def showReconstruct(self):
'''
load window for reconstruction window
'''
self.write = xrftomo.SaveOptions()
self.actions.x_shifts = self.x_shifts
self.actions.y_shifts = self.y_shifts
self.actions.centers = self.centers
self.y_range = self.data.shape[2]
self.ViewControl.combo1.clear()
self.ViewControl.method.clear()
methodname = [
"mlem", "gridrec", "art", "pml_hybrid", "pml_quad", "fbp", "sirt",
"tv"
]
for j in self.elements:
self.ViewControl.combo1.addItem(j)
for k in arange(len(methodname)):
self.ViewControl.method.addItem(methodname[k])
self.elementChanged()
# self.ViewControl.centerTextBox.setText(str(self.centers[2]))
self.ViewControl.mulBtn.setEnabled(False)
self.ViewControl.divBtn.setEnabled(False)
self.ViewControl.end_indx.setText((str(self.data.shape[2])))
self.sld.setRange(0, self.y_range - 1)
self.lcd.display(0)
def showReconstruct(self):
'''
load window for reconstruction window
'''
self.write = xrftomo.SaveOptions()
self.actions.x_shifts = self.x_shifts
self.actions.y_shifts = self.y_shifts
self.actions.centers = self.centers
self.y_range = self.data.shape[2]
self.ViewControl.combo1.clear()
self.ViewControl.method.clear()
self.ViewControl.reconGroup.clear()
self.ViewControl.reconGroup.disconnect()
methodname = [
"mlem", "gridrec", "art", "pml_hybrid", "pml_quad", "fbp", "sirt",
"tv"
]
for j in self.elements:
self.ViewControl.combo1.addItem(j)
for k in range(len(methodname)):
self.ViewControl.method.addItem(methodname[k])
for l in self.elements:
self.ViewControl.reconGroup.addItem(l)
self.recon_array = np.zeros((len(self.elements), self.y_range,
self.data.shape[3], self.data.shape[3]))
self.ViewControl.reconGroup.currentIndexChanged.connect(
self.recon_combobox_changed)
self.elementChanged()
#TODO: recon_array will need to update with any changes to data dimensions as well as re-initialization
# self.ViewControl.centerTextBox.setText(str(self.centers[2]))
self.ViewControl.mulBtn.setEnabled(False)
self.ViewControl.divBtn.setEnabled(False)
self.ViewControl.end_indx.setText((str(self.data.shape[2])))
self.ViewControl.mid_indx.setText((str(self.data.shape[2] // 2)))
self.sld.setRange(0, self.y_range - 1)
self.lcd.display(0)
def initUI(self):
exitAction = QtGui.QAction('Exit', self)
exitAction.triggered.connect(self.close)
exitAction.setShortcut('Ctrl+Q')
closeAction = QtGui.QAction('Quit', self)
closeAction.triggered.connect(sys.exit)
closeAction.setShortcut('Ctrl+X')
openH5Action = QtGui.QAction('open h5 file', self)
openH5Action.triggered.connect(self.openH5)
openExchangeAction = QtGui.QAction('open exchange file', self)
openExchangeAction.triggered.connect(self.openExchange)
openTiffAction = QtGui.QAction('open tiff files', self)
openTiffAction.triggered.connect(self.openTiffs)
openThetaAction = QtGui.QAction('open thetas file', self)
openThetaAction.triggered.connect(self.openThetas)
#openTiffFolderAction = QtGui.QAction("Open Tiff Folder", self)
#openTiffFolderAction.triggered.connect(self.openTiffFolder)
saveProjectionAction = QtGui.QAction('Projections', self)
saveProjectionAction.triggered.connect(self.saveProjections)
# saveHotSpotPosAction = QtGui.QAction('save hotspot positions',self)
# saveHotSpotPosAction.triggered.connect(self.save_hotspot_positions)
saveSinogramAction = QtGui.QAction('Sinogram', self)
saveSinogramAction.triggered.connect(self.saveSinogram)
saveSinogram2Action = QtGui.QAction('Sinogram stack', self)
saveSinogram2Action.triggered.connect(self.saveSinogram2)
saveReconstructionAction = QtGui.QAction('Reconstruction', self)
saveReconstructionAction.triggered.connect(self.saveReconstruction)
saveToHDFAction = QtGui.QAction('as HDF file', self)
saveToHDFAction.triggered.connect(self.saveToHDF)
saveThetasAction = QtGui.QAction('Angle information to .txt', self)
saveThetasAction.triggered.connect(self.saveThetas)
saveToNumpyAction = QtGui.QAction("as Numpy file", self)
saveToNumpyAction.triggered.connect(self.saveToNumpy)
saveAlignemtInfoAction = QtGui.QAction("Alignment", self)
saveAlignemtInfoAction.triggered.connect(self.saveAlignemnt)
saveCorrAnalysisAction = QtGui.QAction("Corelation Analysis", self)
saveCorrAnalysisAction.triggered.connect(self.saveCorrAlsys)
runTransRecAction = QtGui.QAction("Transmission Recon", self)
#runTransRecAction.triggered.connect(self.runTransReconstruct)
# selectImageTagAction = QtGui.QAction("Select Image Tag", self)
#selectImageTagAction.triggered.connect(self.selectImageTag)
undoAction = QtGui.QAction('Undo (Ctrl+Z)', self)
undoAction.triggered.connect(self.undo)
undoAction.setShortcut('Ctrl+Z')
preferencesAction = QtGui.QAction("exit preferences")
restoreAction = QtGui.QAction("Restore", self)
restoreAction.triggered.connect(self.restore)
keyMapAction = QtGui.QAction('key map settings', self)
keyMapAction.triggered.connect(self.keyMapSettings)
configAction = QtGui.QAction('load configuration settings', self)
configAction.triggered.connect(self.configSettings)
# matcherAction = QtGui.QAction("match template", self)
#matcherAction.triggered.connect(self.match_window)
# saveHotSpotPosAction = QtGui.QAction("Save Hot Spot Pos", self)
#saveHotSpotPosAction.triggered.connect(self.saveHotSpotPos)
wienerAction = QtGui.QAction("Wiener", self)
#wienerAction.triggered.connect(self.ipWiener)
# externalImageRegAction = QtGui.QAction("External Image Registaration", self)
#externalImageRegAction.triggered.connect(self.externalImageReg)
###
self.frame = QtWidgets.QFrame()
self.vl = QtWidgets.QVBoxLayout()
# theta_auto_completes = seshowImgProcesslf.config.get(STR_CONFIG_THETA_STRS)
# theta_auto_completes = self.params.theta_pv
# if theta_auto_completes is None:
# theta_auto_completes = []
self.fileTableWidget = xrftomo.FileTableWidget(self)
self.imageProcessWidget = xrftomo.ImageProcessWidget()
self.sinogramWidget = xrftomo.SinogramWidget()
self.reconstructionWidget = xrftomo.ReconstructionWidget()
self.writer = xrftomo.SaveOptions()
#refresh UI
self.imageProcessWidget.refreshSig.connect(self.refreshUI)
#sinogram changed
self.sinogramWidget.sinoChangedSig.connect(self.update_sino)
#slider change
self.imageProcessWidget.sliderChangedSig.connect(
self.imageProcessWidget.updateSliderSlot)
#element dropdown change
self.imageProcessWidget.elementChangedSig.connect(
self.sinogramWidget.updateElementSlot)
self.sinogramWidget.elementChangedSig.connect(
self.reconstructionWidget.updateElementSlot)
self.reconstructionWidget.elementChangedSig.connect(
self.imageProcessWidget.updateElementSlot)
# data update
self.imageProcessWidget.dataChangedSig.connect(self.update_history)
self.sinogramWidget.dataChangedSig.connect(self.update_history)
# theta update
self.imageProcessWidget.thetaChangedSig.connect(self.update_theta)
self.imageProcessWidget.thetaChangedSig.connect(
self.sinogramWidget.updateImgSldRange)
#data dimensions changed
# self.imageProcessWidget.ySizeChangedSig.connect(self.imageProcessWidget.ySizeChanged)
# self.imageProcessWidget.ySizeChangedSig.connect(self.sinogramWidget.ySizeChanged)
# self.imageProcessWidget.ySizeChangedSig.connect(self.reconstructionWidget.ySizeChanged)
#alignment changed
self.imageProcessWidget.alignmentChangedSig.connect(
self.update_alignment)
self.sinogramWidget.alignmentChangedSig.connect(self.update_alignment)
self.sinogramWidget.restoreSig.connect(self.restore)
#fnames changed
self.imageProcessWidget.fnamesChanged.connect(self.update_filenames)
#update_reconstructed_data
self.reconstructionWidget.reconChangedSig.connect(self.update_recon)
self.prevTab = 0
self.TAB_FILE = 0
self.TAB_IMAGE_PROC = 1
self.TAB_SINOGRAM = 2
self.TAB_RECONSTRUCTION = 3
self.tab_widget = QtWidgets.QTabWidget()
self.tab_widget.addTab(self.fileTableWidget, 'Files')
self.tab_widget.addTab(self.imageProcessWidget, "Pre Processing")
self.tab_widget.addTab(self.sinogramWidget, "Alignment")
self.tab_widget.addTab(self.reconstructionWidget, "Reconstruction")
self.tab_widget.setTabEnabled(1, False)
self.tab_widget.setTabEnabled(2, False)
self.tab_widget.setTabEnabled(3, False)
self.tab_widget.currentChanged.connect(self.onTabChanged)
self.fileTableWidget.saveDataBtn.clicked.connect(self.updateImages)
self.vl.addWidget(self.tab_widget)
#self.vl.addWidget(self.createMessageWidget())
self.frame.setLayout(self.vl)
self.setCentralWidget(self.frame)
## Top menu bar [file Convert Option Alignment After saving in memory]
menubar = self.menuBar()
menubar.setNativeMenuBar(True)
self.fileMenu = menubar.addMenu('&File')
self.fileMenu.addAction(openH5Action)
self.fileMenu.addAction(openExchangeAction)
self.fileMenu.addAction(openTiffAction)
self.fileMenu.addAction(openThetaAction)
##self.fileMenu.addAction(openFileAction)
#self.fileMenu.addAction(openFolderAction)
#self.fileMenu.addAction(openTiffFolderAction)
self.fileMenu.addAction(exitAction)
self.fileMenu.addAction(closeAction)
self.editMenu = menubar.addMenu("Edit")
self.editMenu.addAction(undoAction)
self.editMenu.addAction(preferencesAction)
# self.editMenu.addAction(matcherAction)
# self.editMenu.addAction(saveHotSpotPosAction)
# self.editMenu.addAction(alignHotSpotPosAction)
# self.editMenu.addAction(externalImageRegAction)
self.editMenu.addAction(restoreAction)
self.editMenu.setDisabled(True)
analysis = QtGui.QMenu('Analysis', self)
corrElemAction = QtGui.QAction('Correlate Elements', self)
analysis.addAction(corrElemAction)
corrElemAction.triggered.connect(self.corrElem)
self.toolsMenu = menubar.addMenu("Tools")
self.toolsMenu.addMenu(analysis)
self.toolsMenu.setDisabled(True)
self.afterConversionMenu = menubar.addMenu('Save')
self.afterConversionMenu.addAction(saveProjectionAction)
# self.afterConversionMenu.addAction(saveHotSpotPosAction)
self.afterConversionMenu.addAction(saveReconstructionAction)
self.afterConversionMenu.addAction(saveAlignemtInfoAction)
self.afterConversionMenu.addAction(saveSinogramAction)
self.afterConversionMenu.addAction(saveSinogram2Action)
self.afterConversionMenu.addAction(saveThetasAction)
self.afterConversionMenu.addAction(saveToHDFAction)
self.afterConversionMenu.addAction(saveToNumpyAction)
self.afterConversionMenu.addAction(saveCorrAnalysisAction)
self.helpMenu = menubar.addMenu('&Help')
self.helpMenu.addAction(keyMapAction)
self.helpMenu.addAction(configAction)
self.afterConversionMenu.setDisabled(True)
add = 0
if sys.platform == "win32":
add = 50
self.setGeometry(add, add, 1100 + add, 500 + add)
self.setWindowTitle('xrftomo')
self.show()
#_______________________Help/config_options______________________
self.config_options = QtWidgets.QWidget()
self.config_options.resize(300, 400)
self.config_options.setWindowTitle('config options')
self.legacy_chbx = QtWidgets.QCheckBox("Load as legacy data")
self.directory_chbx = QtWidgets.QCheckBox("Load last directory")
self.element_chbx = QtWidgets.QCheckBox("Load last elements")
self.image_tag_chbx = QtWidgets.QCheckBox("Load last image_tag")
self.data_tag_chbx = QtWidgets.QCheckBox("Load last data_tag")
self.alingmen_chbx = QtWidgets.QCheckBox("Load alignment information")
self.iter_align_param_chbx = QtWidgets.QCheckBox(
"Load last iter-align parameters")
self.recon_method_chbx = QtWidgets.QCheckBox(
"Load last-used reconstruction method")
self.checkbox_states = eval(self.params.load_settings)
self.legacy_chbx.setChecked(self.checkbox_states[0])
self.directory_chbx.setChecked(self.checkbox_states[1])
self.element_chbx.setChecked(self.checkbox_states[2])
self.image_tag_chbx.setChecked(self.checkbox_states[3])
self.data_tag_chbx.setChecked(self.checkbox_states[4])
self.alingmen_chbx.setChecked(self.checkbox_states[5])
self.iter_align_param_chbx.setChecked(self.checkbox_states[6])
self.recon_method_chbx.setChecked(self.checkbox_states[7])
self.toggleDebugMode()
self.legacy_chbx.stateChanged.connect(self.loadSettingsChanged)
self.legacy_chbx.stateChanged.connect(self.refresh_filetable)
self.directory_chbx.stateChanged.connect(self.loadSettingsChanged)
self.element_chbx.stateChanged.connect(self.loadSettingsChanged)
self.image_tag_chbx.stateChanged.connect(self.loadSettingsChanged)
self.data_tag_chbx.stateChanged.connect(self.loadSettingsChanged)
self.alingmen_chbx.stateChanged.connect(self.loadSettingsChanged)
self.iter_align_param_chbx.stateChanged.connect(
self.loadSettingsChanged)
self.recon_method_chbx.stateChanged.connect(self.loadSettingsChanged)
vbox = QtWidgets.QVBoxLayout()
vbox.addWidget(self.legacy_chbx)
vbox.addWidget(self.directory_chbx)
vbox.addWidget(self.element_chbx)
vbox.addWidget(self.image_tag_chbx)
vbox.addWidget(self.data_tag_chbx)
vbox.addWidget(self.alingmen_chbx)
vbox.addWidget(self.iter_align_param_chbx)
vbox.addWidget(self.recon_method_chbx)
self.config_options.setLayout(vbox)
#_______________________Help/keymap_options______________________
self.keymap_options = QtWidgets.QWidget()
self.keymap_options.resize(600, 400)
self.keymap_options.setWindowTitle('key map')
text = QtWidgets.QLabel(
"Undo: \t\t Ctr+Z \t\t previous image: \t A \n\n"
"shift image up: \t up \t\t next image: \t D \n\n"
"shift image down: \t down \t\t skip (hotspot): \t S \n\n"
"shift image left: \t left \t\t next (hotspot): \t N \n\n"
"shift image right: \t right \n\n"
"shift stack up: \t Shift + up \n\n"
"shift stack down: \t Shift + down \n\n"
"shift stack left: \t Shift + left \n\n"
"shift stack right: \t Shift + right \n\n"
"exclude image: \t Delete \n\n"
"copy background: \t Ctrl + C \n\npaste background: Ctrl + V")
vbox = QtWidgets.QVBoxLayout()
vbox.addWidget(text)
self.keymap_options.setLayout(vbox)
def __init__(self):
super(ReconstructionActions, self).__init__()
self.writer = xrftomo.SaveOptions()
def initUI(self):
self.ViewControl = xrftomo.ReconstructionControlsWidget()
self.ReconView = xrftomo.ReconView(self)
self.actions = xrftomo.ReconstructionActions()
self.actions2 = xrftomo.ImageProcessActions()
self.writer = xrftomo.SaveOptions()
self.file_name_title = QtWidgets.QLabel("_")
lbl1 = QtWidgets.QLabel("x pos:")
self.lbl2 = QtWidgets.QLabel("")
lbl3 = QtWidgets.QLabel("y pos:")
self.lbl4 = QtWidgets.QLabel("")
lbl5 = QtWidgets.QLabel("Slice")
lbl6 = QtWidgets.QLabel("value:")
self.lbl7 = QtWidgets.QLabel("")
self.ReconView.mouseMoveSig.connect(self.updatePanel)
#get pixel value from Histogram widget's projview
self.sld = QtWidgets.QSlider(QtCore.Qt.Horizontal, self)
self.lcd = QtWidgets.QLCDNumber(self)
self.hist = pyqtgraph.HistogramLUTWidget()
self.hist.setMinimumSize(120, 120)
self.hist.setMaximumWidth(120)
self.hist.setImageItem(self.ReconView.projView)
self.ViewControl.combo1.currentIndexChanged.connect(
self.elementChanged)
self.ViewControl.reconGroup.currentIndexChanged.connect(
self.recon_combobox_changed)
self.ViewControl.btn.clicked.connect(self.reconstruct_params)
self.ViewControl.equalizeBtn.clicked.connect(self.equalize_params)
self.ViewControl.rmHotspotBtn.clicked.connect(self.rm_hotspot_params)
self.ViewControl.setThreshBtn.clicked.connect(self.set_thresh_params)
self.ViewControl.btn2.clicked.connect(self.reconstruct_all_params)
self.ViewControl.recon2npy.clicked.connect(
self.reconstruct_all_npy_params)
self.ViewControl.mulBtn.clicked.connect(self.call_reconMultiply)
self.ViewControl.divBtn.clicked.connect(self.call_reconDivide)
self.ViewControl.end_indx.editingFinished.connect(self.update_y_range)
self.ViewControl.start_indx.editingFinished.connect(
self.update_y_range)
self.ViewControl.mid_indx.editingFinished.connect(
self.update_middle_index)
self.ViewControl.recon_stats.clicked.connect(self.toggle_middle_index)
self.sld.valueChanged.connect(self.update_recon_image)
self.x_shifts = None
self.y_shifts = None
self.centers = None
self.recon = None
self.recon_array = None
self.data = None
self.data_original = None
hb0 = QtWidgets.QHBoxLayout()
hb0.addWidget(lbl1)
hb0.addWidget(self.lbl2)
hb0.addWidget(lbl3)
hb0.addWidget(self.lbl4)
hb0.addWidget(lbl6)
hb0.addWidget(self.lbl7)
hb1 = QtWidgets.QHBoxLayout()
hb1.addWidget(lbl5)
hb1.addWidget(self.lcd)
hb1.addWidget(self.sld)
vb1 = QtWidgets.QVBoxLayout()
vb1.addWidget(self.file_name_title)
vb1.addLayout(hb0)
vb1.addWidget(self.ReconView)
vb1.addLayout(hb1)
hb2 = QtWidgets.QHBoxLayout()
hb2.addWidget(self.ViewControl)
hb2.addLayout(vb1)
hb2.addWidget(self.hist, 10)
self.setLayout(hb2)