From 1aaf8ebb47760af376ac91fb9021f25dc9a9e1a3 Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Thu, 3 Oct 2019 09:48:54 +0200
Subject: [PATCH] Fix issues in region attributes
---
scripts/attributes/region_attributes.py | 17 ++++++-----------
scripts/attributes/util.py | 3 +--
update_patch.py | 1 +
3 files changed, 8 insertions(+), 13 deletions(-)
diff --git a/scripts/attributes/region_attributes.py b/scripts/attributes/region_attributes.py
index 2965797..b5f6916 100644
--- a/scripts/attributes/region_attributes.py
+++ b/scripts/attributes/region_attributes.py
@@ -11,7 +11,6 @@ def write_region_table(label_ids, label_list, semantic_mapping_list, out_path):
assert len(label_list) == len(semantic_mapping_list)
n_labels = len(label_ids)
assert all(len(labels) == n_labels for labels in label_list)
-
col_names = ['label_id'] + [name for mapping in semantic_mapping_list
for name in mapping.keys()]
n_cols = len(col_names)
@@ -49,16 +48,13 @@ def muscle_attributes(muscle_path, key_muscle,
# we count everything that has at least 25 % overlap as muscle
overlap_threshold = .25
muscle_labels = normalize_overlap_dict(muscle_labels)
- label_ids = [k for k in sorted(muscle_labels.keys())]
- muscle_labels = np.array([foreground_id if muscle_labels[label_id].get(foreground_id, 0) > overlap_threshold
- else 0 for label_id in label_ids])
+ label_ids = np.array([k for k in sorted(muscle_labels.keys())])
+ overlap_values = np.array([muscle_labels[label_id].get(foreground_id, 0.) for label_id in label_ids])
+ overlap_labels = label_ids[overlap_values > overlap_threshold]
- # print()
- # print()
- # print(np.sum(muscle_labels == foreground_id))
- # print(muscle_labels.size)
- # print()
- # print()
+ n_labels = int(label_ids.max()) + 1
+ muscle_labels = np.zeros(n_labels, dtype='uint8')
+ muscle_labels[overlap_labels] = foreground_id
semantic_muscle = {'muscle': [foreground_id]}
return muscle_labels, semantic_muscle
@@ -86,7 +82,6 @@ def region_attributes(seg_path, region_out,
ids = f['semantic_mapping'][:]
semantics_to_carved_ids = {name: idx.tolist()
for name, idx in zip(names, ids)}
-
label_list = [carved_labels]
semantic_mapping_list = [semantics_to_carved_ids]
diff --git a/scripts/attributes/util.py b/scripts/attributes/util.py
index 70024b9..c34cf32 100644
--- a/scripts/attributes/util.py
+++ b/scripts/attributes/util.py
@@ -53,8 +53,7 @@ def node_labels(seg_path, seg_key,
data = ds_out[:]
else:
n_chunks = ds_out.number_of_chunks
- out_path = ds_out.path
- data = [ndist.deserializeOverlapChunk(out_path, (chunk_id,))[0]
+ data = [ndist.deserializeOverlapChunk(out_path, out_key, (chunk_id,))[0]
for chunk_id in range(n_chunks)]
data = {label_id: overlaps
for chunk_data in data
diff --git a/update_patch.py b/update_patch.py
index 5340967..23716e9 100755
--- a/update_patch.py
+++ b/update_patch.py
@@ -155,6 +155,7 @@ def update_patch(update_seg_names, update_table_names,
update_tables(folder, new_folder, table_updates,
target=target, max_jobs=max_jobs)
+ print("All updates were successfull. Making bdv file and adding version tag")
make_bdv_server_file(new_folder, os.path.join(new_folder, 'misc', 'bdv_server.txt'),
relative_paths=True)
add_version(new_tag)
--
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