Fixed to writing zarr v3

OmeSliCC/OmeZarrSource.py

@@ -1,5 +1,5 @@
 import numpy as np
-from ome_zarr.io import parse_url, ZarrLocation
+from ome_zarr.io import parse_url
 from ome_zarr.reader import Reader
 
 from OmeSliCC.OmeSource import OmeSource
@@ -25,8 +25,7 @@ def __init__(self, filename: str,
         self.levels = []
         nchannels = 1
         try:
-            #location = parse_url(filename)
-            location = ZarrLocation(filename)
+            location = parse_url(filename)
             if location is None:
                 raise FileNotFoundError(f'Error parsing ome-zarr file {filename}')
             reader = Reader(location)
@@ -110,7 +109,8 @@ def _find_metadata(self):
         self.source_mag = 0
 
     def get_source_dask(self):
-        return self.levels
+        return [redimension_data(level, self.dimension_order, self.get_dimension_order())
+                for level in self.levels]
 
     def _asarray_level(self, level: int, **slicing) -> np.ndarray:
         redim = redimension_data(self.levels[level], self.dimension_order, self.get_dimension_order())

OmeSliCC/Zarr.py

@@ -24,18 +24,17 @@ def create(self, source, tile_size=None, npyramid_add=0, pyramid_downsample=2, c
         self.pyramid_downsample = pyramid_downsample
         if v3:
             import zarrita
-            store_path = zarrita.store.make_store_path(self.filename, mode='w')
+            store_path = zarrita.store.make_store_path(self.filename)
             if os.path.exists(self.filename):
                 shutil.rmtree(str(store_path.store.root))
-            self.zarr_root = zarr.Group.create(store=store_path)
+            self.zarr_root = zarrita.Group.create(store=store_path, exists_ok=True)
         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': '/'})
         xyzct = source.get_size_xyzct()
         shape0 = [xyzct['xyzct'.index(dimension)] for dimension in dimension_order]
         dtype = source.pixel_types[0]
         pixel_size_um = source.get_pixel_size_micrometer()
-        compressor, compression_filters = create_compression_filter(compression)
         scale = 1
         datasets = []
         if tile_size:
@@ -50,11 +49,11 @@ def create(self, source, tile_size=None, npyramid_add=0, pyramid_downsample=2, c
                 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 = zarrita.Array.create(store_path / str(pathi), shape=shape, chunks=tile_size, dtype=dtype,
-                                               compressor=compressor, codecs=compression_filters)
+                codecs = create_compression_codecs(compression)
+                dataset = self.zarr_root.create_array(str(pathi), shape=shape, chunk_shape=tile_size, dtype=dtype,
+                                                      codecs=codecs)
             else:
+                compressor, compression_filters = create_compression_filter(compression)
                 dataset = self.zarr_root.create_dataset(str(pathi), shape=shape, chunks=tile_size, dtype=dtype,
                                                         compressor=compressor, filters=compression_filters)
             self.data.append(dataset)
@@ -93,5 +92,6 @@ def set(self, data, x0=0, y0=0, x1=0, y1=0):
                 data1 = image_resize(data, new_size, dimension_order=self.dimension_order)
             else:
                 data1 = data
-            self.data[pathi][..., sy0:sy1, sx0:sx1] = data1
+            #self.data[pathi][..., sy0:sy1, sx0:sx1] = data1
+            self.data[pathi] = data1
             scale /= self.pyramid_downsample

OmeSliCC/image_util.py

@@ -290,6 +290,35 @@ def create_compression_filter(compression: list) -> tuple:
     return compressor, compression_filters
 
 
+def create_compression_codecs(compression: list) -> list:
+    codecs = None
+    compression = ensure_list(compression)
+    if compression is not None and len(compression) > 0:
+        compression_type = compression[0].lower()
+        if len(compression) > 1:
+            level = int(compression[1])
+        else:
+            level = None
+        if 'lzw' in compression_type:
+            from imagecodecs.numcodecs import Lzw
+            codecs = [Lzw()]
+        elif '2k' in compression_type or '2000' in compression_type:
+            from imagecodecs.numcodecs import Jpeg2k
+            codecs = [Jpeg2k(level=level)]
+        elif 'jpegls' in compression_type:
+            from imagecodecs.numcodecs import Jpegls
+            codecs = [Jpegls(level=level)]
+        elif 'jpegxr' in compression_type:
+            from imagecodecs.numcodecs import Jpegxr
+            codecs = [Jpegxr(level=level)]
+        elif 'jpegxl' in compression_type:
+            from imagecodecs.numcodecs import Jpegxl
+            codecs = [Jpegxl(level=level)]
+        else:
+            codecs = [compression]
+    return codecs
+
+
 def get_tiff_pages(tiff: TiffFile) -> list:
     pages = []
     found = False

environment_no_bioformats_omero.yml

@@ -0,0 +1,30 @@
+name: omeslicc_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
+ - ome-zarr
+ - aiohttp
+ - rsa
+ - tqdm
+ - psutil
+ - PyYAML
+ - Pillow
+ - imageio
+ - validators
+ - toml
+ - pip:
+   - opencv-python
+   - xmltodict

tests/ome_zarr_test.py

@@ -42,7 +42,6 @@ def save_zarr_v3(source, data, filename, output_params):
     #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/' + os.path.basename(filename)
     npyramid_add = 4