From be225b82775f0e4e9985ff5756869c8d099f3af8 Mon Sep 17 00:00:00 2001
From: Constantin Pape <c.pape@gmx.net>
Date: Thu, 6 Feb 2020 09:07:28 +0100
Subject: [PATCH] More work on migration scripts
---
mmpb/files/migration.py | 3 ++-
mmpb/files/name_lookup.py | 39 ++++++++++++++++++++++++++++++++++-----
2 files changed, 36 insertions(+), 6 deletions(-)
diff --git a/mmpb/files/migration.py b/mmpb/files/migration.py
index 7225a7e..3efdb7f 100644
--- a/mmpb/files/migration.py
+++ b/mmpb/files/migration.py
@@ -66,7 +66,7 @@ def move_image_file(image_folder, xml_path):
copy_xml_with_newpath(new_xml_path, new_xml_path, new_rel_data_path)
# update the h5 path in the new xml
- return {new_name: get_image_properties(name)}
+ return {new_name: get_image_properties(new_name)}
def update_image_dict(image_folder, image_dict):
@@ -145,6 +145,7 @@ def migrate_version(version):
# - remove segmentations folder (make sure it's empty)
# - remove bdv server config
clean_up(version_folder)
+ # TODO make README for version
# migrate all the data in the raw folder
diff --git a/mmpb/files/name_lookup.py b/mmpb/files/name_lookup.py
index cda2812..e9e91e2 100644
--- a/mmpb/files/name_lookup.py
+++ b/mmpb/files/name_lookup.py
@@ -79,6 +79,9 @@ def update_name_lut():
# get rid of '-ariande' tag [sic]
if '-ariande' in new_name:
new_name = new_name.replace('-ariande', '')
+ # replace '-mask' with '-segmented'
+ if '-mask' in new_name:
+ new_name = new_name.replace('-mask', '-segmented')
# update the gene / region names for prospr
# and make everything lowercase
@@ -102,19 +105,45 @@ def update_name_lut():
def update_image_properties():
global IMAGE_PROPERTIES
- for name in FILE_NAME_LUT:
+ for name in FILE_NAME_LUT.values():
properties = {}
+ table_folder = 'tables/%s' % name
# prospr: Color Magenta
# value range 0 - 1000
if name.startswith('prospr'):
if 'virtual-cells' in name:
- vc_table_folder = 'tables/%s' % name
- properties.update({'ColorMap': 'Glasbey', 'TableFolder': vc_table_folder})
+ properties.update({'ColorMap': 'Glasbey', 'TableFolder': table_folder})
else:
properties.update({'Color': 'Magenta', 'MinValue': 0, 'MaxValue': 1000})
- # TODO handle segmentations / masks
- # TODO segmented / mask is not consistent, get rid of '-mask' tag?
+
+ # handle all special segmentations:
+ # - dynamic and with tables:
+ # -- cells
+ # -- cilia
+ # -- nuclei
+ elif 'segmented-cells' in name:
+ paintera_project = ''
+ table_update_function = ''
+ # TODO postprocessing options in Dynamic
+ properties.update({'ColorMap': 'Glasbey',
+ 'TableFolder': table_folder,
+ 'Dynamic': {'PainteraProject': paintera_project,
+ 'TableUpdateFunction': table_update_function}})
+ # - static but with tables:
+ # -- chromatin
+ # -- tissue
+ # -- ganglia
+ elif ('segmented-chromatin' in name
+ or 'segmented-tissue' in name
+ or 'segmented-ganglia' in name):
+ properties.update({'ColorMap': 'Glasbey', 'TableFolder': table_folder})
+
+ # TODO is white correct ?
+ # all other segmentations are binary masks
+ elif '-segmented' in name:
+ properties.update({'Color': 'White', 'MinValue': 0, 'MaxValue': 1})
+
# em-raw: Color White
# value range 0 - 255
else:
--
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