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Recon.py
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# -*- coding: utf-8 -*-
"""
Created on Tue Jun 03 10:56:26 2014
Class to reconstruct and manipulate phantom data
@author: Hannah Erdevig
"""
import sys
import os #operating system file/directory names
from PyQt4 import QtGui, QtCore
from ReconGUI05 import Ui_ReconGUI # GUI module
from ImageList import ImageList # file import and export helper module
import numpy as np
import scipy
import pyqtgraph as pg
import pyqtgraph.opengl as gl
import pyqtgraph.functions as fn
class Recon(QtGui.QMainWindow):
def __init__(self , parent = None):
super(Recon, self).__init__()
pg.setConfigOption('background', 0.2) #Background on plots 0 = black, 1 = white
pg.setConfigOption('foreground', 'w')
self.ui = Ui_ReconGUI()
self.ui.setupUi(self)
self.dataSetIsNew = False
#window 1
self.imv1 = self.ui.widget_k1
#self.imv1.getView().setLabel('bottom',"H","mm") # labels that keep the window from sizing properly
#self.imv1.getView().setLabel('left',"V","mm")
# self.imv1.ui.normBtn.hide()
self.imv1.ui.roiBtn.setText("Line scan")
self.imv1.vLine = pg.InfiniteLine(pos=None, angle=90, pen=None, movable=False, bounds=None) #cross hairs
self.imv1.hLine = pg.InfiniteLine(pos=None, angle=0, pen=None, movable=False, bounds=None)
self.imv1.addItem(self.imv1.vLine, ignoreBounds=True)
self.imv1.addItem(self.imv1.hLine, ignoreBounds=True)
if self.dataSetIsNew == False:
self.proxy = pg.SignalProxy(self.imv1.view.scene().sigMouseMoved, rateLimit=60, slot=self.mouseMoved)
#window 2
self.imv2 = self.ui.widget_k2
#self.imv2.getView().setLabel('bottom',"H","mm")
#self.imv2.getView().setLabel('left',"V","mm")
# self.imv2.ui.normBtn.hide()
self.imv2.ui.roiBtn.setText("Line scan")
self.imv2.vLine = pg.InfiniteLine(pos=None, angle=90, pen=None, movable=False, bounds=None)
self.imv2.hLine = pg.InfiniteLine(pos=None, angle=0, pen=None, movable=False, bounds=None)
self.imv2.addItem(self.imv2.vLine, ignoreBounds=True)
self.imv2.addItem(self.imv2.hLine, ignoreBounds=True)
if self.dataSetIsNew == False:
self.proxy2 = pg.SignalProxy(self.imv2.view.scene().sigMouseMoved, rateLimit=60, slot=self.mouseMoved2)
#window 3
self.imv3 = self.ui.widget_imag
#self.imv3.getView().setLabel('bottom',"H","mm")
#self.imv3.getView().setLabel('left',"V","mm")
# self.imv3.ui.normBtn.hide()
self.imv3.ui.roiBtn.setText("Line scan")
self.imv3.vLine = pg.InfiniteLine(pos=None, angle=90, pen=None, movable=False, bounds=None)
self.imv3.hLine = pg.InfiniteLine(pos=None, angle=0, pen=None, movable=False, bounds=None)
self.imv3.addItem(self.imv3.vLine, ignoreBounds=True)
self.imv3.addItem(self.imv3.hLine, ignoreBounds=True)
if self.dataSetIsNew == False:
self.proxy3 = pg.SignalProxy(self.imv3.view.scene().sigMouseMoved, rateLimit=60, slot=self.mouseMoved3)
#window 4
self.imv4=self.ui.widget_iphase
#self.imv4.getView().setLabel('bottom',"H","mm")
#self.imv4.getView().setLabel('left',"V","mm")
# self.imv4.ui.normBtn.hide()
self.imv4.ui.roiBtn.setText("Line scan")
self.imv4.vLine = pg.InfiniteLine(pos=None, angle=90, pen=None, movable=False, bounds=None)
self.imv4.hLine = pg.InfiniteLine(pos=None, angle=0, pen=None, movable=False, bounds=None)
self.imv4.addItem(self.imv4.vLine, ignoreBounds=True)
self.imv4.addItem(self.imv4.hLine, ignoreBounds=True)
if self.dataSetIsNew == False:
self.proxy4 = pg.SignalProxy(self.imv4.view.scene().sigMouseMoved, rateLimit=60, slot=self.mouseMoved4)
self.nImages = 0
self.nCurrentImage = 0
self.dicomHeader = "DICOM Header"
self.ui.lineEdit_nimages.setText((str(self.nImages)))
self.ui.label.setText("none")
self.dsRe = ImageList() # Use ImageList.py to create list of image data sets
self.dsIm = ImageList()
self.dsMg = ImageList()
self.dsPh = ImageList()
self.dsOriginalComplex = ImageList()
self.dsComplex = ImageList()
self.dsComplexImage = ImageList()
self.dsImageMag = ImageList()
self.dsImagePhase = ImageList()
self.seriesFileNames = []
self.windows = [0,0,0,0]
self.dataSet = [0,0,0,0]
#signals and slots
# self.ui.actionNew.triggered.connect(self.NewFile)
self.ui.actionOpenRI.triggered.connect(self.OpenFileReIm)
self.ui.actionOpenMP.triggered.connect(self.OpenFileMgPh)
self.ui.actionSave12.triggered.connect(self.writeDicomFiles12)
self.ui.actionSave34.triggered.connect(self.writeDicomFiles34)
self.ui.actionClear.triggered.connect(self.ClearImages)
self.ui.actionDeleteCurrent.triggered.connect(self.deleteCurrentImage)
self.ui.verticalSlider_slice.valueChanged.connect(self.ImageSlider)
self.ui.radioButton_ri.clicked.connect(self.SwitchDisplaytoRI)#(self.dsRe, self.dsIm))
self.ui.radioButton_mp.clicked.connect(self.SwitchDisplaytoMP)#(self.dsMg, self.dsPh))
self.ui.pushButton_reconstructI.clicked.connect(self.ReconstructImageData)
self.ui.pushButton_reconstructK.clicked.connect(self.ReconstructRawData)
self.ui.pushButton_reset.clicked.connect(self.ResetData)
self.ui.pushButton_apply.clicked.connect(self.EditData)
# def NewFile (self):
# self.dataSetIsNew = True
# self.dsRe = ImageList() # Use ImageList.py to create list of image data sets
# self.dsIm = ImageList()
# self.dsMg = ImageList()
# self.dsPh = ImageList()
# self.dsOriginalComplex = ImageList()
# self.dsComplex = ImageList()
# self.dsComplexImage = ImageList()
# self.dsImageMag = ImageList()
# self.dsImagePhase = ImageList()
# self.dsMg.PA.append(np.zeros([256,256]))
# self.dsPh.PA.append(np.zeros([256,256]))
# self.dsRe.PA.append(np.zeros([256,256]))
# self.dsIm.PA.append(np.zeros([256,256]))
# self.dsImageMag.PA.append(np.zeros([256,256]))
# self.dsImagePhase.PA.append(np.zeros([256,256]))
# self.dataSet = self.dsMg, self.dsPh, self.dsImageMag, self.dsImagePhase
# self.windows = [1,1,1,1]
# self.nImages = 1
# self.ui.lineEdit_nimages.setText(str(self.nImages))
# self.ui.verticalSlider_slice.setMinimum(1) #set slider to go from 1 to the number of images
# self.ui.verticalSlider_slice.setMaximum(self.nImages)
# self.nCurrentImage = 1
# self.ui.verticalSlider_slice.setValue(self.nCurrentImage)
# self.DisplayCurrentImage(self.imv1, self.dsMg)
# self.DisplayCurrentImage(self.imv2, self.dsPh)
# self.DisplayCurrentImage(self.imv3, self.dsImageMag)
# self.DisplayCurrentImage(self.imv4, self.dsImagePhase)
# self.ui.label_k1.setText("K-Space [Magnitude]")
# self.ui.label_k2.setText("K-Space [Phase]")
def OpenFileReIm (self):
self.dataSetIsNew = False
self.dsRe = ImageList() # Use ImageList.py to create list of image data sets
self.dsIm = ImageList()
self.dsMg = ImageList()
self.dsPh = ImageList()
self.dsOriginalComplex = ImageList()
self.dsComplex = ImageList()
self.dsComplexImage = ImageList()
self.dsImageMag = ImageList()
self.dsImagePhase = ImageList()
#REAL FILES
self.fileNamesRe = QtGui.QFileDialog.getOpenFileNames(self,"Open Real Image Files", "/home/file", "Image Files (*.dcm *.DCM *.bmp *.tif *.fdf)")
if not self.fileNamesRe: #if cancel is pressed return
return None
self.seriesFileNames.extend(self.fileNamesRe) #concatenate new file list with previous file list
for i in range(len(self.fileNamesRe)):
fileName = self.fileNamesRe[i]
self.dsRe.addFile(fileName)
self.dsOriginalComplex.addFile(fileName)
self.dsComplex.addFile(fileName)
self.dsComplexImage.addFile(fileName)
self.dsImageMag.addFile(fileName)
self.dsImagePhase.addFile(fileName)
self.dsMg.addFile(fileName)
self.dsPh.addFile(fileName)
self.windows[0] = 1
self.dataSet[0] = self.dsRe
self.nImages=self.nImages+len(self.fileNamesRe)
self.ui.lineEdit_nimages.setText(str(self.nImages))
self.ui.verticalSlider_slice.setMinimum(1) #set slider to go from 1 to the number of images
self.ui.verticalSlider_slice.setMaximum(self.nImages)
self.nCurrentImage=1
self.ui.verticalSlider_slice.setValue(self.nCurrentImage)
self.DisplayCurrentImage(self.imv1, self.dsRe)
self.ui.label_k1.setText("K-Space [Real]")
#IMAGINARY FILES
self.fileNamesIm = QtGui.QFileDialog.getOpenFileNames(self,"Open Imaginary Image Files", "/home/file", "Image Files (*.dcm *.DCM *.bmp *.tif *.fdf)")
if not self.fileNamesIm: #if cancel is pressed return
return None
self.seriesFileNames.extend(self.fileNamesIm) #concatenate new file list with previous file list
for i in range(len(self.fileNamesIm)):
fileName = self.fileNamesIm[i]
self.dsIm.addFile(fileName)
self.windows[1] = 1
self.dataSet[1] = self.dsIm
self.ui.lineEdit_nimages.setText(str(self.nImages))
self.ui.verticalSlider_slice.setMinimum(1) #set slider to go from 1 to the number of images
self.ui.verticalSlider_slice.setMaximum(self.nImages)
self.nCurrentImage=1
self.ui.verticalSlider_slice.setValue(self.nCurrentImage)
self.DisplayCurrentImage(self.imv2,self.dsIm)
self.ui.label_k2.setText("K-Space [Imaginary]")
#CREATE COMPLEX ARRAY
# self.dsMg = self.dataSet[0]
# self.dsPh = self.dataSet[0]
# self.dsImageMag = self.dataSet[0]
# self.dsImagePhase = self.dataSet[0]
for i in range(1, len(self.dsMg.PA)):
self.dsOriginalComplex.PA[i] = self.dsRe.PA[i] + 1j*self.dsIm.PA[i]
self.dsComplex.PA[i] = self.dsRe.PA[i] + 1j*self.dsIm.PA[i]
self.dsMg.PA[i] = np.absolute(self.dsComplex.PA[i])
self.dsPh.PA[i] = np.angle(self.dsComplex.PA[i])
self.dsComplexImage.PA[i] = np.fft.fft2(self.dsComplex.PA[i])
self.dsImageMag.PA[i] = np.absolute(self.dsComplexImage.PA[i])
self.dsImagePhase.PA[i] = np.angle(self.dsComplexImage.PA[i])
def OpenFileMgPh (self):
self.dataSetIsNew = False
self.dsRe = ImageList() # Use ImageList.py to create list of image data sets
self.dsIm = ImageList()
self.dsMg = ImageList()
self.dsPh = ImageList()
self.dsOriginalComplex = ImageList()
self.dsComplex = ImageList()
self.dsComplexImage = ImageList()
self.dsImageMag = ImageList()
self.dsImagePhase = ImageList()
#MAGNITUDE FILES
self.fileNamesMg = QtGui.QFileDialog.getOpenFileNames(self,"Open Magnitude Image Files", "/home/file", "Image Files (*.dcm *.DCM *.bmp *.tif *.fdf)")
if not self.fileNamesMg: #if cancel is pressed return
return None
self.seriesFileNames.extend(self.fileNamesMg) #concatenate new file list with previous file list
d1Mg= [] #d1 is 3d data stack for 3d images
for i in range(len(self.fileNamesMg)):
fileName = self.fileNamesMg[i]
self.dsMg.addFile(fileName)
self.dsOriginalComplex.addFile(fileName)
self.dsComplex.addFile(fileName)
self.dsComplexImage.addFile(fileName)
self.dsImageMag.addFile(fileName)
self.dsImagePhase.addFile(fileName)
self.dsRe.addFile(fileName)
self.dsIm.addFile(fileName)
d1Mg.append(self.dsMg.PA[i+1])
self.windows[0] = 1
self.dataSet[0] = self.dsMg
self.nImages=self.nImages+len(self.fileNamesMg)
self.ui.lineEdit_nimages.setText(str(self.nImages))
self.ui.verticalSlider_slice.setMinimum(1) #set slider to go from 1 to the number of images
self.ui.verticalSlider_slice.setMaximum(self.nImages)
self.nCurrentImage=1
self.ui.verticalSlider_slice.setValue(self.nCurrentImage)
self.DisplayCurrentImage(self.imv1,self.dsMg)
self.ui.label_k1.setText("K-Space [Magnitude]")
self.image3D = np.dstack(d1Mg)
# self.msgPrint("image size" + str(d1Mg[0].shape) + "; image3D size" + str(self.image3D.shape)+ os.linesep)
#PHASE FILES
self.fileNamesPh = QtGui.QFileDialog.getOpenFileNames(self,"Open Phase Image Files", "/home/file", "Image Files (*.dcm *.DCM *.bmp *.tif *.fdf)")
if not self.fileNamesPh: #if cancel is pressed return
return None
self.seriesFileNames.extend(self.fileNamesPh) #concatenate new file list with previous file list
for i in range(len(self.fileNamesPh)):
fileName = self.fileNamesPh[i]
self.dsPh.addFile(fileName)
self.windows[1] = 1
self.dataSet[1] = self.dsPh
self.ui.lineEdit_nimages.setText(str(self.nImages))
self.ui.verticalSlider_slice.setMinimum(1) #set slider to go from 1 to the number of images
self.ui.verticalSlider_slice.setMaximum(self.nImages)
self.nCurrentImage=1 # 0th item is dummy image
self.ui.verticalSlider_slice.setValue(self.nCurrentImage)
self.DisplayCurrentImage(self.imv2, self.dsPh)
self.ui.label_k2.setText("K-Space [Phase]")
#CREATE COMPLEX ARRAY
for i in range(1, len(self.dsMg.PA)):
self.dsOriginalComplex.PA[i] = np.multiply(self.dsMg.PA[i],np.exp(1j*self.dsPh.PA[i]))
self.dsComplex.PA[i] = np.multiply(self.dsMg.PA[i],np.exp(1j*self.dsPh.PA[i]))
self.dsRe.PA[i] = self.dsComplex.PA[i].real
self.dsIm.PA[i] = self.dsComplex.PA[i].imag
self.dsComplexImage.PA[i] = np.fft.fft2(self.dsComplex.PA[i])
self.dsComplexImage.PA[i] = np.fft.fftshift(self.dsComplexImage.PA[i])
self.dsImageMag.PA[i] = np.absolute(self.dsComplexImage.PA[i])
self.dsImagePhase.PA[i] = np.angle(self.dsComplexImage.PA[i])
def writeDicomFiles12 (self):
fileName = QtGui.QFileDialog.getSaveFileName(parent=None, caption="Dicom File Name")
if not fileName: #if cancel is pressed return
return None
self.dataSet[0].writeDicomFiles(fileName + "kmag") #write current image list in DICOM format to filename+ imagenumber + .dcm
self.dataSet[1].writeDicomFiles(fileName + "kphase") #write current image list in DICOM format to filename+ imagenumber + .dcm
def writeDicomFiles34 (self):
fileName = QtGui.QFileDialog.getSaveFileName(parent=None, caption="Dicom File Name")
if not fileName: #if cancel is pressed return
return None
self.dataSet[2].writeDicomFiles(fileName + "rmag") #write current image list in DICOM format to filename+ imagenumber + .dcm
self.dataSet[3].writeDicomFiles(fileName + "rphase") #write current image list in DICOM format to filename+ imagenumber + .dcm
def EditData (self):
if self.ui.radioButton_setValue.isChecked():
val = float(self.ui.lineEdit_setValue.text())
if self.ui.groupBox_voxelSelection.isChecked(): #if voxel selection is selected
rstart, rend = int(self.ui.lineEdit_voxelRowStart.text()), int(self.ui.lineEdit_voxelRowEnd.text())
cstart, cend = int(self.ui.lineEdit_voxelColStart.text()), int(self.ui.lineEdit_voxelColEnd.text())
if self.ui.checkBox_w1.isChecked(): # only apply editing to window if corresponding checkBox is checked
for i in range(1, len(self.dsMg.PA)): # for each image in the stack (same for all types)
for c in range(cstart-1, cend): # user inputs pixels numbered 1:imagesize
for r in range(rstart-1, rend):
self.dataSet[0].PA[i][c, r] = val
self.DisplayCurrentImage(self.imv1,self.dataSet[0])
if self.ui.checkBox_w2.isChecked():
for i in range(1, len(self.dsMg.PA)): # for each image in the stack (same for all types)
for c in range(cstart-1, cend): # user inputs pixels numbered 1:imagesize
for r in range(rstart-1, rend):
self.dataSet[1].PA[i][c, r] = val
self.DisplayCurrentImage(self.imv2,self.dataSet[1])
if self.ui.groupBox_regionSelection.isChecked(): #if region selection is selected
xCenter, yCenter, radius = int(self.ui.lineEdit_Xpos.text()), int(self.ui.lineEdit_Ypos.text()), int(self.ui.lineEdit_radius.text())
# selects a circular region in coordinate system where x and y range from [-ImageSize/2, ImageSize/2]
if self.ui.checkBox_w1.isChecked(): # only apply editing to window if corresponding checkBox is checked
for i in range(1, len(self.dataSet[0].PA)): # iterate through arrays
if (self.ui.radioButton_interior.isChecked()): # voxel is inside circle
lx, ly = self.dataSet[0].PA[i].shape
X, Y = np.ogrid[0:lx, 0:ly]
mask = (X - lx/2-xCenter)**2 + (Y - ly/2+yCenter)**2 <= radius**2
self.dataSet[0].PA[i][mask] = val
elif (self.ui.radioButton_exterior.isChecked()): # voxel is outside circle
lx, ly = self.dataSet[0].PA[i].shape
X, Y = np.ogrid[0:lx, 0:ly]
mask = (X - lx/2-xCenter)**2 + (Y - ly/2+yCenter)**2 > radius**2
self.dataSet[0].PA[i][mask] = val
self.DisplayCurrentImage(self.imv1,self.dataSet[0])
if self.ui.checkBox_w2.isChecked(): # only apply editing to window if corresponding checkBox is checked
for i in range(1, len(self.dataSet[1].PA)): # iterate through arrays
if (self.ui.radioButton_interior.isChecked()): # voxel is inside circle
lx, ly = self.dataSet[1].PA[i].shape
X, Y = np.ogrid[0:lx, 0:ly]
mask = (X - lx/2-xCenter)**2 + (Y - ly/2+yCenter)**2 <= radius**2
self.dataSet[1].PA[i][mask] = val
elif (self.ui.radioButton_exterior.isChecked()): # voxel is outside circle
lx, ly = self.dataSet[1].PA[i].shape
X, Y = np.ogrid[0:lx, 0:ly]
mask = (X - lx/2-xCenter)**2 + (Y - ly/2+yCenter)**2 > radius**2
self.dataSet[1].PA[i][mask] = val
self.DisplayCurrentImage(self.imv2,self.dataSet[1])
if self.ui.radioButton_addValue.isChecked():
val = float(self.ui.lineEdit_addValue.text())
if self.ui.groupBox_voxelSelection.isChecked(): #if voxel selection is selected
rstart, rend = int(self.ui.lineEdit_voxelRowStart.text()), int(self.ui.lineEdit_voxelRowEnd.text())
cstart, cend = int(self.ui.lineEdit_voxelColStart.text()), int(self.ui.lineEdit_voxelColEnd.text())
if self.ui.checkBox_w1.isChecked(): # only apply editing to window if corresponding checkBox is checked
for i in range(1, len(self.dsMg.PA)): # for each image in the stack (same for all types)
for c in range(cstart-1, cend): # user inputs pixels numbered 1:imagesize
for r in range(rstart-1, rend):
self.dataSet[0].PA[i][c, r] += val
self.DisplayCurrentImage(self.imv1,self.dataSet[0])
if self.ui.checkBox_w2.isChecked():
for i in range(1, len(self.dsMg.PA)): # for each image in the stack (same for all types)
for c in range(cstart-1, cend): # user inputs pixels numbered 1:imagesize
for r in range(rstart-1, rend):
self.dataSet[1].PA[i][c, r] += val
self.DisplayCurrentImage(self.imv2,self.dataSet[1])
if self.ui.groupBox_regionSelection.isChecked(): #if region selection is selected
xCenter, yCenter, radius = int(self.ui.lineEdit_Xpos.text()), int(self.ui.lineEdit_Ypos.text()), int(self.ui.lineEdit_radius.text())
# selects a circular region in coordinate system where x and y range from [-ImageSize/2, ImageSize/2]
if self.ui.checkBox_w1.isChecked(): # only apply editing to window if corresponding checkBox is checked
for i in range(1, len(self.dataSet[0].PA)): # iterate through arrays
if (self.ui.radioButton_interior.isChecked()): # voxel is inside circle
lx, ly = self.dataSet[0].PA[i].shape
X, Y = np.ogrid[0:lx, 0:ly]
mask = (X - lx/2-xCenter)**2 + (Y - ly/2+yCenter)**2 <= radius**2
self.dataSet[0].PA[i][mask] += val
elif (self.ui.radioButton_exterior.isChecked()): # voxel is outside circle
lx, ly = self.dataSet[0].PA[i].shape
X, Y = np.ogrid[0:lx, 0:ly]
mask = (X - lx/2-xCenter)**2 + (Y - ly/2+yCenter)**2 > radius**2
self.dataSet[0].PA[i][mask] += val
self.DisplayCurrentImage(self.imv1,self.dataSet[0])
if self.ui.checkBox_w2.isChecked(): # only apply editing to window if corresponding checkBox is checked
for i in range(1, len(self.dataSet[1].PA)): # iterate through arrays
if (self.ui.radioButton_interior.isChecked()): # voxel is inside circle
lx, ly = self.dataSet[1].PA[i].shape
X, Y = np.ogrid[0:lx, 0:ly]
mask = (X - lx/2-xCenter)**2 + (Y - ly/2+yCenter)**2 <= radius**2
self.dataSet[1].PA[i][mask] += val
elif (self.ui.radioButton_exterior.isChecked()): # voxel is outside circle
lx, ly = self.dataSet[1].PA[i].shape
X, Y = np.ogrid[0:lx, 0:ly]
mask = (X - lx/2-xCenter)**2 + (Y - ly/2+yCenter)**2 > radius**2
self.dataSet[1].PA[i][mask] += val
self.DisplayCurrentImage(self.imv2,self.dataSet[1])
#RECREATE COMPLEX ARRAY
if self.dataSet[0] == self.dsMg:
for i in range(1, len(self.dsMg.PA)):
self.dsComplex.PA[i] = np.multiply(self.dsMg.PA[i],np.exp(1j*self.dsPh.PA[i]))
self.dsRe.PA[i] = self.dsComplex.PA[i].real
self.dsIm.PA[i] = self.dsComplex.PA[i].imag
self.dsComplexImage.PA[i] = np.fft.fft2(self.dsComplex.PA[i])
self.dsComplexImage.PA[i] = np.fft.fftshift(self.dsComplexImage.PA[i])
self.dsImageMag.PA[i] = np.absolute(self.dsComplexImage.PA[i])
self.dsImagePhase.PA[i] = np.angle(self.dsComplexImage.PA[i])
if self.dataSet[0] == self.dsRe:
for i in range(1, len(self.dsMg.PA)):
self.dsComplex.PA[i] = self.dsRe.PA[i] + 1j*self.dsIm.PA[i]
self.dsMg.PA[i] = np.absolute(self.dsComplex.PA[i])
self.dsPh.PA[i] = np.angle(self.dsComplex.PA[i])
self.dsComplexImage.PA[i] = np.fft.fft2(self.dsComplex.PA[i])
self.dsComplexImage.PA[i] = np.fft.fftshift(self.dsComplexImage.PA[i])
self.dsImageMag.PA[i] = np.absolute(self.dsComplexImage.PA[i])
self.dsImagePhase.PA[i] = np.angle(self.dsComplexImage.PA[i])
def ResetData (self):
for i in range(1, len(self.dsMg.PA)):
self.dsRe.PA[i] = self.dsOriginalComplex.PA[i].real
self.dsIm.PA[i] = self.dsOriginalComplex.PA[i].imag
self.dsMg.PA[i] = np.absolute(self.dsOriginalComplex.PA[i])
self.dsPh.PA[i] = np.angle(self.dsOriginalComplex.PA[i])
self.dsComplexImage.PA[i] = np.fft.fft2(self.dsOriginalComplex.PA[i])
self.dsComplexImage.PA[i] = np.fft.fftshift(self.dsComplexImage.PA[i])
self.dsImageMag.PA[i] = np.absolute(self.dsComplexImage.PA[i])
self.dsImagePhase.PA[i] = np.angle(self.dsComplexImage.PA[i])
if self.ui.radioButton_mp.isChecked():
self.dataSet[0] = self.dsRe
self.dataSet[1] = self.dsIm
if self.ui.radioButton_ri.isChecked():
self.dataSet[0] = self.dsMg
self.dataSet[1] = self.dsPh
self.dataSet[2] = self.dsImageMag
self.dataSet[3] = self.dsImagePhase
self.DisplayCurrentImage(self.imv1, self.dataSet[0])
self.DisplayCurrentImage(self.imv2, self.dataSet[1])
if self.windows[2] == 1:
self.DisplayCurrentImage(self.imv3, self.dataSet[2])
if self.windows[3] == 1:
self.DisplayCurrentImage(self.imv4, self.dataSet[3])
def ReconstructImageData (self):
self.windows[2] = 1
self.windows[3] = 1
self.dataSet[2] = self.dsImageMag
self.dataSet[3] = self.dsImagePhase
self.DisplayCurrentImage(self.imv3, self.dataSet[2])
self.DisplayCurrentImage(self.imv4, self.dataSet[3])
def ReconstructRawData (self):
for i in range(1, len(type.PA)):
self.dsComplexImage.PA[i] = np.multiply(self.dsImageMag.PA[i],np.exp(1j*self.dsImagePhase.PA[i]))
self.dsComplexImage.PA[i] = np.fft.ifft2(self.dsComplex.PA[i])
self.dsComplexImage.PA[i] = np.fft.fftshift(self.dsComplexImage.PA[i])
self.dsRe.PA[i] = self.dsComplex.PA[i].real
self.dsIm.PA[i] = self.dsComplex.PA[i].imag
self.windows[2] = 1
self.windows[3] = 1
self.dataSet[2] = self.dsImageMag
self.dataSet[3] = self.dsImagePhase
self.DisplayCurrentImage(self.imv3, self.dataSet[2])
self.DisplayCurrentImage(self.imv4, self.dataSet[3])
def SwitchDisplaytoRI (self):#,data1,data2): # updates windows 1&2 to display current k-space pair
if (self.windows[0] == 1):
self.dataSet[0] = self.dsRe
self.DisplayCurrentImage(self.imv1, self.dsRe)#data1)
self.ui.label_k1.setText("K-Space [Real]")
if (self.windows[1] == 1):
self.dataSet[1] = self.dsIm
self.DisplayCurrentImage(self.imv2, self.dsIm)#data2
self.ui.label_k2.setText("K-Space [Imaginary]")
def SwitchDisplaytoMP (self):#,data1,data2): # updates windows 1&2 to display current k-space pair
if (self.windows[0] == 1):
self.dataSet[0] = self.dsMg
self.DisplayCurrentImage(self.imv1, self.dsMg)#data1)
self.ui.label_k1.setText("K-Space [Magnitude]")
if (self.windows[1] == 1):
self.dataSet[1] = self.dsPh
self.DisplayCurrentImage(self.imv2, self.dsPh)#data2
self.ui.label_k2.setText("K-Space [Phase]")
def ImageSlider (self):
self.nCurrentImage = self.ui.verticalSlider_slice.value()
if (self.windows[0] == 1):
self.DisplayCurrentImage(self.imv1, self.dataSet[0])
if (self.windows[1] == 1):
self.DisplayCurrentImage(self.imv2, self.dataSet[1])
if (self.windows[2] == 1):
self.DisplayCurrentImage(self.imv3, self.dataSet[2])
if (self.windows[3] == 1):
self.DisplayCurrentImage(self.imv4, self.dataSet[3])
def DisplayCurrentImage (self,win,dstype): # display the current image from the data "dstype" in window "win"
i = self.nCurrentImage
self.ui.label.setText(str(self.nCurrentImage))
if self.dataSetIsNew == False:
self.ui.lineEdit_date.setText(format(dstype.StudyDate[i]))
self.ui.textEdit_filename.setText(self.seriesFileNames[i-1]) if i > 0 else self.ui.textEdit_filename.setText("")
self.ui.lineEdit_manufacturer.setText(dstype.Manufacturer[i])
self.ui.lineEdit_series.setText(dstype.SeriesDescription[i])
self.ui.lineEdit_institution.setText(dstype.InstitutionName[i])
self.ui.lineEdit_fieldT.setText(str(dstype.MagneticFieldStrength[i]))
self.ui.lineEdit_receivecoil.setText(str(dstype.ReceiveCoilName[i]))
#self.ui.lblPatient.setText(dstype.PatientName[i])
self.ui.lineEdit_protocol.setText(str(dstype.ProtocolName[i]))
self.ui.lineEdit_bandwidth.setText(str(dstype.PixelBandwidth[i]))
self.ui.lineEdit_TE.setStyleSheet("background-color: white") if (self.checkEqual(dstype.TE)) else self.ui.lineEdit_TE.setStyleSheet("background-color: yellow")
self.ui.lineEdit_TE.setText(str(dstype.TE[i]))
self.ui.lineEdit_TR.setStyleSheet("background-color: white") if (self.checkEqual(dstype.TR)) else self.ui.lineEdit_TR.setStyleSheet("background-color: yellow")
self.ui.lineEdit_TR.setText(str(dstype.TR[i]))
self.ui.lineEdit_imagesize_col.setText(str(dstype.Columns[i]))
self.ui.lineEdit_imagesize_row.setText(str(dstype.Rows[i]))
self.ui.lineEdit_TI.setStyleSheet("background-color: white") if (self.checkEqual(dstype.TI)) else self.ui.lineEdit_TI.setStyleSheet("background-color: yellow")
self.ui.lineEdit_TI.setText(str(dstype.TI[i]))
self.ui.lineEdit_slicethick.setText(str(dstype.SliceThickness[i]))
self.ui.lineEdit_sliceloc.setStyleSheet("background-color: white") if (self.checkEqual(dstype.SliceLocation)) else self.ui.lineEdit_sliceloc.setStyleSheet("background-color: yellow")
self.ui.lineEdit_sliceloc.setText(str(dstype.SliceLocation[i]))
self.ui.lineEdit_pixsize_row.setText(str(dstype.PixelSpacingX[i]))
self.ui.lineEdit_pixsize_col.setText(str(dstype.PixelSpacingY[i]))
# self.ui.lblFA.setStyleSheet("background-color: white") if (self.checkEqual(dstype.FA)) else self.ui.lblFA.setStyleSheet("background-color: yellow")
# self.ui.lblFA.setText(str(dstype.FA[i]))
self.ui.lineEdit_phasedir.setText(str(dstype.InPlanePhaseEncodingDirection[i]))
self.ui.lineEdit_FoVX.setText(str(dstype.FoVX[i]))
self.ui.lineEdit_FoVY.setText(str(dstype.FoVY[i]))
self.ui.lineEdit_b.setText(str(dstype.bValue[i]))
self.ui.textEdit_header.setText(dstype.header[i])
data = dstype.PA[i] #not sure why we need to transpose]
# xscale = dstype.PixelSpacingX[i] if (dstype.PixelSpacingX[i] > 0.) else 1
# yscale = dstype.PixelSpacingY[i] if (dstype.PixelSpacingY[i] > 0.) else 1
# xmin = -dstype.FoVX[i]/2 #set origin to center of image, need to upgrade to set by DICOM tag
# ymin = -dstype.FoVY[i]/2
# textEdit_results was lblUpperLeft in the line below
#self.ui.textEdit_results.setText("UL=" + "{:.1f}".format(dstype.ImagePosition[i][0]) + "," + "{:.1f}".format(dstype.ImagePosition[i][1]) + "," + "{:.1f}".format(dstype.ImagePosition[i][2]))
# setImage(img, autoRange=True, autoLevels=True, levels=None, axes=None, xvals=None, pos=None, scale=None, transform=None, autoHistogramRange=True)
win.setImage(data, autoRange=True, autoLevels=True, autoHistogramRange=True)#pos = (xmin,ymin), scale = (xscale,yscale), autoHistogramRange=True)
# self.imv1.getView().setLabel('bottom',self.DirectionLabel(dstype.RowDirection[i]),"mm")
# self.imv1.getView().setLabel('left',self.DirectionLabel(dstype.ColumnDirection[i]),"mm")
def checkEqual(self, lst): #returns True if all elemments (except the 0th element) of the list are equal
return lst[2:] == lst[1:-1]
def ClearImages (self): #Deletes all images except default image at index 1
self.ds = ImageList() #list of data sets, can be dicom, tiff, fdf
self.dsRe = ImageList() # Uses separate module to create list of image data sets
self.dsIm = ImageList()
self.dsMg = ImageList()
self.dsPh = ImageList()
self.dsComplex = ImageList()
self.dsOriginalComplex = ImageList()
self.dsComplexImage = ImageList()
self.dsImageMag = ImageList()
self.dsImagePhase = ImageList()
del self.seriesFileNames[:]
self.windows = [0,0,0,0]
self.nCurrentImage=0
self.nImages=0
# self.image3D.zeros[1,1,1]
self.DisplayCurrentImage(self.imv1, self.ds)
self.DisplayCurrentImage(self.imv2, self.ds)
self.DisplayCurrentImage(self.imv3, self.ds)
self.DisplayCurrentImage(self.imv4, self.ds)
self.ui.lineEdit_nimages.setText(str(self.nImages))
self.ui.verticalSlider_slice.setMaximum(0)
def deleteCurrentImage(self):
if self.nCurrentImage > 0:
self.dsRe.deleteImage(self.nCurrentImage)
self.dsIm.deleteImage(self.nCurrentImage)
self.dsMg.deleteImage(self.nCurrentImage)
self.dsPh.deleteImage(self.nCurrentImage)
self.dsComplex.deleteImage(self.nCurrentImage)
self.dsOriginalComplex.deleteImage(self.nCurrentImage)
self.dsComplexImage.deleteImage(self.nCurrentImage)
self.dsImageMag.deleteImage(self.nCurrentImage)
self.dsImagePhase.deleteImage(self.nCurrentImage)
self.nImages -= 1
self.ui.lineEdit_nimages.setText(str(self.nImages))
self.ui.verticalSlider_slice.setMinimum(1) #set slider to go from 1 to the number of images
self.ui.verticalSlider_slice.setMaximum(self.nImages)
if self.nImages == 0:
self.nCurrentImage=0
self.windows = [0,0,0,0]
self.ds = ImageList()
self.DisplayCurrentImage(self.imv1, self.ds)
else:
self.nCurrentImage = 1
self.ui.verticalSlider_slice.setValue(self.nCurrentImage)
self.DisplayCurrentImage(self.imv1, self.dataSet[0])
self.DisplayCurrentImage(self.imv2, self.dataSet[1])
def ViewDicomHeader (self):
if self.ui.rbViewDicomHeader.isChecked():
self.ui.textEdit_header.setHidden(False)
dh = str(self.ds.header[self.nCurrentImage])
if dh == '':
dh="DICOM Header"
self.ui.textEdit_header.setText(dh)
else:
self.ui.textEdit_header.setHidden(True)
# def View3d(self):
# w = gl.GLViewWidget()
# w.opts['distance'] = 200
# w.show()
# w.setWindowTitle('3D View')
# g = gl.GLGridItem()
# g.scale(10, 10, 10)
# w.addItem(g)
# data=self.image3D
# #positive = np.log(np.clip(data, 0, data.max())**2)
# #negative = np.log(np.clip(-data, 0, -data.min())**2)
# d2 = np.empty(data.shape + (4,), dtype=np.ubyte)
# d2[..., 0] = data * (255./data.max())
# d2[..., 1] = data * (255./data.max())
# d2[..., 2] = d2[...,1]
# d2[..., 3] = d2[..., 0]*0.3 + d2[..., 1]*0.3
# d2[..., 3] = (d2[..., 3].astype(float) / 255.) **2 * 255
#
# d2[:, 0, 0] = [255,0,0,100]
# d2[0, :, 0] = [0,255,0,100]
# d2[0, 0, :] = [0,0,255,100]
#
# v = gl.GLVolumeItem(d2)
# v.translate(-128,-128,0)
# w.addItem(v)
# ax = gl.GLAxisItem()
# w.addItem(ax)
def mouseMoved(self,evt): #mouse move event to move crosshairs and display location and values
if self.dataSetIsNew == False:
if (self.windows[0] == 1):
self.ds = self.dataSet[0]
pos = evt[0] ## using signal proxy turns original arguments into a tuple
if self.imv1.view.sceneBoundingRect().contains(pos):
mousePoint = self.imv1.view.mapSceneToView(pos)
self.ui.lineEdit_h.setText("{:.2f}".format(mousePoint.x()))
self.ui.lineEdit_v.setText("{:.2f}".format(mousePoint.y()))
if abs(mousePoint.x()) < self.ds.FoVX[self.nCurrentImage]/2 and abs(mousePoint.y()) < self.ds.FoVY[self.nCurrentImage]/2:
Xindex = int((mousePoint.x()+self.ds.FoVX[self.nCurrentImage]/2)/self.ds.PixelSpacingX[self.nCurrentImage]) #if self.ds.PixelSpacingX[self.nCurrentImage] > 0. else Xindex = int(mousePoint.x())
Yindex = int((mousePoint.y()+self.ds.FoVY[self.nCurrentImage]/2)/self.ds.PixelSpacingY[self.nCurrentImage]) #if self.ds.PixelSpacingY[self.nCurrentImage] > 0. else Yindex = int(mousePoint.y())
value= self.ds.PA[self.nCurrentImage][Xindex,Yindex]
self.ui.lineEdit_value.setText("{:.1f}".format(value))
rc= self.ReltoGlobal(mousePoint.x(), mousePoint.y(), self.nCurrentImage, self.ds)
self.ui.lineEdit_x.setText("{:.2f}".format(rc[0]))
self.ui.lineEdit_y.setText("{:.2f}".format(rc[1]))
self.ui.lineEdit_z.setText("{:.2f}".format(rc[2]))
self.imv1.vLine.setPos(mousePoint.x())
self.imv1.hLine.setPos(mousePoint.y())
def mouseMoved2(self,evt): #mouse move event to move crosshairs and display location and values
if self.dataSetIsNew == False:
if (self.windows[1] == 1):
self.ds = self.dataSet[1]
pos = evt[0] ## using signal proxy turns original arguments into a tuple
if self.imv2.view.sceneBoundingRect().contains(pos):
mousePoint = self.imv2.view.mapSceneToView(pos)
self.ui.lineEdit_h.setText("{:.2f}".format(mousePoint.x()))
self.ui.lineEdit_v.setText("{:.2f}".format(mousePoint.y()))
if abs(mousePoint.x()) < self.ds.FoVX[self.nCurrentImage]/2 and abs(mousePoint.y()) < self.ds.FoVY[self.nCurrentImage]/2:
Xindex = int((mousePoint.x()+self.ds.FoVX[self.nCurrentImage]/2)/self.ds.PixelSpacingX[self.nCurrentImage]) #if self.ds.PixelSpacingX[self.nCurrentImage] > 0. else Xindex = int(mousePoint.x())
Yindex = int((mousePoint.y()+self.ds.FoVY[self.nCurrentImage]/2)/self.ds.PixelSpacingY[self.nCurrentImage]) #if self.ds.PixelSpacingY[self.nCurrentImage] > 0. else Yindex = int(mousePoint.y())
value= self.ds.PA[self.nCurrentImage][Xindex,Yindex]
self.ui.lineEdit_value.setText("{:.1f}".format(value))
rc= self.ReltoGlobal(mousePoint.x(), mousePoint.y(), self.nCurrentImage, self.ds)
self.ui.lineEdit_x.setText("{:.2f}".format(rc[0]))
self.ui.lineEdit_y.setText("{:.2f}".format(rc[1]))
self.ui.lineEdit_z.setText("{:.2f}".format(rc[2]))
self.imv2.vLine.setPos(mousePoint.x())
self.imv2.hLine.setPos(mousePoint.y())
def mouseMoved3(self,evt): #mouse move event to move crosshairs and display location and values
if self.dataSetIsNew == False:
if (self.windows[2] == 1):
self.ds = self.dataSet[2]
pos = evt[0] ## using signal proxy turns original arguments into a tuple
if self.imv3.view.sceneBoundingRect().contains(pos):
mousePoint = self.imv3.view.mapSceneToView(pos)
self.ui.lineEdit_h.setText("{:.2f}".format(mousePoint.x()))
self.ui.lineEdit_v.setText("{:.2f}".format(mousePoint.y()))
if abs(mousePoint.x()) < self.ds.FoVX[self.nCurrentImage]/2 and abs(mousePoint.y()) < self.ds.FoVY[self.nCurrentImage]/2:
Xindex = int((mousePoint.x()+self.ds.FoVX[self.nCurrentImage]/2)/self.ds.PixelSpacingX[self.nCurrentImage]) #if self.ds.PixelSpacingX[self.nCurrentImage] > 0. else Xindex = int(mousePoint.x())
Yindex = int((mousePoint.y()+self.ds.FoVY[self.nCurrentImage]/2)/self.ds.PixelSpacingY[self.nCurrentImage]) #if self.ds.PixelSpacingY[self.nCurrentImage] > 0. else Yindex = int(mousePoint.y())
value= self.ds.PA[self.nCurrentImage][Xindex,Yindex]
self.ui.lineEdit_value.setText("{:.1f}".format(value))
rc= self.ReltoGlobal(mousePoint.x(), mousePoint.y(), self.nCurrentImage, self.ds)
self.ui.lineEdit_x.setText("{:.2f}".format(rc[0]))
self.ui.lineEdit_y.setText("{:.2f}".format(rc[1]))
self.ui.lineEdit_z.setText("{:.2f}".format(rc[2]))
self.imv3.vLine.setPos(mousePoint.x())
self.imv3.hLine.setPos(mousePoint.y())
def mouseMoved4(self,evt): #mouse move event to move crosshairs and display location and values
if self.dataSetIsNew == False:
if (self.windows[3] == 1):
self.ds = self.dataSet[3]
pos = evt[0] ## using signal proxy turns original arguments into a tuple
if self.imv4.view.sceneBoundingRect().contains(pos):
mousePoint = self.imv4.view.mapSceneToView(pos)
self.ui.lineEdit_h.setText("{:.2f}".format(mousePoint.x()))
self.ui.lineEdit_v.setText("{:.2f}".format(mousePoint.y()))
if abs(mousePoint.x()) < self.ds.FoVX[self.nCurrentImage]/2 and abs(mousePoint.y()) < self.ds.FoVY[self.nCurrentImage]/2:
Xindex = int((mousePoint.x()+self.ds.FoVX[self.nCurrentImage]/2)/self.ds.PixelSpacingX[self.nCurrentImage]) #if self.ds.PixelSpacingX[self.nCurrentImage] > 0. else Xindex = int(mousePoint.x())
Yindex = int((mousePoint.y()+self.ds.FoVY[self.nCurrentImage]/2)/self.ds.PixelSpacingY[self.nCurrentImage]) #if self.ds.PixelSpacingY[self.nCurrentImage] > 0. else Yindex = int(mousePoint.y())
value= self.ds.PA[self.nCurrentImage][Xindex,Yindex]
self.ui.lineEdit_value.setText("{:.1f}".format(value))
rc= self.ReltoGlobal(mousePoint.x(), mousePoint.y(), self.nCurrentImage, self.ds)
self.ui.lineEdit_x.setText("{:.2f}".format(rc[0]))
self.ui.lineEdit_y.setText("{:.2f}".format(rc[1]))
self.ui.lineEdit_z.setText("{:.2f}".format(rc[2]))
self.imv4.vLine.setPos(mousePoint.x())
self.imv4.hLine.setPos(mousePoint.y())
def ReltoGlobal (self, h,v,n, dstype): #given relative coordinate x,y of image n returns np vector of global coordinates
rc= ((h+dstype.FoVX[n]/2) * dstype.RowDirection[n]+(v+dstype.FoVX[n]/2)*dstype.ColumnDirection[n])+dstype.ImagePosition[n]
return rc
# UNUSED FUNCTION
def GlobaltoRel(self,r,n, dstype): #Given r vector in global coordinates returns h,v in image plane of image n
h=np.dot(r-dstype.ImageCenter[n],dstype.RowDirection[n])
v=np.dot(r-dstype.ImageCenter[n],dstype.ColumnDirection[n])
return [h,v]
if __name__ == '__main__':
app = QtGui.QApplication(sys.argv)
main = Recon()
main.show()
sys.exit(app.exec_())