format and comment interfile module

mu_map/file/interfile.py

@@ -58,6 +58,7 @@ class Interfile:
     Interfile data type wrapping the header and the image
     into an object.
     """
+
     header: Dict[str, str]
     image: np.ndarray
 
@@ -70,6 +71,7 @@ class _InterfileKeys:
     """
     Data class defining keys for an Interfile header.
     """
+
     placeholder: str = "{_}"
 
     _dim: str = f"matrix size [{placeholder}]"
@@ -88,6 +90,8 @@ class _InterfileKeys:
 
     def spacing(self, index: int) -> str:
         return self._spacing.replace(self.placeholder, str(index))
+
+
 InterfileKeys = _InterfileKeys()
 
 
@@ -103,7 +107,9 @@ def type_by_format(number_format: str, bytes_per_pixel: int) -> type:
     if number_format == "float" and bytes_per_pixel == 4:
         return np.float32
 
-    raise ValueError("Unknown mapping from format {number_format} with {bytes_per_pixel} bytes to numpy type")
+    raise ValueError(
+        "Unknown mapping from format {number_format} with {bytes_per_pixel} bytes to numpy type"
+    )
 
 
 def parse_interfile_header_str(header: str) -> Dict[str, str]:
@@ -139,13 +145,17 @@ def load_interfile(filename: str) -> Interfile:
     Load an INTERFILE header and its image as a numpy array.
 
     :param filename: the filename of the INTERFILE header file
-    :return: the header as a dict and the image as a numpy array
+    :return: the interfile image
     """
     header = parse_interfile_header(filename)
 
     dim_x = int(header[InterfileKeys.dim(1)])
     dim_y = int(header[InterfileKeys.dim(2)])
-    dim_z = int(header[InterfileKeys.dim(3)]) if InterfileKeys.dim(3) in header else int(header[InterfileKeys.n_projections])
+    dim_z = (
+        int(header[InterfileKeys.dim(3)])
+        if InterfileKeys.dim(3) in header
+        else int(header[InterfileKeys.n_projections])
+    )
 
     bytes_per_pixel = int(header[InterfileKeys.bytes_per_pixel])
     num_format = header[InterfileKeys.number_format]
@@ -170,6 +180,16 @@ def load_interfile_img(filename: str) -> np.ndarray:
 
 
 def write_interfile(filename: str, interfile: Interfile):
+    """
+    Write an interfile image.
+    Note that custom extensions to the filename are removed and the defaults
+    from this module are used (.hv for the header and .v for the image).
+    This method also sanitizes the header by making sure that
+    dimensions match the image.
+
+    :param filename: the filename where the interfile image is written to
+    :param interfile: the interfile saved
+    """
     filename = os.path.splitext(filename)[0]
     filename_data = f"{filename}{EXTENSION_INTERFILE_IMAGE}"
     filename_header = f"{filename}{EXTENSION_INTERFILE_HEADER}"
@@ -195,11 +215,29 @@ if __name__ == "__main__":
     import argparse
     import math
 
-    parser = argparse.ArgumentParser(description="Modify an interfile image")
-    parser.add_argument("--interfile", type=str, required=True, help="the interfile input")
-    parser.add_argument("--out", type=str, help="the interfile output - if not set the input file will be overwritte")
-    parser.add_argument("--cmd", choices=["fill", "crop", "pad", "flip"], help="the modification to perform")
-    parser.add_argument("--param", type=int, required=True, help="the parameters for the modification [fill: value, crop & pad: target size of z dimension]")
+    parser = argparse.ArgumentParser(
+        description="Modify an interfile image",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+    parser.add_argument(
+        "--interfile", type=str, required=True, help="the interfile input"
+    )
+    parser.add_argument(
+        "--out",
+        type=str,
+        help="the interfile output - if not set the input file will be overwritte",
+    )
+    parser.add_argument(
+        "--cmd",
+        choices=["fill", "crop", "pad", "flip"],
+        help="the modification to perform",
+    )
+    parser.add_argument(
+        "--param",
+        type=int,
+        required=True,
+        help="the parameters for the modification [fill: value, crop & pad: target size of z dimension]",
+    )
     args = parser.parse_args()
     args.out = args.interfile if args.out is None else args.out
 
@@ -211,16 +249,22 @@ if __name__ == "__main__":
     if args.cmd == "pad":
         target_size = args.param
         real_size = interfile.image.shape[0]
-        assert target_size > real_size, f"Cannot pad from a larger size {real_size} to a smaller size {target_size}"
+        assert (
+            target_size > real_size
+        ), f"Cannot pad from a larger size {real_size} to a smaller size {target_size}"
 
         diff = target_size - real_size
         pad_lower = math.ceil(diff / 2)
         pad_upper = math.floor(diff / 2)
-        interfile.image = np.pad(interfile.image, ((pad_lower, pad_upper), (0, 0), (0, 0)))
+        interfile.image = np.pad(
+            interfile.image, ((pad_lower, pad_upper), (0, 0), (0, 0))
+        )
     if args.cmd == "crop":
         target_size = args.param
         real_size = interfile.image.shape[0]
-        assert target_size < real_size, f"Cannot crop from a smaller size {real_size} to a larger size {target_size}"
+        assert (
+            target_size < real_size
+        ), f"Cannot crop from a smaller size {real_size} to a larger size {target_size}"
 
         diff = target_size / 2
         center = real_size // 2
@@ -231,7 +275,3 @@ if __name__ == "__main__":
         interfile.image = interfile.image[:, :, ::-1]
 
     write_interfile(args.out, interfile)
-
-
-
-