Added zarr v2_3 env

OmeSliCC/OmeZarrSource.py

@@ -1,6 +1,5 @@
-#import dask.array as da
 import numpy as np
-from ome_zarr.io import parse_url
+from ome_zarr.io import parse_url, ZarrLocation
 from ome_zarr.reader import Reader
 
 from OmeSliCC.OmeSource import OmeSource
@@ -26,7 +25,8 @@ def __init__(self, filename: str,
         self.levels = []
         nchannels = 1
         try:
-            location = parse_url(filename)
+            #location = parse_url(filename)
+            location = ZarrLocation(filename)
             if location is None:
                 raise FileNotFoundError(f'Error parsing ome-zarr file {filename}')
             reader = Reader(location)

OmeSliCC/Zarr.py

@@ -1,7 +1,8 @@
 import numpy as np
+import os.path
 import pathlib
+import shutil
 import zarr
-from zarr.store import make_store_path
 
 from OmeSliCC.image_util import *
 from OmeSliCC.ome_zarr_util import *
@@ -22,8 +23,11 @@ def create(self, source, tile_size=None, npyramid_add=0, pyramid_downsample=2, c
         self.npyramid_add = npyramid_add
         self.pyramid_downsample = pyramid_downsample
         if v3:
-            store_path = make_store_path(self.filename, mode='w')
-            self.zarr_root = zarr.Group.create(store=store_path, zarr_format=3)
+            import zarrita
+            store_path = zarrita.store.make_store_path(self.filename, mode='w')
+            if os.path.exists(self.filename):
+                shutil.rmtree(str(store_path.store.root))
+            self.zarr_root = zarr.Group.create(store=store_path)
         else:
             file_url = pathlib.Path(self.filename, mode='w').as_uri()
             self.zarr_root = zarr.open_group(store=file_url, mode='w', storage_options={'dimension_separator': '/'})
@@ -43,10 +47,13 @@ def create(self, source, tile_size=None, npyramid_add=0, pyramid_downsample=2, c
         for pathi in range(1 + npyramid_add):
             shape = calc_shape_scale(shape0, dimension_order, scale)
             if v3:
+                import zarrita
                 shape = np.array(shape).tolist()    # convert to basic int
                 tile_size = np.array(tile_size).tolist()  # convert to basic int
-                dataset = self.zarr_root.create_array(str(pathi), shape=shape, chunks=tile_size, dtype=dtype,
-                                                      compressor=compressor, codecs=compression_filters)
+                #dataset = self.zarr_root.create_array(str(pathi), shape=shape, chunks=tile_size, dtype=dtype,
+                #                                      compressor=compressor, codecs=compression_filters)
+                dataset = zarrita.Array.create(store_path / str(pathi), shape=shape, chunks=tile_size, dtype=dtype,
+                                               compressor=compressor, codecs=compression_filters)
             else:
                 dataset = self.zarr_root.create_dataset(str(pathi), shape=shape, chunks=tile_size, dtype=dtype,
                                                         compressor=compressor, filters=compression_filters)

environmentv2_3.yml

@@ -0,0 +1,31 @@
+name: omesliccv2_3_env
+channels:
+ - ome
+ - conda-forge
+ - defaults
+dependencies:
+ - python=3.10
+ - pip
+ - numpy
+ - pandas
+ - scikit-image
+ - scikit-learn
+ - imagecodecs>=2023.3.16
+ - numcodecs
+ - dask
+ - tifffile>=2023.9.26
+ - zarr==2.18
+ - ome-zarr==0.9
+ - aiohttp
+ - rsa
+ - tqdm
+ - psutil
+ - PyYAML
+ - Pillow
+ - imageio
+ - validators
+ - toml
+ - pip:
+   - opencv-python
+   - xmltodict
+   - zarrita

tests/ome_zarr_test.py

@@ -1,3 +1,4 @@
+import os.path
 import numpy as np
 from tqdm import tqdm
 
@@ -38,10 +39,12 @@ def save_zarr_v3(source, data, filename, output_params):
 
 if __name__ == '__main__':
     #filename = 'E:/Personal/Crick/slides/TCGA_KIRC/0f450938-5604-4af6-8783-c385ea647569/TCGA-A3-3358-01Z-00-DX1.1bd1c720-f6db-4837-8f83-e7476dd2b0a3.svs'
-    filename = 'E:/Personal/Crick/slides/test_images/zarr test.zarr'
+    #filename = 'E:/Personal/Crick/slides/test_images/zarr test.zarr'
+    filename = 'https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr'
     source = create_source(filename, {})
+    #source = ZarrSource(filename)
     w, h = source.get_size()
-    output_filename = 'D:/slides/test/test.ome.zarr'
+    output_filename = 'D:/slides/test/' + os.path.basename(filename)
     npyramid_add = 4
     pyramid_downsample = 2
     tile_size = 16