Error in importing "_cpmorphology" module

[zhouhao-learning]

I'm trying to run your Processplate. sh file, but I encountered a module import error in the CellProfiler / cellprofiler / cpmath / cpmorphology. py file. The cpmorphology. py file imported itself as a module, but I couldn't run it. I got the following error:

Traceback (most recent call last):
  File "./CellProfiler/CellProfiler.py", line 252, in main
    run_pipeline_headless(options, args)
  File "./CellProfiler/CellProfiler.py", line 790, in run_pipeline_headless
    from cellprofiler.pipeline import Pipeline, EXIT_STATUS, M_PIPELINE
  File "/project/hit_cell/process-plate/CellProfiler/cellprofiler/pipeline.py", line 52, in <module>
    import cellprofiler.objects as cpo
  File "/project/hit_cell/process-plate/CellProfiler/cellprofiler/objects.py", line 19, in <module>
    from cellprofiler.cpmath.cpmorphology import all_connected_components
  File "/project/hit_cell/process-plate/CellProfiler/cellprofiler/cpmath/cpmorphology.py", line 20, in <module>
    import _cpmorphology
ImportError: No module named _cpmorphology

Similar modules are from _cpmorphology2 import skeletonize_loop, table_lookup_index, but I don't see a cpmorphology2.py file, just see a _cpmorphology2.pyx file

What should I do with this error? Thank you very much.

[roelWuyts]

It is a CellProfiler error that I cannot remember seeing.

However I have added some more instructions and files to get CellProfiler 2.1.1 running correctly. Can you check out the latest release of process-plate and follow the instructions in the readme (both installing the missing dependencies and then initializing CellProfiler) ? That may solve the import problems.

[zhouhao-learning]

@roelWuyts
Hello, I started again according to the content of your updated document, and I got the following error during the same period:

Traceback (most recent call last):
  File "./CellProfiler/CellProfiler.py", line 249, in main
    run_pipeline_headless(options, args)
  File "./CellProfiler/CellProfiler.py", line 787, in run_pipeline_headless
    from cellprofiler.pipeline import Pipeline, EXIT_STATUS, M_PIPELINE
  File "/project/hit_cell/test/process-plate/CellProfiler/cellprofiler/pipeline.py", line 58, in <module>
    from bioformats.omexml import OMEXML
  File "/project/hit_cell/test/process-plate/CellProfiler/bioformats/__init__.py", line 150, in <module>
    start_cellprofiler_jvm()
  File "/project/hit_cell/test/process-plate/CellProfiler/bioformats/__init__.py", line 68, in start_cellprofiler_jvm
    jar_files = get_cellprofiler_jars()
  File "/project/hit_cell/test/process-plate/CellProfiler/external_dependencies.py", line 315, in get_cellprofiler_jars
    "Can't determine CellProfiler java dependencies because %s is missing. Please re-run external_dependencies with the -o switch" % path)
RuntimeError: Can't determine CellProfiler java dependencies because /project/hit_cell/test/process-plate/CellProfiler/imagej/jars/cellprofiler-dependencies-classpath.txt is missing. Please re-run external_dependencies with the -o switch
Failed to stop Ilastik
Failed to stop the JVM

And I didn't produce the CellProfiler / ImageJ / jars / cellprofiler - dependencies - classpath. txt file mentioned in the error when I did it your way.

Then I rerun Python Cell Profiler / Cell Profiler. py -- build - and - exit to get a lot of errors, some of which are as follows:

Traceback (most recent call last):
  File "/project/hit_cell/test/process-plate/CellProfiler/external_dependencies.py", line 142, in fetch_external_dependencies
    fetchfile(path, url)
  File "/project/hit_cell/test/process-plate/CellProfiler/external_dependencies.py", line 106, in fetchfile
    src = urllib2.urlopen(url)
  File "/home/zh/anaconda2/lib/python2.7/urllib2.py", line 154, in urlopen
    return opener.open(url, data, timeout)
  File "/home/zh/anaconda2/lib/python2.7/urllib2.py", line 429, in open
    response = self._open(req, data)
  File "/home/zh/anaconda2/lib/python2.7/urllib2.py", line 447, in _open
    '_open', req)
  File "/home/zh/anaconda2/lib/python2.7/urllib2.py", line 407, in _call_chain
    result = func(*args)
  File "/home/zh/anaconda2/lib/python2.7/urllib2.py", line 1336, in file_open
    return self.open_local_file(req)
  File "/home/zh/anaconda2/lib/python2.7/urllib2.py", line 1376, in open_local_file
    raise URLError(msg)
URLError: <urlopen error [Errno 2] No such file or directory: '/CP/dependencies/apache-maven-3.0.4-bin.zip'>
Could not fetch external binary dependency /project/hit_cell/test/process-plate/CellProfiler/imagej/apache-maven-3.0.4-bin.zip from file:///CP/dependencies/apache-maven-3.0.4-bin.zip.  Some functionality may be missing.  You might try installing it by hand.
fetching file:///CP/dependencies/blitz.jar to /project/hit_cell/test/process-plate/CellProfiler/imagej/jars/blitz.jar

What should I do? Why do you have no problem there?