Plate conversion

merge.py

@@ -1,41 +1,81 @@
 #!/usr/bin/env python
 import os
-import sys
 import glob
 import json
 import argparse
-p = argparse.ArgumentParser()
-p.add_argument("dir", nargs="+")
-a = p.parse_args()
-rv = dict()
-
-for dir in a.dir:
-    if os.path.exists(f"{dir}/.zattrs"):
-        with open(f"{dir}/.zattrs") as o:
+
+
+def update_zattrs(zarr_dir, omero_json=None, dry_run=False):
+    rv = dict()
+    if os.path.exists(f"{zarr_dir}/.zattrs"):
+        with open(f"{zarr_dir}/.zattrs") as o:
             rv.update(json.load(o))
     else:
         multiscale = {"datasets":[],"version":"0.1"}
-        for path in sorted(glob.glob(f"{dir}/[0-9]*")):
+        for path in sorted(glob.glob(f"{zarr_dir}/[0-9]*")):
             path = path.split("/")[-1]
             multiscale["datasets"].append({"path": path})
         rv["multiscales"] = [multiscale]
 
-    with open(f"{dir}/omero.json", "r") as o:
-        omero = json.load(o)
+    if not omero_json:
+        with open(f"{zarr_dir}/omero.json", "r") as o:
+            omero_json = json.load(o)
 
     rv["omero"] = {}
-    if "version" not in omero:
-        omero["version" ] = "0.1"
+    if "version" not in omero_json:
+        omero_json["version" ] = "0.1"
     for x in ("version", "channels", "rdefs"):
-        rv["omero"][x] = omero[x]
+        rv["omero"][x] = omero_json[x]
 
-    rv["omero"]["id"] = omero["id"]
-    rv["omero"]["name"] = omero["meta"]["imageName"]
+    rv["omero"]["id"] = omero_json["id"]
+    rv["omero"]["name"] = omero_json["meta"]["imageName"]
     for ch in rv["omero"]["channels"]:
         for x in ("reverseIntensity", "emissionWave"):
             ch.pop(x, None)
     rv["omero"]["rdefs"].pop("invertAxis", None)
     rv["omero"]["rdefs"].pop("projection", None)
 
-    with open(f"{dir}/.zattrs", "w") as o:
+    if args.dry_run:
+        print(f"Updating {zarr_dir}/.zattrs")
+    with open(f"{zarr_dir}/.zattrs", "w") as o:
         o.write(json.dumps(rv, indent=4, sort_keys=True))
+
+
+def get_zarr_directories(top_dirs, recursive):
+    if not recursive:
+       return top_dirs
+
+    if len(top_dirs) > 1:
+        raise Exception("Recursive option can only be used with one directory")
+
+    paths = []
+    for root, dirs, files in os.walk(top_dirs[0]):
+        for f in files:
+            if f.lower() == '.zattrs':
+                paths.append(root)
+    return(paths)
+
+
+def get_omero_json(json_file):
+    if json_file:
+        with open(f"{json_file}", "r") as o:
+            return json.load(o)
+    else:
+        return None
+
+
+if __name__ == "__main__":
+    p = argparse.ArgumentParser()
+    p.add_argument("dir", nargs="+", help="the Zarr directory")
+    p.add_argument('--file',
+                   help="a JSON file containing the rendering settings")
+    p.add_argument("--dry-run", "-n", action='store_true',
+                   help="dry-run")
+    p.add_argument("--recursive", "-r", action='store_true',
+                   help="apply recursively to all Zarr sub-directories")
+    args = p.parse_args()
+
+    zarr_dirs = get_zarr_directories(args.dir, args.recursive)
+    omero_json = get_omero_json(args.file)
+    for zarr_dir in zarr_dirs:
+        update_zattrs(zarr_dir, omero_json=omero_json, dry_run=False)