Black formatting

yuriyzubov · Oct 25, 2024 · 5fe4953 · 5fe4953
1 parent b2b0fb9
commit 5fe4953
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Showing 3 changed files with 22 additions and 39 deletions.
diff --git a/tif_to_zarr/conversion_lib.py b/tif_to_zarr/conversion_lib.py
@@ -1,4 +1,5 @@
 """This module contains the Conversion class used to convert tiff file to OME-NGFF Zarr (contains chunked array)."""
+
 import dask.array as da
 import numpy as np
 from tifffile import imwrite, TiffFile
@@ -11,15 +12,15 @@
 
 class Conversion:
     """A class used to convert tiff file to zarr array with properly formatted OME-NGFF metadata."""
-    
+
     def __init__(
         self,
-        input_filepath : str,
-        output_filepath : str,
-        axes : List[str],
-        translation : List[float],
-        scale : List[float],
-        units : List[str]
+        input_filepath: str,
+        output_filepath: str,
+        axes: List[str],
+        translation: List[float],
+        scale: List[float],
+        units: List[str],
     ):
         """Construct all the necessary attributes for the proper conversion of tiff to OME-NGFF Zarr.
 
@@ -40,12 +41,11 @@ def __init__(
             "units": units,
         }
 
-
     def read_tiff(self):
         """Read tiff file and store array, axes and metadata in a dictionary.
 
         Returns:
-            [numpy.array, [str], dict]: returns tiff image as numpy array object, axis naming and order, and imagej style metadata. 
+            [numpy.array, [str], dict]: returns tiff image as numpy array object, axis naming and order, and imagej style metadata.
         """
         try:
             with TiffFile(self.input_filepath) as tiff:
@@ -60,11 +60,11 @@ def read_tiff(self):
             sys.exit(1)
         return [volume_numpy, axes, imagej_metadata]
 
-    def dask_to_zarray(self, tiff_data : List, chunks : List):
+    def dask_to_zarray(self, tiff_data: List, chunks: List):
         """Store dask array in a zarr file.
 
         Args:
-            tiff_data (List): a list containing tiff image as numpy array object, axis naming and order, and imagej style metadata. 
+            tiff_data (List): a list containing tiff image as numpy array object, axis naming and order, and imagej style metadata.
             chunks (List): what chunk size to use for output zarr array
         """
         # create root group
@@ -95,7 +95,7 @@ def numpy_to_zarray(self, tiff_data, chunks):
         """Store numpy array in a zarr file.
 
         Args:
-            tiff_data (List): a list containing tiff image as numpy array object, axis naming and order, and imagej style metadata. 
+            tiff_data (List): a list containing tiff image as numpy array object, axis naming and order, and imagej style metadata.
             chunks (List): what chunk size to use for output zarr array
         """
         # create root group

diff --git a/tif_to_zarr/n5_attrs_template.json b/tif_to_zarr/n5_attrs_template.json
@@ -1,21 +1,9 @@
 {
-    "axes": [
-        "x",
-        "y",
-        "z"
-    ],
-    "multiscales": [
-        {
-            "datasets": [
-
-            ],
-            "name": "em/fibsem-uint8"
-        }
-    ],
-
-"pixelResolution":{"dimensions":[0.0,0.0,0.0],"unit":"nm"},
-"ordering":"C",
-"scales":[],
-"units":["nm","nm","nm"],
-"translate":[0,0,0]
+    "axes": ["x", "y", "z"],
+    "multiscales": [{"datasets": [], "name": "em/fibsem-uint8"}],
+    "pixelResolution": {"dimensions": [0.0, 0.0, 0.0], "unit": "nm"},
+    "ordering": "C",
+    "scales": [],
+    "units": ["nm", "nm", "nm"],
+    "translate": [0, 0, 0]
 }
diff --git a/tif_to_zarr/zarr_attrs_template.json b/tif_to_zarr/zarr_attrs_template.json
@@ -4,13 +4,8 @@
             "version": "",
             "name": "",
             "axes": [],
-            "datasets": [
-
-            ],
-            "coordinateTransformations": [
-
-            ]
-
+            "datasets": [],
+            "coordinateTransformations": []
         }
     ]
-}
+}