def main_InteractivelySetParameters():
#######################################################################################################################
############################################### User Parameters ######################################################
#######################################################################################################################
# GENFIRE's reconstruction parameters can be edited here by the user and run interactively, any inputs provided
# by either the command line or the GUI will override these momentarily
print ("starting main_InteractivelySetParameters")
filename_projections = 'projections.mrc' #filename of projections, which should be size NxNxN_projections where N_projections is the number of projections
filename_angles = 'angles.txt' #angles can be either a 1xN_projections array containing a single tilt series, or 3xN_projections array containing 3 Euler angles for each projections in the form [phi;theta;psi]
filename_support = '' #NxNxN binary array specifying a region of 1's in which the reconstruction can exist
filename_initialObject = None #initial object to use in reconstruction; set to None to provide no initial guess
filename_results = 'GENFIRE_rec.mrc' #filename to save results
resolutionExtensionSuppressionState = 2 # 1) Turn on resolution extension/suppression, 2) No resolution extension/suppression, 3) Just resolution extension
numIterations = 100 #number of iterations to run in iterative reconstruction
oversamplingRatio = 3 #input projections will be padded internally to match this oversampling ratio. If you prepad your projections, set this to 1
interpolationCutoffDistance = 0.7 #radius of spherical interpolation kernel (in pixels) within which to include measured datapoints
doYouWantToDisplayFigure = True
displayFigure = genfire.reconstruct.DisplayFigure()
displayFigure.DisplayFigureON = doYouWantToDisplayFigure
calculateRFree = True
if filename_support is None:
useDefaultSupport = True
else:
useDefaultSupport = False
reconstruction_parameters = ReconstructionParameters()
reconstruction_parameters.projections = filename_projections
reconstruction_parameters.eulerAngles = filename_angles
reconstruction_parameters.support = filename_support
reconstruction_parameters.interpolationCutoffDistance = interpolationCutoffDistance
reconstruction_parameters.numIterations = numIterations
reconstruction_parameters.oversamplingRatio = oversamplingRatio
reconstruction_parameters.displayFigure = displayFigure
reconstruction_parameters.calculateRfree = calculateRFree
reconstruction_parameters.resolutionExtensionSuppressionState = resolutionExtensionSuppressionState
reconstruction_parameters.useDefaultSupport = useDefaultSupport
if os.path.isfile(filename_results): # If a valid initial object was provided, use it
reconstruction_parameters.initialObject = filename_results
main(reconstruction_parameters)
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)
filename_support=''
useDefaultSupport = True
#end
try:
filename_results
except NameError as e:
filename_results='GENFIRE_rec.mrc'
#end
try:
interpolationCutoffDistance = float(interpolationCutoffDistance)
except NameError as e:
interpolationCutoffDistance = 0.7
#end
reconstruction_parameters = ReconstructionParameters()
reconstruction_parameters.projections = filename_projections
reconstruction_parameters.eulerAngles = filename_angles
reconstruction_parameters.support = filename_support
reconstruction_parameters.interpolationCutoffDistance = interpolationCutoffDistance
reconstruction_parameters.numIterations = numIterations
reconstruction_parameters.oversamplingRatio = oversamplingRatio
reconstruction_parameters.displayFigure = displayFigure
reconstruction_parameters.calculateRfree = calculateRFree
reconstruction_parameters.resolutionExtensionSuppressionState = resolutionExtensionSuppressionState
reconstruction_parameters.methodState = methodState
reconstruction_parameters.useDefaultSupport = useDefaultSupport
if os.path.isfile(filename_results): # If a valid initial object was provided, use it
reconstruction_parameters.initialObject = filename_results
try:
class GenfireMainWindow(QtWidgets.QMainWindow):
stop_threads = QtCore.pyqtSignal()
def closeEvent(self, QCloseEvent):
self.stop_threads.emit()
GF_logger.listener_thread.wait()
GF_error_logger.listener_thread.wait()
import matplotlib.pyplot as plt
plt.close("all")
QCloseEvent.accept()
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 safeSetInterpDistance(self):
try:
val = toFloat(self.ui.lineEdit_interpolationCutoffDistance.text())
except:
val = 1.0
self.ui.lineEdit_interpolationCutoffDistance.setText('1.0')
self.GENFIRE_ReconstructionParameters.setInterpolationCutoffDistance(
val)
def safeSetNumIterations(self):
try:
val = toInt(self.ui.lineEdit_numIterations.text())
except:
val = 1
self.ui.lineEdit_numIterations.setText('1')
self.GENFIRE_ReconstructionParameters.setNumberOfIterations(val)
def safeSetOversamplingRatio(self):
try:
val = toInt(self.ui.lineEdit_oversamplingRatio.text())
except:
val = 1
self.ui.lineEdit_oversamplingRatio.setText('1')
self.GENFIRE_ReconstructionParameters.setOversamplingRatio(val)
def setNumberOfIterations(self, value):
number_of_iterations = toInt(value)
self.GENFIRE_ReconstructionParameters.setNumberOfIterations(
number_of_iterations)
def calculateRfree(self):
if self.ui.checkBox_rfree.isChecked() == True:
self.GENFIRE_ReconstructionParameters.calculateRfree = True
else:
self.GENFIRE_ReconstructionParameters.calculateRfree = False
def launchProjectionCalculator(self):
from functools import partial
self.GENFIRE_ProjectionCalculator = ProjectionCalculator.ProjectionCalculator(
self)
self.GENFIRE_ProjectionCalculator.model_loading_signal.connect(
partial(self.receive_msg, "Loading Model..."))
self.GENFIRE_ProjectionCalculator.emit_message_signal.connect(
self.receive_msg)
self.GENFIRE_ProjectionCalculator.update_filenames_signal.connect(
self.updateFilenames)
self.GENFIRE_ProjectionCalculator.show()
def setGriddingMethod(self):
if self.ui.radioButton_DFT.isChecked():
self.GENFIRE_ReconstructionParameters.griddingMethod = "DFT"
else:
self.GENFIRE_ReconstructionParameters.griddingMethod = "FFT"
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 launchVolumeSlicer(self):
import genfire.fileio
filename, _ = QtWidgets.QFileDialog.getOpenFileName(
QtWidgets.QFileDialog(),
"Select Volume",
filter="Volume files (*.mat *.mrc *.npy);;All Files (*)")
if filename:
filename = toString(filename)
volume = genfire.fileio.readVolume(filename)
self.VolumeSlicer = VolumeSlicer.VolumeSlicer(volume)
self.VolumeSlicer.show()
def toggleResCircle(self):
if self.ui.checkBox_resCircle.isChecked():
self.GENFIRE_ReconstructionParameters.enforceResolutionCircle = True
else:
self.GENFIRE_ReconstructionParameters.enforceResolutionCircle = False
def toggleMultiGridding(self):
if self.ui.checkBox_multiGridding.isChecked():
self.GENFIRE_ReconstructionParameters.permitMultipleGridding = True
else:
self.GENFIRE_ReconstructionParameters.permitMultipleGridding = False
def toggleSelectIO(self):
if self.ui.lineEdit_io.isEnabled():
self.ui.lineEdit_io.setStyleSheet("background-color: gray")
self.ui.lineEdit_io.setEnabled(False)
self.GENFIRE_ReconstructionParameters.initialObjectFilename = ""
else:
self.ui.lineEdit_io.setStyleSheet("background-color: white")
self.ui.lineEdit_io.setEnabled(True)
def toggleSupportConstraint(self):
if self.ui.checkBox_support_constraint.isChecked():
self.GENFIRE_ReconstructionParameters.constraintSupport = True
else:
self.GENFIRE_ReconstructionParameters.constraintSupport = False
def togglePositivityConstraint(self):
if self.ui.checkBox_positivity_constraint.isChecked():
self.GENFIRE_ReconstructionParameters.constraintPositivity = True
else:
self.GENFIRE_ReconstructionParameters.constraintPositivity = False
def toggleUseDefaultSupport(self):
if self.ui.checkBox_default_support.isChecked():
self.GENFIRE_ReconstructionParameters.useDefaultSupport = True
self.ui.lineEdit_support.setDisabled(True)
self.ui.lineEdit_support.setStyleSheet("background-color: gray")
else:
self.GENFIRE_ReconstructionParameters.useDefaultSupport = False
self.ui.lineEdit_support.setDisabled(False)
self.ui.lineEdit_support.setStyleSheet("background-color: white")
def messageWritten(self, message):
print(message)
def __del__(self):
import sys
sys.stdout = sys.__stdout__ # Restore output stream to default upon exiting the GUI
sys.stderr = sys.__stderr__
#Functions for selecting input files using QFileDialog
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 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 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 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))
#Define constraint enforcement mode
def selectResolutionExtensionSuppressionState(self):
if self.ui.radioButton_on.isChecked():
self.GENFIRE_ReconstructionParameters.setResolutionExtensionSuppressionState(
1)
elif self.ui.radioButton_extension.isChecked():
self.GENFIRE_ReconstructionParameters.setResolutionExtensionSuppressionState(
3)
else:
self.GENFIRE_ReconstructionParameters.setResolutionExtensionSuppressionState(
2)
def checkParameters(self):
parametersAreGood = self.GENFIRE_ReconstructionParameters.checkParameters(
)
if parametersAreGood: #update "go" button if we are ready
self.ui.btn_reconstruct.setEnabled(True)
self.ui.btn_reconstruct.setStyleSheet(
"background-color: GREEN; color:#ffffff;font-size:30px")
# GF_window.ui.btn_reconstruct.setStyleSheet("color: WHITE")
self.ui.btn_reconstruct.setText("Launch Reconstruction!")
#Function to run GENFIRE reconstruction once all parameters are accounted for
@QtCore.pyqtSlot()
def startReconstruction(self):
print('Launching GENFIRE reconstruction')
# Launch the reconstruction in a separate thread to prevent the GUI blocking while reconstructing
from threading import Thread
from functools import partial
import genfire.main
t = Thread(target=partial(genfire.main.main,
self.GENFIRE_ReconstructionParameters))
t.start()
def displayResults(self):
outputfilename, _ = QtWidgets.QFileDialog.getOpenFileName(
QtWidgets.QFileDialog(),
"Select Reconstruction",
filter=
"Volume files (*.mrc *.mat *.npy) ;; MATLAB files (*.mat);;text files (*.txt *.tiff);;MRC (*.mrc);;All Files (*)"
)
outputfilename = toString(outputfilename)
if outputfilename:
import numpy as np
import os
import genfire.fileio
import matplotlib.pyplot as plt
plt.close('all')
initialObject = genfire.fileio.readVolume(outputfilename)
dims = np.shape(initialObject)
n_half_x = int(dims[0] / 2) #this assumes even-sized arrays
n_half_y = int(dims[1] / 2)
n_half_z = int(dims[2] / 2)
reconstructionDisplayWindowSize = dims[0] # array should be cubic
half_window_x = reconstructionDisplayWindowSize // 2
half_window_y = reconstructionDisplayWindowSize // 2
half_window_z = reconstructionDisplayWindowSize // 2
plt.figure()
plt.subplot(233)
plt.imshow(
np.squeeze(initialObject[n_half_x,
n_half_y - half_window_y:n_half_y +
half_window_y,
n_half_z - half_window_z:n_half_z +
half_window_z]))
plt.title("central YZ slice")
plt.subplot(232)
plt.imshow(
np.squeeze(initialObject[n_half_x - half_window_x:n_half_x +
half_window_x, n_half_y,
n_half_z - half_window_z:n_half_z +
half_window_z]))
plt.title("central XZ slice")
plt.subplot(231)
plt.title("central XY slice")
plt.imshow(
np.squeeze(initialObject[n_half_x - half_window_x:n_half_x +
half_window_x,
n_half_y - half_window_y:n_half_y +
half_window_y, n_half_z]))
plt.subplot(236)
plt.title("YZ projection")
plt.imshow(
np.squeeze(
np.sum(initialObject[n_half_x - half_window_x:n_half_x +
half_window_x,
n_half_y - half_window_y:n_half_y +
half_window_y,
n_half_z - half_window_z:n_half_z +
half_window_z],
axis=0)))
plt.subplot(235)
plt.title("XZ projection")
plt.imshow(
np.squeeze(
np.sum(initialObject[n_half_x - half_window_x:n_half_x +
half_window_x,
n_half_y - half_window_y:n_half_y +
half_window_y,
n_half_z - half_window_z:n_half_z +
half_window_z],
axis=1)))
plt.subplot(234)
plt.title("XY projection")
plt.imshow(
np.squeeze(
np.sum(initialObject[n_half_x - half_window_x:n_half_x +
half_window_x,
n_half_y - half_window_y:n_half_y +
half_window_y,
n_half_z - half_window_z:n_half_z +
half_window_z],
axis=2)))
plt.get_current_fig_manager().window.setGeometry(25, 25, 600, 1200)
# now load error curves if they exist
output_base, output_ext = os.path.splitext(outputfilename)
errK_filename = output_base + '_errK.txt'
if os.path.isfile(errK_filename):
errK = np.loadtxt(errK_filename)
numIterations = np.shape(errK)[0]
plt.figure()
plt.plot(range(0, numIterations), errK)
mngr = plt.get_current_fig_manager()
mngr.window.setGeometry(700, 25, 550, 250)
plt.title("Reciprocal Error vs Iteration Number")
plt.xlabel("Iteration Num")
plt.ylabel("Reciprocal Error")
# plt.setp(plt.gcf(),)
Rfree_total_filename = output_base + '_Rfree_total.txt'
Rfree_bybin_filename = output_base + '_Rfree_bybin.txt'
if os.path.isfile(Rfree_total_filename):
Rfree_total = np.loadtxt(Rfree_total_filename)
numIterations = np.shape(Rfree_total)[0]
plt.figure()
plt.title("R-free vs Iteration Number")
mngr = plt.get_current_fig_manager()
mngr.window.setGeometry(700, 350, 550, 250)
plt.plot(range(0, numIterations), Rfree_total)
plt.title("Mean R-free Value vs Iteration Number")
plt.xlabel("Iteration Num")
plt.ylabel('Mean R-free')
if os.path.isfile(Rfree_bybin_filename):
Rfree_bybin = np.loadtxt(Rfree_bybin_filename)
plt.figure()
mngr = plt.get_current_fig_manager()
mngr.window.setGeometry(700, 650, 550, 250)
X = np.linspace(0, 1, np.shape(Rfree_bybin)[0])
plt.plot(X, Rfree_bybin[:, -1])
plt.title("Final Rfree Value vs Spatial Frequency")
plt.xlabel("Spatial Frequency (% of Nyquist)")
plt.ylabel('Rfree')
plt.draw()
plt.pause(1e-30) # slight pause forces redraw
@QtCore.pyqtSlot(str)
def receive_msg(self, msg):
global process_finished
if not process_finished:
self.ui.log.moveCursor(QtGui.QTextCursor.End)
formatted_msg = "<span style=\" font-size:14pt; font-weight:600; color:#000000;\" >" + msg + "</span/>"
self.ui.log.append(formatted_msg)
@QtCore.pyqtSlot(str)
def receive_error_msg(self, msg):
global process_finished
if not process_finished:
self.ui.log.moveCursor(QtGui.QTextCursor.End)
formatted_msg = "<span style=\" font-size:14pt; font-weight:600; color:#ff0000;\" >" + msg + "</span/>"
self.ui.log.append(formatted_msg)
@QtCore.pyqtSlot()
def stopRunning(self):
global process_finished
process_finished = True