Small fixes, unify style for script arguments

Author: schilling40

flamingo_tools/segmentation/unet_prediction.py

@@ -295,7 +295,7 @@ def calc_mean_and_std(input_path: str, input_key: str, output_folder: str) -> No
     mean, std = parallel.mean_and_std(
         input_, block_shape=tuple([2 * i for i in chunks]), n_threads=n_threads, verbose=True, mask=image_mask
     )
-    ddict = {"mean": mean, "std": std}
+    ddict = {"mean": float(mean), "std": float(std)}
     with open(json_file, "w") as f:
         json.dump(ddict, f)
 
@@ -369,9 +369,9 @@ def run_unet_prediction_preprocess_slurm(
         )
 
     if not os.path.isdir(os.path.join(output_folder, "mask.zarr")):
-        find_mask(input_path, input_key, output_folder, s3=s3)
+        find_mask(input_path, input_key, output_folder)
 
-    calc_mean_and_std(input_path, input_key, output_folder, s3=s3)
+    calc_mean_and_std(input_path, input_key, output_folder)
 
 
 def run_unet_prediction_slurm(
@@ -420,7 +420,7 @@ def run_unet_prediction_slurm(
         raise ValueError("The SLURM_ARRAY_TASK_ID is not set. Ensure that you are using the '-a' option with SBATCH.")
 
     if not os.path.isdir(os.path.join(output_folder, "mask.zarr")):
-        find_mask(input_path, input_key, output_folder, s3=s3)
+        find_mask(input_path, input_key, output_folder)
 
     # get pre-computed mean and standard deviation of full volume from JSON file
     if os.path.isfile(os.path.join(output_folder, "mean_std.json")):

scripts/convert_tif_to_n5.py

@@ -19,9 +19,8 @@ def main(input_path: str, output_path: str = None) -> None:
     if input_path.split(".")[-1] not in ["TIFF", "TIF", "tiff", "tif"]:
         sys.exit("Input file must be in tif format.")
 
-    basename = "".join(input_path.split("/")[-1].split(".")[:-1])
-    input_dir = input_path.split(basename)[0]
-    input_dir = os.path.abspath(input_dir)
+    basename = ".".join(input_path.split("/")[-1].split(".")[:-1])
+    input_dir = os.path.abspath(input_path).split(basename)[0]
 
     if output_path is None:
         output_path = os.path.join(input_dir, basename + ".n5")

scripts/resize_wrongly_scaled_cochleas.py

@@ -14,7 +14,7 @@
 
 def main(
         input_path: str,
-        output_folder: str,
+        output_dir: str = None,
         scale: float = 0.38,
         input_key: str = "setup0/timepoint0/s0",
         interpolation_order: int = 3
@@ -23,7 +23,7 @@ def main(
 
     Args:
         input_path: Input path to tif file or n5 folder.
-        output_folder: Output folder for rescaled data in n5 format.
+        output_dir: Output folder for rescaled data in n5 format.
         scale: Scale of output data.
         input_key: The key / internal path of the image data.
         interpolation_order: Interpolation order for resizing function.
@@ -36,8 +36,13 @@ def main(
         input_chunks = input_.chunks
 
     abs_path = os.path.abspath(input_path)
-    basename = "".join(os.path.basename(abs_path).split(".")[:-1])
-    output_path = os.path.join(output_folder, basename + "_resized.n5")
+    basename = ".".join(os.path.basename(abs_path).split(".")[:-1])
+    input_dir = os.path.abspath(input_path).split(basename)[0]
+
+    if output_dir is None:
+        output_path = os.path.join(input_dir, basename + "_resized.n5")
+    else:
+        output_path = os.path.abspath(output_dir)
 
     shape = input_.shape
     ndim = len(shape)
@@ -78,15 +83,14 @@ def copy_chunk(block_index):
     parser = argparse.ArgumentParser(
         description="Script for resizing microscoopy data in n5 format.")
 
-    parser.add_argument("input_file", type=str, required=True, help="Input tif file or n5 folder.")
-    parser.add_argument(
-        "output_folder", type=str, help="Output folder. Default resized output is '<basename>_resized.n5'."
-    )
+    parser.add_argument("-i", "--input", required=True, type=str, help="Input tif file or n5 folder.")
+    parser.add_argument("-o", "--output", type=str,
+                        help="Output n5 folder. Default resized output is '<basename>_resized.n5'.")
 
     parser.add_argument("-s", "--scale", type=float, default=0.38, help="Scale of input. Re-scaled to 1.")
     parser.add_argument("-k", "--input_key", type=str, default="setup0/timepoint0/s0", help="Input key for n5 file.")
-    parser.add_argument("-i", "--interpolation_order", type=float, default=3, help="Interpolation order.")
+    parser.add_argument("--interpolation_order", type=float, default=3, help="Interpolation order.")
 
     args = parser.parse_args()
 
-    main(args.input_file, args.output_folder, args.scale, args.input_key, args.interpolation_order)
+    main(args.input, args.output, args.scale, args.input_key, args.interpolation_order)