CellProfiler/CellProfiler — Issue #60: JIRA [IMG-1525] MeasureObjectSizeShape error
Author: thouis
Created: 2011-11-23 20:49:45+00:00
State: open
Labels: current

********
Traceback (most recent call last):
File"C:\Trunk\CellProfiler_11429_patched_with_11448\cellprofiler\gui\pipelinecontroller.py", line 1000, in do_step
module.run(workspace)
File"C:\Trunk\CellProfiler_11429_patched_with_11448\cellprofiler\modules\measureobjectsizeshape.py", line 290, in run
self.run_on_objects(object_group.name.value, workspace)
File"C:\Trunk\CellProfiler_11429_patched_with_11448\cellprofiler\modules\measureobjectsizeshape.py", line 340, in run_on_objects
distances = distance_to_edge(labels)
File"C:\Trunk\CellProfiler_11429_patched_with_11448\cellprofiler\cpmath\cpmorphology.py", line 3475, in distance_to_edge
colors = color_labels(labels)
File"C:\Trunk\CellProfiler_11429_patched_with_11448\cellprofiler\cpmath\cpmorphology.py", line 3262, in color_labels
v_count, v_index, v_neighbor = find_neighbors(dt_labels)
File"C:\Trunk\CellProfiler_11429_patched_with_11448\cellprofiler\cpmath\cpmorphology.py", line 3205, in find_neighbors
np.arange(max_label,dtype=np.int32)+1))
File"C:\Python26\lib\site-packages\scipy\ndimage\measurements.py", line 358, in sum
count, sum = _stats(input, labels, index)
File"C:\Python26\lib\site-packages\scipy\ndimage\measurements.py", line 302, in _stats
unique_labels, new_labels = numpy.unique1d(labels, return_inverse=True)
AttributeError:'module' object has no attribute'unique1d'
*******
Def input: \\iodine\imaging|analysis\2010_05_25_Synapse_Formation_Nieland_Bernardo_Sabatini_Lab_HMS\2011_01_25_SynapseScreen_1_2\images_selected_wells
Pipeline: \\iodine\imaging|analysis\2010_05_25_Synapse_Formation_Nieland_Bernardo_Sabatini_Lab_HMS\2011_01_25_SynapseScreen_1_2\Analysis\test_G1p4_P0p8_S0p65_11429_v3_\PIPE_LowThresholds_11429_BGthresh_3.cp

Original reporter: dlogan
Jira link: https://jira.broadinstitute.org/browse/IMG-1525
Fix version: Current
Assignee: leek

**Comment from leek on Mon, 12 Sep 2011 15:53:23 -0400:**
OK - I will check on the Windows VM. Possibly has to be tomorrow.
On 9/12/2011 1:48 PM, David Logan (JIRA) wrote:
> [https://jira.broadinstitute.org/browse/IMG-1525?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=147826#comment-147826]
>
> David Logan commented onIMG-1525:
> ----------------------------------
>
> I haven't tried this on my machine, as I am using the Windows VM. So this numpy was installed by Mark via the same template as all the VM's I think, and has been fine. I just checked and it uses numpy version 1.6.1.
>
>
>
>> MeasureObjectSizeShape error
>> ----------------------------
>>
>> Key:IMG-1525
>> URL:https://jira.broadinstitute.org/browse/IMG-1525
>> Project: Imaging
>> Issue Type: Bug
>> Components: CellProfiler
>> Affects Versions: Current
>> Environment: Win7
>> Reporter: David Logan
>> Assignee: Lee Kamentsky
>> Priority: Major
>> Fix For: Current
>>
>>
>> ********
>> Traceback (most recent call last):
>> File"C:\Trunk\CellProfiler_11429_patched_with_11448\cellprofiler\gui\pipelinecontroller.py", line 1000, in do_step
>> module.run(workspace)
>> File"C:\Trunk\CellProfiler_11429_patched_with_11448\cellprofiler\modules\measureobjectsizeshape.py", line 290, in run
>> self.run_on_objects(object_group.name.value, workspace)
>> File"C:\Trunk\CellProfiler_11429_patched_with_11448\cellprofiler\modules\measureobjectsizeshape.py", line 340, in run_on_objects
>> distances = distance_to_edge(labels)
>> File"C:\Trunk\CellProfiler_11429_patched_with_11448\cellprofiler\cpmath\cpmorphology.py", line 3475, in distance_to_edge
>> colors = color_labels(labels)
>> File"C:\Trunk\CellProfiler_11429_patched_with_11448\cellprofiler\cpmath\cpmorphology.py", line 3262, in color_labels
>> v_count, v_index, v_neighbor = find_neighbors(dt_labels)
>> File"C:\Trunk\CellProfiler_11429_patched_with_11448\cellprofiler\cpmath\cpmorphology.py", line 3205, in find_neighbors
>> np.arange(max_label,dtype=np.int32)+1))
>> File"C:\Python26\lib\site-packages\scipy\ndimage\measurements.py", line 358, in sum
>> count, sum = _stats(input, labels, index)
>> File"C:\Python26\lib\site-packages\scipy\ndimage\measurements.py", line 302, in _stats
>> unique_labels, new_labels = numpy.unique1d(labels, return_inverse=True)
>> AttributeError:'module' object has no attribute'unique1d'
>> *******
>> Def input: \\iodine\imaging|analysis\2010_05_25_Synapse_Formation_Nieland_Bernardo_Sabatini_Lab_HMS\2011_01_25_SynapseScreen_1_2\images_selected_wells
>> Pipeline: \\iodine\imaging|analysis\2010_05_25_Synapse_Formation_Nieland_Bernardo_Sabatini_Lab_HMS\2011_01_25_SynapseScreen_1_2\Analysis\test_G1p4_P0p8_S0p65_11429_v3_\PIPE_LowThresholds_11429_BGthresh_3.cp
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