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)