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Commit f137ab3f authored by lucas_miranda's avatar lucas_miranda
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Fixes issues with MMD implementation

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/workspace.xml
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DeepOF
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<settings>
<option name="USE_PROJECT_PROFILE" value="false" />
<version value="1.0" />
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<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="ProjectModuleManager">
<modules>
<module fileurl="file://$PROJECT_DIR$/.idea/DeepOF.iml" filepath="$PROJECT_DIR$/.idea/DeepOF.iml" />
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<project version="4">
<component name="RGraphicsSettings">
<option name="height" value="1050" />
<option name="resolution" value="75" />
<option name="version" value="1" />
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<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="RSettings">
<option name="interpreterPath" value="/usr/local/bin/R" />
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<option name="enabledRepositoryUrls">
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<option value="@CRAN@" />
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<mapping directory="$PROJECT_DIR$" vcs="Git" />
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.ipynb_checkpoints/main-checkpoint.ipynb 0 → 100644
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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"%load_ext autoreload\n",
"%autoreload 2\n",
"\n",
"import warnings\n",
"warnings.filterwarnings(\"ignore\")"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"#from source.utils import *\n",
"from source.preprocess import *\n",
"import pickle\n",
"import matplotlib.pyplot as plt\n",
"import pandas as pd\n",
"from collections import defaultdict\n",
"from tqdm import tqdm_notebook as tqdm"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Set up and design the project"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"with open('../../Desktop/DLC_social_1/DLC_social_1_exp_conditions.pickle', 'rb') as handle:\n",
" Treatment_dict = pickle.load(handle)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"#Which angles to compute?\n",
"bp_dict = {'B_Nose':['B_Left_ear','B_Right_ear'],\n",
" 'B_Left_ear':['B_Nose','B_Right_ear','B_Center','B_Left_flank'],\n",
" 'B_Right_ear':['B_Nose','B_Left_ear','B_Center','B_Right_flank'],\n",
" 'B_Center':['B_Left_ear','B_Right_ear','B_Left_flank','B_Right_flank','B_Tail_base'],\n",
" 'B_Left_flank':['B_Left_ear','B_Center','B_Tail_base'],\n",
" 'B_Right_flank':['B_Right_ear','B_Center','B_Tail_base'],\n",
" 'B_Tail_base':['B_Center','B_Left_flank','B_Right_flank']}"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"CPU times: user 2.71 s, sys: 837 ms, total: 3.54 s\n",
"Wall time: 1.13 s\n"
]
}
],
"source": [
"%%time\n",
"DLC_social_1 = project(path='../../Desktop/DLC_social_1/',#Path where to find the required files\n",
" smooth_alpha=0.85, #Alpha value for exponentially weighted smoothing\n",
" distances=['B_Center','B_Nose','B_Left_ear','B_Right_ear','B_Left_flank',\n",
" 'B_Right_flank','B_Tail_base'],\n",
" ego=False,\n",
" angles=True,\n",
" connectivity=bp_dict,\n",
" arena='circular', #Type of arena used in the experiments\n",
" arena_dims=[380], #Dimensions of the arena. Just one if it's circular\n",
" video_format='.mp4',\n",
" table_format='.h5',\n",
" exp_conditions=Treatment_dict)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Run project"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Loading trajectories...\n",
"Smoothing trajectories...\n",
"Computing distances...\n",
"Computing angles...\n",
"Done!\n",
"Coordinates of 47 videos across 4 conditions\n",
"CPU times: user 9.19 s, sys: 562 ms, total: 9.75 s\n",
"Wall time: 10 s\n"
]
},
{
"data": {
"text/plain": [
"source.preprocess.coordinates"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"%%time\n",
"DLC_social_1_coords = DLC_social_1.run(verbose=True)\n",
"print(DLC_social_1_coords)\n",
"type(DLC_social_1_coords)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Generate coords"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"CPU times: user 832 ms, sys: 72.8 ms, total: 905 ms\n",
"Wall time: 857 ms\n"
]
},
{
"data": {
"text/plain": [
"'coords'"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"%%time\n",
"ptest = DLC_social_1_coords.get_coords(center=True, polar=False, speed=0, length='00:10:00')\n",
"ptest._type"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"CPU times: user 525 ms, sys: 365 ms, total: 890 ms\n",
"Wall time: 889 ms\n"
]
},
{
"data": {
"text/plain": [
"'dists'"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"%%time\n",
"dtest = DLC_social_1_coords.get_distances(speed=0, length='00:10:00')\n",
"dtest._type"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"CPU times: user 140 ms, sys: 80.3 ms, total: 221 ms\n",
"Wall time: 220 ms\n"
]
},
{
"data": {
"text/plain": [
"'angles'"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"%%time\n",
"atest = DLC_social_1_coords.get_angles(degrees=True, speed=0, length='00:10:00')\n",
"atest._type"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Visualization playground"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"ptest.plot_heatmaps(['B_Center', 'W_Center'], i=1)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"#Plot animation of trajectory over time with different smoothings\n",
"plt.plot(ptest['Day2Test13DLC']['B_Center'].iloc[:5000]['x'],\n",
" ptest['Day2Test13DLC']['B_Center'].iloc[:5000]['y'], label='alpha=0.85')\n",
"\n",
"plt.xlabel('x')\n",
"plt.ylabel('y')\n",
"plt.title('Mouse Center Trajectory using different exponential smoothings')\n",
"plt.legend()\n",
"plt.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Dimensionality reduction playground"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"pca = ptest.pca(4, 1000)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"plt.scatter(*pca[0].T)\n",
"plt.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Preprocessing playground"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"mtest = merge_tables(DLC_social_1_coords.get_coords(center=True, polar=True, length='00:10:00'))#,\n",
"# DLC_social_1_coords.get_distances(speed=0, length='00:10:00'),\n",
"# DLC_social_1_coords.get_angles(degrees=True, speed=0, length='00:10:00'))"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"pptest = mtest.preprocess(window_size=51, filter='gaussian', sigma=10, shift=20)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"pttest = mtest.preprocess(window_size=51, filter=None)\n",
"pttest.shape"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"plt.plot(pttest[2,:,2], label='normal')\n",
"plt.plot(pptest[2,:,2], label='gaussian')\n",
"plt.legend()\n",
"plt.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Trained models playground"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Seq 2 seq Variational Auto Encoder"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"pttest = pttest[:1000]"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"CONV_filters = 64\n",
"LSTM_units_1 = 128\n",
"LSTM_units_2 = 64\n",
"DENSE_1 = 64\n",
"DENSE_2 = 32\n",
"ENCODING = 20\n",
"DROPOUT_RATE = 0.2\n",
"\n",
"original_dim = pttest.shape[1:]\n",
"batch_size = 256"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from source.hypermodels import *\n",
"import tensorflow as tf\n",
"from tensorflow.keras import Input, Model\n",
"from tensorflow.keras.layers import Dense, Lambda, Bidirectional, LSTM\n",
"from tensorflow.keras import backend as K\n",
"K.clear_session()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"class KLDivergenceLayer(Layer):\n",
"\n",
" \"\"\" Identity transform layer that adds KL divergence\n",
" to the final model loss.\n",
" \"\"\"\n",
"\n",
" def __init__(self, *args, **kwargs):\n",
" self.is_placeholder = True\n",
" super(KLDivergenceLayer, self).__init__(*args, **kwargs)\n",
"\n",
" def call(self, inputs):\n",
"\n",
" mu, log_var = inputs\n",
"\n",
" kl_batch = - .5 * K.sum(1 + log_var -\n",
" K.square(mu) -\n",
" K.exp(log_var), axis=-1)\n",
"\n",
" self.add_loss(K.mean(kl_batch), inputs=inputs)\n",
"\n",
" return inputs"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"class MMDiscrepancyLayer(Layer):\n",
"\n",
" \"\"\" Identity transform layer that adds MM discrepancy\n",
" to the final model loss.\n",
" \"\"\"\n",
"\n",
" def __init__(self, *args, **kwargs):\n",
" self.is_placeholder = True\n",
" super(MMDiscrepancyLayer, self).__init__(*args, **kwargs)\n",
"\n",
" def call(self, z):\n",
" \n",
" true_samples = K.random_normal(K.shape(z), mean=0., stddev=2./K.cast_to_floatx(K.shape(z)[1])) \n",
" mmd_batch = compute_mmd(z, true_samples)\n",
" \n",
" self.add_loss(K.mean(mmd_batch), inputs=z)\n",
"\n",
" return z"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Encoder Layers\n",
"Model_E0 = tf.keras.layers.Conv1D(\n",
" filters=CONV_filters,\n",
" kernel_size=5,\n",
" strides=1,\n",
" padding=\"causal\",\n",
" activation=\"relu\",\n",
")\n",
"Model_E1 = Bidirectional(\n",
" LSTM(\n",
" LSTM_units_1,\n",
" activation=\"tanh\",\n",
" return_sequences=True,\n",
" kernel_constraint=UnitNorm(axis=0),\n",
" )\n",
")\n",
"Model_E2 = Bidirectional(\n",
" LSTM(\n",
" LSTM_units_2,\n",
" activation=\"tanh\",\n",
" return_sequences=False,\n",
" kernel_constraint=UnitNorm(axis=0),\n",
" )\n",
")\n",
"Model_E3 = Dense(DENSE_1, activation=\"relu\", kernel_constraint=UnitNorm(axis=0))\n",
"Model_E4 = Dense(DENSE_2, activation=\"relu\", kernel_constraint=UnitNorm(axis=0))\n",
"Model_E5 = Dense(\n",
" ENCODING,\n",
" activation=\"relu\",\n",
" kernel_constraint=UnitNorm(axis=1),\n",
" activity_regularizer=UncorrelatedFeaturesConstraint(3, weightage=1.0),\n",
" )\n",
"\n",
"# Decoder layers\n",
"Model_D4 = Bidirectional(\n",
" LSTM(\n",
" LSTM_units_1,\n",
" activation=\"tanh\",\n",
" return_sequences=True,\n",
" kernel_constraint=UnitNorm(axis=1),\n",
" )\n",
")\n",
"Model_D5 = Bidirectional(\n",
" LSTM(\n",
" LSTM_units_1,\n",
" activation=\"sigmoid\",\n",
" return_sequences=True,\n",
" kernel_constraint=UnitNorm(axis=1),\n",
" )\n",
")\n",
"\n",
"# Define and instanciate encoder\n",
"x = Input(shape=original_dim)\n",
"encoder = Model_E0(x)\n",
"encoder = Model_E1(encoder)\n",
"encoder = Model_E2(encoder)\n",
"encoder = Model_E3(encoder)\n",
"encoder = Dropout(DROPOUT_RATE)(encoder)\n",
"encoder = Model_E4(encoder)\n",
"encoder = Model_E5(encoder)\n",
"z_mean = Dense(ENCODING)(encoder)\n",
"z_log_sigma = Dense(ENCODING)(encoder)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"def sampling(args, epsilon_std=1.):\n",
" z_mean, z_log_sigma = args\n",
" epsilon = K.random_normal(shape=K.shape(z_mean),\n",
" mean=0., stddev=epsilon_std)\n",
" return z_mean + K.exp(z_log_sigma) * epsilon\n",
"\n",
"# note that \"output_shape\" isn't necessary with the TensorFlow backend\n",
"# so you could write `Lambda(sampling)([z_mean, z_log_sigma])`\n",
"\n",
"z_mean, z_log_sigma = KLDivergenceLayer()([z_mean, z_log_sigma])\n",
"z = Lambda(sampling)([z_mean, z_log_sigma])\n",
"z = MMDiscrepancyLayer()(z)"
]
},
{
"cell_type": "code",