Write ome-ngff metadata to .zattrs

yuriyzubov · Jan 16, 2025 · b660f44 · b660f44
1 parent ec08282
commit b660f44
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Showing 8 changed files with 98 additions and 423 deletions.
diff --git a/src/conversion_lib.py b/src/conversion_lib.py
diff --git a/src/n5_attrs_template.json b/src/n5_attrs_template.json
diff --git a/src/tif_to_zarr.py b/src/tif_to_zarr.py
diff --git a/src/tiff_stack.py b/src/tiff_stack.py
@@ -7,28 +7,37 @@
 import dask.array as da
 from natsort import natsorted
 from glob import glob
+from tiff_volume import TiffVolume
 
-class TiffStack():
+class TiffStack(TiffVolume):
 
     def __init__(self,
-                src_path: str):
+                src_path: str,
+                axes : list[str],
+                scale : list[float],
+                translation : list[float],
+                units : list[str]):
         """Construct all the necessary attributes for the proper conversion of tiff to OME-NGFF Zarr.
 
         Args:
             input_filepath (str): path to source tiff file.
         """
-        self.input_filepath = src_path
-
-
+        self.src_path = src_path
         self.stack_list = natsorted(glob(os.path.join(src_path, '*.tif*')))
         probe_image_store = imread(os.path.join(src_path, self.stack_list[0]), aszarr=True)
         probe_image_arr = da.from_zarr(probe_image_store)
 
         self.dtype = probe_image_arr.dtype
         self.shape =  [len(self.stack_list)] + list(probe_image_arr.shape)
-
-
-
+
+        #metadata
+        self.zarr_metadata = {
+            "axes": axes,
+            "translation": translation,
+            "scale": scale,
+            "units": units,
+        }
+
     def write_tile_slab_to_zarr(self,
                             chunk_num : int,
                             zarray : zarr.Array,
@@ -52,16 +61,16 @@ def write_tile_slab_to_zarr(self,
                 print(f'Tiff tile with index {slab_index} is not present in tiff stack.')
             np_slab[slab_index - chunk_num, :, :] = image_tile
 
-        # write a tiff stack slab into zarr array        
+        # write a tiff stack slab into a zarr array        
         zarray[chunk_num : chunk_num+ zarray.chunks[0], :, :] = np_slab
 
 
 
     #parallel writing of tiff stack into zarr array
     def write_to_zarr(self,
-                            zarray : zarr.Group,
-                            client : Client
-                            ):
+                        zarray : zarr.Array,
+                        client : Client
+                        ):
         chunks_list = np.arange(0, zarray.shape[0], zarray.chunks[0])
         print(chunks_list)