Runtime Error at MeasureObjectSizeShape (Linux 32)

First of all, I just wanted to say that CP is a great tool and I hope you keep up the good work.
I’m using it for a couple of month already with no issues under Microsoft Win 7 inside a Virtual Box.
Now I wanted to try get it running on a Linux 32 bit system (Ubuntu 10.04): I followed instructions at the developers wiki and also some instructions from this post http://www.cellprofiler.org/forum/viewtopic.php?f=14&t=1080&p=4364&hilit=linux+32#p4364 concerning the java library…

It starts up (more or less) fine, just the vigra-package ist not found, but this should’nt be problematic for my pipeline.

Here’s the terminal log at start up.

[code]michael@HAL:~/Media/CellProfiler/CellProfiler$ python CellProfiler.py
running build_ext
Using jdk_home = None
Using jdk_home = None
running build_ext
running build_ext
/usr/lib/python2.6/dist-packages/pytz/init.py:32: UserWarning: Module _mysql was already imported from /usr/lib/pymodules/python2.6/_mysql.so, but /usr/lib/pymodules/python2.6 is being added to sys.path
from pkg_resources import resource_stream
/usr/lib/python2.6/dist-packages/pytz/init.py:32: UserWarning: Module decorator was already imported from /home/michael/Media/CellProfiler/CellProfiler/decorator.pyc, but /usr/lib/pymodules/python2.6 is being added to sys.path
from pkg_resources import resource_stream
vigra import: failed to import the vigra library. Please follow the instructions on
http://hci.iwr.uni-heidelberg.de/vigra/” to install vigra
Traceback (most recent call last):
File “/home/michael/Media/CellProfiler/CellProfiler/cellprofiler/modules/classifypixels.py”, line 14, in
import vigra
ImportError: No module named vigra
Traceback (most recent call last):
File “/home/michael/Media/CellProfiler/CellProfiler/cellprofiler/modules/init.py”, line 278, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/home/michael/Media/CellProfiler/CellProfiler/cellprofiler/modules/classifypixels.py”, line 20, in
raise vigraImport
ImportError: No module named vigra
None
could not load these modules (‘cellprofiler.modules.classifypixels’, ImportError(‘No module named vigra’,))]

(python:10947): Gtk-CRITICAL **: gtk_range_set_range: assertion `min < max’ failed
Subversion revision: 10583
[/code]

Now, when I run my pipeline (attached) I encounter “RuntimeError: data type not supported” at module “MeasureObjectSizeShape”, details here:

Traceback (most recent call last): File "/home/michael/Media/CellProfiler/CellProfiler/cellprofiler/pipeline.py", line 309, in run self.module.run(self.workspace) File "/home/michael/Media/CellProfiler/CellProfiler/cellprofiler/modules/measureobjectsizeshape.py", line 238, in run self.run_on_objects(object_group.name.value, workspace) File "/home/michael/Media/CellProfiler/CellProfiler/cellprofiler/modules/measureobjectsizeshape.py", line 275, in run_on_objects object_name, F_SOLIDITY) File "/home/michael/Media/CellProfiler/CellProfiler/cellprofiler/modules/measureobjectsizeshape.py", line 326, in perform_measurement data = objects.fn_of_label_and_index(function) File "<string>", line 2, in fn_of_label_and_index File "/home/michael/Media/CellProfiler/CellProfiler/cellprofiler/objects.py", line 36, in memoize_method d[function][args[1:]] = function(*args) File "/home/michael/Media/CellProfiler/CellProfiler/cellprofiler/objects.py", line 243, in fn_of_label_and_index return function(self.segmented,self.indices) File "/home/michael/Media/CellProfiler/CellProfiler/cellprofiler/cpmath/cpmorphology.py", line 1825, in calculate_solidity convex_hull_areas = calculate_convex_hull_areas(labels, indexes) File "/home/michael/Media/CellProfiler/CellProfiler/cellprofiler/cpmath/cpmorphology.py", line 1727, in calculate_convex_hull_areas hull, counts = convex_hull(labels, indexes) File "/home/michael/Media/CellProfiler/CellProfiler/cellprofiler/cpmath/cpmorphology.py", line 327, in convex_hull return convex_hull_ijv(pixel_labels, indexes) File "/home/michael/Media/CellProfiler/CellProfiler/cellprofiler/cpmath/cpmorphology.py", line 360, in convex_hull_ijv scind.mean(i.astype(float), labels_per_point.astype(int), indexes)) File "/usr/lib/python2.6/dist-packages/scipy/ndimage/measurements.py", line 145, in mean return _nd_image.statistics(input, labels, index, 1) RuntimeError: data type not supported

I kicked the “MeasueObjectSizeShape” out of the pipeline and it runs through completely without errors.
Is there any chance to fix this, it certainly is a problem of CP under Linux 32bit…?

Im using CellProfiler build 10583, the pipeline from Win 7 machine is version 10415, but this should not be the reason, as a freshly set up pipeline doesnt work either…

Hope you can help to run CP more native on my Linux, all the best,
Michael
example_images.zip (646 KB)
IdentifyShmoo_Fluorescence_Stricter.cp (16.8 KB)

Hi Michael,
It looks like you may be using an older version of scipy, possibly 0.70. There are some critical changes since 0.70; if you build from source, you should probably check out scipy directly (svn co svn.scipy.org/svn/scipy/trunk/sc … rements.py

If you have some patience, you might try following the directions at the bottom of this post: How to install cellprofiller2.0 in a Linux Cluster
I haven’t tried this on a 32-bit Linux, but Mario Emmenlauer and I have succeeding in building on two different Unix distributions.

–Lee

Hi Lee,
thanks for the reply, i’ll check out your suggestions and tell what happens,

Best regards
Michael

Hello again,

Concerning your suggestions I just wanted to say you are absolutely right: my version of scipy (and also numpy) is quite outdated, it’s 0.7.
Unfortunately my experiences with building these items from source are fairly limited and it seems to be some effort… I think I postpone this until they update the repository version to 0.8 or something and stay at windows for a while…

Thanks anyway, best regards,
Michael