adapt NEMA PET fitting example to new submodule structure

gschramm · Feb 13, 2020 · 1c818e7 · 1c818e7
1 parent 3f263cd
commit 1c818e7
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Showing 2 changed files with 13 additions and 4 deletions.
diff --git a/examples/pet/nema_pet.py b/examples/pet/nema_pet.py
@@ -5,7 +5,7 @@
 import pylab as py
 import matplotlib.patches as patches
 
-import pymirc.registration     as pymr
+import pymirc.metrics     as pymr
 
 from pymirc.image_operations import kul_aff, aff_transform
 
@@ -1210,7 +1210,7 @@ def fit_WB_NEMA_sphere_profiles(vol,
     bgCOVs  = np.array([x.bgcov  for x in fitres])
 
     retvals = {'fitres':fitres, 'fwhms':fwhms, 'Rs':Rs, 'Bs': Bs, 'Ss':Ss, 'a50RCs':a50RCs,
-               'meanRCs':meanRCs, 'maxRCs':maxRCs, 'bgCOVs':bgCOVs, 'subvols':subvols}
+               'meanRCs':meanRCs, 'maxRCs':maxRCs, 'bgCOVs':bgCOVs, 'subvols':subvols, 'vol':vol}
 
     if showprofiles: 
         retvals['fig']  = fig

diff --git a/examples/pet/wb_nema.py b/examples/pet/wb_nema.py
@@ -7,11 +7,20 @@
 from scipy.io import readsav
 
 import pymirc.fileio as pmf
+import pymirc.viewer as pv
 
 from nema_pet import fit_WB_NEMA_sphere_profiles
 
-dcm     = pmf.DicomVolume('mydcm_dir*.dcm')
+dcm     = pmf.DicomVolume('my_dcm_dir/*.dcm')
 vol     = dcm.get_data() 
 voxsize = dcm.voxsize 
 
-res = fit_WB_NEMA_sphere_profiles(vol, voxsize, Sfix = 16800, sm_fwhm = 4.5)
+#res = fit_WB_NEMA_sphere_profiles(vol, voxsize, sm_fwhm = 4.5)
+#res = fit_WB_NEMA_sphere_profiles(vol, voxsize, sm_fwhm = 4.5, Rfix = [18.5, 14., 11., 8.5, 6.5, 5.])
+res = fit_WB_NEMA_sphere_profiles(vol, voxsize, sm_fwhm = 4.5, Rfix = [18.5, 14., 11., 8.5, 6.5, 5.], Sfix = 16914)
+
+# show the n-th sphere sub volume
+#pv.ThreeAxisViewer(res['subvols'][5], voxsize = voxsize, imshow_kwargs = {'vmin': 0, 'vmax': res['Ss'][0]})
+
+# show the whole volume
+#pv.ThreeAxisViewer(res['vol'], voxsize = voxsize, imshow_kwargs = {'vmin': 0, 'vmax': res['Ss'][0]})