add possibility to show the background ROI

gschramm · Aug 24, 2020 · dc4fafe · dc4fafe
1 parent 53cb07c
commit dc4fafe
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Showing 2 changed files with 22 additions and 6 deletions.
diff --git a/examples/wb_nema.py b/examples/wb_nema.py
@@ -34,7 +34,8 @@
 
 # try also doing the fit without fixing the radii
 fitres, sphere_results = nema.fit_WB_NEMA_sphere_profiles(vol, voxsize, sameSignal = True,
-                                                          Rfix = [18.5, 14.0, 11.0, 8.5, 6.5, 5.])
+                                                          Rfix = [18.5, 14.0, 11.0, 8.5, 6.5, 5.],
+                                                          showBGROI = True)
 
 print('fit with same signal and fixed radii')
 print(sphere_results)

diff --git a/pynemaiqpet/nema_wb.py b/pynemaiqpet/nema_wb.py
@@ -13,7 +13,7 @@
 
 from lmfit    import Model
 
-def find_background_roi(vol, voxsize, Rcenter = 82, edge_margin = 28.):
+def find_background_roi(vol, voxsize, Rcenter = 82, edge_margin = 28., showROI= False):
   """ find the 2D background ROI for a NEMA sphere phantom
 
   Parameters
@@ -31,6 +31,9 @@ def find_background_roi(vol, voxsize, Rcenter = 82, edge_margin = 28.):
   edge_margin : float (optional)
     margin (mm) to stay away from the boarder of the phantom - default 28.
 
+  showROI : bool (optional)
+    whether to show 2D background ROI in a figure - default False
+
   Returns
   -------
 
@@ -71,6 +74,14 @@ def find_background_roi(vol, voxsize, Rcenter = 82, edge_margin = 28.):
   tmp[...,sphere_sl] = bg_mask
   bg_inds = np.where(tmp == 1)
 
+  if showROI:
+    fig, ax = py.subplots(figsize = (5,5))
+    ax.imshow(sphere_2d_img.T, cmap = py.cm.Greys, vmin = 0, vmax = np.percentile(sphere_2d_img,99.9))
+    ax.contour(bg_mask.T)
+    ax.set_title(f'background ROI slice {sphere_sl}')
+    fig.tight_layout()
+    fig.show()
+
   return bg_inds
 
 #--------------------------------------------------------------------------------------------------
@@ -648,7 +659,8 @@ def fit_WB_NEMA_sphere_profiles(vol,
                                 FWHMfix   = None,
                                 wm           = 'dist',
                                 nmax_spheres = 6,
-                                sameSignal   = False):
+                                sameSignal   = False,
+                                showBGROI    = False):
     """ Analyse the sphere profiles of a NEMA scan
 
     Parameters
@@ -674,11 +686,14 @@ def fit_WB_NEMA_sphere_profiles(vol,
     wm : str, optional
       the weighting method of the data (equal, dist, sqdist)
 
-    nmax_spheres: int (optional)
+    nmax_spheres: int, optional
       maximum number of spheres to consider (default 6)
 
     sameSignal : bool, optional
-       whether to forace all spheres to have the signal from the biggest sphere
+      whether to forace all spheres to have the signal from the biggest sphere
+
+    showBGROI : bool ,optional
+      whether to show the background ROI in a separate figure - default False 
 
     Returns
     -------
@@ -695,7 +710,7 @@ def fit_WB_NEMA_sphere_profiles(vol,
         vol      = gaussian_filter(vol, sigma = sigmas)
 
     # find the 2D background ROI
-    bg_inds = find_background_roi(vol, voxsizes)
+    bg_inds = find_background_roi(vol, voxsizes, showROI = showBGROI)
     bg_mean = vol[bg_inds].mean()
     bg_cov  = vol[bg_inds].std() / bg_mean