From e535cbfb59fabc743e67f55d8c64426a81c95161 Mon Sep 17 00:00:00 2001 From: "hugo.marques" Date: Mon, 4 Nov 2024 17:22:38 +0000 Subject: [PATCH] Updated documentation of BonFly3MPTracker. --- Marta/BonFly3MPTracker/README.md | 4 + .../bonsai/Bonsai.config | 142 +++++ .../bonsai/NuGet.config | 8 + .../bonsai/Setup.cmd | 1 + .../bonsai/SetupPS.ps1 | 9 + .../src/MatingIdentification.bonsai | 504 ++++++++++++++++++ .../src/MatingIdentification.bonsai.layout | 501 +++++++++++++++++ 7 files changed, 1169 insertions(+) create mode 100644 Vasconcelos/MatingIdentification-INDP2024/bonsai/Bonsai.config create mode 100644 Vasconcelos/MatingIdentification-INDP2024/bonsai/NuGet.config create mode 100644 Vasconcelos/MatingIdentification-INDP2024/bonsai/Setup.cmd create mode 100644 Vasconcelos/MatingIdentification-INDP2024/bonsai/SetupPS.ps1 create mode 100644 Vasconcelos/MatingIdentification-INDP2024/src/MatingIdentification.bonsai create mode 100644 Vasconcelos/MatingIdentification-INDP2024/src/MatingIdentification.bonsai.layout diff --git a/Marta/BonFly3MPTracker/README.md b/Marta/BonFly3MPTracker/README.md index a3636e3..8070eec 100644 --- a/Marta/BonFly3MPTracker/README.md +++ b/Marta/BonFly3MPTracker/README.md @@ -16,6 +16,10 @@ These should only need to be installed once on a fresh new system, and are not r You can download the latest release of tensorflow.dll [here](https://www.tensorflow.org/install/lang_c#download_and_extract) and copy it inside your Extensions folder. You can click [here](https://github.com/bonsai-rx/sleap) for further instructions on install sleap in Bonsai. + +## Running the parallel code +Currently, to parallelise the workflows, you need to manually divide your files across different directories in a given parent directory. Each of working directory will run independently from the others. This can be improved in the future, but we should test whether this is a good strategy to handle the data. + ## Acknowledgements This code was modified from the original one created by Bruno Cruz. diff --git a/Vasconcelos/MatingIdentification-INDP2024/bonsai/Bonsai.config b/Vasconcelos/MatingIdentification-INDP2024/bonsai/Bonsai.config new file mode 100644 index 0000000..d68881e --- /dev/null +++ b/Vasconcelos/MatingIdentification-INDP2024/bonsai/Bonsai.config @@ -0,0 +1,142 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/Vasconcelos/MatingIdentification-INDP2024/bonsai/NuGet.config b/Vasconcelos/MatingIdentification-INDP2024/bonsai/NuGet.config new file mode 100644 index 0000000..d577787 --- /dev/null +++ b/Vasconcelos/MatingIdentification-INDP2024/bonsai/NuGet.config @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/Vasconcelos/MatingIdentification-INDP2024/bonsai/Setup.cmd b/Vasconcelos/MatingIdentification-INDP2024/bonsai/Setup.cmd new file mode 100644 index 0000000..9004f5c --- /dev/null +++ b/Vasconcelos/MatingIdentification-INDP2024/bonsai/Setup.cmd @@ -0,0 +1 @@ +powershell -ExecutionPolicy Bypass -File .\SetupPS.ps1 \ No newline at end of file diff --git a/Vasconcelos/MatingIdentification-INDP2024/bonsai/SetupPS.ps1 b/Vasconcelos/MatingIdentification-INDP2024/bonsai/SetupPS.ps1 new file mode 100644 index 0000000..38b755d --- /dev/null +++ b/Vasconcelos/MatingIdentification-INDP2024/bonsai/SetupPS.ps1 @@ -0,0 +1,9 @@ +if (!(Test-Path "./Bonsai.exe")) { + Invoke-WebRequest "https://github.com/bonsai-rx/bonsai/releases/download/2.8.5/Bonsai.zip" -OutFile "temp.zip" + Move-Item -Path "NuGet.config" "temp.config" + Expand-Archive "temp.zip" -DestinationPath "." -Force + Move-Item -Path "temp.config" "NuGet.config" -Force + Remove-Item -Path "temp.zip" + Remove-Item -Path "Bonsai32.exe" +} +& .\Bonsai.exe --no-editor \ No newline at end of file diff --git a/Vasconcelos/MatingIdentification-INDP2024/src/MatingIdentification.bonsai b/Vasconcelos/MatingIdentification-INDP2024/src/MatingIdentification.bonsai new file mode 100644 index 0000000..88ea905 --- /dev/null +++ b/Vasconcelos/MatingIdentification-INDP2024/src/MatingIdentification.bonsai @@ -0,0 +1,504 @@ + + + + + + + C:\Users\HugoMarques\Documents\Code\MyReps\cf.labs\Vasconcelos\MatingIdentification-INDP2024\data\Video1.avi + 10000 + 0 + Frames + false + true + + + + + + + + 985 + 518 + + + 982 + 518 + + + 982 + 518 + + + 985 + 518 + + + + + 594 + 824 + + + 594 + 824 + + + 594 + 820 + + + 594 + 820 + + + + + 783 + 767 + + + 783 + 767 + + + 783 + 763 + + + 783 + 763 + + + + + 1160 + 525 + + + 1151 + 611 + + + 1129 + 692 + + + 1092 + 771 + + + 1041 + 840 + + + 978 + 901 + + + 905 + 950 + + + 825 + 986 + + + 740 + 1007 + + + 653 + 1016 + + + 565 + 1007 + + + 480 + 986 + + + 400 + 950 + + + 327 + 901 + + + 264 + 840 + + + 213 + 771 + + + 176 + 692 + + + 154 + 611 + + + 146 + 526 + + + 154 + 440 + + + 176 + 359 + + + 213 + 280 + + + 264 + 211 + + + 327 + 150 + + + 400 + 101 + + + 480 + 65 + + + 565 + 44 + + + 652 + 36 + + + 740 + 44 + + + 825 + 65 + + + 905 + 101 + + + 978 + 150 + + + 1041 + 211 + + + 1092 + 280 + + + 1129 + 359 + + + 1151 + 440 + + + + ToZero + + 255 + 255 + 255 + 255 + + + + + Frames + + + + + + + + + + + + 83 + 255 + BinaryInv + + + + + External + ChainApproxNone + + 0 + 0 + + 50 + 2000 + + + + + + + + + + Count + + + + 1 + + + + + + + + + + Item1 + + + + 5 + + + + Centroid + + + Smallest Countour + + + + 0 + + + + Centroid + + + Largest Countour + + + + + + ContourCentroidExtrema.csv + false + true + None + false + + + + + + Source1 + + + + + + Centroid + + + + + + + + + + + + + + + + ContourCentroids.csv + false + true + None + false + + + + + + Frames + + + Size + + + + + + + + + + 1015 + 981 + + U8 + 3 + + 0 + 0 + 0 + 0 + + + + + + + + + + + + 0 + 0 + 0 + 0 + + Linear + + + + Smallest Countour + + + + + + + + + + 738 + 297 + + 20 + + 0 + 0 + 255 + 255 + + 2 + Connected8 + 0 + + + + Largest Countour + + + + + + + + + + 715 + 220 + + 20 + + 0 + 255 + 0 + 255 + + 2 + Connected8 + 0 + + + + + + + Frames + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/Vasconcelos/MatingIdentification-INDP2024/src/MatingIdentification.bonsai.layout b/Vasconcelos/MatingIdentification-INDP2024/src/MatingIdentification.bonsai.layout new file mode 100644 index 0000000..0a924d2 --- /dev/null +++ b/Vasconcelos/MatingIdentification-INDP2024/src/MatingIdentification.bonsai.layout @@ -0,0 +1,501 @@ + + + + false + + 2039 + 256 + + + 326 + 352 + + Normal + Bonsai.Vision.Design.FileCaptureVisualizer + + + + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 1968 + 52 + + + 334 + 278 + + Normal + + + false + + 2477 + 364 + + + 334 + 278 + + Normal + + + false + + 2703 + 509 + + + 294 + 326 + + Normal + + + true + + 2660 + 180 + + + 334 + 278 + + Normal + Bonsai.Vision.Design.ConnectedComponentCollectionVisualizer + + + + + + false + + 2064 + 156 + + + 334 + 278 + + Normal + Bonsai.Vision.Design.ConnectedComponentCollectionVisualizer + + + + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + false + + 2122 + 260 + + + 440 + 224 + + Normal + + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + true + + 2217 + 149 + + + 415 + 461 + + Normal + Bonsai.Vision.Design.IplImageVisualizer + + + + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + + false + + 0 + 0 + + + 0 + 0 + + Normal + + \ No newline at end of file