Merge branch 'main' of github.com:rs-station/laue-dials

src/laue_dials/command_line/optimize_indexing.py

@@ -8,9 +8,9 @@
 import time
 from itertools import repeat
 from multiprocessing import Pool
-import numpy as np
 
 import libtbx.phil
+import numpy as np
 from dials.array_family.flex import reflection_table
 from dials.util import show_mail_handle_errors
 from dials.util.options import (ArgumentParser,
@@ -252,7 +252,7 @@ def run(args=None, *, phil=working_phil):
     ids = list(np.unique(reflections["id"]).astype(np.int32))
     expts_arr = []
     refls_arr = []
-    for i in ids: # Split DIALS objects into lists
+    for i in ids:  # Split DIALS objects into lists
         expts_arr.append(ExperimentList([experiments[i]]))
         refls_arr.append(reflections.select(reflections["id"] == i))
     inputs = list(zip(repeat(params), refls_arr, expts_arr))

src/laue_dials/command_line/predict.py

@@ -86,6 +86,7 @@ def predict_spots(params, refls, expts):
     A function for predicting spots given a geometry
     """
     from laue_dials.algorithms.laue import LauePredictor
+
     img_num = refls["id"][0]
 
     # Remove outliers
@@ -174,8 +175,10 @@ def predict_spots(params, refls, expts):
         preds = preds.select(flex.bool(sel))
         new_lams = new_lams[sel]
     except:
-        logger.warning(f"WARNING: Could not predict reflections for experiment {img_num}. Image skipped.")
-        return reflection_table() # Return empty on failure
+        logger.warning(
+            f"WARNING: Could not predict reflections for experiment {img_num}. Image skipped."
+        )
+        return reflection_table()  # Return empty on failure
 
     # Append image predictions to dataset
     final_preds.extend(preds)
@@ -256,7 +259,7 @@ def run(args=None, *, phil=working_phil):
     ids = list(np.unique(reflections["id"]).astype(np.int32))
     expts_arr = []
     refls_arr = []
-    for i in range(len(ids)): # Split DIALS objects into lists
+    for i in range(len(ids)):  # Split DIALS objects into lists
         expts_arr.append(ExperimentList([experiments[i]]))
         refls_arr.append(reflections.select(reflections["id"] == ids[i]))
     inputs = list(zip(repeat(params), refls_arr, expts_arr))

src/laue_dials/command_line/refine.py

@@ -6,11 +6,11 @@
 import logging
 import sys
 import time
-import numpy as np
 from itertools import repeat
 from multiprocessing import Pool
 
 import libtbx.phil
+import numpy as np
 from dials.array_family import flex
 from dials.array_family.flex import reflection_table
 from dials.command_line.refine import run_dials_refine
@@ -109,6 +109,7 @@
 
 working_phil = main_phil.fetch(sources=[refiner_phil])
 
+
 def refine_image(params, expts, refls):
     img_num = refls["id"][0]
     original_ids = refls["id"]
@@ -123,8 +124,10 @@ def refine_image(params, expts, refls):
             multi_expts, multi_refls, params
         )
     except:
-        logger.warning(f"WARNING: Experiment {img_num} could not be refined. Skipping image.")
-        return ExperimentList(), reflection_table() # Return empty
+        logger.warning(
+            f"WARNING: Experiment {img_num} could not be refined. Skipping image."
+        )
+        return ExperimentList(), reflection_table()  # Return empty
 
     crystals = refined_expts.crystals()
 
@@ -140,7 +143,6 @@ def refine_image(params, expts, refls):
     return refined_expts, refined_refls
 
 
-
 @show_mail_handle_errors()
 def run(args=None, *, phil=working_phil):
     # Parse arguments