reorganizing configs

.gitignore

@@ -9,9 +9,6 @@ Desktop.ini
 # Recycle Bin used on file shares
 $RECYCLE.BIN/
 
-./CAPTURE_analysis/
-./CAPTURE_data/
-
 *.mat
 *.sh
 *.out
@@ -34,14 +31,13 @@ $RECYCLE.BIN/
 !/tutorials/
 /tutorials/*
 !/tutorials/tutorial.ipynb
+/configs/*
+!/configs/tutorial.yaml
 
 /dappy/wandb/
 /dappy/models/
 /dappy/artifcats/
 
-!configs/param_configs/fitsne.yaml
-!configs/path_configs/example_path.yaml
-
 *.egg-info
 
 # Windows shortcuts

README.md

@@ -13,6 +13,7 @@ conda env create -f environment.yml
 conda activate dappy
 pip install -e .
 ```
+Note that `pip` and `setuptools` must be updated to the most recent versions.
 
 To begin gaining familiarity with the functionality of this package, run through the code in `tutorial/tutorial.ipynb`.
 

configs/tutorial.yaml

@@ -0,0 +1,37 @@
+# Folder path of data location
+data_path: '/home/exx/Desktop/GitHub/CAPTURE_data/ensemble_healthy/'
+
+# File path of predictions file
+pose_path: '/home/exx/Desktop/GitHub/CAPTURE_data/ensemble_healthy/predictions.mat'
+
+# File path of metadata file
+meta_path: '/home/exx/Desktop/GitHub/CAPTURE_data/ensemble_healthy/metadata.csv'
+
+# Output folder of all plots
+out_path: '/home/exx/Desktop/GitHub/results/ensemble_healthy/'
+
+# Path of list of behavior heuristics
+heuristics_path: '/home/exx/Desktop/GitHub/dappy/src/dappy/behavior_heuristics.py'
+
+# File path of skeletal specifications
+skeleton_path: '/home/exx/Desktop/GitHub/dappy/src/dappy/skeletons.py'
+
+# Key of skeleton in the skeletons file
+skeleton_name: 'mouse20_notail'
+
+label: 'fitsne'
+
+analysis: 'embed'
+
+downsample: 10
+
+single_embed:
+  method: 'fitsne'
+  perplexity: 50
+  lr: 'auto'
+  sigma: 15
+
+transform_embed: 
+  method: 'knn'
+  k: 5
+  sigma: 15

tutorials/tutorial.ipynb

@@ -18,15 +18,23 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Neurodegenerative diseases (like Parkinson's) are characterized by a wide variety of behavioral defects or movement deficits. However, behavior and movement have historically been difficult to quantify and measure."
+    "Neurodegenerative diseases (like Parkinson's) are characterized by a wide variety of behavioral defects or movement deficits. However, behavior and movement have historically been difficult to quantify and measure. Recent developments in hardware and machine learning have enabled more objective behavioral metrics by providing continuous 3D measurements of naturalistic animal behavior through multi-view videos. These new modalities of data offer a means by which we can comprehensively characterize behavioral phenotypes of neural (dys)-function. We present `dappy` to establish an open-source API with easy access to machine learning methods for the analysis of 3D pose sequences."
    ]
   },
   {
    "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "This notebook implements a Python version of CAPTURE (Marshall, 2020), which was based on earlier work MotionMapper (Berman, 2014) for the analysis of behavioral data, which can interface with future frameworks."
+    "This notebook implements a Python version of [CAPTURE (Marshall, 2020)](https://www.cell.com/neuron/fulltext/S0896-6273(20)30894-1?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0896627320308941%3Fshowall%3Dtrue), which was based on earlier work [MotionMapper (Berman, 2014)](https://royalsocietypublishing.org/doi/full/10.1098/rsif.2014.0672) for the analysis of behavioral data, which can interface with future frameworks."
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "First, we import the necessary modules."
    ]
   },
   {
@@ -35,7 +43,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import this\n",
     "from dappy import features, read, write\n",
     "import dappy.DataStruct as ds\n",
     "import dappy.visualization as vis\n",
@@ -61,7 +68,7 @@
    "outputs": [],
    "source": [
     "analysis_key = \"tutorial\"\n",
-    "config = read.config(\"../../dappy/configs/\" + analysis_key + \".yaml\")\n",
+    "config = read.config(\"../../configs/\" + analysis_key + \".yaml\")\n",
     "\n",
     "pose, ids = read.pose_h5(config[\"data_path\"] + \"pose_aligned.h5\")\n",
     "\n",
@@ -72,45 +79,6 @@
     "meta, meta_by_frame = read.meta(config[\"meta_path\"], id=ids)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 8,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "array([[1.    , 0.5217, 0.    , 0.5   ],\n",
-       "       [1.    , 0.5217, 0.    , 0.5   ],\n",
-       "       [1.    , 0.5217, 0.    , 0.5   ],\n",
-       "       [1.    , 0.5217, 0.    , 0.5   ],\n",
-       "       [1.    , 0.5217, 0.    , 0.5   ],\n",
-       "       [1.    , 0.5217, 0.    , 0.5   ],\n",
-       "       [0.4348, 1.    , 0.    , 0.5   ],\n",
-       "       [0.1739, 1.    , 0.    , 0.5   ],\n",
-       "       [0.    , 1.    , 0.6087, 0.5   ],\n",
-       "       [0.    , 1.    , 0.8696, 0.5   ],\n",
-       "       [0.    , 1.    , 1.    , 0.5   ],\n",
-       "       [0.    , 0.2609, 1.    , 0.5   ],\n",
-       "       [0.    , 0.3478, 1.    , 0.5   ],\n",
-       "       [0.    , 0.5217, 1.    , 0.5   ],\n",
-       "       [0.4348, 0.    , 1.    , 0.5   ],\n",
-       "       [0.4348, 0.    , 1.    , 0.5   ],\n",
-       "       [0.1739, 0.    , 1.    , 0.5   ],\n",
-       "       [0.9565, 0.    , 1.    , 0.5   ],\n",
-       "       [1.    , 0.    , 0.7826, 0.5   ],\n",
-       "       [1.    , 0.    , 0.5217, 0.5   ]], dtype=float32)"
-      ]
-     },
-     "execution_count": 8,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "connectivity.colors"
-   ]
-  },
   {
    "attachments": {},
    "cell_type": "markdown",
@@ -488,7 +456,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.8.13"
   },
   "orig_nbformat": 4,
   "vscode": {