From 0090bb5b61cb2e3e4e4b06c7a713232b642e7aaf Mon Sep 17 00:00:00 2001
From: James Beilsten-Edmands
 <30625594+jbeilstenedmands@users.noreply.github.com>
Date: Mon, 14 Oct 2024 09:56:26 +0100
Subject: [PATCH] Fix bad merge

---
 src/dials/algorithms/correlation/analysis.py |  7 --
 src/dials/algorithms/scaling/scaleit.py      | 75 --------------------
 2 files changed, 82 deletions(-)
 delete mode 100644 src/dials/algorithms/scaling/scaleit.py

diff --git a/src/dials/algorithms/correlation/analysis.py b/src/dials/algorithms/correlation/analysis.py
index 1bd25789ab..81a159a998 100644
--- a/src/dials/algorithms/correlation/analysis.py
+++ b/src/dials/algorithms/correlation/analysis.py
@@ -48,11 +48,6 @@
 absolute_angle_tolerance = 2
   .type = float(value_min=0)
   .help = "Datasets are only accepted if unit cell angles fall within this absolute tolerance of the median cell angles."
-<<<<<<< HEAD
-
-min_reflections = 10
-  .type = int(value_min=1)
-  .help = "The minimum number of reflections per experiment."
 
 dimensionality_assessment {
   outlier_rejection = True
@@ -71,8 +66,6 @@
     .type = float(value_min=0, value_max=1)
     .help = "Buffer for minimum number of points required for a cluster in OPTICS algorithm: min_points=(number_of_datasets/number_of_dimensions)*buffer"
 }
-=======
->>>>>>> 10544d54f (Remove duplicate from phil scope)
 """,
     process_includes=True,
 )
diff --git a/src/dials/algorithms/scaling/scaleit.py b/src/dials/algorithms/scaling/scaleit.py
deleted file mode 100644
index ef736c06b7..0000000000
--- a/src/dials/algorithms/scaling/scaleit.py
+++ /dev/null
@@ -1,75 +0,0 @@
-mtz1 = "merged_3.mtz"
-mtz2 = "merged_1.mtz"
-expts = "scaled.expt"
-
-anomalous = False
-
-from dials.array_family import flex
-from dxtbx.model import Experiment, ExperimentList
-from dials.util.reference import intensities_from_reference_data_file
-from iotbx.mtz.crystal_symmetry_from_mtz import extract_from
-from dxtbx.model import Crystal
-from iotbx import mtz
-from dxtbx.serialize import load
-elist = load.experiment_list(expts)
-from copy import deepcopy
-from unittest.mock import Mock
-from dials.algorithms.scaling.model.model import KBScalingModel
-from dxtbx.util import ersatz_uuid4
-
-from dials.util.options import ArgumentParser
-from libtbx import Auto, phil
-import logging
-from dials.util import log
-log.config()
-logger = logging.getLogger("dials")
-
-def datafiles_from_mtz(mtzfile, id_=0):
-    intensities = intensities_from_reference_data_file(mtzfile)
-    if anomalous:
-        intensities = intensities.as_non_anomalous_array().merge_equivalents().array()
-    table = flex.reflection_table()
-    table["intensity"] = intensities.data()
-    table["miller_index"] = intensities.indices()
-    table["id"] = flex.int(table.size(), id_)
-    table["d"] = intensities.d_spacings().data()
-    table["variance"] = intensities.sigmas() ** 2
-    table.set_flags(flex.bool(table.size(), False), table.flags.bad_for_scaling)
-    table.set_flags(flex.bool(table.size(), True), table.flags.integrated)
-
-    expt = Experiment()
-    expt.crystal = deepcopy(elist[0].crystal)
-    phil_scope = phil.parse(
-        """
-    include scope dials.algorithms.scaling.scaling_options.phil_scope
-    include scope dials.algorithms.scaling.model.model.model_phil_scope
-    include scope dials.algorithms.scaling.scaling_refiner.scaling_refinery_phil_scope
-""",
-        process_includes=True,
-    )
-    parser = ArgumentParser(phil=phil_scope, check_format=False)
-    params, _ = parser.parse_args(args=[], quick_parse=True)
-    params.model = "KB"
-    params.KB.decay_correction = False
-    expt.scaling_model = KBScalingModel.from_data(params, [], [])
-    #expt.scaling_model.set_scaling_model_as_scaled()  # Set as scaled to fix scale.
-    expt.identifier = ersatz_uuid4()
-    table.experiment_identifiers()[id_] = expt.identifier
-    return table, expt
-
-t1,e1 = datafiles_from_mtz(mtz1, 0)
-e1 = ExperimentList([e1])
-t2,e2 = datafiles_from_mtz(mtz2, 1)
-e2 = ExperimentList([e2])
-t1["intensity.sum.value"] = t1["intensity"]
-t1["intensity.sum.variance"] = t1["variance"]
-t2["intensity.sum.value"] = t2["intensity"]
-t2["intensity.sum.variance"] = t2["variance"]
-from dials.algorithms.scaling.scaling_library import scale_against_target
-
-result = scale_against_target(t1,e1,t2,e2)
-print(e1.scaling_models()[0].to_dict())
-print(e1.scaling_models()[1].to_dict())
-
-
-print("done")
\ No newline at end of file