omero import script, updated UI

src/app.py

@@ -659,6 +659,7 @@ def is_mask_ok(mask):
 
 
 @app.route('/')
+@nocache
 def root():
     """
     Serves the minerva-author web UI

src/convert_omero_channels.py

@@ -0,0 +1,101 @@
+import pathlib
+import json
+import os
+import argparse
+from json.decoder import JSONDecodeError
+
+def make_channel(ch_key, ch):
+    ch_id = 0
+    try:
+        # Minerva Author uses a zero-based index
+        ch_id = int(ch_key) - 1
+    except ValueError as e:
+        print(e)
+        print(f'Skipping channel: "{ch_key}" is not an integer')
+        return {}
+    return {
+        "color": ch['color'],
+        "label": ch['label'],
+        "min": ch['start'] / ch['max'],
+        "max": ch['end'] / ch['max'],
+        "id": ch_id,
+    }
+
+def make_group(channels):
+    all_channels = [
+        make_channel(ch_key, ch) for (ch_key, ch) in channels.items()
+    ]
+    all_channels = [ch for ch in all_channels if 'id' in ch]
+    all_channels.sort(key= lambda ch: ch['id'])
+    return {
+        "channels": all_channels,
+        "label": "imported omero channels"
+    }
+
+def main(omero_json, author_json):
+
+    story_json_checks = [
+        (author_json, ['.json']),
+        (pathlib.Path(author_json.stem), ['.groups', '.story'])
+        ]
+    test_suffix = lambda check: check[0].suffix in check[1]
+    if not all(map(test_suffix, story_json_checks)):
+        print(' '.join([
+            'Invalid output path.',
+            'It must end in .story.json or .groups.json'
+        ]))
+        return
+
+    if os.path.exists(author_json):
+        print(f'Overwriting existing save file {author_json}')
+    else:
+        print(f'Writing to new save file {author_json}')
+
+    if not author_json.parent.exists():
+        author_json.parent.mkdir(parents=True)
+
+    omero_channels = {}
+    try:
+        with open(omero_json) as rf:
+            loaded = json.load(rf)
+        omero_channels = loaded['channels']
+    except (FileNotFoundError, JSONDecodeError, KeyError) as e:
+        logger.error(e)
+        logger.error(f'Invalid input file: cannot parse {omero_json}')
+        return
+
+    with open(author_json, 'w') as wf:
+        json.dump({
+            "in_file": "",
+            "csv_file": "",
+            "groups": [
+                make_group(omero_channels)
+            ],
+            "masks": [],
+            "waypoints": [],
+            "sample_info": {
+                "rotation": 0,
+                "name": "",
+                "text": ""
+            }
+        }, wf)
+
+        print(f'Success! {author_json} written')
+
+if __name__ == '__main__':
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "omero_json", metavar="omero_json", type=pathlib.Path,
+        help="Input path to exported omero channels",
+    )
+    parser.add_argument(
+        "author_json", metavar="author_json", type=pathlib.Path,
+        help="Output Minerva Author save file with channels from omero",
+    )
+    args = parser.parse_args()
+
+    omero_json = args.omero_json
+    author_json = args.author_json
+
+    main(omero_json, author_json)

src/save_exhibit_pyramid.py

@@ -6,6 +6,7 @@
 import argparse
 from distutils import file_util
 from distutils.errors import DistutilsFileError
+from tifffile.tifffile import TiffFileError
 from json.decoder import JSONDecodeError
 from render_jpg import render_color_tiles
 from storyexport import deduplicate_data