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CellProfiler / stitching

Image stitching
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Problem of Nonetype execute stitching #9

Open JmonkG opened 5 years ago

JmonkG commented 5 years ago

I am having issues regarding the execution of this script to get the tif images of my cif file. I installed the dependencies explained on the readme, and try to stitch the images from the cellprofiler example, named example.cif. When I executed it, I get the following error: log4j:WARN No appenders could be found for logger (loci.common.NIOByteBufferProvider). log4j:WARN Please initialize the log4j system properly. log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info. /Users/carlosjordan/Google Drive/MscBioinformatics/6th Semester/Master Thesis/CellProfiler_IFC/step1/stitching-master/venv/lib/python2.7/site-packages/skimage/io/_io.py:140: UserWarning: ../../../output/Ch1_1.tif is a low contrast image warn('%s is a low contrast image' % fname) /Users/carlosjordan/Google Drive/MscBioinformatics/6th Semester/Master Thesis/CellProfiler_IFC/step1/stitching-master/venv/lib/python2.7/site-packages/skimage/io/_io.py:140: UserWarning: ../../../output/Ch2_1.tif is a low contrast image warn('%s is a low contrast image' % fname) /Users/carlosjordan/Google Drive/MscBioinformatics/6th Semester/Master Thesis/CellProfiler_IFC/step1/stitching-master/venv/lib/python2.7/site-packages/skimage/io/_io.py:140: UserWarning: ../../../output/Ch3_1.tif is a low contrast image warn('%s is a low contrast image' % fname) /Users/carlosjordan/Google Drive/MscBioinformatics/6th Semester/Master Thesis/CellProfiler_IFC/step1/stitching-master/venv/lib/python2.7/site-packages/skimage/io/_io.py:140: UserWarning: ../../../output/Ch4_1.tif is a low contrast image warn('%s is a low contrast image' % fname) /Users/carlosjordan/Google Drive/MscBioinformatics/6th Semester/Master Thesis/CellProfiler_IFC/step1/stitching-master/venv/lib/python2.7/site-packages/skimage/io/_io.py:140: UserWarning: ../../../output/Ch5_1.tif is a low contrast image warn('%s is a low contrast image' % fname) /Users/carlosjordan/Google Drive/MscBioinformatics/6th Semester/Master Thesis/CellProfiler_IFC/step1/stitching-master/venv/lib/python2.7/site-packages/skimage/io/_io.py:140: UserWarning: ../../../output/Ch6_1.tif is a low contrast image warn('%s is a low contrast image' % fname) TypeError: 'NoneType' object is not callable Exception TypeError: "'NoneType' object is not callable" in '_javabridge.JB_Object.__dealloc__' ignored TypeError: 'NoneType' object is not callable Exception TypeError: "'NoneType' object is not callable" in '_javabridge.JB_Object.__dealloc__' ignored TypeError: 'NoneType' object is not callable Exception TypeError: "'NoneType' object is not callable" in '_javabridge.JB_Object.__dealloc__' ignored

I an runing it in a virtualenv environment using python 2.7. Thank you.

schaefed commented 5 years ago

I got the same errors using Python 2.7. Running the program under Python 3.7 worked without the javabridge exceptions

JmonkG commented 5 years ago

Thanks for the tip. I try it with Python 3.5 and it didnt work, I'll try it with the version you mentioned. If it's not too much to ask, what version of Java are you using for your workable stitching?.

I got the same errors using Python 2.7. Running the program under Python 3.7 worked without the javabridge exceptions

schaefed commented 5 years ago

I am using OpenJDK version 1.8 on Linux

JmonkG commented 5 years ago

Thank you.