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, 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 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 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)
