def orthoStackFrom4D(imp):
stkA = ArrayList()
for i in range(1, imp.getNFrames()+1):
e4d = Extractfrom4D()
e4d.setGstarttimepoint(i)
IJ.log("current time point" + str(i))
aframe = e4d.coreheadless(imp, 3)
ortho = XYZMaxProject(aframe)
orthoimp = ortho.getXYZProject()
stkA.add(orthoimp)
#orthoimp.show()
stk = ImageStack(stkA.get(0).getWidth(), stkA.get(0).getHeight())
for item in stkA:
stk.addSlice("slcie", item.getProcessor())
out = ImagePlus("out", stk)
return out
for item in ls:
data.add(item)
return data
# extracting stack time frames and convert to ortho
imp = IJ.getImage()
stkA = ArrayList()
for i in range(1, 4):
#for i in range(1, imp.getNFrames()):
e4d = Extractfrom4D()
e4d.setGstarttimepoint(i)
IJ.log("current time point" + str(i))
aframe = e4d.coreheadless(imp, 3)
ortho = XYZMaxProject(aframe)
orthoimp = ortho.getXYZProject()
stkA.add(orthoimp)
#orthoimp.show()
stk = ImageStack(stkA.get(0).getWidth(), stkA.get(0).getHeight())
for item in stkA:
stk.addSlice("slcie", item.getProcessor())
out = ImagePlus("out", stk)
#out.setCalibration(imp.getCalibration().copy())
IJ.run(out, "Grays", "");
IJ.run(out, "RGB Color", "");
# load data from file
filepath = '/Users/miura/Dropbox/Mette/20_23h/20_23hrfull_corrected_1_6_6_netdispZ40.csv'
filename = os.path.basename(filepath)
