updates

Author: bugraoezdemir

__init__.py

@@ -16,8 +16,7 @@
 import itertools
 from pathlib import Path
 import glob, zarr
-from ome_zarr_io.ngff.multiscales import Pyramid, Multimeta
-from ome_zarr_io.base.readers import ImageReader
+from zarr_parallel_processing.multiscales import Multimeta
 from typing import Callable, Any
 from collections import defaultdict
 

convert_to_ngff.py

@@ -0,0 +1,66 @@
+
+default_axes = 'tczyx'
+
+unit_map = {
+    't': 'Frame',
+    'c': 'Channel',
+    'z': 'Slice',
+    'y': 'Pixel',
+    'x': 'Pixel'
+}
+
+scale_factor_map = {
+    't': 1,
+    'c': 1,
+    'z': 1,
+    'y': 2,
+    'x': 2
+}
+
+scale_map = {
+    't': 1,
+    'c': 1,
+    'z': 1,
+    'y': 1,
+    'x': 1
+}
+
+type_map = {
+    't': 'time',
+    'c': 'channel',
+    'z': 'space',
+    'y': 'space',
+    'x': 'space'
+}
+
+datasets_archetype = {
+                '0': {
+                    'array': None,
+                    'axis_order': None,
+                    'scale': None,
+                    'unit_list': None,
+                    'chunks': None,
+                    'dtype': None
+                },
+                '1': {
+                    'array': None,
+                    'axis_order': None,
+                    'scale': None,
+                    'unit_list': None,
+                    'chunks': None,
+                    'dtype': None
+                }
+        }
+
+NotMultiscalesException = Exception('Not applicable as this group is not a single image or label.')
+NotImageException = Exception('Not applicable as this group is not an image.')
+AxisNotFoundException = Exception('Axis information not provided in the metadata.')
+
+TempDir = '/tmp/OME-Zarr'
+
+refpath = '0'
+
+rechunker_maxmem = '1G'
+
+array_meta_keys = ['chunks', 'shape', 'compressor', 'dtype', 'dimension_separator']
+