def main(): workDir = sys.argv[1] with open(workDir + "Input_Args.txt", "r") as inputFile: lines = inputFile.readlines() if len(lines) == 4: fileName1 = lines[0].strip("\n") fileName2 = lines[1].strip("\n") myROI = eval(lines[2]) upsamplingFactor = eval(lines[3]) rawStack1, rawStack2, sumImg1, sumImg2, diffImg, sx, sy = calc_DIFF_images( fileName1, fileName2, myROI, upsamplingFactor ) elif len(lines) == 5: fileName1 = lines[0].strip("\n") fileName2 = lines[1].strip("\n") fileNameNorm = lines[2].strip("\n") myROI = eval(lines[3]) upsamplingFactor = eval(lines[4]) rawStack1, rawStack2, sumImg1, sumImg2, diffImg, sx, sy = calc_DIFF_images( fileName1, fileName2, fileNameNorm, myROI, upsamplingFactor ) fileNameRoot1 = fileName1[fileName1.rfind("/") :].strip("/") fileNameRoot2 = fileName2[fileName2.rfind("/") :].strip("/") skimage.io.imsave(workDir + fileNameRoot1 + "_RAW_stack1.tif", rawStack1) skimage.io.imsave(workDir + fileNameRoot2 + "_RAW_stack2.tif", rawStack2) skimage.io.imsave(workDir + fileNameRoot1 + "_CORR1.tif", np.array(sumImg1)) skimage.io.imsave(workDir + fileNameRoot2 + "_CORR2.tif", np.array(sumImg2)) skimage.io.imsave(workDir + fileNameRoot1 + "_DIFF.tif", np.array(diffImg)) xpeemreg.saveShifts(workDir, fileName1, sx, sy)
def main(): workDir = sys.argv[1] with open(workDir+'Input_Args.txt','r') as inputFile: lines = inputFile.readlines() if len(lines) == 4: fileName1 = lines[0].strip('\n') fileName2 = lines[1].strip('\n') myROI = eval(lines[2]) upsamplingFactor = eval(lines[3]) rawStack1,rawStack2,corrStack1,corrStack2,diffStack,sx,sy = calc_DIFF_spectra(fileName1,fileName2,myROI,upsamplingFactor) elif len(lines) == 5: fileName1 = lines[0].strip('\n') fileName2 = lines[1].strip('\n') fileNameNorm = lines[2].strip('\n') myROI = eval(lines[3]) upsamplingFactor = eval(lines[4]) rawStack1,rawStack2,corrStack1,corrStack2,diffStack,sx,sy = calc_DIFF_spectra(fileName1,fileName2,fileNameNorm,myROI,upsamplingFactor) fileNameRoot1 = fileName1[fileName1.rfind('/'):].strip('/') fileNameRoot2 = fileName2[fileName2.rfind('/'):].strip('/') skimage.io.imsave(workDir+fileNameRoot1+'_RAW_stack1.tif',rawStack1) skimage.io.imsave(workDir+fileNameRoot2+'_RAW_stack2.tif',rawStack2) skimage.io.imsave(workDir+fileNameRoot1+'_CORR1.tif',np.array(corrStack1)) skimage.io.imsave(workDir+fileNameRoot2+'_CORR2.tif',np.array(corrStack2)) skimage.io.imsave(workDir+fileNameRoot1+'_DIFF.tif',np.array(diffStack)) xpeemreg.saveShifts(workDir,fileName1,sx,sy)
def load4files(self): self.loadContext = 'FOUR FILES' self.fileName1 = str(QtGui.QFileDialog.getOpenFileName(self,'Pick a DATA file',self.dataDirectory, 'NeXuS (*.nxs)')) self.noSlice1,self.imgStack1,self.myShape1,self.xValues1 = xpeem.loadHDF5(self.fileName1) if self.xValues1 == None: self.imageView.setImage(self.imgStack1) else: self.imageView.setImage(self.imgStack1,xvals=self.xValues1) self.changeLabelText(self.fileName1) self.fileName2 = str(QtGui.QFileDialog.getOpenFileName(self,'Pick a DATA file',self.dataDirectory, 'NeXuS (*.nxs)')) self.noSlice2,self.imgStack2,self.myShape2,self.xValues2 = xpeem.loadHDF5(self.fileName2) if self.xValues2 == None: self.imageView.setImage(self.imgStack2) else: self.imageView.setImage(self.imgStack2,xvals=self.xValues2) self.changeLabelText(self.fileName2) self.fileName3 = str(QtGui.QFileDialog.getOpenFileName(self,'Pick a DATA file',self.dataDirectory, 'NeXuS (*.nxs)')) self.noSlice3,self.imgStack3,self.myShape3,self.xValues3 = xpeem.loadHDF5(self.fileName3) if self.xValues3 == None: self.imageView.setImage(self.imgStack3) else: self.imageView.setImage(self.imgStack3,xvals=self.xValues3) self.changeLabelText(self.fileName3) self.fileName4 = str(QtGui.QFileDialog.getOpenFileName(self,'Pick a DATA file',self.dataDirectory, 'NeXuS (*.nxs)')) self.noSlice4,self.imgStack4,self.myShape4,self.xValues4 = xpeem.loadHDF5(self.fileName4) if self.xValues4 == None: self.imageView.setImage(self.imgStack4) else: self.imageView.setImage(self.imgStack4,xvals=self.xValues4) self.changeLabelText(self.fileName4)
def main(): workDir = sys.argv[1] with open(workDir + 'Input_Args.txt', 'r') as inputFile: lines = inputFile.readlines() if len(lines) == 4: fileName1 = lines[0].strip('\n') fileName2 = lines[1].strip('\n') myROI = eval(lines[2]) upsamplingFactor = eval(lines[3]) rawStack1, rawStack2, sumImg1, sumImg2, diffImg, sx, sy = calc_DIFF_images( fileName1, fileName2, myROI, upsamplingFactor) elif len(lines) == 5: fileName1 = lines[0].strip('\n') fileName2 = lines[1].strip('\n') fileNameNorm = lines[2].strip('\n') myROI = eval(lines[3]) upsamplingFactor = eval(lines[4]) rawStack1, rawStack2, sumImg1, sumImg2, diffImg, sx, sy = calc_DIFF_images( fileName1, fileName2, fileNameNorm, myROI, upsamplingFactor) fileNameRoot1 = fileName1[fileName1.rfind('/'):].strip('/') fileNameRoot2 = fileName2[fileName2.rfind('/'):].strip('/') skimage.io.imsave(workDir + fileNameRoot1 + '_RAW_stack1.tif', rawStack1) skimage.io.imsave(workDir + fileNameRoot2 + '_RAW_stack2.tif', rawStack2) skimage.io.imsave(workDir + fileNameRoot1 + '_CORR1.tif', np.array(sumImg1)) skimage.io.imsave(workDir + fileNameRoot2 + '_CORR2.tif', np.array(sumImg2)) skimage.io.imsave(workDir + fileNameRoot1 + '_DIFF.tif', np.array(diffImg)) xpeemreg.saveShifts(workDir, fileName1, sx, sy)
def calc_single_spectrum(*args): if len(args) == 3: noSlice,myImgStack,myShape,xValues = xpeemreg.loadHDF5(args[0]) refImg = myImgStack[0] regImg,shiftX,shiftY = xpeemreg.reduce_DRIFT(noSlice,myImgStack,myShape,refImg,args[1],args[2]) elif len(args) == 4: noSlice,myImgStack,myShape,xValues = xpeemreg.loadHDF5(args[0]) refImg = myImgStack[0] noSliceNorm,imgStackNorm,myShapeNorm,xValuesNorm = xpeemreg.loadHDF5(args[1]) imgNorm = np.sum(imgStackNorm,axis=0,dtype='float32')/len(imgStackNorm) imgNormStack = [myImgStack[theSlice].astype('float32')/imgNorm for theSlice in range(noSlice)] imgNormStack = np.array(imgNormStack) regImg,shiftX,shiftY = xpeemreg.reduce_DRIFT(noSlice,imgNormStack,myShape,refImg,args[2],args[3]) return myImgStack,regImg,shiftX,shiftY
def load4files(self): self.loadContext = 'FOUR FILES' self.fileName1 = str( QtGui.QFileDialog.getOpenFileName(self, 'Pick a DATA file', self.dataDirectory, 'NeXuS (*.nxs)')) self.noSlice1, self.imgStack1, self.myShape1, self.xValues1 = xpeem.loadHDF5( self.fileName1) if self.xValues1 == None: self.imageView.setImage(self.imgStack1) else: self.imageView.setImage(self.imgStack1, xvals=self.xValues1) self.changeLabelText(self.fileName1) self.fileName2 = str( QtGui.QFileDialog.getOpenFileName(self, 'Pick a DATA file', self.dataDirectory, 'NeXuS (*.nxs)')) self.noSlice2, self.imgStack2, self.myShape2, self.xValues2 = xpeem.loadHDF5( self.fileName2) if self.xValues2 == None: self.imageView.setImage(self.imgStack2) else: self.imageView.setImage(self.imgStack2, xvals=self.xValues2) self.changeLabelText(self.fileName2) self.fileName3 = str( QtGui.QFileDialog.getOpenFileName(self, 'Pick a DATA file', self.dataDirectory, 'NeXuS (*.nxs)')) self.noSlice3, self.imgStack3, self.myShape3, self.xValues3 = xpeem.loadHDF5( self.fileName3) if self.xValues3 == None: self.imageView.setImage(self.imgStack3) else: self.imageView.setImage(self.imgStack3, xvals=self.xValues3) self.changeLabelText(self.fileName3) self.fileName4 = str( QtGui.QFileDialog.getOpenFileName(self, 'Pick a DATA file', self.dataDirectory, 'NeXuS (*.nxs)')) self.noSlice4, self.imgStack4, self.myShape4, self.xValues4 = xpeem.loadHDF5( self.fileName4) if self.xValues4 == None: self.imageView.setImage(self.imgStack4) else: self.imageView.setImage(self.imgStack4, xvals=self.xValues4) self.changeLabelText(self.fileName4)
def calc_DIFF_images(*args): if len(args) == 4: noSlice1, myImgStack1, myShape1, xValues1 = xpeemreg.loadHDF5(args[0]) noSlice2, myImgStack2, myShape2, xValues2 = xpeemreg.loadHDF5(args[1]) noSlice = noSlice1 + noSlice2 myImgStack = np.concatenate((myImgStack1, myImgStack2), axis=0) myShape = np.shape(myImgStack) refImg = myImgStack[0] regImg, shiftX, shiftY = xpeemreg.reduce_DRIFT(noSlice, myImgStack, myShape, refImg, args[2], args[3]) elif len(args) == 5: noSlice1, myImgStack1, myShape1, xValues1 = xpeemreg.loadHDF5(args[0]) noSlice2, myImgStack2, myShape2, xValues2 = xpeemreg.loadHDF5(args[1]) noSlice = noSlice1 + noSlice2 myImgStack = np.concatenate((myImgStack1, myImgStack2), axis=0) myShape = np.shape(myImgStack) refImg = myImgStack[0] noSliceNorm, imgStackNorm, myShapeNorm, xValuesNorm = xpeemreg.loadHDF5(args[2]) imgNorm = np.sum(imgStackNorm, axis=0, dtype="float32") / len(imgStackNorm) imgNormStack = [myImgStack[theSlice].astype("float32") / imgNorm for theSlice in range(noSlice)] imgNormStack = np.array(imgNormStack) regImg, shiftX, shiftY = xpeemreg.reduce_DRIFT(noSlice, imgNormStack, myShape, refImg, args[3], args[4]) regImg1 = regImg[: noSlice / 2] regImg2 = regImg[noSlice / 2 :] regImgSum1 = np.sum(regImg1, axis=0, dtype="float32") / (noSlice / 2) regImgSum2 = np.sum(regImg2, axis=0, dtype="float32") / (noSlice / 2) diffImgArray = (regImgSum1 - regImgSum2) / (regImgSum1 + regImgSum2) return myImgStack[: noSlice / 2], myImgStack[noSlice / 2 :], regImgSum1, regImgSum2, diffImgArray, shiftX, shiftY
def calc_DIFF_spectra(*args): if len(args) == 4: noSlice1,myImgStack1,myShape1,xValues1 = xpeemreg.loadHDF5(args[0]) noSlice2,myImgStack2,myShape2,xValues2 = xpeemreg.loadHDF5(args[1]) noSlice = noSlice1+noSlice2 myImgStack = np.concatenate((myImgStack1,myImgStack2),axis=0) myShape = np.shape(myImgStack) refImg = myImgStack[0] regImg,shiftX,shiftY = xpeemreg.reduce_DRIFT(noSlice,myImgStack,myShape,refImg,args[2],args[3]) elif len(args) == 5: noSlice1,myImgStack1,myShape1,xValues1 = xpeemreg.loadHDF5(args[0]) noSlice2,myImgStack2,myShape2,xValues2 = xpeemreg.loadHDF5(args[1]) noSlice = noSlice1+noSlice2 myImgStack = np.concatenate((myImgStack1,myImgStack2),axis=0) myShape = np.shape(myImgStack) refImg = myImgStack[0] noSliceNorm,imgStackNorm,myShapeNorm,xValuesNorm = xpeemreg.loadHDF5(args[2]) imgNorm = np.sum(imgStackNorm,axis=0,dtype='float32')/len(imgStackNorm) imgNormStack = [myImgStack[theSlice].astype('float32')/imgNorm for theSlice in range(noSlice)] imgNormStack = np.array(imgNormStack) regImg,shiftX,shiftY = xpeemreg.reduce_DRIFT(noSlice,imgNormStack,myShape,refImg,args[3],args[4]) regImg1 = regImg[:noSlice/2] regImg2 = regImg[noSlice/2:] diffStack = [(regImg1[theSlice].astype('float32')-regImg2[theSlice].astype('float32'))/(regImg1[theSlice].astype('float32')+regImg2[theSlice].astype('float32')) for theSlice in range(noSlice/2)] return myImgStack[:noSlice/2],myImgStack[noSlice/2:],regImg1,regImg2,diffStack,shiftX,shiftY
def load1file(self): self.loadContext = 'ONE FILE' self.fileName = str(QtGui.QFileDialog.getOpenFileName(self,'Pick a DATA file',self.dataDirectory, 'NeXuS HDF5 (*.nxs *.hdf5)')) self.noSlice,self.imgStack,self.myShape,self.xValues = xpeem.loadHDF5(self.fileName) if self.xValues == None: self.imageView.setImage(self.imgStack) else: self.imageView.setImage(self.imgStack,xvals=self.xValues) self.changeLabelText(self.fileName)
def main(): workDir = sys.argv[1] with open(workDir + 'Input_Args.txt', 'r') as inputFile: lines = inputFile.readlines() if len(lines) == 6: fileName1 = lines[0].strip('\n') fileName2 = lines[1].strip('\n') fileName3 = lines[2].strip('\n') fileName4 = lines[3].strip('\n') myROI = eval(lines[4]) upsamplingFactor = eval(lines[5]) rawStack1, rawStack2, rawStack3, rawStack4, sumImg1, sumImg2, sumImg3, sumImg4, diffImg, sx, sy = calc_ABS_NORM_DIFF_images( fileName1, fileName2, fileName3, fileName4, myROI, upsamplingFactor) elif len(lines) == 7: fileName1 = lines[0].strip('\n') fileName2 = lines[1].strip('\n') fileName3 = lines[2].strip('\n') fileName4 = lines[3].strip('\n') fileNameNorm = lines[4].strip('\n') myROI = eval(lines[5]) upsamplingFactor = eval(lines[6]) rawStack1, rawStack2, rawStack3, rawStack4, sumImg1, sumImg2, sumImg3, sumImg4, diffImg, sx, sy = calc_ABS_NORM_DIFF_images( fileName1, fileName2, fileName3, fileName4, fileNameNorm, myROI, upsamplingFactor) fileNameRoot1 = fileName1[fileName1.rfind('/'):].strip('/') fileNameRoot2 = fileName2[fileName2.rfind('/'):].strip('/') fileNameRoot3 = fileName3[fileName3.rfind('/'):].strip('/') fileNameRoot4 = fileName4[fileName4.rfind('/'):].strip('/') skimage.io.imsave(workDir + fileNameRoot1 + '_RAW_stack1.tif', rawStack1) skimage.io.imsave(workDir + fileNameRoot2 + '_RAW_stack2.tif', rawStack2) skimage.io.imsave(workDir + fileNameRoot3 + '_RAW_stack3.tif', rawStack3) skimage.io.imsave(workDir + fileNameRoot4 + '_RAW_stack4.tif', rawStack4) skimage.io.imsave(workDir + fileNameRoot1 + '_CORR1.tif', np.array(sumImg1)) skimage.io.imsave(workDir + fileNameRoot2 + '_CORR2.tif', np.array(sumImg2)) skimage.io.imsave(workDir + fileNameRoot3 + '_CORR3.tif', np.array(sumImg3)) skimage.io.imsave(workDir + fileNameRoot4 + '_CORR4.tif', np.array(sumImg4)) skimage.io.imsave(workDir + fileNameRoot1 + '_DIFF.tif', np.array(diffImg)) xpeemreg.saveShifts(workDir, fileName1, sx, sy)
def loadNormFile(self): self.fileNameNorm = str( QtGui.QFileDialog.getOpenFileName(self, 'Pick a NORMALIZATION file', self.dataDirectory, 'NeXuS (*.nxs)')) self.noSliceNorm, self.imgStackNorm, self.myShapeNorm, self.xValuesNorm = xpeem.loadHDF5( self.fileNameNorm) self.imgNorm = np.sum(self.imgStackNorm, axis=0, dtype='float32') / len(self.imgStackNorm)
def load1file(self): self.loadContext = 'ONE FILE' self.fileName = str( QtGui.QFileDialog.getOpenFileName(self, 'Pick a DATA file', self.dataDirectory, 'NeXuS HDF5 (*.nxs *.hdf5)')) self.noSlice, self.imgStack, self.myShape, self.xValues = xpeem.loadHDF5( self.fileName) if self.xValues == None: self.imageView.setImage(self.imgStack) else: self.imageView.setImage(self.imgStack, xvals=self.xValues) self.changeLabelText(self.fileName)
def main(): workDir = sys.argv[1] with open(workDir+'Input_Args.txt','r') as inputFile: lines = inputFile.readlines() if len(lines) == 3: fileName = lines[0].strip('\n') myROI = eval(lines[1]) upsamplingFactor = eval(lines[2]) rawStack,corrStack,sx,sy = calc_single_spectrum(fileName,myROI,upsamplingFactor) elif len(lines) == 4: fileName = lines[0].strip('\n') fileNameNorm = lines[1].strip('\n') myROI = eval(lines[2]) upsamplingFactor = eval(lines[3]) rawStack,corrStack,sx,sy = calc_single_spectrum(fileName,fileNameNorm,myROI,upsamplingFactor) fileNameRoot = fileName[fileName.rfind('/'):].strip('/') #xpeemreg.apply_Mask(rawStack) #xpeemreg.apply_Mask(corrStack) skimage.io.imsave(workDir+fileNameRoot+'_RAW.tif',rawStack) skimage.io.imsave(workDir+fileNameRoot+'_CORR1.tif',np.array(corrStack)) xpeemreg.saveShifts(workDir,fileName,sx,sy)
def main(): workDir = sys.argv[1] with open(workDir+'Input_Args.txt','r') as inputFile: lines = inputFile.readlines() if len(lines) == 6: fileName1 = lines[0].strip('\n') fileName2 = lines[1].strip('\n') fileName3 = lines[2].strip('\n') fileName4 = lines[3].strip('\n') myROI = eval(lines[4]) upsamplingFactor = eval(lines[5]) rawStack1,rawStack2,rawStack3,rawStack4,sumImg1,sumImg2,sumImg3,sumImg4,diffImg,sx,sy = calc_ABS_NORM_DIFF_images(fileName1,fileName2,fileName3,fileName4,myROI,upsamplingFactor) elif len(lines) == 7: fileName1 = lines[0].strip('\n') fileName2 = lines[1].strip('\n') fileName3 = lines[2].strip('\n') fileName4 = lines[3].strip('\n') fileNameNorm = lines[4].strip('\n') myROI = eval(lines[5]) upsamplingFactor = eval(lines[6]) rawStack1,rawStack2,rawStack3,rawStack4,sumImg1,sumImg2,sumImg3,sumImg4,diffImg,sx,sy = calc_ABS_NORM_DIFF_images(fileName1,fileName2,fileName3,fileName4,fileNameNorm,myROI,upsamplingFactor) fileNameRoot1 = fileName1[fileName1.rfind('/'):].strip('/') fileNameRoot2 = fileName2[fileName2.rfind('/'):].strip('/') fileNameRoot3 = fileName3[fileName3.rfind('/'):].strip('/') fileNameRoot4 = fileName4[fileName4.rfind('/'):].strip('/') skimage.io.imsave(workDir+fileNameRoot1+'_RAW_stack1.tif',rawStack1) skimage.io.imsave(workDir+fileNameRoot2+'_RAW_stack2.tif',rawStack2) skimage.io.imsave(workDir+fileNameRoot3+'_RAW_stack3.tif',rawStack3) skimage.io.imsave(workDir+fileNameRoot4+'_RAW_stack4.tif',rawStack4) skimage.io.imsave(workDir+fileNameRoot1+'_CORR1.tif',np.array(sumImg1)) skimage.io.imsave(workDir+fileNameRoot2+'_CORR2.tif',np.array(sumImg2)) skimage.io.imsave(workDir+fileNameRoot3+'_CORR3.tif',np.array(sumImg3)) skimage.io.imsave(workDir+fileNameRoot4+'_CORR4.tif',np.array(sumImg4)) skimage.io.imsave(workDir+fileNameRoot1+'_DIFF.tif',np.array(diffImg)) xpeemreg.saveShifts(workDir,fileName1,sx,sy)
def calc_ABS_NORM_DIFF_images(*args): if len(args) == 6: noSlice1, myImgStack1, myShape1, xValues1 = xpeemreg.loadHDF5(args[0]) noSlice2, myImgStack2, myShape2, xValues2 = xpeemreg.loadHDF5(args[1]) noSlice3, myImgStack3, myShape3, xValues3 = xpeemreg.loadHDF5(args[2]) noSlice4, myImgStack4, myShape4, xValues4 = xpeemreg.loadHDF5(args[3]) noSlice = noSlice1 + noSlice2 + noSlice3 + noSlice4 myImgStack = np.concatenate( (myImgStack1, myImgStack2, myImgStack3, myImgStack4), axis=0) myShape = np.shape(myImgStack) refImg = myImgStack[0] regImg, shiftX, shiftY = xpeemreg.reduce_DRIFT(noSlice, myImgStack, myShape, refImg, args[4], args[5]) elif len(args) == 7: noSlice1, myImgStack1, myShape1, xValues1 = xpeemreg.loadHDF5(args[0]) noSlice2, myImgStack2, myShape2, xValues2 = xpeemreg.loadHDF5(args[1]) noSlice3, myImgStack3, myShape3, xValues3 = xpeemreg.loadHDF5(args[2]) noSlice4, myImgStack4, myShape4, xValues4 = xpeemreg.loadHDF5(args[3]) noSlice = noSlice1 + noSlice2 + noSlice3 + noSlice4 myImgStack = np.concatenate( (myImgStack1, myImgStack2, myImgStack3, myImgStack4), axis=0) myShape = np.shape(myImgStack) refImg = myImgStack[0] noSliceNorm, imgStackNorm, myShapeNorm, xValuesNorm = xpeemreg.loadHDF5( args[4]) imgNorm = np.sum(imgStackNorm, axis=0, dtype='float32') / len(imgStackNorm) imgNormStack = [ myImgStack[theSlice].astype('float32') / imgNorm for theSlice in range(noSlice) ] imgNormStack = np.array(imgNormStack) regImg, shiftX, shiftY = xpeemreg.reduce_DRIFT(noSlice, imgNormStack, myShape, refImg, args[5], args[6]) regImg1 = regImg[:noSlice / 4] regImg2 = regImg[noSlice / 4:2 * noSlice / 4] regImg3 = regImg[2 * noSlice / 4:3 * noSlice / 4] regImg4 = regImg[3 * noSlice / 4:] regImgSum1 = np.sum(regImg1, axis=0, dtype='float32') / (noSlice / 4) regImgSum2 = np.sum(regImg2, axis=0, dtype='float32') / (noSlice / 4) regImgSum3 = np.sum(regImg3, axis=0, dtype='float32') / (noSlice / 4) regImgSum4 = np.sum(regImg4, axis=0, dtype='float32') / (noSlice / 4) diffImgArray = ((regImgSum2 - regImgSum1) / (regImgSum2 + regImgSum1) - (regImgSum4 - regImgSum3) / (regImgSum4 + regImgSum3)) return myImgStack[:noSlice / 4], myImgStack[ noSlice / 4:2 * noSlice / 4], myImgStack[2 * noSlice / 4:3 * noSlice / 4], myImgStack[ 3 * noSlice / 4:], regImgSum1, regImgSum2, regImgSum3, regImgSum4, diffImgArray, shiftX, shiftY
def calc_ABS_NORM_DIFF_images(*args): if len(args) == 6: noSlice1,myImgStack1,myShape1,xValues1 = xpeemreg.loadHDF5(args[0]) noSlice2,myImgStack2,myShape2,xValues2 = xpeemreg.loadHDF5(args[1]) noSlice3,myImgStack3,myShape3,xValues3 = xpeemreg.loadHDF5(args[2]) noSlice4,myImgStack4,myShape4,xValues4 = xpeemreg.loadHDF5(args[3]) noSlice = noSlice1+noSlice2+noSlice3+noSlice4 myImgStack = np.concatenate((myImgStack1,myImgStack2,myImgStack3,myImgStack4),axis=0) myShape = np.shape(myImgStack) refImg = myImgStack[0] regImg,shiftX,shiftY = xpeemreg.reduce_DRIFT(noSlice,myImgStack,myShape,refImg,args[4],args[5]) elif len(args) == 7: noSlice1,myImgStack1,myShape1,xValues1 = xpeemreg.loadHDF5(args[0]) noSlice2,myImgStack2,myShape2,xValues2 = xpeemreg.loadHDF5(args[1]) noSlice3,myImgStack3,myShape3,xValues3 = xpeemreg.loadHDF5(args[2]) noSlice4,myImgStack4,myShape4,xValues4 = xpeemreg.loadHDF5(args[3]) noSlice = noSlice1+noSlice2+noSlice3+noSlice4 myImgStack = np.concatenate((myImgStack1,myImgStack2,myImgStack3,myImgStack4),axis=0) myShape = np.shape(myImgStack) refImg = myImgStack[0] noSliceNorm,imgStackNorm,myShapeNorm,xValuesNorm = xpeemreg.loadHDF5(args[4]) imgNorm = np.sum(imgStackNorm,axis=0,dtype='float32')/len(imgStackNorm) imgNormStack = [myImgStack[theSlice].astype('float32')/imgNorm for theSlice in range(noSlice)] imgNormStack = np.array(imgNormStack) regImg,shiftX,shiftY = xpeemreg.reduce_DRIFT(noSlice,imgNormStack,myShape,refImg,args[5],args[6]) regImg1 = regImg[:noSlice/4] regImg2 = regImg[noSlice/4:2*noSlice/4] regImg3 = regImg[2*noSlice/4:3*noSlice/4] regImg4 = regImg[3*noSlice/4:] regImgSum1 = np.sum(regImg1,axis=0,dtype='float32')/(noSlice/4) regImgSum2 = np.sum(regImg2,axis=0,dtype='float32')/(noSlice/4) regImgSum3 = np.sum(regImg3,axis=0,dtype='float32')/(noSlice/4) regImgSum4 = np.sum(regImg4,axis=0,dtype='float32')/(noSlice/4) diffImgArray = ((regImgSum2-regImgSum1)/(regImgSum2+regImgSum1)-(regImgSum4-regImgSum3)/(regImgSum4+regImgSum3)) return myImgStack[:noSlice/4],myImgStack[noSlice/4:2*noSlice/4],myImgStack[2*noSlice/4:3*noSlice/4],myImgStack[3*noSlice/4:],regImgSum1,regImgSum2,regImgSum3,regImgSum4, diffImgArray,shiftX,shiftY
def loadNormFile(self): self.fileNameNorm = str(QtGui.QFileDialog.getOpenFileName(self,'Pick a NORMALIZATION file',self.dataDirectory, 'NeXuS (*.nxs)')) self.noSliceNorm,self.imgStackNorm,self.myShapeNorm,self.xValuesNorm = xpeem.loadHDF5(self.fileNameNorm) self.imgNorm = np.sum(self.imgStackNorm,axis=0,dtype='float32')/len(self.imgStackNorm)