Update source logic

data/sources.json

+[{"modality": "sbem", "stage": "6dpf", "id": "1", "region": "whole"},
+ {"modality": "prospr", "stage": "6dpf", "id": "1", "region": "whole"},
+ {"modality": "fibsem", "stage": "6dpf", "id": "1", "region": "parapod"}]

extract_from_platybrowser.py

+#! /g/arendt/pape/miniconda3/envs/platybrowser/bin/python
+
 import argparse
 import os
 import pandas as pd

make_data_sources.py

+#! /g/arendt/pape/miniconda3/envs/platybrowser/bin/python
+
 import os
 import glob
-from scripts.files import get_h5_path_from_xml, copy_xml_with_newpath, write_simple_xml
 from shutil import copyfile
+from scripts.files import get_h5_path_from_xml, copy_xml_with_newpath, write_simple_xml
 
 
 def copy_xmls_and_symlink_h5(name_dict, src_folder, trgt_folder):

scripts/default_config.py

@@ -2,8 +2,9 @@ import os
 import json
 from cluster_tools.cluster_tasks import BaseClusterTask
 
-DEFAULT_GROUP = 'kreshuk'
-DEFAULT_SHEBANG = '#! /g/arendt/pape/miniconda3/envs/platybrowser/bin/python'
+DEFAULT_GROUP = os.environ.get('PLATYBROWSER_GROUP', 'kreshuk')
+DEFAULT_SHEBANG = os.environ.get('PLATYBROWSER_SHEBANG',
+                                 '#! /g/arendt/pape/miniconda3/envs/platybrowser/bin/python')
 DEFAULT_BLOCK_SHAPE = [64, 512, 512]
 
 

scripts/sources.py

-# this folder contains information about the current data sources, see
-# https://git.embl.de/tischer/platy-browser-tables/blob/dev/README.md#file-naming
+import json
 
-# TODO maybe store this as exteral file in json
-# list of the current data sources
-SOURCES = [{'modality': 'sbem', 'stage': '6dpf', 'id': '1', 'region': 'whole'},
-           {'modality': 'prospr', 'stage': '6dpf', 'id': '1', 'region': 'whole'},
-           {'modality': 'fibsem', 'stage': '6dpf', 'id': '1', 'region': 'parapod'}]
+SOURCE_FILE = '../data/sources.json'
+SEGMENTATION_FILE = '../data/segmentations.json'
+IMAGE_FILE = '../data/images.json'
 
 
 def get_sources():
-    return SOURCES
+    """ Get names of the current data sources.
+
+    See https://git.embl.de/tischer/platy-browser-tables/README.md#file-naming
+    for the source naming conventions.
+    """
+    with open(SOURCE_FILE) as f:
+        sources = json.load(f)
+    return sources
+
+
+def add_source(modality, stage, id=1, region='whole'):
+    """ Add a new data source
+
+    See https://git.embl.de/tischer/platy-browser-tables/README.md#file-naming
+    for the source naming conventions.
+    """
+    if not isinstance(modality, str):
+        raise ValueError("Expected modality to be a string, not %s" % type(modality))
+    if not isinstance(stage, str):
+        raise ValueError("Expected stage to be a string, not %s" % type(id))
+    if not isinstance(id, int):
+        raise ValueError("Expected id to be an integer, not %s" % type(id))
+    if not isinstance(region, str):
+        raise ValueError("Expected region to be a string, not %s" % type(id))
+    sources = get_sources()
+    sources.append({'modality': modality, 'stage': stage, 'id': str(id), 'region': region})
+    with open(SOURCE_FILE, 'w') as f:
+        json.dump(sources, f)
 
 
 def source_to_prefix(source):
@@ -20,6 +44,20 @@ def source_to_prefix(source):
 
 
 def get_name_prefixes():
+    """ Get the name prefixes corresponding to all sources.
+    """
     sources = get_sources()
     prefixes = [source_to_prefix(source) for source in sources]
     return prefixes
+
+
+def add_image(input_path):
+    """ Add image volume to the platy browser data.
+    """
+    pass
+
+
+def add_segmentation():
+    """ Add segmentation volume to the platy browser data.
+    """
+    pass

update_platy_browser.py

-#! /g/kreshuk/pape/Work/software/conda/miniconda3/envs/cluster_env37/bin/python
+#! /g/arendt/pape/miniconda3/envs/platybrowser/bin/python
 
 import os
 import argparse