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SCaVis manual

Image manipulation

The example below shows how to load an image and apply a filter. It also show how to access its internals. Look at the complete API of the IJ package.

from ij import *
from ij.process import *
from ij.measure import *
# we open the file manually. Generate  ImagePlus object
imp = IJ.openImage(file)
print dir(imp) # check image manipulation methods
# display it
print imp.getWidth()
# do manipulations with the clone
imp.getProcessor().setThreshold(174, 174, ImageProcessor.NO_LUT_UPDATE),"Convert to Mask",""),"Watershed", "")
# get all the pixels
pix = imp.getProcessor().getPixels()

Next we can perform a detailed analysis of images. For example, one can create a histogram:

from ij import *
imp = IJ.openImage(""), "Histogram", "")
stats = imp.getStatistics()
print stats.histogram

One can extract data from image and perform manipulation. Then a new modified array can be used to build a new image. Look at the example:

Code example

  Download for this example is disabled for non-members
 1: # Images.   Subtract the minimal value to an image
 3: from ij import *
 4: from ij.process import *
 5: from ij.measure import *
 6: from ij.gui import *
 7: from java.lang import Math
 9: imp = IJ.openImage("")
10: #
12: # get pixel array
13: pix = imp.getProcessor().convertToFloat().getPixels()
14: print pix
15: # find out the minimal pixel value
16: min = reduce(Math.min, pix)
18: # create a new pixel array with the minimal value subtracted
19: pix2 = map(lambda x: x - min, pix)
21: img1=ImagePlus("min subtracted", FloatProcessor(imp.width, imp.height, pix2, None))

Edge detection of images

In this example, let's detect edges of the image of Scavis logo. Below we show 2 examples: one reads this logo using the URL, and the second example reads this logo from local file.

Unregistered users have a limited access to this section. One can unlock this example after becoming a full member.

The output of these scripts are below:

Note that it makes sense to convert the image into back-white. Also, one can swap the colors.

There is a very good tutorial about how to use Jython for image manipulation To avoid plagiarism, we will stop this description here and continue with the subject of how to perform analysis of images using SCaVis API.

man/images/images_advanced.txt · Last modified: 2013/12/17 21:19 by admin
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