def Normalization(reconspace, backprojector, sinogram):
sinseg = sinogram.get_segment_by_sinogram(0)
filler = np.ones(np.shape(stirextra.to_numpy(sinseg)))
fillStirSpace(sinseg, filler)
sinogram.set_segment(sinseg)
backprojector.back_project(reconspace, sinogram)
npReconSpace = stirextra.to_numpy(reconspace)
pyvpx.numpy2vpx(npReconSpace, 'NormMap.vpx')
return reconspace
def test_ProjData():
s=Scanner.get_scanner_from_name("ECAT 962")
#ProjDataInfoCTI(const shared_ptr<Scanner>& scanner_ptr,
# const int span, const int max_delta,
# const int num_views, const int num_tangential_poss,
#
projdatainfo=ProjDataInfo.ProjDataInfoCTI(s,3,9,8,6)
#print projdatainfo
projdata=ProjDataInMemory(ExamInfo(), projdatainfo)
np=stirextra.to_numpy(projdata)
np+=2
projdata.fill(np.flat)
seg0=stirextra.to_numpy(projdata.get_segment_by_sinogram(0))
assert(seg0.max() == 2)
def test_ProjData():
s = Scanner.get_scanner_from_name("ECAT 962")
#construct_proj_data_info(const shared_ptr<Scanner>& scanner_ptr,
# const int span, const int max_delta,
# const int num_views, const int num_tangential_poss,
#
projdatainfo = ProjDataInfo.construct_proj_data_info(s, 3, 9, 8, 6)
#print projdatainfo
projdata = ProjDataInMemory(ExamInfo(), projdatainfo)
np = stirextra.to_numpy(projdata)
np += 2
projdata.fill(np.flat)
seg0 = stirextra.to_numpy(projdata.get_segment_by_sinogram(0))
assert (seg0.max() == 2)
def test_Array3Diterator():
a=FloatArray3D(IndexRange3D(Int3BasicCoordinate((1,3,-1)), Int3BasicCoordinate((3,9,5))))
for i1,i2 in zip(a.flat(), range(a.size_all())):
i1=i2;
np=stirextra.to_numpy(a);
for i1,i2 in zip(a.flat(), np.flat):
assert abs(i1-i2)<.01
def plot_sinogram_profiles(projection_data_list, sumaxis=0, select=0):
"""
Plot a profile through STIR.ProjData.
Average over all sinograms to reduce noise
projection_data_list: list of sinogram file names or stir.ProjData objects to load and plot
sumaxis: axes to sum over (passed to numpy.sum(..., axis))
select: element to select after summing
"""
plt.figure()
ax = plt.subplot(111)
for f in projection_data_list:
label = ""
if isinstance(f, str):
print(f"Handling:\n {f}")
label = f
f = stir.ProjData_read_from_file(f)
if isinstance(f, stir.ProjData):
f = stirextra.to_numpy(f)
else:
raise ValueError("wrong type of argument")
plt.plot(np.sum(f, axis=sumaxis)[select,:], label=label)
plt.title(f"Summing over axis {sumaxis} with element {select}")
ax.legend()
plt.show()
def test_Array3Diterator():
a=FloatArray3D(IndexRange3D(Int3BasicCoordinate((1,3,-1)), Int3BasicCoordinate((3,9,5))))
for i1,i2 in zip(a.flat(), range(a.size_all())):
i1=i2;
np=stirextra.to_numpy(a);
for i1,i2 in zip(a.flat(), np.flat):
assert abs(i1-i2)<.01
def test_Array2Diterator():
a=FloatArray2D(IndexRange2D(Int2BasicCoordinate((1,3)), Int2BasicCoordinate((3,9))))
for i1,i2 in itertools.izip(a.flat(), range(a.size_all())):
i1=i2;
np=stirextra.to_numpy(a);
for i1,i2 in itertools.izip(a.flat(), np.flat):
assert abs(i1-i2)<.01
def test_Array2Diterator():
a = FloatArray2D(
IndexRange2D(Int2BasicCoordinate((1, 3)), Int2BasicCoordinate((3, 9))))
for i1, i2 in zip(a.flat(), range(a.size_all())):
i1 = i2
np = stirextra.to_numpy(a)
for i1, i2 in zip(a.flat(), np.flat):
assert abs(i1 - i2) < .01
def test_Array2D():
minind=Int2BasicCoordinate((3,3));
a=FloatArray2D(IndexRange2D(minind, Int2BasicCoordinate((9,8))))
a.fill(2);
ind=Int2BasicCoordinate((4,5));
a[ind]=4
np=stirextra.to_numpy(a);
assert np[(0,0)]==2
npind=(ind[1]-minind[1], ind[2]-minind[2])
assert np[npind]==a[ind]
def test_Array2D():
minind = Int2BasicCoordinate((3, 3))
a = FloatArray2D(IndexRange2D(minind, Int2BasicCoordinate((9, 8))))
a.fill(2)
ind = Int2BasicCoordinate((4, 5))
a[ind] = 4
np = stirextra.to_numpy(a)
assert np[(0, 0)] == 2
npind = (ind[1] - minind[1], ind[2] - minind[2])
assert np[npind] == a[ind]
def _call(self, volume, out):
"""Forward project a volume."""
# Set volume data
self.volume.fill(volume.asarray().flat)
# project
with StirVerbosity(0):
self.projector.forward_project(self.proj_data, self.volume)
# make ODL data
out[:] = stirextra.to_numpy(self.proj_data)
def _call(self, projections, out):
"""Back project."""
# Set projection data
self.proj_data.fill(projections.asarray().flat)
# back-project
with StirVerbosity(0):
self.back_projector.back_project(self.volume, self.proj_data)
# make ODL data
out[:] = stirextra.to_numpy(self.volume)
def _call(self, volume, out):
"""Forward project a volume."""
# Set volume data
self.volume.fill(volume.asarray().flat)
# project
with StirVerbosity(0):
self.projector.forward_project(self.proj_data, self.volume)
# make ODL data
out[:] = stirextra.to_numpy(self.proj_data)
def _call(self, projections, out):
"""Back project."""
# Set projection data
self.proj_data.fill(projections.asarray().flat)
# back-project
with StirVerbosity(0):
self.back_projector.back_project(self.volume, self.proj_data)
# make ODL data
out[:] = stirextra.to_numpy(self.volume)
def call_with_stir_buffer(function,
b_in,
b_out,
v_in,
subset_num=0,
num_subsets=1,
clear_buffer=False):
b_in.fill(v_in.asarray().flat)
if clear_buffer:
b_out.fill(0)
function(b_out, b_in, subset_num, num_subsets)
return to_numpy(b_out)
def test_Array3D():
minind=Int3BasicCoordinate((3,3,5));
a=FloatArray3D(IndexRange3D(minind, Int3BasicCoordinate((9,8,7))))
a.fill(2);
ind=Int3BasicCoordinate((4,5,6));
a[ind]=4
np=stirextra.to_numpy(a);
assert np[(0,0,1)]==2
npind=(ind[1]-minind[1], ind[2]-minind[2], ind[3]-minind[3])
assert np[npind]==a[ind]
np+=2
a.fill(np.flat)
assert np[(0,0,1)]==4
assert np[npind]==a[ind]
def test_Array3D():
minind = Int3BasicCoordinate((3, 3, 5))
a = FloatArray3D(IndexRange3D(minind, Int3BasicCoordinate((9, 8, 7))))
a.fill(2)
ind = Int3BasicCoordinate((4, 5, 6))
a[ind] = 4
np = stirextra.to_numpy(a)
assert np[(0, 0, 1)] == 2
npind = (ind[1] - minind[1], ind[2] - minind[2], ind[3] - minind[3])
assert np[npind] == a[ind]
np += 2
a.fill(np.flat)
assert np[(0, 0, 1)] == 4
assert np[npind] == a[ind]
def MLEMRecon(normMap, reconspace, imspaceError, forwardprojector, backprojector, sinogram, measurement, nIter = 30):
imspaceError.fill(1)
meascomp = measurement.get_segment_by_sinogram(0)
npNormMap = stirextra.to_numpy(normMap)
for iter in range(nIter):
sinogram.fill(0)
forwardprojector.forward_project(sinogram, reconspace);
sinocomp = sinogram.get_segment_by_sinogram(0)
#populate error sinogram
error = stirextra.to_numpy(meascomp) /stirextra.to_numpy(sinocomp)
error[np.isnan(error)] = 1
error[np.isinf(error)] = 1
#error[error > 1E10] = 1;
#error[error < 1E-10] = 1;
sinocompy = fillStirSpace(sinocomp, error)
sinogram.set_segment(sinocompy)
#backproject error
backprojector.back_project(imspaceError, sinogram)
image = stirextra.to_numpy(reconspace)
error = stirextra.to_numpy(imspaceError)
error = error/npNormMap
#error[error > 1E10] = 0
error[np.isinf(error)] = 0
error[np.isnan(error)] = 1
#pylab.imshow(error[0,:,:]), pylab.show()
#update image
image = image * error
reconspace = fillStirSpace(reconspace, image)
return reconspace
def forwardProjectionShiftError(yShift, forwardProjector, shiftingSino, referenceSino, image, shiftImage, iter, iFrame):
npimage = stirextra.to_numpy(image)
npshiftim = np.zeros(np.shape(npimage))
ndimage.shift(npimage, [0, yShift, 0], output = npshiftim)
shiftImage = fillStirSpace(shiftImage, npshiftim)
#Forward project
forwardProjector.forward_project(shiftingSino, shiftImage)
#Calculate error measure
shiftingSinoExtr = stirextra.to_numpy(shiftingSino.get_segment_by_sinogram(0))
shiftingSinoExtr /= np.sum(shiftingSinoExtr)
referenceSinoExtr = stirextra.to_numpy(referenceSino.get_segment_by_sinogram(0))
referenceSinoExtr /= np.sum(referenceSinoExtr)
npShiftingSino =shiftingSinoExtr - referenceSinoExtr
npShiftingSino[np.isnan(npShiftingSino)] = 0
npShiftingSino[np.isinf(npShiftingSino)] = 0
return np.sum(npShiftingSino**2)
def test_sinogram():
"""
Make sure that the sinogram offsets are correct.
"""
scanner = mCT()
compression, proj, projections = get_projections(scanner)
sinfo = compression._get_sinogram_info()
seg_ind = np.random.randint(len(sinfo))
segment = sinfo[seg_ind][0]
ax_ind = np.random.randint(sinfo[seg_ind][1])
offset = compression.get_offset(segment, ax_ind)
computed = projections[offset].asarray()
expected = stirextra.to_numpy(proj.proj_data.get_sinogram(ax_ind, segment))
assert pytest.approx(computed) == expected
import stirextra
#%% You could set "interactive display" on
# This would mean that plots are generated and the program immediatelly continues,
# as opposed to waiting for you to close a figure.
#pylab.ion()
#%% image display
# read an image using STIR
image = stir.FloatVoxelsOnCartesianGrid.read_from_file(
'../../recon_test_pack/test_image_3.hv')
# convert data to numpy 3d array
npimage = stirextra.to_numpy(image)
# make some plots
# first a bitmap
pylab.figure()
pylab.imshow(npimage[10, :, :], cmap='hot')
pylab.title('slice 10 (starting from 0)')
pylab.show()
# now a profile
pylab.figure()
pylab.plot(npimage[10, 45, :])
pylab.xlabel('x')
pylab.title('slice 10, line 45 (starting from 0)')
pylab.show()
#%% Let's read some projection data
#%% create projection data for output of forward projection
# We'll just create the data in memory here
projdataout = stir.ProjDataInMemory(projdata.get_exam_info(),
projdata.get_proj_data_info())
# Note: we could write to file, but it is right now a bit complicated to open a
# file for read/write:
# inout=stir.ios.trunc|stir.ios.ios_base_in|stir.ios.out;
# projdataout=stir.ProjDataInterfile(projdata.get_exam_info(), projdata.get_proj_data_info(), 'my_test_python_projection.hs',inout);
#%% forward project an image. Here just some uniform data
target.fill(2)
forwardprojector.set_up(projdataout.get_proj_data_info(), target)
forwardprojector.forward_project(projdataout, target)
#%% display
seg = projdataout.get_segment_by_sinogram(0)
seg_array = stirextra.to_numpy(seg)
pylab.figure()
pylab.subplot(1, 2, 1)
pylab.imshow(seg_array[10, :, :])
pylab.title('Forward projection')
pylab.subplot(1, 2, 2)
pylab.plot(seg_array[10, 0, :])
pylab.show()
#%% backproject this projection data
# we need to set the target to zero first, otherwise it will add to existing numbers.
target.fill(0)
backprojector.set_up(projdataout.get_proj_data_info(), target)
backprojector.back_project(target, projdataout)
#%% display
# This shows a beautiful pattern, a well-known feature of a ray-tracing matrix
target_array = stirextra.to_numpy(target)
# Without it, the python shell will wait after every pylab.show() for you
# to close the window.
try:
pylab.ion()
except:
print("Enabling interactive-mode for plotting failed. Continuing.")
s = recon.set_up(target)
if (s == stir.Succeeded(stir.Succeeded.yes)):
pylab.figure()
for iter in range(1, 4):
print('\n--------------------- Subiteration ', iter)
recon.set_start_subiteration_num(iter)
recon.set_num_subiterations(iter)
s = recon.reconstruct(target)
# currently we need to explicitly prevent recomputing sensitivity
# when we call reconstruct() again in the next iteration
poissonobj.set_recompute_sensitivity(False)
# extract to python for plotting
npimage = stirextra.to_numpy(target)
pylab.plot(npimage[10, 30, :])
pylab.show()
# plot slice of final image
pylab.figure()
pylab.imshow(npimage[10, :, :])
# Keep figures open until user closes them
pylab.show(block=True)
else:
print('Error setting-up reconstruction object')
import stir
import stirextra
#%% You could set "interactive display" on
# This would mean that plots are generated and the program immediatelly continues,
# as opposed to waiting for you to close a figure.
#pylab.ion()
#%% image display
# read an image using STIR
image=stir.FloatVoxelsOnCartesianGrid.read_from_file('../../recon_test_pack/test_image_3.hv')
# convert data to numpy 3d array
npimage=stirextra.to_numpy(image);
# make some plots
# first a bitmap
pylab.figure()
pylab.imshow(npimage[10,:,:], cmap='hot');
pylab.title('slice 10 (starting from 0)')
pylab.show()
# now a profile
pylab.figure();
pylab.plot(npimage[10,45,:]);
pylab.xlabel('x')
pylab.title('slice 10, line 45 (starting from 0)')
pylab.show()
def volume_from_voxels(_voxels):
space = space_from_stir_domain(_voxels)
arr = to_numpy(_voxels)
element = space.element(arr)
return element
def forwardProject(npSource):
guessVolume.fill(npSource.flat)
forwardSino2D.fill(0)
forwardprojector2D.forward_project(forwardSino2D, guessVolume)
return stirextra.to_numpy(forwardSino2D)
def backProject(npSino):
guessVolume.fill(0)
forwardSino2D.fill(npSino.flat)
backprojector2D.back_project(guessVolume, forwardSino2D)
return stirextra.to_numpy(guessVolume)
'''
image = np.zeros((160,160))
image[65:95, 65:95] = 1
'''
## TEST: Recons maken na verschillende iteraties -> som berekenen
testList = []
sumList = []
test = stir.FloatVoxelsOnCartesianGrid(projdata_info, 1,
stir.FloatCartesianCoordinate3D(stir.make_FloatCoordinate(0,0,0)),
stir.IntCartesianCoordinate3D(stir.make_IntCoordinate(1,200,200))) # Lengte moet je gokken/weten
for i in range(8):
test = test.read_from_file('output_config_Proj_1_{0}.hv'.format(i+1))
testList.append(stirextra.to_numpy(test))
sumList.append(np.sum(stirextra.to_numpy(test)[0,:,:]))
axisX = range(1,9,1)
plt.plot(axisX, sumList, axisX, [np.sum(image)]*len(axisX)), plt.title('Sum of OSMAPOSL recon (blue), sum of original image (green)'), plt.xlabel('Iteration number')
plt.savefig('./Plaatjes/OSMAPOSLSumAfterIterations.png')
plt.show()
for i in range(8):
plt.subplot(2,4,i+1), plt.imshow(testList[i][0,:,:], cmap=plt.cm.Greys_r, interpolation=None, vmin = 0), plt.title('Iteration {0}'.format(i))
plt.savefig('./Plaatjes/OSMAPOSLReconAfterIterations.png'.format(trueShiftPixels))
plt.show()
##
# Image shape ##
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 = []
MotionModel.setOffset(0.0)
for i in range(nFrames):
forwardprojector.forward_project(measurement, phantomS[i])
measurement.write_to_file('sinoMeas_{}.hs'.format(i + 1))
measurementS = measurement.get_segment_by_sinogram(0)
measurementP = stirextra.to_numpy(measurementS)
#measurementP /= np.sum(measurementP)
if (noise):
measurementP = sp.random.poisson(measurementP)
measurementListP.append(measurementP)
plt.subplot(2, nFrames / 2 + 1,
i + 1), plt.imshow(measurementP[0, :, :],
cmap=plt.cm.Greys_r,
interpolation=None,
vmin=0), plt.title('Meas. TF0')
plt.savefig(figSaveDir + 'Fig{}_TrueShift{}_Measurements.png'.format(
numFigures, trueShiftAmplitude))
numFigures += 1
plt.close()
# Define the time frames - we are just defining one timeframe starting at 0 and ending at 10s.
time_frames = stir.TimeFrameDefinitions()
time_frames.set_num_time_frames(1)
time_frames.set_time_frame(1, 0, 10)
lm_to_projdata.set_time_frame_definitions(time_frames)
# Read template ProjData.
template_projdata = stir.ProjData.read_from_file("../../recon_test_pack/Siemens_mMR_seg2.hs")
lm_to_projdata.set_template_proj_data_info(template_projdata.get_proj_data_info())
# Perform the actual processing.
lm_to_projdata.set_up()
lm_to_projdata.process_data()
# Read in the generated proj data and visualise them (looks a bit like abstract art,
# as there are very few counts in this example data).
generated_projdata = stir.ProjData.read_from_file("output_projdata_f1g1d0b0.hs")
first_segment = generated_projdata.get_segment_by_sinogram(0)
projdata_np = stirextra.to_numpy(first_segment)
plt.figure()
plt.imshow(projdata_np[projdata_np.shape[0] // 2, :, :]) # plot the middle slice
plt.title("sinogram 10 (starting from 0)")
plt.clim(0, projdata_np.max() * 0.9)
plt.colorbar()
plt.show(block=True)
# Finally, let's keep the example folder clean.
os.remove("output_projdata_f1g1d0b0.hs")
os.remove("output_projdata_f1g1d0b0.s")
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(
stir.make_IntCoordinate(
np.shape(originalImageP)[0],
np.shape(originalImageP)[1],
np.shape(originalImageP)[2])))
backprojector.back_project(finalImageS, measurement)
finalImageP = stirextra.to_numpy(finalImageS)
# create a coordinate for the centre (note the z,y,x order)
centre=stir.FloatCartesianCoordinate3D(z_centre,0,0)
# create a geometrical shape
shape=stir.EllipsoidalCylinder(length, radius, radius,
centre)
#%% we set the image to a discretised version of this shape
# (the last argument means we'll sample every voxel only once)
shape.construct_volume(image_data, stir.IntCartesianCoordinate3D(1,1,1))
#%% Let's add another translated cylinder
# The way to do this is currently still awkward. Apologies.
shape.translate(stir.FloatCartesianCoordinate3D(15,90,40))
# make a clone and fill that one with the second shape
image_data2=image_data.clone()
shape.construct_volume(image_data2, stir.IntCartesianCoordinate3D(1,1,1))
# now add that to the previous one (currently messy as we need to pass through numpy, sorry)
image_data_array=stirextra.to_numpy(image_data);
image_data_array+=stirextra.to_numpy(image_data2);
image_data.fill(image_data_array.flat)
#%% display 2 transaxial slices of the volume
maxforplot=image_data.find_max(); # save for display
image_data_array=stirextra.to_numpy(image_data);
plt.figure();
plt.subplot(1,2,1)
plt.imshow(image_data_array[middle_slice,:,:]);
plt.clim(0,maxforplot)
plt.title('slice %d' % middle_slice)
plt.subplot(1,2,2)
plt.imshow(image_data_array[middle_slice+5,:,:]);
plt.title('slice %d' % (middle_slice+5))
plt.clim(0,maxforplot)
import os
import numpy as np
import time
#%% go to directory with input files
print("\nRunning ROI_demo.py")
os.chdir('../recon_demo')
image_filename = 'init.hv'
# Load image from file (for shape)
print(f"Loading {image_filename} as image...")
image = stir.FloatVoxelsOnCartesianGrid.read_from_file(image_filename)
print("Populating image with random values...")
# Make a copy in numpy, populate random voxel value and back-fill STIR FloatVoxelsOnCartesianGrid object
image_numpy = stirextra.to_numpy(image)
image_numpy = np.random.random(image_numpy.shape)
image.fill(image_numpy.flat)
# Construct an example shape
print(
"Creating a EllipsoidalCylinder object as the Region Of Interest (ROI)...")
ROI_shape = stir.EllipsoidalCylinder(10, 5, 4,
stir.FloatCartesianCoordinate3D(0, 0, 0))
# number_of_sample needs to be a 3D Int CartesianCoordinate
n = 10
print(f"Setting the number of samples of each axis to be {n}...")
number_of_samples = stir.IntCartesianCoordinate3D(n, n, n)
print(
forwardprojector=stir.ForwardProjectorByBinUsingProjMatrixByBin(projmatrix);
backprojector=stir.BackProjectorByBinUsingProjMatrixByBin(projmatrix);
#%% create projection data for output of forward projection
# We'll just create the data in memory here
projdataout=stir.ProjDataInMemory(projdata.get_exam_info(), projdata.get_proj_data_info());
# Note: we could write to file, but it is right now a bit complicated to open a
# file for read/write:
# inout=stir.ios.trunc|stir.ios.ios_base_in|stir.ios.out;
# projdataout=stir.ProjDataInterfile(projdata.get_exam_info(), projdata.get_proj_data_info(), 'my_test_python_projection.hs',inout);
#%% forward project an image. Here just some uniform data
target.fill(2);
forwardprojector.forward_project(projdataout, target);
#%% display
seg=projdataout.get_segment_by_sinogram(0);
seg_array=stirextra.to_numpy(seg);
pylab.figure();
pylab.subplot(1,2,1)
pylab.imshow(seg_array[10,:,:]);
pylab.title('Forward projection')
pylab.subplot(1,2,2)
pylab.plot(seg_array[10,0,:])
pylab.show()
#%% backproject this projection data
# we need to set the target to zero first, otherwise it will add to existing numbers.
target.fill(0)
backprojector.back_project(target, projdataout);
#%% display
# This shows a beautiful pattern, a well-known feature of a ray-tracing matrix
target_array=stirextra.to_numpy(target);
pylab.figure();
NormSpace, backprojector,
stir.ProjDataInMemory(stir.ExamInfo(), projdata_info))
locationList = []
#sinosum = np.zeros((1,252,344))
for iFrame in range(nFrames):
reconList[iFrame] = MLEMRecon(NormSpace,
reconList[iFrame],
imspaceError,
forwardprojector,
backprojector,
sinogramList[iFrame],
measurementList[iFrame],
nIter=5)
#sinosum += stirextra.to_numpy(measurementList[iFrame].get_segment_by_sinogram(0))
recon = pyvpx.numpy2vpx(stirextra.to_numpy(reconList[0]), 'Recon0.vpx')
recon = pyvpx.numpy2vpx(stirextra.to_numpy(reconList[1]), 'Recon1.vpx')
recon = pyvpx.numpy2vpx(
stirextra.to_numpy(reconList[1]) - stirextra.to_numpy(reconList[0]),
'ReconDiff.vpx')
#recnp = stirextra.to_numpy(reconList[0])
#plt.imshow(recnp[0,:,:]), plt.show()
'''
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] )))
vShift = np.array([0,0,0])
vShiftOut, errorLog = OptimizeSinogramError(vShift, forwardprojector,sinogramList ,measurementList ,reconList[0], guestimatespace, SurrogateSignal)
print(vShiftOut)
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)
#_________________________FIRST RECONSTRUCTION________________________
# Measurement/projections of inital time frame
measurement = stir.ProjDataInMemory(stir.ExamInfo(), projdata_info)
forwardprojector.forward_project(measurement, phantomS[0])
measurement.write_to_file('sino_1.hs')
measurementS = measurement.get_segment_by_sinogram(0)
measurementP = stirextra.to_numpy(measurementS)
# Image reconstruction using OSMAPOSL
reconImageS = stir.FloatVoxelsOnCartesianGrid(projdata_info, 1,
stir.FloatCartesianCoordinate3D(stir.make_FloatCoordinate(0,0,0)),
stir.IntCartesianCoordinate3D(stir.make_IntCoordinate(np.shape(originalImageP)[0],np.shape(originalImageP)[1],np.shape(originalImageP)[2] )))
reconImageS.fill(1) # moet er staan
MotionModel.setOffset(0.0)
reconOSMAPOSL = stir.OSMAPOSLReconstruction3DFloat(projmatrix, 'config_Image_1.par')
s = reconOSMAPOSL.set_up(reconImageS)
reconOSMAPOSL.reconstruct(reconImageS)
reconImagePRef = stirextra.to_numpy(reconImageS) # reference time frame
#_________________________SECOND RECONSTRUCTION________________________
z_centre = middle_slice * image_data.get_voxel_size().z()
# create a coordinate for the centre (note the z,y,x order)
centre = stir.FloatCartesianCoordinate3D(z_centre, 0, 0)
# create a geometrical shape
shape = stir.EllipsoidalCylinder(length, radius, radius, centre)
#%% we set the image to a discretised version of this shape
# (the last argument means we'll sample every voxel only once)
shape.construct_volume(image_data, stir.IntCartesianCoordinate3D(1, 1, 1))
#%% Let's add another translated cylinder
# The way to do this is currently still awkward. Apologies.
shape.translate(stir.FloatCartesianCoordinate3D(15, 90, 40))
# make a clone and fill that one with the second shape
image_data2 = image_data.clone()
shape.construct_volume(image_data2, stir.IntCartesianCoordinate3D(1, 1, 1))
# now add that to the previous one (currently messy as we need to pass through numpy, sorry)
image_data_array = stirextra.to_numpy(image_data)
image_data_array += stirextra.to_numpy(image_data2)
image_data.fill(image_data_array.flat)
#%% display 2 transaxial slices of the volume
maxforplot = image_data.find_max()
# save for display
image_data_array = stirextra.to_numpy(image_data)
plt.figure()
plt.subplot(1, 2, 1)
plt.imshow(image_data_array[middle_slice, :, :])
plt.clim(0, maxforplot)
plt.title('slice %d' % middle_slice)
plt.subplot(1, 2, 2)
plt.imshow(image_data_array[middle_slice + 5, :, :])
plt.title('slice %d' % (middle_slice + 5))
plt.clim(0, maxforplot)
# Switch 'interactive' mode on for pylab.
# Without it, the python shell will wait after every pylab.show() for you
# to close the window.
pylab.ion()
s=recon.set_up(target);
if (s==stir.Succeeded(stir.Succeeded.yes)):
pylab.figure()
pylab.hold(True)
for iter in range(1,4):
print '\n--------------------- Subiteration ', iter
recon.set_start_subiteration_num(iter)
recon.set_num_subiterations(iter)
s=recon.reconstruct(target);
# currently we need to explicitly prevent recomputing sensitivity when we
# call reconstruct() again in the next iteration
poissonobj.set_recompute_sensitivity(False)
# extract to python for plotting
npimage=stirextra.to_numpy(target);
pylab.plot(npimage[10,30,:])
pylab.show()
# plot slice of final image
pylab.figure()
pylab.imshow(npimage[10,:,:])
pylab.show()
else:
print 'Error setting-up reconstruction object'
# This file is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# See STIR/LICENSE.txt for details
import numpy
import pylab
import stir
import stirextra
# read an image using STIR
image=stir.FloatVoxelsOnCartesianGrid.read_from_file('../../recon_test_pack/test_image_3.hv')
# convert data to numpy 3d array
npimage=stirextra.to_numpy(image);
# make some plots
# first a bitmap
pylab.figure()
pylab.imshow(npimage[10,:,:]);
pylab.title('slice 10 (starting from 0)')
pylab.show()
# now a profile
pylab.figure()
pylab.plot(npimage[10,45,:]);
pylab.xlabel('x')
pylab.title('slice 10, line 45 (starting from 0)')
pylab.show()
def test_load():
volume_file = base / 'initial.hv'
vol = volume_from_file(volume_file.as_posix())
stir_vol = stir.FloatVoxelsOnCartesianGrid.read_from_file(volume_file.as_posix())
assert pytest.approx(vol.asarray(), stirextra.to_numpy(stir_vol))