148 exception fail fast

docker/bidsapp/run.py

@@ -158,6 +158,38 @@ def check_and_return_valid_nb_of_cores(openmp_nb_of_cores, nipype_nb_of_cores, o
     return openmp_nb_of_cores, nipype_nb_of_cores
 
 
+def check_participants_params(participants_params):
+    """Check the participants_params input json to see
+    if the custom_interfaces have only allowed keys, i.e.
+    keys that are used somewhere in mialsrtk.
+
+    Parameters
+    ----------
+    pariticipants_params: dict
+        A dictionary corresponding to the json config file.
+    """
+    allowed_keys = [
+        "skip_svr",
+        "do_refine_hr_mask",
+        "do_nlm_denoising",
+        "skip_stacks_ordering",
+        "do_reconstruct_labels",
+        "do_anat_orientation",
+        "do_multi_parameters",
+        "do_srr_assessment"
+        ]
+    for sub, sub_list in participants_params.items():
+        for config in sub_list:
+            if "custom_interfaces" in config.keys():
+                for k in config["custom_interfaces"].keys():
+                    if k not in allowed_keys:
+                        raise RuntimeError(
+                            f"Invalid custom interface key {k} for subject "
+                            f"{sub}. Valid keys are \n" +
+                            ", ".join(allowed_keys)
+                            )
+
+
 def main(bids_dir, output_dir,
          subject,
          session,
@@ -170,6 +202,7 @@ def main(bids_dir, output_dir,
          labels_derivatives_dir='',
          masks_desc=None,
          dict_custom_interfaces=None,
+         verbose=None,
          nipype_number_of_cores=1,
          openmp_number_of_cores=1,
          memory=0
@@ -241,7 +274,6 @@ def main(bids_dir, output_dir,
 
     if sr_id is None:
         sr_id = 1
-
     # Initialize an instance of AnatomicalPipeline
     if run_type == "sr":
         pipeline = SRReconPipeline(
@@ -257,6 +289,7 @@ def main(bids_dir, output_dir,
             labels_derivatives_dir,
             masks_desc,
             p_dict_custom_interfaces=dict_custom_interfaces,
+            p_verbose=verbose,
             p_openmp_number_of_cores=openmp_number_of_cores,
             p_nipype_number_of_cores=nipype_number_of_cores
             )
@@ -272,6 +305,7 @@ def main(bids_dir, output_dir,
             masks_derivatives_dir,
             masks_desc,
             p_dict_custom_interfaces=dict_custom_interfaces,
+            p_verbose=verbose,
             p_openmp_number_of_cores=openmp_number_of_cores,
             p_nipype_number_of_cores=nipype_number_of_cores,
             )
@@ -307,28 +341,29 @@ def main(bids_dir, output_dir,
     print("INFO: Environment variable OMP_NUM_THREADS set to: "
           "{}".format(os.environ["OMP_NUM_THREADS"]))
 
-    print(args.param_file)
-    with open(args.param_file, "r") as f:
+    with open(args.param_file, 'r') as f:
         participants_params = json.load(f)
-        print(participants_params)
-        print(participants_params.keys())
-    print()
-
+    check_participants_params(participants_params)
     subjects_to_analyze = []
     # only for a subset of subjects
     if args.participant_label:
         subjects_to_analyze = args.participant_label
     # for all subjects
     else:
         subject_dirs = glob(os.path.join(args.bids_dir, "sub-*"))
-        subjects_to_analyze = [
+        subjects_to_analyze = sorted([
             subject_dir.split("-")[-1] for subject_dir in subject_dirs
-        ]
+        ])
+    success_dict = {}
+    failed_dict = {}
 
     for sub in subjects_to_analyze:
+        success_dict[sub] = []
+        failed_dict[sub] = []
         if sub in participants_params.keys():
 
             sr_list = participants_params[sub]
+            print(f"Processing subject {sub}.")
             print(sr_list)
 
             for sr_params in sr_list:
@@ -349,29 +384,57 @@ def main(bids_dir, output_dir,
                     if "custom_interfaces" in sr_params.keys() else None
 
                 if sr_id is None:
-                    print(f"WARNING: Do not process subjects {sub} "
-                          "because of missing parameters.")
+                    e = f'Subject {sub} was not processed ' \
+                        f'because of missing parameters.'
+                    failed_dict[sub] += [e]
+                    print(e)
                     continue
-
-                res = main(bids_dir=args.bids_dir,
-                           output_dir=args.output_dir,
-                           subject=sub,
-                           session=ses,
-                           run_type=args.run_type,
-                           p_ga=ga,
-                           p_stacks=stacks,
-                           param_TV=param_TV,
-                           sr_id=sr_id,
-                           masks_derivatives_dir=args.masks_derivatives_dir,
-                           labels_derivatives_dir=args.labels_derivatives_dir,
-                           masks_desc=masks_desc,
-                           dict_custom_interfaces=dict_custom_interfaces,
-                           nipype_number_of_cores=nipype_nb_of_cores,
-                           openmp_number_of_cores=openmp_nb_of_cores,
-                           memory=args.memory
-                           )
+                try:
+                    res = main(
+                        bids_dir=args.bids_dir,
+                        output_dir=args.output_dir,
+                        subject=sub,
+                        session=ses,
+                        run_type=args.run_type,
+                        p_ga=ga,
+                        p_stacks=stacks,
+                        param_TV=param_TV,
+                        sr_id=sr_id,
+                        masks_derivatives_dir=args.masks_derivatives_dir,
+                        labels_derivatives_dir=args.labels_derivatives_dir,
+                        masks_desc=masks_desc,
+                        dict_custom_interfaces=dict_custom_interfaces,
+                        verbose=args.verbose,
+                        nipype_number_of_cores=nipype_nb_of_cores,
+                        openmp_number_of_cores=openmp_nb_of_cores,
+                        memory=args.memory
+                        )
+                    out = f"Subject {sub} with parameters {sr_params} " \
+                          f"succeeded."
+                    success_dict[sub] += [out]
+                except Exception as e:
+                    e = f"Subject {sub} with parameters {sr_params} failed "\
+                        f"with message \n\t {e}"
+                    failed_dict[sub] += [e]
+                    print(e)
         else:
-            print(f"WARNING: Do not process subjects {sub} "
-                  "because of missing configuration.")
+            e = f"Subject {sub} was not processed because of missing "\
+                f"configuration."
+            failed_dict[sub] += [e]
+            print(e)
+
+    if not all(v == [] for v in success_dict.values()):
+        print("\n" + "-"*15 + "\nSUCCESSFUL RUNS\n" +
+              "-"*15)
+        for sub, v in success_dict.items():
+            for out in v:
+                print("-> ", out)
+
+    if not all(v == [] for v in failed_dict.values()):
+        print("\n" + "-"*24 + "\nWARNING: SOME RUN FAILED\n" +
+              "-"*24)
+        for sub, v in failed_dict.items():
+            for error in v:
+                print("-> ", error)
 
     sys.exit(0)

documentation/usage.rst

@@ -70,9 +70,9 @@ where:
     * ``"session"`` (optional) It MUST be specified if you have a BIDS dataset composed of multiple sessions with the *sub-XX/ses-YY* structure.
 
     * ``"ga"`` (optional but mandatory when ``do_anat_orientation`` is true) subject's gestational age in weeks.
-
+    
     * ``"run_type"`` (optional): defines the type of run that should be done. It can be set between `sr` (super-resolution) and `preprocessing` (preprocessing-only). (default is ``"sr"``)
-
+    
     * ``"custom_interfaces"`` (optional): indicates weither optional interfaces of the pipeline should be performed.
 
         * ``"skip_svr"`` (optional) the Slice-to-Volume Registration should be skipped in the image reconstruction. (default is False)
@@ -89,7 +89,13 @@ where:
         If True, path to a directory containing STA atlas (Gholipour et al., 2017 [1]_, [2]_) must be mounted to `/sta`.
 
         * ``"preproc_do_registration"`` (optional) indicates whether the Slice-to-Volume Registration should be computed in the ``"preprocessing"`` run (default is False).
+
+        * ``"do_multi_parameters"`` (optional) enables running the super-resolution reconstruction with lists of parameters. The algorithm will
+        then run a grid search over all combinations of parameters. (default is False)
 
+        * ``"do_srr_assessment"`` (optional) enables comparing the quality of the super-resolution reconstruction with a reference image. (default is False)
+        If True, it will require a reference isotropic T2w image, mask and labels located in the data folder.
+
 References
 ----------
 .. [1] Gholipour et al.; A normative spatiotemporal MRI atlas of the fetal brain for automatic segmentation and analysis of early brain growth, Scientific Reports 7, Article number: 476 (2017). `(link to article)<http://www.nature.com/articles/s41598-017-00525-w>`_ .

pymialsrtk/cli/mialsuperresolutiontoolkit_docker.py

@@ -107,14 +107,8 @@ def main():
         tracker.start()
 
     # Execute the docker run command
-    try:
-        print(f'... cmd: {cmd}')
-        run(cmd)
-        exit_code = 0
-    except Exception as e:
-        print('Failed')
-        print(e)
-        exit_code = 1
+    print(f'... cmd: {cmd}')
+    run(cmd)
 
     if args.track_carbon_footprint:
         emissions: float = tracker.stop()
@@ -139,7 +133,7 @@ def main():
         print("Results can be visualized with the codecarbon visualization tool using following command:\n")
         print(f'\t$ carbonboard --filepath="{args.bids_dir}/code/emissions.csv" --port=9999\n')
 
-    return exit_code
+    return 0
 
 
 if __name__ == '__main__':

pymialsrtk/cli/mialsuperresolutiontoolkit_singularity.py

@@ -106,14 +106,8 @@ def main():
         tracker.start()
 
     # Execute the singularity run command
-    try:
-        print(f'... cmd: {cmd}')
-        run(cmd)
-        exit_code = 0
-    except Exception as e:
-        print('Failed')
-        print(e)
-        exit_code = 1
+    print(f'... cmd: {cmd}')
+    run(cmd)
 
     if args.track_carbon_footprint:
         emissions: float = tracker.stop()
@@ -138,7 +132,7 @@ def main():
         print("Results can be visualized with the codecarbon visualization tool using following command:\n")
         print(f'\t$ carbonboard --filepath="{args.bids_dir}/code/emissions.csv" --port=9999\n')
 
-    return exit_code
+    return 0
 
 
 if __name__ == '__main__':