Update name lookup scripts

mmpb/files/__init__.py

 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

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)

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)