# 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))
Esempio n. 2
0
# 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))