def __openFolder(self, mode):
""" Called when user wants to open a sequence of KEST files.
NOTE: a thread is started when this function is invoked.
"""
try:
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
options |= QFileDialog.ShowDirsOnly
folder = QFileDialog.getExistingDirectory(self,"Open KEST sequence",
"", options=options)
if folder:
# Disable buttons:
self.sidebar.reconstructionTab.button.setEnabled(False)
self.sidebar.preprocessingTab.btnApply.setEnabled(False)
# Read the file (on a separate thread):
self.readThread = ReadThread(self, folder, mode, True)
self.readThread.readDone.connect(self.readJobDone)
self.readThread.logOutput.connect(self.handleOutputLog)
self.readThread.error.connect(self.handleThreadError)
self.readThread.start()
# Open the related HDF5 (if exists):
#self.sidebar.hdfViewerTab.setHDF5File("C:\\Temp\\test.kest")
except Exception as e:
eprint(str(e))
# Restore the buttons:
self.sidebar.reconstructionTab.button.setEnabled(True)
self.sidebar.preprocessingTab.btnApply.setEnabled(True)
def __openFile(self, mode): """ Called when user wants to open a new KEST file. NOTE: a thread is started when this function is invoked. """ try: options = QFileDialog.Options() options |= QFileDialog.DontUseNativeDialog filename, _ = QFileDialog.getOpenFileName(self,"Open KEST file", "","KEST Files (*.dat);;All Files (*)", options=options) if filename: # Disable buttons: self.sidebar.reconstructionTab.button.setEnabled(False) self.sidebar.preprocessingTab.btnApply.setEnabled(False) # Read the file (on a separate thread): self.readThread = ReadThread(self, filename, mode, False) self.readThread.readDone.connect(self.readJobDone) self.readThread.logOutput.connect(self.handleOutputLog) self.readThread.error.connect(self.handleThreadError) self.readThread.start() except Exception as e: eprint(str(e)) # Restore the buttons: self.sidebar.reconstructionTab.button.setEnabled(True) self.sidebar.preprocessingTab.btnApply.setEnabled(True)
def _toolBarBtnPressed(self, button):
if button.text() == ZOOM_IN_TOOLTIP:
self.imagePanel.performZoom(min(400.0,self.imagePanel.zoomFactor*1.15))
elif button.text() == ZOOM_OUT_TOOLTIP:
self.imagePanel.performZoom(max(1.0,self.imagePanel.zoomFactor/1.15))
elif button.text() == ZOOM_RESET_TOOLTIP:
self.imagePanel.performZoom(1.0)
elif button.text() == EXPORT_TOOLTIP:
# Open a Save As dialog:
try:
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
filename, _ = QFileDialog.getSaveFileName(self,"Save as TIFF",
"","TIFF Files (*.tif);;All Files (*)", options=options)
if filename:
# Call the method to save the current displayed image:
self.imagePanel.saveAsTIFF(filename)
except Exception as e:
eprint(str(e))
elif button.text() == EXPORTALL_TOOLTIP:
# Open a Save As dialog:
try:
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
options |= QFileDialog.DirectoryOnly
folder = QFileDialog.getExistingDirectory(self, "Select Folder for TIFF sequence")
if folder:
for i in range(0,self.__data.shape[2]):
# Prepare filename:
filename = os.path.join(folder, "image_" + "{:04d}".format(i) + ".tif")
# Save as TIFF with tiffile library:
tifffile.imsave(filename, data=self.__data[:,:,i])
except Exception as e:
eprint(str(e))
def onQApplicationStarted(self):
""" Things done as the main window is fully loaded.
"""
try:
# Startup message:
platf = platform.uname()
cpus = psutil.cpu_count()
stat = psutil.virtual_memory()
ram = (stat.total) / (1024.0 * 1024 * 1024) # GB
# system, node, release, version, machine, and processor.
val = "KEST started on " + platf.node + " (# of CPUs: " + str(cpus) + \
", RAM: " + "{:.2f}".format(ram) + " GB)"
# Log string:
self.mainPanel.log.logOutput(val)
# Read settings:
#self.read_settings()
except Exception as e:
eprint(str(e))
pass
def applyReconstruction(self):
""" Called when user wants to perform the reconstruction on current flat-fielded image:
NOTE: the current image should be a 'pre-processed' image. The UI should avoid
to let this method callable when current image is not a 'pre-processed'.
NOTE: a thread is started when this function is invoked.
"""
try:
# Disable buttons:
self.sidebar.reconstructionTab.button.setEnabled(False)
self.sidebar.preprocessingTab.btnApply.setEnabled(False)
# Get current left image:
curr_tab = self.mainPanel.getCurrentTab()
im = curr_tab.getData()
sourceFile = curr_tab.getSourceFile()
mode = curr_tab.getOriginalMode()
# Get parameters from UI:
method = self.sidebar.reconstructionTab.getValue("ReconstructionAlgorithm_Method")
iterations = self.sidebar.reconstructionTab.getValue("ReconstructionAlgorithm_Iterations")
filter = self.sidebar.reconstructionTab.getValue("ReconstructionAlgorithm_FDK-Filter")
weights = self.sidebar.reconstructionTab.getValue("ReconstructionAlgorithm_Weights")
angles = self.sidebar.reconstructionTab.getValue("Reconstruction_Angles")
angles_shift = self.sidebar.reconstructionTab.getValue("Reconstruction_Angles_Shift")
angles_decimation = self.sidebar.reconstructionTab.getValue("Reconstruction_Angles_Decimation")
nr_proj = self.sidebar.reconstructionTab.getValue("Reconstruction_Projections")
upsampling = self.sidebar.reconstructionTab.getValue("ReconstructionAlgorithm_Upsampling")
overpadding = self.sidebar.reconstructionTab.getValue("ReconstructionAlgorithm_Overpadding")
geometry = self.sidebar.reconstructionTab.getValue("Geometry_Type")
ssd = float(self.sidebar.reconstructionTab.getValue("Geometry_Source-Sample"))
sdd = float(self.sidebar.reconstructionTab.getValue("Geometry_Source-Detector"))
px = float(self.sidebar.reconstructionTab.getValue("Geometry_DetectorPixelSize"))
det_u = float(self.sidebar.reconstructionTab.getValue("Offsets_Detector-u"))
det_v = float(self.sidebar.reconstructionTab.getValue("Offsets_Detector-v"))
roll = float(self.sidebar.reconstructionTab.getValue("Offsets_Detector-Roll"))
pitch = float(self.sidebar.reconstructionTab.getValue("Offsets_Detector-Pitch"))
yaw = float(self.sidebar.reconstructionTab.getValue("Offsets_Detector-Yaw"))
# Remove extra projections:
im = im[:,:,:nr_proj]
im = im[:,:,::angles_decimation]
# Convert from degrees to radians:
angles = angles * numpy.pi / 180.0
angles_shift = angles_shift * numpy.pi / 180.0
# Convert to boolean for short_scan:
short_scan = False if (weights == 0) else True
# Call reconstruction (on a separate thread):
self.reconThread = ReconThread(self, im, sourceFile, angles, geometry, \
ssd, sdd, px, det_u, det_v, short_scan, method, iterations, mode, \
overpadding, angles_shift )
self.reconThread.reconDone.connect(self.reconstructJobDone)
self.reconThread.logOutput.connect(self.handleOutputLog)
self.reconThread.error.connect(self.handleThreadError)
self.reconThread.start()
# Only for debug:
#rec = recon_tigre_fdk(im, ssd, sdd - ssd, px, angles, \
# angles_shift, det_u, det_v, roll, pitch,
# yaw, short_scan, overpadding, filter)
#self.reconstructJobDone(rec, sourceFile, RECON_TABLABEL, mode)
except Exception as e:
# Print the exception:
eprint("Error while performing reconstruction: " + str(e))
# Restore the buttons:
self.sidebar.reconstructionTab.button.setEnabled(True)
self.sidebar.preprocessingTab.btnApply.setEnabled(True)
def applyPreprocessing(self):
""" Called when user wants to apply the preprocessing on current image.
NOTE: the current image should be a 'raw' image. The UI should avoid
to let this method callable when current image is not a 'raw'.
NOTE: a thread is started when this function is invoked.
"""
try:
# Disable buttons:
self.sidebar.reconstructionTab.button.setEnabled(False)
self.sidebar.preprocessingTab.btnApply.setEnabled(False)
# Get current left image:
curr_tab = self.mainPanel.getCurrentTab()
sourceFile = curr_tab.getSourceFile()
mode = curr_tab.getOriginalMode()
# Get params from UI:
crop_top = self.sidebar.preprocessingTab.getValue("Crop_Top")
crop_bottom = self.sidebar.preprocessingTab.getValue("Crop_Bottom")
crop_left = self.sidebar.preprocessingTab.getValue("Crop_Left")
crop_right = self.sidebar.preprocessingTab.getValue("Crop_Right")
proj_avg_mode = self.sidebar.preprocessingTab.getValue("ProjectionAveraging_Mode")
proj_avg_alpha = self.sidebar.preprocessingTab.getValue("ProjectionAveraging_AlphaTrimmed")
rebinning = self.sidebar.preprocessingTab.getValue("MatrixManipulation_Rebinning2x2")
flatfielding_window = self.sidebar.preprocessingTab.getValue("FlatFielding_Window")
despeckle_thresh = self.sidebar.preprocessingTab.getValue("Despeckle_Threshold")
ringremoval_thresh = self.sidebar.preprocessingTab.getValue("RingRemoval_Threshold")
output_low = self.sidebar.preprocessingTab.getValue("Output_LowEnergy")
output_high = self.sidebar.preprocessingTab.getValue("Output_HighEnergy")
output_diff = self.sidebar.preprocessingTab.getValue("Output_LogSubtraction")
output_sum = self.sidebar.preprocessingTab.getValue("Output_EnergyIntegration")
## Call pre-processing (on a separate thread):
#self.preprocessThread = PreprocessThread(self, self.dset, rebinning, \
# flatfielding_window, despeckle_thresh, output_low, output_high, \
# output_diff, output_sum, mode, crop_top, crop_bottom, crop_left, \
# crop_right, proj_avg_mode, proj_avg_alpha )
#self.preprocessThread.processDone.connect(self.preprocessJobDone)
#self.preprocessThread.logOutput.connect(self.handleOutputLog)
#self.preprocessThread.error.connect(self.handleThreadError)
#self.preprocessThread.start()
# For debug:
low, high, diff, sum = pre_processing(self.dset, rebinning, \
flatfielding_window, despeckle_thresh, output_low, \
output_high, output_diff, output_sum, mode, \
[crop_top, crop_bottom, crop_left, crop_right], \
proj_avg_mode, proj_avg_alpha, ringremoval_thresh )
self.preprocessJobDone( low, high, diff, sum, output_low, output_high, \
output_diff, output_sum, sourceFile, PREPROC_TABLABEL, mode )
except Exception as e:
eprint("Error while pre-processing: " + str(e))
# Restore the buttons:
self.sidebar.reconstructionTab.button.setEnabled(True)
self.sidebar.preprocessingTab.btnApply.setEnabled(True)