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Merged
maximpavliv merged 3 commits into from
Feb 11, 2025
Merged

Merges main into pytorch_dlc #2876

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c483526
Pin TensorFlow according to OS; Fix DeepLabCut install in Colab to de…
n-poulsen Feb 7, 2025
5203360
Remove nwb from analyze videos tab (#2875)
maximpavliv Feb 11, 2025
6f1cb1e
Merge branch 'main' into maxim/merge_main_20250211
maximpavliv Feb 11, 2025
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18 changes: 0 additions & 18 deletions deeplabcut/gui/tabs/analyze_videos.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -115,12 +115,6 @@ def _generate_layout_other_options(self, layout):

tmp_layout.addWidget(self.save_as_csv)

self.save_as_nwb = QtWidgets.QCheckBox("Save result(s) as nwb")
self.save_as_nwb.setCheckState(Qt.Unchecked)
self.save_as_nwb.stateChanged.connect(self.update_nwb_choice)

tmp_layout.addWidget(self.save_as_csv)

# Filter predictions
self.filter_predictions = QtWidgets.QCheckBox("Filter predictions")
self.filter_predictions.setCheckState(Qt.Unchecked)
Expand Down Expand Up @@ -223,10 +217,6 @@ def update_csv_choice(self, state):
s = "ENABLED" if Qt.CheckState(state) == Qt.Checked else "DISABLED"
self.root.logger.info(f"Save results as CSV {s}")

def update_nwb_choice(self, state):
s = "ENABLED" if Qt.CheckState(state) == Qt.Checked else "DISABLED"
self.root.logger.info(f"Save results as NWB {s}")

def update_filter_choice(self, state):
s = "ENABLED" if Qt.CheckState(state) == Qt.Checked else "DISABLED"
self.root.logger.info(f"Filtering predictions {s}")
Expand Down Expand Up @@ -331,7 +321,6 @@ def run_enabled(self):

videos = list(self.files)
save_as_csv = self.save_as_csv.isChecked()
save_as_nwb = self.save_as_nwb.isChecked()
filter_data = self.filter_predictions.isChecked()
videotype = self.video_selection_widget.videotype_widget.currentText()
try:
Expand Down Expand Up @@ -382,10 +371,3 @@ def run_enabled(self):
videos,
listofvideos=True,
)

if save_as_nwb:
deeplabcut.analyze_videos_converth5_to_nwb(
config,
videos,
listofvideos=True,
)
50 changes: 45 additions & 5 deletions examples/COLAB/COLAB_3miceDemo.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,9 @@
"- 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/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"
"### To get started, please go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n",
"\n",
"As the COLAB environments were updated to CUDA 12.X and Python 3.11, we need to install DeepLabCut and TensorFlow in a distinct way to get TensorFlow to connect to the GPU."
]
},
{
Expand All @@ -43,11 +45,49 @@
},
"outputs": [],
"source": [
"# Installs a CUDA version compatible with tensorflow on COLAB\n",
"!apt update && apt install cuda-11-8\n",
"# Install TensorFlow, tensorpack and tf_slim versions compatible with DeepLabCut\n",
"!pip install \"tensorflow==2.12.1\" \"tensorpack>=0.11\" \"tf_slim>=1.1.0\""
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Downgrade PyTorch to a version using CUDA 11.8 and cudnn 8\n",
"# This will also install the required CUDA libraries, for both PyTorch and TensorFlow\n",
"!pip install torch==2.3.1 torchvision --index-url https://download.pytorch.org/whl/cu118"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Install the latest version of DeepLabCut\n",
"!pip install \"git+https://github.com/DeepLabCut/DeepLabCut.git\""
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# As described in https://www.tensorflow.org/install/pip#step-by-step_instructions, \n",
"# create symbolic links to NVIDIA shared libraries:\n",
"!ln -svf /usr/local/lib/python3.11/dist-packages/nvidia/*/lib/*.so* /usr/local/lib/python3.11/dist-packages/tensorflow"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Important - Restart the Runtime for the updated packages to be imported!\n",
"\n",
"# Install the latest DeepLabCut version:\n",
"!pip install \"deeplabcut[tf]\""
"PLEASE, click \"restart runtime\" from the output above before proceeding!"
]
},
{
Expand Down
8 changes: 4 additions & 4 deletions examples/COLAB/COLAB_DEMO_SuperAnimal.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,15 +43,15 @@
"\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"
"*Also, be sure you are connected to a GPU: go to menu, click Runtime > Change Runtime Type > select \"GPU\"*\n",
"\n",
"As the COLAB environments were updated to CUDA 12.X and Python 3.11, we need to install DeepLabCut and TensorFlow in a distinct way to get TensorFlow to connect to the GPU.\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "03ylSyQ4O9Ee"
},
"metadata": {},
"outputs": [],
"source": [
"!pip install deeplabcut==3.0.0rc5"
Expand Down
32 changes: 28 additions & 4 deletions examples/COLAB/COLAB_DEMO_mouse_openfield.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,30 @@
"id": "txoddlM8hLKm"
},
"source": [
"## First, go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\""
"## First, go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n",
"\n",
"As the COLAB environments were updated to CUDA 12.X and Python 3.11, we need to install DeepLabCut and TensorFlow in a distinct way to get TensorFlow to connect to the GPU."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Install TensorFlow, tensorpack and tf_slim versions compatible with DeepLabCut\n",
"!pip install \"tensorflow==2.12.1\" \"tensorpack>=0.11\" \"tf_slim>=1.1.0\""
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Downgrade PyTorch to a version using CUDA 11.8 and cudnn 8\n",
"# This will also install the required CUDA libraries, for both PyTorch and TensorFlow\n",
"!pip install torch==2.3.1 torchvision --index-url https://download.pytorch.org/whl/cu118"
]
},
{
Expand All @@ -51,8 +74,9 @@
"metadata": {},
"outputs": [],
"source": [
"# Installs a CUDA version compatible with tensorflow on COLAB\n",
"!apt update && apt install cuda-11-8"
"# As described in https://www.tensorflow.org/install/pip#step-by-step_instructions, \n",
"# create symbolic links to NVIDIA shared libraries:\n",
"!ln -svf /usr/local/lib/python3.11/dist-packages/nvidia/*/lib/*.so* /usr/local/lib/python3.11/dist-packages/tensorflow"
]
},
{
Expand Down Expand Up @@ -91,7 +115,7 @@
"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]\""
"!pip install \".\""
]
},
{
Expand Down
53 changes: 42 additions & 11 deletions examples/COLAB/COLAB_DLC_ModelZoo.ipynb
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -45,29 +45,60 @@
"\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\"*"
"*Also, be sure you are connected to a GPU: go to menu, click Runtime > Change Runtime Type > select \"GPU\"*\n",
"\n",
"As the COLAB environments were updated to CUDA 12.X and Python 3.11, we need to install DeepLabCut and TensorFlow in a distinct way to get TensorFlow to connect to the GPU."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "q23BzhA6CXxu"
},
"metadata": {},
"outputs": [],
"source": [
"# Install TensorFlow, tensorpack and tf_slim versions compatible with DeepLabCut\n",
"!pip install \"tensorflow==2.12.1\" \"tensorpack>=0.11\" \"tf_slim>=1.1.0\""
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"#click the play icon (this will take a few minutes to install all the dependencies!)\n",
"!apt update && apt install cuda-11-8\n",
"!pip install deeplabcut[tf,modelzoo]"
"# Downgrade PyTorch to a version using CUDA 11.8 and cudnn 8\n",
"# This will also install the required CUDA libraries, for both PyTorch and TensorFlow\n",
"!pip install torch==2.3.1 torchvision --index-url https://download.pytorch.org/whl/cu118"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Install the latest version of DeepLabCut\n",
"!pip install \"git+https://github.com/DeepLabCut/DeepLabCut.git#egg=deeplabcut[modelzoo]\""
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# As described in https://www.tensorflow.org/install/pip#step-by-step_instructions, \n",
"# create symbolic links to NVIDIA shared libraries:\n",
"!ln -svf /usr/local/lib/python3.11/dist-packages/nvidia/*/lib/*.so* /usr/local/lib/python3.11/dist-packages/tensorflow"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "zYm6DljQB0Y7"
},
"metadata": {},
"source": [
"###proTip: be sure to click \"restart runtime button\" if it appears above ^"
"### Important - Restart the Runtime for the updated packages to be imported!\n",
"\n",
"PLEASE, click \"restart runtime\" from the output above before proceeding!"
]
},
{
Expand Down
47 changes: 38 additions & 9 deletions examples/COLAB/COLAB_YOURDATA_TrainNetwork_VideoAnalysis.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,22 +48,51 @@
"id": "txoddlM8hLKm"
},
"source": [
"## First, go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n"
"## First, go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n",
"\n",
"As the COLAB environments were updated to CUDA 12.X and Python 3.11, we need to install DeepLabCut and TensorFlow in a distinct way to get TensorFlow to connect to the GPU."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "q23BzhA6CXxu"
},
"metadata": {},
"outputs": [],
"source": [
"# Install TensorFlow, tensorpack and tf_slim versions compatible with DeepLabCut\n",
"!pip install \"tensorflow==2.12.1\" \"tensorpack>=0.11\" \"tf_slim>=1.1.0\""
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Downgrade PyTorch to a version using CUDA 11.8 and cudnn 8\n",
"# This will also install the required CUDA libraries, for both PyTorch and TensorFlow\n",
"!pip install torch==2.3.1 torchvision --index-url https://download.pytorch.org/whl/cu118"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Install the latest version of DeepLabCut\n",
"!pip install \"git+https://github.com/DeepLabCut/DeepLabCut.git\""
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"#(this will take a few minutes to install all the dependences!)\n",
"!apt update && apt install cuda-11-8\n",
"!pip install \"deeplabcut[tf]\""
"# As described in https://www.tensorflow.org/install/pip#step-by-step_instructions, \n",
"# create symbolic links to NVIDIA shared libraries:\n",
"!ln -svf /usr/local/lib/python3.11/dist-packages/nvidia/*/lib/*.so* /usr/local/lib/python3.11/dist-packages/tensorflow"
]
},
{
Expand Down
47 changes: 31 additions & 16 deletions examples/COLAB/COLAB_maDLC_TrainNetwork_VideoAnalysis.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -46,36 +46,51 @@
"id": "txoddlM8hLKm"
},
"source": [
"## First, go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n"
"## First, go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n",
"\n",
"As the COLAB environments were updated to CUDA 12.X and Python 3.11, we need to install DeepLabCut and TensorFlow in a distinct way to get TensorFlow to connect to the GPU."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "q23BzhA6CXxu"
},
"metadata": {},
"outputs": [],
"source": [
"#(this will take a few minutes to install all the dependences!)\n",
"!apt update && apt install cuda-11-8\n",
"!pip install \"deeplabcut[tf]\"\n",
"%reload_ext numpy\n",
"%reload_ext scipy\n",
"%reload_ext matplotlib\n",
"%reload_ext mpl_toolkits"
"# Install TensorFlow, tensorpack and tf_slim versions compatible with DeepLabCut\n",
"!pip install \"tensorflow==2.12.1\" \"tensorpack>=0.11\" \"tf_slim>=1.1.0\""
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "-MVvZ13_FMvP"
},
"metadata": {},
"outputs": [],
"source": [
"# Downgrade PyTorch to a version using CUDA 11.8 and cudnn 8\n",
"# This will also install the required CUDA libraries, for both PyTorch and TensorFlow\n",
"!pip install torch==2.3.1 torchvision --index-url https://download.pytorch.org/whl/cu118"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Install the latest version of DeepLabCut\n",
"!pip install \"git+https://github.com/DeepLabCut/DeepLabCut.git\""
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"#a few colab specific things needed:\n",
"!pip install --upgrade scikit-image"
"# As described in https://www.tensorflow.org/install/pip#step-by-step_instructions, \n",
"# create symbolic links to NVIDIA shared libraries:\n",
"!ln -svf /usr/local/lib/python3.11/dist-packages/nvidia/*/lib/*.so* /usr/local/lib/python3.11/dist-packages/tensorflow"
]
},
{
Expand Down
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