`_
10 | **************************************************************
11 |
--------------------------------------------------------------------------------
/examples/bca.py:
--------------------------------------------------------------------------------
1 | from matplotlib import rc
2 | rc("font", family="serif", size=12)
3 | rc("text", usetex=True)
4 | import daft
5 |
6 | if __name__ == "__main__":
7 | pgm = daft.PGM([1.1, 3.15], origin=[0.45, 2.2])
8 | pgm.add_node(daft.Node("a", r"$a$", 1, 5))
9 | pgm.add_node(daft.Node("b", r"$b$", 1, 4))
10 | pgm.add_node(daft.Node("c", r"$c_n$", 1, 3, observed=True))
11 | pgm.add_plate(daft.Plate([0.5, 2.25, 1, 1.25], label=r"data $n$"))
12 | pgm.add_edge("a", "b")
13 | pgm.add_edge("b", "c")
14 | pgm.render()
15 | pgm.figure.savefig("bca.pdf")
16 | pgm.figure.savefig("bca.png", dpi=150)
17 |
--------------------------------------------------------------------------------
/examples/nocircles.py:
--------------------------------------------------------------------------------
1 | """
2 | Nodes can go free
3 | =================
4 |
5 | You don't need to put ellipses or circles around your node contents,
6 | if you don't want to.
7 |
8 | """
9 |
10 | from matplotlib import rc
11 | rc("font", family="serif", size=12)
12 | rc("text", usetex=True)
13 |
14 | import daft
15 |
16 | pgm = daft.PGM([3.6, 2.4], origin = [1.15, 0.8], node_ec="none")
17 | pgm.add_node(daft.Node("cloudy", r"cloudy", 3, 3))
18 | pgm.add_node(daft.Node("rain", r"rain", 2, 2))
19 | pgm.add_node(daft.Node("sprinkler", r"sprinkler", 4, 2))
20 | pgm.add_node(daft.Node("wet", r"grass wet", 3, 1))
21 | pgm.add_edge("cloudy", "rain")
22 | pgm.add_edge("cloudy", "sprinkler")
23 | pgm.add_edge("rain", "wet")
24 | pgm.add_edge("sprinkler", "wet")
25 | pgm.render()
26 | pgm.figure.savefig("nocircles.pdf")
27 | pgm.figure.savefig("nocircles.png", dpi=150)
28 |
--------------------------------------------------------------------------------
/docs/api.rst:
--------------------------------------------------------------------------------
1 | .. _api:
2 |
3 | API
4 | ===
5 |
6 | .. module:: daft
7 |
8 | The PGM Object
9 | --------------
10 |
11 | All daft scripts will start with the creation of a :class:`PGM` object. This
12 | object contains a list of :class:`Node` objects and :class:`Edge` objects
13 | connecting them. You can also specify rendering parameters and other default
14 | parameters when you initialize your :class:`PGM`.
15 |
16 | .. autoclass:: PGM
17 | :inherited-members:
18 |
19 |
20 | Nodes
21 | -----
22 |
23 | .. autoclass:: Node
24 | :inherited-members:
25 |
26 |
27 | Edges
28 | -----
29 |
30 | .. autoclass:: Edge
31 | :inherited-members:
32 |
33 |
34 | Plates
35 | ------
36 |
37 | .. autoclass:: Plate
38 | :inherited-members:
39 |
40 |
41 | The Rendering Context
42 | ---------------------
43 |
44 | .. autoclass:: _rendering_context
45 | :inherited-members:
46 |
--------------------------------------------------------------------------------
/examples/logo.py:
--------------------------------------------------------------------------------
1 | #!/usr/bin/env python
2 | """
3 | That's an awfully DAFT logo!
4 |
5 | """
6 |
7 | from matplotlib import rc
8 | rc("font", family="serif", size=12)
9 | rc("text", usetex=True)
10 |
11 | import os
12 | import sys
13 | sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
14 |
15 | import daft
16 |
17 |
18 | if __name__ == "__main__":
19 | # Instantiate the PGM.
20 | pgm = daft.PGM((3.7, 0.7), origin=(0.15, 0.15))
21 |
22 | pgm.add_node(daft.Node("d", r"$D$", 0.5, 0.5))
23 | pgm.add_node(daft.Node("a", r"$a$", 1.5, 0.5, observed=True))
24 | pgm.add_node(daft.Node("f", r"$f$", 2.5, 0.5))
25 | pgm.add_node(daft.Node("t", r"$t$", 3.5, 0.5))
26 |
27 | pgm.add_edge("d", "a")
28 | pgm.add_edge("a", "f")
29 | pgm.add_edge("f", "t")
30 |
31 | pgm.render()
32 | pgm.figure.savefig("logo.pdf")
33 | pgm.figure.savefig("logo.png", dpi=200, transparent=True)
34 |
--------------------------------------------------------------------------------
/examples/wordy.py:
--------------------------------------------------------------------------------
1 | """
2 | Nodes can contain words
3 | =======================
4 |
5 | We here at **Daft** headquarters tend to put symbols (variable
6 | names) in our graph nodes. But you don't have to if you don't
7 | want to.
8 |
9 | """
10 |
11 | from matplotlib import rc
12 | rc("font", family="serif", size=12)
13 | rc("text", usetex=True)
14 |
15 | import daft
16 |
17 | pgm = daft.PGM([3.6, 2.7], origin=[1.15, 0.65])
18 | pgm.add_node(daft.Node("cloudy", r"cloudy", 3, 3, aspect=1.8))
19 | pgm.add_node(daft.Node("rain", r"rain", 2, 2, aspect=1.2))
20 | pgm.add_node(daft.Node("sprinkler", r"sprinkler", 4, 2, aspect=2.1))
21 | pgm.add_node(daft.Node("wet", r"grass wet", 3, 1, aspect=2.4, observed=True))
22 | pgm.add_edge("cloudy", "rain")
23 | pgm.add_edge("cloudy", "sprinkler")
24 | pgm.add_edge("rain", "wet")
25 | pgm.add_edge("sprinkler", "wet")
26 | pgm.render()
27 | pgm.figure.savefig("wordy.pdf")
28 | pgm.figure.savefig("wordy.png", dpi=150)
29 |
--------------------------------------------------------------------------------
/examples/gaia.py:
--------------------------------------------------------------------------------
1 | from matplotlib import rc
2 | rc("font", family="serif", size=12)
3 | rc("text", usetex=True)
4 | import daft
5 |
6 | if __name__ == "__main__":
7 | pgm = daft.PGM([3.7, 3.15], origin=[-0.35, 2.2])
8 | pgm.add_node(daft.Node("omega", r"$\omega$", 2, 5))
9 | pgm.add_node(daft.Node("true", r"$\tilde{X}_n$", 2, 4))
10 | pgm.add_node(daft.Node("obs", r"$X_n$", 2, 3, observed=True))
11 | pgm.add_node(daft.Node("alpha", r"$\alpha$", 3, 4))
12 | pgm.add_node(daft.Node("Sigma", r"$\Sigma$", 0, 3))
13 | pgm.add_node(daft.Node("sigma", r"$\sigma_n$", 1, 3))
14 | pgm.add_plate(daft.Plate([0.5, 2.25, 2, 2.25], label=r"stars $n$"))
15 | pgm.add_edge("omega", "true")
16 | pgm.add_edge("true", "obs")
17 | pgm.add_edge("alpha", "true")
18 | pgm.add_edge("Sigma", "sigma")
19 | pgm.add_edge("sigma", "obs")
20 | pgm.render()
21 | pgm.figure.savefig("gaia.pdf")
22 | pgm.figure.savefig("gaia.png", dpi=150)
23 |
--------------------------------------------------------------------------------
/examples/mrf.py:
--------------------------------------------------------------------------------
1 | """
2 | An undirected graph
3 | ===================
4 |
5 | This makes the simple point that you don't have to have directions on
6 | your edges; you can have *undirected* graphs. (Also, the nodes don't
7 | need to have labels!)
8 |
9 | """
10 |
11 | import itertools
12 | import numpy as np
13 |
14 | import daft
15 |
16 | # Instantiate the PGM.
17 | pgm = daft.PGM([3.6, 3.6], origin=[0.7, 0.7], node_unit=0.4, grid_unit=1,
18 | directed=False)
19 |
20 | for i, (xi, yi) in enumerate(itertools.product(range(1, 5), range(1, 5))):
21 | pgm.add_node(daft.Node(str(i), "", xi, yi))
22 |
23 |
24 | for e in [(4, 9), (6, 7), (3, 7), (10, 11), (10, 9), (10, 14),
25 | (10, 6), (10, 7), (1, 2), (1, 5), (1, 0), (1, 6), (8, 12), (12, 13),
26 | (13, 14), (15, 11)]:
27 | pgm.add_edge(str(e[0]), str(e[1]))
28 |
29 | # Render and save.
30 | pgm.render()
31 | pgm.figure.savefig("mrf.pdf")
32 | pgm.figure.savefig("mrf.png", dpi=150)
33 |
--------------------------------------------------------------------------------
/examples/badfont.py:
--------------------------------------------------------------------------------
1 | """
2 | You can use arbitrarily shitty fonts
3 | ====================================
4 |
5 | Any fonts that LaTeX or matplotlib supports can be used. Do not take
6 | this example as any kind of implied recommendation unless you plan on
7 | announcing a *huge* discovery!
8 |
9 | """
10 |
11 | from matplotlib import rc
12 |
13 | ff = "comic sans ms"
14 | # ff = "impact"
15 | # ff = "times new roman"
16 |
17 | rc("font", family=ff, size=12)
18 | rc("text", usetex=False)
19 |
20 | import daft
21 |
22 | pgm = daft.PGM([3.6, 1.8], origin=[2.2, 1.6], aspect=2.1)
23 | pgm.add_node(daft.Node("confused", r"confused", 3.0, 3.0))
24 | pgm.add_node(daft.Node("ugly", r"ugly font", 3.0, 2.0, observed=True))
25 | pgm.add_node(daft.Node("bad", r"bad talk", 5.0, 2.0, observed=True))
26 | pgm.add_edge("confused", "ugly")
27 | pgm.add_edge("ugly", "bad")
28 | pgm.add_edge("confused", "bad")
29 | pgm.render()
30 | pgm.figure.savefig("badfont.pdf")
31 | pgm.figure.savefig("badfont.png", dpi=150)
32 |
--------------------------------------------------------------------------------
/docs/examples/nocircles.rst:
--------------------------------------------------------------------------------
1 | .. _nocircles:
2 |
3 |
4 | Nodes can go free
5 | =================
6 |
7 | .. figure:: /_static/examples/nocircles.png
8 |
9 |
10 | Nodes can go free
11 | =================
12 |
13 | You don't need to put ellipses or circles around your node contents,
14 | if you don't want to.
15 |
16 |
17 |
18 | ::
19 |
20 |
21 | from matplotlib import rc
22 | rc("font", family="serif", size=12)
23 | rc("text", usetex=True)
24 |
25 | import daft
26 |
27 | pgm = daft.PGM([3.6, 2.4], origin = [1.15, 0.8], node_ec="none")
28 | pgm.add_node(daft.Node("cloudy", r"cloudy", 3, 3))
29 | pgm.add_node(daft.Node("rain", r"rain", 2, 2))
30 | pgm.add_node(daft.Node("sprinkler", r"sprinkler", 4, 2))
31 | pgm.add_node(daft.Node("wet", r"grass wet", 3, 1))
32 | pgm.add_edge("cloudy", "rain")
33 | pgm.add_edge("cloudy", "sprinkler")
34 | pgm.add_edge("rain", "wet")
35 | pgm.add_edge("sprinkler", "wet")
36 | pgm.render()
37 | pgm.figure.savefig("nocircles.pdf")
38 | pgm.figure.savefig("nocircles.png", dpi=150)
39 |
40 |
41 |
--------------------------------------------------------------------------------
/LICENSE.rst:
--------------------------------------------------------------------------------
1 | Copyright (c) 2012 Daniel Foreman-Mackey, David W. Hogg, and contributors
2 |
3 | Permission is hereby granted, free of charge, to any person obtaining a copy of
4 | this software and associated documentation files (the "Software"), to deal in
5 | the Software without restriction, including without limitation the rights to
6 | use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
7 | the Software, and to permit persons to whom the Software is furnished to do so,
8 | subject to the following conditions:
9 |
10 | The above copyright notice and this permission notice shall be included in all
11 | copies or substantial portions of the Software.
12 |
13 | **THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
14 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
15 | FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
16 | COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
17 | IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
18 | CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.**
19 |
--------------------------------------------------------------------------------
/docs/_static/examples.js:
--------------------------------------------------------------------------------
1 | function shuffle(array) {
2 | // Based on: http://d3js.org
3 | var m = array.length, t, i;
4 |
5 | // While there remain elements to shuffle
6 | while (m) {
7 | // Pick a remaining element…
8 | i = Math.floor(Math.random() * m--);
9 |
10 | // And swap it with the current element.
11 | t = array[m];
12 | array[m] = array[i];
13 | array[i] = t;
14 | }
15 |
16 | return array;
17 | }
18 |
19 | function show_examples(N) {
20 | d3.json("/_static/examples.json", function (examples) {
21 | var k, names = [];
22 | for (k in examples) {
23 | names.push(k);
24 | }
25 |
26 | if (typeof(N) !== "undefined")
27 | names = shuffle(names).slice(0, N);
28 |
29 | d3.select("#examples").selectAll(".example")
30 | .data(names)
31 | .enter().append("a")
32 | .attr("class", "example")
33 | .attr("href", function (d) { return "/examples/" + d + "/"; })
34 | .append("img")
35 | .attr("src", function (d) { return "/_static/examples/" + d + "-thumb.png"; });
36 | });
37 | }
38 |
--------------------------------------------------------------------------------
/docs/examples/wordy.rst:
--------------------------------------------------------------------------------
1 | .. _wordy:
2 |
3 |
4 | Nodes can contain words
5 | =======================
6 |
7 | .. figure:: /_static/examples/wordy.png
8 |
9 |
10 | Nodes can contain words
11 | =======================
12 |
13 | We here at **Daft** headquarters tend to put symbols (variable
14 | names) in our graph nodes. But you don't have to if you don't
15 | want to.
16 |
17 |
18 |
19 | ::
20 |
21 |
22 | from matplotlib import rc
23 | rc("font", family="serif", size=12)
24 | rc("text", usetex=True)
25 |
26 | import daft
27 |
28 | pgm = daft.PGM([3.6, 2.7], origin=[1.15, 0.65])
29 | pgm.add_node(daft.Node("cloudy", r"cloudy", 3, 3, aspect=1.8))
30 | pgm.add_node(daft.Node("rain", r"rain", 2, 2, aspect=1.2))
31 | pgm.add_node(daft.Node("sprinkler", r"sprinkler", 4, 2, aspect=2.1))
32 | pgm.add_node(daft.Node("wet", r"grass wet", 3, 1, aspect=2.4, observed=True))
33 | pgm.add_edge("cloudy", "rain")
34 | pgm.add_edge("cloudy", "sprinkler")
35 | pgm.add_edge("rain", "wet")
36 | pgm.add_edge("sprinkler", "wet")
37 | pgm.render()
38 | pgm.figure.savefig("wordy.pdf")
39 | pgm.figure.savefig("wordy.png", dpi=150)
40 |
41 |
42 |
--------------------------------------------------------------------------------
/docs/examples/mrf.rst:
--------------------------------------------------------------------------------
1 | .. _mrf:
2 |
3 |
4 | An undirected graph
5 | ===================
6 |
7 | .. figure:: /_static/examples/mrf.png
8 |
9 |
10 | An undirected graph
11 | ===================
12 |
13 | This makes the simple point that you don't have to have directions on
14 | your edges; you can have *undirected* graphs. (Also, the nodes don't
15 | need to have labels!)
16 |
17 |
18 |
19 | ::
20 |
21 |
22 | import itertools
23 | import numpy as np
24 |
25 | import daft
26 |
27 | # Instantiate the PGM.
28 | pgm = daft.PGM([3.6, 3.6], origin=[0.7, 0.7], node_unit=0.4, grid_unit=1,
29 | directed=False)
30 |
31 | for i, (xi, yi) in enumerate(itertools.product(range(1, 5), range(1, 5))):
32 | pgm.add_node(daft.Node(str(i), "", xi, yi))
33 |
34 |
35 | for e in [(4, 9), (6, 7), (3, 7), (10, 11), (10, 9), (10, 14),
36 | (10, 6), (10, 7), (1, 2), (1, 5), (1, 0), (1, 6), (8, 12), (12, 13),
37 | (13, 14), (15, 11)]:
38 | pgm.add_edge(str(e[0]), str(e[1]))
39 |
40 | # Render and save.
41 | pgm.render()
42 | pgm.figure.savefig("mrf.pdf")
43 | pgm.figure.savefig("mrf.png", dpi=150)
44 |
45 |
46 |
--------------------------------------------------------------------------------
/examples/classic.py:
--------------------------------------------------------------------------------
1 | """
2 | The Quintessential PGM
3 | ======================
4 |
5 | This is a demonstration of a very common structure found in graphical models.
6 | It has been rendered using Daft's default settings for all the parameters
7 | and it shows off how much beauty is baked in by default.
8 |
9 | """
10 |
11 | from matplotlib import rc
12 | rc("font", family="serif", size=12)
13 | rc("text", usetex=True)
14 |
15 | import daft
16 |
17 | # Instantiate the PGM.
18 | pgm = daft.PGM([2.3, 2.05], origin=[0.3, 0.3])
19 |
20 | # Hierarchical parameters.
21 | pgm.add_node(daft.Node("alpha", r"$\alpha$", 0.5, 2, fixed=True))
22 | pgm.add_node(daft.Node("beta", r"$\beta$", 1.5, 2))
23 |
24 | # Latent variable.
25 | pgm.add_node(daft.Node("w", r"$w_n$", 1, 1))
26 |
27 | # Data.
28 | pgm.add_node(daft.Node("x", r"$x_n$", 2, 1, observed=True))
29 |
30 | # Add in the edges.
31 | pgm.add_edge("alpha", "beta")
32 | pgm.add_edge("beta", "w")
33 | pgm.add_edge("w", "x")
34 | pgm.add_edge("beta", "x")
35 |
36 | # And a plate.
37 | pgm.add_plate(daft.Plate([0.5, 0.5, 2, 1], label=r"$n = 1, \cdots, N$",
38 | shift=-0.1))
39 |
40 | # Render and save.
41 | pgm.render()
42 | pgm.figure.savefig("classic.pdf")
43 | pgm.figure.savefig("classic.png", dpi=150)
44 |
--------------------------------------------------------------------------------
/docs/examples/badfont.rst:
--------------------------------------------------------------------------------
1 | .. _badfont:
2 |
3 |
4 | You can use arbitrarily shitty fonts
5 | ====================================
6 |
7 | .. figure:: /_static/examples/badfont.png
8 |
9 |
10 | You can use arbitrarily shitty fonts
11 | ====================================
12 |
13 | Any fonts that LaTeX or matplotlib supports can be used. Do not take
14 | this example as any kind of implied recommendation unless you plan on
15 | announcing a *huge* discovery!
16 |
17 |
18 |
19 | ::
20 |
21 |
22 | from matplotlib import rc
23 |
24 | ff = "comic sans ms"
25 | # ff = "impact"
26 | # ff = "times new roman"
27 |
28 | rc("font", family=ff, size=12)
29 | rc("text", usetex=False)
30 |
31 | import daft
32 |
33 | pgm = daft.PGM([3.6, 1.8], origin=[2.2, 1.6], aspect=2.1)
34 | pgm.add_node(daft.Node("confused", r"confused", 3.0, 3.0))
35 | pgm.add_node(daft.Node("ugly", r"ugly font", 3.0, 2.0, observed=True))
36 | pgm.add_node(daft.Node("bad", r"bad talk", 5.0, 2.0, observed=True))
37 | pgm.add_edge("confused", "ugly")
38 | pgm.add_edge("ugly", "bad")
39 | pgm.add_edge("confused", "bad")
40 | pgm.render()
41 | pgm.figure.savefig("badfont.pdf")
42 | pgm.figure.savefig("badfont.png", dpi=150)
43 |
44 |
45 |
--------------------------------------------------------------------------------
/examples/yike.py:
--------------------------------------------------------------------------------
1 | """
2 | Yike's model
3 | ============
4 |
5 | This is Yike Tang's model for weak lensing.
6 |
7 | """
8 |
9 | from matplotlib import rc
10 | rc("font", family="serif", size=12)
11 | rc("text", usetex=True)
12 |
13 | import daft
14 |
15 | pgm = daft.PGM([5.20, 2.95], origin=[-1.70, 1.65])
16 | pgm.add_node(daft.Node("obs", r"$\epsilon^{\mathrm{obs}}_n$", 2, 3, observed=True))
17 | pgm.add_node(daft.Node("true", r"$\epsilon^{\mathrm{true}}_n$", 1, 3))
18 | pgm.add_edge("true", "obs")
19 | pgm.add_node(daft.Node("alpha", r"$\alpha,\beta$", -0.25, 3))
20 | pgm.add_edge("alpha", "true")
21 | pgm.add_node(daft.Node("shape prior", r"$p(\alpha, \beta)$", -1.25, 3, fixed=True))
22 | pgm.add_edge("shape prior", "alpha")
23 | pgm.add_node(daft.Node("gamma", r"$\gamma_m$", 2, 4))
24 | pgm.add_edge("gamma", "obs")
25 | pgm.add_node(daft.Node("gamma prior", r"$p(\gamma)$", -0.25, 4, fixed=True))
26 | pgm.add_edge("gamma prior", "gamma")
27 | pgm.add_node(daft.Node("sigma", r"$\sigma_{\epsilon}$", 3.25, 3, fixed=True))
28 | pgm.add_edge("sigma", "obs")
29 | pgm.add_plate(daft.Plate([0.5, 2.25, 2, 1.25],
30 | label=r"galaxies $n$"))
31 | pgm.add_plate(daft.Plate([0.25, 1.75, 2.5, 2.75],
32 | label=r"patches $m$"))
33 | pgm.render()
34 | pgm.figure.savefig("yike.pdf")
35 | pgm.figure.savefig("yike.png", dpi=150)
36 |
--------------------------------------------------------------------------------
/examples/nogray.py:
--------------------------------------------------------------------------------
1 | """
2 | Alternative Observed Node Styles
3 | ================================
4 |
5 | .. module:: daft
6 |
7 | This model is the same as `the classic `_ model but the
8 | "observed" :class:`Node` is indicated by a double outline instead of shading.
9 | This particular example uses the ``inner`` style but ``outer`` is also an
10 | option for a different look.
11 |
12 | """
13 |
14 | from matplotlib import rc
15 | rc("font", family="serif", size=12)
16 | rc("text", usetex=True)
17 |
18 | import daft
19 |
20 | pgm = daft.PGM([2.3, 2.05], origin=[0.3, 0.3], observed_style="inner")
21 |
22 | # Hierarchical parameters.
23 | pgm.add_node(daft.Node("alpha", r"$\alpha$", 0.5, 2, fixed=True))
24 | pgm.add_node(daft.Node("beta", r"$\beta$", 1.5, 2))
25 |
26 | # Latent variable.
27 | pgm.add_node(daft.Node("w", r"$w_n$", 1, 1))
28 |
29 | # Data.
30 | pgm.add_node(daft.Node("x", r"$x_n$", 2, 1, observed=True))
31 |
32 | # Add in the edges.
33 | pgm.add_edge("alpha", "beta")
34 | pgm.add_edge("beta", "w")
35 | pgm.add_edge("w", "x")
36 | pgm.add_edge("beta", "x")
37 |
38 | # And a plate.
39 | pgm.add_plate(daft.Plate([0.5, 0.5, 2, 1], label=r"$n = 1, \ldots, N$",
40 | shift=-0.1))
41 |
42 | # Render and save.
43 | pgm.render()
44 | pgm.figure.savefig("nogray.pdf")
45 | pgm.figure.savefig("nogray.png", dpi=150)
46 |
--------------------------------------------------------------------------------
/examples/thicklines.py:
--------------------------------------------------------------------------------
1 | """
2 | T-shirt style
3 | =============
4 |
5 | Don't like dainty thin lines? Need to make graphical-model-themed
6 | conference schwag? Then `line_width` is the parameter for you. Also
7 | check out the `preamble` option in the `matplotlib.rc` command.
8 |
9 | """
10 |
11 | from matplotlib import rc
12 | rc("font", family="serif", size=14)
13 | rc("text", usetex=True)
14 | rc('text.latex',
15 | preamble="\usepackage{amssymb}\usepackage{amsmath}\usepackage{mathrsfs}")
16 |
17 | import daft
18 |
19 | # Instantiate the PGM.
20 | pgm = daft.PGM([2.3, 2.05], origin=[0.3, 0.3], line_width=2.5)
21 |
22 | # Hierarchical parameters.
23 | pgm.add_node(daft.Node("alpha", r"$\boldsymbol{\alpha}$", 0.5, 2, fixed=True))
24 | pgm.add_node(daft.Node("beta", r"$\boldsymbol{\beta}$", 1.5, 2))
25 |
26 | # Latent variable.
27 | pgm.add_node(daft.Node("w", r"$\boldsymbol{w_n}$", 1, 1))
28 |
29 | # Data.
30 | pgm.add_node(daft.Node("x", r"$\boldsymbol{x_n}$", 2, 1, observed=True))
31 |
32 | # Add in the edges.
33 | pgm.add_edge("alpha", "beta")
34 | pgm.add_edge("beta", "w")
35 | pgm.add_edge("w", "x")
36 | pgm.add_edge("beta", "x")
37 |
38 | # And a plate.
39 | pgm.add_plate(daft.Plate([0.5, 0.5, 2, 1], label=r"$\boldsymbol{n = 1, \cdots, N}$",
40 | shift=-0.1))
41 |
42 | # Render and save.
43 | pgm.render()
44 | pgm.figure.savefig("thicklines.pdf")
45 | pgm.figure.savefig("thicklines.png", dpi=150)
46 |
--------------------------------------------------------------------------------
/setup.py:
--------------------------------------------------------------------------------
1 | #!/usr/bin/env python
2 |
3 |
4 | try:
5 | from setuptools import setup, Extension
6 | setup, Extension
7 | except ImportError:
8 | from distutils.core import setup
9 | from distutils.extension import Extension
10 | setup, Extension
11 |
12 | import os
13 | import re
14 | import sys
15 |
16 | if sys.argv[-1] == "publish":
17 | os.system("python setup.py sdist upload")
18 | sys.exit()
19 |
20 | vre = re.compile("__version__ = \"(.*?)\"")
21 | m = open(os.path.join(os.path.dirname(os.path.abspath(__file__)),
22 | "daft.py")).read()
23 | version = vre.findall(m)[0]
24 |
25 |
26 | setup(
27 | name="daft",
28 | version=version,
29 | description="PGM rendering at its finest.",
30 | long_description=open("README.rst").read(),
31 | author="David W. Hogg & Daniel Foreman-Mackey",
32 | author_email="danfm@nyu.edu",
33 | url="http://daft-pgm.org",
34 | py_modules=["daft"],
35 | package_data={"": ["LICENSE.rst"]},
36 | include_package_data=True,
37 | install_requires=[
38 | "numpy",
39 | "matplotlib"
40 | ],
41 | classifiers=[
42 | "Development Status :: 3 - Alpha",
43 | "Intended Audience :: Developers",
44 | "Intended Audience :: Science/Research",
45 | "License :: OSI Approved :: MIT License",
46 | "Operating System :: OS Independent",
47 | "Programming Language :: Python",
48 | ],
49 | )
50 |
--------------------------------------------------------------------------------
/docs/examples/classic.rst:
--------------------------------------------------------------------------------
1 | .. _classic:
2 |
3 |
4 | The Quintessential PGM
5 | ======================
6 |
7 | .. figure:: /_static/examples/classic.png
8 |
9 |
10 | The Quintessential PGM
11 | ======================
12 |
13 | This is a demonstration of a very common structure found in graphical models.
14 | It has been rendered using Daft's default settings for all the parameters
15 | and it shows off how much beauty is baked in by default.
16 |
17 |
18 |
19 | ::
20 |
21 |
22 | from matplotlib import rc
23 | rc("font", family="serif", size=12)
24 | rc("text", usetex=True)
25 |
26 | import daft
27 |
28 | # Instantiate the PGM.
29 | pgm = daft.PGM([2.3, 2.05], origin=[0.3, 0.3])
30 |
31 | # Hierarchical parameters.
32 | pgm.add_node(daft.Node("alpha", r"$\alpha$", 0.5, 2, fixed=True))
33 | pgm.add_node(daft.Node("beta", r"$\beta$", 1.5, 2))
34 |
35 | # Latent variable.
36 | pgm.add_node(daft.Node("w", r"$w_n$", 1, 1))
37 |
38 | # Data.
39 | pgm.add_node(daft.Node("x", r"$x_n$", 2, 1, observed=True))
40 |
41 | # Add in the edges.
42 | pgm.add_edge("alpha", "beta")
43 | pgm.add_edge("beta", "w")
44 | pgm.add_edge("w", "x")
45 | pgm.add_edge("beta", "x")
46 |
47 | # And a plate.
48 | pgm.add_plate(daft.Plate([0.5, 0.5, 2, 1], label=r"$n = 1, \cdots, N$",
49 | shift=-0.1))
50 |
51 | # Render and save.
52 | pgm.render()
53 | pgm.figure.savefig("classic.pdf")
54 | pgm.figure.savefig("classic.png", dpi=150)
55 |
56 |
57 |
--------------------------------------------------------------------------------
/examples/weaklensing.py:
--------------------------------------------------------------------------------
1 | """
2 | A model for weak lensing
3 | ========================
4 |
5 | This is (**Daft** co-author) Hogg's model for the obsevational
6 | cosmology method known as *weak gravitational lensing*, if that method
7 | were properly probabilistic (which it usually isn't). Hogg put the
8 | model here for one very important reason: *Because he can*. Oh, and
9 | it demonstrates that you can represent non-trivial scientific projects
10 | with **Daft**.
11 |
12 | """
13 |
14 | from matplotlib import rc
15 | rc("font", family="serif", size=12)
16 | rc("text", usetex=True)
17 |
18 | import daft
19 |
20 | pgm = daft.PGM([4.7, 2.35], origin=[-1.35, 2.2])
21 | pgm.add_node(daft.Node("Omega", r"$\Omega$", -1, 4))
22 | pgm.add_node(daft.Node("gamma", r"$\gamma$", 0, 4))
23 | pgm.add_node(daft.Node("obs", r"$\epsilon^{\mathrm{obs}}_n$", 1, 4,
24 | observed=True))
25 | pgm.add_node(daft.Node("alpha", r"$\alpha$", 3, 4))
26 | pgm.add_node(daft.Node("true", r"$\epsilon^{\mathrm{true}}_n$", 2, 4))
27 | pgm.add_node(daft.Node("sigma", r"$\sigma_n$", 1, 3))
28 | pgm.add_node(daft.Node("Sigma", r"$\Sigma$", 0, 3))
29 | pgm.add_node(daft.Node("x", r"$x_n$", 2, 3, observed=True))
30 | pgm.add_plate(daft.Plate([0.5, 2.25, 2, 2.25],
31 | label=r"galaxies $n$"))
32 | pgm.add_edge("Omega", "gamma")
33 | pgm.add_edge("gamma", "obs")
34 | pgm.add_edge("alpha", "true")
35 | pgm.add_edge("true", "obs")
36 | pgm.add_edge("x", "obs")
37 | pgm.add_edge("Sigma", "sigma")
38 | pgm.add_edge("sigma", "obs")
39 | pgm.render()
40 | pgm.figure.savefig("weaklensing.pdf")
41 | pgm.figure.savefig("weaklensing.png", dpi=150)
42 |
--------------------------------------------------------------------------------
/docs/examples/nogray.rst:
--------------------------------------------------------------------------------
1 | .. _nogray:
2 |
3 |
4 | Alternative Observed Node Styles
5 | ================================
6 |
7 | .. figure:: /_static/examples/nogray.png
8 |
9 |
10 | Alternative Observed Node Styles
11 | ================================
12 |
13 | .. module:: daft
14 |
15 | This model is the same as `the classic `_ model but the
16 | "observed" :class:`Node` is indicated by a double outline instead of shading.
17 | This particular example uses the ``inner`` style but ``outer`` is also an
18 | option for a different look.
19 |
20 |
21 |
22 | ::
23 |
24 |
25 | from matplotlib import rc
26 | rc("font", family="serif", size=12)
27 | rc("text", usetex=True)
28 |
29 | import daft
30 |
31 | pgm = daft.PGM([2.3, 2.05], origin=[0.3, 0.3], observed_style="inner")
32 |
33 | # Hierarchical parameters.
34 | pgm.add_node(daft.Node("alpha", r"$\alpha$", 0.5, 2, fixed=True))
35 | pgm.add_node(daft.Node("beta", r"$\beta$", 1.5, 2))
36 |
37 | # Latent variable.
38 | pgm.add_node(daft.Node("w", r"$w_n$", 1, 1))
39 |
40 | # Data.
41 | pgm.add_node(daft.Node("x", r"$x_n$", 2, 1, observed=True))
42 |
43 | # Add in the edges.
44 | pgm.add_edge("alpha", "beta")
45 | pgm.add_edge("beta", "w")
46 | pgm.add_edge("w", "x")
47 | pgm.add_edge("beta", "x")
48 |
49 | # And a plate.
50 | pgm.add_plate(daft.Plate([0.5, 0.5, 2, 1], label=r"$n = 1, \ldots, N$",
51 | shift=-0.1))
52 |
53 | # Render and save.
54 | pgm.render()
55 | pgm.figure.savefig("nogray.pdf")
56 | pgm.figure.savefig("nogray.png", dpi=150)
57 |
58 |
59 |
--------------------------------------------------------------------------------
/examples/huey_p_newton.py:
--------------------------------------------------------------------------------
1 | """
2 | n-body particle inference
3 | =========================
4 |
5 | Dude.
6 | """
7 |
8 | from matplotlib import rc
9 | rc("font", family="serif", size=12)
10 | rc("text", usetex=True)
11 |
12 | import daft
13 |
14 | pgm = daft.PGM([5.4, 2.0], origin=[0.65, 0.35])
15 |
16 | kx, ky = 1.5, 1.
17 | nx, ny = kx + 3., ky + 0.
18 | hx, hy, dhx = kx - 0.5, ky + 1., 1.
19 |
20 | pgm.add_node(daft.Node("dyn", r"$\theta_{\mathrm{dyn}}$", hx + 0. * dhx, hy + 0.))
21 | pgm.add_node(daft.Node("ic", r"$\theta_{\mathrm{I.C.}}$", hx + 1. * dhx, hy + 0.))
22 | pgm.add_node(daft.Node("sun", r"$\theta_{\odot}$", hx + 2. * dhx, hy + 0.))
23 | pgm.add_node(daft.Node("bg", r"$\theta_{\mathrm{bg}}$", hx + 3. * dhx, hy + 0.))
24 | pgm.add_node(daft.Node("Sigma", r"$\Sigma^2$", hx + 4. * dhx, hy + 0.))
25 |
26 | pgm.add_plate(daft.Plate([kx - 0.5, ky - 0.6, 2., 1.1], label=r"model points $k$"))
27 | pgm.add_node(daft.Node("xk", r"$x_k$", kx + 0., ky + 0.))
28 | pgm.add_edge("dyn", "xk")
29 | pgm.add_edge("ic", "xk")
30 | pgm.add_node(daft.Node("yk", r"$y_k$", kx + 1., ky + 0.))
31 | pgm.add_edge("sun", "yk")
32 | pgm.add_edge("xk", "yk")
33 |
34 | pgm.add_plate(daft.Plate([nx - 0.5, ny - 0.6, 2., 1.1], label=r"data points $n$"))
35 | pgm.add_node(daft.Node("sigman", r"$\sigma^2_n$", nx + 1., ny + 0., observed=True))
36 | pgm.add_node(daft.Node("Yn", r"$Y_n$", nx + 0., ny + 0., observed=True))
37 | pgm.add_edge("bg", "Yn")
38 | pgm.add_edge("Sigma", "Yn")
39 | pgm.add_edge("Sigma", "Yn")
40 | pgm.add_edge("yk", "Yn")
41 | pgm.add_edge("sigman", "Yn")
42 |
43 | # Render and save.
44 | pgm.render()
45 | pgm.figure.savefig("huey_p_newton.pdf")
46 | pgm.figure.savefig("huey_p_newton.png", dpi=150)
47 |
--------------------------------------------------------------------------------
/docs/_themes/daft/search.html:
--------------------------------------------------------------------------------
1 | {% extends "layout.html" %}
2 |
3 | {% set title = _('Search') %}
4 |
5 | {% set script_files = script_files + ['_static/searchtools.js'] %}
6 |
7 | {% block extrahead %}
8 |
11 | {{ super() }}
12 | {% endblock %}
13 |
14 | {% block body %}
15 | {{ _('Search') }}
16 |
17 |
18 |
19 | {% trans %}Please activate JavaScript to enable the search
20 | functionality.{% endtrans %}
21 |
22 |
24 | {% trans %}From here you can search these documents. Enter your search
25 | words into the box below. Note that the search
26 | function will automatically search for all of the words. Pages
27 | containing fewer words won't appear in the result list.{% endtrans %}
28 |
29 |
33 | {% if search_performed %}
34 | {{ _('Search Results') }}
35 | {% if not search_results %}
36 | {{ _('Your search did not match any results.') }}
37 | {% endif %}
38 | {% endif %}
39 |
40 | {% if search_results %}
41 |
42 | {% for href, caption, context in search_results %}
43 | {{ caption }}
44 | {{ context|e }}
45 |
48 | {% endif %}
49 |
21 |
22 |
{{ theme_tagline }}
23 |
37 |
41 |
42 |
55 |
56 | {%- endblock %}
57 |
--------------------------------------------------------------------------------
/docs/examples/weaklensing.rst:
--------------------------------------------------------------------------------
1 | .. _weaklensing:
2 |
3 |
4 | A model for weak lensing
5 | ========================
6 |
7 | .. figure:: /_static/examples/weaklensing.png
8 |
9 |
10 | A model for weak lensing
11 | ========================
12 |
13 | This is (**Daft** co-author) Hogg's model for the obsevational
14 | cosmology method known as *weak gravitational lensing*, if that method
15 | were properly probabilistic (which it usually isn't). Hogg put the
16 | model here for one very important reason: *Because he can*. Oh, and
17 | it demonstrates that you can represent non-trivial scientific projects
18 | with **Daft**.
19 |
20 |
21 |
22 | ::
23 |
24 |
25 | from matplotlib import rc
26 | rc("font", family="serif", size=12)
27 | rc("text", usetex=True)
28 | rc("./weaklensing.tex")
29 |
30 | import daft
31 |
32 | pgm = daft.PGM([4.7, 2.35], origin=[-1.35, 2.2])
33 | pgm.add_node(daft.Node("Omega", r"$\Omega$", -1, 4))
34 | pgm.add_node(daft.Node("gamma", r"$\gamma$", 0, 4))
35 | pgm.add_node(daft.Node("obs", r"$\epsilon^{\mathrm{obs}}_n$", 1, 4, observed=True))
36 | pgm.add_node(daft.Node("alpha", r"$\alpha$", 3, 4))
37 | pgm.add_node(daft.Node("true", r"$\epsilon^{\mathrm{true}}_n$", 2, 4))
38 | pgm.add_node(daft.Node("sigma", r"$\sigma_n$", 1, 3))
39 | pgm.add_node(daft.Node("Sigma", r"$\Sigma$", 0, 3))
40 | pgm.add_node(daft.Node("x", r"$x_n$", 2, 3, observed=True))
41 | pgm.add_plate(daft.Plate([0.5, 2.25, 2, 2.25],
42 | label=r"galaxies $n$"))
43 | pgm.add_edge("Omega", "gamma")
44 | pgm.add_edge("gamma", "obs")
45 | pgm.add_edge("alpha", "true")
46 | pgm.add_edge("true", "obs")
47 | pgm.add_edge("x", "obs")
48 | pgm.add_edge("Sigma", "sigma")
49 | pgm.add_edge("sigma", "obs")
50 | pgm.render()
51 | pgm.figure.savefig("weaklensing.pdf")
52 | pgm.figure.savefig("weaklensing.png", dpi=150)
53 |
54 |
55 |
--------------------------------------------------------------------------------
/docs/examples/recursive.rst:
--------------------------------------------------------------------------------
1 | .. _recursive:
2 |
3 |
4 | Recursively generated graph
5 | ===========================
6 |
7 | .. figure:: /_static/examples/recursive.png
8 |
9 |
10 | Recursively generated graph
11 | ===========================
12 |
13 | **Daft** is Python, so you can do anything Python can do. This graph is
14 | generated by recursive code.
15 |
16 |
17 |
18 | ::
19 |
20 |
21 | from matplotlib import rc
22 | rc("font", family="serif", size=12)
23 | rc("text", usetex=True)
24 |
25 | import daft
26 |
27 | def recurse(pgm, nodename, level, c):
28 | if level > 4:
29 | return nodename
30 | r = c / 2
31 | r1nodename = "r{0:02d}{1:04d}".format(level, r)
32 | if 2 * r == c:
33 | print("adding {0}".format(r1nodename))
34 | pgm.add_node(daft.Node(r1nodename, r"reduce",
35 | 2 ** level * (r + 0.5) - 0.5,
36 | 3 - 0.7 * level, aspect=1.9))
37 | pgm.add_edge(nodename, r1nodename)
38 | if 2 * r == c:
39 | return recurse(pgm, r1nodename, level + 1, r)
40 |
41 | pgm = daft.PGM([16.2, 8], origin=[-0.6, -1.5])
42 |
43 | pgm.add_node(daft.Node("query", r'\texttt{"kittens?"}', 3, 6., aspect=3.,
44 | plot_params={"ec": "none"}))
45 | pgm.add_node(daft.Node("input", r"input", 7.5, 6., aspect=3.))
46 | pgm.add_edge("query", "input")
47 |
48 | for c in range(16):
49 | nodename = "map {0:02d}".format(c)
50 | pgm.add_node(daft.Node(nodename, str(nodename), c, 3., aspect=1.9))
51 | pgm.add_edge("input", nodename)
52 | level = 1
53 | recurse(pgm, nodename, level, c)
54 |
55 | pgm.add_node(daft.Node("output", r"output", 7.5, -1., aspect=3.))
56 | pgm.add_edge("r040000", "output")
57 | pgm.add_node(daft.Node("answer", r'\texttt{"http://dwh.gg/"}', 12., -1.,
58 | aspect=4.5, plot_params={"ec": "none"}))
59 | pgm.add_edge("output", "answer")
60 |
61 | pgm.render()
62 | pgm.figure.savefig("recursive.pdf")
63 | pgm.figure.savefig("recursive.png", dpi=200)
64 |
65 |
66 |
--------------------------------------------------------------------------------
/docs/examples/exoplanets.rst:
--------------------------------------------------------------------------------
1 | .. _exoplanets:
2 |
3 |
4 | The Fergus model of exoplanet detection
5 | =======================================
6 |
7 | .. figure:: /_static/examples/exoplanets.png
8 |
9 |
10 | The Fergus model of exoplanet detection
11 | =======================================
12 |
13 | Besides being generally awesome, this example also demonstrates how you can
14 | color the nodes and add arbitrary labels to the figure.
15 |
16 |
17 |
18 | ::
19 |
20 |
21 | from matplotlib import rc
22 | rc("font", family="serif", size=12)
23 | rc("text", usetex=True)
24 |
25 | import daft
26 |
27 | # Colors.
28 | p_color = {"ec": "#46a546"}
29 | s_color = {"ec": "#f89406"}
30 |
31 | pgm = daft.PGM([3.6, 3.5], origin=[0.7, 0])
32 |
33 | n = daft.Node("phi", r"$\phi$", 1, 3, plot_params=s_color)
34 | n.va = "baseline"
35 | pgm.add_node(n)
36 | pgm.add_node(daft.Node("speckle_coeff", r"$z_i$", 2, 3, plot_params=s_color))
37 | pgm.add_node(daft.Node("speckle_img", r"$x_i$", 2, 2, plot_params=s_color))
38 |
39 | pgm.add_node(daft.Node("spec", r"$s$", 4, 3, plot_params=p_color))
40 | pgm.add_node(daft.Node("shape", r"$g$", 4, 2, plot_params=p_color))
41 | pgm.add_node(daft.Node("planet_pos", r"$\mu_i$", 3, 3, plot_params=p_color))
42 | pgm.add_node(daft.Node("planet_img", r"$p_i$", 3, 2, plot_params=p_color))
43 |
44 | pgm.add_node(daft.Node("pixels", r"$y_i ^j$", 2.5, 1, observed=True))
45 |
46 | # Edges.
47 | pgm.add_edge("phi", "speckle_coeff")
48 | pgm.add_edge("speckle_coeff", "speckle_img")
49 | pgm.add_edge("speckle_img", "pixels")
50 |
51 | pgm.add_edge("spec", "planet_img")
52 | pgm.add_edge("shape", "planet_img")
53 | pgm.add_edge("planet_pos", "planet_img")
54 | pgm.add_edge("planet_img", "pixels")
55 |
56 | # And a plate.
57 | pgm.add_plate(daft.Plate([1.5, 0.2, 2, 3.2], label=r"exposure $i$",
58 | shift=-0.1))
59 | pgm.add_plate(daft.Plate([2, 0.5, 1, 1], label=r"pixel $j$",
60 | shift=-0.1))
61 |
62 | # Render and save.
63 | pgm.render()
64 | pgm.figure.savefig("exoplanets.pdf")
65 | pgm.figure.savefig("exoplanets.png", dpi=150)
66 |
67 |
68 |
--------------------------------------------------------------------------------
/docs/index.rst:
--------------------------------------------------------------------------------
1 | Daft
2 | ====
3 |
4 | .. raw:: html
5 |
6 |
7 |
10 |
11 |
12 |
15 |
16 |
17 | Summary
18 | -------
19 |
20 | **Daft** is a Python package that uses `matplotlib `_:
34 |
35 | ::
36 |
37 | pip install daft
38 |
39 | Otherwise, you can download the source (`tar
40 | `_, `zip
41 | `_) and run:
42 |
43 | ::
44 |
45 | python setup.py install
46 |
47 | in the root directory.
48 |
49 | Daft only depends on `matplotlib `_. These are standard components of the
51 | scientific Python stack but if you don't already have them installed ``pip``
52 | will try to install them for you but sometimes it's easier to do that part
53 | yourself.
54 |
55 |
56 | Issues
57 | ------
58 |
59 | If you have any problems or questions, `open an "issue" on Github
60 | `_.
61 |
62 |
63 | Authors & Contributions
64 | -----------------------
65 |
66 | **Daft** is being developed and supported by `Dan Foreman-Mackey
67 | `_ and `David W. Hogg `_.
68 |
69 | For the hackers in the house, development happens on `Github
70 | `_ and we welcome pull requests. In particular,
71 | we'd love to see examples of how you're using Daft in your work.
72 |
73 |
74 | License
75 | -------
76 |
77 | *Copyright 2012 Dan Foreman-Mackey, David W. Hogg, and contributors.*
78 |
79 | **Daft** is free software made available under the *MIT License*. For details
80 | see `the LICENSE file `_.
81 |
82 | If you use Daft in academic projects, acknowledgements are greatly
83 | appreciated.
84 |
85 |
86 | API
87 | ---
88 |
89 | .. toctree::
90 | :maxdepth: 2
91 |
92 | api
93 |
--------------------------------------------------------------------------------
/examples/galex.py:
--------------------------------------------------------------------------------
1 | """
2 | The GALEX Photon Catalog
3 | ========================
4 |
5 | This is the Hogg \& Schiminovich model for how photons turn into
6 | counts in the GALEX satellite data stream. Note the use of relative
7 | positioning.
8 |
9 | """
10 |
11 | from matplotlib import rc
12 | rc("font", family="serif", size=12)
13 | rc("text", usetex=True)
14 | import daft
15 | pgm = daft.PGM([5.4, 5.4], origin=[1.2, 1.2])
16 | wide = 1.5
17 | verywide = 1.5 * wide
18 | dy = 0.75
19 |
20 | # electrons
21 | el_x, el_y = 2., 2.
22 | pgm.add_plate(daft.Plate([el_x - 0.6, el_y - 0.6, 2.2, 2 * dy + 0.3], label="electrons $i$"))
23 | pgm.add_node(daft.Node("xabc", r"xa$_i$,xabc$_i$,ya$_i$,\textit{etc}", el_x + 0.5, el_y + 0 * dy, aspect=2.3 * wide, observed=True))
24 | pgm.add_node(daft.Node("xyti", r"$x_i,y_i,t_i$", el_x + 1., el_y + 1 * dy, aspect=wide))
25 | pgm.add_edge("xyti", "xabc")
26 |
27 | # intensity fields
28 | ph_x, ph_y = el_x + 2.5, el_y + 3 * dy
29 | pgm.add_node(daft.Node("Ixyt", r"$I_{\nu}(x,y,t)$", ph_x, ph_y, aspect=verywide))
30 | pgm.add_edge("Ixyt", "xyti")
31 | pgm.add_node(daft.Node("Ixnt", r"$I_{\nu}(\xi,\eta,t)$", ph_x, ph_y + 1 * dy, aspect=verywide))
32 | pgm.add_edge("Ixnt", "Ixyt")
33 | pgm.add_node(daft.Node("Iadt", r"$I_{\nu}(\alpha,\delta,t)$", ph_x, ph_y + 2 * dy, aspect=verywide))
34 | pgm.add_edge("Iadt", "Ixnt")
35 |
36 | # s/c
37 | sc_x, sc_y = ph_x + 1.5, ph_y - 1.5 * dy
38 | pgm.add_node(daft.Node("dark", r"dark", sc_x, sc_y - 1 * dy, aspect=wide))
39 | pgm.add_edge("dark", "xyti")
40 | pgm.add_node(daft.Node("flat", r"flat", sc_x, sc_y, aspect=wide))
41 | pgm.add_edge("flat", "xyti")
42 | pgm.add_node(daft.Node("att", r"att", sc_x, sc_y + 3 * dy))
43 | pgm.add_edge("att", "Ixnt")
44 | pgm.add_node(daft.Node("optics", r"optics", sc_x, sc_y + 2 * dy, aspect=wide))
45 | pgm.add_edge("optics", "Ixyt")
46 | pgm.add_node(daft.Node("psf", r"psf", sc_x, sc_y + 1 * dy))
47 | pgm.add_edge("psf", "xyti")
48 | pgm.add_node(daft.Node("fee", r"f.e.e.", sc_x, sc_y - 2 * dy, aspect=wide))
49 | pgm.add_edge("fee", "xabc")
50 |
51 | # sky
52 | pgm.add_node(daft.Node("sky", r"sky", sc_x, sc_y + 4 * dy))
53 | pgm.add_edge("sky", "Iadt")
54 |
55 | # stars
56 | star_x, star_y = el_x, el_y + 4 * dy
57 | pgm.add_plate(daft.Plate([star_x - 0.6, star_y - 0.6, 2.2, 2 * dy + 0.3], label="stars $n$"))
58 | pgm.add_node(daft.Node("star adt", r"$I_{\nu,n}(\alpha,\delta,t)$", star_x + 0.5, star_y + 1 * dy, aspect=verywide))
59 | pgm.add_edge("star adt", "Iadt")
60 | pgm.add_node(daft.Node("star L", r"$L_{\nu,n}(t)$", star_x + 1, star_y, aspect=wide))
61 | pgm.add_edge("star L", "star adt")
62 | pgm.add_node(daft.Node("star pos", r"$\vec{x_n}$", star_x, star_y))
63 | pgm.add_edge("star pos", "star adt")
64 |
65 | # done
66 | pgm.render()
67 | pgm.figure.savefig("galex.pdf")
68 | pgm.figure.savefig("galex.png", dpi=150)
69 |
--------------------------------------------------------------------------------
/docs/gen_example.py:
--------------------------------------------------------------------------------
1 | #!/usr/bin/env python
2 |
3 | from __future__ import print_function
4 |
5 | import os
6 | import sys
7 | import json
8 | from subprocess import check_call
9 |
10 |
11 | this_path = os.path.dirname(os.path.abspath(__file__))
12 | daft_path = os.path.dirname(this_path)
13 | sys.path.insert(0, daft_path)
14 |
15 | example_dir = os.path.join(daft_path, "examples")
16 | out_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "examples")
17 | img_out_dir = os.path.join(this_path, "_static", "examples")
18 |
19 | try:
20 | os.makedirs(out_dir)
21 | except os.error:
22 | pass
23 |
24 | try:
25 | os.makedirs(img_out_dir)
26 | except os.error:
27 | pass
28 |
29 | example_template = """.. _{example}:
30 |
31 | {title}
32 |
33 | .. figure:: /_static/examples/{example}.png
34 |
35 | {doc}
36 |
37 | ::
38 |
39 | {src}
40 |
41 | """
42 |
43 |
44 | def main(fn, thumb_info):
45 | # Run the code.
46 | pyfn = os.path.join(example_dir, fn + ".py")
47 | src = open(pyfn).read()
48 | print("Executing: " + pyfn)
49 |
50 | ns = {}
51 | exec src in ns
52 | pgm = ns["pgm"]
53 |
54 | # Generate the RST source file.
55 | src = src.split("\n")
56 | if ns["__doc__"] is None:
57 | title = fn.title() + "\n" + "=" * len(fn)
58 | doc = ""
59 | else:
60 | doc = ns["__doc__"].split("\n")
61 | title = "\n".join(doc[:3])
62 | doc = "\n".join(doc)
63 | src = src[len(ns["__doc__"].split("\n")):]
64 |
65 | fmt_src = "\n".join([" " + l for l in src])
66 | img_path = os.path.join(img_out_dir, fn + ".png")
67 | thumb_path = os.path.join(img_out_dir, fn + "-thumb.png")
68 |
69 | rst = example_template.format(title=title, doc=doc, example=fn,
70 | src=fmt_src, img_path=img_path)
71 |
72 | # Write the RST file.
73 | rstfn = os.path.join(out_dir, fn + ".rst")
74 | print("Writing: " + rstfn)
75 | with open(rstfn, "w") as f:
76 | f.write(rst)
77 |
78 | # Remove the generated plots.
79 | try:
80 | os.remove(fn + ".png")
81 | except os.error:
82 | pass
83 | try:
84 | os.remove(fn + ".pdf")
85 | except os.error:
86 | pass
87 |
88 | # Save the new figure.
89 | print("Saving: " + img_path)
90 | pgm.figure.savefig(img_path, dpi=150)
91 |
92 | # Crop the thumbnail.
93 | cmd = " ".join(["convert",
94 | "-crop 190x190+{0[0]:d}+{0[1]:d}".format(thumb_info),
95 | img_path, thumb_path])
96 | print(cmd)
97 | check_call(cmd, shell=True)
98 |
99 |
100 | if __name__ == "__main__":
101 | m = json.load(open(os.path.join(this_path, "_static", "examples.json")))
102 | if len(sys.argv) == 1:
103 | # Build all the examples.
104 | argv = m.keys()
105 | else:
106 | argv = sys.argv[1:]
107 |
108 | for k in argv:
109 | assert k in m, "Add {0} to _static/examples.json".format(k)
110 | main(k, m[k])
111 |
--------------------------------------------------------------------------------
/docs/_themes/daft/static/daft.css:
--------------------------------------------------------------------------------
1 | @import url("normalize.css");
2 | @import url(http://fonts.googleapis.com/css?family=Lato:100,300,700,300italic);
3 | @import url(http://fonts.googleapis.com/css?family=Source+Code+Pro:300,400,600);
4 |
5 | body {
6 | font-family: Lato, "Helvetica Neue", Helvetica, sans-serif;
7 | font-weight: 300;
8 | line-height: 1.55;
9 | font-size: 16px;
10 | color: #333;
11 |
12 | background: #dbe0df;
13 | background: -moz-linear-gradient(left, #dbe0df 0%, #ffffff 50%, #dbe0df 100%);
14 | background: -webkit-gradient(linear, left top, right top, color-stop(0%,#dbe0df), color-stop(50%,#ffffff), color-stop(100%,#dbe0df));
15 | background: -webkit-linear-gradient(left, #dbe0df 0%,#ffffff 50%,#dbe0df 100%);
16 | background: -o-linear-gradient(left, #dbe0df 0%,#ffffff 50%,#dbe0df 100%);
17 | background: -ms-linear-gradient(left, #dbe0df 0%,#ffffff 50%,#dbe0df 100%);
18 | background: linear-gradient(to right, #dbe0df 0%,#ffffff 50%,#dbe0df 100%);
19 | filter: progid:DXImageTransform.Microsoft.gradient( startColorstr='#dbe0df', endColorstr='#dbe0df',GradientType=1 );
20 | }
21 |
22 | a {
23 | color: #383;
24 | text-decoration: underline;
25 | }
26 |
27 | a:hover {
28 | color: #5a5;
29 | }
30 |
31 | a.headerlink {
32 | padding-left: 10px;
33 | font-size: 80%;
34 | text-decoration: none;
35 | color: #bbb;
36 | }
37 |
38 | a.headerlink:hover {
39 | color: #aaa;
40 | }
41 |
42 | .pre, pre {
43 | font-size: 14px;
44 | font-weight: 400;
45 | font-family: "Source Code Pro", Courier, monospace;
46 | }
47 |
48 | .document, .footer, .related {
49 | width: 600px;
50 | margin: 0 auto;
51 | }
52 |
53 | .body:first-child h1 {
54 | display: none;
55 | }
56 |
57 | .main-logo {
58 | padding: 30px 0 10px;
59 | border-bottom: 1px dashed #e1e1e1;
60 | text-align: center;
61 | }
62 |
63 | .main-logo h1 {
64 | font-size: 48px;
65 | font-weight: 300;
66 | line-height: 0;
67 | text-transform: uppercase;
68 | }
69 |
70 | .main-logo a, .main-logo a:hover {
71 | color: #333;
72 | text-decoration: none;
73 | }
74 |
75 | .main-logo h2 {
76 | color: #888;
77 | font-size: 16px;
78 | font-weight: 300;
79 | line-height: 1;
80 | text-transform: uppercase;
81 | }
82 |
83 | #examples h2 {
84 | display: none;
85 | }
86 |
87 | #examples {
88 | line-height: 0;
89 | margin-top: 5px;
90 | }
91 |
92 | #examples img {
93 | border: 1px solid #ccc;
94 | margin: 5px 0 5px 0;
95 | }
96 |
97 | #examples a:not(:nth-of-type(3n)) img {
98 | margin-right: 8px;
99 | }
100 |
101 | #summary h2 {
102 | display: none;
103 | }
104 |
105 | .related {
106 | margin: 10px 0 0;
107 | padding: 10px 0 0;
108 | border-top: 1px dashed #e1e1e1;
109 | }
110 |
111 | .related .previous {
112 | float: left;
113 | }
114 |
115 | .related .next {
116 | float: right;
117 | }
118 |
119 | .related:after {
120 | content: ".";
121 | display: block;
122 | clear: both;
123 | visibility: hidden;
124 | line-height: 0;
125 | height: 0;
126 | }
127 |
128 | #searchbox {
129 | margin: 10px 0;
130 | text-align: center;
131 | }
132 |
133 | input.searchfield {
134 | border: 1px solid #999;
135 | -moz-border-radius: 15px;
136 | border-radius: 15px;
137 | padding: 3px 10px;
138 | font-weight: normal;
139 | }
140 |
141 | input.searchfield:focus {
142 | outline: 0;
143 | outline: thin dotted \9;
144 | border-color: #ddd;
145 | -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 3px #5a5;
146 | -moz-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 3px #5a5;
147 | box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 3px #5a5;
148 | }
149 |
150 | .footer {
151 | text-align: center;
152 | font-size: 11px;
153 | padding: 20px 0;
154 | }
155 |
156 | .figure {
157 | background: white;
158 | text-align: center;
159 | padding: 15px;
160 | margin: 15px 0;
161 | border: 1px solid #DDD;
162 | overflow: auto;
163 | }
164 |
165 | /* API */
166 |
167 | .field-body {
168 | margin: 0;
169 | padding: 0;
170 | padding-left: 10px;
171 | }
172 |
173 | .field-body ul {
174 | margin: 0;
175 | padding: 0;
176 | list-style: none;
177 | }
178 |
179 | .field-body ul li {
180 | margin: 0;
181 | padding: 0;
182 | }
183 |
--------------------------------------------------------------------------------
/docs/Makefile:
--------------------------------------------------------------------------------
1 | # Makefile for Sphinx documentation
2 | #
3 |
4 | # You can set these variables from the command line.
5 | SPHINXOPTS =
6 | SPHINXBUILD = sphinx-build
7 | PAPER =
8 | BUILDDIR = _build
9 |
10 | # Internal variables.
11 | PAPEROPT_a4 = -D latex_paper_size=a4
12 | PAPEROPT_letter = -D latex_paper_size=letter
13 | ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
14 | # the i18n builder cannot share the environment and doctrees with the others
15 | I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
16 |
17 | .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
18 |
19 | help:
20 | @echo "Please use \`make ' where is one of"
21 | @echo " html to make standalone HTML files"
22 | @echo " dirhtml to make HTML files named index.html in directories"
23 | @echo " singlehtml to make a single large HTML file"
24 | @echo " pickle to make pickle files"
25 | @echo " json to make JSON files"
26 | @echo " htmlhelp to make HTML files and a HTML help project"
27 | @echo " qthelp to make HTML files and a qthelp project"
28 | @echo " devhelp to make HTML files and a Devhelp project"
29 | @echo " epub to make an epub"
30 | @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
31 | @echo " latexpdf to make LaTeX files and run them through pdflatex"
32 | @echo " text to make text files"
33 | @echo " man to make manual pages"
34 | @echo " texinfo to make Texinfo files"
35 | @echo " info to make Texinfo files and run them through makeinfo"
36 | @echo " gettext to make PO message catalogs"
37 | @echo " changes to make an overview of all changed/added/deprecated items"
38 | @echo " linkcheck to check all external links for integrity"
39 | @echo " doctest to run all doctests embedded in the documentation (if enabled)"
40 |
41 | clean:
42 | -rm -rf $(BUILDDIR)/*
43 |
44 | html:
45 | $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
46 | @echo
47 | @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
48 |
49 | dirhtml:
50 | $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
51 | @echo
52 | @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
53 |
54 | singlehtml:
55 | $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
56 | @echo
57 | @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
58 |
59 | pickle:
60 | $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
61 | @echo
62 | @echo "Build finished; now you can process the pickle files."
63 |
64 | json:
65 | $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
66 | @echo
67 | @echo "Build finished; now you can process the JSON files."
68 |
69 | htmlhelp:
70 | $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
71 | @echo
72 | @echo "Build finished; now you can run HTML Help Workshop with the" \
73 | ".hhp project file in $(BUILDDIR)/htmlhelp."
74 |
75 | qthelp:
76 | $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
77 | @echo
78 | @echo "Build finished; now you can run "qcollectiongenerator" with the" \
79 | ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
80 | @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/Daft.qhcp"
81 | @echo "To view the help file:"
82 | @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Daft.qhc"
83 |
84 | devhelp:
85 | $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
86 | @echo
87 | @echo "Build finished."
88 | @echo "To view the help file:"
89 | @echo "# mkdir -p $$HOME/.local/share/devhelp/Daft"
90 | @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Daft"
91 | @echo "# devhelp"
92 |
93 | epub:
94 | $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
95 | @echo
96 | @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
97 |
98 | latex:
99 | $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
100 | @echo
101 | @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
102 | @echo "Run \`make' in that directory to run these through (pdf)latex" \
103 | "(use \`make latexpdf' here to do that automatically)."
104 |
105 | latexpdf:
106 | $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
107 | @echo "Running LaTeX files through pdflatex..."
108 | $(MAKE) -C $(BUILDDIR)/latex all-pdf
109 | @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
110 |
111 | text:
112 | $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
113 | @echo
114 | @echo "Build finished. The text files are in $(BUILDDIR)/text."
115 |
116 | man:
117 | $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
118 | @echo
119 | @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
120 |
121 | texinfo:
122 | $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
123 | @echo
124 | @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
125 | @echo "Run \`make' in that directory to run these through makeinfo" \
126 | "(use \`make info' here to do that automatically)."
127 |
128 | info:
129 | $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
130 | @echo "Running Texinfo files through makeinfo..."
131 | make -C $(BUILDDIR)/texinfo info
132 | @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
133 |
134 | gettext:
135 | $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
136 | @echo
137 | @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
138 |
139 | changes:
140 | $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
141 | @echo
142 | @echo "The overview file is in $(BUILDDIR)/changes."
143 |
144 | linkcheck:
145 | $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
146 | @echo
147 | @echo "Link check complete; look for any errors in the above output " \
148 | "or in $(BUILDDIR)/linkcheck/output.txt."
149 |
150 | doctest:
151 | $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
152 | @echo "Testing of doctests in the sources finished, look at the " \
153 | "results in $(BUILDDIR)/doctest/output.txt."
154 |
155 | examples: ../examples/*.py _static/examples.json
156 | python gen_example.py
157 |
--------------------------------------------------------------------------------
/docs/conf.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
3 | import os
4 | import sys
5 |
6 | # If extensions (or modules to document with autodoc) are in another directory,
7 | # add these directories to sys.path here. If the directory is relative to the
8 | # documentation root, use os.path.abspath to make it absolute, like shown here.
9 | sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
10 |
11 |
12 | import daft
13 |
14 |
15 | extensions = ["sphinx.ext.autodoc", "sphinx.ext.intersphinx",
16 | "sphinx.ext.mathjax"]
17 |
18 | # Add any paths that contain templates here, relative to this directory.
19 | templates_path = ["_templates"]
20 |
21 | # The suffix of source filenames.
22 | source_suffix = ".rst"
23 |
24 | # The master toctree document.
25 | master_doc = "index"
26 |
27 | # General information about the project.
28 | project = u"Daft"
29 | copyright = u"2012, Dan Foreman-Mackey & David W. Hogg"
30 | version = daft.__version__
31 | release = daft.__version__
32 |
33 | # There are two options for replacing |today|: either, you set today to some
34 | # non-false value, then it is used:
35 | #today = ''
36 | # Else, today_fmt is used as the format for a strftime call.
37 | #today_fmt = '%B %d, %Y'
38 |
39 | # List of patterns, relative to source directory, that match files and
40 | # directories to ignore when looking for source files.
41 | exclude_patterns = ["_build"]
42 |
43 | # If true, '()' will be appended to :func: etc. cross-reference text.
44 | #add_function_parentheses = True
45 |
46 | # If true, the current module name will be prepended to all description
47 | # unit titles (such as .. function::).
48 | #add_module_names = True
49 |
50 | # If true, sectionauthor and moduleauthor directives will be shown in the
51 | # output. They are ignored by default.
52 | #show_authors = False
53 |
54 | # The name of the Pygments (syntax highlighting) style to use.
55 | pygments_style = "sphinx"
56 |
57 | # A list of ignored prefixes for module index sorting.
58 | #modindex_common_prefix = []
59 |
60 | # The theme to use for HTML and HTML Help pages. See the documentation for
61 | # a list of builtin themes.
62 | html_theme = "daft"
63 |
64 | # Theme options are theme-specific and customize the look and feel of a theme
65 | # further. For a list of options available for each theme, see the
66 | # documentation.
67 | html_theme_options = {
68 | "tagline": "Beautifully rendered probabilistic graphical models.",
69 | }
70 |
71 | # Add any paths that contain custom themes here, relative to this directory.
72 | html_theme_path = ["_themes"]
73 |
74 | # The name for this set of Sphinx documents. If None, it defaults to
75 | # " v documentation".
76 | #html_title = None
77 |
78 | # A shorter title for the navigation bar. Default is the same as html_title.
79 | #html_short_title = None
80 |
81 | # The name of an image file (relative to this directory) to place at the top
82 | # of the sidebar.
83 | #html_logo = None
84 |
85 | # The name of an image file (within the static path) to use as favicon of the
86 | # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
87 | # pixels large.
88 | #html_favicon = None
89 |
90 | # Add any paths that contain custom static files (such as style sheets) here,
91 | # relative to this directory. They are copied after the builtin static files,
92 | # so a file named "default.css" will overwrite the builtin "default.css".
93 | html_static_path = ["_static"]
94 |
95 | # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
96 | # using the given strftime format.
97 | #html_last_updated_fmt = '%b %d, %Y'
98 |
99 | # If true, SmartyPants will be used to convert quotes and dashes to
100 | # typographically correct entities.
101 | #html_use_smartypants = True
102 |
103 | # Custom sidebar templates, maps document names to template names.
104 | html_sidebars = {
105 | "**": ["relations.html", "searchbox.html"]
106 | }
107 |
108 | # Additional templates that should be rendered to pages, maps page names to
109 | # template names.
110 | #html_additional_pages = {}
111 |
112 | # If false, no module index is generated.
113 | #html_domain_indices = True
114 |
115 | # If false, no index is generated.
116 | #html_use_index = True
117 |
118 | # If true, the index is split into individual pages for each letter.
119 | #html_split_index = False
120 |
121 | # If true, links to the reST sources are added to the pages.
122 | html_show_sourcelink = False
123 |
124 | # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
125 | #html_show_sphinx = True
126 |
127 | # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
128 | #html_show_copyright = True
129 |
130 | # If true, an OpenSearch description file will be output, and all pages will
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--------------------------------------------------------------------------------
40 |
41 |
42 |
55 |
56 | {%- endblock %}
57 |
--------------------------------------------------------------------------------
/docs/examples/weaklensing.rst:
--------------------------------------------------------------------------------
1 | .. _weaklensing:
2 |
3 |
4 | A model for weak lensing
5 | ========================
6 |
7 | .. figure:: /_static/examples/weaklensing.png
8 |
9 |
10 | A model for weak lensing
11 | ========================
12 |
13 | This is (**Daft** co-author) Hogg's model for the obsevational
14 | cosmology method known as *weak gravitational lensing*, if that method
15 | were properly probabilistic (which it usually isn't). Hogg put the
16 | model here for one very important reason: *Because he can*. Oh, and
17 | it demonstrates that you can represent non-trivial scientific projects
18 | with **Daft**.
19 |
20 |
21 |
22 | ::
23 |
24 |
25 | from matplotlib import rc
26 | rc("font", family="serif", size=12)
27 | rc("text", usetex=True)
28 | rc("./weaklensing.tex")
29 |
30 | import daft
31 |
32 | pgm = daft.PGM([4.7, 2.35], origin=[-1.35, 2.2])
33 | pgm.add_node(daft.Node("Omega", r"$\Omega$", -1, 4))
34 | pgm.add_node(daft.Node("gamma", r"$\gamma$", 0, 4))
35 | pgm.add_node(daft.Node("obs", r"$\epsilon^{\mathrm{obs}}_n$", 1, 4, observed=True))
36 | pgm.add_node(daft.Node("alpha", r"$\alpha$", 3, 4))
37 | pgm.add_node(daft.Node("true", r"$\epsilon^{\mathrm{true}}_n$", 2, 4))
38 | pgm.add_node(daft.Node("sigma", r"$\sigma_n$", 1, 3))
39 | pgm.add_node(daft.Node("Sigma", r"$\Sigma$", 0, 3))
40 | pgm.add_node(daft.Node("x", r"$x_n$", 2, 3, observed=True))
41 | pgm.add_plate(daft.Plate([0.5, 2.25, 2, 2.25],
42 | label=r"galaxies $n$"))
43 | pgm.add_edge("Omega", "gamma")
44 | pgm.add_edge("gamma", "obs")
45 | pgm.add_edge("alpha", "true")
46 | pgm.add_edge("true", "obs")
47 | pgm.add_edge("x", "obs")
48 | pgm.add_edge("Sigma", "sigma")
49 | pgm.add_edge("sigma", "obs")
50 | pgm.render()
51 | pgm.figure.savefig("weaklensing.pdf")
52 | pgm.figure.savefig("weaklensing.png", dpi=150)
53 |
54 |
55 |
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/docs/examples/recursive.rst:
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1 | .. _recursive:
2 |
3 |
4 | Recursively generated graph
5 | ===========================
6 |
7 | .. figure:: /_static/examples/recursive.png
8 |
9 |
10 | Recursively generated graph
11 | ===========================
12 |
13 | **Daft** is Python, so you can do anything Python can do. This graph is
14 | generated by recursive code.
15 |
16 |
17 |
18 | ::
19 |
20 |
21 | from matplotlib import rc
22 | rc("font", family="serif", size=12)
23 | rc("text", usetex=True)
24 |
25 | import daft
26 |
27 | def recurse(pgm, nodename, level, c):
28 | if level > 4:
29 | return nodename
30 | r = c / 2
31 | r1nodename = "r{0:02d}{1:04d}".format(level, r)
32 | if 2 * r == c:
33 | print("adding {0}".format(r1nodename))
34 | pgm.add_node(daft.Node(r1nodename, r"reduce",
35 | 2 ** level * (r + 0.5) - 0.5,
36 | 3 - 0.7 * level, aspect=1.9))
37 | pgm.add_edge(nodename, r1nodename)
38 | if 2 * r == c:
39 | return recurse(pgm, r1nodename, level + 1, r)
40 |
41 | pgm = daft.PGM([16.2, 8], origin=[-0.6, -1.5])
42 |
43 | pgm.add_node(daft.Node("query", r'\texttt{"kittens?"}', 3, 6., aspect=3.,
44 | plot_params={"ec": "none"}))
45 | pgm.add_node(daft.Node("input", r"input", 7.5, 6., aspect=3.))
46 | pgm.add_edge("query", "input")
47 |
48 | for c in range(16):
49 | nodename = "map {0:02d}".format(c)
50 | pgm.add_node(daft.Node(nodename, str(nodename), c, 3., aspect=1.9))
51 | pgm.add_edge("input", nodename)
52 | level = 1
53 | recurse(pgm, nodename, level, c)
54 |
55 | pgm.add_node(daft.Node("output", r"output", 7.5, -1., aspect=3.))
56 | pgm.add_edge("r040000", "output")
57 | pgm.add_node(daft.Node("answer", r'\texttt{"http://dwh.gg/"}', 12., -1.,
58 | aspect=4.5, plot_params={"ec": "none"}))
59 | pgm.add_edge("output", "answer")
60 |
61 | pgm.render()
62 | pgm.figure.savefig("recursive.pdf")
63 | pgm.figure.savefig("recursive.png", dpi=200)
64 |
65 |
66 |
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/docs/examples/exoplanets.rst:
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1 | .. _exoplanets:
2 |
3 |
4 | The Fergus model of exoplanet detection
5 | =======================================
6 |
7 | .. figure:: /_static/examples/exoplanets.png
8 |
9 |
10 | The Fergus model of exoplanet detection
11 | =======================================
12 |
13 | Besides being generally awesome, this example also demonstrates how you can
14 | color the nodes and add arbitrary labels to the figure.
15 |
16 |
17 |
18 | ::
19 |
20 |
21 | from matplotlib import rc
22 | rc("font", family="serif", size=12)
23 | rc("text", usetex=True)
24 |
25 | import daft
26 |
27 | # Colors.
28 | p_color = {"ec": "#46a546"}
29 | s_color = {"ec": "#f89406"}
30 |
31 | pgm = daft.PGM([3.6, 3.5], origin=[0.7, 0])
32 |
33 | n = daft.Node("phi", r"$\phi$", 1, 3, plot_params=s_color)
34 | n.va = "baseline"
35 | pgm.add_node(n)
36 | pgm.add_node(daft.Node("speckle_coeff", r"$z_i$", 2, 3, plot_params=s_color))
37 | pgm.add_node(daft.Node("speckle_img", r"$x_i$", 2, 2, plot_params=s_color))
38 |
39 | pgm.add_node(daft.Node("spec", r"$s$", 4, 3, plot_params=p_color))
40 | pgm.add_node(daft.Node("shape", r"$g$", 4, 2, plot_params=p_color))
41 | pgm.add_node(daft.Node("planet_pos", r"$\mu_i$", 3, 3, plot_params=p_color))
42 | pgm.add_node(daft.Node("planet_img", r"$p_i$", 3, 2, plot_params=p_color))
43 |
44 | pgm.add_node(daft.Node("pixels", r"$y_i ^j$", 2.5, 1, observed=True))
45 |
46 | # Edges.
47 | pgm.add_edge("phi", "speckle_coeff")
48 | pgm.add_edge("speckle_coeff", "speckle_img")
49 | pgm.add_edge("speckle_img", "pixels")
50 |
51 | pgm.add_edge("spec", "planet_img")
52 | pgm.add_edge("shape", "planet_img")
53 | pgm.add_edge("planet_pos", "planet_img")
54 | pgm.add_edge("planet_img", "pixels")
55 |
56 | # And a plate.
57 | pgm.add_plate(daft.Plate([1.5, 0.2, 2, 3.2], label=r"exposure $i$",
58 | shift=-0.1))
59 | pgm.add_plate(daft.Plate([2, 0.5, 1, 1], label=r"pixel $j$",
60 | shift=-0.1))
61 |
62 | # Render and save.
63 | pgm.render()
64 | pgm.figure.savefig("exoplanets.pdf")
65 | pgm.figure.savefig("exoplanets.png", dpi=150)
66 |
67 |
68 |
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/docs/index.rst:
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1 | Daft
2 | ====
3 |
4 | .. raw:: html
5 |
6 |
7 |