Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk
/work/CaPTk/bin/install/appdir/usr/bin/captk /work/CaPTk/bin/install/appdir/usr/bin/BreastTexturePipeline.cwl -i /images/{image}.dcm -o /output or /work/CaPTk/bin/install/appdir/usr/bin/libra /images/{image}.dcm /output
See error
Expected behavior
Expect the LIBRA or BreastTexturePipeline to execute completely
CaPTk Version
CaPTk v1.9.0.RC
Desktop (please complete the following information):
OS: Ubuntu 20.04.6
Additional context
The code executes successfully to the same point with either command:
Running LIBRA-1.0.4 (Revision: 603) on MATLAB R2014b
>> Analzying single file...
>> Processing File 1/1: /images/{image}.dcm
> Checking header
> WARNING: Age information is missing. Use Default.
> Checking passed.
...identifying appropriate training model
...using model:Hologic-Processed...
Masking out Breast
Running 15-class FCM
...Getting dense-cluster metrics (i.e. hierarchical agglomeration)
------------------------------------------------------------------------
Illegal instruction detected at Mon Oct 16 23:21:28 2023
------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled
Current Visual : None
Default Encoding : UTF-8
GNU C Library : 2.17 stable
MATLAB Architecture: glnxa64
MATLAB Root : /work/CaPTk/bin/install/appdir/usr/libexec/MCR/v84
MATLAB Version : 8.4.0.150421 (R2014b)
Operating System : Linux 5.4.0-153-generic #170-Ubuntu SMP Fri Jun 16 13:43:31 UTC 2023 x86_64
Processor ID : x86 Family 143 Model 49 Stepping 0, AuthenticAMD
Software OpenGL : 0
Virtual Machine : Java 1.7.0_11-b21 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
Window System : No active display
Fault Count: 1
Describe the bug When trying to run either the BreastTexturePipeline or LIBRA from the CLI from the latest CaPTK Docker container I get a fatal error
To Reproduce Steps to reproduce the behavior:
docker run --rm -it -v $(pwd)/test:/app -v {local_img_dir}:/images -v {local_out_dir}:/output --entrypoint /bin/bash cbica/captk/work/CaPTk/bin/install/appdir/usr/bin/captk /work/CaPTk/bin/install/appdir/usr/bin/BreastTexturePipeline.cwl -i /images/{image}.dcm -o /outputor/work/CaPTk/bin/install/appdir/usr/bin/libra /images/{image}.dcm /outputExpected behavior Expect the LIBRA or BreastTexturePipeline to execute completely
CaPTk Version CaPTk v1.9.0.RC
Desktop (please complete the following information):
Additional context The code executes successfully to the same point with either command:
Stack Trace