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updated COLAB notebooks to install a CUDA version compatible with DLC #2506

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Merged
MMathisLab merged 1 commit into from
Feb 2, 2024
Merged

updated COLAB notebooks to install a CUDA version compatible with DLC #2506

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3 changes: 3 additions & 0 deletions examples/COLAB/COLAB_3miceDemo.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,9 @@
},
"outputs": [],
"source": [
"# Installs a CUDA version compatible with tensorflow on COLAB\n",
"!apt update && apt install cuda-11-8\n",
"\n",
"# Install the latest DeepLabCut version:\n",
"!pip install \"deeplabcut[tf]\""
]
Expand Down
47 changes: 24 additions & 23 deletions examples/COLAB/COLAB_DEMO_SuperAnimal.ipynb
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Expand Up @@ -54,6 +54,7 @@
},
"outputs": [],
"source": [
"!apt update && apt install cuda-11-8\n",
"!pip install deeplabcut[tf,modelzoo]"
]
},
Expand All @@ -80,12 +81,12 @@
},
{
"cell_type": "markdown",
"source": [
"## Please select a video you want to run SuperAnimal-X on:"
],
"metadata": {
"id": "GXf8N4v28Xqo"
}
},
"source": [
"## Please select a video you want to run SuperAnimal-X on:"
]
},
{
"cell_type": "code",
Expand All @@ -110,14 +111,14 @@
},
{
"cell_type": "markdown",
"metadata": {
"id": "A8sDYMa08f62"
},
"source": [
"## Next select the model you want to use, Quadruped or TopViewMouse\n",
"- See http://modelzoo.deeplabcut.org/ for more details on these models\n",
"- The pcutoff is for visualization only, namely only keypoints with a value over what you set are shown. 0 is low confidience, 1 is perfect confidience of the model."
],
"metadata": {
"id": "A8sDYMa08f62"
}
]
},
{
"cell_type": "code",
Expand All @@ -133,12 +134,12 @@
},
{
"cell_type": "markdown",
"source": [
"## Okay, let's go! 🐭🦓🐻"
],
"metadata": {
"id": "zsB0pGtj9Luq"
}
},
"source": [
"## Okay, let's go! 🐭🦓🐻"
]
},
{
"cell_type": "code",
Expand All @@ -163,18 +164,23 @@
},
{
"cell_type": "markdown",
"metadata": {
"id": "gPLZSBpD34Mj"
},
"source": [
"## Let's view the video in Colab:\n",
"- otherwise, you can download and look at the video from the left side of your screen! It will end with _labeled.mp4\n",
"- If your data doesn't work as well as you'd like, consider fine-tuning our model on your data, changing the pcutoff, changing the scale-range\n",
"(pick values smaller and larger than your video image input size). See our repo for more details."
],
"metadata": {
"id": "gPLZSBpD34Mj"
}
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "ejFJ1Pbg33i6"
},
"outputs": [],
"source": [
"from base64 import b64encode\n",
"from IPython.display import HTML\n",
Expand All @@ -186,12 +192,7 @@
" <source src=\"%s\" type=\"video/mp4\">\n",
"</video>\n",
"\"\"\" % data_url)"
],
"metadata": {
"id": "ejFJ1Pbg33i6"
},
"execution_count": null,
"outputs": []
]
}
],
"metadata": {
Expand Down Expand Up @@ -225,4 +226,4 @@
},
"nbformat": 4,
"nbformat_minor": 0
}
}
130 changes: 70 additions & 60 deletions examples/COLAB/COLAB_DEMO_mouse_openfield.ipynb
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@@ -1,37 +1,10 @@
{
"nbformat": 4,
"nbformat_minor": 0,
"metadata": {
"accelerator": "GPU",
"colab": {
"name": "Colab_DEMO_mouse_openfield.ipynb",
"provenance": [],
"collapsed_sections": []
},
"kernelspec": {
"display_name": "Python [default]",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.9"
}
},
"cells": [
{
"cell_type": "markdown",
"metadata": {
"id": "view-in-github",
"colab_type": "text"
"colab_type": "text",
"id": "view-in-github"
},
"source": [
"<a href=\"https://colab.research.google.com/github/DeepLabCut/DeepLabCut/blob/master/examples/COLAB/COLAB_DEMO_mouse_openfield.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
Expand Down Expand Up @@ -74,42 +47,52 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Installs a CUDA version compatible with tensorflow on COLAB\n",
"!apt update && apt install cuda-11-8"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "Ew6r4hotoQjt"
},
"outputs": [],
"source": [
"# Clone the entire deeplabcut repo so we can use the demo data:\n",
"!git clone -l -s https://github.com/DeepLabCut/DeepLabCut.git cloned-DLC-repo\n",
"%cd cloned-DLC-repo\n",
"!ls"
],
"execution_count": null,
"outputs": []
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "yDaY78dFoxyD"
},
"outputs": [],
"source": [
"%cd /content/cloned-DLC-repo/examples/openfield-Pranav-2018-10-30\n",
"!ls"
],
"execution_count": null,
"outputs": []
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "q23BzhA6CXxu"
},
"outputs": [],
"source": [
"# Install the latest DeepLabCut version (this will take a few minutes to install all the dependencies!)\n",
"%cd /content/cloned-DLC-repo/\n",
"!pip install \".[tf]\""
],
"execution_count": null,
"outputs": []
]
},
{
"cell_type": "markdown",
Expand All @@ -122,29 +105,29 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "sXufoX6INe6w"
},
"outputs": [],
"source": [
"import deeplabcut"
],
"execution_count": null,
"outputs": []
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "Z7ZlDr3wV4D1"
},
"outputs": [],
"source": [
"#create a path variable that links to the config file:\n",
"path_config_file = '/content/cloned-DLC-repo/examples/openfield-Pranav-2018-10-30/config.yaml'\n",
"\n",
"# Loading example data set:\n",
"deeplabcut.load_demo_data(path_config_file)"
],
"execution_count": null,
"outputs": []
]
},
{
"cell_type": "markdown",
Expand All @@ -158,9 +141,11 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "_pOvDq_2oEJW"
},
"outputs": [],
"source": [
"#let's also change the display and save_iters just in case Colab takes away the GPU... \n",
"#if that happens, you can reload from a saved point. Typically, you want to train to 200,000 + iterations.\n",
Expand All @@ -170,9 +155,7 @@
"\n",
"#this will run until you stop it (CTRL+C), or hit \"STOP\" icon, or when it hits the end (default, 1.03M iterations). \n",
"#Whichever you chose, you will see what looks like an error message, but it's not an error - don't worry...."
],
"execution_count": null,
"outputs": []
]
},
{
"cell_type": "markdown",
Expand All @@ -196,17 +179,17 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "nv4zlbrnoEJg"
},
"outputs": [],
"source": [
"%matplotlib notebook\n",
"deeplabcut.evaluate_network(path_config_file,plotting=True)\n",
"\n",
"# Here you want to see a low pixel error! Of course, it can only be as good as the labeler, so be sure your labels are good!"
],
"execution_count": null,
"outputs": []
]
},
{
"cell_type": "markdown",
Expand Down Expand Up @@ -234,15 +217,15 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "Y_LZiS_0oEJl"
},
"outputs": [],
"source": [
"videofile_path = ['/content/cloned-DLC-repo/examples/openfield-Pranav-2018-10-30/videos/m3v1mp4.mp4'] #Enter the list of videos to analyze.\n",
"deeplabcut.analyze_videos(path_config_file,videofile_path, videotype='.mp4')"
],
"execution_count": null,
"outputs": []
]
},
{
"cell_type": "markdown",
Expand All @@ -256,14 +239,14 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "6aDF7Q7KoEKE"
},
"outputs": [],
"source": [
"deeplabcut.create_labeled_video(path_config_file,videofile_path)"
],
"execution_count": null,
"outputs": []
]
},
{
"cell_type": "markdown",
Expand All @@ -277,14 +260,41 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "gX21zZbXoEKJ"
},
"outputs": [],
"source": [
"deeplabcut.plot_trajectories(path_config_file,videofile_path)"
],
"execution_count": null,
"outputs": []
]
}
],
"metadata": {
"accelerator": "GPU",
"colab": {
"collapsed_sections": [],
"name": "Colab_DEMO_mouse_openfield.ipynb",
"provenance": []
},
"kernelspec": {
"display_name": "Python [default]",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.9"
}
]
},
"nbformat": 4,
"nbformat_minor": 0
}
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