Re: Python iteration through Pixel/ROI to slow ... ?

Posted by Andreas Rzepecki on Oct 22, 2013; 4:00pm
URL: http://imagej.273.s1.nabble.com/Python-iteration-through-Pixel-ROI-to-slow-tp5005274p5005267.html

Dear Mr. Street,

thank you very much for the mask-hint. I tried to change my code to avoid roi.contains() and instead use mask.get:


for j in range(x):
  IJ.showProgress(j, x)
  sumpix_sap = 0
  for i in range(y):
    sap_row = 0
    for roi in RoiManager.getInstance().getRoisAsArray():
      mask = roi.getMask()
      if mask.get(j, i)!= 0:      
        pix_sap = rt.getValue("Sapflow per Pixel", sap_row)
        sumpix_sap = sumpix_sap + pix_sap
      else:
      sap_row = sap_row + 1
  table.incrementCounter()
  table.addValue("Sapflow sum", sumpix_sap * 1000000)
IJ.showProgress(1)
table.show("IASF-Results")


This unfortunately leads to the following Java-error:

Traceback (most recent call last):
  File "<iostream>", line 44, in <module>
        at ij.process.ByteProcessor.get(ByteProcessor.java:262)
        at sun.reflect.GeneratedMethodAccessor21.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
java.lang.ArrayIndexOutOfBoundsException: java.lang.ArrayIndexOutOfBoundsException: 30

So I'm at this point  not sure if I have completely misunderstood the mask command.

Best regards

Andreas Rzepecki

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