update documentation of method to calculated rod ROIs

gschramm · Mar 21, 2022 · a2ea86c · a2ea86c
1 parent 888abc1
commit a2ea86c
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Showing 2 changed files with 8 additions and 4 deletions.
diff --git a/pynemaiqpet/nema_smallanimal.py b/pynemaiqpet/nema_smallanimal.py
@@ -232,9 +232,11 @@ def nema_2008_small_animal_pet_rois(vol, voxsize, lp_voxel = 'max', rod_th = 0.1
     containing the voxel size
 
   lp_voxel: string, optional
-    method of how to compute the pixel used to draw the line profiles
-    in the rods. 'max' means the maximum voxels in the summed 2D image.
-    anything else means use the center of mass.
+    method of how to compute the ROIs around the line profiles
+    in the summed images of the hot rods.
+    'max' means the maximum voxels in the summed 2D image.
+    anything else means use all pixels that are within the rod radius
+    around the center of mass
  
   rod_th : float, optional
     threshold to find the rod in the summed 2D image relative to the

diff --git a/scripts/analyze_small_animal.py b/scripts/analyze_small_animal.py
@@ -22,6 +22,8 @@
 output_dir = Path('results') 
 # verbose output
 verbose    = True
+# method for ROI to calculate recovery for hot rods (max or mean)
+lp_voxel   = 'mean'
 #-----------------------------------------------------------------------------------------
 
 if not output_dir.exists():
@@ -56,7 +58,7 @@
   vol_aligned = nsa.align_nema_2008_small_animal_iq_phantom(vol, voxsize, version = phantom_name)
 
   # generate the ROI label volume
-  roi_vol = nsa.nema_2008_small_animal_pet_rois(vol_aligned, voxsize, phantom = phantom_name)
+  roi_vol = nsa.nema_2008_small_animal_pet_rois(vol_aligned, voxsize, phantom = phantom_name, lp_voxel = lp_voxel)
 
   # generate the report
   res = nsa.nema_2008_small_animal_iq_phantom_report(vol_aligned, roi_vol)