Comments (6)
If you go to ClearMap\ClearMap you should find Settings.py. Starting line 29 you should see where to set the path to elastix:
Line 29 in ae57ca9
Then just set it to where you have it built/installed on your machine. For example, mine is:
ElastixPath = '/home/asus/software/elastix-4.9.0-linux/';
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thank you, vzickus by following your instruction. I was able to run sudo python setup.py install. it ran the setup fine. the other part, where do I go to launch the clearmap software? I see a couple of new folders created after I ran setup.
build ClearMap ClearMap.egg-info dist
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I suggest you have a read of this, where they point you to the relevant files
https://github.com/ChristophKirst/ClearMap/blob/master/docs/tutorial.rst
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thank you, I have read the tutorials a few times. I kind of left everything as default just see how it works besides changing the path to this:
#load the parameters:
execfile('/home/moduk/ClearMap/build/lib.linux-x86_64-2.7/ClearMap/Scripts/parameter_file_template.py')
then I ran: python process_template.py
could help me see if this suppose to happen?
Elastix sucessfully initialized from path: /home/moduk/elastix490
Ilastik sucessfully initialized from path: /home/moduk/ilastik-1.3.0-Linux
Traceback (most recent call last):
File "process_template.py", line 7, in
execfile('/home/moduk/ClearMap/build/lib.linux-x86_64-2.7/ClearMap/Scripts/parameter_file_template.py')
File "/home/moduk/ClearMap/build/lib.linux-x86_64-2.7/ClearMap/Scripts/parameter_file_template.py", line 17, in
from ClearMap.Analysis.Label import countPointsInRegions
File "/usr/local/lib/python2.7/dist-packages/ClearMap-0.9.2-py2.7-linux-x86_64.egg/ClearMap/Analysis/Label.py", line 164, in
Label = LabelInfo();
File "/usr/local/lib/python2.7/dist-packages/ClearMap-0.9.2-py2.7-linux-x86_64.egg/ClearMap/Analysis/Label.py", line 86, in init
slf.initialize(annotationFile = annotationFile);
File "/usr/local/lib/python2.7/dist-packages/ClearMap-0.9.2-py2.7-linux-x86_64.egg/ClearMap/Analysis/Label.py", line 91, in initialize
with open(annotationFile) as dfile:
IOError: [Errno 2] No such file or directory: '/usr/local/lib/python2.7/dist-packages/ClearMap-0.9.2-py2.7-linux-x86_64.egg/ClearMap/Data/ARA2_annotation_info_collapse.csv'
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@AbsolemPillar I am trying Clearmap as well and got the same error. I then copied the Data
folder from your git clone download
ls Data/
ARA2_annotation_info_collapse.csv ARA2_annotation_statistics.csv lightsheet_line_intensty_profiles_y.csv
ARA2_annotation_info.csv lightsheet_flatfield_correction.csv lightsheet_peak_intensity_profile_y.csv
cp -r Data /usr/local/lib/python2.7/dist-packages/ClearMap-0.9.2-py2.7-linux-x86_64.egg/ClearMap/
it should work.
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It does.
For some reason, when python installs the repository it does not copy the Data folder. You need to add it manually as per @crazyhottommy code.
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Related Issues (20)
- No module named 'Cython' HOT 8
- Region specific heatmaps HOT 2
- elastix library not loaded (MacOSX) despite existing in path HOT 1
- Python crashes during resampling
- TIFFReadDirectory warning: Unknown field with tag 50838 HOT 1
- 'OverflowError('cannot serialize a string larger than 2 GiB',)
- annotated counts not registering to csv
- Too many files open
- itk::ERROR: RandomCoordinateSampler Please select a smaller SampleRegionSize!
- no
- Two of the Unlabelled regions actually labels parts of two different regions
- Problems with Elastix HOT 2
- problems with the Analysis script HOT 2
- findCenterOfMaxima returns non integer center coordinates, which are not valid in voxelizePixel function
- Issue with Installation, setting.py specifically HOT 3
- Interfacing Ilastik
- ClearMap can't find my .ilp file for celldetection
- Elastix runtime error
- ImportError: cannot import name 'Texture3D' from 'vispy.visuals.volume' HOT 2
- Error during Transform point coordinates with 'elastix_input.txt'
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