Merge pull request #30 from txusser/fix/wholebody

Fix/wholebody

utils/tools.py

@@ -1001,3 +1001,11 @@ def change_format(image_hdr, newFormat, logfile):
         hdr.set_data_shape(data.shape)
         imageToWrite = nib.AnalyzeImage(data, img.affine, hdr)    
         nib.save(imageToWrite, image_hdr)
+
+def fix_4d_data(data):
+    shape = data.shape
+
+    if len(shape) == 3:
+        return data
+    else:
+        return data[:, :, :, 0]

utils/wb_tools.py

@@ -1,8 +1,12 @@
+import sys
 from os.path import join, dirname
 import nibabel as nib
 import numpy as np
 from scipy.ndimage import gaussian_filter
 from scipy.ndimage import median_filter
+from pyprojroot import here
+
+sys.path.append(str(here()))
 from utils import resources as rsc
 from utils import spm_tools as spm
 from utils import tools
@@ -222,14 +226,14 @@ def join_beds_wb(recons_beds, joint_beds):
 
     bed_0_data = bed_0_data[:, :, :-slices_to_remove]
 
-    for i in range(1, len(recons_beds) - 1):
-        print(i)
+    for i in range(1, len(recons_beds)):
+        print(f"Bed: {i}")
 
         bed = nib.load(recons_beds[i])
         bed_data = tools.fix_4d_data(bed.get_fdata())
         bed_data = bed_data[:, :, slices_to_remove:-slices_to_remove]
         bed_0_data = np.append(bed_0_data, bed_data, axis=2)
-    print(len(recons_beds) - 1)
+
     bed_last = nib.load(recons_beds[len(recons_beds) - 1])
     bed_data = tools.fix_4d_data(bed_last.get_fdata())
     bed_data = bed_data[:, :, slices_to_remove:]
@@ -243,7 +247,7 @@ def join_beds_wb(recons_beds, joint_beds):
     hdr1.set_data_dtype(dtype)
     hdr1.set_data_shape(bed_0_data.shape)
     affine = bed_0.get_affine()
-    hdr1.set_zooms((affine[0, 0], affine[1, 1], affine[2, 2]))
+    hdr1.set_zooms((abs(affine[0, 0]), abs(affine[1, 1]), abs(affine[2, 2])))
 
     analyze_img = nib.AnalyzeImage(bed_0_data, hdr1.get_base_affine(), hdr1)
     nib.save(analyze_img, joint_beds)

wholebody.py

@@ -28,7 +28,8 @@ def __init__(self, cfg: DictConfig):
         self.params = self.cfg["params"]
         self.config = {k: v for k, v in self.cfg.items() if k != "params"}
         self.scanner = self.cfg["params"]["scanner"]
-        self.scanner_model = self.params.get("scanner")
+        self.scanner_model = str(self.params["scanner"]["scanner_name"]).lower().replace(" ", "_")
+        self.cfg_omega.params.scanner.scanner_name = self.scanner_model
 
         # The following lines will read the general, scanner and config parameters
         self.sim_type = self.params.get("sim_type")
@@ -82,8 +83,8 @@ def run(self):
             if not exists(bed_dir):
                 os.makedirs(bed_dir)
 
-            self.params['center_slice'] = cs
-            self.params['output_dir'] = output_name + "/Bed_cs_%s" % cs
+            self.cfg_omega.params.center_slice = int(cs)
+            self.cfg_omega.params.output_dir = output_name + "/Bed_cs_%s" % cs
 
             print("Simulating bed %s with center slice %s" % (j, cs))