def main(): #filename = sys.argv[1] #exportDir = sys.argv[2] inputDir = "/mnt/med-groups-lmu/ls1/users/l/lsalomie/" defaultName = "lif.lif" outputDir = "/home/hajaalin/tmp/lifexporttest" filename = OpenDialog("Choose LIF",inputDir,defaultName).getPath() if not filename: # user canceled dialog return chooser = DirectoryChooser("Choose export directory") chooser.setDefaultDirectory(outputDir) exportDir = chooser.getDirectory() if not exportDir: # user canceled dialog return # EDF parameters params = Parameters() params.setQualitySettings(params.QUALITY_HIGH) params.nScales = 10 worker = EdfWorker(exportDir,params) iterateLif(filename,worker)
import glob import os.path import sys from ij import IJ, ImagePlus, ImageStack, WindowManager from ij.io import DirectoryChooser from edfgui import ExtendedDepthOfField, Parameters file_in = sys.argv[1] file_out = sys.argv[2] # EDF parameters params = Parameters() params.setQualitySettings(params.QUALITY_HIGH) params.nScales = 10 # read input image imp = ImagePlus(file_in) # make all-in-focus image edf = ExtendedDepthOfField(imp,params) edf.process() # save output imp = WindowManager.getCurrentImage() IJ.saveAsTiff(imp,file_out) imp.close()
from ij import IJ, ImagePlus, ImageStack, WindowManager from edf import EdfComplexWavelets, PostProcessing, Tools from edfgui import ExtendedDepthOfField, Parameters from imageware import Builder, ImageWare from optparse import OptionParser # REAL_WAVELETS = 2 COMPLEX_WAVELETS = 3 # EDF parameters params = Parameters() params.setQualitySettings(params.QUALITY_HIGH) params.nScales = 10 # # this is a reproduction of method "process" in edfgui.ExtendedDepthOfField. # def process(imp): isExtended = False waveletMethod = params.edfMethod == REAL_WAVELETS \ or params.edfMethod == COMPLEX_WAVELETS stackConverted = None impConverted = None impBW = imp if params.color: