From 881918f9c7ad86c3787fcf7150e6fbb36526c452 Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Thu, 15 Aug 2019 16:56:15 +0200
Subject: [PATCH] add_segmentation is working for dynamic segmentations and
added existing dynamic segmentations
---
add_existing_data.py | 37 ++++++++++++++++++++++++++++++-------
data/segmentations.json | 2 +-
scripts/files/checks.py | 4 ++--
3 files changed, 33 insertions(+), 10 deletions(-)
diff --git a/add_existing_data.py b/add_existing_data.py
index 8ae4351..0a61b25 100644
--- a/add_existing_data.py
+++ b/add_existing_data.py
@@ -37,10 +37,10 @@ def add_static_segmentations():
source = 'sbem-6dpf-1-whole'
# chromatin segmentation
- # chromatin_tables = {'default': './data/0.2.0/tables/sbem-6dpf-1-whole-segmented-chromatin-labels/default.csv'}
- # add_segmentation(source, 'segmented-chromatin-labels',
- # segmentation_path='./data/rawdata/sbem-6dpf-1-whole-segmented-chromatin-labels.xml',
- # table_path_dict=chromatin_tables, copy_data=False)
+ chromatin_tables = {'default': './data/0.2.0/tables/sbem-6dpf-1-whole-segmented-chromatin-labels/default.csv'}
+ add_segmentation(source, 'segmented-chromatin-labels',
+ segmentation_path='./data/rawdata/sbem-6dpf-1-whole-segmented-chromatin-labels.xml',
+ table_path_dict=chromatin_tables, copy_data=False)
# tissue segmentation
tissue_tables = {'default': './data/0.1.0/tables/sbem-6dpf-1-whole-segmented-tissue-labels/base.csv'}
@@ -53,17 +53,40 @@ def add_static_segmentations():
segmentation_path='./data/rawdata/sbem-6dpf-1-whole-segmented-muscle.xml', copy_data=False)
+def add_dynamic_segmentations():
+ source = 'sbem-6dpf-1-whole'
+ paintera_root = '/g/kreshuk/data/arendt/platyneris_v1/data.n5'
+
+ # cell segmentation
+ add_segmentation(source, 'segmented-cells-labes',
+ paintera_project=(paintera_root, 'volumes/paintera/proofread_cells'),
+ resolution=[.025, .02, .02],
+ table_update_function='make_cell_tables')
+
+ # nucleus segmentation
+ add_segmentation(source, 'segmented-nuclei-labels',
+ paintera_project=(paintera_root, 'volumes/paintera/nuclei'),
+ resolution=[.1, .08, .08],
+ table_update_function='make_nucleus_tables')
+
+ # cilia segmentation
+ add_segmentation(source, 'segmented-cilia-labels',
+ paintera_project=(paintera_root, 'volumes/paintera/cilia'),
+ resolution=[.025, .01, .01],
+ table_update_function='make_cilia_tables')
+
+
def add_segmentations():
add_static_segmentations()
- # add_dynamic_segmentations()
+ add_dynamic_segmentations()
def add_existing_data():
""" Add existing data to the json files that keep track of
sources, image data and segmentations.
"""
- # add_sources()
- # add_images()
+ add_sources()
+ add_images()
add_segmentations()
diff --git a/data/segmentations.json b/data/segmentations.json
index 78f4601..12391cf 100644
--- a/data/segmentations.json
+++ b/data/segmentations.json
@@ -1 +1 @@
-{"sbem-6dpf-1-whole-segmented-chromatin-labels": {"is_static": true, "has_tables": true}, "sbem-6dpf-1-whole-segmented-tissue-labels": {"is_static": true, "has_tables": true}, "sbem-6dpf-1-whole-segmented-muscle": {"is_static": true, "has_tables": false}}
\ No newline at end of file
+{"sbem-6dpf-1-whole-segmented-chromatin-labels": {"is_static": true, "has_tables": true}, "sbem-6dpf-1-whole-segmented-tissue-labels": {"is_static": true, "has_tables": true}, "sbem-6dpf-1-whole-segmented-muscle": {"is_static": true, "has_tables": false}, "sbem-6dpf-1-whole-segmented-cells-labes": {"is_static": false, "paintera_project": ["/g/kreshuk/data/arendt/platyneris_v1/data.n5", "volumes/paintera/proofread_cells"], "resolution": [0.025, 0.02, 0.02], "table_update_function": "make_cell_tables"}, "sbem-6dpf-1-whole-segmented-nuclei-labels": {"is_static": false, "paintera_project": ["/g/kreshuk/data/arendt/platyneris_v1/data.n5", "volumes/paintera/nuclei"], "resolution": [0.1, 0.08, 0.08], "table_update_function": "make_nucleus_tables"}, "sbem-6dpf-1-whole-segmented-cilia-labels": {"is_static": false, "paintera_project": ["/g/kreshuk/data/arendt/platyneris_v1/data.n5", "volumes/paintera/cilia"], "resolution": [0.025, 0.01, 0.01], "table_update_function": "make_cilia_tables"}}
\ No newline at end of file
diff --git a/scripts/files/checks.py b/scripts/files/checks.py
index f8bb35c..073ab88 100644
--- a/scripts/files/checks.py
+++ b/scripts/files/checks.py
@@ -35,10 +35,10 @@ def check_paintera(paintera_project):
except TypeError:
return False
try:
- f = z5py.File(path)
+ f = z5py.File(path, 'r')
group = f[key]
# check for expected paintera keys
- for kk in ('data', 'label-block-mapping', 'unique-labels'):
+ for kk in ('data', 'label-to-block-mapping', 'unique-labels'):
if kk not in group:
return False
except Exception:
--
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