refactor(process_pipeline): use filename without extension for TIFF output

This change extracts the base file name without its extension when creating TIFF output files. Previously, the full file path with an extension was used, which could lead to redundant extensions in output filenames. This update ensures clearer and more concise naming conventions for generated files.

process_pipeline.py

@@ -78,6 +78,9 @@ def process_czi_file(file_path, config):
     x_idx = dims.index('X')
     y_idx = dims.index('Y')
 
+    # Extract the file name without the extension
+    input_filename = os.path.splitext(os.path.basename(file_path))[0]
+
     num_series = len(czi.get_dims_shape())
     print(f"Number of detected series (S): {num_series}")
 
@@ -128,7 +131,7 @@ def process_czi_file(file_path, config):
             mosaic_image[pos_y:pos_y + height, pos_x:pos_x + width] = tile[0, 0, 0, 0, :, :, 1]
 
         # Save the assembled mosaic as a TIFF with a series suffix
-        output_filename = os.path.join(config['output_dir'], f"{os.path.basename(file_path)}_series_{s}.tif")
+        output_filename = os.path.join(config['output_dir'], f"{input_filename}_series_{s}.tif")
         tiff.imwrite(output_filename, mosaic_image, compression=config['compression'])
 
         print(f"Generated TIFF for series {s}: {output_filename}")