Using openCARP's docker container

# Using openCARP's docker container Assume you want to run `openCARP` on a file called `carpf_laplace_PA.par`, that is located on a folder `$LAPath`, then: **Using openCARP installed on your machine**. This is equivalent to using the AppImage, only the name changes: ```shell! cd $LAPath openCARP +F carpf_laplace_PA.par --simID PA_UAC ``` **Using openCARP's docker** We'll display the command in multiple lines to be more understandable: ```shell docker run \ --rm \ --volume=$LAPath:/shared:z --workdir=/shared \ docker.opencarp.org/opencarp/opencarp:latest \ openCARP \ +F carpf_laplace_PA.par --simID PA_UAC ``` > In a single line: ```shell docker run --rm --volume=$LAPath:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_PA.par --simID PA_UAC ``` # Another example Paste your code below: ```shell # #!/bin/bash # EXAMPLE 1 echo "==== Using local meshtool ==== " meshtool convert -imsh="$LAPath/Labelled" -ifmt=carp_txt -omsh="$LAPath/Labelled" -ofmt=carp_txt -scale=1000 echo "==== Using meshtool inside openCARP docker ====" docker run --rm --volume=$LAPath:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest meshtool convert -imsh="Labelled" -ifmt=carp_txt -omsh="Labelled" -ofmt=carp_txt -scale=1000 # EXAMPLE 2 echo "==== Using openCARP AppImage ====" cd "$LAPath/" openCARP-v13.0-x86_64.AppImage +F carpf_laplace_PV1.par -simID MV_PV1 echo "==== Using docker openCARP ====" docker run --rm --volume=$LAPath:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_PV1.par -simID MV_PV1 ``` Try it yourself! ## Additional Question When I ran the script, Docker is not running in the background. Is this the problem? ## Directory Structure ``` root (Project root Folder) ├─UAC_code(UAC code folder) ├─Data │ ├─CardioInsight_clipped.stl │ ├─CardioInsight_Landmarks.txt │ ├─CardioInsight_Regions.txt │ ├─Ensite_clipped.stl │ ├─Ensite_Landmarks.txt │ └─Ensite_Regions.txt └─umc-lav_CardioInsight.sh ``` ## Changed Segment Line 64 - 74 ```shell= docker run --rm --volume=/mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject/Data/:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_PV1.par -simID MV_PV1 docker run --rm --volume=/mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject/Data/:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_PV2.par -simID MV_PV2 docker run --rm --volume=/mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject/Data/:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_PV3.par -simID MV_PV3 docker run --rm --volume=/mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject/Data/:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_PV4.par -simID MV_PV4 docker run --rm --volume=/mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject/Data/:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_LAA.par -simID MV_LAA # openCARP-v13.0-x86_64.AppImage +F carpf_laplace_PV1.par -simID MV_PV1 # openCARP-v13.0-x86_64.AppImage +F carpf_laplace_PV2.par -simID MV_PV2 # openCARP-v13.0-x86_64.AppImage +F carpf_laplace_PV3.par -simID MV_PV3 # openCARP-v13.0-x86_64.AppImage +F carpf_laplace_PV4.par -simID MV_PV4 # openCARP-v13.0-x86_64.AppImage +F carpf_laplace_LAA.par -simID MV_LAA ``` ## umc-lav_CardioInsight.sh ```shell= #!/bin/bash echo "Variables" # Variables PROJECT=UAC_code # UAC project directory DATA=Data # data directory PYTHON_PATH2=UAC_code/carpusers-bdx-tools # carpusers-bdx-tools directory export PYTHONPATH=$PROJECT RA_Mesh_Name="Labelled_6" ES_dir="$PROJECT/extra_structures" RAendofib_dir="$PROJECT/fibre_files/ra/endo/l/" RAepifib_dir="$PROJECT/fibre_files/ra/epi/l/" RAbbfib_dir="$PROJECT/fibre_files/bb/ra/" LAendofib_dir="$PROJECT/fibre_files/la/endo/l/" LAepifib_dir="$PROJECT/fibre_files/la/epi/l/" LAbbfib_dir="$PROJECT/fibre_files/bb/la/" MeshName="Labelled" LandmarksRA="CardioInsight_Landmarks.txt" RegionRA="CardioInsight_Regions.txt" LandmarksLA="CardioInsight_Landmarks.txt" RegionLA="CardioInsight_Regions.txt" index=1 pvThreshold=0.85 LAAThreshold=0.9 #Bigger number = smaller area defined From 0 to 1 # Variables LAPath='Data/' LAFile='CardioInsight_clipped.stl' # Using openCARP installed on local machine # cd $LAPath # openCARP +F carpf_laplace_PA.par --simID PA_UAC # Shared folder absolute path: # /mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject/Data/ # Create shared folder and set the working directory inside the container shared folder # docker run --rm --volume=$LAPath:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_PA.par --simID PA_UAC # Combined: docker run --rm --volume=/mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject/Data/:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_PA.par --simID PA_UAC echo $LAPath python $PYTHON_PATH2/trans_mod.py --from-format=stl --to-format=carp "$LAPath/$LAFile" "$LAPath/Labelled.pts" meshtool convert -imsh="$LAPath/Labelled" -ifmt=carp_txt -omsh="$LAPath/Labelled" -ofmt=carp_txt -scale=1000 python $PROJECT/scripts/labels_la_1.py $LAPath "$PROJECT/fibre_files/la/endo/" "$PROJECT/laplace_files/" Labelled $pvThreshold $LAAThreshold $RegionLA 1000 cp "$PROJECT/laplace_files/carpf_laplace_PV1.par" "$LAPath/carpf_laplace_PV1.par" cp "$PROJECT/laplace_files/carpf_laplace_PV2.par" "$LAPath/carpf_laplace_PV2.par" cp "$PROJECT/laplace_files/carpf_laplace_PV3.par" "$LAPath/carpf_laplace_PV3.par" cp "$PROJECT/laplace_files/carpf_laplace_PV4.par" "$LAPath/carpf_laplace_PV4.par" cp "$PROJECT/laplace_files/carpf_laplace_LAA.par" "$LAPath/carpf_laplace_LAA.par" cd "$LAPath/" docker run --rm --volume=/mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject/Data/:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_PV1.par -simID MV_PV1 docker run --rm --volume=/mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject/Data/:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_PV2.par -simID MV_PV2 docker run --rm --volume=/mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject/Data/:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_PV3.par -simID MV_PV3 docker run --rm --volume=/mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject/Data/:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_PV4.par -simID MV_PV4 docker run --rm --volume=/mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject/Data/:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_LAA.par -simID MV_LAA # openCARP-v13.0-x86_64.AppImage +F carpf_laplace_PV1.par -simID MV_PV1 # openCARP-v13.0-x86_64.AppImage +F carpf_laplace_PV2.par -simID MV_PV2 # openCARP-v13.0-x86_64.AppImage +F carpf_laplace_PV3.par -simID MV_PV3 # openCARP-v13.0-x86_64.AppImage +F carpf_laplace_PV4.par -simID MV_PV4 # openCARP-v13.0-x86_64.AppImage +F carpf_laplace_LAA.par -simID MV_LAA python $PROJECT/scripts/labels_la_2.py "$LAPath/" "$PROJECT/fibre_files/la/endo/" "$PROJECT/laplace_files/" Labelled $pvThreshold $LAAThreshold $RegionLA 1000 cp "$LAPath/Labelled_Labels.elem" "$LAPath/Labelled.elem" cp "$PROJECT/laplace_files/carpf_laplace_LS.par" "$LAPath/carpf_laplace_LS.par" cp "$PROJECT/laplace_files/carpf_laplace_PA.par" "$LAPath/carpf_laplace_PA.par" python $PROJECT/scripts/1_la.py "$LAPath/" "$PROJECT/fibre_files/la/endo/" "$PROJECT/laplace_files/" Labelled 11 13 21 23 25 27 $LandmarksLA 1000 echo "=====Old UAC approximation - openCARP command line ($i)=====" cd "$LAPath/" docker run --rm --volume=/mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject/Data/:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_PA.par -simID PA_UAC_N2 docker run --rm --volume=/mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject/Data/:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_LS.par -simID LR_UAC_N2 echo "=====New UAC=====" cp "$PROJECT/laplace_files/carpf_laplace_single_LR_P.par" "$LAPath/carpf_laplace_single_LR_P.par" cp "$PROJECT/laplace_files/carpf_laplace_single_UD_P.par" "$LAPath/carpf_laplace_single_UD_P.par" cp "$PROJECT/laplace_files/carpf_laplace_single_LR_A.par" "$LAPath/carpf_laplace_single_LR_A.par" cp "$PROJECT/laplace_files/carpf_laplace_single_UD_A.par" "$LAPath/carpf_laplace_single_UD_A.par" python $PROJECT/scripts/2a_la.py "$LAPath/" "$PROJECT/fibre_files/la/endo/" "$PROJECT/laplace_files/" Labelled 11 13 21 23 25 27 $LandmarksLA 1000 docker run --rm --volume=/mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject/Data/:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_single_LR_A.par -simID LR_Ant_UAC docker run --rm --volume=/mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject/Data/:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_single_LR_P.par -simID LR_Post_UAC docker run --rm --volume=/mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject/Data/:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_single_UD_A.par -simID UD_Ant_UAC docker run --rm --volume=/mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject/Data/:/shared:z --workdir=/shared docker.opencarp.org/opencarp/opencarp:latest openCARP +F carpf_laplace_single_UD_P.par -simID UD_Post_UAC echo "=====New UAC part 2=====" python $PROJECT/scripts/2b_la.py "$LAPath/" "$PROJECT/fibre_files/la/endo/" "$PROJECT/laplace_files/" Labelled 11 13 21 23 25 27 1000 echo "=====Add fibres2 =====" python $PROJECT/scripts/fibre_mapping.py "$LAPath/" "$PROJECT/fibre_files/la/endo/l/" "$PROJECT/laplace_files/" Labelled Labelled.lon Fibre_l echo "=====Add LAT field ($i)=====" python $PROJECT/scripts/lat_field.py "$LAPath/" LAT_Spiral4_B.dat Fibre_l echo "=====Make PV stimulus files .vtx ($i)=====" ``` ## Error Code ``` (uac) zack@MSI:/mnt/c/Users/catsk$ cd OneDrive/桌面/PCAL_NonInvasiveMappingProject (uac) zack@MSI:/mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject$ sh umc-lav_CardioInsight.sh Variables Data/ Reading Data//CardioInsight_clipped.stl in stl format Finished reading Data//CardioInsight_clipped.stl <meshio mesh object> Number of points: 3430 Number of cells: triangle: 6539 Cell data: facet_normals Writing Data//Labelled.pts in carp ASCII format OpenMP thread utilization: 16 / 16 threads. Reading mesh: Data//Labelled Reading elements in text CARP format: [============] 00h:00m:00s FIN Reading points in text CARP format: [============] 00h:00m:00s FIN Reading fibers (1 directions) in text CARP format: [============] 00h:00m:00s FIN Done in 0.01252 sec Processing mesh .. Pass 1: Corrected 0 inside-out elements. Done in 4.2e-05 sec Writing mesh: Data//Labelled Writing elements in text CARP format: [============] 00h:00m:00s FIN Writing points in text CARP format: [============] 00h:00m:00s FIN Writing fibers (1 direction) in text CARP format: [============] 00h:00m:00s FIN Done in 0.135395 sec Traceback (most recent call last): File "UAC_code/scripts/labels_la_1.py", line 7, in <module> from uac import utils File "/mnt/c/Users/catsk/OneDrive/桌面/PCAL_NonInvasiveMappingProject/UAC_code/uac/utils.py", line 10, in <module> import vtk File "/home/zack/anaconda3/envs/uac/lib/python3.8/site-packages/vtk.py", line 30, in <module> all_m = importlib.import_module('vtkmodules.all') File "/home/zack/anaconda3/envs/uac/lib/python3.8/importlib/__init__.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "/home/zack/anaconda3/envs/uac/lib/python3.8/site-packages/vtkmodules/all.py", line 23, in <module> from .vtkRenderingVtkJS import * ImportError: libGL.so.1: cannot open shared object file: No such file or directory The command 'docker' could not be found in this WSL 2 distro. We recommend to activate the WSL integration in Docker Desktop settings. For details about using Docker Desktop with WSL 2, visit: https://docs.docker.com/go/wsl2/ The command 'docker' could not be found in this WSL 2 distro. We recommend to activate the WSL integration in Docker Desktop settings. For details about using Docker Desktop with WSL 2, visit: https://docs.docker.com/go/wsl2/ The command 'docker' could not be found in this WSL 2 distro. We recommend to activate the WSL integration in Docker Desktop settings. For details about using Docker Desktop with WSL 2, visit: https://docs.docker.com/go/wsl2/ The command 'docker' could not be found in this WSL 2 distro. We recommend to activate the WSL integration in Docker Desktop settings. For details about using Docker Desktop with WSL 2, visit: https://docs.docker.com/go/wsl2/ The command 'docker' could not be found in this WSL 2 distro. We recommend to activate the WSL integration in Docker Desktop settings. For details about using Docker Desktop with WSL 2, visit: https://docs.docker.com/go/wsl2/ python: can't open file 'UAC_code/scripts/labels_la_2.py': [Errno 2] No such file or directory cp: cannot stat 'Data//Labelled_Labels.elem': No such file or directory cp: cannot stat 'UAC_code/laplace_files/carpf_laplace_LS.par': No such file or directory cp: cannot stat 'UAC_code/laplace_files/carpf_laplace_PA.par': No such file or directory python: can't open file 'UAC_code/scripts/1_la.py': [Errno 2] No such file or directory =====Old UAC approximation - openCARP command line ()===== umc-lav_CardioInsight.sh: 88: cd: can't cd to Data// The command 'docker' could not be found in this WSL 2 distro. We recommend to activate the WSL integration in Docker Desktop settings. For details about using Docker Desktop with WSL 2, visit: https://docs.docker.com/go/wsl2/ The command 'docker' could not be found in this WSL 2 distro. We recommend to activate the WSL integration in Docker Desktop settings. For details about using Docker Desktop with WSL 2, visit: https://docs.docker.com/go/wsl2/ =====New UAC===== cp: cannot stat 'UAC_code/laplace_files/carpf_laplace_single_LR_P.par': No such file or directory cp: cannot stat 'UAC_code/laplace_files/carpf_laplace_single_UD_P.par': No such file or directory cp: cannot stat 'UAC_code/laplace_files/carpf_laplace_single_LR_A.par': No such file or directory cp: cannot stat 'UAC_code/laplace_files/carpf_laplace_single_UD_A.par': No such file or directory python: can't open file 'UAC_code/scripts/2a_la.py': [Errno 2] No such file or directory The command 'docker' could not be found in this WSL 2 distro. We recommend to activate the WSL integration in Docker Desktop settings. For details about using Docker Desktop with WSL 2, visit: https://docs.docker.com/go/wsl2/ The command 'docker' could not be found in this WSL 2 distro. We recommend to activate the WSL integration in Docker Desktop settings. For details about using Docker Desktop with WSL 2, visit: https://docs.docker.com/go/wsl2/ The command 'docker' could not be found in this WSL 2 distro. We recommend to activate the WSL integration in Docker Desktop settings. For details about using Docker Desktop with WSL 2, visit: https://docs.docker.com/go/wsl2/ The command 'docker' could not be found in this WSL 2 distro. We recommend to activate the WSL integration in Docker Desktop settings. For details about using Docker Desktop with WSL 2, visit: https://docs.docker.com/go/wsl2/ =====New UAC part 2===== python: can't open file 'UAC_code/scripts/2b_la.py': [Errno 2] No such file or directory =====Add fibres2 ===== python: can't open file 'UAC_code/scripts/fibre_mapping.py': [Errno 2] No such file or directory =====Add LAT field ()===== python: can't open file 'UAC_code/scripts/lat_field.py': [Errno 2] No such file or directory =====Make PV stimulus files .vtx ()===== ```

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