if os.path.splitext(warpFile)[1] == '.tif':
print('calculating warp parameters from image: '+warpFile)
warpFilePath = os.path.split(warpFile[:-len(os.path.splitext(warpFile)[1])]+'.warp')[1]
saveWarp(warpFile, pixLens, warpFilePath, linearWarp)
warpFile = warpFilePath
elif os.path.splitext(warpFile)[1] == '.warp':
print('using previously-calculated warp parameters from file: '+warpFile)
print('Processing the sequence in folder: ' + workingPath)
print('Saving the sequence to folder: ' + savePath)
#---------------------------------------------------------------------------
if batchMode == 0:
print('Processing raw LF image: ')
single_stacker(magnification, NA, workingPath, pixLens, warpFile, numSlices, umPerSlice, savePath)
elif batchMode == 1:
folder_stacker(workingPath, startTP, warpFile, linearWarp, emailInterval, magnification, NA, pixLens, numSlices, umPerSlice, savePath)
elif batchMode == 2: #*** needs work
# ask for folder of folders location with GUI...
root = Tkinter.Tk()
root.withdraw()
pathFolder = askdirectory(initialdir=pathInit) # title='choose folder folder')
print('Processing folder: ' + pathFolder)
folder_stacker(pathFolder, startTP, usePrevWarp, emailInterval, magnification, NA, pixLens, numSlices, umPerSlice)
elif batchMode == 3:
pathDate = workingPath
date_stacker(pathDate, warpFile, linearWarp, emailInterval, magnification, NA, pixLens, numSlices, umPerSlice, savePath)