From f860222d7937d10a4bd5011ddce95f1d0903fd6e Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Fri, 7 Feb 2020 13:37:26 +0100
Subject: [PATCH] Update name lookup scripts
---
mmpb/files/__init__.py | 2 --
mmpb/files/migration.py | 14 ++++++--------
mmpb/files/name_lookup.py | 18 +++++++++---------
3 files changed, 15 insertions(+), 19 deletions(-)
diff --git a/mmpb/files/__init__.py b/mmpb/files/__init__.py
index 7559d6a..d804933 100644
--- a/mmpb/files/__init__.py
+++ b/mmpb/files/__init__.py
@@ -1,8 +1,6 @@
from .copy_helper import (copy_tables, copy_segmentation, copy_image_data,
copy_misc_data, copy_release_folder)
-from .bdv_server import make_bdv_server_file
-
from .folders import make_folder_structure
from .sources import add_image, add_segmentation, add_postprocessing, add_source
diff --git a/mmpb/files/migration.py b/mmpb/files/migration.py
index 1ae5b19..de842db 100644
--- a/mmpb/files/migration.py
+++ b/mmpb/files/migration.py
@@ -191,20 +191,20 @@ def migrate_version(version):
version_folder = os.path.join(ROOT, version)
# 1.) make new folder structure
- new_folder_structure(version_folder)
+ # new_folder_structure(version_folder)
# 2.) iterate over all images and segmentations, replace names (if necessary),
# move the files and make the new images.json dict
- update_image_data(version_folder)
+ # update_image_data(version_folder)
# 3.) iterate over all table links and repair them
- update_segmentation_data(version_folder)
+ # update_segmentation_data(version_folder)
# 4.) update the tables
update_tables(version_folder)
# 5.) clean up:
- clean_up(version_folder)
+ # clean_up(version_folder)
# migrate all the data in the raw folder
@@ -366,15 +366,13 @@ if __name__ == '__main__':
# change names and xmls in the rawfolder
# migrate_rawfolder()
- # version = '0.0.1'
- # migrate_version(version)
+ version = '0.6.5'
+ migrate_version(version)
version = '0.6.5'
copied = make_n5_files(version)
with open('/g/kreshuk/pape/copied_to_n5.json', 'w') as f:
json.dump(copied, f)
- # x = json.dumps(copied, indent=2, sort_keys=True)
- # print(x)
# version = '0.6.5'
# update_n5_xmls(version)
diff --git a/mmpb/files/name_lookup.py b/mmpb/files/name_lookup.py
index 8a68fd8..34a5998 100644
--- a/mmpb/files/name_lookup.py
+++ b/mmpb/files/name_lookup.py
@@ -50,6 +50,7 @@ DYNAMIC_SEGMENTATIONS = ['sbem-6dpf-1-whole-segmented-cells',
ROOT = '/g/arendt/EM_6dpf_segmentation/platy-browser-data/data'
FILE_NAME_LUT = {}
+LUT_PATH = os.path.join(ROOT, 'new_name_lut.json')
IMAGE_PROPERTIES = {}
@@ -60,18 +61,19 @@ IMAGE_PROPERTIES = {}
# - segmentations -> get rid of '-labels' postifx
def update_name_lut():
global FILE_NAME_LUT
+ if os.path.exists(LUT_PATH):
+ with open(LUT_PATH, 'r') as f:
+ FILE_NAME_LUT.update(json.load(f))
+ return
# update files according to the last version folder
folder = os.path.join(ROOT, '0.6.5')
image_names = os.listdir(os.path.join(folder, 'images'))
image_names = [os.path.splitext(name)[0] for name in image_names
if os.path.splitext(name)[1] == '.xml']
- if os.path.exists(os.path.join(folder, 'segmentations')):
- seg_names = os.listdir(os.path.join(folder, 'segmentations'))
- seg_names = [os.path.splitext(name)[0] for name in seg_names
- if os.path.splitext(name)[1] == '.xml']
- else:
- seg_names = []
+ seg_names = os.listdir(os.path.join(folder, 'segmentations'))
+ seg_names = [os.path.splitext(name)[0] for name in seg_names
+ if os.path.splitext(name)[1] == '.xml']
file_names = image_names + seg_names
for name in file_names:
@@ -213,7 +215,5 @@ def get_dynamic_segmentation_properties(name):
if __name__ == '__main__':
- # x = json.dumps(FILE_NAME_LUT, sort_keys=True, indent=2)
- # print(x)
- with open('/g/kreshuk/pape/new_names.json', 'w') as f:
+ with open(LUT_PATH, 'w') as f:
json.dump(FILE_NAME_LUT, f, sort_keys=True, indent=2)
--
GitLab