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Merged
MMathisLab merged 3 commits into from
Oct 10, 2023
Merged

update notebooks and COLAB #2411

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90b1d59
updated notebooks
n-poulsen Oct 10, 2023
5a5b589
updated viewer to use QT6, new labeling code and removed manual extra…
n-poulsen Oct 10, 2023
15b89f9
found last wx
n-poulsen Oct 10, 2023
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4 changes: 2 additions & 2 deletions examples/COLAB/COLAB_3miceDemo.ipynb
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Expand Up @@ -27,10 +27,10 @@
"- assemble animals and tracklets.\n",
"- create quality check plots and video.\n",
"\n",
"### To create a full maDLC pipeline please see our full docs: https://deeplabcut.github.io/DeepLabCut/docs/intro.html \n",
"### To create a full maDLC pipeline please see our full docs: https://deeplabcut.github.io/DeepLabCut/README.html\n",
"- Of interest is a full how-to for maDLC: https://deeplabcut.github.io/DeepLabCut/docs/maDLC_UserGuide.html\n",
"- a quick guide to maDLC: https://deeplabcut.github.io/DeepLabCut/docs/tutorial.html\n",
"- a demo COLAB for how to use maDLC on your own data: https://github.com/DeepLabCut/DeepLabCut/blob/master/examples/COLAB_maDLC_TrainNetwork_VideoAnalysis.ipynb\n",
"- a demo COLAB for how to use maDLC on your own data: https://github.com/DeepLabCut/DeepLabCut/blob/main/examples/COLAB/COLAB_maDLC_TrainNetwork_VideoAnalysis.ipynb\n",
"\n",
"### To get started, please go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n"
]
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2 changes: 1 addition & 1 deletion examples/COLAB/COLAB_YOURDATA_TrainNetwork_VideoAnalysis.ipynb
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Expand Up @@ -27,7 +27,7 @@
"- create simple quality check plots\n",
"- analyze novel videos!\n",
"\n",
"###This notebook assumes you already have a project folder with labeled data! \n",
"### This notebook assumes you already have a project folder with labeled data! \n",
"\n",
"This notebook demonstrates the necessary steps to use DeepLabCut for your own project.\n",
"\n",
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44 changes: 22 additions & 22 deletions examples/COLAB/COLAB_maDLC_TrainNetwork_VideoAnalysis.ipynb
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@@ -1,19 +1,4 @@
{
"nbformat": 4,
"nbformat_minor": 0,
"metadata": {
"accelerator": "GPU",
"colab": {
"collapsed_sections": [],
"include_colab_link": true,
"name": "COLAB_maDLC_TrainNetwork_VideoAnalysis.ipynb",
"provenance": []
},
"kernelspec": {
"display_name": "Python 3",
"name": "python3"
}
},
"cells": [
{
"cell_type": "markdown",
Expand Down Expand Up @@ -44,7 +29,7 @@
"- assemble animals and tracklets\n",
"- create quality check plots!\n",
"\n",
"###This notebook assumes you already have a DLC project folder with labeled data and you uploaded it to your own Google Drive.\n",
"### This notebook assumes you already have a DLC project folder with labeled data and you uploaded it to your own Google Drive.\n",
"\n",
"This notebook demonstrates the necessary steps to use DeepLabCut for your own project.\n",
"\n",
Expand Down Expand Up @@ -82,16 +67,16 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "-MVvZ13_FMvP"
},
"outputs": [],
"source": [
"#a few colab specific things needed:\n",
"!pip install --upgrade scikit-image\n",
"!pip3 install pickle5"
],
"execution_count": null,
"outputs": []
]
},
{
"cell_type": "markdown",
Expand All @@ -106,16 +91,16 @@
"cell_type": "code",
"execution_count": 2,
"metadata": {
"id": "oTwAcbq2-FZz",
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "oTwAcbq2-FZz",
"outputId": "9cfd8dcf-a0a8-4801-ed1d-fbcd5ec056af"
},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"output_type": "stream",
"text": [
"DLC loaded in light mode; you cannot use any GUI (labeling, relabeling and standalone GUI)\n"
]
Expand Down Expand Up @@ -501,5 +486,20 @@
" filtered=True)"
]
}
]
],
"metadata": {
"accelerator": "GPU",
"colab": {
"collapsed_sections": [],
"include_colab_link": true,
"name": "COLAB_maDLC_TrainNetwork_VideoAnalysis.ipynb",
"provenance": []
},
"kernelspec": {
"display_name": "Python 3",
"name": "python3"
}
},
"nbformat": 4,
"nbformat_minor": 0
}
4 changes: 2 additions & 2 deletions examples/COLAB/COLAB_transformer_reID.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -27,10 +27,10 @@
"- use the transformer to do unsupervised ID tracking.\n",
"- create quality check plots and video.\n",
"\n",
"### To create a full maDLC pipeline please see our full docs: https://deeplabcut.github.io/DeepLabCut/docs/intro.html \n",
"### To create a full maDLC pipeline please see our full docs: https://deeplabcut.github.io/DeepLabCut/README.html\n",
"- Of interest is a full how-to for maDLC: https://deeplabcut.github.io/DeepLabCut/docs/maDLC_UserGuide.html\n",
"- a quick guide to maDLC: https://deeplabcut.github.io/DeepLabCut/docs/tutorial.html\n",
"- a demo COLAB for how to use maDLC on your own data: https://github.com/DeepLabCut/DeepLabCut/blob/master/examples/COLAB_maDLC_TrainNetwork_VideoAnalysis.ipynb\n",
"- a demo COLAB for how to use maDLC on your own data: https://github.com/DeepLabCut/DeepLabCut/blob/main/examples/COLAB/COLAB_maDLC_TrainNetwork_VideoAnalysis.ipynb\n",
"\n",
"### To get started, please go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n"
]
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2 changes: 1 addition & 1 deletion examples/JUPYTER/Demo_labeledexample_Openfield.ipynb
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Expand Up @@ -528,7 +528,7 @@
},
"outputs": [],
"source": [
"%gui wx\n",
"%gui qt6\n",
"deeplabcut.refine_labels(path_config_file)"
]
},
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4 changes: 2 additions & 2 deletions examples/JUPYTER/Demo_napari.ipynb
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Expand Up @@ -192,7 +192,7 @@
"outputs": [],
"source": [
"# napari will pop up! Please go to plugin > deeplabcut to start:\n",
"%gui qt5\n",
"%gui qt6\n",
"import napari\n",
"napari.Viewer()"
]
Expand Down Expand Up @@ -400,7 +400,7 @@
"source": [
"#now you can edit the \"machine-labeled file\" within napari; \n",
"#just again drop the file and images into the workspace after you load the plugin\n",
"%gui qt5\n",
"%gui qt6\n",
"import napari\n",
"napari.Viewer()"
]
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52 changes: 23 additions & 29 deletions examples/JUPYTER/Demo_yourowndata.ipynb
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Expand Up @@ -65,7 +65,7 @@
},
{
"cell_type": "code",
"execution_count": 0,
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
Expand Down Expand Up @@ -129,7 +129,7 @@
},
{
"cell_type": "code",
"execution_count": 0,
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
Expand All @@ -144,18 +144,6 @@
"deeplabcut.extract_frames(path_config_file) "
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"#AND/OR:\n",
"#SELECT RARE EVENTS MANUALLY:\n",
"%gui wx\n",
"deeplabcut.extract_frames(path_config_file,'manual')"
]
},
{
"cell_type": "markdown",
"metadata": {
Expand All @@ -170,16 +158,22 @@
},
{
"cell_type": "code",
"execution_count": 0,
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "iyROSOiEoEJI"
},
"outputs": [],
"source": [
"%gui wx\n",
"deeplabcut.label_frames(path_config_file)"
"# napari will pop up!\n",
"# Please go to plugin > deeplabcut to start\n",
"# then, drag-and-drop the project configuration file into the viewer (the value of path_config_file)\n",
"# finally, drop the folder containing the images (in 'labeled-data') in the viewer\n",
"\n",
"%gui qt6\n",
"import napari\n",
"napari.Viewer()"
]
},
{
Expand All @@ -196,7 +190,7 @@
},
{
"cell_type": "code",
"execution_count": 0,
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
Expand Down Expand Up @@ -237,7 +231,7 @@
},
{
"cell_type": "code",
"execution_count": 0,
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
Expand All @@ -264,7 +258,7 @@
},
{
"cell_type": "code",
"execution_count": 0,
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
Expand All @@ -289,7 +283,7 @@
},
{
"cell_type": "code",
"execution_count": 0,
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
Expand All @@ -315,7 +309,7 @@
},
{
"cell_type": "code",
"execution_count": 0,
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
Expand Down Expand Up @@ -351,7 +345,7 @@
},
{
"cell_type": "code",
"execution_count": 0,
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
Expand All @@ -375,15 +369,15 @@
},
{
"cell_type": "code",
"execution_count": 0,
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "n_FpEXtyoEJy"
},
"outputs": [],
"source": [
"%gui wx\n",
"%gui qt6\n",
"deeplabcut.refine_labels(path_config_file)"
]
},
Expand All @@ -406,7 +400,7 @@
},
{
"cell_type": "code",
"execution_count": 0,
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
Expand All @@ -432,7 +426,7 @@
},
{
"cell_type": "code",
"execution_count": 0,
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
Expand Down Expand Up @@ -471,7 +465,7 @@
},
{
"cell_type": "code",
"execution_count": 0,
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
Expand All @@ -495,7 +489,7 @@
},
{
"cell_type": "code",
"execution_count": 0,
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
Expand Down