[WIP] Fix out_path argument and describe TOOLPATH pointing location (#135)

* Fix out_path argument and describe TOOLPATH pointing location

Signed-off-by: Gabriel Ziegler <[email protected]>

* Standardize arguments in examples to output_path

Signed-off-by: Gabriel Ziegler <[email protected]>

Author: gabrielziegler3

fastmri_examples/cs/README.md

@@ -12,14 +12,15 @@ which was used as a baseline model in
 The implementation uses the BART toolkit. To install BART, please follow the
 [installation instructions][bartlink].
 
-Once BART is installed, set the `TOOLBOX_PATH` environment variable and point
-`PYTHONPATH` to the python wrapper for BART:
+Once BART is installed, set the `TOOLBOX_PATH` environment variable to point to the location where the repo was cloned and `PYTHONPATH` to the python wrapper for BART:
 
 ```bash
 export TOOLBOX_PATH=/path/to/bart
 export PYTHONPATH=${TOOLBOX_PATH}/python:${PYTHONPATH}
 ```
 
+where `/path/to/bart` is the path to the cloned BART repository, not your OS installed BART program.
+
 To run the reconstruction algorithm on the validation data, run:
 
 ```bash

fastmri_examples/cs/run_bart.py

@@ -191,7 +191,7 @@ def run_bart(args):
             time_taken = time.perf_counter() - start_time
 
     logging.info(f"Run Time = {time_taken:} s")
-    save_outputs(outputs, args.out_path)
+    save_outputs(outputs, args.output_path)
 
 
 def create_arg_parser():
@@ -204,7 +204,7 @@ def create_arg_parser():
         help="Path to the data",
     )
     parser.add_argument(
-        "--out_path",
+        "--output_path",
         type=pathlib.Path,
         required=True,
         help="Path to save the reconstructions to",

fastmri_examples/zero_filled/README.md

@@ -10,7 +10,7 @@ To generate the zero-filled submissions, run:
 python run_zero_filled.py \
     --challenge CHALLENGE \
     --data_path DATA \
-    --out_path RECONS
+    --output_path RECONS
 ```
 
 where `CHALLENGE` is either `singlecoil` or `multicoil`.

fastmri_examples/zero_filled/run_zero_filled.py

@@ -63,7 +63,7 @@ def create_arg_parser():
         help="Path to the data",
     )
     parser.add_argument(
-        "--out_path",
+        "--output_path",
         type=Path,
         required=True,
         help="Path to save the reconstructions to",
@@ -80,4 +80,4 @@ def create_arg_parser():
 
 if __name__ == "__main__":
     args = create_arg_parser().parse_args()
-    save_zero_filled(args.data_path, args.out_path, args.challenge)
+    save_zero_filled(args.data_path, args.output_path, args.challenge)