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():
index = 0
# Chose a file to open
srcDir = DirectoryChooser("Choose directory containing sequence to split").getDirectory()
# Chose a directory to store each slice as a file
targetDir = DirectoryChooser("Chose folder in which to save sequence").getDirectory()
if targetDir is None:
# User canceled the diolog
return
if srcDir is None:
# User canceled dialog
return
#path = os.path.join(srcDir, od.getFileName())
for f in os.listdir(srcDir):
path = os.path.join(srcDir, f)
# Ready:
cs = ChannelSeparator()
cs.setId(path)
bf = BFVirtualStack(path, cs, False, False, False)
fname = "%06d"%(index-index%200)
path = os.path.join(targetDir,fname)
try:
os.mkdir(path)
except Exception, e:
print "Couldn't make directory:",e
for sliceIndex in xrange(1,bf.getSize() +1):
print "Well done. Processing slice", sliceIndex
ip = bf.getProcessor(sliceIndex)
string = "%06d.tif"%index
sliceFileName = os.path.join(path, string)
FileSaver(ImagePlus(str(sliceIndex), ip)).saveAsTiff(sliceFileName)
index +=1
print "Finished:",path
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(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():
# Chose a file to open
od = OpenDialog("Chose File to Split", None)
srcDir = od.getDirectory()
if srcDir is None:
# User canceled dialog
return
path = os.path.join(srcDir, od.getFileName())
# Chose a directory to store each slice as a file
targetDir = DirectoryChooser("Chose folder in which to save").getDirectory()
if targetDir is None:
# User canceled the diolog
return
# Ready:
cs = ChannelSeparator()
cs.setId(path)
bf = BFVirtualStack(path, cs, False, False, False)
for sliceIndex in xrange(1,bf.getSize() +1):
print "Well done. Processing slice", sliceIndex
ip = bf.getProcessor(sliceIndex)
sliceFileName = os.path.join(targetDir, 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
if targetDir is None: # User canceled the diolog return if srcDir is None: # User canceled dialog return try: os.mkdir(targetDir) except Exception, e: print "Couldn't make directory:",e for f in os.listdir(srcDir): path = os.path.join(srcDir, f) # Ready: cs = ChannelSeparator() cs.setId(path) bf = BFVirtualStack(path, cs, False, False, False) fname = "%06d"%(index-index%200) path = os.path.join(targetDir,fname) try: os.mkdir(path) except Exception, e: print "Couldn't make directory:",e for sliceIndex in xrange(1,bf.getSize() +1): print "Well done. Processing slice", sliceIndex ip = bf.getProcessor(sliceIndex) string = "%06d.tif"%index sliceFileName = os.path.join(path, string) FileSaver(ImagePlus(str(sliceIndex), ip)).saveAsTiff(sliceFileName) index +=1 print "Finished:",path run(sys.argv[1])
import os
from loci.plugins.util import BFVirtualStack, ImageProcessorReader
print '---------------------------------------------------------------------------------------'
base = '/scratch/imageproc/data/paolo/FluoView_stitching/oib_format/TVA4vglut2_n2_4X_20140126_234209'
infile = 'Slide1sec001/Slide1sec001_01.oib'
path = os.path.join(base, infile)
#print 'file: %s' % path
irdr = ImageProcessorReader()
irdr.setId(path)
bf = BFVirtualStack(path, irdr, False, False, False)
print 'Successfully created virtual stack.'
width = bf.getWidth()
height = bf.getHeight()
size = bf.getSize()
procreader = bf.getReader()
# meta = procreader.getMetadata()
# print meta
absposx = procreader.getMetadataValue('AbsPositionValueX')
absposy = procreader.getMetadataValue('AbsPositionValueY')
print 'Dimensions (x, y, size): %s, %s, %s' % (width, height, size)
print 'Absolute positions: %s, %s' % (absposx, absposy)