From 181976dfea551220571cd66ebaa6a2ca47505865 Mon Sep 17 00:00:00 2001
From: Kimberly Meechan <kimberly.meechan@embl.de>
Date: Tue, 28 Jan 2020 10:19:08 +0100
Subject: [PATCH] split main function into two
---
.../extension/attributes/morphology_impl.py | 154 +++++++++++++++++-
1 file changed, 147 insertions(+), 7 deletions(-)
diff --git a/scripts/extension/attributes/morphology_impl.py b/scripts/extension/attributes/morphology_impl.py
index 0298a9d..d9e33fe 100644
--- a/scripts/extension/attributes/morphology_impl.py
+++ b/scripts/extension/attributes/morphology_impl.py
@@ -99,7 +99,7 @@ def load_data(ds, row, scale):
# load the data from the bounding box
return ds[bb]
-
+# @profile
def morphology_row_features(mask, scale):
# Calculate stats from skimage
ski_morph = regionprops(mask.astype('uint8'))
@@ -131,7 +131,7 @@ def morphology_row_features(mask, scale):
return (volume_in_microns, extent, equiv_diameter, major_axis,
minor_axis, surface_area, sphericity, max_radius)
-
+# @profile
def intensity_row_features(raw, mask):
intensity_vals_in_mask = raw[mask]
# mean and stdev - use float64 to avoid silent overflow errors
@@ -146,7 +146,7 @@ def intensity_row_features(raw, mask):
return mean_intensity, st_dev, median_intensity, interquartile_range_intensity, total
-
+# @profile
def radial_intensity_row_features(raw, mask, scale, stops=(0.0, 0.25, 0.5, 0.75, 1.0)):
result = ()
@@ -163,7 +163,7 @@ def radial_intensity_row_features(raw, mask, scale, stops=(0.0, 0.25, 0.5, 0.75,
return result
-
+# @profile
def texture_row_features(raw, mask):
# errors if there are small, isolated spots (because I'm using ignore zeros as true)
# so here remove components that are < 10 pixels
@@ -187,7 +187,7 @@ def texture_row_features(raw, mask):
return tuple(hara)
-
+# @profile
def radial_distribution(edt, mask, stops=(0.0, 0.25, 0.5, 0.75, 1.0)):
result = ()
@@ -201,7 +201,7 @@ def radial_distribution(edt, mask, stops=(0.0, 0.25, 0.5, 0.75, 1.0)):
return result
-
+# @profile
def chromatin_row_features(chromatin, edt, raw, scale_chromatin):
result = ()
@@ -224,7 +224,7 @@ def chromatin_row_features(chromatin, edt, raw, scale_chromatin):
return result
-
+# @profile
# compute morphology (and intensity features) for label range
def morphology_features_for_label_range(table, ds, ds_raw,
ds_chromatin,
@@ -404,6 +404,145 @@ def compute_morphology_features(table, segmentation_path, raw_path,
return stats
+
+def morphology_impl_nucleus (nucleus_segmentation_path, raw_path, chromatin_path,
+ table,
+ min_size, max_size,
+ max_bb,
+ nucleus_resolution, chromatin_resolution,
+ nucleus_seg_scale, raw_scale, chromatin_scale,
+ label_starts, label_stops):
+
+ # keys for the different scales
+ nucleus_seg_key_full = 't00000/s00/0/cells'
+ nucleus_seg_key = 't00000/s00/%i/cells' % nucleus_seg_scale
+ raw_key_full = 't00000/s00/0/cells'
+ raw_key = 't00000/s00/%i/cells' % raw_scale
+ chromatin_key_full = 't00000/s00/0/cells'
+ chromatin_key = 't00000/s00/%i/cells' % chromatin_scale
+
+ # get scale factors
+ scale_factor_nucleus_seg = get_scale_factor(nucleus_segmentation_path, nucleus_seg_key_full, nucleus_seg_key,
+ nucleus_resolution)
+
+ if raw_path is not None:
+ log("Have raw path; compute intensity features")
+ # NOTE for now we can hard-code the resolution for the raw data here,
+ # but we might need to change this if we get additional dataset(s)
+ raw_resolution = [0.025, 0.01, 0.01]
+ scale_factor_raw = get_scale_factor(raw_path, raw_key_full, raw_key, raw_resolution)
+ else:
+ log("Don't have raw path; do not compute intensity features")
+ scale_factor_raw = None
+
+ if chromatin_path is not None:
+ log("Have chromatin path; compute chromatin features")
+ scale_factor_chromatin = get_scale_factor(chromatin_path, chromatin_key_full, chromatin_key,
+ chromatin_resolution)
+ else:
+ log("Don't have chromatin path; do not compute chromatin features")
+ scale_factor_chromatin = None
+
+ # 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])
+
+ log("Computing morphology features")
+ stats = compute_morphology_features(table, segmentation_path, raw_path,
+ chromatin_path, exclude_nuc_path,
+ seg_key, raw_key, chromatin_key,
+ exclude_key,
+ scale_factor_seg, scale_factor_raw,
+ scale_factor_chromatin,
+ scale_factor_exclude,
+ label_starts, label_stops)
+ return stats
+
+def morphology_impl_cell (cell_segmentation_path, raw_path,
+ nucleus_segmentation_path,
+ table, mapping_path,
+ region_mapping_path,
+ min_size, max_size,
+ max_bb,
+ cell_resolution, nucleus_resolution,
+ cell_seg_scale, raw_scale, nucleus_seg_scale,
+ label_starts, label_stops):
+
+ # keys for the different scales
+ cell_seg_key_full = 't00000/s00/0/cells'
+ cell_seg_key = 't00000/s00/%i/cells' % cell_seg_scale
+ raw_key_full = 't00000/s00/0/cells'
+ raw_key = 't00000/s00/%i/cells' % raw_scale
+ nucleus_seg_key_full = 't00000/s00/0/cells'
+ nucleus_seg_key = 't00000/s00/%i/cells' % nucleus_seg_scale
+
+ # get scale factors
+ cell_seg_scale_factor = get_scale_factor(cell_segmentation_path, cell_seg_key_full, cell_seg_key, cell_resolution)
+
+ if raw_path is not None:
+ log("Have raw path; compute intensity features")
+ # NOTE for now we can hard-code the resolution for the raw data here,
+ # but we might need to change this if we get additional dataset(s)
+ raw_resolution = [0.025, 0.01, 0.01]
+ scale_factor_raw = get_scale_factor(raw_path, raw_key_full, raw_key, raw_resolution)
+ else:
+ log("Don't have raw path; do not compute intensity features")
+ scale_factor_raw = None
+
+ if nucleus_segmentation_path is not None:
+ log("Have nucleus path; exclude nucleus for intensity measures")
+ scale_factor_nucleus = get_scale_factor(nucleus_segmentation_path, nucleus_seg_key_full, nucleus_seg_key,
+ nucleus_resolution)
+ else:
+ log("Don't have exclude path; don't exclude nucleus area for intensity measures")
+ scale_factor_nucleus = None
+
+ # 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])
+
+ log("Computing morphology features")
+ stats = compute_morphology_features(table, segmentation_path, raw_path,
+ chromatin_path, exclude_nuc_path,
+ seg_key, raw_key, chromatin_key,
+ exclude_key,
+ scale_factor_seg, scale_factor_raw,
+ scale_factor_chromatin,
+ scale_factor_exclude,
+ label_starts, label_stops)
+ return stats
+
+
def morphology_impl(segmentation_path, raw_path, chromatin_path,
exclude_nuc_path,
table, mapping_path,
@@ -530,5 +669,6 @@ def morphology_impl(segmentation_path, raw_path, chromatin_path,
return stats
+
if __name__ == '__main__':
pass
--
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