postBIBSnet improvement and bug fixes

- Added dataset_description.json file copying into precomputed
- Added functionality to choose template file with age closest to subject's for LR registration
- Fixed bug where BIBSnet fails even after correctly making segmentation (by catching and ignoring the exception)

Still need to test
- running BIBSnet from CABINET, and
- template file selection on subjects whose age doesn't exactly match a template file age

run.py

@@ -7,7 +7,6 @@
 Created: 2021-11-12
 Updated: 2022-06-17
 """
-
 # Import standard libraries
 import argparse
 from datetime import datetime
@@ -47,9 +46,9 @@ def find_myself(flg):
     as_cli_attr, as_cli_arg, correct_chirality, create_anatomical_average,
     crop_image, dict_has, dilate_LR_mask, exit_with_time_info,
     extract_from_json, get_and_make_preBIBSnet_work_dirs, get_optional_args_in,
-    get_stage_name, get_subj_ID_and_session, make_given_or_default_dir,
-    resize_images, run_all_stages, valid_readable_json,
-    validate_parameter_types, valid_readable_dir, will_run_stage
+    get_stage_name, get_subj_ID_and_session, get_template_age_closest_to,
+    make_given_or_default_dir, resize_images, run_all_stages,
+    valid_readable_json, validate_parameter_types, valid_readable_dir
 )
 
 
@@ -356,12 +355,22 @@ def run_BIBSnet(j_args, logger):
         #sys.path.append("/home/cabinet/SW/BIBSnet")
         #from BIBSnet.run import run_nnUNet_predict
 
-        # Run BIBSnet
-        run_nnUNet_predict({"model": j_args["BIBSnet"]["model"],
-                    "nnUNet": j_args["BIBSnet"]["nnUNet_predict_path"],
-                    "input": dir_BIBS.format("in"),
-                    "output": dir_BIBS.format("out"),
-                    "task": str(j_args["BIBSnet"]["task"])})
+        try:  # Run BIBSnet
+            inputs_BIBSnet = {"model": j_args["BIBSnet"]["model"],
+                              "nnUNet": j_args["BIBSnet"]["nnUNet_predict_path"],
+                              "input": dir_BIBS.format("in"),
+                              "output": dir_BIBS.format("out"),
+                              "task": str(j_args["BIBSnet"]["task"])}
+            run_nnUNet_predict(**inputs_BIBSnet)
+        except subprocess.CalledProcessError as e:
+            # BIBSnet will crash even after correctly creating a segmentation,
+            # so only crash CABINET if that segmentation is not made.
+            outfpath = os.path.join(dir_BIBS.format("out"),
+                                    "{}_{}_optimal_resized.nii.gz".format(*sub_ses))
+            if not os.path.exists(outfpath):
+                logger.error("BIBSnet failed to create this segmentation file...\n{}\n...from these inputs:\n{}".format(outfpath, inputs_BIBSnet))
+                sys.exit(e)
+
 
         # TODO hardcoded below call to run_nnUNet_predict. Will likely want to change and integrate into j_args
         #run_nnUNet_predict({"model": "3d_fullres",
@@ -384,12 +393,18 @@ def run_postBIBSnet(j_args, logger):
     # Template selection values
     age_months = j_args["common"]["age_months"]
     logger.info("Age of participant: {} months".format(age_months))
-    if age_months > 33:
-        age_months = "34-38"
+
+    # Get template closest to age
+    tmpl_age = get_template_age_closest_to(
+        age_months, os.path.join(SCRIPT_DIR, "data", "chirality_masks")
+    )
+    if j_args["common"]["verbose"]:
+        logger.info("Closest template-age is {} months".format(tmpl_age))
+    # if age_months > 33: age_months = "34-38"
 
     # Run left/right registration script and chirality correction
     left_right_mask_nifti_fpath = run_left_right_registration(
-        j_args, sub_ses, age_months, 2 if int(age_months) < 22 else 1, logger  # NOTE 22 cutoff might change
+        j_args, sub_ses, tmpl_age, 2 if int(age_months) < 22 else 1, logger  # NOTE 22 cutoff might change
     )
     logger.info("Left/right image registration completed")
 
@@ -463,13 +478,18 @@ def run_left_right_registration(j_args, sub_ses, age_months, t1or2, logger):
     msg = "{} left/right registration on {}"
     if (j_args["common"]["overwrite"] or not
             os.path.exists(left_right_mask_nifti_fpath)):
-        logger.info(msg.format("Running", first_subject_head))
+        # logger.info(msg.format("Running", first_subject_head))
         try:
             # SubjectHead TemplateHead TemplateMask OutputMaskFile
-            subprocess.check_call((LR_REGISTR_PATH, first_subject_head,
-                                   tmpl_head.format(age_months, t1or2),
-                                   tmpl_mask.format(age_months),
-                                   left_right_mask_nifti_fpath))
+            cmd_LR_reg = (LR_REGISTR_PATH, first_subject_head,
+                        tmpl_head.format(age_months, t1or2),
+                        tmpl_mask.format(age_months),
+                        left_right_mask_nifti_fpath)
+            if j_args["common"]["verbose"]:
+                logger.info(msg.format("Now running", "\n".join(
+                    (first_subject_head, " ".join(cmd_LR_reg))
+                )))
+            subprocess.check_call(cmd_LR_reg)
 
         # Tell the user if ANTS crashes due to a memory error
         except subprocess.CalledProcessError as e:
@@ -484,6 +504,7 @@ def run_left_right_registration(j_args, sub_ses, age_months, t1or2, logger):
         )))
     logger.info(msg.format("Finished", first_subject_head))  # TODO Only print this message if not skipped (and do the same for all other stages)
     return left_right_mask_nifti_fpath
+
 
 
 def run_chirality_correction(l_r_mask_nifti_fpath, j_args, logger):

src/utilities.py

@@ -614,6 +614,29 @@ def get_subj_ses(j_args):
     return "_".join(get_subj_ID_and_session(j_args))
 
 
+def get_template_age_closest_to(age, templates_dir):
+    template_ages = list()
+    template_ranges = dict()
+
+    # Get list of all int ages (in months) that have template files
+    for tmpl_path in glob(os.path.join(templates_dir,
+                                        "*mo_template_LRmask.nii.gz")):
+        tmpl_age = os.path.basename(tmpl_path).split("mo", 1)[0]
+        if "-" in tmpl_age: # len(tmpl_age) <3:
+            for each_age in tmpl_age.split("-"):
+                template_ages.append(int(each_age))
+                template_ranges[template_ages[-1]] = tmpl_age
+            # template_ages.append(int(tmpl_age.split("-")))
+        else:
+            template_ages.append(int(tmpl_age))
+
+    # Get template age closest to subject age, then return template age
+    closest_age = template_ages[np.argmin(np.abs(np.array(template_ages)-age))]
+    return (template_ranges[closest_age] if closest_age
+            in template_ranges else str(closest_age)) #final_template_age
+    # template_ages = [os.path.basename(f).split("mo", 1)[0] for f in glob(globber)]
+
+
 def glob_and_copy(dest_dirpath, *path_parts_to_glob):
     """
     Collect all files matching a glob string, then copy those files