root.withdraw()
workingPath = askdirectory(initialdir=pathInit) # title='choose bout folder')
# get path to save folder for tiff stacks...
if savePath=='':
# ask for bout folder location with GUI...
print 'Please choose save folder...'
root = Tkinter.Tk()
root.withdraw()
savePath = askdirectory(initialdir=pathInit) # title='choose bout folder')
#if warpFile ext is .tif, calculate a .warp file
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)
import os #import socket # for getting system name #from focal_stacker import findNonStackedRaws from focal_stacker import saveWarp, applyWarp # stimulation record processer #f = '/Users/todicus/Documents/LF/Data/20100603 - ogb1/visual stimulation/' #name = '1.01 response_tester.txt (23-12-23).txt' rectTiff = '/Users/logangrosenick/Documents/Data/20100720_ogb1/Raw_60x/AVG_2.01.tif' rectTiffName = os.path.split(rectTiff)[1] rectTiffFolder = os.path.split(rectTiff)[0] warpFileName = rectTiffName[:-len(os.path.splitext(rectTiffName)[1])]+'.warp' print(rectTiffFolder+' | '+warpFileName) saveWarp(rectTiff, 9, rectTiffFolder+'/'+warpFileName)
