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Merged
MMathisLab merged 2 commits into from
Sep 14, 2023
Merged

updated Model Zoo Colab notebook #2381

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0870387
Created using Colaboratory
MMathisLab Sep 14, 2023
32bd685
Created using Colaboratory
MMathisLab Sep 14, 2023
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42 changes: 34 additions & 8 deletions examples/COLAB/COLAB_DEMO_SuperAnimal.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,9 +1,10 @@
{
"cells": [
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"metadata": {
"id": "3G1Nx3YLOVaZ"
},
"source": [
"<a target=\"_blank\" href=\"https://colab.research.google.com/github/DeepLabCut/DeepLabCut/blob/main/examples/COLAB/COLAB_DEMO_SuperAnimal.ipynb\">\n",
" <img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/>\n",
Expand All @@ -16,7 +17,32 @@
"id": "23v-XAUNQIPY"
},
"source": [
"# First, go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\""
"# **DeepLabCut Model Zoo: SuperAnimal models\n",
"\n",
"![alt text](https://images.squarespace-cdn.com/content/v1/57f6d51c9f74566f55ecf271/1616492373700-PGOAC72IOB6AUE47VTJX/ke17ZwdGBToddI8pDm48kB8JrdUaZR-OSkKLqWQPp_YUqsxRUqqbr1mOJYKfIPR7LoDQ9mXPOjoJoqy81S2I8N_N4V1vUb5AoIIIbLZhVYwL8IeDg6_3B-BRuF4nNrNcQkVuAT7tdErd0wQFEGFSnBqyW03PFN2MN6T6ry5cmXqqA9xITfsbVGDrg_goIDasRCalqV8R3606BuxERAtDaQ/modelzoo.png?format=1000w)\n",
"\n",
"http://modelzoo.deeplabcut.org\n",
"\n",
"You can use this notebook to analyze videos with pretrained networks from our model zoo - NO local installation of DeepLabCut is needed!\n",
"\n",
"- **What you need:** a video of your favorite dog, cat, human, etc: check the list of currently available models here: http://modelzoo.deeplabcut.org\n",
"\n",
"- **What to do:** (1) in the top right corner, click \"CONNECT\". Then, just hit run (play icon) on each cell below and follow the instructions!\n",
"\n",
"## **Please consider giving back and labeling a little data to help make each network even better!**\n",
"\n",
"We have a WebApp, so no need to install anything, just a few clicks! We'd really appreciate your help!\n",
" \n",
"https://contrib.deeplabcut.org/\n",
"\n",
"\n",
"- **Note, if you performance is less that you would like:** firstly check the labeled_video parameters (i.e. \"pcutoff\" in the config.yaml file that will set the video plotting) - see the end of this notebook. You can also use the model in your own projects locally. Please be sure to cite the papers for the model, and http://modelzoo.deeplabcut.org (paper forthcoming!)\n",
"\n",
"\n",
"\n",
"## **Let's get going: install DeepLabCut into COLAB:**\n",
"\n",
"*Also, be sure you are connected to a GPU: go to menu, click Runtime > Change Runtime Type > select \"GPU\"*\n"
]
},
{
Expand All @@ -36,12 +62,12 @@
"id": "TguLMTJpQx1_"
},
"source": [
"## PLEASE, click \"restart runtime\" from the output above before proceeding! "
"## PLEASE, click \"restart runtime\" from the output above before proceeding!"
]
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": null,
"metadata": {
"id": "4BejjXKFO2Zg"
},
Expand All @@ -67,13 +93,13 @@
"video_path = os.path.abspath(filepath)\n",
"\n",
"# If this cell fails (e.g., when using Safari in place of Google Chrome),\n",
"# manually upload your video via the Files menu to the left \n",
"# manually upload your video via the Files menu to the left\n",
"# and define `video_path` yourself with right click > copy path on the video."
]
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": null,
"metadata": {
"id": "ge589yC4v9yX"
},
Expand Down Expand Up @@ -135,4 +161,4 @@
},
"nbformat": 4,
"nbformat_minor": 0
}
}
32 changes: 17 additions & 15 deletions examples/COLAB/COLAB_DLC_ModelZoo.ipynb
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,11 @@
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "view-in-github"
"id": "view-in-github",
"colab_type": "text"
},
"source": [
"<a href=\"https://colab.research.google.com/github/DeepLabCut/DeepLabCut/blob/main/examples/COLAB/COLAB_DLC_ModelZoo.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
"<a href=\"https://colab.research.google.com/github/MMathisLab/DeepLabCut/blob/main/examples/COLAB/COLAB_DLC_ModelZoo.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
]
},
{
Expand All @@ -16,19 +16,21 @@
"id": "RK255E7YoEIt"
},
"source": [
"# **DeepLabCut Model Zoo!**\n",
"# **DeepLabCut Model Zoo: (mainly) user-contributed models**\n",
"\n",
"🚨 **WARNING** -- this is using the old version from 2020-2023. Please see the SuperAnimal notebook for more features\n",
"\n",
"![alt text](https://images.squarespace-cdn.com/content/v1/57f6d51c9f74566f55ecf271/1616492373700-PGOAC72IOB6AUE47VTJX/ke17ZwdGBToddI8pDm48kB8JrdUaZR-OSkKLqWQPp_YUqsxRUqqbr1mOJYKfIPR7LoDQ9mXPOjoJoqy81S2I8N_N4V1vUb5AoIIIbLZhVYwL8IeDg6_3B-BRuF4nNrNcQkVuAT7tdErd0wQFEGFSnBqyW03PFN2MN6T6ry5cmXqqA9xITfsbVGDrg_goIDasRCalqV8R3606BuxERAtDaQ/modelzoo.png?format=1000w)\n",
"\n",
"http://modelzoo.deeplabcut.org\n",
"\n",
"You can use this notebook to analyze videos with pretrained networks from our model zoo - NO local installation of DeepLabCut is needed! \n",
"You can use this notebook to analyze videos with pretrained networks from our model zoo - NO local installation of DeepLabCut is needed!\n",
"\n",
"- **What you need:** a video of your favorite dog, cat, human, etc: check the list of currently available models here: http://modelzoo.deeplabcut.org\n",
"\n",
"- **What to do:** (1) in the top right corner, click \"CONNECT\". Then, just hit run (play icon) on each cell below and follow the instructions!\n",
"\n",
"## **Please consider giving back and labeling a little data to help make each network even better!** \n",
"## **Please consider giving back and labeling a little data to help make each network even better!**\n",
"\n",
"We have a WebApp, so no need to install anything, just a few clicks! We'd really appreciate your help!\n",
" \n",
Expand Down Expand Up @@ -64,7 +66,7 @@
"id": "zYm6DljQB0Y7"
},
"source": [
"###proTip: be sure to click \"restart runtime button\" if it appears above ^ "
"###proTip: be sure to click \"restart runtime button\" if it appears above ^"
]
},
{
Expand All @@ -73,7 +75,7 @@
"id": "ZT4PwGSbYQEO"
},
"source": [
"## Now let's set the backend & import the DeepLabCut package \n",
"## Now let's set the backend & import the DeepLabCut package\n",
"#### (if colab is buggy/throws an error, just rerun this cell):"
]
},
Expand Down Expand Up @@ -114,7 +116,7 @@
"video_path = os.path.abspath(filepath)\n",
"\n",
"# If this cell fails (e.g., when using Safari in place of Google Chrome),\n",
"# manually upload your video via the Files menu to the left \n",
"# manually upload your video via the Files menu to the left\n",
"# and define `video_path` yourself with right click > copy path on the video."
]
},
Expand Down Expand Up @@ -168,7 +170,7 @@
"id": "JQxko-t3uMVO"
},
"source": [
"## Attention on this step !! \n",
"## Attention on this step !!\n",
"- Please note that for optimal performance your videos should contain frames that are around ~300-600 pixels (on one edge). If you have a larger video (like from an iPhone, first downsize by running this please! :)\n",
"\n",
"- Thus, if you're using an iPhone, or such, you'll need to downsample the video first by running the code below**\n",
Expand Down Expand Up @@ -223,7 +225,7 @@
"id": "WS-KxhBMvEBj"
},
"source": [
"Now, you can move this project from Colab (i.e. download it to your GoogleDrive), and use it like a normal standard project! \n",
"Now, you can move this project from Colab (i.e. download it to your GoogleDrive), and use it like a normal standard project!\n",
"\n",
"You can analyze more videos, extract outliers, refine then, and/or then add new key points + label new frames, and retrain if desired. We hope this gives you a good launching point for your work!\n",
"\n",
Expand All @@ -237,7 +239,7 @@
"id": "KPOqiLmo6d7t"
},
"source": [
"## More advanced options: \n",
"## More advanced options:\n",
"\n",
"- If you would now like to customize the video/plots - i.e., color, dot size, threshold for the point to be plotted (pcutoff), please simply edit the \"config.yaml\" file by updating the values below:"
]
Expand Down Expand Up @@ -285,10 +287,10 @@
],
"metadata": {
"colab": {
"include_colab_link": true,
"name": "Copy of COLAB_DLC_ModelZoo.ipynb",
"provenance": [],
"toc_visible": true
"toc_visible": true,
"include_colab_link": true
},
"gpuClass": "standard",
"kernelspec": {
Expand All @@ -311,4 +313,4 @@
},
"nbformat": 4,
"nbformat_minor": 0
}
}