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updating docs
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andrewheusser committed Jun 14, 2017
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2 changes: 1 addition & 1 deletion docs/_build/html/.buildinfo
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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 27f69a987af6cebd72c9ce04198515dc
config: 91bba5725d2ee2f6e7e8d9d4495368c7
tags: 645f666f9bcd5a90fca523b33c5a78b7
2 changes: 1 addition & 1 deletion docs/_build/html/_downloads/animate.ipynb
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"execution_count": null,
"cell_type": "code",
"source": [
"# Code source: Andrew Heusser\n# License: MIT\n\nimport hypertools as hyp\nimport scipy.io as sio\nimport numpy as np\n\ndata = hyp.tools.load('weights')\naligned_w = hyp.tools.align(data)\n\nw1 = np.mean(aligned_w[:17],0)\nw2 = np.mean(aligned_w[18:],0)\n\nhyp.plot([w1, w2], animate=True)"
"# Code source: Andrew Heusser\n# License: MIT\n\n# import\nimport hypertools as hyp\nimport numpy as np\n\n# load example data\ndata = hyp.tools.load('weights', align=True)\n\n# average into two groups\nw1 = np.mean(data[:17],0)\nw2 = np.mean(data[18:],0)\n\n# plot\nhyp.plot([w1, w2], animate=True)"
],
"outputs": [],
"metadata": {
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12 changes: 7 additions & 5 deletions docs/_build/html/_downloads/animate.py
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# Code source: Andrew Heusser
# License: MIT

# import
import hypertools as hyp
import scipy.io as sio
import numpy as np

data = hyp.tools.load('weights')
aligned_w = hyp.tools.align(data)
# load example data
data = hyp.tools.load('weights', align=True)

w1 = np.mean(aligned_w[:17],0)
w2 = np.mean(aligned_w[18:],0)
# average into two groups
w1 = np.mean(data[:17],0)
w2 = np.mean(data[18:],0)

# plot
hyp.plot([w1, w2], animate=True)
54 changes: 54 additions & 0 deletions docs/_build/html/_downloads/animate_MDS.ipynb
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{
"nbformat_minor": 0,
"nbformat": 4,
"cells": [
{
"execution_count": null,
"cell_type": "code",
"source": [
"%matplotlib inline"
],
"outputs": [],
"metadata": {
"collapsed": false
}
},
{
"source": [
"\n# Animated trajectory plotted with multidimensional scaling\n\n\nThis is a trajectory of brain data, hyperaligned and then plotted in 3D\nwith multidimensional scaling.\n\n"
],
"cell_type": "markdown",
"metadata": {}
},
{
"execution_count": null,
"cell_type": "code",
"source": [
"# Code source: Andrew Heusser\n# License: MIT\n\nimport hypertools as hyp\nimport scipy.io as sio\nimport numpy as np\n\ndata = hyp.tools.load('weights')\naligned_w = hyp.tools.align(data)\n\nw1 = np.mean(aligned_w[:17],0)\nw2 = np.mean(aligned_w[18:],0)\n\nhyp.plot([w1, w2], animate=True, model='MDS')"
],
"outputs": [],
"metadata": {
"collapsed": false
}
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 2",
"name": "python2",
"language": "python"
},
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"name": "python",
"file_extension": ".py",
"version": "2.7.11",
"pygments_lexer": "ipython2",
"codemirror_mode": {
"version": 2,
"name": "ipython"
}
}
}
}
24 changes: 24 additions & 0 deletions docs/_build/html/_downloads/animate_MDS.py
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# -*- coding: utf-8 -*-
"""
=============================
Animated trajectory plotted with multidimensional scaling
=============================
This is a trajectory of brain data, hyperaligned and then plotted in 3D
with multidimensional scaling.
"""

# Code source: Andrew Heusser
# License: MIT

import hypertools as hyp
import scipy.io as sio
import numpy as np

data = hyp.tools.load('weights')
aligned_w = hyp.tools.align(data)

w1 = np.mean(aligned_w[:17],0)
w2 = np.mean(aligned_w[18:],0)

hyp.plot([w1, w2], animate=True, model='MDS')
2 changes: 1 addition & 1 deletion docs/_build/html/_downloads/animate_spin.ipynb
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"execution_count": null,
"cell_type": "code",
"source": [
"# Code source: Andrew Heusser\n# License: MIT\n\n# load\nimport hypertools as hyp\n\n# load data\ndata = hyp.tools.load('weights_sample')\n\n# plot\nhyp.plot(data, '.', animate='spin')"
"# Code source: Andrew Heusser\n# License: MIT\n\n# import\nimport hypertools as hyp\n\n# load example data\ndata = hyp.tools.load('weights_sample')\n\n# plot\nhyp.plot(data, '.', animate='spin')"
],
"outputs": [],
"metadata": {
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4 changes: 2 additions & 2 deletions docs/_build/html/_downloads/animate_spin.py
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# Code source: Andrew Heusser
# License: MIT

# load
# import
import hypertools as hyp

# load data
# load example data
data = hyp.tools.load('weights_sample')

# plot
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2 changes: 1 addition & 1 deletion docs/_build/html/_downloads/explore.ipynb
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"execution_count": null,
"cell_type": "code",
"source": [
"# Code source: Andrew Heusser\n# License: MIT\n\nimport hypertools as hyp\nimport scipy.io as sio\nimport numpy as np\n\ndata = hyp.tools.load('weights_sample')\n\nhyp.plot(data, '.', explore=True)"
"# Code source: Andrew Heusser\n# License: MIT\n\n# import\nimport hypertools as hyp\n\n# load example data\ndata = hyp.tools.load('weights_sample')\n\n# plot\nhyp.plot(data, '.', explore=True)"
],
"outputs": [],
"metadata": {
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5 changes: 3 additions & 2 deletions docs/_build/html/_downloads/explore.py
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# Code source: Andrew Heusser
# License: MIT

# import
import hypertools as hyp
import scipy.io as sio
import numpy as np

# load example data
data = hyp.tools.load('weights_sample')

# plot
hyp.plot(data, '.', explore=True)
2 changes: 1 addition & 1 deletion docs/_build/html/_downloads/plot_PPCA.ipynb
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"execution_count": null,
"cell_type": "code",
"source": [
"# Code source: Andrew Heusser\n# License: MIT\n\nfrom scipy.linalg import toeplitz\nimport numpy as np\nfrom copy import copy\nimport hypertools as hyp\n\nK = 10 - toeplitz(np.arange(10))\n\ndata1 = np.cumsum(np.random.multivariate_normal(np.zeros(10), K, 250), axis=0)\ndata2 = copy(data1)\n\nmissing = .1\ninds = [(i,j) for i in range(data2.shape[0]) for j in range(data2.shape[1])]\nmissing_data = [inds[i] for i in np.random.choice(int(len(inds)), int(len(inds)*missing))]\nfor i,j in missing_data:\n data2[i,j]=np.nan\n\nhyp.plot([data1, data2], linestyle=['-',':'], legend=['Original', 'PPCA'])"
"# Code source: Andrew Heusser\n# License: MIT\n\n# import\nfrom scipy.linalg import toeplitz\nimport numpy as np\nfrom copy import copy\nimport hypertools as hyp\n\n# simulate data\nK = 10 - toeplitz(np.arange(10))\ndata1 = np.cumsum(np.random.multivariate_normal(np.zeros(10), K, 250), axis=0)\ndata2 = copy(data1)\n\n# simulate missing data\nmissing = .1\ninds = [(i,j) for i in range(data2.shape[0]) for j in range(data2.shape[1])]\nmissing_data = [inds[i] for i in np.random.choice(int(len(inds)), int(len(inds)*missing))]\nfor i,j in missing_data:\n data2[i,j]=np.nan\n\n# plot\nhyp.plot([data1, data2], linestyle=['-',':'], legend=['Original', 'PPCA'])"
],
"outputs": [],
"metadata": {
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5 changes: 4 additions & 1 deletion docs/_build/html/_downloads/plot_PPCA.py
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# Code source: Andrew Heusser
# License: MIT

# import
from scipy.linalg import toeplitz
import numpy as np
from copy import copy
import hypertools as hyp

# simulate data
K = 10 - toeplitz(np.arange(10))

data1 = np.cumsum(np.random.multivariate_normal(np.zeros(10), K, 250), axis=0)
data2 = copy(data1)

# simulate missing data
missing = .1
inds = [(i,j) for i in range(data2.shape[0]) for j in range(data2.shape[1])]
missing_data = [inds[i] for i in np.random.choice(int(len(inds)), int(len(inds)*missing))]
for i,j in missing_data:
data2[i,j]=np.nan

# plot
hyp.plot([data1, data2], linestyle=['-',':'], legend=['Original', 'PPCA'])
54 changes: 54 additions & 0 deletions docs/_build/html/_downloads/plot_TSNE.ipynb
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{
"nbformat_minor": 0,
"nbformat": 4,
"cells": [
{
"execution_count": null,
"cell_type": "code",
"source": [
"%matplotlib inline"
],
"outputs": [],
"metadata": {
"collapsed": false
}
},
{
"source": [
"\n# Visualizing the digits dataset using t-SNE\n\n\nThis example loads in some data from the scikit-learn digits dataset and plots\nit using t-SNE.\n\n"
],
"cell_type": "markdown",
"metadata": {}
},
{
"execution_count": null,
"cell_type": "code",
"source": [
"# Code source: Andrew Heusser\n# License: MIT\n\nfrom sklearn import datasets\nimport hypertools as hyp\n\ndigits = datasets.load_digits(n_class=6)\ndata = digits.data\ngroup = digits.target.astype('str')\n\nhyp.plot(data, '.', model='TSNE', group=group, ndims=2)"
],
"outputs": [],
"metadata": {
"collapsed": false
}
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 2",
"name": "python2",
"language": "python"
},
"language_info": {
"mimetype": "text/x-python",
"nbconvert_exporter": "python",
"name": "python",
"file_extension": ".py",
"version": "2.7.11",
"pygments_lexer": "ipython2",
"codemirror_mode": {
"version": 2,
"name": "ipython"
}
}
}
}
21 changes: 21 additions & 0 deletions docs/_build/html/_downloads/plot_TSNE.py
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# -*- coding: utf-8 -*-
"""
=============================
Visualizing the digits dataset using t-SNE
=============================
This example loads in some data from the scikit-learn digits dataset and plots
it using t-SNE.
"""

# Code source: Andrew Heusser
# License: MIT

from sklearn import datasets
import hypertools as hyp

digits = datasets.load_digits(n_class=6)
data = digits.data
group = digits.target.astype('str')

hyp.plot(data, '.', model='TSNE', group=group, ndims=2)
2 changes: 1 addition & 1 deletion docs/_build/html/_downloads/plot_align.ipynb
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"execution_count": null,
"cell_type": "code",
"source": [
"# Code source: Andrew Heusser\n# License: MIT\n\nimport hypertools as hyp\nimport scipy.io as sio\nimport numpy as np\n\ndata = hyp.tools.load('weights')\naligned_data = hyp.tools.align(data)\n\ngroup1 = np.mean(aligned_data[:17],0)\ngroup2 = np.mean(aligned_data[18:],0)\n\nhyp.plot([group1[:100,:],group2[:100,:]])"
"# Code source: Andrew Heusser\n# License: MIT\n\n# import\nimport hypertools as hyp\nimport numpy as np\n\n# load example data\ndata = hyp.tools.load('weights', align=True)\n\n# average into two groups\ngroup1 = np.mean(data[:17], 0)\ngroup2 = np.mean(data[18:], 0)\n\n# plot\nhyp.plot([group1[:100, :], group2[:100, :]])"
],
"outputs": [],
"metadata": {
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14 changes: 8 additions & 6 deletions docs/_build/html/_downloads/plot_align.py
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# Code source: Andrew Heusser
# License: MIT

# import
import hypertools as hyp
import scipy.io as sio
import numpy as np

data = hyp.tools.load('weights')
aligned_data = hyp.tools.align(data)
# load example data
data = hyp.tools.load('weights', align=True)

group1 = np.mean(aligned_data[:17],0)
group2 = np.mean(aligned_data[18:],0)
# average into two groups
group1 = np.mean(data[:17], 0)
group2 = np.mean(data[18:], 0)

hyp.plot([group1[:100,:],group2[:100,:]])
# plot
hyp.plot([group1[:100, :], group2[:100, :]])
2 changes: 1 addition & 1 deletion docs/_build/html/_downloads/plot_basic.ipynb
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"execution_count": null,
"cell_type": "code",
"source": [
"# Code source: Andrew Heusser\n# License: MIT\n\nimport hypertools as hyp\n\ndata = hyp.tools.load('weights_sample')\n\nhyp.plot(data, '.')"
"# Code source: Andrew Heusser\n# License: MIT\n\n# import\nimport hypertools as hyp\n\n# load example data\ndata = hyp.tools.load('weights_sample')\n\n# plot\nhyp.plot(data, '.')"
],
"outputs": [],
"metadata": {
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3 changes: 3 additions & 0 deletions docs/_build/html/_downloads/plot_basic.py
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# Code source: Andrew Heusser
# License: MIT

# import
import hypertools as hyp

# load example data
data = hyp.tools.load('weights_sample')

# plot
hyp.plot(data, '.')
2 changes: 1 addition & 1 deletion docs/_build/html/_downloads/plot_clusters.ipynb
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"execution_count": null,
"cell_type": "code",
"source": [
"# Code source: Andrew Heusser\n# License: MIT\n\nimport hypertools as hyp\nimport pandas as pd\n\ndata = hyp.tools.load('mushrooms')\n\nhyp.plot(data, '.', n_clusters=10)"
"# Code source: Andrew Heusser\n# License: MIT\n\n# import\nimport hypertools as hyp\nimport pandas as pd\n\n# load example data\ndata = hyp.tools.load('mushrooms')\n\n# plot\nhyp.plot(data, '.', n_clusters=10)"
],
"outputs": [],
"metadata": {
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3 changes: 3 additions & 0 deletions docs/_build/html/_downloads/plot_clusters.py
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# Code source: Andrew Heusser
# License: MIT

# import
import hypertools as hyp
import pandas as pd

# load example data
data = hyp.tools.load('mushrooms')

# plot
hyp.plot(data, '.', n_clusters=10)
2 changes: 1 addition & 1 deletion docs/_build/html/_downloads/plot_clusters2.ipynb
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"execution_count": null,
"cell_type": "code",
"source": [
"# Code source: Andrew Heusser\n# License: MIT\n\nimport hypertools as hyp\nimport numpy as np\nfrom scipy.stats import multivariate_normal\n\ncluster1 = np.random.multivariate_normal(np.zeros(3), np.eye(3), size=100)\ncluster2 = np.random.multivariate_normal(np.zeros(3)+3, np.eye(3), size=100)\ndata = np.vstack([cluster1,cluster2])\n\ncluster_labels = hyp.tools.cluster(data, n_clusters=2)\nhyp.plot(data, '.', group=cluster_labels)"
"# Code source: Andrew Heusser\n# License: MIT\n\n# import\nimport hypertools as hyp\nimport numpy as np\nfrom scipy.stats import multivariate_normal\n\n# simulate clusters\ncluster1 = np.random.multivariate_normal(np.zeros(3), np.eye(3), size=100)\ncluster2 = np.random.multivariate_normal(np.zeros(3)+3, np.eye(3), size=100)\ndata = np.vstack([cluster1, cluster2])\n\n# get cluster labels\ncluster_labels = hyp.tools.cluster(data, n_clusters=2)\n\n# plot\nhyp.plot(data, '.', group=cluster_labels)"
],
"outputs": [],
"metadata": {
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7 changes: 6 additions & 1 deletion docs/_build/html/_downloads/plot_clusters2.py
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Expand Up @@ -12,13 +12,18 @@
# Code source: Andrew Heusser
# License: MIT

# import
import hypertools as hyp
import numpy as np
from scipy.stats import multivariate_normal

# simulate clusters
cluster1 = np.random.multivariate_normal(np.zeros(3), np.eye(3), size=100)
cluster2 = np.random.multivariate_normal(np.zeros(3)+3, np.eye(3), size=100)
data = np.vstack([cluster1,cluster2])
data = np.vstack([cluster1, cluster2])

# get cluster labels
cluster_labels = hyp.tools.cluster(data, n_clusters=2)

# plot
hyp.plot(data, '.', group=cluster_labels)
2 changes: 1 addition & 1 deletion docs/_build/html/_downloads/plot_dataframe.ipynb
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Expand Up @@ -24,7 +24,7 @@
"execution_count": null,
"cell_type": "code",
"source": [
"# Code source: Andrew Heusser\n# License: MIT\n\nimport hypertools as hyp\nimport pandas as pd\n\ndata = hyp.tools.load('mushrooms')\n\ngroup = data.pop('class')\n\nhyp.plot(data, '.', group=group)"
"# Code source: Andrew Heusser\n# License: MIT\n\n# import\nimport hypertools as hyp\n\n# load example data\ndata = hyp.tools.load('mushrooms')\n\n# pop off the class (poisonousness)\ngroup = data.pop('class')\n\n# plot\nhyp.plot(data, '.', group=group)"
],
"outputs": [],
"metadata": {
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