From 00f80aef211dc9d927a23a2b56d663a1d82850ee Mon Sep 17 00:00:00 2001 From: DLS Jenkins Date: Mon, 24 Jun 2024 23:21:18 +0100 Subject: [PATCH] htdocs update (master) --- .../dials/algorithms/indexing/indexer.html | 36 +- .../dials/algorithms/indexing/max_cell.html | 2 + .../algorithms/indexing/model_evaluation.html | 4 +- .../algorithms/indexing/nearest_neighbor.html | 18 +- .../dials/algorithms/refinement/refiner.html | 21 +- .../refinement/reflection_manager.html | 585 ++++++++++++++++-- .../dials/algorithms/refinement/target.html | 200 +++++- .../refinement/weighting_strategies.html | 64 ++ .../algorithms/dials.algorithms.indexing.html | 6 +- .../dials.algorithms.refinement.html | 150 +++++ .../library_reference/algorithms/index.html | 6 + documentation/programs/dials_index.html | 4 + documentation/programs/dials_refine.html | 4 + .../dials_refine_bravais_settings.html | 4 + genindex.html | 94 ++- searchindex.js | 2 +- 16 files changed, 1105 insertions(+), 95 deletions(-) diff --git a/_modules/dials/algorithms/indexing/indexer.html b/_modules/dials/algorithms/indexing/indexer.html index 8797c5721..d32276e86 100644 --- a/_modules/dials/algorithms/indexing/indexer.html +++ b/_modules/dials/algorithms/indexing/indexer.html @@ -52,7 +52,7 @@

Source code for dials.algorithms.indexing.indexer

import iotbx.phil import libtbx from cctbx import sgtbx -from dxtbx.model import ExperimentList, ImageSequence +from dxtbx.model import ExperimentList, ImageSequence, tof_helpers import dials.util from dials.algorithms.indexing import ( @@ -931,7 +931,7 @@

Source code for dials.algorithms.indexing.indexer

refined_reflections = reflections.select(imgset_sel) panel_numbers = flex.size_t(refined_reflections["panel"]) xyzcal_mm = refined_reflections["xyzcal.mm"] - x_mm, y_mm, z_rad = xyzcal_mm.parts() + x_mm, y_mm, z = xyzcal_mm.parts() xy_cal_mm = flex.vec2_double(x_mm, y_mm) xy_cal_px = flex.vec2_double(len(xy_cal_mm)) for i_panel in range(len(expt.detector)): @@ -942,10 +942,18 @@

Source code for dials.algorithms.indexing.indexer

) x_px, y_px = xy_cal_px.parts() if expt.scan is not None: - z_px = expt.scan.get_array_index_from_angle(z_rad, deg=False) + if expt.scan.has_property("time_of_flight"): + tof = expt.scan.get_property("time_of_flight") + frames = list(range(len(tof))) + tof_to_frame = tof_helpers.tof_to_frame_interpolator(tof, frames) + z.set_selected(z < min(tof), min(tof)) + z.set_selected(z > max(tof), max(tof)) + z_px = flex.double(tof_to_frame(z)) + else: + z_px = expt.scan.get_array_index_from_angle(z, deg=False) else: # must be a still image, z centroid not meaningful - z_px = z_rad + z_px = z xyzcal_px = flex.vec3_double(x_px, y_px, z_px) reflections["xyzcal.px"].set_selected(imgset_sel, xyzcal_px) @@ -1004,6 +1012,25 @@

Source code for dials.algorithms.indexing.indexer

self.params.max_cell = params.multiplier * max(uc_params[:3]) logger.info("Using max_cell: %.1f Angstrom", self.params.max_cell) else: + + convert_reflections_z_to_deg = True + all_tof_experiments = False + for expt in self.experiments: + if expt.scan is not None and expt.scan.has_property( + "time_of_flight" + ): + all_tof_experiments = True + elif all_tof_experiments: + raise ValueError( + "Cannot find max cell for ToF and non-ToF experiments at the same time" + ) + + if all_tof_experiments: + if params.step_size < 100: + logger.info("Setting default ToF step size to 500 usec") + params.step_size = 500 + convert_reflections_z_to_deg = False + self.params.max_cell = find_max_cell( self.reflections, max_cell_multiplier=params.multiplier, @@ -1015,6 +1042,7 @@

Source code for dials.algorithms.indexing.indexer

filter_ice=params.filter_ice, filter_overlaps=params.filter_overlaps, overlaps_border=params.overlaps_border, + convert_reflections_z_to_deg=convert_reflections_z_to_deg, ).max_cell logger.info("Found max_cell: %.1f Angstrom", self.params.max_cell)
diff --git a/_modules/dials/algorithms/indexing/max_cell.html b/_modules/dials/algorithms/indexing/max_cell.html index bc5cf8440..34f13672a 100644 --- a/_modules/dials/algorithms/indexing/max_cell.html +++ b/_modules/dials/algorithms/indexing/max_cell.html @@ -68,6 +68,7 @@

Source code for dials.algorithms.indexing.max_cell

filter_ice=True, filter_overlaps=True, overlaps_border=0, + convert_reflections_z_to_deg=True, ): logger.debug("Finding suitable max_cell based on %i reflections", len(reflections)) # Exclude potential ice-ring spots from nearest neighbour analysis if needed @@ -109,6 +110,7 @@

Source code for dials.algorithms.indexing.max_cell

percentile=nearest_neighbor_percentile, histogram_binning=histogram_binning, nn_per_bin=nn_per_bin, + convert_reflections_z_to_deg=convert_reflections_z_to_deg, ) except AssertionError as e: raise DialsIndexError("Failure in nearest neighbour analysis:\n" + str(e)) diff --git a/_modules/dials/algorithms/indexing/model_evaluation.html b/_modules/dials/algorithms/indexing/model_evaluation.html index d99031ec9..176556999 100644 --- a/_modules/dials/algorithms/indexing/model_evaluation.html +++ b/_modules/dials/algorithms/indexing/model_evaluation.html @@ -322,7 +322,7 @@

Source code for dials.algorithms.indexing.model_evaluation

def score_by_rmsd_xy(self, reverse=False): # smaller rmsds = better rmsd_x, rmsd_y, rmsd_z = flex.vec3_double( - s.rmsds for s in self.all_solutions + s.rmsds[:3] for s in self.all_solutions ).parts() rmsd_xy = flex.sqrt(flex.pow2(rmsd_x) + flex.pow2(rmsd_y)) score = flex.log(rmsd_xy) / math.log(2) @@ -384,7 +384,7 @@

Source code for dials.algorithms.indexing.model_evaluation

perm = flex.sort_permutation(combined_scores) rmsd_x, rmsd_y, rmsd_z = flex.vec3_double( - s.rmsds for s in self.all_solutions + s.rmsds[:3] for s in self.all_solutions ).parts() rmsd_xy = flex.sqrt(flex.pow2(rmsd_x) + flex.pow2(rmsd_y)) diff --git a/_modules/dials/algorithms/indexing/nearest_neighbor.html b/_modules/dials/algorithms/indexing/nearest_neighbor.html index 6ff491238..7809a798f 100644 --- a/_modules/dials/algorithms/indexing/nearest_neighbor.html +++ b/_modules/dials/algorithms/indexing/nearest_neighbor.html @@ -61,6 +61,7 @@

Source code for dials.algorithms.indexing.nearest_neighbor

percentile=None, histogram_binning="linear", nn_per_bin=5, + convert_reflections_z_to_deg=True, ): self.tolerance = tolerance # Margin of error for max unit cell estimate from scitbx.array_family import flex @@ -76,7 +77,10 @@

Source code for dials.algorithms.indexing.nearest_neighbor

else: entering_flags = flex.bool(reflections.size(), True) rs_vectors = reflections["rlp"] - phi_deg = reflections["xyzobs.mm.value"].parts()[2] * (180 / math.pi) + + z = reflections["xyzobs.mm.value"].parts()[2] + if convert_reflections_z_to_deg: + z = z * (180 / math.pi) d_spacings = flex.double() # nearest neighbor analysis @@ -86,16 +90,16 @@

Source code for dials.algorithms.indexing.nearest_neighbor

sel_imageset = reflections["imageset_id"] == imageset_id if sel_imageset.count(True) == 0: continue - phi_min = flex.min(phi_deg.select(sel_imageset)) - phi_max = flex.max(phi_deg.select(sel_imageset)) - d_phi = phi_max - phi_min - n_steps = max(int(math.ceil(d_phi / step_size)), 1) + z_min = flex.min(z.select(sel_imageset)) + z_max = flex.max(z.select(sel_imageset)) + d_z = z_max - z_min + n_steps = max(int(math.ceil(d_z / step_size)), 1) for n in range(n_steps): sel_step = ( sel_imageset - & (phi_deg >= (phi_min + n * step_size)) - & (phi_deg < (phi_min + (n + 1) * step_size)) + & (z >= (z_min + n * step_size)) + & (z < (z_min + (n + 1) * step_size)) ) for entering in (True, False): diff --git a/_modules/dials/algorithms/refinement/refiner.html b/_modules/dials/algorithms/refinement/refiner.html index 5479550de..ae537a119 100644 --- a/_modules/dials/algorithms/refinement/refiner.html +++ b/_modules/dials/algorithms/refinement/refiner.html @@ -290,6 +290,9 @@

Source code for dials.algorithms.refinement.refiner

"flags", "shoebox", "delpsical.weights", + "wavelength", + "wavelength_cal", + "s0", ] # NB xyzobs.px.value & xyzcal.px required by SauterPoon outlier rejector # NB delpsical.weights is used by ExternalDelPsiWeightingStrategy @@ -435,6 +438,7 @@

Source code for dials.algorithms.refinement.refiner

obs["x_resid"] = x_calc - x_obs obs["y_resid"] = y_calc - y_obs obs["phi_resid"] = phi_calc - phi_obs + refman.update_residuals() # determine whether to do basic centroid analysis to automatically # determine outlier rejection block @@ -925,6 +929,9 @@

Source code for dials.algorithms.refinement.refiner

if units == "mm": header.append(name + "\n(mm)") rmsd_multipliers.append(1.0) + elif units == "A": + header.append(name + "\n(A)") + rmsd_multipliers.append(1.0) elif units == "rad": # convert radians to degrees for reporting header.append(name + "\n(deg)") rmsd_multipliers.append(RAD2DEG) @@ -1006,6 +1013,8 @@

Source code for dials.algorithms.refinement.refiner

# will convert other angles in radians to degrees (e.g. for # RMSD_DeltaPsi and RMSD_2theta) header.append(name + "\n(deg)") + elif name == "RMSD_wavelength" and units == "frame": + header.append(name + "\n(frame)") else: # skip other/unknown RMSDs pass @@ -1027,7 +1036,7 @@

Source code for dials.algorithms.refinement.refiner

scan = exp.scan try: images_per_rad = 1.0 / abs(scan.get_oscillation(deg=False)[1]) - except (AttributeError, ZeroDivisionError): + except (AttributeError, ZeroDivisionError, RuntimeError): images_per_rad = None raw_rmsds = self._target.rmsds_for_experiment(iexp) @@ -1044,6 +1053,8 @@

Source code for dials.algorithms.refinement.refiner

rmsds.append(rmsd * px_per_mm[1]) elif name == "RMSD_Phi" and units == "rad": rmsds.append(rmsd * images_per_rad) + elif name == "RMSD_wavelength" and units == "frame": + rmsds.append(rmsd) elif units == "rad": rmsds.append(rmsd * RAD2DEG) rows.append([str(iexp), str(num)] + [f"{r:.5g}" for r in rmsds]) @@ -1072,14 +1083,14 @@

Source code for dials.algorithms.refinement.refiner

def print_panel_rmsd_table(self): """print useful output about refinement steps in the form of a simple table""" - if len(self._experiments.scans()) > 1: + if len(self._experiments.scans()) > 1 and not self._experiments.all_tof(): logger.warning( "Multiple scans present. Only the first scan will be used " "to determine the image width for reporting RMSDs" ) scan = self._experiments.scans()[0] images_per_rad = None - if scan: + if scan and scan.has_property("oscillation"): if scan.get_oscillation(deg=False)[1] != 0.0: images_per_rad = 1.0 / abs(scan.get_oscillation(deg=False)[1]) @@ -1100,6 +1111,8 @@

Source code for dials.algorithms.refinement.refiner

name == "RMSD_DeltaPsi" and units == "rad" ): # convert radians to degrees for reporting of stills header.append(name + "\n(deg)") + elif name == "RMSD_wavelength" and units == "frame": + header.append(name + "\n(frame)") else: # skip RMSDs that cannot be expressed in image/scan space pass @@ -1126,6 +1139,8 @@

Source code for dials.algorithms.refinement.refiner

rmsds.append(rmsd * images_per_rad) elif name == "RMSD_DeltaPsi" and units == "rad": rmsds.append(rmsd * RAD2DEG) + elif name == "RMSD_wavelength" and units == "frame": + rmsds.append(rmsd) rows.append([str(ipanel), str(num)] + [f"{r:.5g}" for r in rmsds]) if len(rows) > 0: diff --git a/_modules/dials/algorithms/refinement/reflection_manager.html b/_modules/dials/algorithms/refinement/reflection_manager.html index c32357460..578b10be1 100644 --- a/_modules/dials/algorithms/refinement/reflection_manager.html +++ b/_modules/dials/algorithms/refinement/reflection_manager.html @@ -52,6 +52,8 @@

Source code for dials.algorithms.refinement.reflection_manager

import random import libtbx +from dxtbx.model import tof_helpers +from dxtbx.model.experiment_list import ExperimentList from libtbx.phil import parse from scitbx import matrix from scitbx.math import five_number_summary @@ -146,6 +148,10 @@

Source code for dials.algorithms.refinement.reflection_manager

"whether the case is for stills or scans. The default gives" "unit weighting." .type = floats(size = 3, value_min = 0) + wavelength_weight = 1e4 + .help = "Weight for the wavelength term in the target function for" + "Laue refinement" + .type = float(value_min = 0) } %(outlier_phil)s @@ -288,32 +294,99 @@

Source code for dials.algorithms.refinement.reflection_manager

flex.set_random_seed(params.random_seed) logger.debug("Random seed set to %d", params.random_seed) - # check whether we deal with stills or scans - if do_stills: - refman = StillsReflectionManager - # check incompatible weighting strategy - if params.weighting_strategy.override == "statistical": - raise DialsRefineConfigError( - 'The "statistical" weighting strategy is not compatible ' - "with stills refinement" - ) + if "wavelength" in reflections: + return ReflectionManagerFactory.laue_manager( + experiments, reflections, params + ) + + elif do_stills: + return ReflectionManagerFactory.stills_manager( + experiments, reflections, params + ) + else: - refman = ReflectionManager - # check incompatible weighting strategy - if params.weighting_strategy.override in ["stills", "external_deltapsi"]: - msg = ( - 'The "{}" weighting strategy is not compatible with ' - "scan refinement" - ).format(params.weighting_strategy.override) - raise DialsRefineConfigError(msg) - - # set automatic outlier rejection options + return ReflectionManagerFactory.rotation_scan_manager( + experiments, reflections, params + )
+ + +
+[docs] + @staticmethod + def stills_manager( + experiments: ExperimentList, + reflections: flex.reflection_table, + params: libtbx.phil.scope_extract, + ) -> StillsReflectionManager: + + refman = StillsReflectionManager + + ## Outlier detection + if params.outlier.algorithm in ("auto", libtbx.Auto): - if do_stills: - params.outlier.algorithm = "sauter_poon" - else: - params.outlier.algorithm = "mcd" + params.outlier.algorithm = "sauter_poon" + if params.outlier.sauter_poon.px_sz is libtbx.Auto: + # get this from the first panel of the first detector + params.outlier.sauter_poon.px_sz = experiments.detectors()[0][ + 0 + ].get_pixel_size() + if params.outlier.algorithm in ("null", None): + outlier_detector = None + else: + colnames = ["x_resid", "y_resid"] + params.outlier.block_width = None + from dials.algorithms.refinement.outlier_detection import ( + CentroidOutlierFactory, + ) + + outlier_detector = CentroidOutlierFactory.from_parameters_and_colnames( + params, colnames + ) + + ## Weighting strategy + + # check incompatible weighting strategy + if params.weighting_strategy.override == "statistical": + raise DialsRefineConfigError( + 'The "statistical" weighting strategy is not compatible ' + "with stills refinement" + ) + if params.weighting_strategy.override == "constant": + params.weighting_strategy.override = "constant_stills" + + weighting_strategy = ReflectionManagerFactory.get_weighting_strategy_override( + params + ) + + return refman( + reflections=reflections, + experiments=experiments, + nref_per_degree=params.reflections_per_degree, + max_sample_size=params.maximum_sample_size, + min_sample_size=params.minimum_sample_size, + close_to_spindle_cutoff=params.close_to_spindle_cutoff, + scan_margin=params.scan_margin, + outlier_detector=outlier_detector, + weighting_strategy_override=weighting_strategy, + )
+ + +
+[docs] + @staticmethod + def rotation_scan_manager( + experiments: ExperimentList, + reflections: flex.reflection_table, + params: libtbx.phil.scope_extract, + ) -> ReflectionManager: + + refman = ReflectionManager + + ## Outlier detection + + if params.outlier.algorithm in ("auto", libtbx.Auto): + params.outlier.algorithm = "mcd" if params.outlier.algorithm == "sauter_poon": if params.outlier.sauter_poon.px_sz is libtbx.Auto: # get this from the first panel of the first detector @@ -321,15 +394,19 @@

Source code for dials.algorithms.refinement.reflection_manager

0 ].get_pixel_size() - # do outlier rejection? + ## Weighting strategy + + # check incompatible weighting strategy + if params.weighting_strategy.override in ["stills", "external_deltapsi"]: + msg = ( + 'The "{}" weighting strategy is not compatible with ' "scan refinement" + ).format(params.weighting_strategy.override) + raise DialsRefineConfigError(msg) + if params.outlier.algorithm in ("null", None): outlier_detector = None else: - if do_stills: - colnames = ["x_resid", "y_resid"] - params.outlier.block_width = None - else: - colnames = ["x_resid", "y_resid", "phi_resid"] + colnames = ["x_resid", "y_resid", "phi_resid"] from dials.algorithms.refinement.outlier_detection import ( CentroidOutlierFactory, ) @@ -338,36 +415,87 @@

Source code for dials.algorithms.refinement.reflection_manager

params, colnames ) - # override default weighting strategy? - weighting_strategy = None - if params.weighting_strategy.override == "statistical": - from dials.algorithms.refinement.weighting_strategies import ( - StatisticalWeightingStrategy, - ) + weighting_strategy = ReflectionManagerFactory.get_weighting_strategy_override( + params + ) - weighting_strategy = StatisticalWeightingStrategy() - elif params.weighting_strategy.override == "stills": - from dials.algorithms.refinement.weighting_strategies import ( - StillsWeightingStrategy, - ) + return refman( + reflections=reflections, + experiments=experiments, + nref_per_degree=params.reflections_per_degree, + max_sample_size=params.maximum_sample_size, + min_sample_size=params.minimum_sample_size, + close_to_spindle_cutoff=params.close_to_spindle_cutoff, + scan_margin=params.scan_margin, + outlier_detector=outlier_detector, + weighting_strategy_override=weighting_strategy, + )
- weighting_strategy = StillsWeightingStrategy( - params.weighting_strategy.delpsi_constant + +
+[docs] + @staticmethod + def laue_manager( + experiments: ExperimentList, + reflections: flex.reflection_table, + params: libtbx.phil.scope_extract, + ) -> LaueReflectionManager: + + all_tof_experiments = False + for expt in experiments: + if expt.scan is not None and expt.scan.has_property("time_of_flight"): + all_tof_experiments = True + elif all_tof_experiments: + raise ValueError( + "Cannot refine ToF and non-ToF experiments at the same time" + ) + + if all_tof_experiments: + refman = TOFReflectionManager + else: + refman = LaueReflectionManager + + ## Outlier detection + if params.outlier.algorithm in ("auto", libtbx.Auto): + params.outlier.algorithm = "mcd" + if params.outlier.sauter_poon.px_sz is libtbx.Auto: + # get this from the first panel of the first detector + params.outlier.sauter_poon.px_sz = experiments.detectors()[0][ + 0 + ].get_pixel_size() + + if params.outlier.algorithm in ("null", None): + outlier_detector = None + else: + colnames = ["x_resid", "y_resid"] + params.outlier.block_width = None + from dials.algorithms.refinement.outlier_detection import ( + CentroidOutlierFactory, ) - elif params.weighting_strategy.override == "external_deltapsi": - from dials.algorithms.refinement.weighting_strategies import ( - ExternalDelPsiWeightingStrategy, + + outlier_detector = CentroidOutlierFactory.from_parameters_and_colnames( + params, colnames ) - weighting_strategy = ExternalDelPsiWeightingStrategy() + ## Weighting strategy + + if params.weighting_strategy.override == "statistical": + params.weighting_strategy.override = "statistical_laue" elif params.weighting_strategy.override == "constant": - from dials.algorithms.refinement.weighting_strategies import ( - ConstantWeightingStrategy, - ) + params.weighting_strategy.override = "constant_laue" + + if params.weighting_strategy.override is not None: + if params.weighting_strategy.override not in [ + "constant_laue", + "statistical_laue", + ]: + raise ValueError( + f"{params.weighting_strategy.override} not compatible with Laue data" + ) - weighting_strategy = ConstantWeightingStrategy( - *params.weighting_strategy.constants, stills=do_stills - ) + weighting_strategy = ReflectionManagerFactory.get_weighting_strategy_override( + params + ) return refman( reflections=reflections, @@ -379,7 +507,49 @@

Source code for dials.algorithms.refinement.reflection_manager

scan_margin=params.scan_margin, outlier_detector=outlier_detector, weighting_strategy_override=weighting_strategy, + wavelength_weight=params.weighting_strategy.wavelength_weight, )
+ + +
+[docs] + @staticmethod + def get_weighting_strategy_override( + params: libtbx.phil.scope_extract, + ) -> weighting_strategies.StatisticalWeightingStrategy | weighting_strategies.ConstantWeightingStrategy: + + if params.weighting_strategy.override == "statistical": + return weighting_strategies.StatisticalWeightingStrategy() + + elif params.weighting_strategy.override == "stills": + return weighting_strategies.StillsWeightingStrategy( + params.weighting_strategy.delpsi_constant + ) + + elif params.weighting_strategy.override == "external_deltapsi": + return weighting_strategies.ExternalDelPsiWeightingStrategy() + + elif params.weighting_strategy.override == "constant": + return weighting_strategies.ConstantWeightingStrategy( + *params.weighting_strategy.constants + ) + + elif params.weighting_strategy.override == "constant_stills": + return weighting_strategies.ConstantStillsWeightingStrategy( + *params.weighting_strategy.constants + ) + + elif params.weighting_strategy.override == "statistical_laue": + return weighting_strategies.LaueStatisticalWeightingStrategy( + params.weighting_strategy.wavelength_weight, + ) + + elif params.weighting_strategy.override == "constant_laue": + return weighting_strategies.LaueMixedWeightingStrategy( + params.weighting_strategy.wavelength_weight, + ) + + return None
@@ -680,7 +850,11 @@

Source code for dials.algorithms.refinement.reflection_manager

nrefs = sample_size = len(isel) # set sample size according to nref_per_degree (per experiment) - if exp.scan and self._nref_per_degree: + if ( + exp.scan + and exp.scan.has_property("oscillation") + and self._nref_per_degree + ): sequence_range_rad = exp.scan.get_oscillation_range(deg=False) width = abs(sequence_range_rad[1] - sequence_range_rad[0]) * RAD2DEG if self._nref_per_degree is libtbx.Auto: @@ -829,6 +1003,16 @@

Source code for dials.algorithms.refinement.reflection_manager

self._reflections = self._reflections.select(sel) return self._reflections
+ + +
+[docs] + def update_residuals(self): + x_obs, y_obs, phi_obs = self._reflections["xyzobs.mm.value"].parts() + x_calc, y_calc, phi_calc = self._reflections["xyzcal.mm"].parts() + self._reflections["x_resid"] = x_calc - x_obs + self._reflections["y_resid"] = y_calc - y_obs + self._reflections["phi_resid"] = phi_calc - phi_obs
@@ -909,6 +1093,301 @@

Source code for dials.algorithms.refinement.reflection_manager

logger.info(dials.util.tabulate(rows, header) + "\n")
+ + +
+[docs] +class LaueReflectionManager(ReflectionManager): + + _weighting_strategy = weighting_strategies.LaueStatisticalWeightingStrategy() + experiment_type = "laue" + +
+[docs] + def __init__( + self, + reflections, + experiments, + nref_per_degree=None, + max_sample_size=None, + min_sample_size=0, + close_to_spindle_cutoff=0.02, + scan_margin=0.0, + outlier_detector=None, + weighting_strategy_override=None, + wavelength_weight=1e7, + ): + + if len(reflections) == 0: + raise ValueError("Empty reflections table provided to ReflectionManager") + + # keep track of models + self._experiments = experiments + goniometers = [e.goniometer for e in self._experiments] + self._axes = [ + matrix.col(g.get_rotation_axis()) if g else None for g in goniometers + ] + + # unset the refinement flags (creates flags field if needed) + reflections.unset_flags( + flex.size_t_range(len(reflections)), + flex.reflection_table.flags.used_in_refinement, + ) + + # check that the observed beam vectors are stored: if not, compute them + n_s1_set = set_obs_s1(reflections, experiments) + if n_s1_set > 0: + logger.debug("Set scattering vectors for %d reflections", n_s1_set) + + # keep track of the original indices of the reflections + reflections["iobs"] = flex.size_t_range(len(reflections)) + + # Check for monotonically increasing value range. If not, ref_table isn't sorted, + # and proceed to sort by id and panel. This is required for the C++ extension + # modules to allow for nlogn subselection of values used in refinement. + l_id = reflections["id"] + id0 = l_id[0] + for id_x in l_id[1:]: + if id0 <= id_x: + id0 = id_x + else: + reflections.sort("id") # Ensuring the ref_table is sorted by id + reflections.subsort( + "id", "panel" + ) # Ensuring that within each sorted id block, sorting is next performed by panel + break + + # set up the reflection inclusion criteria + self._close_to_spindle_cutoff = close_to_spindle_cutoff # close to spindle + self._scan_margin = DEG2RAD * scan_margin # close to the scan edge + self._outlier_detector = outlier_detector # for outlier rejection + self._nref_per_degree = nref_per_degree # random subsets + self._max_sample_size = max_sample_size # sample size ceiling + self._min_sample_size = min_sample_size # sample size floor + + # exclude reflections that fail some inclusion criteria + refs_to_keep = self._id_refs_to_keep(reflections) + self._accepted_refs_size = len(refs_to_keep) + + # set entering flags for all reflections + reflections.calculate_entering_flags(self._experiments) + + # reset all use flags + self.reset_accepted_reflections(reflections) + + # put full list of indexed reflections aside and select only the reflections + # that were not excluded to manage + self._indexed = reflections + self._reflections = reflections.select(refs_to_keep) + + # set exclusion flag for reflections that failed the tests + refs_to_excl = flex.bool(len(self._indexed), True) + refs_to_excl.set_selected(refs_to_keep, False) + self._indexed.set_flags( + refs_to_excl, self._indexed.flags.excluded_for_refinement + ) + + # set weights for all kept reflections + if weighting_strategy_override is not None: + self._weighting_strategy = weighting_strategy_override + else: + self._weighting_strategy = ( + weighting_strategies.LaueStatisticalWeightingStrategy(wavelength_weight) + ) + self._weighting_strategy.calculate_weights(self._reflections) + + # not known until the manager is finalised + self._sample_size = None
+ + + def _id_refs_to_keep(self, obs_data): + """Create a selection of observations that pass certain conditions. + Stills-specific version removes checks relevant only to experiments + with a rotation axis.""" + + # first exclude reflections with miller index set to 0,0,0 + sel1 = obs_data["miller_index"] != (0, 0, 0) + + # exclude reflections with overloads, as these have worse centroids + sel2 = ~obs_data.get_flags(obs_data.flags.overloaded) + + # combine selections + sel = sel1 & sel2 + inc = flex.size_t_range(len(obs_data)).select(sel) + + return inc + +
+[docs] + def print_stats_on_matches(self): + """Print some basic statistics on the matches""" + + l = self.get_matches() + nref = len(l) + if nref == 0: + logger.warning( + "Unable to calculate summary statistics for zero observations" + ) + return + + from scitbx.math import five_number_summary + + try: + x_resid = l["x_resid"] + y_resid = l["y_resid"] + wavelength_resid = l["wavelength_resid"] + w_x, w_y, w_z = l["xyzobs.mm.weights"].parts() + except KeyError: + return + + header = ["", "Min", "Q1", "Med", "Q3", "Max"] + rows = [] + row_data = five_number_summary(x_resid) + rows.append(["Xc - Xo (mm)"] + [f"{e:.4g}" for e in row_data]) + row_data = five_number_summary(y_resid) + rows.append(["Yc - Yo (mm)"] + [f"{e:.4g}" for e in row_data]) + row_data = five_number_summary(wavelength_resid) + rows.append(["Wavelengthc - Wavelengtho (A)"] + [f"{e:.4g}" for e in row_data]) + row_data = five_number_summary(w_x) + rows.append(["X weights"] + [f"{e:.4g}" for e in row_data]) + row_data = five_number_summary(w_y) + rows.append(["Y weights"] + [f"{e:.4g}" for e in row_data]) + row_data = five_number_summary(w_z) + rows.append(["Wavelength weights"] + [f"{e:.4g}" for e in row_data]) + + msg = ( + f"\nSummary statistics for {nref} observations" + " matched to predictions:" + ) + logger.info(msg) + logger.info(dials.util.tabulate(rows, header) + "\n")
+ + +
+[docs] + def update_residuals(self): + x_obs, y_obs, _ = self._reflections["xyzobs.mm.value"].parts() + x_calc, y_calc, _ = self._reflections["xyzcal.mm"].parts() + wavelength_obs = self._reflections["wavelength"] + wavelength_cal = self._reflections["wavelength_cal"] + self._reflections["x_resid"] = x_calc - x_obs + self._reflections["y_resid"] = y_calc - y_obs + self._reflections["wavelength_resid"] = wavelength_cal - wavelength_obs + self._reflections["wavelength_resid2"] = ( + self._reflections["wavelength_resid"] ** 2 + )
+
+ + + +
+[docs] +class TOFReflectionManager(LaueReflectionManager): +
+[docs] + def __init__( + self, + reflections, + experiments, + nref_per_degree=None, + max_sample_size=None, + min_sample_size=0, + close_to_spindle_cutoff=0.02, + scan_margin=0.0, + outlier_detector=None, + weighting_strategy_override=None, + wavelength_weight=1e7, + ): + + super().__init__( + reflections=reflections, + experiments=experiments, + nref_per_degree=nref_per_degree, + max_sample_size=max_sample_size, + min_sample_size=min_sample_size, + close_to_spindle_cutoff=close_to_spindle_cutoff, + scan_margin=scan_margin, + outlier_detector=outlier_detector, + weighting_strategy_override=weighting_strategy_override, + wavelength_weight=wavelength_weight, + ) + + tof_to_frame_interpolators = [] + sample_to_source_distances = [] + tof_ranges = [] + for expt in self._experiments: + tof = expt.scan.get_property("time_of_flight") # (usec) + tof_range = (min(tof), max(tof)) + tof_ranges.append(tof_range) + frames = list(range(len(tof))) + tof_to_frame = tof_helpers.tof_to_frame_interpolator(tof, frames) + tof_to_frame_interpolators.append(tof_to_frame) + sample_to_source_distances.append( + expt.beam.get_sample_to_source_distance() * 10**-3 # (m) + ) + + self._tof_to_frame_interpolators = tof_to_frame_interpolators + self._sample_to_source_distances = sample_to_source_distances + self._tof_ranges = tof_ranges
+ + +
+[docs] + def update_residuals(self): + x_obs, y_obs, _ = self._reflections["xyzobs.mm.value"].parts() + x_calc, y_calc, _ = self._reflections["xyzcal.mm"].parts() + wavelength_obs = self._reflections["wavelength"] + wavelength_cal = self._reflections["wavelength_cal"] + L2 = self._reflections["s1"].norms() * 10**-3 + self._reflections["x_resid"] = x_calc - x_obs + self._reflections["y_resid"] = y_calc - y_obs + self._reflections["wavelength_resid"] = wavelength_cal - wavelength_obs + self._reflections["wavelength_resid2"] = ( + self._reflections["wavelength_resid"] ** 2 + ) + + frame_resid = flex.double(len(self._reflections)) + frame_resid2 = flex.double(len(self._reflections)) + for idx, expt in enumerate(self._experiments): + if "imageset_id" in self._reflections: + r_expt = self._reflections["imageset_id"] == idx + else: + r_expt = self._reflections["id"] == idx + + L_expt = self._sample_to_source_distances[idx] + L2.select(r_expt) + + tof_obs_expt = ( + tof_helpers.tof_from_wavelength(L_expt, wavelength_obs.select(r_expt)) + * 10**6 + ) # (usec) + tof_obs_expt.set_selected( + tof_obs_expt < self._tof_ranges[idx][0], self._tof_ranges[idx][0] + ) + tof_obs_expt.set_selected( + tof_obs_expt > self._tof_ranges[idx][1], self._tof_ranges[idx][1] + ) + + tof_cal_expt = ( + tof_helpers.tof_from_wavelength(L_expt, wavelength_cal.select(r_expt)) + * 10**6 + ) # (usec) + tof_cal_expt.set_selected( + tof_cal_expt < self._tof_ranges[idx][0], self._tof_ranges[idx][0] + ) + tof_cal_expt.set_selected( + tof_cal_expt > self._tof_ranges[idx][1], self._tof_ranges[idx][1] + ) + + tof_to_frame = self._tof_to_frame_interpolators[idx] + frame_resid_expt = flex.double( + tof_to_frame(tof_cal_expt) - tof_to_frame(tof_obs_expt) + ) + frame_resid.set_selected(r_expt, frame_resid_expt) + frame_resid2.set_selected(r_expt, frame_resid_expt**2) + + self._reflections["frame_resid"] = frame_resid + self._reflections["frame_resid2"] = frame_resid2
+
+
diff --git a/_modules/dials/algorithms/refinement/target.html b/_modules/dials/algorithms/refinement/target.html index 2de49b1f0..591ec6bf3 100644 --- a/_modules/dials/algorithms/refinement/target.html +++ b/_modules/dials/algorithms/refinement/target.html @@ -49,7 +49,7 @@

Source code for dials.algorithms.refinement.target

from __future__ import annotations import math -from typing import Any, Tuple, Union +from typing import Any, Optional, Tuple, Union from libtbx.phil import parse from scitbx import sparse @@ -125,9 +125,23 @@

Source code for dials.algorithms.refinement.target

+ " not recognised" ) + all_tof_experiments = False + for expt in experiments: + if expt.scan is not None and expt.scan.has_property("time_of_flight"): + all_tof_experiments = True + elif all_tof_experiments: + raise ValueError( + "Cannot refine ToF and non-ToF experiments at the same time" + ) + + if all_tof_experiments: + from dials.algorithms.refinement.target import ( + TOFLeastSquaresResidualWithRmsdCutoff as targ, + ) + # Determine whether the target is in X, Y, Phi space or just X, Y to choose # the right Target to instantiate - if do_stills: + elif do_stills: if do_sparse: from dials.algorithms.refinement.target_stills import ( LeastSquaresStillsResidualWithRmsdCutoffSparse as targ, @@ -296,7 +310,11 @@

Source code for dials.algorithms.refinement.target

sel = reflections["id"] == iexp # keep all reflections if there is no rotation axis - if exp.goniometer is None: + if ( + exp.goniometer is None + or exp.scan is None + or not exp.scan.has_property("oscillation") + ): to_keep.set_selected(sel, True) continue @@ -826,6 +844,182 @@

Source code for dials.algorithms.refinement.target

pass
+ + +
+[docs] +class LaueLeastSquaresResidualWithRmsdCutoff(Target): + + """A Laue implementation of the target class providing a least squares + residual in terms of detector impact position X, Y, and observed + wavelength""" + + _grad_names = ["dX_dp", "dY_dp", "dwavelength_dp"] + rmsd_names = ["RMSD_X", "RMSD_Y", "RMSD_wavelength"] + rmsd_units = ["mm", "mm", "A"] + +
+[docs] + def __init__( + self, + experiments, + predictor, + reflection_manager, + prediction_parameterisation, + restraints_parameterisation, + frac_binsize_cutoff: float = 0.33333, + absolute_cutoffs: Optional[list] = None, + gradient_calculation_blocksize=None, + ): + + Target.__init__( + self, + experiments, + predictor, + reflection_manager, + prediction_parameterisation, + restraints_parameterisation, + gradient_calculation_blocksize, + ) + + """ + Set up the RMSD achieved criterion. + For simplicity, we take models from the first Experiment only. + If this is not appropriate for refinement over all experiments + then absolute cutoffs should be used instead. + """ + + detector = experiments[0].detector + + if not absolute_cutoffs: + # Pixel cutoffs + pixel_sizes = [p.get_pixel_size() for p in detector] + min_px_size_x = min(e[0] for e in pixel_sizes) + min_px_size_y = min(e[1] for e in pixel_sizes) + self._binsize_cutoffs = [ + min_px_size_x * frac_binsize_cutoff, + min_px_size_y * frac_binsize_cutoff, + ] + # Wavelength cutoff + self._binsize_cutoffs.append(0) + else: + assert len(absolute_cutoffs) == 3 + self._binsize_cutoffs = absolute_cutoffs
+ + + @staticmethod + def _extract_residuals_and_weights(matches): + + # return residuals and weights as 1d flex.double vectors + residuals = flex.double.concatenate(matches["x_resid"], matches["y_resid"]) + + residuals = flex.double.concatenate(residuals, matches["wavelength_resid"]) + + weights, w_y, w_z = matches["xyzobs.mm.weights"].parts() + weights.extend(w_y) + weights.extend(w_z) + + return residuals, weights + + @staticmethod + def _extract_squared_residuals(matches): + + return flex.double.concatenate( + matches["x_resid2"], + flex.double.concatenate(matches["y_resid2"], matches["wavelength_resid2"]), + ) + + def _rmsds_core(self, reflections): + + """calculate unweighted RMSDs for the specified reflections""" + + resid_x = flex.sum(reflections["x_resid2"]) + resid_y = flex.sum(reflections["y_resid2"]) + resid_wavelength = flex.sum(reflections["wavelength_resid2"]) + n = len(reflections) + + rmsds = ( + math.sqrt(resid_x / n), + math.sqrt(resid_y / n), + math.sqrt(abs(resid_wavelength) / n), + ) + return rmsds + + def _predict_core(self, reflections, skip_derivatives=False): + """perform prediction for the specified reflections""" + + # If the prediction parameterisation has a compose method (true for the scan + # varying case) then call it. Prefer hasattr to try-except duck typing to + # avoid masking AttributeErrors that could be raised within the method. + if hasattr(self._prediction_parameterisation, "compose"): + self._prediction_parameterisation.compose(reflections, skip_derivatives) + + # do prediction (updates reflection table in situ). Scan-varying prediction + # is done automatically if the crystal has scan-points (assuming reflections + # have ub_matrix set) + self._reflection_predictor(reflections) + + x_obs, y_obs, _ = reflections["xyzobs.mm.value"].parts() + x_calc, y_calc, _ = reflections["xyzcal.mm"].parts() + + # calculate residuals and assign columns + reflections["x_resid"] = x_calc - x_obs + reflections["x_resid2"] = reflections["x_resid"] ** 2 + reflections["y_resid"] = y_calc - y_obs + reflections["y_resid2"] = reflections["y_resid"] ** 2 + wavelength_obs = reflections["wavelength"] + wavelength_cal = reflections["wavelength_cal"] + reflections["wavelength_resid"] = wavelength_cal - wavelength_obs + reflections["wavelength_resid2"] = reflections["wavelength_resid"] ** 2 + + return reflections + +
+[docs] + def achieved(self): + """RMSD criterion for target achieved""" + r = self._rmsds if self._rmsds else self.rmsds() + + # reset cached rmsds to avoid getting out of step + self._rmsds = None + + if ( + r[0] < self._binsize_cutoffs[0] + and r[1] < self._binsize_cutoffs[1] + and r[2] < self._binsize_cutoffs[2] + ): + return True + return False
+
+ + + +
+[docs] +class TOFLeastSquaresResidualWithRmsdCutoff(LaueLeastSquaresResidualWithRmsdCutoff): + + _grad_names = ["dX_dp", "dY_dp", "dwavelength_dp"] + rmsd_names = ["RMSD_X", "RMSD_Y", "RMSD_wavelength", "RMSD_wavelength"] + rmsd_units = ["mm", "mm", "A", "frame"] + + def _rmsds_core(self, reflections): + + """calculate unweighted RMSDs for the specified reflections""" + + resid_x = flex.sum(reflections["x_resid2"]) + resid_y = flex.sum(reflections["y_resid2"]) + resid_wavelength = flex.sum(reflections["wavelength_resid2"]) + resid_frame = flex.sum(reflections["frame_resid2"]) + n = len(reflections) + + rmsds = ( + math.sqrt(resid_x / n), + math.sqrt(resid_y / n), + math.sqrt(abs(resid_wavelength) / n), + math.sqrt(abs(resid_frame) / n), + ) + return rmsds
+
diff --git a/_modules/dials/algorithms/refinement/weighting_strategies.html b/_modules/dials/algorithms/refinement/weighting_strategies.html index ec63076a0..033f1d87c 100644 --- a/_modules/dials/algorithms/refinement/weighting_strategies.html +++ b/_modules/dials/algorithms/refinement/weighting_strategies.html @@ -170,6 +170,70 @@

Source code for dials.algorithms.refinement.weighting_strategies

return reflections
+ + +
+[docs] +class LaueStatisticalWeightingStrategy(StatisticalWeightingStrategy): + + """ + Variance in z estimated from sqrt(x^2+y^2) + """ + +
+[docs] + def __init__( + self, + wavelength_weight: float = 1e7, + ): + self._wavelength_weight = wavelength_weight
+ + +
+[docs] + def calculate_weights(self, reflections): + + reflections = super().calculate_weights(reflections) + + wx, wy, _ = reflections["xyzobs.mm.weights"].parts() + wz = flex.sqrt(wx * wx + wy * wy) * self._wavelength_weight + reflections["xyzobs.mm.weights"] = flex.vec3_double(wx, wy, wz) + + return reflections
+
+ + + +
+[docs] +class LaueMixedWeightingStrategy(StatisticalWeightingStrategy): + + """ + Use statistical weighting for x and y, and constant weighting for z + """ + +
+[docs] + def __init__( + self, + wavelength_weight: float = 1e7, + ): + self._wavelength_weight = wavelength_weight
+ + +
+[docs] + def calculate_weights(self, reflections): + + reflections = super().calculate_weights(reflections) + + wx, wy, wz = reflections["xyzobs.mm.weights"].parts() + wz = wz * 0 + self._wavelength_weight + reflections["xyzobs.mm.weights"] = flex.vec3_double(wx, wy, wz) + + return reflections
+
+
diff --git a/documentation/library_reference/algorithms/dials.algorithms.indexing.html b/documentation/library_reference/algorithms/dials.algorithms.indexing.html index 52bdf3d66..2574a02dc 100644 --- a/documentation/library_reference/algorithms/dials.algorithms.indexing.html +++ b/documentation/library_reference/algorithms/dials.algorithms.indexing.html @@ -907,16 +907,16 @@

dials.algorithms.indexing.max_cell¶

-dials.algorithms.indexing.max_cell.find_max_cell(reflections, max_cell_multiplier=1.3, step_size=45, nearest_neighbor_percentile=None, histogram_binning='linear', nn_per_bin=5, max_height_fraction=0.25, filter_ice=True, filter_overlaps=True, overlaps_border=0)[source]¶
+dials.algorithms.indexing.max_cell.find_max_cell(reflections, max_cell_multiplier=1.3, step_size=45, nearest_neighbor_percentile=None, histogram_binning='linear', nn_per_bin=5, max_height_fraction=0.25, filter_ice=True, filter_overlaps=True, overlaps_border=0, convert_reflections_z_to_deg=True)[source]¶
-class dials.algorithms.indexing.nearest_neighbor.NeighborAnalysis(reflections, step_size=45, tolerance=1.5, max_height_fraction=0.25, percentile=None, histogram_binning='linear', nn_per_bin=5)[source]¶
+class dials.algorithms.indexing.nearest_neighbor.NeighborAnalysis(reflections, step_size=45, tolerance=1.5, max_height_fraction=0.25, percentile=None, histogram_binning='linear', nn_per_bin=5, convert_reflections_z_to_deg=True)[source]¶

Bases: object

-__init__(reflections, step_size=45, tolerance=1.5, max_height_fraction=0.25, percentile=None, histogram_binning='linear', nn_per_bin=5)[source]¶
+__init__(reflections, step_size=45, tolerance=1.5, max_height_fraction=0.25, percentile=None, histogram_binning='linear', nn_per_bin=5, convert_reflections_z_to_deg=True)[source]¶
diff --git a/documentation/library_reference/algorithms/dials.algorithms.refinement.html b/documentation/library_reference/algorithms/dials.algorithms.refinement.html index 8b5532ee9..592b11347 100644 --- a/documentation/library_reference/algorithms/dials.algorithms.refinement.html +++ b/documentation/library_reference/algorithms/dials.algorithms.refinement.html @@ -75,6 +75,33 @@
+
+
+class dials.algorithms.refinement.reflection_manager.LaueReflectionManager(reflections, experiments, nref_per_degree=None, max_sample_size=None, min_sample_size=0, close_to_spindle_cutoff=0.02, scan_margin=0.0, outlier_detector=None, weighting_strategy_override=None, wavelength_weight=10000000.0)[source]¶
+

Bases: ReflectionManager

+
+
+__init__(reflections, experiments, nref_per_degree=None, max_sample_size=None, min_sample_size=0, close_to_spindle_cutoff=0.02, scan_margin=0.0, outlier_detector=None, weighting_strategy_override=None, wavelength_weight=10000000.0)[source]¶
+
+ +
+
+experiment_type = 'laue'¶
+
+ +
+
+print_stats_on_matches()[source]¶
+

Print some basic statistics on the matches

+
+ +
+
+update_residuals()[source]¶
+
+ +
+
class dials.algorithms.refinement.reflection_manager.ReflectionManager(reflections, experiments, nref_per_degree=None, max_sample_size=None, min_sample_size=0, close_to_spindle_cutoff=0.02, scan_margin=0.0, outlier_detector=None, weighting_strategy_override=None)[source]¶
@@ -169,6 +196,11 @@ predictions

+
+
+update_residuals()[source]¶
+
+
@@ -190,6 +222,26 @@
+
+
+static get_weighting_strategy_override(params: scope_extract) → StatisticalWeightingStrategy | ConstantWeightingStrategy[source]¶
+
+ +
+
+static laue_manager(experiments: ExperimentList, reflections: reflection_table, params: scope_extract) → LaueReflectionManager[source]¶
+
+ +
+
+static rotation_scan_manager(experiments: ExperimentList, reflections: reflection_table, params: scope_extract) → ReflectionManager[source]¶
+
+ +
+
+static stills_manager(experiments: ExperimentList, reflections: reflection_table, params: scope_extract) → StillsReflectionManager[source]¶
+
+
@@ -212,6 +264,22 @@
+
+
+class dials.algorithms.refinement.reflection_manager.TOFReflectionManager(reflections, experiments, nref_per_degree=None, max_sample_size=None, min_sample_size=0, close_to_spindle_cutoff=0.02, scan_margin=0.0, outlier_detector=None, weighting_strategy_override=None, wavelength_weight=10000000.0)[source]¶
+

Bases: LaueReflectionManager

+
+
+__init__(reflections, experiments, nref_per_degree=None, max_sample_size=None, min_sample_size=0, close_to_spindle_cutoff=0.02, scan_margin=0.0, outlier_detector=None, weighting_strategy_override=None, wavelength_weight=10000000.0)[source]¶
+
+ +
+
+update_residuals()[source]¶
+
+ +
+

Contains classes used to provide weighting schemes as strategies for ReflectionManagers.

@@ -250,6 +318,42 @@
+
+
+class dials.algorithms.refinement.weighting_strategies.LaueMixedWeightingStrategy(wavelength_weight: float = 10000000.0)[source]¶
+

Bases: StatisticalWeightingStrategy

+

Use statistical weighting for x and y, and constant weighting for z

+
+
+__init__(wavelength_weight: float = 10000000.0)[source]¶
+
+ +
+
+calculate_weights(reflections)[source]¶
+

set ‘statistical weights’, that is w(x) = 1/var(x)

+
+ +
+ +
+
+class dials.algorithms.refinement.weighting_strategies.LaueStatisticalWeightingStrategy(wavelength_weight: float = 10000000.0)[source]¶
+

Bases: StatisticalWeightingStrategy

+

Variance in z estimated from sqrt(x^2+y^2)

+
+
+__init__(wavelength_weight: float = 10000000.0)[source]¶
+
+ +
+
+calculate_weights(reflections)[source]¶
+

set ‘statistical weights’, that is w(x) = 1/var(x)

+
+ +
+
class dials.algorithms.refinement.weighting_strategies.StatisticalWeightingStrategy[source]¶
@@ -931,6 +1035,36 @@

Contains classes used to construct a target function for refinement, principally Target and ReflectionManager.

+
+
+class dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff(experiments, predictor, reflection_manager, prediction_parameterisation, restraints_parameterisation, frac_binsize_cutoff: float = 0.33333, absolute_cutoffs: list | None = None, gradient_calculation_blocksize=None)[source]¶
+

Bases: Target

+

A Laue implementation of the target class providing a least squares +residual in terms of detector impact position X, Y, and observed +wavelength

+
+
+__init__(experiments, predictor, reflection_manager, prediction_parameterisation, restraints_parameterisation, frac_binsize_cutoff: float = 0.33333, absolute_cutoffs: list | None = None, gradient_calculation_blocksize=None)[source]¶
+
+ +
+
+achieved()[source]¶
+

RMSD criterion for target achieved

+
+ +
+
+rmsd_names = ['RMSD_X', 'RMSD_Y', 'RMSD_wavelength']¶
+
+ +
+
+rmsd_units = ['mm', 'mm', 'A']¶
+
+ +
+
class dials.algorithms.refinement.target.LeastSquaresPositionalResidualWithRmsdCutoff(experiments, predictor, reflection_manager, prediction_parameterisation, restraints_parameterisation, frac_binsize_cutoff=0.33333, absolute_cutoffs=None, gradient_calculation_blocksize=None)[source]¶
@@ -969,6 +1103,22 @@ that employed sparse storage.

+
+
+class dials.algorithms.refinement.target.TOFLeastSquaresResidualWithRmsdCutoff(experiments, predictor, reflection_manager, prediction_parameterisation, restraints_parameterisation, frac_binsize_cutoff: float = 0.33333, absolute_cutoffs: list | None = None, gradient_calculation_blocksize=None)[source]¶
+

Bases: LaueLeastSquaresResidualWithRmsdCutoff

+
+
+rmsd_names = ['RMSD_X', 'RMSD_Y', 'RMSD_wavelength', 'RMSD_wavelength']¶
+
+ +
+
+rmsd_units = ['mm', 'mm', 'A', 'frame']¶
+
+ +
+
class dials.algorithms.refinement.target.Target(experiments, predictor, reflection_manager, prediction_parameterisation, restraints_parameterisation=None, gradient_calculation_blocksize=None)[source]¶
diff --git a/documentation/library_reference/algorithms/index.html b/documentation/library_reference/algorithms/index.html index 63ee51b2d..41d3880ba 100644 --- a/documentation/library_reference/algorithms/index.html +++ b/documentation/library_reference/algorithms/index.html @@ -94,11 +94,15 @@

Algorithmsdials.algorithms.profile_model
  • dials.algorithms.refinement
    • -
  • achieved() (dials.algorithms.refinement.target.LeastSquaresPositionalResidualWithRmsdCutoff method) +
  • achieved() (dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff method)
      +
    • all_tof() (dxtbx.model.ExperimentList method) +
    • append() (dials.algorithms.indexing.model_evaluation.ModelRank method) + -
      • compute_functional_gradients_diag() (dials.algorithms.refinement.engine.LBFGScurvs method)
          +
        • export_as_json() (dials.algorithms.indexing.indexer.Indexer method) +
        • export_mtz() (in module dials.util.export_mtz)
        • export_reflections() (dials.algorithms.indexing.indexer.Indexer method) @@ -1764,6 +1782,8 @@

          G

        • get_vendor() (dxtbx.imageset.ImageSetData method)
        • get_vendortype() (dxtbx.imageset.ImageSet method) +
          • +
        • get_weighting_strategy_override() (dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory static method)
        • Goniometer (class in dxtbx.model.goniometer)
          • @@ -2021,7 +2041,17 @@

          K

          L

          + - - + - + - +
          diff --git a/searchindex.js b/searchindex.js index 08a794487..e0b81bb61 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"About": [[0, "about"]], "Acknowledgements": [[0, "acknowledgements"], [77, "acknowledgements"], [78, "acknowledgements"], [81, "acknowledgements"], [83, "acknowledgements"]], "Adding new format classes": [[4, "adding-new-format-classes"]], "Advanced use - Choosing reflections to use for minimisation": [[1, "advanced-use-choosing-reflections-to-use-for-minimisation"]], "Advanced use - Controlling the scaling models": [[1, "advanced-use-controlling-the-scaling-models"]], "Algorithms": [[19, "algorithms"]], "Almost there": [[84, "almost-there"]], "Analysis of individually processed datasets": [[83, "analysis-of-individually-processed-datasets"]], "Analysis of jointly refined datasets": [[83, "analysis-of-jointly-refined-datasets"]], "Applying the corrected metrology": [[81, "applying-the-corrected-metrology"]], "Array Family": [[20, "array-family"]], "Attendees": [[98, "attendees"]], "Basic parameters": [[34, "basic-parameters"], [36, "basic-parameters"], [37, "basic-parameters"], [38, "basic-parameters"], [39, "basic-parameters"], [40, "basic-parameters"], [41, "basic-parameters"], [42, "basic-parameters"], [43, "basic-parameters"], [44, "basic-parameters"], [45, "basic-parameters"], [46, "basic-parameters"], [47, "basic-parameters"], [49, "basic-parameters"], [50, "basic-parameters"], [51, "basic-parameters"], [52, "basic-parameters"], [53, "basic-parameters"], [54, "basic-parameters"], [55, "basic-parameters"], [57, "basic-parameters"], [58, "basic-parameters"], [59, "basic-parameters"], [60, "basic-parameters"], [61, "basic-parameters"], [62, "basic-parameters"], [63, "basic-parameters"], [64, "basic-parameters"], [65, "basic-parameters"], [66, "basic-parameters"], [67, "basic-parameters"], [68, "basic-parameters"], [69, "basic-parameters"], [70, "basic-parameters"], [72, "basic-parameters"]], "Basis vector search strategies": [[4, "basis-vector-search-strategies"]], "Bookkeeping": [[76, "bookkeeping"]], "Bravais Lattice Refinement": [[82, "bravais-lattice-refinement"], [86, "bravais-lattice-refinement"], [87, "bravais-lattice-refinement"]], "Bravais lattice determination": [[88, "bravais-lattice-determination"]], "Build instructions": [[48, "build-instructions"]], "Built-in help": [[7, "built-in-help"]], "Centred or pseudocentred?": [[77, "centred-or-pseudocentred"]], "Check indexing symmetry": [[78, "check-indexing-symmetry"]], "Checking the symmetry": [[87, "checking-the-symmetry"]], "Class Methods": [[4, "class-methods"]], "Cluster Comparisons": [[76, "cluster-comparisons"]], "Conclusions": [[77, "conclusions"], [78, "conclusions"]], "Contact": [[90, "contact"]], "Contents": [[4, "contents"]], "Conventions": [[2, "conventions"]], "Converting to a centred lattice": [[77, "converting-to-a-centred-lattice"]], "Coordinate frames": [[2, "coordinate-frames"]], "DIALS 1: 12th-13th June 2012 (Diamond Light Source, UK)": [[97, "dials-1-12th-13th-june-2012-diamond-light-source-uk"]], "DIALS Application to XFEL Crystallography": [[95, "dials-application-to-xfel-crystallography"]], "DIALS East": [[0, "dials-east"]], "DIALS How-To guides": [[89, "dials-how-to-guides"]], "DIALS Journal Articles": [[95, "dials-journal-articles"]], "DIALS License": [[92, "dials-license"]], "DIALS Newsletter Articles": [[95, "dials-newsletter-articles"]], "DIALS Reports": [[95, "dials-reports"]], "DIALS Synchrotron Applications": [[95, "dials-synchrotron-applications"]], "DIALS West": [[0, "dials-west"]], "DIALS for neutron diffraction": [[94, "dials-for-neutron-diffraction"]], "DIALS-3: 22nd May 2013 (Cambridge, UK)": [[98, "dials-3-22nd-may-2013-cambridge-uk"]], "DIALS: Diffraction Integration for Advanced Light Sources": [[90, "dials-diffraction-integration-for-advanced-light-sources"]], "DPF3 Part 1: Correcting poor initial geometry": [[78, "dpf3-part-1-correcting-poor-initial-geometry"]], "DPF3 Part 2: A question of centring": [[77, "dpf3-part-2-a-question-of-centring"]], "Data": [[74, "data"], [75, "data"], [76, "data"], [88, "data"]], "Data collection videos": [[73, "data-collection-videos"]], "Data files": [[3, "data-files"]], "Dataset 1": [[75, "dataset-1"], [75, "id1"], [75, "id11"]], "Dataset 2": [[75, "dataset-2"], [75, "id2"], [75, "id12"]], "Dataset 3": [[75, "dataset-3"], [75, "id3"], [75, "id13"]], "Dataset 4": [[75, "dataset-4"], [75, "id4"], [75, "id14"]], "Dataset 5": [[75, "dataset-5"], [75, "id5"], [75, "id15"]], "Dataset 6": [[75, "dataset-6"], [75, "id6"], [75, "id8"], [75, "id10"], [75, "id16"]], "Dataset 7": [[75, "dataset-7"], [75, "id7"], [75, "id17"]], "Datasets 1-5 & 7": [[75, "datasets-1-5-7"], [75, "id9"]], "Defining a scaling model": [[4, "defining-a-scaling-model"]], "Delta CC-half": [[76, "delta-cc-half"]], "Details": [[35, "details"]], "Detector distance": [[74, "detector-distance"]], "Determining lattice symmetry": [[74, "determining-lattice-symmetry"]], "Developer Examples": [[5, "developer-examples"]], "Development Builds": [[91, "development-builds"]], "Development Teams": [[0, "development-teams"]], "Dials parameters": [[48, "dials-parameters"]], "Discover a better experimental model": [[78, "discover-a-better-experimental-model"]], "Distl parameters": [[48, "distl-parameters"]], "Documentation": [[8, "documentation"]], "Downloading the DIALS regression test data": [[9, "downloading-the-dials-regression-test-data"]], "Entry points": [[4, "entry-points"]], "Example": [[40, "example"]], "Example use cases": [[43, "example-use-cases"]], "Examples use cases": [[72, "examples-use-cases"]], "Excluding bad frames": [[73, "excluding-bad-frames"]], "Experiment list files": [[3, "experiment-list-files"]], "Explorations of Reciprocal Space": [[76, "explorations-of-reciprocal-space"]], "Exploratory analysis": [[74, "exploratory-analysis"]], "Export": [[93, "export"]], "Export the data": [[73, "export-the-data"]], "Exporting": [[88, "exporting"]], "Exporting as MTZ": [[87, "exporting-as-mtz"]], "Exporting to unmerged MTZ": [[82, "exporting-to-unmerged-mtz"], [86, "exporting-to-unmerged-mtz"]], "Extending DIALS": [[4, "extending-dials"]], "Extending dials.index": [[4, "extending-dials-index"]], "Extending dials.scale": [[4, "extending-dials-scale"]], "Extending profile models": [[4, "extending-profile-models"]], "Extensions": [[31, "extensions"]], "Feedback": [[79, "feedback"]], "Find Spots": [[78, "find-spots"], [82, "find-spots"], [86, "find-spots"], [87, "find-spots"]], "Find spots": [[73, "find-spots"]], "Find the Bravais lattice (optional)": [[73, "find-the-bravais-lattice-optional"]], "Find the beam centre": [[73, "find-the-beam-centre"]], "Full parameter definitions": [[34, "full-parameter-definitions"], [35, "full-parameter-definitions"], [36, "full-parameter-definitions"], [37, "full-parameter-definitions"], [38, 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[75, "indexing"], [78, "indexing"], [82, "indexing"], [85, "indexing"], [86, "indexing"], [87, "indexing"], [88, "indexing"]], "Indexing SSX data with dials.ssx_index": [[96, "indexing-ssx-data-with-dials-ssx-index"]], "Indexing with the corrected beam centre": [[78, "indexing-with-the-corrected-beam-centre"]], "Individual processing": [[83, "individual-processing"]], "Inspecting the results": [[87, "inspecting-the-results"]], "Installation": [[7, "installation"], [91, "installation"], [91, "id1"]], "Installation for Developers": [[9, "installation-for-developers"]], "Integrating SSX data with dials.ssx_integrate": [[96, "integrating-ssx-data-with-dials-ssx-integrate"]], "Integration": [[73, "integration"], [74, "integration"], [75, "integration"], [82, "integration"], [86, "integration"], [87, "integration"], [88, "integration"]], "Intensity Clustering": [[76, "intensity-clustering"]], "Introduction": [[34, "introduction"], [35, "introduction"], [36, "introduction"], [37, "introduction"], [38, "introduction"], [39, "introduction"], [40, "introduction"], [41, "introduction"], [42, "introduction"], [43, "introduction"], [44, "introduction"], [45, "introduction"], [46, "introduction"], [47, "introduction"], [48, "introduction"], [49, "introduction"], [50, "introduction"], [51, "introduction"], [52, "introduction"], [53, "introduction"], [54, "introduction"], [55, "introduction"], [56, "introduction"], [57, "introduction"], [58, "introduction"], [59, "introduction"], [60, "introduction"], [61, "introduction"], [62, "introduction"], [63, "introduction"], [64, "introduction"], [65, "introduction"], [66, "introduction"], [67, "introduction"], [68, "introduction"], [69, "introduction"], [70, "introduction"], [72, "introduction"], [74, "introduction"], [75, "introduction"], [76, "introduction"], [77, "introduction"], [78, "introduction"], [81, "introduction"], [82, "introduction"], [83, "introduction"], [84, "introduction"], [85, "introduction"], [86, "introduction"], [87, "introduction"], [88, "introduction"]], "Joint refinement": [[83, "joint-refinement"]], "Keeping a Development Environment current": [[9, "keeping-a-development-environment-current"]], "Lattice search strategies": [[4, "lattice-search-strategies"]], "Library Reference": [[32, "library-reference"]], "Lysozyme nanocrystals": [[75, "lysozyme-nanocrystals"]], "Mac and Linux binary installers": [[91, "mac-and-linux-binary-installers"]], "Mac graphical binary installers": [[91, "mac-graphical-binary-installers"]], "Manual reprocessing": [[84, "manual-reprocessing"]], "ModuleNotFoundError: No module named \u2018gltbx_gl_ext\u2019": [[9, "modulenotfounderror-no-module-named-gltbx-gl-ext"]], "Multi-crystal analysis with DIALS and BLEND: individual vs joint refinement": [[83, "multi-crystal-analysis-with-dials-and-blend-individual-vs-joint-refinement"]], "Multi-crystal analysis with DIALS and xia2.multiplex": [[76, "multi-crystal-analysis-with-dials-and-xia2-multiplex"]], "Multi-crystal symmetry analysis and scaling with DIALS": [[84, "multi-crystal-symmetry-analysis-and-scaling-with-dials"]], "Multi-dataset symmetry determination": [[73, "multi-dataset-symmetry-determination"]], "Multi-lattice Tutorial": [[85, "multi-lattice-tutorial"]], "Multi-tile refinement": [[81, "multi-tile-refinement"]], "MyD88TIR small wedges": [[74, "myd88tir-small-wedges"]], "Next steps": [[7, "next-steps"]], "Note about pedestal and offset": [[73, "note-about-pedestal-and-offset"]], "Organising committee": [[97, "organising-committee"]], "Orientation matrix": [[2, "orientation-matrix"]], "Orthogonalisation convention": [[2, "orthogonalisation-convention"]], "Other datasets": [[73, "other-datasets"]], "Output for SADABS (alternate path)": [[88, "output-for-sadabs-alternate-path"]], "Parameters": [[7, "parameters"]], "Post Experiment Processing": [[76, "post-experiment-processing"]], "Practicalities for large datasets": [[1, "practicalities-for-large-datasets"]], "Preferential 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"refine-the-geometry"]], "Refinement": [[82, "refinement"], [86, "refinement"], [87, "refinement"], [88, "refinement"], [93, "refinement"]], "Refinement and Integration": [[85, "refinement-and-integration"]], "Refining multi-tile detector metrology with DIALS": [[81, "refining-multi-tile-detector-metrology-with-dials"]], "Refining the detector distance": [[74, "refining-the-detector-distance"]], "Reflection files": [[3, "reflection-files"]], "SARS-CoV-2 main protease (Mpro)": [[82, "sars-cov-2-main-protease-mpro"]], "SSX processing guide": [[96, "ssx-processing-guide"]], "Scale the data together": [[73, "scale-the-data-together"]], "Scaling": [[73, "scaling"], [74, "scaling"], [87, "scaling"], [88, "scaling"]], "Scaling against a reference dataset": [[1, "scaling-against-a-reference-dataset"]], "Scaling and Merging": [[82, "scaling-and-merging"], [86, "scaling-and-merging"]], "Scaling and merging": [[75, "scaling-and-merging"]], "Scan-varying refinement": [[75, "scan-varying-refinement"]], "Scripted processing": [[74, "scripted-processing"]], "Sets 0-9": [[76, "sets-0-9"]], "Sets 10-19": [[76, "sets-10-19"]], "Sets 20-29": [[76, "sets-20-29"]], "Setting up a Development Environment on Linux or Mac": [[9, "setting-up-a-development-environment-on-linux-or-mac"]], "Small-molecule data reduction tutorial": [[88, "small-molecule-data-reduction-tutorial"]], "Solve the structure": [[73, "solve-the-structure"]], "Sourcing the DIALS environment": [[7, "sourcing-the-dials-environment"]], "Spot finding": [[88, "spot-finding"]], "Spot-finding": [[74, "spot-finding"], [75, "spot-finding"]], "Stable Release: DIALS 3.20.0": [[91, "stable-release-dials-3-20-0"]], "Static model refinement": [[75, "static-model-refinement"]], "Summary of coordinate frames": [[2, "summary-of-coordinate-frames"]], "Symmetry Determination": [[88, "symmetry-determination"]], "Symmetry analysis": [[82, "symmetry-analysis"], [86, "symmetry-analysis"]], "Symmetry, Scaling and Merging": [[85, "symmetry-scaling-and-merging"]], "Table of Contents": [[20, "table-of-contents"], [31, "table-of-contents"]], "Testing the server": [[48, "testing-the-server"]], "The DXTBX goniometer model": [[2, "the-dxtbx-goniometer-model"]], "The diffractometer equation": [[2, "the-diffractometer-equation"]], "The laboratory frame": [[2, "the-laboratory-frame"]], "Tilt axis orientation": [[74, "tilt-axis-orientation"]], "Tutorial data": [[82, "tutorial-data"], [86, "tutorial-data"], [87, "tutorial-data"]], "Tutorials": [[80, "tutorials"]], "Unit Cell Comparisons": [[76, "unit-cell-comparisons"]], "Unit cell refinement": [[88, "unit-cell-refinement"]], "User guide for scaling data with DIALS": [[1, "user-guide-for-scaling-data-with-dials"]], "Using DIALS at Diamond Light Source": [[79, "using-dials-at-diamond-light-source"]], "Using DIALS with xia2": [[79, "using-dials-with-xia2"]], "Util": [[33, "util"]], "What to do next": [[81, "what-to-do-next"]], "What to do next?": [[83, "what-to-do-next"]], "Workshops": [[99, "workshops"]], "Writing a new format class": [[4, "writing-a-new-format-class"]], "dials.algorithms.background": [[10, "module-dials.algorithms.background"]], "dials.algorithms.indexing": [[11, "module-dials.algorithms.indexing"]], "dials.algorithms.indexing.basis_vector_search": [[11, "module-dials.algorithms.indexing.basis_vector_search"]], "dials.algorithms.indexing.indexer": [[11, "module-dials.algorithms.indexing.indexer"]], "dials.algorithms.indexing.lattice_search": [[11, "module-dials.algorithms.indexing.lattice_search"]], "dials.algorithms.indexing.max_cell": [[11, "module-dials.algorithms.indexing.max_cell"]], "dials.algorithms.indexing.model_evaluation": [[11, "module-dials.algorithms.indexing.model_evaluation"]], "dials.algorithms.indexing.stills_indexer": [[11, "module-dials.algorithms.indexing.stills_indexer"]], "dials.algorithms.integration": [[12, "module-dials.algorithms.integration.integrator"]], "dials.algorithms.profile_model": [[13, "module-dials.algorithms.profile_model"]], "dials.algorithms.refinement": [[14, "module-dials.algorithms.refinement.reflection_manager"]], "dials.algorithms.scaling": [[15, "module-dials.algorithms.scaling"]], "dials.algorithms.spot_finding": [[16, "module-dials.algorithms.spot_finding.finder"]], "dials.algorithms.spot_prediction": [[17, "module-dials.algorithms.spot_prediction.reflection_predictor"]], "dials.algorithms.symmetry": [[18, "module-dials.algorithms.symmetry"]], "dials.algorithms.symmetry.cosym": [[18, "module-dials.algorithms.symmetry.cosym"]], "dials.align_crystal": [[34, "dials-align-crystal"]], "dials.anvil_correction": [[35, "dials-anvil-correction"]], "dials.apply_mask": [[36, "dials-apply-mask"]], "dials.check_indexing_symmetry": [[37, "dials-check-indexing-symmetry"]], "dials.combine_experiments": [[38, "dials-combine-experiments"]], "dials.compare_orientation_matrices": [[39, "dials-compare-orientation-matrices"]], 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"dials.algorithms.refinement.refiner.RefinerFactory.config_refinery", false]], "config_restraints() (dials.algorithms.refinement.refiner.refinerfactory static method)": [[14, "dials.algorithms.refinement.refiner.RefinerFactory.config_restraints", false]], "config_sparse() (dials.algorithms.refinement.refiner.refinerfactory static method)": [[14, "dials.algorithms.refinement.refiner.RefinerFactory.config_sparse", false]], "config_target() (dials.algorithms.refinement.refiner.refinerfactory static method)": [[14, "dials.algorithms.refinement.refiner.RefinerFactory.config_target", false]], "configdict (dials.algorithms.scaling.model.model.scalingmodelbase property)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.configdict", false]], "configure_components() (dials.algorithms.scaling.model.model.arrayscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.configure_components", false]], "configure_components() (dials.algorithms.scaling.model.model.dosedecay method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.configure_components", false]], "configure_components() (dials.algorithms.scaling.model.model.kbscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel.configure_components", false]], "configure_components() (dials.algorithms.scaling.model.model.physicalscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.configure_components", false]], "configure_components() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.configure_components", false]], "configure_filter() (dials.algorithms.spot_finding.factory.spotfinderfactory static method)": [[16, "dials.algorithms.spot_finding.factory.SpotFinderFactory.configure_filter", false]], "configure_modules (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.configure_modules", false]], "configure_threshold() (dials.algorithms.spot_finding.factory.spotfinderfactory static method)": [[16, "dials.algorithms.spot_finding.factory.SpotFinderFactory.configure_threshold", false]], "consecutive_refinement_order (dials.algorithms.scaling.model.model.arrayscalingmodel property)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.consecutive_refinement_order", false]], "consecutive_refinement_order (dials.algorithms.scaling.model.model.dosedecay property)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.consecutive_refinement_order", false]], "consecutive_refinement_order (dials.algorithms.scaling.model.model.kbscalingmodel property)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel.consecutive_refinement_order", false]], "consecutive_refinement_order (dials.algorithms.scaling.model.model.physicalscalingmodel property)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.consecutive_refinement_order", false]], "consecutive_refinement_order() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.consecutive_refinement_order", false]], "constantweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)": [[14, "dials.algorithms.refinement.weighting_strategies.ConstantWeightingStrategy", false]], "convergence_as_shift_over_esd (dials.algorithms.refinement.engine.gaussnewtoniterations attribute)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations.convergence_as_shift_over_esd", false]], "convert_to_cambridge() (in module dials.util.export_mtz)": [[33, "dials.util.export_mtz.convert_to_cambridge", false]], "copy() (dxtbx.imageset.memreader method)": [[26, "dxtbx.imageset.MemReader.copy", false]], "correlationcoefficientaccumulator (class in dials.algorithms.symmetry.laue_group)": [[18, "dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator", false]], "cosymanalysis (class in dials.algorithms.symmetry.cosym)": [[18, "dials.algorithms.symmetry.cosym.CosymAnalysis", false]], "crystal (class in dxtbx.model)": [[22, "dxtbx.model.Crystal", false]], "crystal (dials.algorithms.indexing.model_evaluation.result attribute)": [[11, "dials.algorithms.indexing.model_evaluation.Result.crystal", false]], "crystal() (in module dxtbx.serialize.load)": [[30, "dxtbx.serialize.load.crystal", false]], "crystalfactory (class in dxtbx.model.crystal)": [[22, "dxtbx.model.crystal.CrystalFactory", false]], "crystals() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.crystals", false]], "curvatures() (dials.algorithms.symmetry.cosym.target.target method)": [[18, "dials.algorithms.symmetry.cosym.target.Target.curvatures", false]], "curvatures_fd() (dials.algorithms.symmetry.cosym.target.target method)": [[18, "dials.algorithms.symmetry.cosym.target.Target.curvatures_fd", false]], "damping_value (dials.algorithms.refinement.engine.gaussnewtoniterations attribute)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations.damping_value", false]], "data (dxtbx.imageset.externallookupitembool property)": [[26, "dxtbx.imageset.ExternalLookupItemBool.data", false]], "data (dxtbx.imageset.externallookupitemdouble property)": [[26, "dxtbx.imageset.ExternalLookupItemDouble.data", false]], "data() (dials.algorithms.integration.integrator.integratorexecutor method)": [[12, "dials.algorithms.integration.integrator.IntegratorExecutor.data", false]], "data() (dials.algorithms.integration.integrator.profilemodellerexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileModellerExecutor.data", false]], "data() (dials.algorithms.integration.integrator.profilevalidatorexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileValidatorExecutor.data", false]], "data() (dials.algorithms.integration.integrator.reflectionmanager method)": [[12, "dials.algorithms.integration.integrator.ReflectionManager.data", false]], "data() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.data", false]], "default (dials.extensions.gaussian_rs_profile_model_ext.gaussianrsprofilemodelext attribute)": [[31, "dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt.default", false]], "default (dials.extensions.simple_centroid_ext.simplecentroidext attribute)": [[31, "dials.extensions.simple_centroid_ext.SimpleCentroidExt.default", false]], "del_last_row() (dials.algorithms.refinement.engine.journal method)": [[14, "dials.algorithms.refinement.engine.Journal.del_last_row", false]], "denominator() (dials.algorithms.symmetry.laue_group.correlationcoefficientaccumulator method)": [[18, "dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator.denominator", false]], "dest_dir_prefix (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.dest_dir_prefix", false]], "detector (class in dxtbx.model)": [[23, "dxtbx.model.Detector", false]], "detectorcomparison (class in dxtbx.model.experiment_list)": [[24, "dxtbx.model.experiment_list.DetectorComparison", false]], "detectorfactory (class in dxtbx.model.detector)": [[23, "dxtbx.model.detector.DetectorFactory", false]], "detectors() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.detectors", false]], "determine_auto_absorption_params() (in module dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.determine_auto_absorption_params", false]], "determine_esq_outlier_index_arrays() (in module dials.algorithms.scaling.outlier_rejection)": [[15, "dials.algorithms.scaling.outlier_rejection.determine_Esq_outlier_index_arrays", false]], "determine_outlier_index_arrays() (in module dials.algorithms.scaling.outlier_rejection)": [[15, "dials.algorithms.scaling.outlier_rejection.determine_outlier_index_arrays", false]], "determine_reindex_operator_against_reference() (in module dials.algorithms.symmetry.reindex_to_reference)": [[18, "dials.algorithms.symmetry.reindex_to_reference.determine_reindex_operator_against_reference", false]], "dials.algorithms.background": [[10, "module-dials.algorithms.background", false]], "dials.algorithms.indexing": [[11, "module-dials.algorithms.indexing", false]], "dials.algorithms.indexing.assign_indices": [[11, "module-dials.algorithms.indexing.assign_indices", false]], "dials.algorithms.indexing.basis_vector_search": [[11, "module-dials.algorithms.indexing.basis_vector_search", false]], "dials.algorithms.indexing.basis_vector_search.combinations": [[11, "module-dials.algorithms.indexing.basis_vector_search.combinations", false]], "dials.algorithms.indexing.basis_vector_search.optimise": [[11, "module-dials.algorithms.indexing.basis_vector_search.optimise", false]], "dials.algorithms.indexing.compare_orientation_matrices": [[11, "module-dials.algorithms.indexing.compare_orientation_matrices", false]], "dials.algorithms.indexing.indexer": [[11, "module-dials.algorithms.indexing.indexer", false]], "dials.algorithms.indexing.lattice_search": [[11, "module-dials.algorithms.indexing.lattice_search", false]], "dials.algorithms.indexing.max_cell": [[11, "module-dials.algorithms.indexing.max_cell", false]], "dials.algorithms.indexing.model_evaluation": [[11, "module-dials.algorithms.indexing.model_evaluation", false]], "dials.algorithms.indexing.nearest_neighbor": [[11, "module-dials.algorithms.indexing.nearest_neighbor", false]], "dials.algorithms.indexing.refinement": [[11, "module-dials.algorithms.indexing.refinement", false]], "dials.algorithms.indexing.stills_indexer": [[11, "module-dials.algorithms.indexing.stills_indexer", false]], "dials.algorithms.indexing.symmetry": [[11, "module-dials.algorithms.indexing.symmetry", false]], "dials.algorithms.integration.integrator": [[12, "module-dials.algorithms.integration.integrator", false]], "dials.algorithms.profile_model": [[13, "module-dials.algorithms.profile_model", false]], "dials.algorithms.refinement.engine": [[14, "module-dials.algorithms.refinement.engine", false]], "dials.algorithms.refinement.refiner": [[14, "module-dials.algorithms.refinement.refiner", false]], "dials.algorithms.refinement.reflection_manager": [[14, "module-dials.algorithms.refinement.reflection_manager", false]], "dials.algorithms.refinement.target": [[14, "module-dials.algorithms.refinement.target", false]], "dials.algorithms.refinement.target_stills": [[14, "module-dials.algorithms.refinement.target_stills", false]], "dials.algorithms.refinement.weighting_strategies": [[14, "module-dials.algorithms.refinement.weighting_strategies", false]], "dials.algorithms.scaling": [[15, "module-dials.algorithms.scaling", false]], "dials.algorithms.scaling.model.model": [[15, "module-dials.algorithms.scaling.model.model", false]], "dials.algorithms.scaling.outlier_rejection": [[15, "module-dials.algorithms.scaling.outlier_rejection", false]], "dials.algorithms.spot_finding.factory": [[16, "module-dials.algorithms.spot_finding.factory", false]], "dials.algorithms.spot_finding.finder": [[16, "module-dials.algorithms.spot_finding.finder", false]], "dials.algorithms.spot_prediction.reflection_predictor": [[17, "module-dials.algorithms.spot_prediction.reflection_predictor", false]], "dials.algorithms.symmetry": [[18, "module-dials.algorithms.symmetry", false]], "dials.algorithms.symmetry.cosym": [[18, "module-dials.algorithms.symmetry.cosym", false]], "dials.algorithms.symmetry.cosym.engine": [[18, "module-dials.algorithms.symmetry.cosym.engine", false]], "dials.algorithms.symmetry.cosym.target": [[18, "module-dials.algorithms.symmetry.cosym.target", false]], "dials.algorithms.symmetry.laue_group": [[18, "module-dials.algorithms.symmetry.laue_group", false]], "dials.algorithms.symmetry.reindex_to_reference": [[18, "module-dials.algorithms.symmetry.reindex_to_reference", false]], "dials.array_family.flex": [[20, "module-dials.array_family.flex", false]], "dials.extensions.dispersion_spotfinder_threshold_ext": [[31, "module-dials.extensions.dispersion_spotfinder_threshold_ext", false]], "dials.extensions.gaussian_rs_profile_model_ext": [[31, "module-dials.extensions.gaussian_rs_profile_model_ext", false]], "dials.extensions.null_background_ext": [[31, "module-dials.extensions.null_background_ext", false]], "dials.extensions.simple_background_ext": [[31, "module-dials.extensions.simple_background_ext", false]], "dials.extensions.simple_centroid_ext": [[31, "module-dials.extensions.simple_centroid_ext", false]], "dials.util.command_line": [[33, "module-dials.util.command_line", false]], "dials.util.export_mtz": [[33, "module-dials.util.export_mtz", false]], "dials.util.export_text": [[33, "module-dials.util.export_text", false]], "dials.util.image": [[33, "module-dials.util.image", false]], "dials.util.installer": [[33, "module-dials.util.installer", false]], "dials.util.ioutil": [[33, "module-dials.util.ioutil", false]], "dials.util.nexus": [[33, "module-dials.util.nexus", false]], "dials.util.options": [[33, "module-dials.util.options", false]], "dialsindexerror": [[11, "dials.algorithms.indexing.DialsIndexError", false]], "dialsindexrefineerror": [[11, "dials.algorithms.indexing.DialsIndexRefineError", false]], "diff_phil (dials.util.options.argumentparser property)": [[33, "dials.util.options.ArgumentParser.diff_phil", false]], "diff_phil (dials.util.options.philcommandparser property)": [[33, "dials.util.options.PhilCommandParser.diff_phil", false]], "difference_rotation_matrix_axis_angle() (in module dials.algorithms.indexing.compare_orientation_matrices)": [[11, "dials.algorithms.indexing.compare_orientation_matrices.difference_rotation_matrix_axis_angle", false]], "dim (dials.algorithms.refinement.target.target property)": [[14, "dials.algorithms.refinement.target.Target.dim", false]], "dim (dials.algorithms.symmetry.cosym.target.target attribute)": [[18, "dials.algorithms.symmetry.cosym.target.Target.dim", false]], "disablempmixin (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.DisableMPmixin", false]], "dispersionspotfinderthresholdext (class in dials.extensions.dispersion_spotfinder_threshold_ext)": [[31, "dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt", false]], "dosedecay (class in dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.DoseDecay", false]], "dump() (in module dials.util.nexus)": [[33, "dials.util.nexus.dump", false]], "dx (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.dx", false]], "dxtbx.imageset": [[26, "module-dxtbx.imageset", false]], "dxtbx.model.beam": [[21, "module-dxtbx.model.beam", false]], "dxtbx.model.crystal": [[22, "module-dxtbx.model.crystal", false]], "dxtbx.model.detector": [[23, "module-dxtbx.model.detector", false]], "dxtbx.model.experiment_list": [[24, "module-dxtbx.model.experiment_list", false]], "dxtbx.model.goniometer": [[25, "module-dxtbx.model.goniometer", false]], "dxtbx.model.profile": [[28, "module-dxtbx.model.profile", false]], "dxtbx.model.scan": [[29, "module-dxtbx.model.scan", false]], "dxtbx.serialize.imageset": [[30, "module-dxtbx.serialize.imageset", false]], "dxtbx.serialize.load": [[30, "module-dxtbx.serialize.load", false]], "dxtbx.serialize.xds": [[30, "module-dxtbx.serialize.xds", false]], "dy (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.dy", false]], "e_refine() (in module dials.algorithms.indexing.stills_indexer)": [[11, "dials.algorithms.indexing.stills_indexer.e_refine", false]], "empty() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.empty", false]], "end() (dials.util.command_line.command class method)": [[33, "dials.util.command_line.Command.end", false]], "error_model (dials.algorithms.scaling.model.model.scalingmodelbase property)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.error_model", false]], "estimate_global_threshold() (in module dials.extensions.dispersion_spotfinder_threshold_ext)": [[31, "dials.extensions.dispersion_spotfinder_threshold_ext.estimate_global_threshold", false]], "evaluate() (dials.algorithms.indexing.model_evaluation.modelevaluation method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelEvaluation.evaluate", false]], "evaluate() (dials.algorithms.indexing.model_evaluation.strategy method)": [[11, "dials.algorithms.indexing.model_evaluation.Strategy.evaluate", false]], "exception (dials.util.options.argumenthandlingerrorinfo attribute)": [[33, "dials.util.options.ArgumentHandlingErrorInfo.exception", false]], "executor (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Executor", false]], "exp_nos (dials.util.export_mtz.wavelengthgroup attribute)": [[33, "dials.util.export_mtz.WavelengthGroup.exp_nos", false]], "experiment_list() (in module dxtbx.serialize.load)": [[30, "dxtbx.serialize.load.experiment_list", false]], "experiment_list_for_crystal() (dials.algorithms.indexing.stills_indexer.stillsindexer method)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexer.experiment_list_for_crystal", false]], "experiment_type (dials.algorithms.refinement.reflection_manager.reflectionmanager attribute)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.experiment_type", false]], "experiment_type (dials.algorithms.refinement.reflection_manager.stillsreflectionmanager attribute)": [[14, "dials.algorithms.refinement.reflection_manager.StillsReflectionManager.experiment_type", false]], "experimentlist (class in dxtbx.model)": [[24, "dxtbx.model.ExperimentList", false]], "experimentlistfactory (class in dxtbx.model.experiment_list)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory", false]], "export_as_json() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.export_as_json", false]], "export_mtz() (in module dials.util.export_mtz)": [[33, "dials.util.export_mtz.export_mtz", false]], "export_reflections() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.export_reflections", false]], "export_text() (in module dials.util.export_text)": [[33, "dials.util.export_text.export_text", false]], "extend() (dials.algorithms.indexing.model_evaluation.modelrank method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRank.extend", false]], "extend() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter.extend", false]], "extend() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.extend", false]], "external_lookup (dxtbx.imageset.imageset property)": [[26, "dxtbx.imageset.ImageSet.external_lookup", false]], "external_lookup (dxtbx.imageset.imagesetdata property)": [[26, "dxtbx.imageset.ImageSetData.external_lookup", false]], "externaldelpsiweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)": [[14, "dials.algorithms.refinement.weighting_strategies.ExternalDelPsiWeightingStrategy", false]], "externallookup (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ExternalLookup", false]], "externallookupitembool (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ExternalLookupItemBool", false]], "externallookupitemdouble (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ExternalLookupItemDouble", false]], "extract_reference_intensities() (in module dials.algorithms.symmetry.cosym)": [[18, "dials.algorithms.symmetry.cosym.extract_reference_intensities", false]], "extractpixelsfromimage (class in dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.ExtractPixelsFromImage", false]], "extractpixelsfromimage2dnoshoeboxes (class in dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.ExtractPixelsFromImage2DNoShoeboxes", false]], "extractspots (class in dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.ExtractSpots", false]], "extractspotsparalleltask (class in dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.ExtractSpotsParallelTask", false]], "fft1d (class in dials.algorithms.indexing.basis_vector_search)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT1D", false]], "fft3d (class in dials.algorithms.indexing.basis_vector_search)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT3D", false]], "filename (dxtbx.imageset.externallookupitembool property)": [[26, "dxtbx.imageset.ExternalLookupItemBool.filename", false]], "filename (dxtbx.imageset.externallookupitemdouble property)": [[26, "dxtbx.imageset.ExternalLookupItemDouble.filename", false]], "filename_or_none() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.filename_or_none", false]], "filename_to_absolute() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.filename_to_absolute", false]], "filter_by_likelihood() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter.filter_by_likelihood", false]], "filter_by_n_indexed() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter.filter_by_n_indexed", false]], "filter_by_volume() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter.filter_by_volume", false]], "filter_doubled_cell() (in module dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.filter_doubled_cell", false]], "filter_known_symmetry() (in module dials.algorithms.indexing.basis_vector_search.combinations)": [[11, "dials.algorithms.indexing.basis_vector_search.combinations.filter_known_symmetry", false]], "filter_obs() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.filter_obs", false]], "filter_similar_orientations() (in module dials.algorithms.indexing.basis_vector_search.combinations)": [[11, "dials.algorithms.indexing.basis_vector_search.combinations.filter_similar_orientations", false]], "filterrunner (class in dials.algorithms.spot_finding.factory)": [[16, "dials.algorithms.spot_finding.factory.FilterRunner", false]], "final_outlier_arrays (dials.algorithms.scaling.outlier_rejection.outlierrejectionbase attribute)": [[15, "dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase.final_outlier_arrays", false]], "finalise() (dials.algorithms.integration.integrator.integrator3dthreaded method)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded.finalise", false]], "finalise() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.finalise", false]], "finalize() (dials.algorithms.integration.integrator.integratorexecutor method)": [[12, "dials.algorithms.integration.integrator.IntegratorExecutor.finalize", false]], "finalize() (dials.algorithms.integration.integrator.profilemodellerexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileModellerExecutor.finalize", false]], "finalize() (dials.algorithms.integration.integrator.profilevalidatorexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileValidatorExecutor.finalize", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integrator2d static method)": [[12, "dials.algorithms.integration.integrator.Integrator2D.finalize_reflections", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integrator3d static method)": [[12, "dials.algorithms.integration.integrator.Integrator3D.finalize_reflections", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integratorflat3d static method)": [[12, "dials.algorithms.integration.integrator.IntegratorFlat3D.finalize_reflections", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integratorsingle2d static method)": [[12, "dials.algorithms.integration.integrator.IntegratorSingle2D.finalize_reflections", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integratorstills static method)": [[12, "dials.algorithms.integration.integrator.IntegratorStills.finalize_reflections", false]], "find() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.find", false]], "find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.fft1d method)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT1D.find_basis_vectors", false]], "find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.fft3d method)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT3D.find_basis_vectors", false]], "find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.realspacegridsearch method)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.find_basis_vectors", false]], "find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.strategy method)": [[11, "dials.algorithms.indexing.basis_vector_search.Strategy.find_basis_vectors", false]], "find_crystal_models() (dials.algorithms.indexing.lattice_search.lowresspotmatch method)": [[11, "dials.algorithms.indexing.lattice_search.LowResSpotMatch.find_crystal_models", false]], "find_crystal_models() (dials.algorithms.indexing.lattice_search.pinkindexer method)": [[11, "dials.algorithms.indexing.lattice_search.PinkIndexer.find_crystal_models", false]], "find_crystal_models() (dials.algorithms.indexing.lattice_search.strategy method)": [[11, "dials.algorithms.indexing.lattice_search.Strategy.find_crystal_models", false]], "find_lattices() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.find_lattices", false]], "find_matching_symmetry() (in module dials.algorithms.indexing.symmetry)": [[11, "dials.algorithms.indexing.symmetry.find_matching_symmetry", false]], "find_max_cell() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.find_max_cell", false]], "find_max_cell() (in module dials.algorithms.indexing.max_cell)": [[11, "dials.algorithms.indexing.max_cell.find_max_cell", false]], "find_spots() (dials.algorithms.spot_finding.finder.spotfinder method)": [[16, "dials.algorithms.spot_finding.finder.SpotFinder.find_spots", false]], "finished() (dials.algorithms.integration.integrator.reflectionmanager method)": [[12, "dials.algorithms.integration.integrator.ReflectionManager.finished", false]], "finished() (dials.util.command_line.progressbar method)": [[33, "dials.util.command_line.ProgressBar.finished", false]], "fit_profiles() (dials.algorithms.integration.integrator.integrator method)": [[12, "dials.algorithms.integration.integrator.Integrator.fit_profiles", false]], "fix_initial_parameter() (dials.algorithms.scaling.model.model.dosedecay method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.fix_initial_parameter", false]], "fix_initial_parameter() (dials.algorithms.scaling.model.model.physicalscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.fix_initial_parameter", false]], "fix_initial_parameter() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.fix_initial_parameter", false]], "fixed_components (dials.algorithms.scaling.model.model.scalingmodelbase property)": [[15, 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"dxtbx.model.experiment_list.ExperimentListFactory.from_args", false]], "from_data() (dials.algorithms.scaling.model.model.arrayscalingmodel class method)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.from_data", false]], "from_data() (dials.algorithms.scaling.model.model.dosedecay class method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.from_data", false]], "from_data() (dials.algorithms.scaling.model.model.kbscalingmodel class method)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel.from_data", false]], "from_data() (dials.algorithms.scaling.model.model.physicalscalingmodel class method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.from_data", false]], "from_data() (dials.algorithms.scaling.model.model.scalingmodelbase class method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.from_data", false]], "from_dict() (dials.algorithms.scaling.model.model.arrayscalingmodel class method)": [[15, 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"dxtbx.model.beam.BeamFactory.from_dict", false]], "from_dict() (dxtbx.model.crystal static method)": [[22, "dxtbx.model.Crystal.from_dict", false]], "from_dict() (dxtbx.model.crystal.crystalfactory static method)": [[22, "dxtbx.model.crystal.CrystalFactory.from_dict", false]], "from_dict() (dxtbx.model.detector static method)": [[23, "dxtbx.model.Detector.from_dict", false]], "from_dict() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.from_dict", false]], "from_dict() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_dict", false]], "from_dict() (dxtbx.model.goniometer.goniometer static method)": [[25, "dxtbx.model.goniometer.Goniometer.from_dict", false]], "from_dict() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.from_dict", false]], "from_dict() (dxtbx.model.goniometer.multiaxisgoniometer static method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.from_dict", false]], "from_dict() (dxtbx.model.mosaiccrystalkabsch2010 class method)": [[22, "dxtbx.model.MosaicCrystalKabsch2010.from_dict", false]], "from_dict() (dxtbx.model.mosaiccrystalsauter2014 class method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.from_dict", false]], "from_dict() (dxtbx.model.profile.profilemodelfactory static method)": [[28, "dxtbx.model.profile.ProfileModelFactory.from_dict", false]], "from_dict() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.from_dict", false]], "from_file() (dxtbx.model.experimentlist static method)": [[24, "dxtbx.model.ExperimentList.from_file", false]], "from_filenames() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_filenames", false]], "from_imageset() (dxtbx.imageset.imagegrid static method)": [[26, "dxtbx.imageset.ImageGrid.from_imageset", false]], "from_imageset_and_crystal() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_imageset_and_crystal", false]], "from_json() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_json", false]], "from_json_file() (dials.algorithms.refinement.engine.journal class method)": [[14, "dials.algorithms.refinement.engine.Journal.from_json_file", false]], "from_json_file() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_json_file", false]], "from_mosflm_matrix() (dxtbx.model.crystal.crystalfactory static method)": [[22, "dxtbx.model.crystal.CrystalFactory.from_mosflm_matrix", false]], "from_parameters() (dials.algorithms.indexing.indexer.indexer static method)": [[11, "dials.algorithms.indexing.indexer.Indexer.from_parameters", false]], "from_parameters() (dials.algorithms.spot_finding.factory.spotfinderfactory static method)": [[16, "dials.algorithms.spot_finding.factory.SpotFinderFactory.from_parameters", false]], "from_parameters_and_experiments() (dials.algorithms.refinement.target.targetfactory static method)": [[14, "dials.algorithms.refinement.target.TargetFactory.from_parameters_and_experiments", false]], "from_parameters_data_experiments() (dials.algorithms.refinement.refiner.refinerfactory class method)": [[14, "dials.algorithms.refinement.refiner.RefinerFactory.from_parameters_data_experiments", false]], "from_parameters_reflections_experiments() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.from_parameters_reflections_experiments", false]], "from_phil() (dials.algorithms.integration.integrator.parameters static method)": [[12, "dials.algorithms.integration.integrator.Parameters.from_phil", false]], "from_phil() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.from_phil", false]], "from_phil() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.from_phil", false]], "from_phil() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.from_phil", false]], "from_phil() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.from_phil", false]], "from_pickle_file() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_pickle_file", false]], "from_sequence_and_crystal() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_sequence_and_crystal", false]], "from_serialized_format() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_serialized_format", false]], "from_stills_and_crystal() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_stills_and_crystal", false]], "from_template() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.from_template", false]], "from_templates() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_templates", false]], "from_templates() (dxtbx.model.experimentlist static method)": [[24, "dxtbx.model.ExperimentList.from_templates", false]], "from_xds() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_xds", false]], "gain (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.gain", false]], "gaussianrsprofilemodelext (class in dials.extensions.gaussian_rs_profile_model_ext)": [[31, "dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt", false]], "gaussnewtoniterations (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations", false]], "generate_from_phil() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.generate_from_phil", false]], "generate_phil_scope() (in module dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.generate_phil_scope", false]], "generate_phil_scope() (in module dials.algorithms.spot_finding.factory)": [[16, "dials.algorithms.spot_finding.factory.generate_phil_scope", false]], "get_a_as_sqr() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.get_A_as_sqr", false]], "get_a_inverse_as_sqr() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.get_A_inverse_as_sqr", false]], "get_accepted_refs_size() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_accepted_refs_size", false]], "get_alpha_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_alpha_angle", false]], "get_angles() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.get_angles", false]], "get_array_range() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_array_range", false]], "get_axes() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.get_axes", false]], "get_beam() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_beam", false]], "get_beam() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_beam", false]], "get_beam() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_beam", false]], "get_beam() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_beam", false]], "get_beam() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_beam", false]], "get_centroid_analyser() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_centroid_analyser", false]], "get_corrected_data() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_corrected_data", false]], "get_corrected_data() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_corrected_data", false]], "get_correlation_matrix_for_step() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.get_correlation_matrix_for_step", false]], "get_crystal_symmetry() (dxtbx.model.crystal method)": [[22, "dxtbx.model.Crystal.get_crystal_symmetry", false]], "get_data() (dials.util.image.reader method)": [[33, "dials.util.image.reader.get_data", false]], "get_data() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_data", false]], "get_detector() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_detector", false]], "get_detector() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_detector", false]], "get_detector() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_detector", false]], "get_detector() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_detector", false]], "get_detector() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_detector", false]], "get_detectorbase() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_detectorbase", false]], "get_direction() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_direction", false]], "get_domain_size_ang() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.get_domain_size_ang", false]], "get_elapsed_time() (dials.util.command_line.progressbartimer method)": [[33, "dials.util.command_line.ProgressBarTimer.get_elapsed_time", false]], "get_entry() (in module dials.util.nexus)": [[33, "dials.util.nexus.get_entry", false]], "get_experiments() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_experiments", false]], "get_fixed_rotation() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_fixed_rotation", false]], "get_format_class() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_format_class", false]], "get_format_class() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_format_class", false]], "get_free_reflections() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_free_reflections", false]], "get_free_reflections() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_free_reflections", false]], "get_gain() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_gain", false]], "get_gain() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_gain", false]], "get_goniometer() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_goniometer", false]], "get_goniometer() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_goniometer", false]], "get_goniometer() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_goniometer", false]], "get_goniometer() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_goniometer", false]], "get_goniometer() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_goniometer", false]], "get_grid_size() (dxtbx.imageset.imagegrid method)": [[26, "dxtbx.imageset.ImageGrid.get_grid_size", false]], "get_half_mosaicity_deg() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.get_half_mosaicity_deg", false]], "get_image_identifier() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_image_identifier", false]], "get_image_identifier() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_image_identifier", false]], "get_indexed() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_indexed", false]], "get_inverse_ub_matrix_from_xparm() (in module dials.util.ioutil)": [[33, "dials.util.ioutil.get_inverse_ub_matrix_from_xparm", false]], "get_kappa_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_kappa_angle", false]], "get_kappa_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_kappa_axis", false]], "get_mask() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_mask", false]], "get_mask() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_mask", false]], "get_master_path() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_master_path", false]], "get_matches() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_matches", false]], "get_matches() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_matches", false]], "get_max_inscribed_resolution() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_max_inscribed_resolution", false]], "get_max_resolution() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_max_resolution", false]], "get_mosaicity() (dxtbx.model.mosaiccrystalkabsch2010 method)": [[22, "dxtbx.model.MosaicCrystalKabsch2010.get_mosaicity", false]], "get_names() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_names", false]], "get_names() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.get_names", false]], "get_nrows() (dials.algorithms.refinement.engine.journal method)": [[14, "dials.algorithms.refinement.engine.Journal.get_nrows", false]], "get_num_matches() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.get_num_matches", false]], "get_num_matches_for_experiment() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.get_num_matches_for_experiment", false]], "get_num_matches_for_panel() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.get_num_matches_for_panel", false]], "get_num_scan_points() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_num_scan_points", false]], "get_num_steps() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.get_num_steps", false]], "get_obs() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_obs", false]], "get_omega_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_omega_angle", false]], "get_omega_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_omega_axis", false]], "get_panel_intersection() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_panel_intersection", false]], "get_param_reporter() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_param_reporter", false]], "get_parameter_correlation_matrix() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_parameter_correlation_matrix", false]], "get_params() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_params", false]], "get_path() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_path", false]], "get_path() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_path", false]], "get_pedestal() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_pedestal", false]], "get_phi_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_phi_angle", false]], "get_phi_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_phi_axis", false]], "get_raw_data() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_raw_data", false]], "get_ray_intersection() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_ray_intersection", false]], "get_rotation_axis() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_rotation_axis", false]], "get_rotation_axis_datum() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_rotation_axis_datum", false]], "get_sample_size() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_sample_size", false]], "get_scan() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_scan", false]], "get_scan() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_scan", false]], "get_scan() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_scan", false]], "get_scan() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_scan", false]], "get_scan() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_scan", false]], "get_scan_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_scan_axis", false]], "get_scan_axis() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.get_scan_axis", false]], "get_setting_rotation() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_setting_rotation", false]], "get_setting_rotation_at_scan_point() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_setting_rotation_at_scan_point", false]], "get_setting_rotation_at_scan_points() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_setting_rotation_at_scan_points", false]], "get_shared_components() (dials.algorithms.scaling.model.model.dosedecay method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.get_shared_components", false]], "get_shared_components() (dials.algorithms.scaling.model.model.physicalscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.get_shared_components", false]], "get_shared_components() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.get_shared_components", false]], "get_space_group_type_from_xparm() (in module dials.util.ioutil)": [[33, "dials.util.ioutil.get_space_group_type_from_xparm", false]], "get_spectrum() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_spectrum", false]], "get_template() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_template", false]], "get_template() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_template", false]], "get_template() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_template", false]], "get_vendor() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_vendor", false]], "get_vendortype() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_vendortype", false]], "goniometer (class in dxtbx.model.goniometer)": [[25, "dxtbx.model.goniometer.Goniometer", false]], "goniometercomparison (class in dxtbx.model.experiment_list)": [[24, "dxtbx.model.experiment_list.GoniometerComparison", false]], "goniometerfactory (class in dxtbx.model.goniometer)": [[25, "dxtbx.model.goniometer.GoniometerFactory", false]], "goniometers() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.goniometers", false]], "gradient_threshold (dials.algorithms.refinement.engine.gaussnewtoniterations attribute)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations.gradient_threshold", false]], "groups_cache() (in module dials.algorithms.indexing.symmetry)": [[11, "dials.algorithms.indexing.symmetry.groups_cache", false]], "has_dynamic_mask() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.has_dynamic_mask", false]], "has_projection_2d() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.has_projection_2d", false]], "has_single_file_reader() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.has_single_file_reader", false]], "heading() (in module dials.util.command_line)": [[33, "dials.util.command_line.heading", false]], "hierarchy() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.hierarchy", false]], "hist() (in module dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.hist", false]], "history (dials.algorithms.refinement.refiner.refiner property)": [[14, "dials.algorithms.refinement.refiner.Refiner.history", false]], "hkl_offset (dials.algorithms.indexing.model_evaluation.result attribute)": [[11, "dials.algorithms.indexing.model_evaluation.Result.hkl_offset", false]], "id_ (dials.algorithms.scaling.model.model.arrayscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.id_", false]], "id_ (dials.algorithms.scaling.model.model.dosedecay attribute)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.id_", false]], "id_ (dials.algorithms.scaling.model.model.kbscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel.id_", false]], "id_ (dials.algorithms.scaling.model.model.physicalscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.id_", false]], "id_ (dials.algorithms.scaling.model.model.scalingmodelbase attribute)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.id_", false]], "identifiers (dials.util.export_mtz.wavelengthgroup attribute)": [[33, "dials.util.export_mtz.WavelengthGroup.identifiers", false]], "identifiers() (dxtbx.imageset.memreader method)": [[26, "dxtbx.imageset.MemReader.identifiers", false]], "identifiers() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.identifiers", false]], "identify_outliers() (dials.algorithms.indexing.stills_indexer.stillsindexer method)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexer.identify_outliers", false]], "imagegrid (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageGrid", false]], "imagesequence (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSequence", false]], "imagesequence_from_dict() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.imagesequence_from_dict", false]], "imagesequence_to_dict() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.imagesequence_to_dict", false]], "imageset (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSet", false]], "imageset() (in module dxtbx.serialize.load)": [[30, "dxtbx.serialize.load.imageset", false]], "imageset_from_anyset() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.imageset_from_anyset", false]], "imageset_from_dict() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.imageset_from_dict", false]], "imageset_to_dict() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.imageset_to_dict", false]], "imagesetdata (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSetData", false]], "imagesetfactory (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSetFactory", false]], "imagesetlazy (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSetLazy", false]], "imagesets() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.imagesets", false]], "imgcif() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.imgCIF", false]], "imgcif() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.imgCIF", false]], "imgcif() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.imgCIF", false]], "imgcif() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.imgCIF", false]], "imgcif_h() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.imgCIF_H", false]], "imgcif_h() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.imgCIF_H", false]], "imgcif_h() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.imgCIF_H", false]], "imgcif_h() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.imgCIF_H", false]], "importer (class in dials.util.options)": [[33, "dials.util.options.Importer", false]], "include_gui_packages (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.include_gui_packages", false]], "indent (dials.util.command_line.command attribute)": [[33, "dials.util.command_line.Command.indent", false]], "index() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.index", false]], "index() (dials.algorithms.indexing.stills_indexer.stillsindexer method)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexer.index", false]], "index_reflections() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.index_reflections", false]], "indexer (class in dials.algorithms.indexing.indexer)": [[11, "dials.algorithms.indexing.indexer.Indexer", false]], "indices() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.indices", false]], "indices() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.indices", false]], "initialise() (dials.algorithms.integration.integrator.integrator3dthreaded method)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded.initialise", false]], "initialise_smooth_input() (in module dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.initialise_smooth_input", false]], "initialize() (dials.algorithms.integration.integrator.integratorexecutor method)": [[12, "dials.algorithms.integration.integrator.IntegratorExecutor.initialize", false]], "initialize() (dials.algorithms.integration.integrator.profilemodellerexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileModellerExecutor.initialize", false]], "initialize() (dials.algorithms.integration.integrator.profilevalidatorexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileValidatorExecutor.initialize", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integrator2d static method)": [[12, "dials.algorithms.integration.integrator.Integrator2D.initialize_reflections", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integrator3d static method)": [[12, "dials.algorithms.integration.integrator.Integrator3D.initialize_reflections", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integratorflat3d static method)": [[12, "dials.algorithms.integration.integrator.IntegratorFlat3D.initialize_reflections", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integratorsingle2d static method)": [[12, "dials.algorithms.integration.integrator.IntegratorSingle2D.initialize_reflections", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integratorstills static method)": [[12, "dials.algorithms.integration.integrator.IntegratorStills.initialize_reflections", false]], "installer (class in dials.util.installer)": [[33, "dials.util.installer.installer", false]], "installer_dir (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.installer_dir", false]], "integrate() (dials.algorithms.integration.integrator.integrator method)": [[12, "dials.algorithms.integration.integrator.Integrator.integrate", false]], "integrate() (dials.algorithms.integration.integrator.integrator3dthreaded method)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded.integrate", false]], "integrator (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Integrator", false]], "integrator2d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Integrator2D", false]], "integrator3d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Integrator3D", false]], "integrator3dthreaded (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded", false]], "integratorexecutor (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.IntegratorExecutor", false]], "integratorflat3d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.IntegratorFlat3D", false]], "integratorsingle2d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.IntegratorSingle2D", false]], "integratorstills (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.IntegratorStills", false]], "inv_d2() (dials.algorithms.background.radialaverage method)": [[10, "dials.algorithms.background.RadialAverage.inv_d2", false]], "invalidphilerror": [[33, "dials.util.options.InvalidPhilError", false]], "is_consistent() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.is_consistent", false]], "is_marked_for_rejection() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.is_marked_for_rejection", false]], "is_marked_for_rejection() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.is_marked_for_rejection", false]], "is_scaled (dials.algorithms.scaling.model.model.scalingmodelbase property)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.is_scaled", false]], "is_similar_to() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.is_similar_to", false]], "is_similar_to() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.is_similar_to", false]], "is_similar_to() (dxtbx.model.mosaiccrystalkabsch2010 method)": [[22, "dxtbx.model.MosaicCrystalKabsch2010.is_similar_to", false]], "is_similar_to() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.is_similar_to", false]], "is_single_file_reader() (dxtbx.imageset.memreader static method)": [[26, "dxtbx.imageset.MemReader.is_single_file_reader", false]], "iter_levelorder() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.iter_levelorder", false]], "iter_panels() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.iter_panels", false]], "iter_preorder() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.iter_preorder", false]], "jacobian_condition_number() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.jacobian_condition_number", false]], "job() (dials.algorithms.integration.integrator.reflectionmanager method)": [[12, "dials.algorithms.integration.integrator.ReflectionManager.job", false]], "joblist (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.JobList", false]], "journal (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.Journal", false]], "kappa() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.kappa", false]], "kappagoniometer (class in dxtbx.model.goniometer)": [[25, "dxtbx.model.goniometer.KappaGoniometer", false]], "kbscalingmodel (class in dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel", false]], "kernel_normalisation() (dials.algorithms.symmetry.symmetry_base static method)": [[18, "dials.algorithms.symmetry.symmetry_base.kernel_normalisation", false]], "known_axis() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.known_axis", false]], "lauegroupanalysis (class in dials.algorithms.symmetry.laue_group)": [[18, "dials.algorithms.symmetry.laue_group.LaueGroupAnalysis", false]], "lbfgs_with_curvs (class in dials.algorithms.symmetry.cosym.engine)": [[18, "dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs", false]], "lbfgscurvs (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.LBFGScurvs", false]], "leastsquarespositionalresidualwithrmsdcutoff (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.LeastSquaresPositionalResidualWithRmsdCutoff", false]], "leastsquarespositionalresidualwithrmsdcutoffsparse (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.LeastSquaresPositionalResidualWithRmsdCutoffSparse", false]], "leastsquaresstillsresidualwithrmsdcutoff (class in dials.algorithms.refinement.target_stills)": [[14, "dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff", false]], "leastsquaresstillsresidualwithrmsdcutoffsparse (class in dials.algorithms.refinement.target_stills)": [[14, "dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoffSparse", false]], "levenbergmarquardtiterations (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.LevenbergMarquardtIterations", false]], "limit_image_range() (dials.algorithms.scaling.model.model.arrayscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.limit_image_range", false]], "limit_image_range() (dials.algorithms.scaling.model.model.dosedecay method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.limit_image_range", false]], "limit_image_range() (dials.algorithms.scaling.model.model.physicalscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.limit_image_range", false]], "limit_image_range() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.limit_image_range", false]], "load() (in module dials.util.nexus)": [[33, "dials.util.nexus.load", false]], "load_error_model() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.load_error_model", false]], "load_image() (dials.algorithms.spot_finding.factory.spotfinderfactory static method)": [[16, "dials.algorithms.spot_finding.factory.SpotFinderFactory.load_image", false]], "log_summary() (in module dials.util.export_mtz)": [[33, "dials.util.export_mtz.log_summary", false]], "lowresspotmatch (class in dials.algorithms.indexing.lattice_search)": [[11, "dials.algorithms.indexing.lattice_search.LowResSpotMatch", false]], "madmergedmtzwriter (class in dials.util.export_mtz)": [[33, "dials.util.export_mtz.MADMergedMTZWriter", false]], "make_apps (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.make_apps", false]], "make_beam() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.make_beam", false]], "make_combined_plots() (in module dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.make_combined_plots", false]], "make_detector() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.make_detector", false]], "make_goniometer() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.make_goniometer", false]], "make_imageset() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.make_imageset", false]], "make_kappa_goniometer() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.make_kappa_goniometer", false]], "make_multi_axis_goniometer() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.make_multi_axis_goniometer", false]], "make_polarized_beam() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.make_polarized_beam", false]], "make_polychromatic_beam() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.make_polychromatic_beam", false]], "make_scan() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.make_scan", false]], "make_scan_from_properties() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.make_scan_from_properties", false]], "make_sequence() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.make_sequence", false]], "mark_for_rejection() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.mark_for_rejection", false]], "mark_for_rejection() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.mark_for_rejection", false]], "mask (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.mask", false]], "masker() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.masker", false]], "masker() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.masker", false]], "master_path() (dxtbx.imageset.memreader static method)": [[26, "dxtbx.imageset.MemReader.master_path", false]], "match_wavelengths() (in module dials.util.export_mtz)": [[33, "dials.util.export_mtz.match_wavelengths", false]], "max_length (dials.util.command_line.command attribute)": [[33, "dials.util.command_line.Command.max_length", false]], "max_possible_wl (dials.util.export_mtz.wavelengthgroup attribute)": [[33, "dials.util.export_mtz.WavelengthGroup.max_possible_wl", false]], "max_shift_over_esd (dials.algorithms.refinement.engine.gaussnewtoniterations attribute)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations.max_shift_over_esd", false]], "mean() (dials.algorithms.background.radialaverage method)": [[10, "dials.algorithms.background.RadialAverage.mean", false]], "median_unit_cell() (in module dials.algorithms.symmetry)": [[18, "dials.algorithms.symmetry.median_unit_cell", false]], "memreader (class in dxtbx.imageset)": [[26, "dxtbx.imageset.MemReader", false]], "merge_panel_scope_extracts_by_id() (in module dxtbx.model.detector)": [[23, "dxtbx.model.detector.merge_panel_scope_extracts_by_id", false]], "mergedmtzwriter (class in dials.util.export_mtz)": [[33, "dials.util.export_mtz.MergedMTZWriter", false]], "message (dials.util.options.argumenthandlingerrorinfo attribute)": [[33, "dials.util.options.ArgumentHandlingErrorInfo.message", false]], "metric_supergroup() (in module dials.algorithms.indexing.symmetry)": [[11, "dials.algorithms.indexing.symmetry.metric_supergroup", false]], "min_wl (dials.util.export_mtz.wavelengthgroup attribute)": [[33, "dials.util.export_mtz.WavelengthGroup.min_wl", false]], "minimize_scipy() (in module dials.algorithms.symmetry.cosym.engine)": [[18, "dials.algorithms.symmetry.cosym.engine.minimize_scipy", false]], "minimize_scitbx_lbfgs() (in module dials.algorithms.symmetry.cosym.engine)": [[18, "dials.algorithms.symmetry.cosym.engine.minimize_scitbx_lbfgs", false]], "ml_aniso_normalisation() (dials.algorithms.symmetry.symmetry_base static method)": [[18, "dials.algorithms.symmetry.symmetry_base.ml_aniso_normalisation", false]], "ml_iso_normalisation() (dials.algorithms.symmetry.symmetry_base static method)": [[18, "dials.algorithms.symmetry.symmetry_base.ml_iso_normalisation", false]], "model_likelihood (dials.algorithms.indexing.model_evaluation.result attribute)": [[11, "dials.algorithms.indexing.model_evaluation.Result.model_likelihood", false]], "modelevaluation (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.ModelEvaluation", false]], "modelrank (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRank", false]], "modelrankfilter (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter", false]], "modelrankweighted (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankWeighted", false]], "module": [[10, "module-dials.algorithms.background", false], [11, "module-dials.algorithms.indexing", false], [11, "module-dials.algorithms.indexing.assign_indices", false], [11, "module-dials.algorithms.indexing.basis_vector_search", false], [11, "module-dials.algorithms.indexing.basis_vector_search.combinations", false], [11, "module-dials.algorithms.indexing.basis_vector_search.optimise", false], [11, "module-dials.algorithms.indexing.compare_orientation_matrices", false], [11, "module-dials.algorithms.indexing.indexer", false], [11, "module-dials.algorithms.indexing.lattice_search", false], [11, "module-dials.algorithms.indexing.max_cell", false], [11, "module-dials.algorithms.indexing.model_evaluation", false], [11, "module-dials.algorithms.indexing.nearest_neighbor", false], [11, "module-dials.algorithms.indexing.refinement", false], [11, "module-dials.algorithms.indexing.stills_indexer", false], [11, "module-dials.algorithms.indexing.symmetry", false], [12, "module-dials.algorithms.integration.integrator", false], [13, "module-dials.algorithms.profile_model", false], [14, "module-dials.algorithms.refinement.engine", false], [14, "module-dials.algorithms.refinement.refiner", false], [14, "module-dials.algorithms.refinement.reflection_manager", false], [14, "module-dials.algorithms.refinement.target", false], [14, "module-dials.algorithms.refinement.target_stills", false], [14, "module-dials.algorithms.refinement.weighting_strategies", false], [15, "module-dials.algorithms.scaling", false], [15, "module-dials.algorithms.scaling.model.model", false], [15, "module-dials.algorithms.scaling.outlier_rejection", false], [16, "module-dials.algorithms.spot_finding.factory", false], [16, "module-dials.algorithms.spot_finding.finder", false], [17, "module-dials.algorithms.spot_prediction.reflection_predictor", false], [18, "module-dials.algorithms.symmetry", false], [18, "module-dials.algorithms.symmetry.cosym", false], [18, "module-dials.algorithms.symmetry.cosym.engine", false], [18, "module-dials.algorithms.symmetry.cosym.target", false], [18, "module-dials.algorithms.symmetry.laue_group", false], [18, "module-dials.algorithms.symmetry.reindex_to_reference", false], [20, "module-dials.array_family.flex", false], [21, "module-dxtbx.model.beam", false], [22, "module-dxtbx.model.crystal", false], [23, "module-dxtbx.model.detector", false], [24, "module-dxtbx.model.experiment_list", false], [25, "module-dxtbx.model.goniometer", false], [26, "module-dxtbx.imageset", false], [28, "module-dxtbx.model.profile", false], [29, "module-dxtbx.model.scan", false], [30, "module-dxtbx.serialize.imageset", false], [30, "module-dxtbx.serialize.load", false], [30, "module-dxtbx.serialize.xds", false], [31, "module-dials.extensions.dispersion_spotfinder_threshold_ext", false], [31, "module-dials.extensions.gaussian_rs_profile_model_ext", false], [31, "module-dials.extensions.null_background_ext", false], [31, "module-dials.extensions.simple_background_ext", false], [31, "module-dials.extensions.simple_centroid_ext", false], [33, "module-dials.util.command_line", false], [33, "module-dials.util.export_mtz", false], [33, "module-dials.util.export_text", false], [33, "module-dials.util.image", false], [33, "module-dials.util.installer", false], [33, "module-dials.util.ioutil", false], [33, "module-dials.util.nexus", false], [33, "module-dials.util.options", false]], "mosaiccrystalkabsch2010 (class in dxtbx.model)": [[22, "dxtbx.model.MosaicCrystalKabsch2010", false]], "mosaiccrystalsauter2014 (class in dxtbx.model)": [[22, "dxtbx.model.MosaicCrystalSauter2014", false]], "mtzwriterbase (class in dials.util.export_mtz)": [[33, "dials.util.export_mtz.MTZWriterBase", false]], "mu (dials.algorithms.refinement.engine.levenbergmarquardtiterations property)": [[14, "dials.algorithms.refinement.engine.LevenbergMarquardtIterations.mu", false]], "multi_axis() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.multi_axis", false]], "multi_axis_goniometer_from_phil() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.multi_axis_goniometer_from_phil", false]], "multiaxisgoniometer (class in dxtbx.model.goniometer)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer", false]], "n() (dials.algorithms.symmetry.laue_group.correlationcoefficientaccumulator method)": [[18, "dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator.n", false]], "n_indexed (dials.algorithms.indexing.model_evaluation.result attribute)": [[11, "dials.algorithms.indexing.model_evaluation.Result.n_indexed", false]], "n_params (dials.algorithms.scaling.model.model.scalingmodelbase property)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.n_params", false]], "name (dials.extensions.dispersion_spotfinder_threshold_ext.dispersionspotfinderthresholdext attribute)": [[31, "dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt.name", false]], "name (dials.extensions.gaussian_rs_profile_model_ext.gaussianrsprofilemodelext attribute)": [[31, "dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt.name", false]], "name (dials.extensions.null_background_ext.nullbackgroundext attribute)": [[31, "dials.extensions.null_background_ext.NullBackgroundExt.name", false]], "name (dials.extensions.simple_background_ext.simplebackgroundext attribute)": [[31, "dials.extensions.simple_background_ext.SimpleBackgroundExt.name", false]], "name (dials.extensions.simple_centroid_ext.simplecentroidext attribute)": [[31, "dials.extensions.simple_centroid_ext.SimpleCentroidExt.name", false]], "name (dials.util.options.argumenthandlingerrorinfo attribute)": [[33, "dials.util.options.ArgumentHandlingErrorInfo.name", false]], "neighboranalysis (class in dials.algorithms.indexing.nearest_neighbor)": [[11, "dials.algorithms.indexing.nearest_neighbor.NeighborAnalysis", false]], "new() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.new", false]], "nframes_hist() (in module dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.nframes_hist", false]], "normdevoutlierrejection (class in dials.algorithms.scaling.outlier_rejection)": [[15, "dials.algorithms.scaling.outlier_rejection.NormDevOutlierRejection", false]], "nullbackgroundext (class in dials.extensions.null_background_ext)": [[31, "dials.extensions.null_background_ext.NullBackgroundExt", false]], "nullify_all_single_file_reader_format_instances() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.nullify_all_single_file_reader_format_instances", false]], "num_reflections() (dials.algorithms.integration.integrator.reflectionmanager method)": [[12, "dials.algorithms.integration.integrator.ReflectionManager.num_reflections", false]], "num_scan_points (dxtbx.model.goniometer.goniometer property)": [[25, "dxtbx.model.goniometer.Goniometer.num_scan_points", false]], "numerator() (dials.algorithms.symmetry.laue_group.correlationcoefficientaccumulator method)": [[18, "dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator.numerator", false]], "optimise_basis_vectors() (in module dials.algorithms.indexing.basis_vector_search.optimise)": [[11, "dials.algorithms.indexing.basis_vector_search.optimise.optimise_basis_vectors", false]], "optionparser (class in dials.util.options)": [[33, "dials.util.options.OptionParser", false]], "outlierrejectionbase (class in dials.algorithms.scaling.outlier_rejection)": [[15, "dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase", false]], "overwrite_from_phil() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.overwrite_from_phil", false]], "p_cc_given_not_s (dials.algorithms.symmetry.laue_group.scorecorrelationcoefficient property)": [[18, "dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient.p_cc_given_not_s", false]], "p_cc_given_s (dials.algorithms.symmetry.laue_group.scorecorrelationcoefficient property)": [[18, "dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient.p_cc_given_s", false]], "p_s_given_cc (dials.algorithms.symmetry.laue_group.scorecorrelationcoefficient property)": [[18, "dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient.p_s_given_cc", false]], "parameter_vector_norm() (dials.algorithms.refinement.engine.adaptlstbx method)": [[14, "dials.algorithms.refinement.engine.AdaptLstbx.parameter_vector_norm", false]], "parameters (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Parameters", false]], "parameters.filter (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Parameters.Filter", false]], "parameters.profile (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Parameters.Profile", false]], "parameters.profile.validation (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Parameters.Profile.Validation", false]], "params() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.params", false]], "parse_args() (dials.util.options.argumentparser method)": [[33, "dials.util.options.ArgumentParser.parse_args", false]], "parse_args() (dials.util.options.philcommandparser method)": [[33, "dials.util.options.PhilCommandParser.parse_args", false]], "parse_known_args() (dials.util.options.argumentparserbase method)": [[33, "dials.util.options.ArgumentParserBase.parse_known_args", false]], "partial_data() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.partial_data", false]], "partial_set() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.partial_set", false]], "partial_set() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.partial_set", false]], "paths() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.paths", false]], "paths() (dxtbx.imageset.memreader method)": [[26, "dxtbx.imageset.MemReader.paths", false]], "peakcentroiddistancefilter (class in dials.algorithms.spot_finding.factory)": [[16, "dials.algorithms.spot_finding.factory.PeakCentroidDistanceFilter", false]], "pedestal (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.pedestal", false]], "per_image() (dials.algorithms.refinement.reflection_manager.blockcalculator method)": [[14, "dials.algorithms.refinement.reflection_manager.BlockCalculator.per_image", false]], "per_width() (dials.algorithms.refinement.reflection_manager.blockcalculator method)": [[14, "dials.algorithms.refinement.reflection_manager.BlockCalculator.per_width", false]], "phil (dials.util.options.argumentparser property)": [[33, "dials.util.options.ArgumentParser.phil", false]], "phil (dials.util.options.philcommandparser property)": [[33, "dials.util.options.PhilCommandParser.phil", false]], "phil() (dials.extensions.dispersion_spotfinder_threshold_ext.dispersionspotfinderthresholdext static method)": [[31, "dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt.phil", false]], "phil() (dials.extensions.gaussian_rs_profile_model_ext.gaussianrsprofilemodelext static method)": [[31, "dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt.phil", false]], "phil() (dials.extensions.simple_background_ext.simplebackgroundext static method)": [[31, "dials.extensions.simple_background_ext.SimpleBackgroundExt.phil", false]], "phil_help (dials.algorithms.indexing.basis_vector_search.fft1d attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT1D.phil_help", false]], "phil_help (dials.algorithms.indexing.basis_vector_search.fft3d attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT3D.phil_help", false]], "phil_help (dials.algorithms.indexing.basis_vector_search.realspacegridsearch attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.phil_help", false]], "phil_help (dials.algorithms.indexing.basis_vector_search.strategy attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.Strategy.phil_help", false]], "phil_help (dials.algorithms.indexing.lattice_search.lowresspotmatch attribute)": [[11, "dials.algorithms.indexing.lattice_search.LowResSpotMatch.phil_help", false]], "phil_help (dials.algorithms.indexing.lattice_search.pinkindexer attribute)": [[11, "dials.algorithms.indexing.lattice_search.PinkIndexer.phil_help", false]], "phil_help (dials.algorithms.indexing.lattice_search.strategy attribute)": [[11, "dials.algorithms.indexing.lattice_search.Strategy.phil_help", false]], "phil_scope (dials.algorithms.indexing.basis_vector_search.fft1d attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT1D.phil_scope", false]], "phil_scope (dials.algorithms.indexing.basis_vector_search.fft3d attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT3D.phil_scope", false]], "phil_scope (dials.algorithms.indexing.basis_vector_search.realspacegridsearch attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.phil_scope", false]], "phil_scope (dials.algorithms.indexing.basis_vector_search.strategy attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.Strategy.phil_scope", false]], "phil_scope (dials.algorithms.indexing.lattice_search.lowresspotmatch attribute)": [[11, "dials.algorithms.indexing.lattice_search.LowResSpotMatch.phil_scope", false]], "phil_scope (dials.algorithms.indexing.lattice_search.pinkindexer attribute)": [[11, "dials.algorithms.indexing.lattice_search.PinkIndexer.phil_scope", false]], "phil_scope (dials.algorithms.indexing.lattice_search.strategy attribute)": [[11, "dials.algorithms.indexing.lattice_search.Strategy.phil_scope", false]], "phil_scope (dials.algorithms.scaling.model.model.arrayscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.phil_scope", false]], "phil_scope (dials.algorithms.scaling.model.model.dosedecay attribute)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.phil_scope", false]], "phil_scope (dials.algorithms.scaling.model.model.kbscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel.phil_scope", false]], "phil_scope (dials.algorithms.scaling.model.model.physicalscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.phil_scope", false]], "philcommandparser (class in dials.util.options)": [[33, "dials.util.options.PhilCommandParser", false]], "physicalscalingmodel (class in dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel", false]], "pinkindexer (class in dials.algorithms.indexing.lattice_search)": [[11, "dials.algorithms.indexing.lattice_search.PinkIndexer", false]], "pixel_list_to_reflection_table() (in module dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.pixel_list_to_reflection_table", false]], "pixel_list_to_shoeboxes() (in module dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.pixel_list_to_shoeboxes", false]], "plot_displacements() (in module dials.algorithms.indexing.stills_indexer)": [[11, "dials.algorithms.indexing.stills_indexer.plot_displacements", false]], "plot_histogram() (dials.algorithms.indexing.nearest_neighbor.neighboranalysis method)": [[11, "dials.algorithms.indexing.nearest_neighbor.NeighborAnalysis.plot_histogram", false]], "plot_model_components() (dials.algorithms.scaling.model.model.arrayscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.plot_model_components", false]], "plot_model_components() (dials.algorithms.scaling.model.model.dosedecay method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.plot_model_components", false]], "plot_model_components() (dials.algorithms.scaling.model.model.physicalscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.plot_model_components", false]], "plot_model_components() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.plot_model_components", false]], "plot_scaling_models() (in module dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.plot_scaling_models", false]], "predict() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.predict", false]], "predict_for_free_reflections() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.predict_for_free_reflections", false]], "predict_for_indexed() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.predict_for_indexed", false]], "predict_for_reflection_table() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.predict_for_reflection_table", false]], "predict_for_reflection_table() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.predict_for_reflection_table", false]], "predict_for_reflection_table() (dials.algorithms.refinement.target_stills.leastsquaresstillsresidualwithrmsdcutoff method)": [[14, "dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff.predict_for_reflection_table", false]], "predictor() (dials.algorithms.spot_prediction.reflection_predictor.reflectionpredictor method)": [[17, "dials.algorithms.spot_prediction.reflection_predictor.ReflectionPredictor.predictor", false]], "prepare_for_step() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.prepare_for_step", false]], "print_exp_rmsd_table() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.print_exp_rmsd_table", false]], "print_out_of_sample_rmsd_table() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.print_out_of_sample_rmsd_table", false]], "print_panel_rmsd_table() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.print_panel_rmsd_table", false]], "print_stats_on_matches() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.print_stats_on_matches", false]], "print_stats_on_matches() (dials.algorithms.refinement.reflection_manager.stillsreflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.StillsReflectionManager.print_stats_on_matches", false]], "print_step_table() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.print_step_table", false]], "print_time (dials.util.command_line.command attribute)": [[33, "dials.util.command_line.Command.print_time", false]], "process() (dials.algorithms.integration.integrator.executor method)": [[12, "dials.algorithms.integration.integrator.Executor.process", false]], "process() (dials.algorithms.integration.integrator.integratorexecutor method)": [[12, "dials.algorithms.integration.integrator.IntegratorExecutor.process", false]], "process() (dials.algorithms.integration.integrator.profilemodellerexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileModellerExecutor.process", false]], "process() (dials.algorithms.integration.integrator.profilevalidatorexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileValidatorExecutor.process", false]], "processor2d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Processor2D", false]], "processor3d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Processor3D", false]], "processorclass (dials.algorithms.integration.integrator.integrator2d attribute)": [[12, "dials.algorithms.integration.integrator.Integrator2D.ProcessorClass", false]], "processorclass (dials.algorithms.integration.integrator.integrator3d attribute)": [[12, "dials.algorithms.integration.integrator.Integrator3D.ProcessorClass", false]], "processorclass (dials.algorithms.integration.integrator.integratorflat3d attribute)": [[12, "dials.algorithms.integration.integrator.IntegratorFlat3D.ProcessorClass", false]], "processorclass (dials.algorithms.integration.integrator.integratorsingle2d attribute)": [[12, "dials.algorithms.integration.integrator.IntegratorSingle2D.ProcessorClass", false]], "processorclass (dials.algorithms.integration.integrator.integratorstills attribute)": [[12, "dials.algorithms.integration.integrator.IntegratorStills.ProcessorClass", false]], "processorflat3d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ProcessorFlat3D", false]], "processorsingle2d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ProcessorSingle2D", false]], "processorstills (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ProcessorStills", false]], "product_name (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.product_name", false]], "product_specific_finalize_install() (dials.util.installer.installer method)": [[33, "dials.util.installer.installer.product_specific_finalize_install", false]], "profilemodelfactory (class in dxtbx.model.profile)": [[28, "dxtbx.model.profile.ProfileModelFactory", false]], "profilemodellerexecutor (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ProfileModellerExecutor", false]], "profiles() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.profiles", false]], "profilevalidatorexecutor (class in dials.algorithms.integration.integrator)": 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(class in dials.algorithms.refinement.refiner)": [[14, "dials.algorithms.refinement.refiner.RefinerFactory", false]], "refinery (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.Refinery", false]], "reflectionmanager (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ReflectionManager", false]], "reflectionmanager (class in dials.algorithms.refinement.reflection_manager)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager", false]], "reflectionmanagerfactory (class in dials.algorithms.refinement.reflection_manager)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory", false]], "reflectionpredictor (class in dials.algorithms.spot_prediction.reflection_predictor)": [[17, "dials.algorithms.spot_prediction.reflection_predictor.ReflectionPredictor", false]], "reflections_after_outlier_rejection() (dials.algorithms.refinement.refiner.refinerfactory class method)": [[14, "dials.algorithms.refinement.refiner.RefinerFactory.reflections_after_outlier_rejection", false]], "reflections_and_experiments_from_files() (in module dials.util.options)": [[33, "dials.util.options.reflections_and_experiments_from_files", false]], "reject_outliers() (in module dials.algorithms.scaling.outlier_rejection)": [[15, "dials.algorithms.scaling.outlier_rejection.reject_outliers", false]], "remove_on_experiment_identifiers() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.remove_on_experiment_identifiers", false]], "remove_sources_default (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.remove_sources_default", false]], "replace() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.replace", false]], "report() (dials.algorithms.integration.integrator.integrator method)": [[12, "dials.algorithms.integration.integrator.Integrator.report", false]], "report() (dials.algorithms.integration.integrator.integrator3dthreaded method)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded.report", false]], "report_progress() (dials.algorithms.refinement.engine.levenbergmarquardtiterations method)": [[14, "dials.algorithms.refinement.engine.LevenbergMarquardtIterations.report_progress", false]], "reset_accepted_reflections() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.reset_accepted_reflections", false]], "reset_scan_points() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.reset_scan_points", false]], "resolution_filter_from_array() (in module dials.algorithms.symmetry)": [[18, "dials.algorithms.symmetry.resolution_filter_from_array", false]], "resolution_filter_from_reflections_experiments() (in module dials.algorithms.symmetry)": [[18, "dials.algorithms.symmetry.resolution_filter_from_reflections_experiments", false]], "restart() (dials.algorithms.refinement.engine.adaptlstbx method)": [[14, "dials.algorithms.refinement.engine.AdaptLstbx.restart", false]], "result (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.Result", false]], "rmsd_names (dials.algorithms.refinement.target.target attribute)": [[14, "dials.algorithms.refinement.target.Target.rmsd_names", false]], "rmsd_names (dials.algorithms.refinement.target_stills.leastsquaresstillsresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff.rmsd_names", false]], "rmsd_units (dials.algorithms.refinement.target.target attribute)": [[14, "dials.algorithms.refinement.target.Target.rmsd_units", false]], "rmsd_units (dials.algorithms.refinement.target_stills.leastsquaresstillsresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff.rmsd_units", false]], "rmsds (dials.algorithms.indexing.model_evaluation.result attribute)": [[11, "dials.algorithms.indexing.model_evaluation.Result.rmsds", false]], "rmsds() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.rmsds", false]], "rmsds() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.rmsds", false]], "rmsds_for_experiment() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.rmsds_for_experiment", false]], "rmsds_for_panel() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.rmsds_for_panel", false]], "rmsds_for_reflection_table() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.rmsds_for_reflection_table", false]], "rmsds_for_reflection_table() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.rmsds_for_reflection_table", false]], "rotate_around_origin() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.rotate_around_origin", false]], "rotate_around_origin() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.rotate_around_origin", false]], "rotate_crystal() (in module dials.util.export_mtz)": [[33, "dials.util.export_mtz.rotate_crystal", false]], "rotation_matrix_differences() (in module dials.algorithms.indexing.compare_orientation_matrices)": [[11, "dials.algorithms.indexing.compare_orientation_matrices.rotation_matrix_differences", false]], "run() (dials.algorithms.refinement.engine.gaussnewtoniterations method)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations.run", false]], "run() (dials.algorithms.refinement.engine.lbfgscurvs method)": [[14, "dials.algorithms.refinement.engine.LBFGScurvs.run", false]], "run() (dials.algorithms.refinement.engine.levenbergmarquardtiterations method)": [[14, "dials.algorithms.refinement.engine.LevenbergMarquardtIterations.run", false]], "run() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.run", false]], "run() (dials.algorithms.refinement.engine.simplelbfgs method)": [[14, "dials.algorithms.refinement.engine.SimpleLBFGS.run", false]], "run() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.run", false]], "run() (dials.algorithms.scaling.outlier_rejection.outlierrejectionbase method)": [[15, "dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase.run", false]], "run() (dials.algorithms.spot_finding.factory.backgroundgradientfilter method)": [[16, "dials.algorithms.spot_finding.factory.BackgroundGradientFilter.run", false]], "run() 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dials.algorithms.symmetry.laue_group)": [[18, "dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient", false]], "scoresubgroup (class in dials.algorithms.symmetry.cosym)": [[18, "dials.algorithms.symmetry.cosym.ScoreSubGroup", false]], "scoresubgroup (class in dials.algorithms.symmetry.laue_group)": [[18, "dials.algorithms.symmetry.laue_group.ScoreSubGroup", false]], "scoresymmetryelement (class in dials.algorithms.symmetry.cosym)": [[18, "dials.algorithms.symmetry.cosym.ScoreSymmetryElement", false]], "scoresymmetryelement (class in dials.algorithms.symmetry.laue_group)": [[18, "dials.algorithms.symmetry.laue_group.ScoreSymmetryElement", false]], "search() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.search", false]], "search_directions (dials.algorithms.indexing.basis_vector_search.realspacegridsearch property)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.search_directions", false]], "search_vectors (dials.algorithms.indexing.basis_vector_search.realspacegridsearch property)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.search_vectors", false]], "select_on_experiment_identifiers() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.select_on_experiment_identifiers", false]], "selection_used_for_refinement() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.selection_used_for_refinement", false]], "sensor() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.sensor", false]], "set_angles() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.set_angles", false]], "set_axes() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.set_axes", false]], "set_beam() (dxtbx.imageset.imagesequence method)": [[26, 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88], "spot_counts_per_imag": 67, "spot_find": 16, "spot_predict": 17, "spotfind": 85, "ssx": 96, "ssx_index": 96, "ssx_integr": 96, "stabl": 91, "start": 7, "static": [4, 75], "step": 7, "stereographic_project": 68, "stills_index": 11, "strategi": 4, "structur": 73, "summari": 2, "symmetri": [18, 69, 73, 74, 77, 78, 82, 84, 85, 86, 87, 88], "synchrotron": 95, "tabl": [20, 31], "team": 0, "test": [9, 48], "tile": 81, "tilt": 74, "togeth": 73, "tutori": [80, 82, 85, 86, 87, 88], "two_theta_refin": 70, "uk": [97, 98], "understand": 4, "unit": [76, 88], "unmerg": [82, 86], "up": 9, "us": [1, 43, 72, 79], "user": 1, "util": 33, "v": 83, "vari": 75, "vector": 4, "video": 73, "wedg": 74, "west": 0, "what": [81, 83], "workshop": 99, "write": 4, "xfel": 95, "xia2": [72, 76, 79, 84]}}) \ No newline at end of file +Search.setIndex({"alltitles": {"About": [[0, "about"]], "Acknowledgements": [[0, "acknowledgements"], [77, "acknowledgements"], [78, "acknowledgements"], [81, "acknowledgements"], [83, "acknowledgements"]], "Adding new format classes": [[4, "adding-new-format-classes"]], "Advanced use - Choosing reflections to use for minimisation": [[1, "advanced-use-choosing-reflections-to-use-for-minimisation"]], "Advanced use - Controlling the scaling models": [[1, "advanced-use-controlling-the-scaling-models"]], "Algorithms": [[19, "algorithms"]], "Almost there": [[84, "almost-there"]], "Analysis of individually processed datasets": [[83, "analysis-of-individually-processed-datasets"]], "Analysis of jointly refined datasets": [[83, "analysis-of-jointly-refined-datasets"]], "Applying the corrected metrology": [[81, "applying-the-corrected-metrology"]], "Array Family": [[20, "array-family"]], "Attendees": [[98, "attendees"]], "Basic parameters": [[34, "basic-parameters"], [36, "basic-parameters"], [37, "basic-parameters"], [38, "basic-parameters"], [39, "basic-parameters"], [40, "basic-parameters"], [41, "basic-parameters"], [42, "basic-parameters"], [43, "basic-parameters"], [44, "basic-parameters"], [45, "basic-parameters"], [46, "basic-parameters"], [47, "basic-parameters"], [49, "basic-parameters"], [50, "basic-parameters"], [51, "basic-parameters"], [52, "basic-parameters"], [53, "basic-parameters"], [54, "basic-parameters"], [55, "basic-parameters"], [57, "basic-parameters"], [58, "basic-parameters"], [59, "basic-parameters"], [60, "basic-parameters"], [61, "basic-parameters"], [62, "basic-parameters"], [63, "basic-parameters"], [64, "basic-parameters"], [65, "basic-parameters"], [66, "basic-parameters"], [67, "basic-parameters"], [68, "basic-parameters"], [69, "basic-parameters"], [70, "basic-parameters"], [72, "basic-parameters"]], "Basis vector search strategies": [[4, "basis-vector-search-strategies"]], "Bookkeeping": [[76, "bookkeeping"]], "Bravais Lattice Refinement": [[82, "bravais-lattice-refinement"], [86, "bravais-lattice-refinement"], [87, "bravais-lattice-refinement"]], "Bravais lattice determination": [[88, "bravais-lattice-determination"]], "Build instructions": [[48, "build-instructions"]], "Built-in help": [[7, "built-in-help"]], "Centred or pseudocentred?": [[77, "centred-or-pseudocentred"]], "Check indexing symmetry": [[78, "check-indexing-symmetry"]], "Checking the symmetry": [[87, "checking-the-symmetry"]], "Class Methods": [[4, "class-methods"]], "Cluster Comparisons": [[76, "cluster-comparisons"]], "Conclusions": [[77, "conclusions"], [78, "conclusions"]], "Contact": [[90, "contact"]], "Contents": [[4, "contents"]], "Conventions": [[2, "conventions"]], "Converting to a centred lattice": [[77, "converting-to-a-centred-lattice"]], "Coordinate frames": [[2, "coordinate-frames"]], "DIALS 1: 12th-13th June 2012 (Diamond Light Source, UK)": [[97, "dials-1-12th-13th-june-2012-diamond-light-source-uk"]], "DIALS Application to XFEL Crystallography": [[95, "dials-application-to-xfel-crystallography"]], "DIALS East": [[0, "dials-east"]], "DIALS How-To guides": [[89, "dials-how-to-guides"]], "DIALS Journal Articles": [[95, "dials-journal-articles"]], "DIALS License": [[92, "dials-license"]], "DIALS Newsletter Articles": [[95, "dials-newsletter-articles"]], "DIALS Reports": [[95, "dials-reports"]], "DIALS Synchrotron Applications": [[95, "dials-synchrotron-applications"]], "DIALS West": [[0, "dials-west"]], "DIALS for neutron diffraction": [[94, "dials-for-neutron-diffraction"]], "DIALS-3: 22nd May 2013 (Cambridge, UK)": [[98, "dials-3-22nd-may-2013-cambridge-uk"]], "DIALS: Diffraction Integration for Advanced Light Sources": [[90, "dials-diffraction-integration-for-advanced-light-sources"]], "DPF3 Part 1: Correcting poor initial geometry": [[78, "dpf3-part-1-correcting-poor-initial-geometry"]], "DPF3 Part 2: A question of centring": [[77, "dpf3-part-2-a-question-of-centring"]], "Data": [[74, "data"], [75, "data"], [76, "data"], [88, "data"]], "Data collection videos": [[73, "data-collection-videos"]], "Data files": [[3, "data-files"]], "Dataset 1": [[75, "dataset-1"], [75, "id1"], [75, "id11"]], "Dataset 2": [[75, "dataset-2"], [75, "id2"], [75, "id12"]], "Dataset 3": [[75, "dataset-3"], [75, "id3"], [75, "id13"]], "Dataset 4": [[75, "dataset-4"], [75, "id4"], [75, "id14"]], "Dataset 5": [[75, "dataset-5"], [75, "id5"], [75, "id15"]], "Dataset 6": [[75, "dataset-6"], [75, "id6"], [75, "id8"], [75, "id10"], [75, "id16"]], "Dataset 7": [[75, "dataset-7"], [75, "id7"], [75, "id17"]], "Datasets 1-5 & 7": [[75, "datasets-1-5-7"], [75, "id9"]], "Defining a scaling model": [[4, "defining-a-scaling-model"]], "Delta CC-half": [[76, "delta-cc-half"]], "Details": [[35, "details"]], "Detector distance": [[74, "detector-distance"]], "Determining lattice symmetry": [[74, "determining-lattice-symmetry"]], "Developer Examples": [[5, "developer-examples"]], "Development Builds": [[91, "development-builds"]], "Development Teams": [[0, "development-teams"]], "Dials parameters": [[48, "dials-parameters"]], "Discover a better experimental model": [[78, "discover-a-better-experimental-model"]], "Distl 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"extending-dials-scale"]], "Extending profile models": [[4, "extending-profile-models"]], "Extensions": [[31, "extensions"]], "Feedback": [[79, "feedback"]], "Find Spots": [[78, "find-spots"], [82, "find-spots"], [86, "find-spots"], [87, "find-spots"]], "Find spots": [[73, "find-spots"]], "Find the Bravais lattice (optional)": [[73, "find-the-bravais-lattice-optional"]], "Find the beam centre": [[73, "find-the-beam-centre"]], "Full parameter definitions": [[34, "full-parameter-definitions"], [35, "full-parameter-definitions"], [36, "full-parameter-definitions"], [37, "full-parameter-definitions"], [38, "full-parameter-definitions"], [39, "full-parameter-definitions"], [40, "full-parameter-definitions"], [41, "full-parameter-definitions"], [42, "full-parameter-definitions"], [43, "full-parameter-definitions"], [44, "full-parameter-definitions"], [45, "full-parameter-definitions"], [46, "full-parameter-definitions"], [47, "full-parameter-definitions"], [49, "full-parameter-definitions"], [50, "full-parameter-definitions"], [51, "full-parameter-definitions"], [52, "full-parameter-definitions"], [53, "full-parameter-definitions"], [54, "full-parameter-definitions"], [55, "full-parameter-definitions"], [56, "full-parameter-definitions"], [57, "full-parameter-definitions"], [58, "full-parameter-definitions"], [59, "full-parameter-definitions"], [60, "full-parameter-definitions"], [61, "full-parameter-definitions"], [62, "full-parameter-definitions"], [63, "full-parameter-definitions"], [64, "full-parameter-definitions"], [65, "full-parameter-definitions"], [66, "full-parameter-definitions"], [67, "full-parameter-definitions"], [68, "full-parameter-definitions"], [69, "full-parameter-definitions"], [70, "full-parameter-definitions"], [72, "full-parameter-definitions"]], "Funding": [[90, "funding"]], "Further processing": [[74, "further-processing"]], "Further refinement": [[74, "further-refinement"]], "General": [[79, "general"]], "General Notes": [[73, "general-notes"]], "Generate a mask for the beam center (optional)": [[73, "generate-a-mask-for-the-beam-center-optional"]], "Getting started": [[7, "getting-started"]], "Guide to common scaling options": [[1, "guide-to-common-scaling-options"]], "HTML report": [[82, "html-report"], [86, "html-report"]], "Import": [[75, "import"], [78, "import"], [82, "import"], [86, "import"], [87, "import"], [88, "import"]], "Import and Spotfinding": [[85, "import-and-spotfinding"]], "Import images": [[73, "import-images"]], "Importing": [[93, "importing"]], "Indexing": [[73, "indexing"], [74, "indexing"], [75, "indexing"], [78, "indexing"], [82, "indexing"], [85, "indexing"], [86, "indexing"], [87, "indexing"], [88, "indexing"]], "Indexing SSX data with dials.ssx_index": [[96, "indexing-ssx-data-with-dials-ssx-index"]], "Indexing with the corrected beam centre": [[78, "indexing-with-the-corrected-beam-centre"]], "Individual processing": [[83, "individual-processing"]], "Inspecting the results": [[87, "inspecting-the-results"]], "Installation": [[7, "installation"], [91, "installation"], [91, "id1"]], "Installation for Developers": [[9, "installation-for-developers"]], "Integrating SSX data with dials.ssx_integrate": [[96, "integrating-ssx-data-with-dials-ssx-integrate"]], "Integration": [[73, "integration"], [74, "integration"], [75, "integration"], [82, "integration"], [86, "integration"], [87, "integration"], [88, "integration"]], "Intensity Clustering": [[76, "intensity-clustering"]], "Introduction": [[34, "introduction"], [35, "introduction"], [36, "introduction"], [37, "introduction"], [38, "introduction"], [39, "introduction"], [40, "introduction"], [41, "introduction"], [42, "introduction"], [43, "introduction"], [44, "introduction"], [45, "introduction"], [46, "introduction"], [47, "introduction"], [48, "introduction"], [49, "introduction"], [50, "introduction"], [51, "introduction"], [52, "introduction"], [53, "introduction"], [54, "introduction"], [55, "introduction"], [56, "introduction"], [57, "introduction"], [58, "introduction"], [59, "introduction"], [60, "introduction"], [61, "introduction"], [62, "introduction"], [63, "introduction"], [64, "introduction"], [65, "introduction"], [66, "introduction"], [67, "introduction"], [68, "introduction"], [69, "introduction"], [70, "introduction"], [72, "introduction"], [74, "introduction"], [75, "introduction"], [76, "introduction"], [77, "introduction"], [78, "introduction"], [81, "introduction"], [82, "introduction"], [83, "introduction"], [84, "introduction"], [85, "introduction"], [86, "introduction"], [87, "introduction"], [88, "introduction"]], "Joint refinement": [[83, "joint-refinement"]], "Keeping a Development Environment current": [[9, "keeping-a-development-environment-current"]], "Lattice search strategies": [[4, "lattice-search-strategies"]], "Library Reference": [[32, "library-reference"]], "Lysozyme nanocrystals": [[75, "lysozyme-nanocrystals"]], "Mac and Linux binary installers": [[91, "mac-and-linux-binary-installers"]], "Mac graphical binary installers": [[91, "mac-graphical-binary-installers"]], "Manual reprocessing": [[84, "manual-reprocessing"]], "ModuleNotFoundError: No module named \u2018gltbx_gl_ext\u2019": [[9, "modulenotfounderror-no-module-named-gltbx-gl-ext"]], "Multi-crystal analysis with DIALS and BLEND: individual vs joint refinement": [[83, "multi-crystal-analysis-with-dials-and-blend-individual-vs-joint-refinement"]], "Multi-crystal analysis with DIALS and xia2.multiplex": [[76, "multi-crystal-analysis-with-dials-and-xia2-multiplex"]], "Multi-crystal symmetry analysis and scaling with DIALS": [[84, "multi-crystal-symmetry-analysis-and-scaling-with-dials"]], "Multi-dataset symmetry determination": [[73, "multi-dataset-symmetry-determination"]], "Multi-lattice Tutorial": [[85, "multi-lattice-tutorial"]], "Multi-tile refinement": [[81, "multi-tile-refinement"]], "MyD88TIR small wedges": [[74, "myd88tir-small-wedges"]], "Next steps": [[7, "next-steps"]], "Note about pedestal and offset": [[73, "note-about-pedestal-and-offset"]], "Organising committee": [[97, "organising-committee"]], "Orientation matrix": [[2, "orientation-matrix"]], "Orthogonalisation convention": [[2, "orthogonalisation-convention"]], "Other datasets": [[73, "other-datasets"]], "Output for SADABS (alternate path)": [[88, "output-for-sadabs-alternate-path"]], "Parameters": [[7, "parameters"]], "Post Experiment Processing": [[76, "post-experiment-processing"]], "Practicalities for large datasets": [[1, "practicalities-for-large-datasets"]], "Preferential Orientation": [[76, "preferential-orientation"]], "Preparing for multi-tile refinement": [[81, "preparing-for-multi-tile-refinement"]], "Process": [[76, "process"]], "Processing Sequences with Missing Images": [[93, "processing-sequences-with-missing-images"]], "Processing Small Molecule MicroED/3DED: Biotin": [[73, "processing-small-molecule-microed-3ded-biotin"]], "Processing in Detail": [[86, "processing-in-detail"]], "Processing in Detail with DUI": [[87, "processing-in-detail-with-dui"]], "Program and presentations": [[97, "program-and-presentations"], [98, "program-and-presentations"]], "Program documentation": [[71, "program-documentation"]], "Projects": [[94, "projects"]], "Publications": [[95, "publications"]], "Questioning the lattice symmetry": [[77, "questioning-the-lattice-symmetry"]], "Re-import with the correct beam center": [[73, "re-import-with-the-correct-beam-center"]], "Reading experiment and data": [[6, "reading-experiment-and-data"]], "Refine the geometry": [[73, "refine-the-geometry"]], "Refinement": [[82, "refinement"], [86, "refinement"], [87, "refinement"], [88, "refinement"], [93, "refinement"]], "Refinement and Integration": [[85, "refinement-and-integration"]], "Refining multi-tile detector metrology with DIALS": [[81, "refining-multi-tile-detector-metrology-with-dials"]], "Refining the detector distance": [[74, "refining-the-detector-distance"]], "Reflection files": [[3, "reflection-files"]], "SARS-CoV-2 main protease (Mpro)": [[82, "sars-cov-2-main-protease-mpro"]], "SSX processing guide": [[96, "ssx-processing-guide"]], "Scale the data together": [[73, "scale-the-data-together"]], "Scaling": [[73, "scaling"], [74, "scaling"], [87, "scaling"], [88, "scaling"]], "Scaling against a reference dataset": [[1, "scaling-against-a-reference-dataset"]], "Scaling and Merging": [[82, "scaling-and-merging"], [86, "scaling-and-merging"]], "Scaling and merging": [[75, "scaling-and-merging"]], "Scan-varying refinement": [[75, "scan-varying-refinement"]], "Scripted processing": [[74, "scripted-processing"]], "Sets 0-9": [[76, "sets-0-9"]], "Sets 10-19": [[76, "sets-10-19"]], "Sets 20-29": [[76, "sets-20-29"]], "Setting up a Development Environment on Linux or Mac": [[9, "setting-up-a-development-environment-on-linux-or-mac"]], "Small-molecule data reduction tutorial": [[88, "small-molecule-data-reduction-tutorial"]], "Solve the structure": 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"dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs.compute_functional_gradients_and_curvatures", false]], "compute_functional_gradients_diag() (dials.algorithms.refinement.engine.lbfgscurvs method)": [[14, "dials.algorithms.refinement.engine.LBFGScurvs.compute_functional_gradients_diag", false]], "compute_functional_gradients_diag() (dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs method)": [[18, "dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs.compute_functional_gradients_diag", false]], "compute_gradients() (dials.algorithms.symmetry.cosym.target.target method)": [[18, "dials.algorithms.symmetry.cosym.target.Target.compute_gradients", false]], "compute_gradients_fd() (dials.algorithms.symmetry.cosym.target.target method)": [[18, "dials.algorithms.symmetry.cosym.target.Target.compute_gradients_fd", false]], "compute_residuals() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.compute_residuals", false]], 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false]], "configure_threshold() (dials.algorithms.spot_finding.factory.spotfinderfactory static method)": [[16, "dials.algorithms.spot_finding.factory.SpotFinderFactory.configure_threshold", false]], "consecutive_refinement_order (dials.algorithms.scaling.model.model.arrayscalingmodel property)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.consecutive_refinement_order", false]], "consecutive_refinement_order (dials.algorithms.scaling.model.model.dosedecay property)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.consecutive_refinement_order", false]], "consecutive_refinement_order (dials.algorithms.scaling.model.model.kbscalingmodel property)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel.consecutive_refinement_order", false]], "consecutive_refinement_order (dials.algorithms.scaling.model.model.physicalscalingmodel property)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.consecutive_refinement_order", false]], 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"module-dials.algorithms.indexing.indexer", false]], "dials.algorithms.indexing.lattice_search": [[11, "module-dials.algorithms.indexing.lattice_search", false]], "dials.algorithms.indexing.max_cell": [[11, "module-dials.algorithms.indexing.max_cell", false]], "dials.algorithms.indexing.model_evaluation": [[11, "module-dials.algorithms.indexing.model_evaluation", false]], "dials.algorithms.indexing.nearest_neighbor": [[11, "module-dials.algorithms.indexing.nearest_neighbor", false]], "dials.algorithms.indexing.refinement": [[11, "module-dials.algorithms.indexing.refinement", false]], "dials.algorithms.indexing.stills_indexer": [[11, "module-dials.algorithms.indexing.stills_indexer", false]], "dials.algorithms.indexing.symmetry": [[11, "module-dials.algorithms.indexing.symmetry", false]], "dials.algorithms.integration.integrator": [[12, "module-dials.algorithms.integration.integrator", false]], "dials.algorithms.profile_model": [[13, "module-dials.algorithms.profile_model", false]], 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"module-dials.algorithms.spot_finding.factory", false]], "dials.algorithms.spot_finding.finder": [[16, "module-dials.algorithms.spot_finding.finder", false]], "dials.algorithms.spot_prediction.reflection_predictor": [[17, "module-dials.algorithms.spot_prediction.reflection_predictor", false]], "dials.algorithms.symmetry": [[18, "module-dials.algorithms.symmetry", false]], "dials.algorithms.symmetry.cosym": [[18, "module-dials.algorithms.symmetry.cosym", false]], "dials.algorithms.symmetry.cosym.engine": [[18, "module-dials.algorithms.symmetry.cosym.engine", false]], "dials.algorithms.symmetry.cosym.target": [[18, "module-dials.algorithms.symmetry.cosym.target", false]], "dials.algorithms.symmetry.laue_group": [[18, "module-dials.algorithms.symmetry.laue_group", false]], "dials.algorithms.symmetry.reindex_to_reference": [[18, "module-dials.algorithms.symmetry.reindex_to_reference", false]], "dials.array_family.flex": [[20, "module-dials.array_family.flex", false]], "dials.extensions.dispersion_spotfinder_threshold_ext": [[31, "module-dials.extensions.dispersion_spotfinder_threshold_ext", false]], "dials.extensions.gaussian_rs_profile_model_ext": [[31, "module-dials.extensions.gaussian_rs_profile_model_ext", false]], "dials.extensions.null_background_ext": [[31, "module-dials.extensions.null_background_ext", false]], "dials.extensions.simple_background_ext": [[31, "module-dials.extensions.simple_background_ext", false]], "dials.extensions.simple_centroid_ext": [[31, "module-dials.extensions.simple_centroid_ext", false]], "dials.util.command_line": [[33, "module-dials.util.command_line", false]], "dials.util.export_mtz": [[33, "module-dials.util.export_mtz", false]], "dials.util.export_text": [[33, "module-dials.util.export_text", false]], "dials.util.image": [[33, "module-dials.util.image", false]], "dials.util.installer": [[33, "module-dials.util.installer", false]], "dials.util.ioutil": [[33, "module-dials.util.ioutil", false]], "dials.util.nexus": [[33, "module-dials.util.nexus", false]], "dials.util.options": [[33, "module-dials.util.options", false]], "dialsindexerror": [[11, "dials.algorithms.indexing.DialsIndexError", false]], "dialsindexrefineerror": [[11, "dials.algorithms.indexing.DialsIndexRefineError", false]], "diff_phil (dials.util.options.argumentparser property)": [[33, "dials.util.options.ArgumentParser.diff_phil", false]], "diff_phil (dials.util.options.philcommandparser property)": [[33, "dials.util.options.PhilCommandParser.diff_phil", false]], "difference_rotation_matrix_axis_angle() (in module dials.algorithms.indexing.compare_orientation_matrices)": [[11, "dials.algorithms.indexing.compare_orientation_matrices.difference_rotation_matrix_axis_angle", false]], "dim (dials.algorithms.refinement.target.target property)": [[14, "dials.algorithms.refinement.target.Target.dim", false]], "dim (dials.algorithms.symmetry.cosym.target.target attribute)": [[18, "dials.algorithms.symmetry.cosym.target.Target.dim", false]], "disablempmixin (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.DisableMPmixin", false]], "dispersionspotfinderthresholdext (class in dials.extensions.dispersion_spotfinder_threshold_ext)": [[31, "dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt", false]], "dosedecay (class in dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.DoseDecay", false]], "dump() (in module dials.util.nexus)": [[33, "dials.util.nexus.dump", false]], "dx (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.dx", false]], "dxtbx.imageset": [[26, "module-dxtbx.imageset", false]], "dxtbx.model.beam": [[21, "module-dxtbx.model.beam", false]], "dxtbx.model.crystal": [[22, "module-dxtbx.model.crystal", false]], "dxtbx.model.detector": [[23, "module-dxtbx.model.detector", false]], "dxtbx.model.experiment_list": [[24, "module-dxtbx.model.experiment_list", false]], "dxtbx.model.goniometer": [[25, "module-dxtbx.model.goniometer", false]], "dxtbx.model.profile": [[28, "module-dxtbx.model.profile", false]], "dxtbx.model.scan": [[29, "module-dxtbx.model.scan", false]], "dxtbx.serialize.imageset": [[30, "module-dxtbx.serialize.imageset", false]], "dxtbx.serialize.load": [[30, "module-dxtbx.serialize.load", false]], "dxtbx.serialize.xds": [[30, "module-dxtbx.serialize.xds", false]], "dy (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.dy", false]], "e_refine() (in module dials.algorithms.indexing.stills_indexer)": [[11, "dials.algorithms.indexing.stills_indexer.e_refine", false]], "empty() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.empty", false]], "end() (dials.util.command_line.command class method)": [[33, "dials.util.command_line.Command.end", false]], "error_model (dials.algorithms.scaling.model.model.scalingmodelbase property)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.error_model", false]], "estimate_global_threshold() (in module dials.extensions.dispersion_spotfinder_threshold_ext)": [[31, "dials.extensions.dispersion_spotfinder_threshold_ext.estimate_global_threshold", false]], "evaluate() (dials.algorithms.indexing.model_evaluation.modelevaluation method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelEvaluation.evaluate", false]], "evaluate() (dials.algorithms.indexing.model_evaluation.strategy method)": [[11, "dials.algorithms.indexing.model_evaluation.Strategy.evaluate", false]], "exception (dials.util.options.argumenthandlingerrorinfo attribute)": [[33, "dials.util.options.ArgumentHandlingErrorInfo.exception", false]], "executor (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Executor", false]], "exp_nos (dials.util.export_mtz.wavelengthgroup attribute)": [[33, "dials.util.export_mtz.WavelengthGroup.exp_nos", false]], "experiment_list() (in module dxtbx.serialize.load)": [[30, "dxtbx.serialize.load.experiment_list", false]], "experiment_list_for_crystal() (dials.algorithms.indexing.stills_indexer.stillsindexer method)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexer.experiment_list_for_crystal", false]], "experiment_type (dials.algorithms.refinement.reflection_manager.lauereflectionmanager attribute)": [[14, "dials.algorithms.refinement.reflection_manager.LaueReflectionManager.experiment_type", false]], "experiment_type (dials.algorithms.refinement.reflection_manager.reflectionmanager attribute)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.experiment_type", false]], "experiment_type (dials.algorithms.refinement.reflection_manager.stillsreflectionmanager attribute)": [[14, "dials.algorithms.refinement.reflection_manager.StillsReflectionManager.experiment_type", false]], "experimentlist (class in dxtbx.model)": [[24, "dxtbx.model.ExperimentList", false]], "experimentlistfactory (class in dxtbx.model.experiment_list)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory", false]], "export_as_json() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.export_as_json", false]], "export_mtz() (in module dials.util.export_mtz)": [[33, "dials.util.export_mtz.export_mtz", false]], "export_reflections() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.export_reflections", false]], "export_text() (in module dials.util.export_text)": [[33, "dials.util.export_text.export_text", false]], "extend() (dials.algorithms.indexing.model_evaluation.modelrank method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRank.extend", false]], "extend() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter.extend", false]], "extend() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.extend", false]], "external_lookup (dxtbx.imageset.imageset property)": [[26, "dxtbx.imageset.ImageSet.external_lookup", false]], "external_lookup (dxtbx.imageset.imagesetdata property)": [[26, "dxtbx.imageset.ImageSetData.external_lookup", false]], "externaldelpsiweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)": [[14, "dials.algorithms.refinement.weighting_strategies.ExternalDelPsiWeightingStrategy", false]], "externallookup (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ExternalLookup", false]], "externallookupitembool (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ExternalLookupItemBool", false]], "externallookupitemdouble (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ExternalLookupItemDouble", false]], "extract_reference_intensities() (in module dials.algorithms.symmetry.cosym)": [[18, "dials.algorithms.symmetry.cosym.extract_reference_intensities", false]], "extractpixelsfromimage (class in dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.ExtractPixelsFromImage", false]], "extractpixelsfromimage2dnoshoeboxes (class in dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.ExtractPixelsFromImage2DNoShoeboxes", false]], "extractspots (class in dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.ExtractSpots", false]], "extractspotsparalleltask (class in dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.ExtractSpotsParallelTask", false]], "fft1d (class in dials.algorithms.indexing.basis_vector_search)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT1D", false]], "fft3d (class in dials.algorithms.indexing.basis_vector_search)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT3D", false]], "filename (dxtbx.imageset.externallookupitembool property)": [[26, "dxtbx.imageset.ExternalLookupItemBool.filename", false]], "filename (dxtbx.imageset.externallookupitemdouble property)": [[26, "dxtbx.imageset.ExternalLookupItemDouble.filename", false]], "filename_or_none() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.filename_or_none", false]], "filename_to_absolute() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.filename_to_absolute", false]], "filter_by_likelihood() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter.filter_by_likelihood", false]], "filter_by_n_indexed() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter.filter_by_n_indexed", false]], "filter_by_volume() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter.filter_by_volume", false]], "filter_doubled_cell() (in module dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.filter_doubled_cell", false]], "filter_known_symmetry() (in module dials.algorithms.indexing.basis_vector_search.combinations)": [[11, "dials.algorithms.indexing.basis_vector_search.combinations.filter_known_symmetry", false]], "filter_obs() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.filter_obs", false]], "filter_similar_orientations() (in module dials.algorithms.indexing.basis_vector_search.combinations)": [[11, "dials.algorithms.indexing.basis_vector_search.combinations.filter_similar_orientations", false]], "filterrunner (class in dials.algorithms.spot_finding.factory)": [[16, "dials.algorithms.spot_finding.factory.FilterRunner", false]], "final_outlier_arrays (dials.algorithms.scaling.outlier_rejection.outlierrejectionbase attribute)": [[15, "dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase.final_outlier_arrays", false]], "finalise() (dials.algorithms.integration.integrator.integrator3dthreaded method)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded.finalise", false]], "finalise() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.finalise", false]], "finalize() (dials.algorithms.integration.integrator.integratorexecutor method)": [[12, "dials.algorithms.integration.integrator.IntegratorExecutor.finalize", false]], "finalize() (dials.algorithms.integration.integrator.profilemodellerexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileModellerExecutor.finalize", false]], "finalize() (dials.algorithms.integration.integrator.profilevalidatorexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileValidatorExecutor.finalize", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integrator2d static method)": [[12, "dials.algorithms.integration.integrator.Integrator2D.finalize_reflections", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integrator3d static method)": [[12, "dials.algorithms.integration.integrator.Integrator3D.finalize_reflections", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integratorflat3d static method)": [[12, "dials.algorithms.integration.integrator.IntegratorFlat3D.finalize_reflections", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integratorsingle2d static method)": [[12, "dials.algorithms.integration.integrator.IntegratorSingle2D.finalize_reflections", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integratorstills static method)": [[12, "dials.algorithms.integration.integrator.IntegratorStills.finalize_reflections", false]], "find() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.find", false]], "find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.fft1d method)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT1D.find_basis_vectors", false]], "find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.fft3d method)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT3D.find_basis_vectors", false]], "find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.realspacegridsearch method)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.find_basis_vectors", false]], "find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.strategy method)": [[11, "dials.algorithms.indexing.basis_vector_search.Strategy.find_basis_vectors", false]], "find_crystal_models() (dials.algorithms.indexing.lattice_search.lowresspotmatch method)": [[11, "dials.algorithms.indexing.lattice_search.LowResSpotMatch.find_crystal_models", false]], "find_crystal_models() (dials.algorithms.indexing.lattice_search.pinkindexer method)": [[11, "dials.algorithms.indexing.lattice_search.PinkIndexer.find_crystal_models", false]], "find_crystal_models() (dials.algorithms.indexing.lattice_search.strategy method)": [[11, "dials.algorithms.indexing.lattice_search.Strategy.find_crystal_models", false]], "find_lattices() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.find_lattices", false]], "find_matching_symmetry() (in module dials.algorithms.indexing.symmetry)": [[11, "dials.algorithms.indexing.symmetry.find_matching_symmetry", false]], "find_max_cell() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.find_max_cell", false]], "find_max_cell() (in module dials.algorithms.indexing.max_cell)": [[11, "dials.algorithms.indexing.max_cell.find_max_cell", false]], "find_spots() (dials.algorithms.spot_finding.finder.spotfinder method)": [[16, "dials.algorithms.spot_finding.finder.SpotFinder.find_spots", false]], "finished() (dials.algorithms.integration.integrator.reflectionmanager method)": [[12, "dials.algorithms.integration.integrator.ReflectionManager.finished", false]], "finished() (dials.util.command_line.progressbar method)": [[33, "dials.util.command_line.ProgressBar.finished", false]], "fit_profiles() (dials.algorithms.integration.integrator.integrator method)": [[12, "dials.algorithms.integration.integrator.Integrator.fit_profiles", false]], "fix_initial_parameter() (dials.algorithms.scaling.model.model.dosedecay method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.fix_initial_parameter", false]], "fix_initial_parameter() (dials.algorithms.scaling.model.model.physicalscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.fix_initial_parameter", false]], "fix_initial_parameter() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.fix_initial_parameter", false]], "fixed_components (dials.algorithms.scaling.model.model.scalingmodelbase property)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.fixed_components", false]], "flatten_experiments() (in module dials.util.options)": [[33, "dials.util.options.flatten_experiments", false]], "flatten_reflections() (in module dials.util.options)": [[33, "dials.util.options.flatten_reflections", false]], "format_epilog() (dials.util.options.argumentparserbase method)": [[33, "dials.util.options.ArgumentParserBase.format_epilog", false]], "format_help() (dials.util.options.argumentparser method)": [[33, "dials.util.options.ArgumentParser.format_help", false]], "fraction_indexed (dials.algorithms.indexing.model_evaluation.result attribute)": [[11, "dials.algorithms.indexing.model_evaluation.Result.fraction_indexed", false]], "frame_hist() (in module dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.frame_hist", false]], "from_args() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_args", false]], "from_data() (dials.algorithms.scaling.model.model.arrayscalingmodel class method)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.from_data", false]], "from_data() (dials.algorithms.scaling.model.model.dosedecay class method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.from_data", false]], "from_data() (dials.algorithms.scaling.model.model.kbscalingmodel class method)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel.from_data", false]], "from_data() (dials.algorithms.scaling.model.model.physicalscalingmodel class method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.from_data", false]], "from_data() (dials.algorithms.scaling.model.model.scalingmodelbase class method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.from_data", false]], "from_dict() (dials.algorithms.scaling.model.model.arrayscalingmodel class method)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.from_dict", false]], "from_dict() (dials.algorithms.scaling.model.model.dosedecay class method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.from_dict", false]], "from_dict() (dials.algorithms.scaling.model.model.kbscalingmodel class method)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel.from_dict", false]], "from_dict() (dials.algorithms.scaling.model.model.physicalscalingmodel class method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.from_dict", false]], "from_dict() (dials.algorithms.scaling.model.model.scalingmodelbase class method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.from_dict", false]], "from_dict() (dials.extensions.gaussian_rs_profile_model_ext.gaussianrsprofilemodelext class method)": [[31, "dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt.from_dict", false]], "from_dict() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.from_dict", false]], "from_dict() (dxtbx.model.crystal static method)": [[22, "dxtbx.model.Crystal.from_dict", false]], "from_dict() (dxtbx.model.crystal.crystalfactory static method)": [[22, "dxtbx.model.crystal.CrystalFactory.from_dict", false]], "from_dict() (dxtbx.model.detector static method)": [[23, "dxtbx.model.Detector.from_dict", false]], "from_dict() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.from_dict", false]], "from_dict() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_dict", false]], "from_dict() (dxtbx.model.goniometer.goniometer static method)": [[25, "dxtbx.model.goniometer.Goniometer.from_dict", false]], "from_dict() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.from_dict", false]], "from_dict() (dxtbx.model.goniometer.multiaxisgoniometer static method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.from_dict", false]], "from_dict() (dxtbx.model.mosaiccrystalkabsch2010 class method)": [[22, "dxtbx.model.MosaicCrystalKabsch2010.from_dict", false]], "from_dict() (dxtbx.model.mosaiccrystalsauter2014 class method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.from_dict", false]], "from_dict() (dxtbx.model.profile.profilemodelfactory static method)": [[28, "dxtbx.model.profile.ProfileModelFactory.from_dict", false]], "from_dict() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.from_dict", false]], "from_file() (dxtbx.model.experimentlist static method)": [[24, "dxtbx.model.ExperimentList.from_file", false]], "from_filenames() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_filenames", false]], "from_imageset() (dxtbx.imageset.imagegrid static method)": [[26, "dxtbx.imageset.ImageGrid.from_imageset", false]], "from_imageset_and_crystal() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_imageset_and_crystal", false]], "from_json() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_json", false]], "from_json_file() (dials.algorithms.refinement.engine.journal class method)": [[14, "dials.algorithms.refinement.engine.Journal.from_json_file", false]], "from_json_file() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_json_file", false]], "from_mosflm_matrix() (dxtbx.model.crystal.crystalfactory static method)": [[22, "dxtbx.model.crystal.CrystalFactory.from_mosflm_matrix", false]], "from_parameters() (dials.algorithms.indexing.indexer.indexer static method)": [[11, "dials.algorithms.indexing.indexer.Indexer.from_parameters", false]], "from_parameters() (dials.algorithms.spot_finding.factory.spotfinderfactory static method)": [[16, "dials.algorithms.spot_finding.factory.SpotFinderFactory.from_parameters", false]], "from_parameters_and_experiments() (dials.algorithms.refinement.target.targetfactory static method)": [[14, "dials.algorithms.refinement.target.TargetFactory.from_parameters_and_experiments", false]], "from_parameters_data_experiments() (dials.algorithms.refinement.refiner.refinerfactory class method)": [[14, "dials.algorithms.refinement.refiner.RefinerFactory.from_parameters_data_experiments", false]], "from_parameters_reflections_experiments() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.from_parameters_reflections_experiments", false]], "from_phil() (dials.algorithms.integration.integrator.parameters static method)": [[12, "dials.algorithms.integration.integrator.Parameters.from_phil", false]], "from_phil() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.from_phil", false]], "from_phil() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.from_phil", false]], "from_phil() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.from_phil", false]], "from_phil() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.from_phil", false]], "from_pickle_file() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_pickle_file", false]], "from_sequence_and_crystal() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_sequence_and_crystal", false]], "from_serialized_format() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_serialized_format", false]], "from_stills_and_crystal() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_stills_and_crystal", false]], "from_template() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.from_template", false]], "from_templates() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_templates", false]], "from_templates() (dxtbx.model.experimentlist static method)": [[24, "dxtbx.model.ExperimentList.from_templates", false]], "from_xds() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_xds", false]], "gain (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.gain", false]], "gaussianrsprofilemodelext (class in dials.extensions.gaussian_rs_profile_model_ext)": [[31, "dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt", false]], "gaussnewtoniterations (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations", false]], "generate_from_phil() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.generate_from_phil", false]], "generate_phil_scope() (in module dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.generate_phil_scope", false]], "generate_phil_scope() (in module dials.algorithms.spot_finding.factory)": [[16, "dials.algorithms.spot_finding.factory.generate_phil_scope", false]], "get_a_as_sqr() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.get_A_as_sqr", false]], "get_a_inverse_as_sqr() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.get_A_inverse_as_sqr", false]], "get_accepted_refs_size() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_accepted_refs_size", false]], "get_alpha_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_alpha_angle", false]], "get_angles() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.get_angles", false]], "get_array_range() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_array_range", false]], "get_axes() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.get_axes", false]], "get_beam() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_beam", false]], "get_beam() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_beam", false]], "get_beam() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_beam", false]], "get_beam() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_beam", false]], "get_beam() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_beam", false]], "get_centroid_analyser() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_centroid_analyser", false]], "get_corrected_data() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_corrected_data", false]], "get_corrected_data() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_corrected_data", false]], "get_correlation_matrix_for_step() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.get_correlation_matrix_for_step", false]], "get_crystal_symmetry() (dxtbx.model.crystal method)": [[22, "dxtbx.model.Crystal.get_crystal_symmetry", false]], "get_data() (dials.util.image.reader method)": [[33, "dials.util.image.reader.get_data", false]], "get_data() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_data", false]], "get_detector() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_detector", false]], "get_detector() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_detector", false]], "get_detector() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_detector", false]], "get_detector() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_detector", false]], "get_detector() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_detector", false]], "get_detectorbase() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_detectorbase", false]], "get_direction() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_direction", false]], "get_domain_size_ang() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.get_domain_size_ang", false]], "get_elapsed_time() (dials.util.command_line.progressbartimer method)": [[33, "dials.util.command_line.ProgressBarTimer.get_elapsed_time", false]], "get_entry() (in module dials.util.nexus)": [[33, "dials.util.nexus.get_entry", false]], "get_experiments() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_experiments", false]], "get_fixed_rotation() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_fixed_rotation", false]], "get_format_class() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_format_class", false]], "get_format_class() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_format_class", false]], "get_free_reflections() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_free_reflections", false]], "get_free_reflections() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_free_reflections", false]], "get_gain() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_gain", false]], "get_gain() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_gain", false]], "get_goniometer() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_goniometer", false]], "get_goniometer() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_goniometer", false]], "get_goniometer() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_goniometer", false]], "get_goniometer() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_goniometer", false]], "get_goniometer() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_goniometer", false]], "get_grid_size() (dxtbx.imageset.imagegrid method)": [[26, "dxtbx.imageset.ImageGrid.get_grid_size", false]], "get_half_mosaicity_deg() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.get_half_mosaicity_deg", false]], "get_image_identifier() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_image_identifier", false]], "get_image_identifier() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_image_identifier", false]], "get_indexed() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_indexed", false]], "get_inverse_ub_matrix_from_xparm() (in module dials.util.ioutil)": [[33, "dials.util.ioutil.get_inverse_ub_matrix_from_xparm", false]], "get_kappa_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_kappa_angle", false]], "get_kappa_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_kappa_axis", false]], "get_mask() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_mask", false]], "get_mask() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_mask", false]], "get_master_path() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_master_path", false]], "get_matches() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_matches", false]], "get_matches() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_matches", false]], "get_max_inscribed_resolution() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_max_inscribed_resolution", false]], "get_max_resolution() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_max_resolution", false]], "get_mosaicity() (dxtbx.model.mosaiccrystalkabsch2010 method)": [[22, "dxtbx.model.MosaicCrystalKabsch2010.get_mosaicity", false]], "get_names() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_names", false]], "get_names() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.get_names", false]], "get_nrows() (dials.algorithms.refinement.engine.journal method)": [[14, "dials.algorithms.refinement.engine.Journal.get_nrows", false]], "get_num_matches() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.get_num_matches", false]], "get_num_matches_for_experiment() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.get_num_matches_for_experiment", false]], "get_num_matches_for_panel() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.get_num_matches_for_panel", false]], "get_num_scan_points() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_num_scan_points", false]], "get_num_steps() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.get_num_steps", false]], "get_obs() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_obs", false]], "get_omega_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_omega_angle", false]], "get_omega_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_omega_axis", false]], "get_panel_intersection() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_panel_intersection", false]], "get_param_reporter() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_param_reporter", false]], "get_parameter_correlation_matrix() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_parameter_correlation_matrix", false]], "get_params() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_params", false]], "get_path() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_path", false]], "get_path() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_path", false]], "get_pedestal() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_pedestal", false]], "get_phi_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_phi_angle", false]], "get_phi_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_phi_axis", false]], "get_raw_data() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_raw_data", false]], "get_ray_intersection() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_ray_intersection", false]], "get_rotation_axis() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_rotation_axis", false]], "get_rotation_axis_datum() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_rotation_axis_datum", false]], "get_sample_size() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_sample_size", false]], "get_scan() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_scan", false]], "get_scan() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_scan", false]], "get_scan() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_scan", false]], "get_scan() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_scan", false]], "get_scan() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_scan", false]], "get_scan_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_scan_axis", false]], "get_scan_axis() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.get_scan_axis", false]], "get_setting_rotation() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_setting_rotation", false]], "get_setting_rotation_at_scan_point() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_setting_rotation_at_scan_point", false]], "get_setting_rotation_at_scan_points() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_setting_rotation_at_scan_points", false]], "get_shared_components() (dials.algorithms.scaling.model.model.dosedecay method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.get_shared_components", false]], "get_shared_components() (dials.algorithms.scaling.model.model.physicalscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.get_shared_components", false]], "get_shared_components() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.get_shared_components", false]], "get_space_group_type_from_xparm() (in module dials.util.ioutil)": [[33, "dials.util.ioutil.get_space_group_type_from_xparm", false]], "get_spectrum() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_spectrum", false]], "get_template() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_template", false]], "get_template() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_template", false]], "get_template() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_template", false]], "get_vendor() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_vendor", false]], "get_vendortype() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_vendortype", false]], "get_weighting_strategy_override() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.get_weighting_strategy_override", false]], "goniometer (class in dxtbx.model.goniometer)": [[25, "dxtbx.model.goniometer.Goniometer", false]], "goniometercomparison (class in dxtbx.model.experiment_list)": [[24, "dxtbx.model.experiment_list.GoniometerComparison", false]], "goniometerfactory (class in dxtbx.model.goniometer)": [[25, "dxtbx.model.goniometer.GoniometerFactory", false]], "goniometers() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.goniometers", false]], "gradient_threshold (dials.algorithms.refinement.engine.gaussnewtoniterations attribute)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations.gradient_threshold", false]], "groups_cache() (in module dials.algorithms.indexing.symmetry)": [[11, "dials.algorithms.indexing.symmetry.groups_cache", false]], "has_dynamic_mask() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.has_dynamic_mask", false]], "has_projection_2d() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.has_projection_2d", false]], "has_single_file_reader() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.has_single_file_reader", false]], "heading() (in module dials.util.command_line)": [[33, "dials.util.command_line.heading", false]], "hierarchy() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.hierarchy", false]], "hist() (in module dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.hist", false]], "history (dials.algorithms.refinement.refiner.refiner property)": [[14, "dials.algorithms.refinement.refiner.Refiner.history", false]], "hkl_offset (dials.algorithms.indexing.model_evaluation.result attribute)": [[11, "dials.algorithms.indexing.model_evaluation.Result.hkl_offset", false]], "id_ (dials.algorithms.scaling.model.model.arrayscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.id_", false]], "id_ (dials.algorithms.scaling.model.model.dosedecay attribute)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.id_", false]], "id_ (dials.algorithms.scaling.model.model.kbscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel.id_", false]], "id_ (dials.algorithms.scaling.model.model.physicalscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.id_", false]], "id_ (dials.algorithms.scaling.model.model.scalingmodelbase attribute)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.id_", false]], "identifiers (dials.util.export_mtz.wavelengthgroup attribute)": [[33, "dials.util.export_mtz.WavelengthGroup.identifiers", false]], "identifiers() (dxtbx.imageset.memreader method)": [[26, "dxtbx.imageset.MemReader.identifiers", false]], "identifiers() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.identifiers", false]], "identify_outliers() (dials.algorithms.indexing.stills_indexer.stillsindexer method)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexer.identify_outliers", false]], "imagegrid (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageGrid", false]], "imagesequence (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSequence", false]], "imagesequence_from_dict() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.imagesequence_from_dict", false]], "imagesequence_to_dict() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.imagesequence_to_dict", false]], "imageset (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSet", false]], "imageset() (in module dxtbx.serialize.load)": [[30, "dxtbx.serialize.load.imageset", false]], "imageset_from_anyset() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.imageset_from_anyset", false]], "imageset_from_dict() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.imageset_from_dict", false]], "imageset_to_dict() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.imageset_to_dict", false]], "imagesetdata (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSetData", false]], "imagesetfactory (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSetFactory", false]], "imagesetlazy (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSetLazy", false]], "imagesets() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.imagesets", false]], "imgcif() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.imgCIF", false]], "imgcif() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.imgCIF", false]], "imgcif() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.imgCIF", false]], "imgcif() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.imgCIF", false]], "imgcif_h() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.imgCIF_H", false]], "imgcif_h() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.imgCIF_H", false]], "imgcif_h() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.imgCIF_H", false]], "imgcif_h() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.imgCIF_H", false]], "importer (class in dials.util.options)": [[33, "dials.util.options.Importer", false]], "include_gui_packages (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.include_gui_packages", false]], "indent (dials.util.command_line.command attribute)": [[33, "dials.util.command_line.Command.indent", false]], "index() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.index", false]], "index() (dials.algorithms.indexing.stills_indexer.stillsindexer method)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexer.index", false]], "index_reflections() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.index_reflections", false]], "indexer (class in dials.algorithms.indexing.indexer)": [[11, "dials.algorithms.indexing.indexer.Indexer", false]], "indices() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.indices", false]], "indices() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.indices", false]], "initialise() (dials.algorithms.integration.integrator.integrator3dthreaded method)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded.initialise", false]], "initialise_smooth_input() (in module dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.initialise_smooth_input", false]], "initialize() (dials.algorithms.integration.integrator.integratorexecutor method)": [[12, "dials.algorithms.integration.integrator.IntegratorExecutor.initialize", false]], "initialize() (dials.algorithms.integration.integrator.profilemodellerexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileModellerExecutor.initialize", false]], "initialize() (dials.algorithms.integration.integrator.profilevalidatorexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileValidatorExecutor.initialize", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integrator2d static method)": [[12, "dials.algorithms.integration.integrator.Integrator2D.initialize_reflections", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integrator3d static method)": [[12, "dials.algorithms.integration.integrator.Integrator3D.initialize_reflections", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integratorflat3d static method)": [[12, "dials.algorithms.integration.integrator.IntegratorFlat3D.initialize_reflections", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integratorsingle2d static method)": [[12, "dials.algorithms.integration.integrator.IntegratorSingle2D.initialize_reflections", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integratorstills static method)": [[12, "dials.algorithms.integration.integrator.IntegratorStills.initialize_reflections", false]], "installer (class in dials.util.installer)": [[33, "dials.util.installer.installer", false]], "installer_dir (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.installer_dir", false]], "integrate() (dials.algorithms.integration.integrator.integrator method)": [[12, "dials.algorithms.integration.integrator.Integrator.integrate", false]], "integrate() (dials.algorithms.integration.integrator.integrator3dthreaded method)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded.integrate", false]], "integrator (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Integrator", false]], "integrator2d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Integrator2D", false]], "integrator3d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Integrator3D", false]], "integrator3dthreaded (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded", false]], "integratorexecutor (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.IntegratorExecutor", false]], "integratorflat3d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.IntegratorFlat3D", false]], "integratorsingle2d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.IntegratorSingle2D", false]], "integratorstills (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.IntegratorStills", false]], "inv_d2() (dials.algorithms.background.radialaverage method)": [[10, "dials.algorithms.background.RadialAverage.inv_d2", false]], "invalidphilerror": [[33, "dials.util.options.InvalidPhilError", false]], "is_consistent() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.is_consistent", false]], "is_marked_for_rejection() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.is_marked_for_rejection", false]], "is_marked_for_rejection() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.is_marked_for_rejection", false]], "is_scaled (dials.algorithms.scaling.model.model.scalingmodelbase property)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.is_scaled", false]], "is_similar_to() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.is_similar_to", false]], "is_similar_to() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.is_similar_to", false]], "is_similar_to() (dxtbx.model.mosaiccrystalkabsch2010 method)": [[22, "dxtbx.model.MosaicCrystalKabsch2010.is_similar_to", false]], "is_similar_to() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.is_similar_to", false]], "is_single_file_reader() (dxtbx.imageset.memreader static method)": [[26, "dxtbx.imageset.MemReader.is_single_file_reader", false]], "iter_levelorder() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.iter_levelorder", false]], "iter_panels() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.iter_panels", false]], "iter_preorder() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.iter_preorder", false]], "jacobian_condition_number() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.jacobian_condition_number", false]], "job() (dials.algorithms.integration.integrator.reflectionmanager method)": [[12, "dials.algorithms.integration.integrator.ReflectionManager.job", false]], "joblist (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.JobList", false]], "journal (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.Journal", false]], "kappa() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.kappa", false]], "kappagoniometer (class in dxtbx.model.goniometer)": [[25, "dxtbx.model.goniometer.KappaGoniometer", false]], "kbscalingmodel (class in dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel", false]], "kernel_normalisation() (dials.algorithms.symmetry.symmetry_base static method)": [[18, "dials.algorithms.symmetry.symmetry_base.kernel_normalisation", false]], "known_axis() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.known_axis", false]], "laue_manager() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.laue_manager", false]], "lauegroupanalysis (class in dials.algorithms.symmetry.laue_group)": [[18, "dials.algorithms.symmetry.laue_group.LaueGroupAnalysis", false]], "laueleastsquaresresidualwithrmsdcutoff (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff", false]], "lauemixedweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)": [[14, "dials.algorithms.refinement.weighting_strategies.LaueMixedWeightingStrategy", false]], "lauereflectionmanager (class in dials.algorithms.refinement.reflection_manager)": [[14, "dials.algorithms.refinement.reflection_manager.LaueReflectionManager", false]], "lauestatisticalweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)": [[14, "dials.algorithms.refinement.weighting_strategies.LaueStatisticalWeightingStrategy", false]], "lbfgs_with_curvs (class in dials.algorithms.symmetry.cosym.engine)": [[18, "dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs", false]], "lbfgscurvs (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.LBFGScurvs", false]], "leastsquarespositionalresidualwithrmsdcutoff (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.LeastSquaresPositionalResidualWithRmsdCutoff", false]], "leastsquarespositionalresidualwithrmsdcutoffsparse (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.LeastSquaresPositionalResidualWithRmsdCutoffSparse", false]], "leastsquaresstillsresidualwithrmsdcutoff (class in dials.algorithms.refinement.target_stills)": [[14, "dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff", false]], "leastsquaresstillsresidualwithrmsdcutoffsparse (class in dials.algorithms.refinement.target_stills)": [[14, "dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoffSparse", false]], "levenbergmarquardtiterations (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.LevenbergMarquardtIterations", false]], "limit_image_range() (dials.algorithms.scaling.model.model.arrayscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.limit_image_range", false]], "limit_image_range() (dials.algorithms.scaling.model.model.dosedecay method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.limit_image_range", false]], "limit_image_range() (dials.algorithms.scaling.model.model.physicalscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.limit_image_range", false]], "limit_image_range() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.limit_image_range", false]], "load() (in module dials.util.nexus)": [[33, "dials.util.nexus.load", false]], "load_error_model() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.load_error_model", false]], "load_image() (dials.algorithms.spot_finding.factory.spotfinderfactory static method)": [[16, "dials.algorithms.spot_finding.factory.SpotFinderFactory.load_image", false]], "log_summary() (in module dials.util.export_mtz)": [[33, "dials.util.export_mtz.log_summary", false]], "lowresspotmatch (class in dials.algorithms.indexing.lattice_search)": [[11, "dials.algorithms.indexing.lattice_search.LowResSpotMatch", false]], "madmergedmtzwriter (class in dials.util.export_mtz)": [[33, "dials.util.export_mtz.MADMergedMTZWriter", false]], "make_apps (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.make_apps", false]], "make_beam() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.make_beam", false]], "make_combined_plots() (in module dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.make_combined_plots", false]], "make_detector() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.make_detector", false]], "make_goniometer() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.make_goniometer", false]], "make_imageset() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.make_imageset", false]], "make_kappa_goniometer() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.make_kappa_goniometer", false]], "make_multi_axis_goniometer() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.make_multi_axis_goniometer", false]], "make_polarized_beam() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.make_polarized_beam", false]], "make_polychromatic_beam() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.make_polychromatic_beam", false]], "make_scan() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.make_scan", false]], "make_scan_from_properties() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.make_scan_from_properties", false]], "make_sequence() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.make_sequence", false]], "mark_for_rejection() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.mark_for_rejection", false]], "mark_for_rejection() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.mark_for_rejection", false]], "mask (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.mask", false]], "masker() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.masker", false]], "masker() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.masker", false]], "master_path() (dxtbx.imageset.memreader static method)": [[26, "dxtbx.imageset.MemReader.master_path", false]], "match_wavelengths() (in module dials.util.export_mtz)": [[33, "dials.util.export_mtz.match_wavelengths", false]], "max_length (dials.util.command_line.command attribute)": [[33, "dials.util.command_line.Command.max_length", false]], "max_possible_wl (dials.util.export_mtz.wavelengthgroup attribute)": [[33, "dials.util.export_mtz.WavelengthGroup.max_possible_wl", false]], "max_shift_over_esd (dials.algorithms.refinement.engine.gaussnewtoniterations attribute)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations.max_shift_over_esd", false]], "mean() (dials.algorithms.background.radialaverage method)": [[10, "dials.algorithms.background.RadialAverage.mean", false]], "median_unit_cell() (in module dials.algorithms.symmetry)": [[18, "dials.algorithms.symmetry.median_unit_cell", false]], "memreader (class in dxtbx.imageset)": [[26, "dxtbx.imageset.MemReader", false]], "merge_panel_scope_extracts_by_id() (in module dxtbx.model.detector)": [[23, "dxtbx.model.detector.merge_panel_scope_extracts_by_id", false]], "mergedmtzwriter (class in dials.util.export_mtz)": [[33, "dials.util.export_mtz.MergedMTZWriter", false]], "message (dials.util.options.argumenthandlingerrorinfo attribute)": [[33, "dials.util.options.ArgumentHandlingErrorInfo.message", false]], "metric_supergroup() (in module dials.algorithms.indexing.symmetry)": [[11, "dials.algorithms.indexing.symmetry.metric_supergroup", false]], "min_wl (dials.util.export_mtz.wavelengthgroup attribute)": [[33, "dials.util.export_mtz.WavelengthGroup.min_wl", false]], "minimize_scipy() (in module dials.algorithms.symmetry.cosym.engine)": [[18, "dials.algorithms.symmetry.cosym.engine.minimize_scipy", false]], "minimize_scitbx_lbfgs() (in module dials.algorithms.symmetry.cosym.engine)": [[18, "dials.algorithms.symmetry.cosym.engine.minimize_scitbx_lbfgs", false]], "ml_aniso_normalisation() (dials.algorithms.symmetry.symmetry_base static method)": [[18, "dials.algorithms.symmetry.symmetry_base.ml_aniso_normalisation", false]], "ml_iso_normalisation() (dials.algorithms.symmetry.symmetry_base static method)": [[18, "dials.algorithms.symmetry.symmetry_base.ml_iso_normalisation", false]], "model_likelihood (dials.algorithms.indexing.model_evaluation.result attribute)": [[11, "dials.algorithms.indexing.model_evaluation.Result.model_likelihood", false]], "modelevaluation (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.ModelEvaluation", false]], "modelrank (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRank", false]], "modelrankfilter (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter", false]], "modelrankweighted (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankWeighted", false]], "module": [[10, "module-dials.algorithms.background", false], [11, "module-dials.algorithms.indexing", false], [11, "module-dials.algorithms.indexing.assign_indices", false], [11, "module-dials.algorithms.indexing.basis_vector_search", false], [11, "module-dials.algorithms.indexing.basis_vector_search.combinations", false], [11, "module-dials.algorithms.indexing.basis_vector_search.optimise", false], [11, "module-dials.algorithms.indexing.compare_orientation_matrices", false], [11, "module-dials.algorithms.indexing.indexer", false], [11, "module-dials.algorithms.indexing.lattice_search", false], [11, "module-dials.algorithms.indexing.max_cell", false], [11, "module-dials.algorithms.indexing.model_evaluation", false], [11, "module-dials.algorithms.indexing.nearest_neighbor", false], [11, "module-dials.algorithms.indexing.refinement", false], [11, "module-dials.algorithms.indexing.stills_indexer", false], [11, "module-dials.algorithms.indexing.symmetry", false], [12, "module-dials.algorithms.integration.integrator", false], [13, "module-dials.algorithms.profile_model", false], [14, "module-dials.algorithms.refinement.engine", false], [14, "module-dials.algorithms.refinement.refiner", false], [14, "module-dials.algorithms.refinement.reflection_manager", false], [14, "module-dials.algorithms.refinement.target", false], [14, "module-dials.algorithms.refinement.target_stills", false], [14, "module-dials.algorithms.refinement.weighting_strategies", false], [15, "module-dials.algorithms.scaling", false], [15, "module-dials.algorithms.scaling.model.model", false], [15, "module-dials.algorithms.scaling.outlier_rejection", false], [16, "module-dials.algorithms.spot_finding.factory", false], [16, "module-dials.algorithms.spot_finding.finder", false], [17, "module-dials.algorithms.spot_prediction.reflection_predictor", false], [18, "module-dials.algorithms.symmetry", false], [18, "module-dials.algorithms.symmetry.cosym", false], [18, "module-dials.algorithms.symmetry.cosym.engine", false], [18, "module-dials.algorithms.symmetry.cosym.target", false], [18, "module-dials.algorithms.symmetry.laue_group", false], [18, "module-dials.algorithms.symmetry.reindex_to_reference", false], [20, "module-dials.array_family.flex", false], [21, "module-dxtbx.model.beam", false], [22, "module-dxtbx.model.crystal", false], [23, "module-dxtbx.model.detector", false], [24, "module-dxtbx.model.experiment_list", false], [25, "module-dxtbx.model.goniometer", false], [26, "module-dxtbx.imageset", false], [28, "module-dxtbx.model.profile", false], [29, "module-dxtbx.model.scan", false], [30, "module-dxtbx.serialize.imageset", false], [30, "module-dxtbx.serialize.load", false], [30, "module-dxtbx.serialize.xds", false], [31, "module-dials.extensions.dispersion_spotfinder_threshold_ext", false], [31, "module-dials.extensions.gaussian_rs_profile_model_ext", false], [31, "module-dials.extensions.null_background_ext", false], [31, "module-dials.extensions.simple_background_ext", false], [31, "module-dials.extensions.simple_centroid_ext", false], [33, "module-dials.util.command_line", false], [33, "module-dials.util.export_mtz", false], [33, "module-dials.util.export_text", false], [33, "module-dials.util.image", false], [33, "module-dials.util.installer", false], [33, "module-dials.util.ioutil", false], [33, "module-dials.util.nexus", false], [33, "module-dials.util.options", false]], "mosaiccrystalkabsch2010 (class in dxtbx.model)": [[22, "dxtbx.model.MosaicCrystalKabsch2010", false]], "mosaiccrystalsauter2014 (class in dxtbx.model)": [[22, "dxtbx.model.MosaicCrystalSauter2014", false]], "mtzwriterbase (class in dials.util.export_mtz)": [[33, "dials.util.export_mtz.MTZWriterBase", false]], "mu (dials.algorithms.refinement.engine.levenbergmarquardtiterations property)": [[14, "dials.algorithms.refinement.engine.LevenbergMarquardtIterations.mu", false]], "multi_axis() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.multi_axis", false]], "multi_axis_goniometer_from_phil() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.multi_axis_goniometer_from_phil", false]], "multiaxisgoniometer (class in dxtbx.model.goniometer)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer", false]], "n() (dials.algorithms.symmetry.laue_group.correlationcoefficientaccumulator method)": [[18, "dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator.n", false]], "n_indexed (dials.algorithms.indexing.model_evaluation.result attribute)": [[11, "dials.algorithms.indexing.model_evaluation.Result.n_indexed", false]], "n_params (dials.algorithms.scaling.model.model.scalingmodelbase property)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.n_params", false]], "name (dials.extensions.dispersion_spotfinder_threshold_ext.dispersionspotfinderthresholdext attribute)": [[31, "dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt.name", false]], "name (dials.extensions.gaussian_rs_profile_model_ext.gaussianrsprofilemodelext attribute)": [[31, "dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt.name", false]], "name (dials.extensions.null_background_ext.nullbackgroundext attribute)": [[31, "dials.extensions.null_background_ext.NullBackgroundExt.name", false]], "name (dials.extensions.simple_background_ext.simplebackgroundext attribute)": [[31, "dials.extensions.simple_background_ext.SimpleBackgroundExt.name", false]], "name (dials.extensions.simple_centroid_ext.simplecentroidext attribute)": [[31, "dials.extensions.simple_centroid_ext.SimpleCentroidExt.name", false]], "name (dials.util.options.argumenthandlingerrorinfo attribute)": [[33, "dials.util.options.ArgumentHandlingErrorInfo.name", false]], "neighboranalysis (class in dials.algorithms.indexing.nearest_neighbor)": [[11, "dials.algorithms.indexing.nearest_neighbor.NeighborAnalysis", false]], "new() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.new", false]], "nframes_hist() (in module dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.nframes_hist", false]], "normdevoutlierrejection (class in dials.algorithms.scaling.outlier_rejection)": [[15, "dials.algorithms.scaling.outlier_rejection.NormDevOutlierRejection", false]], "nullbackgroundext (class in dials.extensions.null_background_ext)": [[31, "dials.extensions.null_background_ext.NullBackgroundExt", false]], "nullify_all_single_file_reader_format_instances() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.nullify_all_single_file_reader_format_instances", false]], "num_reflections() (dials.algorithms.integration.integrator.reflectionmanager method)": [[12, "dials.algorithms.integration.integrator.ReflectionManager.num_reflections", false]], "num_scan_points (dxtbx.model.goniometer.goniometer property)": [[25, "dxtbx.model.goniometer.Goniometer.num_scan_points", false]], "numerator() (dials.algorithms.symmetry.laue_group.correlationcoefficientaccumulator method)": [[18, "dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator.numerator", false]], "optimise_basis_vectors() (in module dials.algorithms.indexing.basis_vector_search.optimise)": [[11, "dials.algorithms.indexing.basis_vector_search.optimise.optimise_basis_vectors", false]], "optionparser (class in dials.util.options)": [[33, "dials.util.options.OptionParser", false]], "outlierrejectionbase (class in dials.algorithms.scaling.outlier_rejection)": [[15, "dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase", false]], "overwrite_from_phil() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.overwrite_from_phil", false]], "p_cc_given_not_s (dials.algorithms.symmetry.laue_group.scorecorrelationcoefficient property)": [[18, "dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient.p_cc_given_not_s", false]], "p_cc_given_s (dials.algorithms.symmetry.laue_group.scorecorrelationcoefficient property)": [[18, "dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient.p_cc_given_s", false]], "p_s_given_cc (dials.algorithms.symmetry.laue_group.scorecorrelationcoefficient property)": [[18, "dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient.p_s_given_cc", false]], "parameter_vector_norm() (dials.algorithms.refinement.engine.adaptlstbx method)": [[14, "dials.algorithms.refinement.engine.AdaptLstbx.parameter_vector_norm", false]], "parameters (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Parameters", false]], "parameters.filter (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Parameters.Filter", false]], "parameters.profile (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Parameters.Profile", false]], "parameters.profile.validation (class in dials.algorithms.integration.integrator)": [[12, 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(dxtbx.imageset.memreader method)": [[26, "dxtbx.imageset.MemReader.paths", false]], "peakcentroiddistancefilter (class in dials.algorithms.spot_finding.factory)": [[16, "dials.algorithms.spot_finding.factory.PeakCentroidDistanceFilter", false]], "pedestal (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.pedestal", false]], "per_image() (dials.algorithms.refinement.reflection_manager.blockcalculator method)": [[14, "dials.algorithms.refinement.reflection_manager.BlockCalculator.per_image", false]], "per_width() (dials.algorithms.refinement.reflection_manager.blockcalculator method)": [[14, "dials.algorithms.refinement.reflection_manager.BlockCalculator.per_width", false]], "phil (dials.util.options.argumentparser property)": [[33, "dials.util.options.ArgumentParser.phil", false]], "phil (dials.util.options.philcommandparser property)": [[33, "dials.util.options.PhilCommandParser.phil", false]], "phil() 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"dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.phil_help", false]], "phil_help (dials.algorithms.indexing.basis_vector_search.strategy attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.Strategy.phil_help", false]], "phil_help (dials.algorithms.indexing.lattice_search.lowresspotmatch attribute)": [[11, "dials.algorithms.indexing.lattice_search.LowResSpotMatch.phil_help", false]], "phil_help (dials.algorithms.indexing.lattice_search.pinkindexer attribute)": [[11, "dials.algorithms.indexing.lattice_search.PinkIndexer.phil_help", false]], "phil_help (dials.algorithms.indexing.lattice_search.strategy attribute)": [[11, "dials.algorithms.indexing.lattice_search.Strategy.phil_help", false]], "phil_scope (dials.algorithms.indexing.basis_vector_search.fft1d attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT1D.phil_scope", false]], "phil_scope (dials.algorithms.indexing.basis_vector_search.fft3d attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT3D.phil_scope", false]], "phil_scope (dials.algorithms.indexing.basis_vector_search.realspacegridsearch attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.phil_scope", false]], "phil_scope (dials.algorithms.indexing.basis_vector_search.strategy attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.Strategy.phil_scope", false]], "phil_scope (dials.algorithms.indexing.lattice_search.lowresspotmatch attribute)": [[11, "dials.algorithms.indexing.lattice_search.LowResSpotMatch.phil_scope", false]], "phil_scope (dials.algorithms.indexing.lattice_search.pinkindexer attribute)": [[11, "dials.algorithms.indexing.lattice_search.PinkIndexer.phil_scope", false]], "phil_scope (dials.algorithms.indexing.lattice_search.strategy attribute)": [[11, "dials.algorithms.indexing.lattice_search.Strategy.phil_scope", false]], "phil_scope (dials.algorithms.scaling.model.model.arrayscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.phil_scope", false]], "phil_scope (dials.algorithms.scaling.model.model.dosedecay attribute)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.phil_scope", false]], "phil_scope (dials.algorithms.scaling.model.model.kbscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel.phil_scope", false]], "phil_scope (dials.algorithms.scaling.model.model.physicalscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.phil_scope", false]], "philcommandparser (class in dials.util.options)": [[33, "dials.util.options.PhilCommandParser", false]], "physicalscalingmodel (class in dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel", false]], "pinkindexer (class in dials.algorithms.indexing.lattice_search)": [[11, "dials.algorithms.indexing.lattice_search.PinkIndexer", false]], "pixel_list_to_reflection_table() (in module 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"dials.algorithms.refinement.reflection_manager.StillsReflectionManager.print_stats_on_matches", false]], "print_step_table() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.print_step_table", false]], "print_time (dials.util.command_line.command attribute)": [[33, "dials.util.command_line.Command.print_time", false]], "process() (dials.algorithms.integration.integrator.executor method)": [[12, "dials.algorithms.integration.integrator.Executor.process", false]], "process() (dials.algorithms.integration.integrator.integratorexecutor method)": [[12, "dials.algorithms.integration.integrator.IntegratorExecutor.process", false]], "process() (dials.algorithms.integration.integrator.profilemodellerexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileModellerExecutor.process", false]], "process() (dials.algorithms.integration.integrator.profilevalidatorexecutor method)": [[12, 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"profilemodelfactory (class in dxtbx.model.profile)": [[28, "dxtbx.model.profile.ProfileModelFactory", false]], "profilemodellerexecutor (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ProfileModellerExecutor", false]], "profiles() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.profiles", false]], "profilevalidatorexecutor (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ProfileValidatorExecutor", false]], "progressbar (class in dials.util.command_line)": [[33, "dials.util.command_line.ProgressBar", false]], "progressbartimer (class in dials.util.command_line)": [[33, "dials.util.command_line.ProgressBarTimer", false]], "radialaverage (class in dials.algorithms.background)": [[10, "dials.algorithms.background.RadialAverage", false]], "read() (dxtbx.imageset.memreader method)": [[26, "dxtbx.imageset.MemReader.read", false]], "read_file() 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"dials.algorithms.indexing.indexer.Indexer.refine", false]], "refine() (dials.algorithms.indexing.stills_indexer.stillsindexer method)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexer.refine", false]], "refine() (in module dials.algorithms.indexing.refinement)": [[11, "dials.algorithms.indexing.refinement.refine", false]], "refiner (class in dials.algorithms.refinement.refiner)": [[14, "dials.algorithms.refinement.refiner.Refiner", false]], "refinerfactory (class in dials.algorithms.refinement.refiner)": [[14, "dials.algorithms.refinement.refiner.RefinerFactory", false]], "refinery (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.Refinery", false]], "reflectionmanager (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ReflectionManager", false]], "reflectionmanager (class in dials.algorithms.refinement.reflection_manager)": [[14, 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(dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.remove_on_experiment_identifiers", false]], "remove_sources_default (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.remove_sources_default", false]], "replace() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.replace", false]], "report() (dials.algorithms.integration.integrator.integrator method)": [[12, "dials.algorithms.integration.integrator.Integrator.report", false]], "report() (dials.algorithms.integration.integrator.integrator3dthreaded method)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded.report", false]], "report_progress() (dials.algorithms.refinement.engine.levenbergmarquardtiterations method)": [[14, "dials.algorithms.refinement.engine.LevenbergMarquardtIterations.report_progress", false]], "reset_accepted_reflections() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.reset_accepted_reflections", false]], "reset_scan_points() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.reset_scan_points", false]], "resolution_filter_from_array() (in module dials.algorithms.symmetry)": [[18, "dials.algorithms.symmetry.resolution_filter_from_array", false]], "resolution_filter_from_reflections_experiments() (in module dials.algorithms.symmetry)": [[18, "dials.algorithms.symmetry.resolution_filter_from_reflections_experiments", false]], "restart() (dials.algorithms.refinement.engine.adaptlstbx method)": [[14, "dials.algorithms.refinement.engine.AdaptLstbx.restart", false]], "result (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.Result", false]], "rmsd_names (dials.algorithms.refinement.target.laueleastsquaresresidualwithrmsdcutoff attribute)": [[14, 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"rmsd_units (dials.algorithms.refinement.target.tofleastsquaresresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target.TOFLeastSquaresResidualWithRmsdCutoff.rmsd_units", false]], "rmsd_units (dials.algorithms.refinement.target_stills.leastsquaresstillsresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff.rmsd_units", false]], "rmsds (dials.algorithms.indexing.model_evaluation.result attribute)": [[11, "dials.algorithms.indexing.model_evaluation.Result.rmsds", false]], "rmsds() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.rmsds", false]], "rmsds() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.rmsds", false]], "rmsds_for_experiment() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.rmsds_for_experiment", false]], 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"dials.algorithms.indexing.compare_orientation_matrices.rotation_matrix_differences", false]], "rotation_scan_manager() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.rotation_scan_manager", false]], "run() (dials.algorithms.refinement.engine.gaussnewtoniterations method)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations.run", false]], "run() (dials.algorithms.refinement.engine.lbfgscurvs method)": [[14, "dials.algorithms.refinement.engine.LBFGScurvs.run", false]], "run() (dials.algorithms.refinement.engine.levenbergmarquardtiterations method)": [[14, "dials.algorithms.refinement.engine.LevenbergMarquardtIterations.run", false]], "run() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.run", false]], "run() (dials.algorithms.refinement.engine.simplelbfgs method)": [[14, "dials.algorithms.refinement.engine.SimpleLBFGS.run", false]], "run() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.run", false]], "run() (dials.algorithms.scaling.outlier_rejection.outlierrejectionbase method)": [[15, "dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase.run", false]], "run() (dials.algorithms.spot_finding.factory.backgroundgradientfilter method)": [[16, "dials.algorithms.spot_finding.factory.BackgroundGradientFilter.run", false]], "run() (dials.algorithms.spot_finding.factory.peakcentroiddistancefilter method)": [[16, "dials.algorithms.spot_finding.factory.PeakCentroidDistanceFilter.run", false]], "run() (dials.algorithms.spot_finding.factory.spotdensityfilter method)": [[16, "dials.algorithms.spot_finding.factory.SpotDensityFilter.run", false]], "run() (dials.algorithms.symmetry.cosym.cosymanalysis method)": [[18, "dials.algorithms.symmetry.cosym.CosymAnalysis.run", false]], "run_lbfgs() 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dials.algorithms.symmetry.cosym)": [[18, "dials.algorithms.symmetry.cosym.ScoreSymmetryElement", false]], "scoresymmetryelement (class in dials.algorithms.symmetry.laue_group)": [[18, "dials.algorithms.symmetry.laue_group.ScoreSymmetryElement", false]], "search() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.search", false]], "search_directions (dials.algorithms.indexing.basis_vector_search.realspacegridsearch property)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.search_directions", false]], "search_vectors (dials.algorithms.indexing.basis_vector_search.realspacegridsearch property)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.search_vectors", false]], "select_on_experiment_identifiers() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.select_on_experiment_identifiers", false]], "selection_used_for_refinement() (dials.algorithms.refinement.refiner.refiner method)": 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"dials.algorithms.scaling.outlier_rejection.SimpleNormDevOutlierRejection", false]], "single_axis() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.single_axis", false]], "single_axis_goniometer_from_phil() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.single_axis_goniometer_from_phil", false]], "single_axis_reverse() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.single_axis_reverse", false]], "single_file() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.single_file", false]], "size() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.size", false]], "source_packages (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.source_packages", false]], "sparsegradientsmixin (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.SparseGradientsMixin", false]], "split() (dials.algorithms.integration.integrator.joblist method)": [[12, "dials.algorithms.integration.integrator.JobList.split", false]], "split() (dials.algorithms.integration.integrator.reflectionmanager method)": [[12, "dials.algorithms.integration.integrator.ReflectionManager.split", false]], "split_jacobian_into_blocks() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.split_jacobian_into_blocks", false]], "split_matches_into_blocks() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.split_matches_into_blocks", false]], "spotdensityfilter (class in dials.algorithms.spot_finding.factory)": [[16, "dials.algorithms.spot_finding.factory.SpotDensityFilter", false]], "spotfinder (class in dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.SpotFinder", false]], "spotfinderfactory (class in dials.algorithms.spot_finding.factory)": [[16, "dials.algorithms.spot_finding.factory.SpotFinderFactory", false]], "stars (dials.algorithms.symmetry.cosym.scoresubgroup property)": [[18, "dials.algorithms.symmetry.cosym.ScoreSubGroup.stars", false]], "stars (dials.algorithms.symmetry.cosym.scoresymmetryelement property)": [[18, "dials.algorithms.symmetry.cosym.ScoreSymmetryElement.stars", false]], "start() (dials.util.command_line.command class method)": [[33, "dials.util.command_line.Command.start", false]], "statisticalweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)": [[14, "dials.algorithms.refinement.weighting_strategies.StatisticalWeightingStrategy", false]], "step_backward() (dials.algorithms.refinement.engine.adaptlstbx method)": [[14, "dials.algorithms.refinement.engine.AdaptLstbx.step_backward", false]], "step_forward() (dials.algorithms.refinement.engine.adaptlstbx method)": [[14, "dials.algorithms.refinement.engine.AdaptLstbx.step_forward", false]], "step_threshold (dials.algorithms.refinement.engine.gaussnewtoniterations attribute)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations.step_threshold", false]], "stills_manager() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.stills_manager", false]], "stillsindexer (class in dials.algorithms.indexing.stills_indexer)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexer", false]], "stillsindexerbasisvectorsearch (class in dials.algorithms.indexing.stills_indexer)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexerBasisVectorSearch", false]], "stillsindexerknownorientation (class in dials.algorithms.indexing.stills_indexer)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexerKnownOrientation", false]], "stillsindexerlatticesearch (class in dials.algorithms.indexing.stills_indexer)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexerLatticeSearch", false]], "stillsreflectionmanager (class in dials.algorithms.refinement.reflection_manager)": [[14, "dials.algorithms.refinement.reflection_manager.StillsReflectionManager", false]], "stillsweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)": [[14, "dials.algorithms.refinement.weighting_strategies.StillsWeightingStrategy", false]], "strategy (class in dials.algorithms.indexing.basis_vector_search)": [[11, "dials.algorithms.indexing.basis_vector_search.Strategy", false]], "strategy (class in dials.algorithms.indexing.lattice_search)": [[11, "dials.algorithms.indexing.lattice_search.Strategy", false]], "strategy (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.Strategy", false]], "subgroups_table() (dials.algorithms.symmetry.cosym.symmetryanalysis static method)": [[18, 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dials.algorithms.indexing.symmetry)": [[11, "dials.algorithms.indexing.symmetry.SymmetryHandler", false]], "system_phil (dials.util.options.argumentparser property)": [[33, "dials.util.options.ArgumentParser.system_phil", false]], "system_phil (dials.util.options.philcommandparser property)": [[33, "dials.util.options.PhilCommandParser.system_phil", false]], "target (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.Target", false]], "target (class in dials.algorithms.symmetry.cosym.target)": [[18, "dials.algorithms.symmetry.cosym.target.Target", false]], "targetedoutlierrejection (class in dials.algorithms.scaling.outlier_rejection)": [[15, "dials.algorithms.scaling.outlier_rejection.TargetedOutlierRejection", false]], "targetfactory (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.TargetFactory", false]], "tau (dials.algorithms.refinement.engine.levenbergmarquardtiterations attribute)": [[14, 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