From c84be4c0d4947ea22e1a2ac6a24395a08417115b Mon Sep 17 00:00:00 2001
From: Kimberly Meechan <kimberly.meechan@embl.de>
Date: Tue, 28 Jan 2020 13:12:48 +0100
Subject: [PATCH] separated filters into own function
---
.../extension/attributes/morphology_impl.py | 71 +++++++++----------
1 file changed, 34 insertions(+), 37 deletions(-)
diff --git a/scripts/extension/attributes/morphology_impl.py b/scripts/extension/attributes/morphology_impl.py
index 734db38..7a45fdf 100644
--- a/scripts/extension/attributes/morphology_impl.py
+++ b/scripts/extension/attributes/morphology_impl.py
@@ -87,6 +87,35 @@ def filter_table_region(table, region_path, regions=('empty', 'yolk', 'neuropil'
return table
+def run_all_filters(table, min_size, max_size, max_bb, mapping_path, region_mapping_path):
+
+ # remove zero label if present
+ table = table.loc[table['label_id'] != 0, :]
+
+ # filter to only keep cells with assigned nuclei)
+ if mapping_path is not None:
+ log("Have mapping path %s" % mapping_path)
+ table = filter_table_from_mapping(table, mapping_path)
+ log("Number of labels after filter with mapping: %i" % table.shape[0])
+
+ # filter to exclude certain regions
+ if region_mapping_path is not None:
+ log("Have region mapping path %s" % region_mapping_path)
+ table = filter_table_region(table, region_mapping_path)
+ log("Number of labels after region filter: %i" % table.shape[0])
+
+ # filter by size of object (no. pixels)
+ if min_size is not None or max_size is not None:
+ table = filter_table(table, min_size, max_size)
+ log("Number of labels after size filter: %i" % table.shape[0])
+
+ # filter by bounding box size
+ if max_bb is not None:
+ table = filter_table_bb(table, max_bb)
+ log("Number of labels after bounding box size filter %i" % table.shape[0])
+
+ return table
+
def load_data(ds, row, scale):
# compute the bounding box from the row information
@@ -364,18 +393,8 @@ def morphology_impl_nucleus (nucleus_segmentation_path, raw_path, chromatin_path
chromatin_key_full = 't00000/s00/0/cells'
chromatin_key = 't00000/s00/%i/cells' % chromatin_scale
- # remove zero label if it exists
- table = table.loc[table['label_id'] != 0, :]
-
- # filter by size
- if min_size is not None or max_size is not None:
- table = filter_table(table, min_size, max_size)
- log("Number of labels after size filter: %i" % table.shape[0])
-
- # filter by bounding box size
- if max_bb is not None:
- table = filter_table_bb(table, max_bb)
- log("Number of labels after bounding box size filter %i" % table.shape[0])
+ # filter table
+ table = run_all_filters(table, min_size, max_size, max_bb, None, None)
# get scale factors
if raw_path is not None:
@@ -447,30 +466,8 @@ def morphology_impl_cell (cell_segmentation_path, raw_path,
nucleus_seg_key_full = 't00000/s00/0/cells'
nucleus_seg_key = 't00000/s00/%i/cells' % nucleus_seg_scale
- # remove zero label if it exists
- table = table.loc[table['label_id'] != 0, :]
-
- # filter to only keep cells with assigned nuclei)
- if mapping_path is not None:
- log("Have mapping path %s" % mapping_path)
- table = filter_table_from_mapping(table, mapping_path)
- log("Number of labels after filter with mapping: %i" % table.shape[0])
-
- # filter to exclude certain regions
- if region_mapping_path is not None:
- log("Have region mapping path %s" % region_mapping_path)
- table = filter_table_region(table, region_mapping_path)
- log("Number of labels after region filter: %i" % table.shape[0])
-
- # filter by size of object (no. pixels)
- if min_size is not None or max_size is not None:
- table = filter_table(table, min_size, max_size)
- log("Number of labels after size filter: %i" % table.shape[0])
-
- # filter by bounding box size
- if max_bb is not None:
- table = filter_table_bb(table, max_bb)
- log("Number of labels after bounding box size filter %i" % table.shape[0])
+ # filter table
+ table = run_all_filters(table, min_size, max_size, max_bb, mapping_path, region_mapping_path)
# get scale factors
if raw_path is not None:
@@ -491,7 +488,7 @@ def morphology_impl_cell (cell_segmentation_path, raw_path,
scale_factor_nucleus = get_scale_factor(nucleus_segmentation_path, nucleus_seg_key_full, nucleus_seg_key,
nucleus_resolution)
f_nucleus = h5py.File(nucleus_segmentation_path, 'r')
- ds_nucleus = f_exclude[nucleus_seg_key]
+ ds_nucleus = f_nucleus[nucleus_seg_key]
else:
log("Don't have exclude path; don't exclude nucleus area for intensity measures")
scale_factor_nucleus = None
--
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