From 779d4241ed3f0bfa034728ff34aa9530aa3b98cb Mon Sep 17 00:00:00 2001
From: "David W. Hogg" <dwhogg@gmail.com>
Date: Tue, 5 Mar 2013 07:31:59 -0500
Subject: [PATCH 1/9] start

---
 examples/xdstars.py | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 examples/xdstars.py

diff --git a/examples/xdstars.py b/examples/xdstars.py
new file mode 100644
index 0000000..d9b3fb3
--- /dev/null
+++ b/examples/xdstars.py
@@ -0,0 +1,39 @@
+"""
+Extreme deconvolution of stars
+==============================
+
+The (very simple) model that transformed SDSS-III.
+
+"""
+
+from matplotlib import rc
+rc("font", family="serif", size=12)
+rc("text", usetex=True)
+
+import daft
+
+# Instantiate the PGM.
+pgm = daft.PGM([2.3, 2.05], origin=[0.3, 0.3])
+
+# Hierarchical parameters.
+pgm.add_node(daft.Node("theta", r"$\theta$", 0.5, 2, fixed=True))
+pgm.add_node(daft.Node("sigma", r"$\Sigma$", 1.5, 2))
+
+# Latent variable.
+pgm.add_node(daft.Node("X", r"$X_n$", 1, 1))
+
+# Data.
+pgm.add_node(daft.Node("x", r"$x_n$", 2, 1, observed=True))
+
+# Add in the edges.
+pgm.add_edge("theta", "X")
+pgm.add_edge("sigma", "x")
+pgm.add_edge("X", "x")
+
+# And a plate.
+pgm.add_plate(daft.Plate([0.5, 0.5, 2, 1], label=r"stars $n$", shift=-0.1))
+
+# Render and save.
+pgm.render()
+pgm.figure.savefig("xdstars.pdf")
+pgm.figure.savefig("xdstars.png", dpi=150)

From 45d2eae9c0881361c5e1b382e3a9c73aca2e7f12 Mon Sep 17 00:00:00 2001
From: "David W. Hogg" <dwhogg@gmail.com>
Date: Tue, 5 Mar 2013 07:32:14 -0500
Subject: [PATCH 2/9] not sure what

---
 examples/weaklensing.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/weaklensing.py b/examples/weaklensing.py
index 655dbee..bb78be8 100644
--- a/examples/weaklensing.py
+++ b/examples/weaklensing.py
@@ -14,7 +14,7 @@
 from matplotlib import rc
 rc("font", family="serif", size=12)
 rc("text", usetex=True)
-rc("./weaklensing.tex")
+# rc("./weaklensing.tex")
 
 import daft
 

From 86db27d879ff80a4dc94edd716d450becb112166 Mon Sep 17 00:00:00 2001
From: "David W. Hogg" <dwhogg@gmail.com>
Date: Tue, 5 Mar 2013 07:53:32 -0500
Subject: [PATCH 3/9] new layout, better for extending

---
 daft.py             |  8 +++++---
 examples/xdstars.py | 12 +++++++-----
 2 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/daft.py b/daft.py
index 81aca5c..091f9f8 100644
--- a/daft.py
+++ b/daft.py
@@ -186,6 +186,8 @@ def __init__(self, name, content, x, y, scale=1, aspect=None,
         # Coordinates and dimensions.
         self.x, self.y = x, y
         self.scale = scale
+        if self.fixed:
+            self.scale = scale / 6. # magic number
         self.aspect = aspect
 
         # Display parameters.
@@ -232,11 +234,9 @@ def render(self, ctx):
         l["ha"] = _pop_multiple(l, "center", "ha", "horizontalalignment")
 
         # Deal with ``fixed`` nodes.
-        scale = self.scale
         if self.fixed:
             # MAGIC: These magic numbers should depend on the grid/node units.
             self.offset[1] += 6
-            scale /= 6.
 
             l["va"] = "baseline"
             l.pop("verticalalignment", None)
@@ -245,7 +245,7 @@ def render(self, ctx):
             if p["fc"] == "none":
                 p["fc"] = "k"
 
-        diameter = ctx.node_unit * scale
+        diameter = ctx.node_unit * self.scale
         if self.aspect is not None:
             aspect = self.aspect
         else:
@@ -347,6 +347,8 @@ def _get_coords(self, ctx):
         dist1 = np.sqrt(dy * dy + dx * dx / float(a1 ** 2))
         dist2 = np.sqrt(dy * dy + dx * dx / float(a2 ** 2))
 
+        print self.node1, self.node2, self.node1.scale, self.node2.scale
+
         # Compute the fractional effect of the radii of the nodes.
         alpha1 = 0.5 * ctx.node_unit * self.node1.scale / dist1
         alpha2 = 0.5 * ctx.node_unit * self.node2.scale / dist2
diff --git a/examples/xdstars.py b/examples/xdstars.py
index d9b3fb3..eea086f 100644
--- a/examples/xdstars.py
+++ b/examples/xdstars.py
@@ -13,25 +13,27 @@
 import daft
 
 # Instantiate the PGM.
-pgm = daft.PGM([2.3, 2.05], origin=[0.3, 0.3])
+pgm = daft.PGM([2.2, 3.55], origin=[0.4, 0.3])
 
 # Hierarchical parameters.
-pgm.add_node(daft.Node("theta", r"$\theta$", 0.5, 2, fixed=True))
-pgm.add_node(daft.Node("sigma", r"$\Sigma$", 1.5, 2))
+pgm.add_node(daft.Node("alpha", r"$\alpha$", 1, 3.5, fixed=True))
+pgm.add_node(daft.Node("theta", r"$\theta$", 1, 2.5))
+pgm.add_node(daft.Node("sigma", r"$\Sigma$", 1, 1))
 
 # Latent variable.
-pgm.add_node(daft.Node("X", r"$X_n$", 1, 1))
+pgm.add_node(daft.Node("X", r"$X_n$", 2, 2))
 
 # Data.
 pgm.add_node(daft.Node("x", r"$x_n$", 2, 1, observed=True))
 
 # Add in the edges.
+pgm.add_edge("alpha", "theta")
 pgm.add_edge("theta", "X")
 pgm.add_edge("sigma", "x")
 pgm.add_edge("X", "x")
 
 # And a plate.
-pgm.add_plate(daft.Plate([0.5, 0.5, 2, 1], label=r"stars $n$", shift=-0.1))
+pgm.add_plate(daft.Plate([1.5, 0.5, 1, 2], label=r"stars $n$", shift=-0.1))
 
 # Render and save.
 pgm.render()

From a9c773940dd28e0ab77d63f3caf81a0a3df19096 Mon Sep 17 00:00:00 2001
From: "David W. Hogg" <dwhogg@gmail.com>
Date: Tue, 5 Mar 2013 07:58:40 -0500
Subject: [PATCH 4/9] move scale setting

---
 daft.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/daft.py b/daft.py
index 091f9f8..71c432a 100644
--- a/daft.py
+++ b/daft.py
@@ -347,8 +347,6 @@ def _get_coords(self, ctx):
         dist1 = np.sqrt(dy * dy + dx * dx / float(a1 ** 2))
         dist2 = np.sqrt(dy * dy + dx * dx / float(a2 ** 2))
 
-        print self.node1, self.node2, self.node1.scale, self.node2.scale
-
         # Compute the fractional effect of the radii of the nodes.
         alpha1 = 0.5 * ctx.node_unit * self.node1.scale / dist1
         alpha2 = 0.5 * ctx.node_unit * self.node2.scale / dist2

From 8b623d6a25cdf5b78b0f53f6ab597cd46633a9bb Mon Sep 17 00:00:00 2001
From: "David W. Hogg" <dwhogg@gmail.com>
Date: Tue, 5 Mar 2013 07:58:55 -0500
Subject: [PATCH 5/9] start, skeleton

---
 examples/xdqso.py | 46 ++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 examples/xdqso.py

diff --git a/examples/xdqso.py b/examples/xdqso.py
new file mode 100644
index 0000000..3a31b4a
--- /dev/null
+++ b/examples/xdqso.py
@@ -0,0 +1,46 @@
+"""
+Extreme deconvolution of stars
+==============================
+
+The (very simple) model that transformed SDSS-III.
+
+"""
+
+from matplotlib import rc
+rc("font", family="serif", size=12)
+rc("text", usetex=True)
+
+import daft
+
+# Instantiate the PGM.
+pgm = daft.PGM([3.2, 3.55], origin=[-0.6, 0.3])
+
+# Hierarchical parameters.
+pgm.add_node(daft.Node("alpha", r"$\alpha$", 1, 3.5, fixed=True))
+pgm.add_node(daft.Node("theta", r"$\theta$", 1, 2.5))
+pgm.add_node(daft.Node("sigma", r"$\Sigma$", 1, 1))
+
+# Latent variables.
+pgm.add_node(daft.Node("q", r"$q_n$", 2, 3))
+pgm.add_node(daft.Node("qt", r"$q_m$", 0, 3))
+pgm.add_node(daft.Node("X", r"$X_n$", 2, 2))
+pgm.add_node(daft.Node("Xt", r"$X_m$", 0, 3))
+
+# Data.
+pgm.add_node(daft.Node("x", r"$x_n$", 2, 1, observed=True))
+pgm.add_node(daft.Node("x", r"$x_n$", 0, 1, observed=True))
+
+# Add in the edges.
+pgm.add_edge("alpha", "theta")
+pgm.add_edge("theta", "X")
+pgm.add_edge("sigma", "x")
+pgm.add_edge("X", "x")
+
+# And plates.
+pgm.add_plate(daft.Plate([-0.5, 0.5, 1, 3], label=r"train", shift=-0.1))
+pgm.add_plate(daft.Plate([1.5, 0.5, 1, 3], label=r"test", shift=-0.1))
+
+# Render and save.
+pgm.render()
+pgm.figure.savefig("xdqso.pdf")
+pgm.figure.savefig("xdqso.png", dpi=150)

From 59f45bb71eb1c7a58e959afe1e6cc31441fa6f7b Mon Sep 17 00:00:00 2001
From: "David W. Hogg" <dwhogg@gmail.com>
Date: Tue, 5 Mar 2013 07:59:53 -0500
Subject: [PATCH 6/9] start, skeleton

---
 examples/xdqso.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/xdqso.py b/examples/xdqso.py
index 3a31b4a..597d72e 100644
--- a/examples/xdqso.py
+++ b/examples/xdqso.py
@@ -22,13 +22,13 @@
 
 # Latent variables.
 pgm.add_node(daft.Node("q", r"$q_n$", 2, 3))
-pgm.add_node(daft.Node("qt", r"$q_m$", 0, 3))
+pgm.add_node(daft.Node("qt", r"$q_m$", 0, 3, observed=True))
 pgm.add_node(daft.Node("X", r"$X_n$", 2, 2))
 pgm.add_node(daft.Node("Xt", r"$X_m$", 0, 3))
 
 # Data.
 pgm.add_node(daft.Node("x", r"$x_n$", 2, 1, observed=True))
-pgm.add_node(daft.Node("x", r"$x_n$", 0, 1, observed=True))
+pgm.add_node(daft.Node("xt", r"$x_n$", 0, 1, observed=True))
 
 # Add in the edges.
 pgm.add_edge("alpha", "theta")

From afdbaf00224e520c26d316867d493eecdf853202 Mon Sep 17 00:00:00 2001
From: "David W. Hogg" <dwhogg@gmail.com>
Date: Tue, 5 Mar 2013 08:07:17 -0500
Subject: [PATCH 7/9] aligning xdstars and xdqso PGMs

---
 examples/xdqso.py   | 17 ++++++++++++-----
 examples/xdstars.py |  8 ++++----
 2 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/examples/xdqso.py b/examples/xdqso.py
index 597d72e..e6e81fc 100644
--- a/examples/xdqso.py
+++ b/examples/xdqso.py
@@ -21,20 +21,27 @@
 pgm.add_node(daft.Node("sigma", r"$\Sigma$", 1, 1))
 
 # Latent variables.
-pgm.add_node(daft.Node("q", r"$q_n$", 2, 3))
-pgm.add_node(daft.Node("qt", r"$q_m$", 0, 3, observed=True))
-pgm.add_node(daft.Node("X", r"$X_n$", 2, 2))
-pgm.add_node(daft.Node("Xt", r"$X_m$", 0, 3))
+pgm.add_node(daft.Node("q", r"$q_m$", 2, 3))
+pgm.add_node(daft.Node("X", r"$X_m$", 2, 2))
+pgm.add_node(daft.Node("Xt", r"$X_n$", 0, 2))
 
 # Data.
-pgm.add_node(daft.Node("x", r"$x_n$", 2, 1, observed=True))
+pgm.add_node(daft.Node("qt", r"$q_n$", 0, 3, observed=True))
+pgm.add_node(daft.Node("x", r"$x_m$", 2, 1, observed=True))
 pgm.add_node(daft.Node("xt", r"$x_n$", 0, 1, observed=True))
 
 # Add in the edges.
 pgm.add_edge("alpha", "theta")
+pgm.add_edge("theta", "q")
+pgm.add_edge("theta", "qt")
 pgm.add_edge("theta", "X")
+pgm.add_edge("theta", "Xt")
 pgm.add_edge("sigma", "x")
+pgm.add_edge("sigma", "xt")
 pgm.add_edge("X", "x")
+pgm.add_edge("Xt", "xt")
+pgm.add_edge("q", "X")
+pgm.add_edge("qt", "Xt")
 
 # And plates.
 pgm.add_plate(daft.Plate([-0.5, 0.5, 1, 3], label=r"train", shift=-0.1))
diff --git a/examples/xdstars.py b/examples/xdstars.py
index eea086f..108aadd 100644
--- a/examples/xdstars.py
+++ b/examples/xdstars.py
@@ -13,7 +13,7 @@
 import daft
 
 # Instantiate the PGM.
-pgm = daft.PGM([2.2, 3.55], origin=[0.4, 0.3])
+pgm = daft.PGM([2.2, 3.55], origin=[-0.6, 0.3])
 
 # Hierarchical parameters.
 pgm.add_node(daft.Node("alpha", r"$\alpha$", 1, 3.5, fixed=True))
@@ -21,10 +21,10 @@
 pgm.add_node(daft.Node("sigma", r"$\Sigma$", 1, 1))
 
 # Latent variable.
-pgm.add_node(daft.Node("X", r"$X_n$", 2, 2))
+pgm.add_node(daft.Node("X", r"$X_n$", 0, 2))
 
 # Data.
-pgm.add_node(daft.Node("x", r"$x_n$", 2, 1, observed=True))
+pgm.add_node(daft.Node("x", r"$x_n$", 0, 1, observed=True))
 
 # Add in the edges.
 pgm.add_edge("alpha", "theta")
@@ -33,7 +33,7 @@
 pgm.add_edge("X", "x")
 
 # And a plate.
-pgm.add_plate(daft.Plate([1.5, 0.5, 1, 2], label=r"stars $n$", shift=-0.1))
+pgm.add_plate(daft.Plate([-0.5, 0.5, 1, 2], label=r"stars $n$", shift=-0.1))
 
 # Render and save.
 pgm.render()

From 6d0f8b5ec3978e30d121bb3075afaffa21118fa5 Mon Sep 17 00:00:00 2001
From: "David W. Hogg" <dwhogg@gmail.com>
Date: Wed, 7 Aug 2013 22:21:13 +0200
Subject: [PATCH 8/9] examples

---
 examples/hayabusa.py   | 48 ++++++++++++++++++++++++++++++++++++++++++
 examples/stochastic.py | 42 ++++++++++++++++++++++++++++++++++++
 examples/xdqso.py      |  7 +++---
 3 files changed, 94 insertions(+), 3 deletions(-)
 create mode 100644 examples/hayabusa.py
 create mode 100644 examples/stochastic.py

diff --git a/examples/hayabusa.py b/examples/hayabusa.py
new file mode 100644
index 0000000..b0c8261
--- /dev/null
+++ b/examples/hayabusa.py
@@ -0,0 +1,48 @@
+"""
+Hayabusa
+========
+
+No comment.
+
+"""
+
+from matplotlib import rc
+rc("font", family="serif", size=12)
+rc("text", usetex=True)
+import daft
+
+pgm = daft.PGM([4.8, 3.2], origin=[-0.4, -0.7])
+
+# Hierarchical parameters.
+pgm.add_node(daft.Node("theta", r"$\theta$", 0, 1))
+pgm.add_node(daft.Node("Omega", r"$\Omega$", 4, 1))
+pgm.add_node(daft.Node("Sigma", r"$\Sigma$", 0, 0))
+
+# spectral measurements
+pgm.add_node(daft.Node("a", r"$a_n$", 1, 2, observed=True))
+pgm.add_node(daft.Node("z", r"$z_n$", 2, 2, observed=True))
+
+# Latent variables.
+pgm.add_node(daft.Node("M", r"$M_n$", 1, 1))
+pgm.add_edge("a", "M")
+pgm.add_edge("theta", "M")
+pgm.add_node(daft.Node("K", r"$K_n$", 2, 1))
+pgm.add_edge("z", "K")
+pgm.add_node(daft.Node("DM", r"$DM_n$", 3, 1))
+pgm.add_edge("z", "DM")
+pgm.add_edge("Omega", "DM")
+
+# Data.
+pgm.add_node(daft.Node("m", r"$m_n$", 2, 0, observed=True))
+pgm.add_edge("M", "m")
+pgm.add_edge("K", "m")
+pgm.add_edge("DM", "m")
+pgm.add_edge("Sigma", "m")
+
+# And a plate.
+pgm.add_plate(daft.Plate([0.5, -0.6, 3, 3], label=r"quasars $n$"))
+
+# Render and save.
+pgm.render()
+pgm.figure.savefig("hayabusa.pdf")
+pgm.figure.savefig("hayabusa.png", dpi=150)
diff --git a/examples/stochastic.py b/examples/stochastic.py
new file mode 100644
index 0000000..4306f61
--- /dev/null
+++ b/examples/stochastic.py
@@ -0,0 +1,42 @@
+"""
+The Quintessential PGM
+======================
+
+This is a demonstration of a very common structure found in graphical models.
+It has been rendered using Daft's default settings for all the parameters
+and it shows off how much beauty is baked in by default.
+
+"""
+
+from matplotlib import rc
+rc("font", family="serif", size=12)
+rc("text", usetex=True)
+
+import daft
+
+# Instantiate the PGM.
+pgm = daft.PGM([5., 3.1], origin=[-0.5, 0.3])
+
+# Hierarchical parameters.
+pgm.add_node(daft.Node("alpha", r"$\alpha$", 0.5, 3., fixed=True))
+pgm.add_node(daft.Node("weather", r"stochastic", 0.5, 2., aspect=2.5))
+pgm.add_node(daft.Node("pop", r"population", 2., 3., aspect=2.5))
+pgm.add_node(daft.Node("science", r"target", 2., 2., aspect=2.5))
+pgm.add_node(daft.Node("data", r"data set", 1.5, 1., aspect=2.5))
+pgm.add_node(daft.Node(r"noise", r"\noindent noise\\ model", 3.7, 1., aspect=2.5))
+
+# Add in the edges.
+pgm.add_edge("alpha", "weather")
+pgm.add_edge("weather", "data")
+pgm.add_edge("pop", "science")
+pgm.add_edge("science", "data")
+pgm.add_edge("noise", "data")
+
+# And a plate.
+pgm.add_plate(daft.Plate([-0.3, 0.5, 3.1, 2.], label=r"data sets",
+    shift=-0.1))
+
+# Render and save.
+pgm.render()
+pgm.figure.savefig("stochastic.pdf")
+pgm.figure.savefig("stochastic.png", dpi=150)
diff --git a/examples/xdqso.py b/examples/xdqso.py
index e6e81fc..7fd6b94 100644
--- a/examples/xdqso.py
+++ b/examples/xdqso.py
@@ -13,12 +13,13 @@
 import daft
 
 # Instantiate the PGM.
-pgm = daft.PGM([3.2, 3.55], origin=[-0.6, 0.3])
+pgm = daft.PGM([4.00, 3.55], origin=[-0.6, 0.3])
 
 # Hierarchical parameters.
 pgm.add_node(daft.Node("alpha", r"$\alpha$", 1, 3.5, fixed=True))
 pgm.add_node(daft.Node("theta", r"$\theta$", 1, 2.5))
-pgm.add_node(daft.Node("sigma", r"$\Sigma$", 1, 1))
+pgm.add_node(daft.Node("Sigma", r"$\Sigma$", 1, 1))
+pgm.add_node(daft.Node("sigma", r"$\sigma$", 3, 1))
 
 # Latent variables.
 pgm.add_node(daft.Node("q", r"$q_m$", 2, 3))
@@ -37,7 +38,7 @@
 pgm.add_edge("theta", "X")
 pgm.add_edge("theta", "Xt")
 pgm.add_edge("sigma", "x")
-pgm.add_edge("sigma", "xt")
+pgm.add_edge("Sigma", "xt")
 pgm.add_edge("X", "x")
 pgm.add_edge("Xt", "xt")
 pgm.add_edge("q", "X")

From 2b6171b96f537dae8884657de3cf555bdc88435c Mon Sep 17 00:00:00 2001
From: "David W. Hogg" <dwhogg@gmail.com>
Date: Thu, 8 Aug 2013 18:40:19 +0200
Subject: [PATCH 9/9] brewer example; punking Plate to label

---
 examples/brewer.py | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 examples/brewer.py

diff --git a/examples/brewer.py b/examples/brewer.py
new file mode 100644
index 0000000..9e3a0d3
--- /dev/null
+++ b/examples/brewer.py
@@ -0,0 +1,30 @@
+"""
+Brewer's project, sort of
+=========================
+
+This uses a HACK of `Plate` to put a label on the plot.
+"""
+
+from matplotlib import rc
+rc("font", family="serif", size=12)
+rc("text", usetex=True)
+
+import daft
+
+pgm = daft.PGM([5., 2.5], origin=[2.0, 0.0], aspect=2.1)
+pgm.add_node(daft.Node("counts", r"$dN/dm$", 6.0, 2.0))
+pgm.add_node(daft.Node("stars", r"stars", 4.5, 2.0,))
+pgm.add_node(daft.Node("pixels", r"pixels", 3.0, 2.0, observed=True))
+pgm.add_node(daft.Node("psf", r"psf", 4.5, 1.0))
+pgm.add_node(daft.Node("noise", r"noise", 3.0, 1.0))
+pgm.add_edge("stars", "pixels")
+pgm.add_edge("psf", "pixels")
+pgm.add_edge("noise", "pixels")
+pgm.add_edge("counts", "stars")
+pgm.add_plate(daft.Plate([2.0, 0.0, 7.0, 2.5],
+                         label=r"$p(\mbox{pixels}\,|\,\mbox{stars})\,p(\mbox{stars}\,|\,dN/dm)\,p(dN/dm)$",
+                         label_offset=[30,10],
+                         rect_params={"ec": "none",}))
+pgm.render()
+pgm.figure.savefig("brewer.pdf")
+pgm.figure.savefig("brewer.png", dpi=300)