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2D/3D biopolymer network extraction and quantification.

Home Page: https://www.lehigh.edu/~div206/soax/

License: BSD 3-Clause "New" or "Revised" License

CMake 1.01% C++ 98.99%

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erkang nosuchprocess tclan8023 frenebo hanhongqing

soax's Issues

soax_batch fails to run on Mac

Hi, I am testing SOAX (v3.6.1) for Mac and find it super useful. When I try to run the batch version of SOAX, however, I get the following error:

dyld: lazy symbol binding failed: Symbol not found: __ZN5boost10filesystem6detail28directory_iterator_constructERNS0_18directory_iteratorERKNS0_4pathEPNS_6system10error_codeE
  Referenced from: /Users/amedyukh/Applications/soax/./batch_soax_v3.6.1
  Expected in: /usr/local/opt/boost/lib/libboost_filesystem-mt.dylib

dyld: Symbol not found: __ZN5boost10filesystem6detail28directory_iterator_constructERNS0_18directory_iteratorERKNS0_4pathEPNS_6system10error_codeE
  Referenced from: /Users/amedyukh/Applications/soax/./batch_soax_v3.6.1
  Expected in: /usr/local/opt/boost/lib/libboost_filesystem-mt.dylib

Abort trap: 6

My Mac version is 10.14.6, and I am downloading the Batch SOAX from here: https://www.lehigh.edu/~div206/soax/downloads.html

building from source fails in Ubuntu 14.04

I am trying to build SOAX from source in Ubuntu 14.04 according to instructions here: https://www.lehigh.edu/~div206/soax/downloads.html

Steps 1-3 have been completed successfully (I installed VTK version 6.3 and ITK version 4.72, as suggested in the section for MacOS). Configuring SOAX with CMake also seemed to be successful. However, when building with make, I get the following error:

/opt/release/viewer.cc: In member function 'vtkPolyData* soax::Viewer::MakePolyData(soax::Snake*, unsigned int, unsigned int)':
/opt/release/viewer.cc:449:3: error: 'vtkFloatingPointType' was not declared in this scope
   vtkFloatingPointType coordinates[3];
   ^
/opt/release/viewer.cc:449:24: error: expected ';' before 'coordinates'
   vtkFloatingPointType coordinates[3];
                        ^
/opt/release/viewer.cc:452:5: error: 'coordinates' was not declared in this scope
     coordinates[0] = snake->GetX(i);
     ^
/opt/release/viewer.cc: In member function 'vtkPolyData* soax::Viewer::MakePolyDataForMultipleSnakes(const SnakeContainer&)':
/opt/release/viewer.cc:487:3: error: 'vtkFloatingPointType' was not declared in this scope
   vtkFloatingPointType coordinates[3];
   ^
/opt/release/viewer.cc:487:24: error: expected ';' before 'coordinates'
   vtkFloatingPointType coordinates[3];
                        ^
/opt/release/viewer.cc:492:7: error: 'coordinates' was not declared in this scope
       coordinates[0] = (*s_iter)->GetX(i);
       ^
/opt/release/viewer.cc: In member function 'vtkPolyData* soax::Viewer::MakeClippedPolyData(unsigned int, double)':
/opt/release/viewer.cc:684:3: error: 'vtkFloatingPointType' was not declared in this scope
   vtkFloatingPointType coordinates[3];
   ^
/opt/release/viewer.cc:684:24: error: expected ';' before 'coordinates'
   vtkFloatingPointType coordinates[3];
                        ^
/opt/release/viewer.cc:689:7: error: 'coordinates' was not declared in this scope
       coordinates[0] = it->first->GetX(i);
       ^
make[2]: *** [CMakeFiles/soax.dir/viewer.cc.o] Error 1

I have tried two different versions of the source code, from here: https://github.com/tix209/SOAX/releases/tag/Version-3.5.2. and from here: https://www.lehigh.edu/~div206/soax/code/release_v3.5.7.zip

Both result in the same error.

I'd appreciate any info on the version of the source code that compiles or any other hints on how to make use of the batch mode.

Thanks

Unable to get the `batch_soax` command to work on Intel as well as M1 MacBook

After running the following command

./batch_soax -i ./select_test/ -s ./result-snakes/ -p default_prams.txt --ridge 0.001 0.005 0.1 --stretch 0.1 0.1 1.0

./batch_soax -i ./select_test/ -s ./result-snakes/ -p default_prams.txt

where,
select_test - Is a folder containing isotropic images (5 of them)
result-snakes - Is an empty folder where all the resultant txt files containing information about snakes is to be stored.
default_prams.txt - file containing default parameter for execution.

I am getting the following error in the terminal

Input may contain multiple images.
dyld[11941]: missing symbol called

When I execute the following command for a single file, it executes properly and output in form of several text files is obtained.

#Sweeping parameter space on a single image
./batch soax -i ../data/image.mha -p ../parameters/parameter.txt -s ../result-snakes/ --ridge 0.001 0.005 0.1 --stretch 0.1 0.1 1.0

Why is it then not working for the batch of files (in a folder)?
What is the meaning of the error "Input may contain multiple images. dyld[11941]: missing symbol called"?
If I want to run this software on a lot of data how do I go about creating such process, should I leverage multiprocessing? Is there internal feature to do that optimally?

tix209 / soax Goto Github PK

soax's People

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soax's Issues

soax_batch fails to run on Mac

building from source fails in Ubuntu 14.04

Unable to get the `batch_soax` command to work on Intel as well as M1 MacBook

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