[bug pathes] Issue #2,3,5,6

BrkRaw · Jun 2, 2020 · 0c2bb6f · 0c2bb6f
1 parent be5f30e
commit 0c2bb6f
Show file tree

Hide file tree

Showing 3 changed files with 21 additions and 18 deletions.
diff --git a/brkraw/__init__.py b/brkraw/__init__.py
@@ -1,6 +1,6 @@
 from .lib import *
 
-__version__ = '0.3.3rc5'
+__version__ = '0.3.3rc6'
 __all__ = ['BrukerLoader', '__version__']
 
 

diff --git a/brkraw/lib/loader.py b/brkraw/lib/loader.py
@@ -10,6 +10,7 @@
 import re
 np.set_printoptions(formatter={'float_kind':'{:f}'.format})
 
+
 def load(path):
     path = pathlib.Path(path)
     if os.path.isdir(path):
@@ -201,15 +202,8 @@ def swap_slice_axis(group_id_, dataobj_):
                         dataobj = np.swapaxes(dataobj, slice_axis, -1)
                         dataobj = np.swapaxes(dataobj, 2, -1)
 
-            elif group_id[0] == 'FG_DIFFUSION':
-                dataobj = swap_slice_axis(group_id, dataobj)
-
-            elif group_id[0] == 'FG_DTI':   # reconstructed
-                dataobj = swap_slice_axis(group_id, dataobj)
-
-            elif group_id[0] == 'FG_MOVIE':
+            elif group_id[0] in ['FG_DIFFUSION', 'FG_DTI', 'FG_MOVIE', 'FG_COIL', 'FG_CYCLE', 'FG_COMPLEX']:
                 dataobj = swap_slice_axis(group_id, dataobj)
-
             else:
                 raise UnexpectedError(message='Unexpected frame group combination;'
                                               f'{ISSUE_REPORT}')
@@ -389,6 +383,18 @@ def save_sitk(self, io_type=None):
     def save_as(self):
         return self.save_nifti
 
+    def _inspect_ids(self, scan_id, reco_id):
+        if scan_id not in self._avail.keys():
+            print(f'Invalid Scan ID.\n'
+                  f'Your input: {scan_id}\n'
+                  f'Available Scan IDs: {list(self._avail.keys())}')
+            raise KeyError
+        else:
+            if reco_id not in self._avail[scan_id]:
+                print(f'Invalid Reco ID.\n'
+                      f'Your input: {reco_id}\n'
+                      f'Available Reco IDs: {self._avail[scan_id]}')
+
     def save_nifti(self, scan_id, reco_id, filename, dir='./', ext='nii.gz',
                 crop=None):
         niiobj = self.get_niftiobj(scan_id, reco_id, crop=crop)
@@ -1050,6 +1056,8 @@ def _get_disk_slice_order(visu_pars):
         return disk_slice_order
 
     def _get_visu_pars(self, scan_id, reco_id):
+        # test validation of scan_id and reco_id here
+        self._inspect_ids(scan_id, reco_id)
         return self._pvobj.get_visu_pars(scan_id, reco_id)
 
     @staticmethod

diff --git a/brkraw/scripts/brkraw.py b/brkraw/scripts/brkraw.py
@@ -53,8 +53,9 @@ def main():
     nii.add_argument("input", help=input_str, type=str)
     nii.add_argument("-b", "--bids", help=bids_opt, action='store_true')
     nii.add_argument("-o", "--output", help=output_fnm_str, type=str, default=False)
-    nii.add_argument("-r", "--recoid", help="RECO ID", type=int, default=1)
-    nii.add_argument("-s", "--scanid", help="Scan ID", type=str)
+    nii.add_argument("-r", "--recoid", help="RECO ID (default=1), option to specify a particular reco to convert",
+                     type=int, default=1)
+    nii.add_argument("-s", "--scanid", help="Scan ID, option to specify a particular scan to convert.", type=str)
 
     niiall.add_argument("input", help=input_dir_str, type=str)
     niiall.add_argument("-o", "--output", help=output_dir_str, type=str)
@@ -153,15 +154,11 @@ def main():
                     os.mkdir(subj_path)
                 except OSError:
                     pass
-                else:
-                    raise UnexpectedError
                 sess_path = os.path.join(subj_path, 'ses-{}'.format(study._pvobj.study_id))
                 try:
                     os.mkdir(sess_path)
                 except OSError:
                     pass
-                else:
-                    raise UnexpectedError
                 for scan_id, recos in study._pvobj.avail_reco_id.items():
                     method = study._pvobj._method[scan_id].parameters['Method']
                     if re.search('epi', method, re.IGNORECASE) and not re.search('dti', method, re.IGNORECASE):
@@ -176,8 +173,6 @@ def main():
                         os.mkdir(output_path)
                     except OSError:
                         pass
-                    else:
-                        raise UnexpectedError
                     filename = 'sub-{}_ses-{}_{}'.format(study._pvobj.subj_id, study._pvobj.study_id,
                                                          str(scan_id).zfill(2))
                     for reco_id in recos:
@@ -188,7 +183,7 @@ def main():
                             if args.bids:
                                 study.save_json(scan_id, reco_id, output_fname)
                             if re.search('dti', method, re.IGNORECASE):
-                                study.save_bdata(scan_id, reco_id, output_fname)
+                                study.save_bdata(scan_id, output_fname)
                         except Exception as e:
                             print(e)
                 print(f'{raw} is converted...')