[bug patch] #10 Position correction apply for PV5 only

BrkRaw · Jun 5, 2020 · b86afb7 · b86afb7
1 parent 8838269
commit b86afb7
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diff --git a/README.md b/README.md
@@ -62,6 +62,7 @@ GNU General Public License v3.0
 Lee, Sung-Ho, Ban, Woomi, & Shih, Yen-Yu Ian. (2020, June 4). BrkRaw/bruker: BrkRaw v0.3.3 (Version 0.3.3). 
 Zenodo. http://doi.org/10.5281/zenodo.3877179
 
+
 **BibTeX**
 ```
 @software{lee_sung_ho_2020_3877179,

diff --git a/brkraw/__init__.py b/brkraw/__init__.py
@@ -1,6 +1,6 @@
 from .lib import *
 
-__version__ = '0.3.3'
+__version__ = '0.3.4b0'
 __all__ = ['BrukerLoader', '__version__']
 
 

diff --git a/brkraw/lib/loader.py b/brkraw/lib/loader.py
@@ -998,7 +998,11 @@ def _get_affine(self, visu_pars, method):
         orient_info = self._get_orient_info(visu_pars, method)
         slice_orient_map = {0: 'sagital', 1: 'coronal', 2: 'axial'}
         num_slice_packs = slice_info['num_slice_packs']
-        subj_pose = orient_info['subject_position']
+        version = get_value(visu_pars, 'VisuVersion')
+        if version == 1:  # PV 5.1 required the position correction
+            subj_pose = orient_info['subject_position']
+        else:             # PV 6.01 does not
+            subj_pose = None
         subj_type = orient_info['subject_type']
 
         if num_slice_packs > 1:

diff --git a/brkraw/lib/utils.py b/brkraw/lib/utils.py
@@ -49,26 +49,26 @@ def build_affine_from_orient_info(resol, rmat, pose,
 
     # convert space from image to subject
     # below positions are all reflext human-based position
-    # if subj_pose == 'Head_Supine':
-    #     affine = apply_rotate(affine, rad_z=np.pi)
-    # elif subj_pose == 'Head_Prone':
-    #     pass
-    # # From here, not urgent, extra work to determine correction matrix needed.
-    # elif subj_pose == 'Head_Left':
-    #     affine = apply_rotate(affine, rad_z=np.pi/2)
-    # elif subj_pose == 'Head_Right':
-    #     affine = apply_rotate(affine, rad_z=-np.pi/2)
-    # elif subj_pose in ['Foot_Supine', 'Tail_Supine']:
-    #     affine = apply_rotate(affine, rad_x=np.pi)
-    # elif subj_pose in ['Foot_Prone', 'Tail_Prone']:
-    #     pass
-    #     # affine = apply_rotate(affine, rad_y=np.pi)
-    # elif subj_pose in ['Foot_Left', 'Tail_Left']:
-    #     affine = apply_rotate(affine, rad_z=np.pi/2)
-    # elif subj_pose in ['Foot_Right', 'Tail_Right']:
-    #     affine = apply_rotate(affine, rad_z=-np.pi/2)
-    # else:  # in case Bruker put additional value for this header
-    #     raise Exception(ERROR_MESSAGES['NotIntegrated'])
+    if subj_pose:
+        if subj_pose == 'Head_Supine':
+            affine = apply_rotate(affine, rad_z=np.pi)
+        elif subj_pose == 'Head_Prone':
+            pass
+        # From here, not urgent, extra work to determine correction matrix needed.
+        elif subj_pose == 'Head_Left':
+            affine = apply_rotate(affine, rad_z=np.pi/2)
+        elif subj_pose == 'Head_Right':
+            affine = apply_rotate(affine, rad_z=-np.pi/2)
+        elif subj_pose in ['Foot_Supine', 'Tail_Supine']:
+            affine = apply_rotate(affine, rad_x=np.pi)
+        elif subj_pose in ['Foot_Prone', 'Tail_Prone']:
+            affine = apply_rotate(affine, rad_y=np.pi)
+        elif subj_pose in ['Foot_Left', 'Tail_Left']:
+            affine = apply_rotate(affine, rad_z=np.pi/2)
+        elif subj_pose in ['Foot_Right', 'Tail_Right']:
+            affine = apply_rotate(affine, rad_z=-np.pi/2)
+        else:  # in case Bruker put additional value for this header
+            raise Exception(ERROR_MESSAGES['NotIntegrated'])
 
     if subj_type != 'Biped':
         # correct subject space if not biped (human or non-human primates)