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_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 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_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
