fillStirSpace(originalImageS, originalImageP)
# Initialize the projection matrix (using ray-tracing)
# Het motion model doet nu niets, maar is nodig omdat Stir anders flipt
MotionModel = stir.MotionModel()
MotionModel.setOffset(0.0)
projmatrix = stir.ProjMatrixByBinUsingRayTracing(MotionModel)
projmatrix.set_num_tangential_LORs(nLOR)
projmatrix.set_up(projdata_info, originalImageS)
# Create projectors
forwardprojector = stir.ForwardProjectorByBinUsingProjMatrixByBin(projmatrix)
backprojector = stir.BackProjectorByBinUsingProjMatrixByBin(projmatrix)
# Creating an instance for the sinogram (measurement), it is not yet filled
measurement = stir.ProjDataInMemory(stir.ExamInfo(), projdata_info)
# Forward project originalImageS and store in measurement
forwardprojector.forward_project(measurement, originalImageS)
# Converting the stir sinogram to a numpy sinogram
measurementS = measurement.get_segment_by_sinogram(0)
measurementP = stirextra.to_numpy(measurementS)
#plt.figure(2), plt.title('Sinogram original image'), plt.imshow(measurementP[0,:,:]), plt.show()
# Backprojecting the sinogram to get an image
finalImageS = stir.FloatVoxelsOnCartesianGrid(
projdata_info, 1,
stir.FloatCartesianCoordinate3D(stir.make_FloatCoordinate(0, 0, 0)),
stir.IntCartesianCoordinate3D(
zoom = 1.2 image_data = stir.FloatVoxelsOnCartesianGrid(proj_data_info, zoom) #%% initialise a projection matrix # Using ray-tracing here # Note that the default is to restrict the projection to a cylindrical FOV projmatrix = stir.ProjMatrixByBinUsingRayTracing() projmatrix.set_up(proj_data_info, image_data) #%% construct projectors forwardprojector = stir.ForwardProjectorByBinUsingProjMatrixByBin(projmatrix) forwardprojector.set_up(proj_data_info, image_data) backprojector = stir.BackProjectorByBinUsingProjMatrixByBin(projmatrix) backprojector.set_up(proj_data_info, image_data) #%% create projection data for output of forward projection # We'll create the data in memory here exam_info = stir.ExamInfo() projdataout = stir.ProjDataInMemory(exam_info, proj_data_info) # Note: we could write to file, but it is right now a bit complicated to open a # projection data file for read/write: # inout=stir.ios.trunc|stir.ios.ios_base_in|stir.ios.out; # projdataout=stir.ProjDataInterfile(exam_info, proj_data_info, 'my_test_python_projection.hs',inout); #%% Done creating data and projectors! # Let's now create an interesting image with 2 cylinders #%% create a first cylinder (note: units are in mm) # we'll put it in the middle of the scanner # This is currently a bit difficult in STIR due to its # choice of origin (the middle of the first ring). length = 60 radius = 40
#_______________________PROJ MATRIX AND PROJECTORS______________________
slope = 0.0
offSet = 0.0
MotionModel = stir.MotionModel(nFrames, slope, offSet) # A motion model is compulsory
projmatrix = stir.ProjMatrixByBinUsingRayTracing(MotionModel)
projmatrix.set_num_tangential_LORs(nLOR)
projmatrix.set_up(projdata_info, originalImageS)
# Create projectors
forwardprojector = stir.ForwardProjectorByBinUsingProjMatrixByBin(projmatrix)
backprojector = stir.BackProjectorByBinUsingProjMatrixByBin(projmatrix)
#_________________________MEASUREMENT_______________________________
measurement = stir.ProjDataInMemory(stir.ExamInfo(), projdata_info)
measurementListP = []
## First time frame
MotionModel.setOffset(0.0)
forwardprojector.forward_project(measurement, phantomS[0])
measurement.write_to_file('sinoMeas_1.hs')
measurementS = measurement.get_segment_by_sinogram(0)
measurementP = stirextra.to_numpy(measurementS)
measurementListP.append(measurementP)
## Second time frame
MotionModel.setOffset(0.0) # Beweging zit al in het plaatje
forwardprojector.forward_project(measurement, phantomS[1])
measurement.write_to_file('sinoMeas_2.hs')
measurementS = measurement.get_segment_by_sinogram(0)
#allocate imagespace guestimates
guestimatespace = stir.FloatVoxelsOnCartesianGrid(
projdata_info, 1,
stir.FloatCartesianCoordinate3D(stir.make_FloatCoordinate(0, 0, 0)),
stir.IntCartesianCoordinate3D(
stir.make_IntCoordinate(
np.shape(p)[0],
np.shape(p)[1],
np.shape(p)[2])))
guestimatespace.fill(1)
reconList.append(guestimatespace)
# We'll just create the data in memory here
measurementList.append(
stir.ProjDataInMemory(stir.ExamInfo(), projdata_info))
#forward project last measurement in list
forwardprojector.forward_project(measurementList[-1], phantomList[-1])
tmp = measurementList[-1].get_segment_by_sinogram(0)
#pyvpx.numpy2vpx(stirextra.to_numpy(tmp), ('MeasuredSinoFrame' + str(iFrame) + '.vpx'))
#append empty sinogram for estimations
sinogramList.append(stir.ProjDataInMemory(stir.ExamInfo(), projdata_info))
SurrogateSignal = np.array(range(nFrames))
#Normalize
NormSpace = stir.FloatVoxelsOnCartesianGrid(
projdata_info, 1,
stir.FloatCartesianCoordinate3D(stir.make_FloatCoordinate(0, 0, 0)),
#projdata_info = stir.ProjDataInfo.ProjDataInfoCTI(scanner, span, max_ring_diff, 168, scanner.get_max_num_non_arccorrected_bins(), False)
projdata_info2D = stir.ProjDataInfo.ProjDataInfoCTI(scanner, span, max_ring_diff, 168, scanner.get_max_num_non_arccorrected_bins(), False)
guessVolume = stir.FloatVoxelsOnCartesianGrid(projdata_info2D, 1,
stir.FloatCartesianCoordinate3D(stir.make_FloatCoordinate(0,0,0)),
stir.IntCartesianCoordinate3D(stir.make_IntCoordinate(sizeOfVolumeInVoxels[0], sizeOfVolumeInVoxels[1], sizeOfVolumeInVoxels[2])))
guessVolume.fill(1)
ErrorVolume = stir.FloatVoxelsOnCartesianGrid(projdata_info2D, 1,
stir.FloatCartesianCoordinate3D(stir.make_FloatCoordinate(0,0,0)),
stir.IntCartesianCoordinate3D(stir.make_IntCoordinate(sizeOfVolumeInVoxels[0], sizeOfVolumeInVoxels[1], sizeOfVolumeInVoxels[2])))
ErrorVolume.fill(0)
forwardSino2D = stir.ProjDataInMemory(stir.ExamInfo(), projdata_info2D)
forwardSino2D.fill(0)
#Initialize the projection matrix (using ray-tracing)
projmatrix2D = stir.ProjMatrixByBinUsingRayTracing()
nLOR = 10
projmatrix2D.set_num_tangential_LORs(nLOR)
projmatrix2D.set_up(projdata_info2D, guessVolume)
#Create projectors
forwardprojector2D = stir.ForwardProjectorByBinUsingProjMatrixByBin(projmatrix2D)
backprojector2D = stir.BackProjectorByBinUsingProjMatrixByBin(projmatrix2D)
def forwardProject(npSource):
guessVolume.fill(npSource.flat)
forwardSino2D.fill(0)
def test_shape():
s = stir.Scanner.get_scanner_from_name("ECAT 962")
projdatainfo = stir.ProjDataInfo.ProjDataInfoCTI(s, 3, 9, 8, 6)
projdata = stir.ProjDataInMemory(stir.ExamInfo(), projdatainfo)
shape = get_shape_from_proj_data(projdata)
assert shape == projdata.to_array().shape()