Create DrumTutorial

5 sets of videos of adults and toddlers drumming

Drum.Tutorial.settings.json

@@ -0,0 +1,32 @@
+{
+    "batchName": "VASC Drumming Data tutorial",
+	"lastUpdate": null,
+	"flags":{
+		"anon": false,
+		"includeHands": true,
+		"cleaned": false
+		},
+	"paths":{
+		"openpose":"C:\\Users\\cas\\openpose-1.5.0-binaries-win64-gpu-python-flir-3d_recommended\\",
+		"project": ".\\DrumTutorial",
+		"videos_in": ".\\DrumTutorial\\videos",
+		"videos_out": ".\\DrumTutorial\\",
+		"videos_out_openpose": ".\\DrumTutorial\\openpose",
+		"videos_out_timeseries": ".\\DrumTutorial\\timeseries",
+		"videos_out_analyses" : ".\\DrumTutorial\\analyses"
+	},
+	"filenames":{
+		"videos_json": "videos.json",
+		"clean_json": "clean.json",
+		"alldatanpz": "allframedata.npz",
+		"lefthandnpz": "lefthandframedata.npz",
+		"righthandnpz": "righthandframedata.npz",
+		"lefthandnpz": "lefthandframedata.npz",
+		"cleannpz": "cleandata.npz",
+		"cleanrightnpz": "cleanrightdata.npz",
+		"cleanleftnpz": "cleanleftdata.npz",
+		"cleandataparquet": "cleandata.parquet",
+		"righthandparquet": "righthand.parquet",
+		"lefthandparquet": "lefthand.parquet"
+	}
+}

Step0.GettingStarted.ipynb

@@ -20,19 +20,11 @@
    "source": [
     "### 0.0 - Jupyter notebook environment\n",
     "\n",
-    "*If you can read this you are probably already running [Jupyter](https://jupyter.org/). Congratulations!*\n",
+    "*If you can read this you are probably already running Jupyter. Congratulations!*\n",
     "\n",
-    "There's a [getting started guide](https://jupyter.readthedocs.io/en/latest/content-quickstart.html) at the [Jupyter documentation page](https://jupyter.readthedocs.io/en/latest/index.html)\n",
+    "We recommend using the Anaconda Data Science platform (Python 3 version) \n",
     "\n",
-    "If you're impatient we recommend using the Anaconda Data Science platform (Python 3 version) \n",
-    "https://www.anaconda.com/distribution/\n",
-    "\n",
-    "and then running the command\n",
-    "```\n",
-    "conda install -c conda-forge jupyterlab\n",
-    "```\n",
-    "\n",
-    "These notebooks will run in the original Jupyter Notebook format or with the newer JupyterLab interface. We recommend the latter. "
+    "https://www.anaconda.com/distribution/\n"
    ]
   },
   {
@@ -45,16 +37,14 @@
     "\n",
     "Additionally, you need to download the trained neural-network models that OpenPose uses. To do this go to the `models` subdirectory of OpenPose directory, and double-click / run the `models.bat` script.\n",
     "\n",
-    "The `openposedemo` bin/exe file can be run manually from the command line. It is worth trying this first so you understand what  `openposedemo` is. See [this guide](https://github.com/CMU-Perceptual-Computing-Lab/openpose/blob/master/doc/demo_overview.md) or open a terminal app or Windows Powershell, navigate to the openpose installation folder and then try this command \n",
+    "The `openposedemo` bin/exe file can be run manually from the command line. It is worth trying this first so you understand what  `openposedemo` is. See [this guide](https://github.com/CMU-Perceptual-Computing-Lab/openpose/blob/master/doc/demo_overview.md) or open a terminal app or Windows Powershell, navigate to the openpose installation folder and then try this command\n",
     "\n",
     "```\n",
     ":: Windows\n",
     "bin\\OpenPoseDemo.exe --video examples\\media\\video.avi --write_json output\n",
     "# Mac/Linux\n",
     "./build/examples/openpose/openpose.bin --video examples/media/video.avi --write_json output\n",
-    "```\n",
-    "\n",
-    "Changing the `examples\\media\\video.avi` to the path to another video on your machine will process that instead. "
+    "```"
    ]
   },
   {
@@ -65,14 +55,14 @@
     "\n",
     "There are a handful of python libraries that we use for things like image manipulation, file operations, maths and stats. Many are probably already installed by default such as `os, math, numpy, pandas, matplotlib`. Others need adding to our python environment. \n",
     "\n",
-    "For example, `PyArrow` is a useful extension for saving Pandas and NumPy data. We need it to move the large array created in Step 2 to Step 3. \n",
+    "PyArrow is a useful extension for saving Pandas and NumPy data. We need it to move the large array created in Step 2 to Step 3. \n",
     "\n",
     "**If you are using conda then run the following command to install all the main libraries.**\n",
     "```\n",
     "conda install glob2 opencv pyarrow xlrd openpyxl\n",
     "```\n",
     "#### Troubleshooting\n",
-    "When you run the code in Steps 1, 2 & 3 you might see an error like `ModuleNotFoundError: No module named 'glob'` this is because that python module needs to be installed on your computer. If you use Anaconda, the missing module can usually be installed with the command `conda install glob`. You then need to restart the script with the problem by choosing `Restart kernel..` from the Kernel menu dropdown."
+    "If when you run the code in Steps 1, 2 & 3 you might see an error like `ModuleNotFoundError: No module named 'glob'` this is because that python module needs to be installed on your computer. If you use Anaconda, the missing module can usually be installed with the command `conda install glob`."
    ]
   },
   {
@@ -89,6 +79,10 @@
     "To make these work with the newer Jupyter Lab we also need to install the widgets lab extension, like so:\n",
     "\n",
     "```\n",
+    "Jupyter 3.0 (current)\n",
+    "conda install -c conda-forge jupyterlab_widgets\n",
+    "\n",
+    "Jupyter 2.0 (older)\n",
     "conda install -c conda-forge nodejs\n",
     "jupyter labextension install @jupyter-widgets/jupyterlab-manager\n",
     "jupyter labextension install @jupyter-widgets/jupyterlab-manager ipycanvas\n",
@@ -106,7 +100,7 @@
    "source": [
     "### 0.4 - JupyText \n",
     "\n",
-    "The standard ipython notebook format (`mynotebook.ipynb`) is a single file that mixes together code, formatting commands and outputs both as the results of running code and embedded binaries (images, graphs). This makes it non-human readable and very hard to tell what changed from one version to the next. `Jupytext` solves this by creating a synchronised plain text version of the file saved as a plain `.py` file (`mynotebook.py`). These are useful for developers (as it helps you track differences between versions more easily) but can mostly be ignored by users. \n",
+    "The standard ipython notebook format (`mynotebook.ipynb`) is a single file that mixes together code, formatting commands and outputs both as the results of running code and embedded binaries (images, graphs). This makes it non-human readable and very hard to tell what changes from one improvement to the next. `Jupytext` solves this by creating a synchronised plain text version of the file saved as a plain `.py` file (`mynotebook.py`). These are useful for developers (as it helps you track differences between versions more easily) but can mostly be ignored by users. \n",
     "\n",
     "\n",
     "Install JupyText by running\n",
@@ -118,7 +112,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### 0.5 Notebook extensions (optional)\n",
+    "### 0.6 Notebook extensions (optional)\n",
     "Installing Jupyter notebook extenstions provide some useful tools for navigating notebooks (e.g. table of contents) and other features.\n",
     "\n",
     "To install, run these commands in terminal window.\n",
@@ -148,7 +142,7 @@
    "formats": "ipynb,py:light"
   },
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -162,7 +156,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.12"
   }
  },
  "nbformat": 4,

Step0.GettingStarted.py

@@ -8,7 +8,7 @@
 #       format_version: '1.5'
 #       jupytext_version: 1.7.1
 #   kernelspec:
-#     display_name: Python 3
+#     display_name: Python 3 (ipykernel)
 #     language: python
 #     name: python3
 # ---
@@ -24,49 +24,40 @@
 
 # ### 0.0 - Jupyter notebook environment
 #
-# *If you can read this you are probably already running [Jupyter](https://jupyter.org/). Congratulations!*
+# *If you can read this you are probably already running Jupyter. Congratulations!*
 #
-# There's a [getting started guide](https://jupyter.readthedocs.io/en/latest/content-quickstart.html) at the [Jupyter documentation page](https://jupyter.readthedocs.io/en/latest/index.html)
+# We recommend using the Anaconda Data Science platform (Python 3 version) 
 #
-# If you're impatient we recommend using the Anaconda Data Science platform (Python 3 version) 
 # https://www.anaconda.com/distribution/
 #
-# and then running the command
-# ```
-# conda install -c conda-forge jupyterlab
-# ```
-#
-# These notebooks will run in the original Jupyter Notebook format or with the newer JupyterLab interface. We recommend the latter. 
 
 # ### 0.1 - OpenPoseDemo application
 #
 # Next we need to download and install the [OpenPoseDemo](https://github.com/CMU-Perceptual-Computing-Lab/openpose/blob/master/doc/demo_overview.md) executable.
 #
 # Additionally, you need to download the trained neural-network models that OpenPose uses. To do this go to the `models` subdirectory of OpenPose directory, and double-click / run the `models.bat` script.
 #
-# The `openposedemo` bin/exe file can be run manually from the command line. It is worth trying this first so you understand what  `openposedemo` is. See [this guide](https://github.com/CMU-Perceptual-Computing-Lab/openpose/blob/master/doc/demo_overview.md) or open a terminal app or Windows Powershell, navigate to the openpose installation folder and then try this command 
+# The `openposedemo` bin/exe file can be run manually from the command line. It is worth trying this first so you understand what  `openposedemo` is. See [this guide](https://github.com/CMU-Perceptual-Computing-Lab/openpose/blob/master/doc/demo_overview.md) or open a terminal app or Windows Powershell, navigate to the openpose installation folder and then try this command
 #
 # ```
 # :: Windows
 # bin\OpenPoseDemo.exe --video examples\media\video.avi --write_json output
 # # Mac/Linux
 # ./build/examples/openpose/openpose.bin --video examples/media/video.avi --write_json output
 # ```
-#
-# Changing the `examples\media\video.avi` to the path to another video on your machine will process that instead. 
 
 # ### 0.2 - Load python libraries
 #
 # There are a handful of python libraries that we use for things like image manipulation, file operations, maths and stats. Many are probably already installed by default such as `os, math, numpy, pandas, matplotlib`. Others need adding to our python environment. 
 #
-# For example, `PyArrow` is a useful extension for saving Pandas and NumPy data. We need it to move the large array created in Step 2 to Step 3. 
+# PyArrow is a useful extension for saving Pandas and NumPy data. We need it to move the large array created in Step 2 to Step 3. 
 #
 # **If you are using conda then run the following command to install all the main libraries.**
 # ```
 # conda install glob2 opencv pyarrow xlrd openpyxl
 # ```
 # #### Troubleshooting
-# When you run the code in Steps 1, 2 & 3 you might see an error like `ModuleNotFoundError: No module named 'glob'` this is because that python module needs to be installed on your computer. If you use Anaconda, the missing module can usually be installed with the command `conda install glob`. You then need to restart the script with the problem by choosing `Restart kernel..` from the Kernel menu dropdown.
+# If when you run the code in Steps 1, 2 & 3 you might see an error like `ModuleNotFoundError: No module named 'glob'` this is because that python module needs to be installed on your computer. If you use Anaconda, the missing module can usually be installed with the command `conda install glob`.
 
 # ### 0.3 - iPyWidgets
 #
@@ -78,6 +69,10 @@
 # To make these work with the newer Jupyter Lab we also need to install the widgets lab extension, like so:
 #
 # ```
+# Jupyter 3.0 (current)
+# conda install -c conda-forge jupyterlab_widgets
+#
+# Jupyter 2.0 (older)
 # conda install -c conda-forge nodejs
 # jupyter labextension install @jupyter-widgets/jupyterlab-manager
 # jupyter labextension install @jupyter-widgets/jupyterlab-manager ipycanvas
@@ -91,14 +86,14 @@
 
 # ### 0.4 - JupyText 
 #
-# The standard ipython notebook format (`mynotebook.ipynb`) is a single file that mixes together code, formatting commands and outputs both as the results of running code and embedded binaries (images, graphs). This makes it non-human readable and very hard to tell what changed from one version to the next. `Jupytext` solves this by creating a synchronised plain text version of the file saved as a plain `.py` file (`mynotebook.py`). These are useful for developers (as it helps you track differences between versions more easily) but can mostly be ignored by users. 
+# The standard ipython notebook format (`mynotebook.ipynb`) is a single file that mixes together code, formatting commands and outputs both as the results of running code and embedded binaries (images, graphs). This makes it non-human readable and very hard to tell what changes from one improvement to the next. `Jupytext` solves this by creating a synchronised plain text version of the file saved as a plain `.py` file (`mynotebook.py`). These are useful for developers (as it helps you track differences between versions more easily) but can mostly be ignored by users. 
 #
 #
 # Install JupyText by running
 #
 # ```conda install -c conda-forge jupytext```
 
-# ### 0.5 Notebook extensions (optional)
+# ### 0.6 Notebook extensions (optional)
 # Installing Jupyter notebook extenstions provide some useful tools for navigating notebooks (e.g. table of contents) and other features.
 #
 # To install, run these commands in terminal window.