diff --git a/documentation/programs/dials_cosym.html b/documentation/programs/dials_cosym.html index 088bac74..9d63c33d 100644 --- a/documentation/programs/dials_cosym.html +++ b/documentation/programs/dials_cosym.html @@ -281,7 +281,7 @@

Example

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DIALS 3.dev.1230-g8e2c33c91
+
DIALS 3.dev.1236-gebb50ee49
 The following parameters have been modified:
 
 input {
diff --git a/documentation/tutorials/mpro_x0692.html b/documentation/tutorials/mpro_x0692.html
index 5e0c5efa..5cd25719 100644
--- a/documentation/tutorials/mpro_x0692.html
+++ b/documentation/tutorials/mpro_x0692.html
@@ -79,7 +79,7 @@ 
Import
 
The output just describes what the software understands of the images it was
 passed, in this case one sequence of data containing 400 images:

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DIALS 3.dev.1230-g8e2c33c91
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DIALS 3.dev.1236-gebb50ee49
 The following parameters have been modified:
 
 input {
@@ -128,7 +128,7 @@ 
Find Spots
 
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  1DIALS 3.dev.1230-g8e2c33c91
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  1DIALS 3.dev.1236-gebb50ee49
   2The following parameters have been modified:
   3
   4spotfinder {
@@ -637,7 +637,7 @@ 
Indexing
 

 
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  1DIALS 3.dev.1230-g8e2c33c91
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  1DIALS 3.dev.1236-gebb50ee49
   2The following parameters have been modified:
   3
   4input {
@@ -1365,7 +1365,7 @@ 
Bravais Lattice Refinement
 
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-
 1DIALS 3.dev.1230-g8e2c33c91
+
 1DIALS 3.dev.1236-gebb50ee49
  2The following parameters have been modified:
  3
  4refinement {
@@ -1474,7 +1474,7 @@ 
Bravais Lattice Refinement
 
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-
 1DIALS 3.dev.1230-g8e2c33c91
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 1DIALS 3.dev.1236-gebb50ee49
  2The following parameters have been modified:
  3
  4refinement {
@@ -1599,7 +1599,7 @@ 
Integration
 
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-
   1DIALS 3.dev.1230-g8e2c33c91
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   1DIALS 3.dev.1236-gebb50ee49
    2The following parameters have been modified:
    3integration {
    4  mp {
@@ -2149,12 +2149,12 @@ 
Integration 548
  549Timing information for reference profile formation
  550+-------------------+---------------+
- 551| Read time         | 20.17 seconds |
- 552| Extract time      | 0.36 seconds  |
+ 551| Read time         | 20.15 seconds |
+ 552| Extract time      | 0.46 seconds  |
  553| Pre-process time  | 0.02 seconds  |
- 554| Process time      | 9.69 seconds  |
+ 554| Process time      | 9.83 seconds  |
  555| Post-process time | 0.00 seconds  |
- 556| Total time        | 30.50 seconds |
+ 556| Total time        | 30.46 seconds |
  557+-------------------+---------------+
  558
  559================================================================================
@@ -2685,12 +2685,12 @@ 
Integration1084
 1085Timing information for integration
 1086+-------------------+----------------+
-1087| Read time         | 23.26 seconds  |
-1088| Extract time      | 6.72 seconds   |
-1089| Pre-process time  | 0.27 seconds   |
-1090| Process time      | 146.74 seconds |
+1087| Read time         | 24.13 seconds  |
+1088| Extract time      | 6.65 seconds   |
+1089| Pre-process time  | 0.28 seconds   |
+1090| Process time      | 147.51 seconds |
 1091| Post-process time | 0.00 seconds   |
-1092| Total time        | 178.05 seconds |
+1092| Total time        | 179.51 seconds |
 1093+-------------------+----------------+
 1094
 1095Removing 22837 unintegrated reflections of 199395 total
@@ -2742,7 +2742,7 @@ 
Symmetry analysis
 
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-
  1DIALS 3.dev.1230-g8e2c33c91
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  1DIALS 3.dev.1236-gebb50ee49
   2The following parameters have been modified:
   3
   4best_monoclinic_beta = False
@@ -2914,7 +2914,7 @@ 
Scaling and Merging
 
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  1DIALS 3.dev.1230-g8e2c33c91
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  1DIALS 3.dev.1236-gebb50ee49
   2The following parameters have been modified:
   3input {
   4  experiments = symmetrized.expt
@@ -2983,7 +2983,7 @@ 
Scaling and Merging 67Components to be refined in this cycle for all datasets: scale, decay, absorption
  68Performing a round of scaling with an LBFGS minimizer. 
  69
- 70Time taken for refinement 7.16
+ 70Time taken for refinement 7.21
  71
  72Refinement steps:
  73+--------+--------+----------+
@@ -3062,7 +3062,7 @@ 
Scaling and Merging146Components to be refined in this cycle for all datasets: scale, decay, absorption
 147Performing a round of scaling with an LBFGS minimizer. 
 148
-149Time taken for refinement 3.15
+149Time taken for refinement 3.16
 150
 151Refinement steps:
 152+--------+--------+----------+
@@ -3125,7 +3125,7 @@ 
Scaling and Merging209Components to be refined in this cycle for all datasets: scale, decay, absorption
 210Performing a round of scaling with a Levenberg-Marquardt minimizer.
 211
-212Time taken for refinement 4.34
+212Time taken for refinement 4.43
 213
 214Refinement steps:
 215+--------+--------+----------+
@@ -3149,7 +3149,7 @@ 
Scaling and Merging233Components to be refined in this cycle for all datasets: scale, decay, absorption
 234Performing a round of scaling with a Levenberg-Marquardt minimizer.
 235
-236Time taken for refinement 0.90
+236Time taken for refinement 0.92
 237
 238Refinement steps:
 239+--------+--------+----------+
@@ -3199,7 +3199,7 @@ 
Scaling and Merging283The reflection table variances have been adjusted to account for the
 284uncertainty in the scaling model
 285
-286Total time taken: 21.2869s 
+286Total time taken: 21.5514s 
 287
 288================================================================================
 289
diff --git a/documentation/tutorials/processing_in_detail_betalactamase.html b/documentation/tutorials/processing_in_detail_betalactamase.html
index 8a73a193..6f7da911 100644
--- a/documentation/tutorials/processing_in_detail_betalactamase.html
+++ b/documentation/tutorials/processing_in_detail_betalactamase.html
@@ -85,7 +85,7 @@ 
Import
 
The output just describes what the software understands of the images it was
 passed, in this case one sequence of data containing 720 images:

-
DIALS 3.dev.1230-g8e2c33c91
+
DIALS 3.dev.1236-gebb50ee49
 The following parameters have been modified:
 
 input {
@@ -134,7 +134,7 @@ 
Find Spots
 
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-
  1DIALS 3.dev.1230-g8e2c33c91
+
  1DIALS 3.dev.1236-gebb50ee49
   2The following parameters have been modified:
   3
   4spotfinder {
@@ -965,7 +965,7 @@ 
Indexing
 

 
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  1DIALS 3.dev.1230-g8e2c33c91
+
  1DIALS 3.dev.1236-gebb50ee49
   2The following parameters have been modified:
   3
   4input {
@@ -1693,7 +1693,7 @@ 
Bravais Lattice Refinement
 
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  1DIALS 3.dev.1230-g8e2c33c91
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  1DIALS 3.dev.1236-gebb50ee49
   2The following parameters have been modified:
   3
   4input {
@@ -1868,7 +1868,7 @@ 
Integration
 
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-
   1DIALS 3.dev.1230-g8e2c33c91
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   1DIALS 3.dev.1236-gebb50ee49
    2The following parameters have been modified:
    3integration {
    4  mp {
@@ -2716,12 +2716,12 @@ 
Integration 846
  847Timing information for reference profile formation
  848+-------------------+---------------+
- 849| Read time         | 64.98 seconds |
- 850| Extract time      | 0.54 seconds  |
+ 849| Read time         | 62.27 seconds |
+ 850| Extract time      | 0.53 seconds  |
  851| Pre-process time  | 0.11 seconds  |
- 852| Process time      | 31.26 seconds |
+ 852| Process time      | 30.86 seconds |
  853| Post-process time | 0.00 seconds  |
- 854| Total time        | 97.13 seconds |
+ 854| Total time        | 94.00 seconds |
  855+-------------------+---------------+
  856
  857================================================================================
@@ -3572,12 +3572,12 @@ 
Integration1702
 1703Timing information for integration
 1704+-------------------+----------------+
-1705| Read time         | 63.27 seconds  |
-1706| Extract time      | 2.87 seconds   |
+1705| Read time         | 60.33 seconds  |
+1706| Extract time      | 2.64 seconds   |
 1707| Pre-process time  | 0.47 seconds   |
-1708| Process time      | 156.80 seconds |
+1708| Process time      | 156.88 seconds |
 1709| Post-process time | 0.00 seconds   |
-1710| Total time        | 224.26 seconds |
+1710| Total time        | 221.31 seconds |
 1711+-------------------+----------------+
 1712
 1713Removing 41622 unintegrated reflections of 368699 total
@@ -3629,7 +3629,7 @@ 
Symmetry analysis
 
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-
  1DIALS 3.dev.1230-g8e2c33c91
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  1DIALS 3.dev.1236-gebb50ee49
   2The following parameters have been modified:
   3
   4input {
@@ -3801,7 +3801,7 @@ 
Scaling and Merging
 
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  1DIALS 3.dev.1230-g8e2c33c91
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  1DIALS 3.dev.1236-gebb50ee49
   2The following parameters have been modified:
   3input {
   4  experiments = symmetrized.expt
@@ -3870,7 +3870,7 @@ 
Scaling and Merging 67Components to be refined in this cycle for all datasets: scale, decay, absorption
  68Performing a round of scaling with an LBFGS minimizer. 
  69
- 70Time taken for refinement 3.58
+ 70Time taken for refinement 3.57
  71
  72Refinement steps:
  73+--------+--------+----------+
@@ -3928,7 +3928,7 @@ 
Scaling and Merging125Components to be refined in this cycle for all datasets: scale, decay, absorption
 126Performing a round of scaling with an LBFGS minimizer. 
 127
-128Time taken for refinement 1.02
+128Time taken for refinement 1.01
 129
 130Refinement steps:
 131+--------+--------+----------+
@@ -3980,7 +3980,7 @@ 
Scaling and Merging177Components to be refined in this cycle for all datasets: scale, decay, absorption
 178Performing a round of scaling with a Levenberg-Marquardt minimizer.
 179
-180Time taken for refinement 3.58
+180Time taken for refinement 3.61
 181
 182Refinement steps:
 183+--------+--------+----------+
@@ -4001,7 +4001,7 @@ 
Scaling and Merging198Components to be refined in this cycle for all datasets: scale, decay, absorption
 199Performing a round of scaling with a Levenberg-Marquardt minimizer.
 200
-201Time taken for refinement 1.12
+201Time taken for refinement 1.15
 202
 203Refinement steps:
 204+--------+--------+----------+
@@ -4051,7 +4051,7 @@ 
Scaling and Merging248The reflection table variances have been adjusted to account for the
 249uncertainty in the scaling model
 250
-251Total time taken: 19.0623s 
+251Total time taken: 19.1268s 
 252
 253================================================================================
 254
diff --git a/searchindex.js b/searchindex.js
index 2c7c0e73..5ccd7dca 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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"dials.algorithms.refinement.target.Target.compute_functional_gradients_and_curvatures", false]], "compute_functional_gradients_and_curvatures() (dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs method)": [[18, "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_functional_score_for_dimension_assessment() (dials.algorithms.symmetry.cosym.target.target method)": [[18, "dials.algorithms.symmetry.cosym.target.Target.compute_functional_score_for_dimension_assessment", 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]], "compute_residuals_and_gradients() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.compute_residuals_and_gradients", false]], "compute_restraints_functional_gradients_and_curvatures() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.compute_restraints_functional_gradients_and_curvatures", false]], "compute_restraints_residuals_and_gradients() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.compute_restraints_residuals_and_gradients", false]], "compute_threshold() (dials.extensions.dispersion_spotfinder_threshold_ext.dispersionspotfinderthresholdext method)": [[31, "dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt.compute_threshold", false]], "config_refinery() (dials.algorithms.refinement.refiner.refinerfactory static method)": [[14, "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.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, "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.lauereflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.LaueReflectionManager.print_stats_on_matches", 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]], 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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)": [[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() (dials.util.image.reader method)": [[33, "dials.util.image.reader.read_file", false]], "reader (class in dials.util.image)": [[33, "dials.util.image.reader", false]], "reader() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.reader", false]], "reader() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.reader", false]], "realspacegridsearch (class in dials.algorithms.indexing.basis_vector_search)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch", false]], "reason_for_termination (dials.algorithms.refinement.engine.journal attribute)": [[14, "dials.algorithms.refinement.engine.Journal.reason_for_termination", false]], "record_intensity_combination_imid() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.record_intensity_combination_Imid", false]], "refine() (dials.algorithms.indexing.indexer.indexer method)": [[11, "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, "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.laueleastsquaresresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff.rmsd_names", false]], "rmsd_names (dials.algorithms.refinement.target.target attribute)": [[14, "dials.algorithms.refinement.target.Target.rmsd_names", false]], "rmsd_names (dials.algorithms.refinement.target.tofleastsquaresresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target.TOFLeastSquaresResidualWithRmsdCutoff.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.laueleastsquaresresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff.rmsd_units", false]], "rmsd_units (dials.algorithms.refinement.target.target attribute)": [[14, "dials.algorithms.refinement.target.Target.rmsd_units", false]], "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]], "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]], "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() (dials.algorithms.refinement.engine.adaptlbfgs method)": [[14, "dials.algorithms.refinement.engine.AdaptLbfgs.run_lbfgs", false]], "scaling_models() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.scaling_models", false]], "scalingmodelbase (class in dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase", false]], "scanfactory (class in dxtbx.model.scan)": [[29, "dxtbx.model.scan.ScanFactory", false]], "scans() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.scans", false]], "scanvaryingrefiner (class in dials.algorithms.refinement.refiner)": [[14, "dials.algorithms.refinement.refiner.ScanVaryingRefiner", false]], "score_by_fraction_indexed() (dials.algorithms.indexing.model_evaluation.modelrankweighted method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankWeighted.score_by_fraction_indexed", false]], "score_by_rmsd_xy() (dials.algorithms.indexing.model_evaluation.modelrankweighted method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankWeighted.score_by_rmsd_xy", false]], "score_by_volume() (dials.algorithms.indexing.model_evaluation.modelrankweighted method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankWeighted.score_by_volume", false]], "score_vectors() (dials.algorithms.indexing.basis_vector_search.realspacegridsearch method)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.score_vectors", false]], "scorecorrelationcoefficient (class in 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, "dxtbx.imageset.ImageSequence.set_beam", false]], "set_beam() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.set_beam", false]], "set_beam() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_beam", false]], "set_cholesky_factor() (dials.algorithms.refinement.engine.adaptlstbx method)": [[14, "dials.algorithms.refinement.engine.AdaptLstbx.set_cholesky_factor", false]], "set_detector() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.set_detector", false]], "set_detector() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.set_detector", false]], "set_detector() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_detector", false]], "set_dimensions() (dials.algorithms.symmetry.cosym.target.target method)": [[18, "dials.algorithms.symmetry.cosym.target.Target.set_dimensions", false]], "set_domain_size_ang() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.set_domain_size_ang", false]], "set_error_model() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.set_error_model", false]], "set_fixed_rotation() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.set_fixed_rotation", false]], "set_format_class() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_format_class", false]], "set_goniometer() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.set_goniometer", false]], "set_goniometer() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.set_goniometer", false]], "set_goniometer() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_goniometer", false]], "set_half_mosaicity_deg() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.set_half_mosaicity_deg", false]], "set_last_cell() (dials.algorithms.refinement.engine.journal method)": [[14, "dials.algorithms.refinement.engine.Journal.set_last_cell", false]], "set_mosaicity() (dxtbx.model.mosaiccrystalkabsch2010 method)": [[22, "dxtbx.model.MosaicCrystalKabsch2010.set_mosaicity", false]], "set_nproc() (dials.algorithms.refinement.engine.disablempmixin method)": [[14, "dials.algorithms.refinement.engine.DisableMPmixin.set_nproc", false]], "set_nproc() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.set_nproc", false]], "set_params() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_params", false]], "set_rotation_axis() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.set_rotation_axis", false]], "set_rotation_axis_datum() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.set_rotation_axis_datum", false]], "set_scaling_model_as_scaled() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.set_scaling_model_as_scaled", false]], "set_scaling_model_as_unscaled() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.set_scaling_model_as_unscaled", false]], "set_scan() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.set_scan", false]], "set_scan() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.set_scan", false]], "set_scan() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_scan", false]], "set_setting_rotation() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.set_setting_rotation", false]], "set_setting_rotation_at_scan_points() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.set_setting_rotation_at_scan_points", false]], "set_shoebox_background_value() (in module dials.algorithms.background)": [[10, "dials.algorithms.background.set_shoebox_background_value", false]], "set_template() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_template", false]], "set_valid_image_range() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.set_valid_image_range", false]], "set_vendor() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_vendor", false]], "setup_indexing() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.setup_indexing", false]], "setup_mu() 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(dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.simple_directional", false]], "simplebackgroundext (class in dials.extensions.simple_background_ext)": [[31, "dials.extensions.simple_background_ext.SimpleBackgroundExt", false]], "simplecentroidext (class in dials.extensions.simple_centroid_ext)": [[31, "dials.extensions.simple_centroid_ext.SimpleCentroidExt", false]], "simplelbfgs (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.SimpleLBFGS", false]], "simplenormdevoutlierrejection (class in dials.algorithms.scaling.outlier_rejection)": [[15, "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, "dials.algorithms.symmetry.cosym.SymmetryAnalysis.subgroups_table", false]], "summary() (dials.algorithms.integration.integrator.integrator method)": [[12, "dials.algorithms.integration.integrator.Integrator.summary", false]], "summary() (dials.algorithms.integration.integrator.integrator3dthreaded method)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded.summary", false]], "summary_table() (dials.algorithms.symmetry.cosym.symmetryanalysis static method)": [[18, "dials.algorithms.symmetry.cosym.SymmetryAnalysis.summary_table", false]], "sym_ops_table() (dials.algorithms.symmetry.cosym.symmetryanalysis static method)": [[18, "dials.algorithms.symmetry.cosym.SymmetryAnalysis.sym_ops_table", false]], "symmetry_base (class in dials.algorithms.symmetry)": [[18, "dials.algorithms.symmetry.symmetry_base", false]], "symmetryanalysis (class in dials.algorithms.symmetry.cosym)": [[18, "dials.algorithms.symmetry.cosym.SymmetryAnalysis", false]], "symmetryhandler (class in 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, "dials.algorithms.refinement.engine.LevenbergMarquardtIterations.tau", false]], "test_for_termination() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.test_for_termination", false]], 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"dxtbx.model.goniometer.Goniometer.to_dict", false]], "to_dict() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.to_dict", false]], "to_dict() (dxtbx.model.mosaiccrystalkabsch2010 method)": [[22, "dxtbx.model.MosaicCrystalKabsch2010.to_dict", false]], "to_dict() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.to_dict", false]], "to_imageset() (in module dxtbx.serialize.xds)": [[30, "dxtbx.serialize.xds.to_imageset", false]], "to_json_file() (dials.algorithms.refinement.engine.journal method)": [[14, "dials.algorithms.refinement.engine.Journal.to_json_file", false]], "to_xds (class in dxtbx.serialize.xds)": [[30, "dxtbx.serialize.xds.to_xds", false]], "tofleastsquaresresidualwithrmsdcutoff (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.TOFLeastSquaresResidualWithRmsdCutoff", false]], "tofreflectionmanager (class in 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\ No newline at end of file
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[[97, null]], "DIALS Application to XFEL Crystallography": [[95, "dials-application-to-xfel-crystallography"]], "DIALS How-To guides": [[88, null]], "DIALS Journal Articles": [[95, "dials-journal-articles"]], "DIALS License": [[91, null]], "DIALS Newsletter Articles": [[95, "dials-newsletter-articles"]], "DIALS Reports": [[95, "dials-reports"]], "DIALS Synchrotron Applications": [[95, "dials-synchrotron-applications"]], "DIALS UK": [[0, "dials-uk"]], "DIALS US": [[0, "dials-us"]], "DIALS for neutron diffraction": [[94, "dials-for-neutron-diffraction"]], "DIALS-3: 22nd May 2013 (Cambridge, UK)": [[98, null]], "DIALS: Diffraction Integration for Advanced Light Sources": [[89, null]], "DPF3 Part 1: Correcting poor initial geometry": [[78, null]], "DPF3 Part 2: A question of centring": [[77, null]], "Data": [[74, "data"], [75, "data"], [76, "data"], [87, "data"]], "Data collection videos": [[73, "data-collection-videos"]], "Data files": [[3, null]], "Dataset 1": [[75, "dataset-1"], [75, 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"compute_functional_and_gradients() (dials.algorithms.indexing.basis_vector_search.optimise.basisvectortarget method)": [[11, "dials.algorithms.indexing.basis_vector_search.optimise.BasisVectorTarget.compute_functional_and_gradients", false]], "compute_functional_and_gradients() (dials.algorithms.refinement.engine.adaptlbfgs method)": [[14, "dials.algorithms.refinement.engine.AdaptLbfgs.compute_functional_and_gradients", false]], "compute_functional_and_gradients() (dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs method)": [[18, "dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs.compute_functional_and_gradients", false]], "compute_functional_gradients_and_curvatures() (dials.algorithms.refinement.engine.adaptlbfgs method)": [[14, "dials.algorithms.refinement.engine.AdaptLbfgs.compute_functional_gradients_and_curvatures", false]], "compute_functional_gradients_and_curvatures() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.compute_functional_gradients_and_curvatures", false]], "compute_functional_gradients_and_curvatures() (dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs method)": [[18, "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_functional_score_for_dimension_assessment() (dials.algorithms.symmetry.cosym.target.target method)": [[18, "dials.algorithms.symmetry.cosym.target.Target.compute_functional_score_for_dimension_assessment", 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]], "compute_residuals_and_gradients() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.compute_residuals_and_gradients", false]], "compute_restraints_functional_gradients_and_curvatures() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.compute_restraints_functional_gradients_and_curvatures", false]], "compute_restraints_residuals_and_gradients() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.compute_restraints_residuals_and_gradients", false]], "compute_threshold() (dials.extensions.dispersion_spotfinder_threshold_ext.dispersionspotfinderthresholdext method)": [[31, "dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt.compute_threshold", false]], "config_refinery() (dials.algorithms.refinement.refiner.refinerfactory static method)": [[14, "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, 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"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.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, "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.lauereflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.LaueReflectionManager.print_stats_on_matches", 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, 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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)": [[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() (dials.util.image.reader method)": [[33, "dials.util.image.reader.read_file", false]], "reader (class in dials.util.image)": [[33, "dials.util.image.reader", false]], "reader() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.reader", false]], "reader() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.reader", false]], "realspacegridsearch (class in dials.algorithms.indexing.basis_vector_search)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch", false]], "reason_for_termination (dials.algorithms.refinement.engine.journal attribute)": [[14, "dials.algorithms.refinement.engine.Journal.reason_for_termination", false]], "record_intensity_combination_imid() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.record_intensity_combination_Imid", false]], "refine() (dials.algorithms.indexing.indexer.indexer method)": [[11, "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, "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.laueleastsquaresresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff.rmsd_names", false]], "rmsd_names (dials.algorithms.refinement.target.target attribute)": [[14, "dials.algorithms.refinement.target.Target.rmsd_names", false]], "rmsd_names (dials.algorithms.refinement.target.tofleastsquaresresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target.TOFLeastSquaresResidualWithRmsdCutoff.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.laueleastsquaresresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff.rmsd_units", false]], "rmsd_units (dials.algorithms.refinement.target.target attribute)": [[14, "dials.algorithms.refinement.target.Target.rmsd_units", false]], "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]], "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]], "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() (dials.algorithms.refinement.engine.adaptlbfgs method)": [[14, "dials.algorithms.refinement.engine.AdaptLbfgs.run_lbfgs", false]], "scaling_models() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.scaling_models", false]], "scalingmodelbase (class in dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase", false]], "scanfactory (class in dxtbx.model.scan)": [[29, "dxtbx.model.scan.ScanFactory", false]], "scans() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.scans", false]], "scanvaryingrefiner (class in dials.algorithms.refinement.refiner)": [[14, "dials.algorithms.refinement.refiner.ScanVaryingRefiner", false]], "score_by_fraction_indexed() (dials.algorithms.indexing.model_evaluation.modelrankweighted method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankWeighted.score_by_fraction_indexed", false]], "score_by_rmsd_xy() (dials.algorithms.indexing.model_evaluation.modelrankweighted method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankWeighted.score_by_rmsd_xy", false]], "score_by_volume() (dials.algorithms.indexing.model_evaluation.modelrankweighted method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankWeighted.score_by_volume", false]], "score_vectors() (dials.algorithms.indexing.basis_vector_search.realspacegridsearch method)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.score_vectors", false]], "scorecorrelationcoefficient (class in 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]], 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"set_axes() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.set_axes", false]], "set_beam() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.set_beam", false]], "set_beam() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.set_beam", false]], "set_beam() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_beam", false]], "set_cholesky_factor() (dials.algorithms.refinement.engine.adaptlstbx method)": [[14, "dials.algorithms.refinement.engine.AdaptLstbx.set_cholesky_factor", false]], "set_detector() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.set_detector", false]], "set_detector() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.set_detector", false]], "set_detector() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_detector", false]], "set_dimensions() (dials.algorithms.symmetry.cosym.target.target method)": [[18, "dials.algorithms.symmetry.cosym.target.Target.set_dimensions", false]], "set_domain_size_ang() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.set_domain_size_ang", false]], "set_error_model() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.set_error_model", false]], "set_fixed_rotation() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.set_fixed_rotation", false]], "set_format_class() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_format_class", false]], "set_goniometer() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.set_goniometer", false]], "set_goniometer() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.set_goniometer", false]], "set_goniometer() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_goniometer", false]], "set_half_mosaicity_deg() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.set_half_mosaicity_deg", false]], "set_last_cell() (dials.algorithms.refinement.engine.journal method)": [[14, "dials.algorithms.refinement.engine.Journal.set_last_cell", false]], "set_mosaicity() (dxtbx.model.mosaiccrystalkabsch2010 method)": [[22, "dxtbx.model.MosaicCrystalKabsch2010.set_mosaicity", false]], "set_nproc() (dials.algorithms.refinement.engine.disablempmixin method)": [[14, "dials.algorithms.refinement.engine.DisableMPmixin.set_nproc", false]], "set_nproc() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.set_nproc", false]], "set_params() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_params", false]], "set_rotation_axis() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.set_rotation_axis", false]], "set_rotation_axis_datum() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.set_rotation_axis_datum", false]], "set_scaling_model_as_scaled() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.set_scaling_model_as_scaled", false]], "set_scaling_model_as_unscaled() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.set_scaling_model_as_unscaled", false]], "set_scan() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.set_scan", false]], "set_scan() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.set_scan", false]], "set_scan() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_scan", false]], "set_setting_rotation() (dxtbx.model.goniometer.goniometer method)": [[25, 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(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() 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