# Read the dimensions from the first image
first_path = os.path.join(sourceDir, tiffImageFilenames(sourceDir).next())
width, height = dimensionsOf(first_path)
# Create the VirtualStack without a specific ColorModel
# (which will be set much later upon loading any slice)
vstack = VirtualStack(width, height, None, sourceDir)
# Add all TIFF images in sourceDir as slices in vstack
for filename in tiffImageFilenames(sourceDir):
vstack.addSlice(filename)
# Visualize the VirtualStack
imp = ImagePlus("virtual stack of images in " + os.path.basename(sourceDir), vstack)
# imp.show()
from mpicbg.ij.plugin import NormalizeLocalContrast
from ij.io import FileSaver
# slice마다 process 후 targetDir에 save
for i in xrange(0, vstack.size()):
ip = vstack.getProcessor(i+1) # slice list는 1부터 시작 (1-based listing)
# NormalizeLocalContrast plugin을 ImageProcessor에 적용
NormalizeLocalContrast.run(ip, 200, 200, 3, True, True)
# 결과 저장
name = vstack.getFileName(i+1)
if not name.lower().endswith(".tif"):
name += ".tif"
FileSaver(ImagePlus(name, ip)).saveAsTiff(os.path.join(targetDir, name))
# Read the dimensions from the first image
first_path = os.path.join(sourceDir, tiffImageFilenames(sourceDir).next())
width, height = dimensionsOf(first_path)
# Create the VirtualStack without a specific ColorModel
# (which will be set much later upon loading any slice)
vstack = VirtualStack(width, height, None, sourceDir)
# Add all TIFF images in sourceDir as slices in vstack
for filename in tiffImageFilenames(sourceDir):
vstack.addSlice(filename)
# Visualize the VirtualStack
imp = ImagePlus("virtual stack of images in " + os.path.basename(sourceDir),
vstack)
imp.show()
from mpicbg.ij.plugin import NormalizeLocalContrast
from ij.io import FileSaver
# Process and save every slice
for i in xrange(0, vstack.size()):
ip = vstack.getProcessor(i + 1) # 1-based listing of slices
# Run the NormalizeLocalConstrast plugin on the ImageProcessor
NormalizeLocalContrast.run(ip, 200, 200, 3, True, True)
# Store the result
name = vstack.getFileName(i + 1)
if not name.lower().endswith(".tif"):
name += ".tif"
FileSaver(ImagePlus(name, ip)).saveAsTiff(os.path.join(targetDir, name))
