Removed deprecated input format arg, simplify format error message, simplify zarr color conversion, generalise well test

Author: folterj

converter.py

@@ -122,10 +122,6 @@ def _convert_single(input_filename, output_folder, alt_output_folder=None,
     writer, output_ext = create_writer(output_format, verbose=verbose)
 
     source.init_metadata()
-    if verbose:
-        total_size = print_hbytes(source.get_total_data_size())
-        print(f'Total data size:    {total_size}')
-
     name = source.get_name()
 
     # For Incucyte sources with plates, organize output in subfolders

src/helper.py

@@ -1,13 +1,12 @@
 import os.path
 
 
-def create_source(filename, input_format=None, **kwargs):
+def create_source(filename, **kwargs):
     """
     Create an image source object based on the input file extension.
 
     Args:
         filename (str): Path to the input file or Incucyte .icarch file.
-        input_format (str, optional): Deprecated - format is auto-detected.
         **kwargs: Source-specific parameters (e.g., plate_id for Incucyte).
 
     Returns:
@@ -48,10 +47,7 @@ def create_source(filename, input_format=None, **kwargs):
         from src.TiffSource import TiffSource
         source = TiffSource(filename)
     else:
-        raise ValueError(
-            f'Unsupported input file format: {input_ext}. '
-            f'Supported formats: .db, .icarch, .tif, .tiff'
-        )
+        raise ValueError(f'Unsupported input file format: {input_ext}')
     return source
 
 

src/ome_zarr_util.py

@@ -98,12 +98,7 @@ def create_channel_metadata(dtype, channels, nchannels, is_rgb, window, ome_vers
         omezarr_channel = {'label': channel.get('label', channel.get('Name', f'{channeli}')), 'active': True}
         color = channel.get('color', channel.get('Color'))
         if color is not None:
-            # If color is already a hex string, use it directly
-            if isinstance(color, str):
-                omezarr_channel['color'] = color.lstrip('#').upper()
-            else:
-                # Otherwise convert from RGBA tuple
-                omezarr_channel['color'] = rgba_to_hexrgb(color)
+            omezarr_channel['color'] = rgba_to_hexrgb(color)
         if dtype.kind == 'f':
             min, max = 0, 1
         else:

test/test_convert.py

@@ -82,7 +82,7 @@ def test_convert(self, tmp_path, input_filename, output_format, alt_output_folde
         assert pixel_size.get('x') == source_pixel_size.get('x')
         assert pixel_size.get('y') == source_pixel_size.get('y')
         if source.is_screen():
-            assert wells == source_wells
+            assert list(wells) == list(source_wells)
 
 
 if __name__ == '__main__':