def openFile(self):
fn = QFileDialog.getOpenFileNames(self, 'Open File')
# If the user has pressed cancel, the first element of the tuple will be empty.
# Quit the method cleanly
if not fn[0]:
return
# Single file selection
if len(fn[0]) == 1:
file = fn[0][0]
reader = vtk.vtkMetaImageReader()
reader.AddObserver("ErrorEvent", self.e)
reader.SetFileName(file)
reader.Update()
# Multiple TIFF files selected
else:
# Make sure that the files are sorted 0 - end
filenames = natsorted(fn[0])
# Basic test for tiff images
for file in filenames:
ftype = imghdr.what(file)
if ftype != 'tiff':
# A non-TIFF file has been loaded, present error message and exit method
self.e('','','When reading multiple files, all files must TIFF formatted.')
file = file
self.displayFileErrorDialog(file)
return
# Have passed basic test, can attempt to load
numpy_image = Converter.tiffStack2numpyEnforceBounds(filenames=filenames)
reader = Converter.numpy2vtkImporter(numpy_image)
reader.Update()
if self.e.ErrorOccurred():
self.displayFileErrorDialog(file)
else:
self.vtkWidget.viewer.setInput3DData(reader.GetOutput())
self.setStatusTip('Ready')
def avgProjections(self, filenames):
'''Returns the average of the input images
Input is passed as filenames pointing to 2D TIFF
Output is numpy array
'''
num = len(filenames)
stack = Converter.tiffStack2numpy(filenames=filenames , extent=extent,
sampleRate=(1,1,1))
avg = (stack.T[0] / float(num) )
for i in range(1,num):
avg += (stack.T[i] / float(num))
return avg
def normalizeProjections(self, projectionFileNames=None,
flatFileNames=None,
darkFileNames=None,
extent=None, sampleRate=None):
if projectionFileNames is not None:
self.setProjectionsFileNames(projectionFileNames)
if flatFileNames is not None:
self.setFlatsFileNames(flatFileNames)
if darkFileNames is not None:
self.setDarksFileNames(darkFileNames)
flat = self.avgProjections(self.flatsFileNames)
dark = self.avgProjections(self.darksFileNames)
self.normalizedProjections = Converter.tiffStack2numpy(filenames=self.projectionsFileNames,
darkField=dark, flatField=flat,
extent=extent, sampleRate=sampleRate)
tot_images = 2203
## create a reduced 3D stack
nreduced = 360
directory = r'D:\Documents\Dataset\Chadwick_Flange_Tomo'
indices = [int(float(num) / float(nreduced) * float(tot_images)) for num in range(nreduced)]
angle_proj = numpy.asarray(indices) * 180 / tot_images
#load data file
reader = vtk.vtkMetaImageReader()
reader.SetFileName("Chadwick_flange_norm_360.mha")
reader.Update()
norm = Converter.vtk2numpy(reader.GetOutput())
pp = ProjectionPreprocessor()
pp.normalizedProjections = norm
norm = pp.getNormalizedProjections()
cor = 175.75
############################################################
#recon.pars['algorithm'] = Reconstructor.Algorithm.CGLS_CONV
#recon.pars['regularize'] = numpy.double(0.1)
#img_cgls_conv = recon.reconstruct()
niterations = 15
threads = 4
data = (norm.T).copy()
print("append", end1 - start)
while (nop.append_for(np.random.uniform(low=-1, high=1, size=3)) < M):
pass
end2 = time.time()
print("append_for", end2 - end1)
#%%
gaussians = [{
'Obj': tp3.Objects3D.PARABOLOID,
'C0': 1.,
'x0': float(nop.apoints[loc][0]),
'y0': float(nop.apoints[loc][1]),
'z0': float(nop.apoints[loc][2]),
'a': .2,
'b': .1,
'c': .15,
'phi1': np.random.uniform(low=0, high=360),
'phi2': np.random.uniform(low=0, high=360),
'phi3': np.random.uniform(low=0, high=360)
} for loc in range(len(nop.apoints))]
vol = tp3.Object(128, gaussians)
plt.imshow(vol[0])
plt.show()
writer = vtk.vtkMetaImageWriter()
conv = Converter.numpy2vtkImporter(vol)
conv.Update()
writer.SetInputData(conv.GetOutput())
writer.SetFileName("dvc_phantom0.mha")
writer.Write()
def openFile(self, progress_callback=None, **kwargs):
"""
Open file(s) based on results from QFileDialog
:param (function) progress_callback:
Callback funtion to emit progress percentage.
"""
if 'filename' not in kwargs.keys():
fn = self.fn
else:
fn = ([kwargs['filename']],)
# If the user has pressed cancel, the first element of the tuple will be empty.
# Quit the method cleanly
if not fn[0]:
return
# Single file selection
if len(fn[0]) == 1:
file = fn[0][0]
if progress_callback:
progress_callback.emit(30)
reader = vtk.vtkMetaImageReader()
reader.AddObserver("ErrorEvent", self.e)
reader.SetFileName(file)
reader.Update()
if progress_callback:
progress_callback.emit(90)
self.mainwindow.setStatusTip('File Read: {}'.format(reader.GetOutput().GetExtent()))
# Multiple TIFF files selected
else:
# Make sure that the files are sorted 0 - end
filenames = natsorted(fn[0])
increment = 30.0 / len(filenames)
# Basic test for tiff images
for n,file in enumerate(filenames,1):
ftype = imghdr.what(file)
if ftype != 'tiff':
# A non-TIFF file has been loaded, present error message and exit method
self.e('','','Problem reading file: {}'.format(file))
raise ReadError("File read error!")
if progress_callback:
progress_callback.emit(int(n * increment))
# Have passed basic test, can attempt to load
numpy_image = Converter.pureTiff2Numpy(filenames=filenames, bounds=(256,256,256), progress_callback=progress_callback)
reader = Converter.numpy2vtkImporter(numpy_image)
reader.Update()
if self.e.ErrorOccurred():
raise ReadError()
else:
self.viewerWidget.viewer.setInput3DData(reader.GetOutput())
if progress_callback:
progress_callback.emit(91)
self.mainwindow.setStatusTip('display 2D')
if progress_callback:
progress_callback.emit(92)
self.viewer3DWidget.viewer.setInput3DData(reader.GetOutput())
if progress_callback:
progress_callback.emit(93)
self.graph_numpy_input_data = Converter.vtk2numpy(reader.GetOutput(), transpose=[2,1,0])
if progress_callback:
progress_callback.emit(94)
self.mainwindow.setStatusTip('convert to numpy')
self.mainwindow.setStatusTip('Ready')
if progress_callback:
progress_callback.emit(95)
self.spacing = reader.GetOutput().GetSpacing()
if progress_callback:
progress_callback.emit(96)
self.origin = reader.GetOutput().GetOrigin()
if progress_callback:
progress_callback.emit(97)
### After successfully opening file, reset the interface ###
# Reset linked state
self.linkViewers(force_linked=True)
# Reset graph if drawn
self.graphWidget.viewer.update(vtk.vtkMutableDirectedGraph())
# Reset graph parameter panel
if self.hasDockableWindow:
for element in self.treeWidgetInitialElements:
element.setEnabled(True)
for element in self.treeWidgetUpdateElements:
element.setEnabled(False)
print ("finished openFile")
surface += 1
# polydata object
trianglePolyData = vtk.vtkPolyData()
trianglePolyData.SetPoints(triangle_vertices)
trianglePolyData.SetPolys(triangles)
return trianglePolyData
reader = vtk.vtkMetaImageReader()
reader.SetFileName("../../data/fuel_uc_python.mha")
reader.Update()
seg = SimpleflexSegmentor()
seg.setInputData(Converter.vtk2numpy(reader.GetOutput()))
seg.calculateContourTree()
#seg.setIsoValuePercent(24.)
seg.setLocalIsoValuePercent(0.)
seg.resetCollapsePriority(seg.PRIORITY_VOLUME)
# 5. Construct the iso-surfaces
print("calling resetCollapsePriority")
#seg.updateTreeFromLogTreeSize(size=0.6, isGlobal=False)
print("calling setlogtreesize")
seg.ct.SetLogTreeSize(1)
print("calling UpdateTreeFromLogTreeSize")
seg.ct.UpdateTreeFromLogTreeSize()