Tof

.travis.yml

@@ -228,7 +228,9 @@ before_install:
  # Use Travis' currently checked-out SIRF commit ID to build.
  # Also no point re-downloading SIRF - just use local URL.
  # N.B.: don't put into build matrix to allow caching.
- - BUILD_FLAGS="$BUILD_FLAGS -DPYVER=$PYMVER -DSIRF_URL=$PWD -DSIRF_TAG=$TRAVIS_COMMIT"
+ # Force ALEXJAZZ008008 repo
+ # Force TOF branch
+ - BUILD_FLAGS="$BUILD_FLAGS -DPYVER=$PYMVER -DSIRF_URL=https://github.com/ALEXJAZZ008008/SIRF.git -DSIRF_TAG=tof"
  # get SuperBuild
  - cd ..
  - git clone https://github.com/CCPPETMR/SIRF-SuperBuild --recursive -b master

src/xSTIR/cSTIR/cstir.cpp

@@ -585,16 +585,20 @@ void* cSTIR_acquisitionDataFromScannerInfo
 extern "C"
 void* cSTIR_getAcquisitionDataDimensions(const void* ptr_acq, size_t ptr_dim)
 {
-	try {
-		int* dim = (int*)ptr_dim;
-		SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, ptr_acq);
-		dim[0] = sptr_ad->get_num_tangential_poss();
-		dim[1] = sptr_ad->get_num_views();
-		dim[2] = sptr_ad->get_num_sinograms();
-		dim[3] = sptr_ad->get_num_TOF_bins();
-		return (void*)new DataHandle;
-	}
-	CATCH;
+    try
+    {
+        int* dim = (int*) ptr_dim;
+
+        SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, ptr_acq);
+
+        dim[0] = sptr_ad->get_num_tangential_poss();
+        dim[1] = sptr_ad->get_num_views();
+        dim[2] = sptr_ad->get_num_sinograms();
+        dim[3] = sptr_ad->get_num_TOF_bins();
+
+        return (void*) new DataHandle;
+    }
+    CATCH;
 }
 
 extern "C"
@@ -1160,4 +1164,4 @@ extern "C"
 void* parameter(const void* ptr, const char* obj, const char* name)
 {
 	return cSTIR_parameter(ptr, obj, name);
-}
+}

src/xSTIR/cSTIR/cstir_p.cpp

@@ -587,6 +587,10 @@ sirf::cSTIR_setOSMAPOSLParameter
 		objectFromHandle<OSMAPOSLReconstruction<Image3DF> >(hp);
 	if (boost::iequals(name, "MAP_model"))
 		recon.set_MAP_model(charDataFromDataHandle(hv));
+        if (boost::iequals(name, "set_maximum_relative_change"))
+                recon.set_maximum_relative_change(dataFromHandle<double>((void*)hv));
+        if (boost::iequals(name, "set_minimum_relative_change"))
+                recon.set_minimum_relative_change(dataFromHandle<double>((void*)hv));
 	else
 		return parameterNotFound(name, __FILE__, __LINE__);
 	return new DataHandle;

src/xSTIR/cSTIR/include/sirf/STIR/stir_data_containers.h

@@ -241,7 +241,7 @@ namespace sirf {
 		}
 		int get_num_TOF_bins()
 		{
-			return 1;
+			return data()->get_num_tof_poss();
 		}
 		int get_max_segment_num() const
 		{

src/xSTIR/cSTIR/stir_data_containers.cpp

@@ -33,26 +33,33 @@ using namespace sirf;
 std::string PETAcquisitionData::_storage_scheme;
 shared_ptr<PETAcquisitionData> PETAcquisitionData::_template;
 
-float
-PETAcquisitionData::norm() const
+float PETAcquisitionData::norm() const
 {
 	double t = 0.0;
+
 	for (int s = 0; s <= get_max_segment_num(); ++s)
 	{
 		SegmentBySinogram<float> seg = get_segment_by_sinogram(s);
 		SegmentBySinogram<float>::full_iterator seg_iter;
-		for (seg_iter = seg.begin_all(); seg_iter != seg.end_all();) {
+
+                for (seg_iter = seg.begin_all(); seg_iter != seg.end_all();)
+                {
 			double r = *seg_iter++;
 			t += r*r;
 		}
-		if (s != 0) {
+
+                if (s != 0)
+                {
 			seg = get_segment_by_sinogram(-s);
-			for (seg_iter = seg.begin_all(); seg_iter != seg.end_all();) {
+
+                        for (seg_iter = seg.begin_all(); seg_iter != seg.end_all();)
+                        {
 				double r = *seg_iter++;
 				t += r*r;
 			}
 		}
 	}
+
 	return sqrt((float)t);
 }
 

src/xSTIR/pSTIR/STIR.py

@@ -785,18 +785,26 @@ def rebin(self, num_segments_to_combine, \
             max_in_segment_num_to_process)
         check_status(ad.handle)
         return ad
-    def show(self, sino = None, title = None):
+
+
+    def show(self, sino = None, tof=0, title = None):
         '''Displays interactively selected sinograms.'''
         assert self.handle is not None
+
         if not HAVE_PYLAB:
             print('pylab not found')
+
             return
+
         data = self.as_array()
         nz = data.shape[0]
+
         if type(sino) == type(1):
             if sino < 0 or sino >= nz:
                 return
-            show_2D_array('sinogram %d' % sino, data[0,sino,:,:])
+
+            show_2D_array('sinogram %d' % sino, data[tof,sino,:,:])
+
             return
         elif sino is None:
             ns = nz
@@ -806,21 +814,28 @@ def show(self, sino = None, title = None):
                 ns = len(sino)
             except:
                 raise error('wrong sinograms list')
+
         if title is None:
             title = 'Selected sinograms'
-        if ns >= 16:
-            tiles = (4, 4)
-        else:
-            tiles = None
+
+        #if ns >= 16:
+            #tiles = (4, 4)
+        #else:
+            #tiles = None
+
         f = 0
+
         while f < ns:
             t = min(f + 16, ns)
-            err = show_3D_array(data[0,:,:,:], \
-                                index = sino[f : t], tile_shape = tiles, \
-                                label = 'sinogram', \
-                                xlabel = 'tang.pos', ylabel = 'view', \
-                                suptitle = title, show = (t == ns))
+
+            #err = show_3D_array(data[0,:,:,:], \
+            #                    index = sino[f : t], tile_shape = tiles, \
+            #                    label = 'sinogram', \
+            #                    xlabel = 'tang.pos', ylabel = 'view', \
+            #                    suptitle = title, show = (t == ns))
+
             f = t
+
     def allocate(self, value=0, **kwargs):
         '''Alias to get_uniform_copy
 
@@ -840,6 +855,7 @@ def allocate(self, value=0, **kwargs):
         else:
             out = self.get_uniform_copy(value)
         return out
+
 ##        print('Please enter sinogram numbers (e.g.: 0, 3-5)')
 ##        print('(a value outside the range 0 to %d will stop this loop)' % \
 ##			(nz - 1))
@@ -857,6 +873,7 @@ def allocate(self, value=0, **kwargs):
 ##					' the loop')
 ##                break
 
+
 DataContainer.register(AcquisitionData)
 
 class ListmodeToSinograms(object):
@@ -1987,15 +2004,21 @@ def __init__(self, filename = ''):
     def __del__(self):
         if self.handle is not None:
             pyiutil.deleteDataHandle(self.handle)
-##    def set_MAP_model(self, model):
-##        parms.set_char_par\
-##            (self.handle, self.name, 'MAP_model', model)
-##    def get_objective_function(self):
-##        obj_fun = PoissonLogLikelihoodWithLinearModelForMean()
-##        obj_fun.handle = pystir.cSTIR_parameter\
-##            (self.handle, self.name, 'objective_function')
-##        check_status(obj_fun.handle)
-##        return obj_fun
+    def set_MAP_model(self, model):
+        parms.set_char_par\
+            (self.handle, self.name, 'MAP_model', model)
+    def set_maximum_relative_change(self, value):
+        parms.set_float_par\
+            (self.handle, self.name, 'set_maximum_relative_change', value)
+    def set_minimum_relative_change(self, value):
+        parms.set_float_par\
+            (self.handle, self.name, 'set_minimum_relative_change', value)
+    def get_objective_function(self):
+        obj_fun = PoissonLogLikelihoodWithLinearModelForMean()
+        obj_fun.handle = pystir.cSTIR_parameter\
+            (self.handle, self.name, 'objective_function')
+        check_status(obj_fun.handle)
+        return obj_fun
 
 class KOSMAPOSLReconstructor(IterativeReconstructor):
     '''