def __init__(self,
calculation_parameters=ProjectionCalculationParameters()):
super(CalculateProjectionSeries_popup, self).__init__()
self.calculationParameters = calculation_parameters
self.ui = CalculateProjectionSeries_Dialog.Ui_CalculateProjectionSeries_Dialog(
)
self.ui.setupUi(self)
self.setModal(True)
import os
from functools import partial
self.calculationParameters.outputFilename = os.path.abspath(
os.getcwd() + '/projections.mrc')
self.ui.lineEdit_outputFilename.setText(
self.calculationParameters.outputFilename)
self.ui.lineEdit_phi.setText(
toQString(str(self.calculationParameters.phi)))
self.ui.lineEdit_psi.setText(
toQString(str(self.calculationParameters.psi)))
self.ui.lineEdit_thetaStart.setText(
toQString(str(self.calculationParameters.thetaStart)))
self.ui.lineEdit_thetaStep.setText(
toQString(str(self.calculationParameters.thetaStep)))
self.ui.lineEdit_thetaStop.setText(
toQString(str(self.calculationParameters.thetaStop)))
self.ui.lineEdit_angleFile.textEdited.connect(
self.setAngleFilename_fromLineEdit)
self.ui.btn_selectAngleFile.clicked.connect(self.selectAngleFile)
self.ui.lineEdit_phi.textEdited.connect(self.setPhi)
self.ui.lineEdit_psi.textEdited.connect(self.setPsi)
self.ui.lineEdit_thetaStart.textEdited.connect(self.setThetaStart)
self.ui.lineEdit_thetaStep.textEdited.connect(self.setThetaStep)
self.ui.lineEdit_thetaStop.textEdited.connect(self.setThetaStop)
self.ui.lineEdit_outputFilename.textEdited.connect(
self.setOutputFilename)
self.ui.checkBox_saveAngles.setChecked(True)
self.ui.checkBox_saveAngles.toggled.connect(self.toggleSaveAngles)
self.ui.buttonBox.button(
QtWidgets.QDialogButtonBox.Ok).setText("Calculate Projections")
self.ui.buttonBox.accepted.connect(partial(self.setStatus, 1))
# validations
self.ui.lineEdit_phi.editingFinished.connect(
partial(self.validateFloatFromLineEdit, self.ui.lineEdit_phi))
self.ui.lineEdit_psi.editingFinished.connect(
partial(self.validateFloatFromLineEdit, self.ui.lineEdit_psi))
self.ui.lineEdit_thetaStart.editingFinished.connect(
partial(self.validateFloatFromLineEdit,
self.ui.lineEdit_thetaStart))
self.ui.lineEdit_thetaStep.editingFinished.connect(
partial(self.validateFloatFromLineEdit,
self.ui.lineEdit_thetaStep))
self.ui.lineEdit_thetaStop.editingFinished.connect(
partial(self.validateFloatFromLineEdit,
self.ui.lineEdit_thetaStop))
self.status = 0
def setAngleFilename_fromLineEdit(self):
filename = self.ui.lineEdit_angleFile.text()
if os.path.isfile(toString(filename)):
self.calculationParameters.angleFilename = filename
self.calculationParameters.angleFileProvided = True
self.ui.lineEdit_angleFile.setText(toQString(filename))
self.disableAngleWidgets()
def selectAngleFile(self):
filename, _ = QtWidgets.QFileDialog.getOpenFileName(
QtWidgets.QFileDialog(),
"Select File Containing Support",
filter=
"Euler Angles (*.txt *.mat);; MATLAB files (*.mat);;text files (*.txt);;All Files (*)"
)
if filename:
self.GENFIRE_ReconstructionParameters.setAngleFilename(filename)
self.ui.lineEdit_angle.setText(toQString(filename))
def updateFilenames(self):
import os
base, file = os.path.split(
toString(self.GENFIRE_ProjectionCalculator.calculationParameters.
outputFilename))
self.ui.lineEdit_angle.setText(
toQString(
str(self.GENFIRE_ProjectionCalculator.calculationParameters.
outputAngleFilename)))
self.ui.lineEdit_angle.textChanged.emit(self.ui.lineEdit_angle.text())
self.ui.lineEdit_pj.setText(
toQString(
str(self.GENFIRE_ProjectionCalculator.calculationParameters.
outputFilename)))
self.ui.lineEdit_pj.textChanged.emit(self.ui.lineEdit_pj.text())
self.ui.lineEdit_results.setText(toQString(str(base + "/results.mrc")))
self.ui.lineEdit_results.textChanged.emit(
self.ui.lineEdit_results.text())
def selectAngleFile(self):
filename, _ = QtWidgets.QFileDialog.getOpenFileName(
QtWidgets.QFileDialog(),
"Select File Containing Angles",
filter="txt files (*.txt);;All Files (*)")
if filename:
self.calculationParameters.angleFilename = filename
self.calculationParameters.angleFileProvided = True
self.ui.lineEdit_angleFile.setText(toQString(filename))
self.disableAngleWidgets()
def selectInitialObjectFile(self):
filename, _ = QtWidgets.QFileDialog.getOpenFileName(
QtWidgets.QFileDialog(),
"Select File Containing Initial Object",
filter=
"Volume Files (*.mrc *.mat *.npy);; MATLAB files (*.mat);;MRC (*.mrc);;All Files (*)"
)
if filename:
self.GENFIRE_ReconstructionParameters.setInitialObjectFilename(
filename)
self.ui.lineEdit_io.setText(toQString(filename))
def selectSupportFile(self):
filename, _ = QtWidgets.QFileDialog.getOpenFileName(
QtWidgets.QFileDialog(),
"Select File Containing Support",
filter=
"Volume Files (*.mrc *.mat *.npy);; MATLAB files (*.mat);;MRC (*.mrc);;All Files (*)"
)
if filename:
self.GENFIRE_ReconstructionParameters.setSupportFilename(filename)
self.ui.lineEdit_support.setText(toQString(filename))
self.ui.checkBox_default_support.setChecked(False)
def __init__(self):
self.modelFilename = toQString('')
self.angleFilename = toQString('')
self.outputFilename = toQString('')
self.outputAngleFilename = toQString('')
self.outputFilesFlag = False
self.angleFileProvided = False
self.modelFilenameProvided = False
self.modelLoadedFlag = False
self.writeAnglesFlag = True
self.interpolator = None
self.model = None
self.ncOut = None
self.phi = 0.0
self.theta = 0.0
self.thetaStart = 0.0
self.thetaStep = 3.0
self.thetaStop = 180.0
self.psi = 0.0
self.calculationMethod = "FFT"
def selectProjectionFile(self):
filename, _ = QtWidgets.QFileDialog.getOpenFileName(
QtWidgets.QFileDialog(),
"Select File Containing Projections",
filter=
"Projection Stacks (*.mrc *.mat *.tif *.npy);; MATLAB files (*.mat);;TIFF images (*.tif *.tiff);;MRC (*.mrc);;All Files (*)"
)
if filename:
self.GENFIRE_ReconstructionParameters.setProjectionFilename(
filename)
self.ui.lineEdit_pj.setText(toQString(filename))
def setTextFromSlider(self, lineedit, value):
lineedit.setText(toQString(value))
def __init__(self):
## Superclass constructor
super(GenfireMainWindow, self).__init__()
## Initialize UI
self.ui = GENFIRE_MainWindow.Ui_GENFIRE_MainWindow()
self.ui.setupUi(self)
## Initialize Reconstruction Parameters
self.GENFIRE_ReconstructionParameters = ReconstructionParameters()
## Initialize file paths in text boxes
self.ui.lineEdit_results.setText(
toQString(os.path.join(os.getcwd(), 'results.mrc')))
self.ui.lineEdit_support.setText(toQString(os.getcwd()))
self.ui.lineEdit_pj.setText(toQString(os.getcwd()))
self.ui.lineEdit_io.setText(toQString(os.getcwd()))
self.ui.lineEdit_angle.setText(toQString(os.getcwd()))
## Push Buttons -- connect each to their main function and check if the reconstruction parameters are good each
## time a parameter is changed
self.ui.btn_projections.clicked.connect(self.selectProjectionFile)
self.ui.btn_projections.clicked.connect(self.checkParameters)
self.ui.btn_angles.clicked.connect(self.selectAngleFile)
self.ui.btn_angles.clicked.connect(self.checkParameters)
self.ui.btn_support.clicked.connect(self.selectSupportFile)
self.ui.btn_support.clicked.connect(self.checkParameters)
self.ui.btn_io.clicked.connect(self.selectInitialObjectFile)
self.ui.btn_io.clicked.connect(self.checkParameters)
self.ui.btn_reconstruct.setEnabled(False)
self.ui.btn_reconstruct.clicked.connect(self.startReconstruction)
self.ui.btn_reconstruct.clicked.connect(self.checkParameters)
self.ui.btn_reconstruct.setStyleSheet("background-color: rgb(221,0,0)")
self.ui.btn_displayResults.clicked.connect(self.displayResults)
## Line Edits -- connect each to their main function and check if the reconstruction parameters are good each
## time a parameter is changed
self.ui.lineEdit_pj.textChanged.connect(
self.GENFIRE_ReconstructionParameters.setProjectionFilename)
self.ui.lineEdit_pj.textChanged.connect(self.checkParameters)
self.ui.lineEdit_angle.textChanged.connect(
self.GENFIRE_ReconstructionParameters.setAngleFilename)
self.ui.lineEdit_angle.textChanged.connect(self.checkParameters)
self.ui.lineEdit_support.textChanged.connect(
self.GENFIRE_ReconstructionParameters.setSupportFilename)
self.ui.lineEdit_support.textChanged.connect(self.checkParameters)
self.ui.lineEdit_io.textChanged.connect(
self.GENFIRE_ReconstructionParameters.setInitialObjectFilename)
self.ui.lineEdit_io.textChanged.connect(self.checkParameters)
self.ui.lineEdit_results.textChanged.connect(
self.GENFIRE_ReconstructionParameters.setResultsFilename)
self.ui.lineEdit_results.textChanged.connect(self.checkParameters)
self.ui.lineEdit_numIterations.setText(toQString("100"))
self.ui.lineEdit_numIterations.textChanged.connect(
self.safeSetNumIterations)
self.ui.lineEdit_numIterations.textChanged.connect(
self.checkParameters)
self.ui.lineEdit_oversamplingRatio.setText(toQString("3"))
self.ui.lineEdit_oversamplingRatio.textChanged.connect(
self.safeSetOversamplingRatio)
self.ui.lineEdit_oversamplingRatio.textChanged.connect(
self.checkParameters)
self.ui.lineEdit_interpolationCutoffDistance.setText(toQString("0.7"))
self.ui.lineEdit_interpolationCutoffDistance.textChanged.connect(
self.safeSetInterpDistance)
self.ui.lineEdit_interpolationCutoffDistance.textChanged.connect(
self.checkParameters)
self.ui.lineEdit_io.setDisabled(True)
self.ui.lineEdit_io.setStyleSheet("background-color: gray")
## Radio Buttons -- default is resolution extension suppression
self.ui.radioButton_on.setChecked(True)
self.ui.radioButton_on.toggled.connect(
self.selectResolutionExtensionSuppressionState)
self.ui.radioButton_off.toggled.connect(
self.selectResolutionExtensionSuppressionState)
self.ui.radioButton_extension.toggled.connect(
self.selectResolutionExtensionSuppressionState)
self.ui.radioButton_FFT.setChecked(True)
self.ui.radioButton_DFT.toggled.connect(self.setGriddingMethod)
self.ui.radioButton_FFT.toggled.connect(self.setGriddingMethod)
## Check Boxes
self.ui.checkBox_rfree.setChecked(True)
self.ui.checkBox_rfree.toggled.connect(self.calculateRfree)
self.ui.checkBox_provide_io.toggled.connect(self.toggleSelectIO)
self.ui.checkBox_default_support.toggled.connect(
self.toggleUseDefaultSupport)
self.ui.checkBox_default_support.setChecked(True)
self.ui.checkBox_support_constraint.setChecked(True)
self.ui.checkBox_positivity_constraint.setChecked(True)
self.ui.checkBox_support_constraint.toggled.connect(
self.toggleSupportConstraint)
self.ui.checkBox_positivity_constraint.toggled.connect(
self.togglePositivityConstraint)
self.ui.checkBox_multiGridding.toggled.connect(
self.toggleMultiGridding)
self.ui.checkBox_resCircle.toggled.connect(self.toggleResCircle)
self.ui.action_Create_Support.triggered.connect(
self.launchProjectionCalculator)
self.ui.action_Volume_Slicer.triggered.connect(self.launchVolumeSlicer)
def __init__(self, parent=None):
super(ProjectionCalculator, self).__init__()
self.ui = ProjectionCalculator_MainWindow.Ui_ProjectionCalculator()
self.ui.setupUi(self) # buid the interface
self.parent = parent
self.calculationParameters = ProjectionCalculationParameters()
self.ui.lineEdit_modelFile.setText(toQString(os.getcwd()))
self.ui.lineEdit_modelFile.editingFinished.connect(
self.setModelFilename_fromLineEdit)
## Push Buttons
self.ui.btn_selectModel.clicked.connect(self.selectModelFile)
## Sliders
self.ui.verticalSlider_phi.setValue(0)
self.ui.verticalSlider_phi.setMinimum(0)
self.ui.verticalSlider_phi.setMaximum(3600)
self.ui.verticalSlider_phi.valueChanged.connect(
self.setPhiLineEditValue)
self.ui.verticalSlider_theta.setValue(0)
self.ui.verticalSlider_theta.setMinimum(0)
self.ui.verticalSlider_theta.setMaximum(3600)
self.ui.verticalSlider_theta.valueChanged.connect(
self.setThetaLineEditValue)
self.ui.verticalSlider_psi.setValue(0)
self.ui.verticalSlider_psi.setMinimum(0)
self.ui.verticalSlider_psi.setMaximum(3600)
self.ui.verticalSlider_psi.valueChanged.connect(
self.setPsiLineEditValue)
## Line edits
self.ui.lineEdit_phi.setText(toQString('0'))
self.ui.lineEdit_theta.setText(toQString('0'))
self.ui.lineEdit_psi.setText(toQString('0'))
self.ui.lineEdit_phi.editingFinished.connect(self.setPhiSliderValue)
self.ui.lineEdit_theta.editingFinished.connect(
self.setThetaSliderValue)
self.ui.lineEdit_psi.editingFinished.connect(self.setPsiSliderValue)
self.calculateProjections_Dialog = CalculateProjectionSeries_popup(
self.calculationParameters)
self.ui.btn_go.clicked.connect(self.showDialog)
self.calculateProjections_Dialog.ui.buttonBox.accepted.connect(
self.readyToCalculateProjections)
self.ui.btn_go.setEnabled(False)
# Create figures for embedded plotting
self.figure = plt.figure(3)
self.figure.clf(
) # clear figure in case it was rendered somewhere else previously
self.canvas = FigureCanvas(self.figure)
self.navigationToolbar = NavigationToolbar(self.canvas, self)
self.ui.verticalLayout_figure.addWidget(self.navigationToolbar)
self.ui.verticalLayout_figure.addWidget(self.canvas)
self.ax = self.figure.add_subplot(111)
self.ax.axes.get_xaxis().set_visible(False)
self.ax.axes.get_yaxis().set_visible(False)
self.ui.btn_clearModel.clicked.connect(self.clearModel)
def setModelFilename(self, filename):
self.calculationParameters.modelFilename = filename
self.ui.lineEdit_modelFile.setText(toQString(filename))
self.loadModel(filename)
self.displayFigure()
def setPsiLineEditValue(self, value):
self.ui.lineEdit_psi.setText(toQString(float(value) / 10))
self.calculationParameters.psi = float(value) / 10
self.updateFigure()
def setThetaLineEditValue(self, value):
self.ui.lineEdit_theta.setText(toQString(float(value) / 10))
self.calculationParameters.theta = float(value) / 10
self.updateFigure()
