Update imports (#89)

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brainglobe · Apr 21, 2020 · 6e2f7dc · 6e2f7dc
1 parent c60650a
commit 6e2f7dc
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Showing 3 changed files with 14 additions and 30 deletions.
diff --git a/cellfinder/summarise/count_summary.py b/cellfinder/summarise/count_summary.py
@@ -13,16 +13,17 @@
 from imlib.image.metadata import define_pixel_sizes
 from imlib.general.config import get_config_obj
 from imlib.IO.structures import load_structures_as_df
-
+from imlib.source.source_files import get_structures_path
 from imlib.anatomy.structures.structures_tree import (
     atlas_value_to_structure_id,
     CellCountMissingCellsException,
     UnknownAtlasValue,
 )
 
+from neuro.atlas_tools.misc import get_atlas_pixel_sizes
+
 import cellfinder.tools.parser as cellfinder_parse
 from cellfinder.tools.prep import prep_atlas_conf, Paths
-from imlib.source.source_files import get_structures_path
 
 LEFT_HEMISPHERE = 2
 RIGHT_HEMISPHERE = 1
@@ -34,7 +35,6 @@ def region_summary_cli_parser():
     )
     parser = cli_parse(parser)
     parser = cellfinder_parse.count_summary_parse(parser)
-    # parser = cellfinder_parse.atlas_parse(parser)
     parser = cellfinder_parse.pixel_parser(parser)
     return parser
 
@@ -208,17 +208,13 @@ def get_structure_from_coordinates(
 def analysis_run(args, file_name="summary_cell_counts.csv"):
     args = prep_atlas_conf(args)
 
-    # if args.structures_file_path is None:
-    #     args.structures_file_path = get_structures_path()
-
     atlas = brainio.load_any(args.paths.registered_atlas_path)
     hemisphere = brainio.load_any(args.paths.hemispheres_atlas_path)
 
     cells = get_cells_data(
         args.paths.classification_out_file, cells_only=args.cells_only,
     )
     max_coords = get_max_coords(cells)  # Useful for debugging dimensions
-    # structures_reference_df = load_structures_as_df(args.structures_file_path)
     structures_reference_df = load_structures_as_df(get_structures_path())
 
     atlas_pixel_sizes = get_atlas_pixel_sizes(args.atlas_config)

diff --git a/cellfinder/utils/roi_transform.py b/cellfinder/utils/roi_transform.py
@@ -23,10 +23,11 @@
 )
 from imlib.general.exceptions import RegistrationError
 from imlib.source.source_files import source_custom_config_cellfinder
+from imlib.source.niftyreg_binaries import get_niftyreg_binaries, get_binary
+from neuro.atlas_tools.misc import get_atlas_pixel_sizes
 from amap.config.atlas import Atlas
-from amap.config.config import get_binary
-from amap.tools.source_files import get_niftyreg_binaries
-import cellfinder.summarise.count_summary as cells_regions
+
+from imlib.source.niftyreg_binaries import get_binary
 
 
 # TODO: get this from amap
@@ -311,9 +312,7 @@ def main():
     atlas = brainio.load_nii(str(destination_image), as_array=False)
     atlas_scale = atlas.header.get_zooms()
 
-    atlas_pixel_sizes = cells_regions.get_atlas_pixel_sizes(
-        args.registration_config
-    )
+    atlas_pixel_sizes = get_atlas_pixel_sizes(args.registration_config)
 
     transformation_matrix = np.eye(4)
     for i, axis in enumerate(("x", "y", "z")):

diff --git a/cellfinder/utils/xml_crop.py b/cellfinder/utils/xml_crop.py
@@ -5,22 +5,21 @@
 from brainio import brainio
 from imlib.general.numerical import check_positive_float, check_positive_int
 
-import cellfinder.summarise.count_summary as cells_regions
 from imlib.IO.cells import cells_to_xml
-from cellfinder.tools.prep import prep_atlas_conf
 from imlib.source.source_files import get_structures_path
 from imlib.IO.structures import load_structures_as_df
+from neuro.atlas_tools.misc import get_atlas_pixel_sizes
+
+from cellfinder.tools.prep import prep_atlas_conf
+import cellfinder.summarise.count_summary as cells_regions
 
 
 def xml_crop(args, df_query="name"):
     args = prep_atlas_conf(args)
 
-    # if args.reference_structures_file_path is None:
-    #     args.reference_structures_file_path = get_structures_path()
     if args.structures_file_path is None:
         args.structures_file_path = get_structures_path()
 
-    # reference_struct_df = pd.read_csv(args.reference_structures_file_path)
     reference_struct_df = pd.read_csv(get_structures_path())
 
     curate_struct_df = pd.read_csv(args.structures_file_path)
@@ -34,12 +33,9 @@ def xml_crop(args, df_query="name"):
     atlas = brainio.load_any(args.registered_atlas_path)
     hemisphere = brainio.load_any(args.hemispheres_atlas_path)
 
-    # structures_reference_df = load_structures_as_df(
-    #     args.reference_structures_file_path
-    # )
     structures_reference_df = load_structures_as_df(get_structures_path())
 
-    atlas_pixel_sizes = cells_regions.get_atlas_pixel_sizes(args.atlas_config)
+    atlas_pixel_sizes = get_atlas_pixel_sizes(args.atlas_config)
     sample_pixel_sizes = args.x_pixel_um, args.y_pixel_um, args.z_pixel_um
 
     scales = cells_regions.get_scales(sample_pixel_sizes, atlas_pixel_sizes)
@@ -107,14 +103,7 @@ def get_parser():
         type=str,
         help="Curated csv structure list (as per the allen brain atlas csv",
     )
-    # parser.add_argument(
-    #     "--ref-structures-file",
-    #     dest="reference_structures_file_path",
-    #     type=str,
-    #     help="The csv file containing the structures "
-    #     "definition (if not using the default "
-    #     "Allen brain atlas).",
-    # )
+
     parser.add_argument(
         "--hemisphere-query",
         dest="hemisphere_query",