added convert options to command line

qim3d/io/convert.py

@@ -184,13 +184,14 @@ class Convert:
         save(nifti_path, z, compression=compression)
 
 
-def convert(input_path: str, output_path: str, chunk_shape: tuple = (64, 64, 64)):
+def convert(input_path: str, output_path: str, chunk_shape: tuple = (64, 64, 64), base_name: str = None):
     """Convert a file to another format without loading the entire file into memory
 
     Args:
         input_path (str): path to the input file
         output_path (str): path to the output file
         chunk_shape (tuple, optional): chunk size for the zarr file. Defaults to (64, 64, 64).
+        base_name (str, optional): base name for the tiff stack. Defaults to None.
     """
-    converter = Convert(chunk_shape=chunk_shape)
+    converter = Convert(chunk_shape=chunk_shape,base_name=base_name)
     converter.convert(input_path, output_path)

qim3d/utils/cli.py

@@ -84,6 +84,8 @@ def main():
     preview_parser = subparsers.add_parser('convert', help= 'Convert files to different formats without loading the entire file into memory')
     preview_parser.add_argument('input_path',type = str, metavar = 'Input path', help = 'Path to image that will be converted')
     preview_parser.add_argument('output_path',type = str, metavar = 'Output path', help = 'Path to save converted image')
+    preview_parser.add_argument('chunk_shape',type = tuple, metavar = 'Chunk shape', help = 'Chunk size for the zarr file', default = (64,64,64))
+    preview_parser.add_argument('base_name',type = str, metavar = 'Base name', help = 'Base name for the zarr file', default = None)
 
     args = parser.parse_args()
 
@@ -171,7 +173,7 @@ def main():
         print("\n")
 
     elif args.subcommand == 'convert':
-        qim3d.io.convert(args.input_path, args.output_path)
+        qim3d.io.convert(args.input_path, args.output_path, args.chunk_shape, args.base_name)
 
 
 if __name__ == "__main__":