fix parameter updates to patch dataset

mu_map/dataset/patches.py

@@ -37,6 +37,7 @@ class MuMapPatchDataset(MuMapDataset):
         self.patches_per_image = patches_per_image
         self.patch_size = patch_size
         self.patch_size_z = patch_size_z
+        self.patch_offset = patch_offset
         self.shuffle = shuffle
 
         self.patches = []
@@ -57,8 +58,14 @@ class MuMapPatchDataset(MuMapDataset):
             z_range = (0, max(recon.shape[0] - self.patch_size_z, 0))
             # sometimes the mu_maps have fewer than 32 slices
             # in this case the z-axis will be padded to the patch size, but this means we only have a single option for z
-            y_range = (20, recon.shape[1] - self.patch_size - 20)
-            x_range = (20, recon.shape[2] - self.patch_size - 20)
+            y_range = (
+                self.patch_offset,
+                recon.shape[1] - self.patch_size - self.patch_offset,
+            )
+            x_range = (
+                self.patch_offset,
+                recon.shape[2] - self.patch_size - self.patch_offset,
+            )
 
             # compute padding for z axis
             padding = [0, 0, 0, 0, 0, 0, 0, 0]
@@ -103,27 +110,44 @@ if __name__ == "__main__":
     from mu_map.util import to_grayscale, grayscale_to_rgb
 
     param_keys = list(MuMapPatchDataset.__init__.__annotations__.keys())[1:]
-    param_defaults = MuMapPatchDataset.__init__.__defaults__[1:]
+    param_defaults = MuMapPatchDataset.__init__.__defaults__
+    param_help = [
+        "number of patches for each image",
+        "patch size in x- and y-direction",
+        "patch size in z-direction",
+        "offset to ignore image borders",
+        "shuffle the dataset",
+    ]
 
     parser = argparse.ArgumentParser(
-        help="Visualize the patches in a MuMapPatchDataset",
+        description="Visualize the patches in a MuMapPatchDataset",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
     )
     parser.add_argument(
-        "dataset_dir",
+        "--dataset_dir",
         type=str,
-        defaul="data/initial/",
+        default="data/initial/",
         help="the directory of the dataset",
     )
-    for key, _default in zip(param_keys, param_defaults):
-        parser.add_argument(f"--{key}", type=type(_default), default=_default)
+    for key, _default, _help in zip(param_keys, param_defaults, param_help):
+        parser.add_argument(
+            f"--{key}", type=type(_default), default=_default, help=_help
+        )
     args = parser.parse_args()
+    print(args)
 
     wname = "Dataset"
     cv.namedWindow(wname, cv.WINDOW_NORMAL)
     cv.resizeWindow(wname, 1600, 900)
 
-    dataset = MuMapPatchDataset("data/initial/", patches_per_image=1)
+    dataset = MuMapPatchDataset(
+        "data/initial/",
+        patches_per_image=args.patches_per_image,
+        patch_size=args.patch_size,
+        patch_size_z=args.patch_size_z,
+        patch_offset=args.patch_offset,
+        shuffle=args.shuffle,
+    )
 
     print(f"Images (Patches) in the dataset {len(dataset)}")