def run():
srcDir = DirectoryChooser("Choose directory").getDirectory()
if not srcDir:
return
targetDir = DirectoryChooser("Choose target directory").getDirectory()
if targetDir is None:
# User canceled the dialog
return
sId = ".tiff"
for root, directories, filenames in os.walk(srcDir):
for filename in filenames:
path = os.path.join(root, filename)
if not (sId in filename):
continue
cs = ChannelSeparator()
cs.setId(path)
print "cs", cs
bf = BFVirtualStack(path, cs, False, False, False)
for sliceIndex in xrange(1, bf.getSize() + 1):
print "Processing slice", sliceIndex
ip = bf.getProcessor(sliceIndex)
sliceFileName = os.path.join(targetDir + filename + "_" +
str(sliceIndex) + ".tiff")
print "writing ", sliceFileName
FileSaver(ImagePlus(str(sliceIndex),
ip)).saveAsTiff(sliceFileName)
def run(FolderName, SaveFolder):
# Find tiffiles in folder
onlyfiles = [f for f in os.listdir(FolderName) if
os.path.isfile(os.path.join(FolderName, f)) and f.lower().endswith('.tif')]
for ii in xrange(0, len(onlyfiles)):
path = os.path.join(FolderName, onlyfiles[ii])
print "Processing file..", path
# Find stimulus, Block, regions from filename for sorting
# Get all underscores
underscores = [m.start() for m in re.finditer('_', onlyfiles[ii])]
# Fish Name
findfish = onlyfiles[ii].find('Fish')
findunderscore = [i for i in underscores if i > findfish][0]
fishnum = onlyfiles[ii][findfish:findunderscore]
print 'Fish Number..', fishnum
# Block
findblock = onlyfiles[ii].find('Block')
findunderscore = [i for i in underscores if i > findblock][0]
blocknum = onlyfiles[ii][findblock:findunderscore]
print 'Block Number..', blocknum
# Stimulus
findstimulus = onlyfiles[ii].find('Blue')
findunderscore = [i for i in underscores if i > findstimulus][0]
stimulustype = onlyfiles[ii][findstimulus:findunderscore]
print 'Stimulus type..', stimulustype
# Region
findregion = onlyfiles[ii].find('Hb')
findunderscore = [i for i in underscores if i > findregion][0]
region = onlyfiles[ii][findregion-1:findunderscore]
print 'Region..', region
targetDir = os.path.join(SaveFolder, fishnum, region) + filesep
print 'Images will be saved in .....', targetDir
if not os.path.exists(targetDir):
os.makedirs(targetDir)
cs = ChannelSeparator()
cs.setId(path)
bf = BFVirtualStack(path, cs, False, False, False)
for sliceIndex in xrange(1,bf.getSize() + 1):
print "Processing slice", sliceIndex
ip = bf.getProcessor(sliceIndex)
sliceFileName = os.path.join(targetDir, "T=" + str(sliceIndex) + ".tif")
FileSaver(ImagePlus(str(sliceIndex), ip)).saveAsTiff(sliceFileName)
def run():
# Choose a file to open
od = OpenDialog("Choose multi-image file", None)
srcDir = od.getDirectory()
if srcDir is None:
# User canceled the dialog
return
path = os.path.join(srcDir, od.getFileName())
# Choose a directory to store each slice as a file
targetDir = DirectoryChooser("Choose target directory").getDirectory()
if targetDir is None:
# User canceled the dialog
return
# Ready:
cs = ChannelSeparator()
cs.setId(path)
print "cs", cs
bf = BFVirtualStack(path, cs, False, False, False)
for sliceIndex in xrange(1, bf.getSize() + 1):
print "Processing slice", sliceIndex
ip = bf.getProcessor(sliceIndex)
sliceFileName = os.path.join(targetDir, str(sliceIndex) + ".tif")
FileSaver(ImagePlus(str(sliceIndex), ip)).saveAsTiff(sliceFileName)
# Approach 1: using the "Raw" command with macro parameters for its dialog
IJ.run(
"Raw...",
"open=%s image=%i-bit width=%i height=%i number=%i offset=%i big-endian" %
(filepath, bitDepth, width, height, num_slices, headerSize + slice_offset))
# Approach 2: using LOCI bio-formats
from loci.plugins.util import BFVirtualStack
from loci.formats import ChannelSeparator
from ij import ImagePlus, ImageStack
try:
cs = ChannelSeparator()
cs.setId(filepath)
bfvs = BFVirtualStack(filepath, cs, False, False, False)
stack = ImageStack(width, height)
for index in xrange(slice_index, slice_index + num_slices):
stack.addSlice(bfvs.getProcessor(index))
title = os.path.split(filepath)[1] + " from slice %i" % slice_index
imp = ImagePlus(title, stack)
imp.show()
finally:
cs.close()
# Approach 3: using low-level ImageJ libraries
from ij.io import FileInfo, FileOpener
fi = FileInfo()
fi.width = width
fi.height = height
