def save_singleplanes(imp, savepath, metainfo, mode='TZC', format='tiff'):
"""
This function is still in testing.
"""
titleext = imp.getTitle()
title = os.path.splitext(titleext)[0]
if mode == 'TZC':
for t in range(metainfo['SizeT']):
for z in range(metainfo['SizeZ']):
for c in range(metainfo['SizeC']):
# set position - channel, slice, frame
imp.setPosition(c + 1, z + 1, t + 1)
numberedtitle = title + "_t" + IJ.pad(t, 2) + "_z" + IJ.pad(z, 4) + "_c" + IJ.pad(c, 4) + "." + format
stackindex = imp.getStackIndex(c + 1, z + 1, t + 1)
aframe = ImagePlus(numberedtitle, imp.getStack().getProcessor(stackindex))
outputpath = os.path.join(savepath, numberedtitle)
IJ.saveAs(aframe, "TIFF", outputpath)
if mode == 'Z':
c = 0
t = 0
for z in range(metainfo['SizeZ']):
# set position - channel, slice, frame
imp.setPosition(c + 1, z + 1, t + 1)
znumber = MiscTools.addzeros(z)
numberedtitle = title + "_z" + znumber + "." + format
stackindex = imp.getStackIndex(c + 1, z + 1, t + 1)
aframe = ImagePlus(numberedtitle, imp.getStack().getProcessor(stackindex))
outputpath = os.path.join(savepath, numberedtitle)
IJ.saveAs(aframe, "TIFF", outputpath)
def save_hyperstack_as_image_sequence(imp, path):
# make dir
if not os.path.isdir(path):
os.mkdir(path)
#imp.show()
ssize = imp.getStackSize()
titleext = imp.getTitle()
#print titleext
title = os.path.splitext(titleext)[0]
dimA = imp.getDimensions()
print "Title",title," ----- Dimensions",dimA
for c in range(dimA[2]):
for z in range(dimA[3]):
for t in range(dimA[4]):
# imagej is one-based and we save zero-based
numberedtitle = \
title + "--C" + IJ.pad(c, 2) + \
"--Z" + IJ.pad(z, 4) + \
"--T" + IJ.pad(t, 4) + ".tif"
stackindex = imp.getStackIndex(c+1, z+1, t+1) # imagej is one-based
aframe = ImagePlus(numberedtitle, imp.getStack().getProcessor(stackindex))
IJ.log("saving: " + os.path.join(path, numberedtitle))
IJ.saveAs(aframe, "TIFF", os.path.join(path, numberedtitle))
def save_hyperstack_as_image_sequence(imp, path):
# make dir
if not os.path.isdir(path):
os.mkdir(path)
#imp.show()
ssize = imp.getStackSize()
titleext = imp.getTitle()
#print titleext
title = os.path.splitext(titleext)[0]
dimA = imp.getDimensions()
print "Title",title," ----- Dimensions",dimA
for c in range(dimA[2]):
for z in range(dimA[3]):
for t in range(dimA[4]):
# imagej is one-based and we save zero-based
numberedtitle = \
title + "--C" + IJ.pad(c, 2) + \
"--Z" + IJ.pad(z, 4) + \
"--T" + IJ.pad(t, 4) + ".tif"
stackindex = imp.getStackIndex(c+1, z+1, t+1) # imagej is one-based
aframe = ImagePlus(numberedtitle, imp.getStack().getProcessor(stackindex))
IJ.log("saving: " + os.path.join(path, numberedtitle))
IJ.saveAs(aframe, "TIFF", os.path.join(path, numberedtitle))
IJ.log("Maximum time lag analyzed: " + str(max_cycle_length) + " frames")
#savepath = IJ.getDirectory("")
#imp = IJ.getImage()
#ssize = imp.getStackSize()
#titleext = imp.getTitle()
title = os.path.splitext(filename)[0] + "_STICS_map" #os.path.splitext(titleext)[0]
save_imp = ImagePlus(title, result_stack)
save_imp.show()
dimA = save_imp.getDimensions()
for c in range(dimA[2]):
for z in range(dimA[3]):
for t in range(dimA[4]):
save_imp.setPosition(c+1, z+1, t+1)
#print c, z, t
numberedtitle = \
title + "_c" + IJ.pad(c, 2) + \
"_z" + IJ.pad(z, 4) + \
"_t" + IJ.pad(t, 4) + ".tif"
stackindex = save_imp.getStackIndex(c + 1, z + 1, t + 1)
aframe = ImagePlus(numberedtitle, save_imp.getStack().getProcessor(stackindex))
IJ.saveAs(aframe, "TIFF", coords_path + numberedtitle)
#IJ.log("saved:" + numberedtitle)
#IJ.saveAs(result_stack, "TIFF", coords_path)
IJ.log("Saved " + str(dimA[3]) + " files at: " + coords_path)
print("Done")
'''
Saves a hyperstack as separate series of 2D images.
Kota Miura
20130408
'''
from ij import IJ
import os
savepath = IJ.getDirectory("")
imp = IJ.getImage()
ssize = imp.getStackSize()
titleext = imp.getTitle()
title = os.path.splitext(titleext)[0]
dimA = imp.getDimensions()
for t in range(1, dimA[4] + 1):
for z in range(1, dimA[3] +1 ):
for w in range(1, dimA[2] +1 ):
#imp.setPosition(w+1, z+1, t+1)
print t, z, w
numberedtitle = \
title + "_t" + IJ.pad(t, 4) + \
"_z" + IJ.pad(z, 4) + \
"_w" + IJ.pad(w, 4) + ".tif"
stackindex = imp.getStackIndex(w, z, t)
aframe = ImagePlus(numberedtitle, imp.getStack().getProcessor(stackindex))
IJ.saveAs(aframe, "TIFF", savepath + numberedtitle)
IJ.log("saved: " + str(stackindex) + ", " + numberedtitle)
