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revamp using style sheets #88

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merged 7 commits into from
Mar 31, 2023
Merged

revamp using style sheets #88

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aec0df4
make cheatsheets column width exactly 57 mm
jimustafa Oct 23, 2021
b20eb40
start refactoring using style sheets
jimustafa Nov 14, 2021
5ea8b48
continue refactoring using style sheets
jimustafa Oct 23, 2021
aeeeb3b
finish (for now) refactoring using style sheets
jimustafa Nov 24, 2021
e4c6b67
small tweaks to size and spacing identified during review
jimustafa Jan 3, 2022
c44d32b
revert some changes
jimustafa Mar 30, 2023
cfa709d
replace `add_gridspec` with `plt.subplots`
jimustafa Mar 31, 2023
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14 changes: 10 additions & 4 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -14,10 +14,16 @@ logos:
figures:
# generate the figures
cd scripts && for script in *.py; do echo $$script; MPLBACKEND="agg" python $$script; done
# crop the figures
cd figures && for figure in *.pdf; do echo $$figure; pdfcrop $$figure $$figure; done
# regenerate some figures that should not be cropped
cd scripts && MPLBACKEND="agg" python styles.py
# crop some of the figures
cd figures && pdfcrop adjustments.pdf adjustments.pdf
cd figures && pdfcrop annotate.pdf annotate.pdf
cd figures && pdfcrop anatomy.pdf anatomy.pdf
cd figures && pdfcrop colornames.pdf colornames.pdf
cd figures && pdfcrop fonts.pdf fonts.pdf
cd figures && pdfcrop markers.pdf markers.pdf
cd figures && pdfcrop text-alignments.pdf text-alignments.pdf
cd figures && pdfcrop tip-font-family.pdf tip-font-family.pdf
cd figures && pdfcrop tip-hatched.pdf tip-hatched.pdf

.PHONY: cheatsheets
cheatsheets:
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2 changes: 1 addition & 1 deletion cheatsheets.tex
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Original file line number Diff line number Diff line change
Expand Up @@ -104,7 +104,7 @@
\setlength\parindent{0pt}
\setlength{\tabcolsep}{2pt}
\baselineskip=0pt
\setlength\columnsep{0.5em}
\setlength\columnsep{1.75mm}


% --- Macros ------------------------------------------------------------------
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71 changes: 45 additions & 26 deletions scripts/adjustements.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,62 +2,82 @@
# Matplotlib cheat sheet
# Released under the BSD License
# -----------------------------------------------------------------------------
import pathlib

import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
from matplotlib.collections import PatchCollection


fig = plt.figure(figsize=(4.25, 4.25 * 95/115))
ax = fig.add_axes([0, 0, 1, 1], frameon=False, aspect=1,
xlim=(0-5, 100+10), ylim=(-10, 80+5), xticks=[], yticks=[])
mpl.style.use([
pathlib.Path(__file__).parent/'../styles/base.mplstyle',
])
mpl.rc('font', size=4)
mpl.rc('lines', linewidth=0.5)
mpl.rc('patch', linewidth=0.5)


subplots_kw = dict(
figsize=(5.7/2.54, 5.7/2.54 * 95/115),
subplot_kw=dict(
frameon=False,
aspect=1,
xlim=(0-5, 100+10),
ylim=(-10, 80+5),
xticks=[],
yticks=[],
),
)

(fig, ax) = plt.subplots(**subplots_kw)


box = mpatches.FancyBboxPatch(
(0, 0), 100, 83, mpatches.BoxStyle("Round", pad=0, rounding_size=2),
linewidth=1., facecolor="0.9", edgecolor="black")
facecolor="0.9", edgecolor="black")
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Why did you remove linewidth=1?

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The linewidth is configured with mpl.rc.

ax.add_artist(box)

box = mpatches.FancyBboxPatch(
(0, 0), 100, 75, mpatches.BoxStyle("Round", pad=0, rounding_size=0),
linewidth=1., facecolor="white", edgecolor="black")
facecolor="white", edgecolor="black")
ax.add_artist(box)


box = mpatches.Rectangle(
(5, 5), 45, 30, zorder=10,
linewidth=1.0, facecolor="white", edgecolor="black")
facecolor="white", edgecolor="black")
ax.add_artist(box)

box = mpatches.Rectangle(
(5, 40), 45, 30, zorder=10,
linewidth=1.0, facecolor="white", edgecolor="black")
facecolor="white", edgecolor="black")
ax.add_artist(box)

box = mpatches.Rectangle(
(55, 5), 40, 65, zorder=10,
linewidth=1.0, facecolor="white", edgecolor="black")
facecolor="white", edgecolor="black")
ax.add_artist(box)

# Window button
X, Y = [5, 10, 15], [79, 79, 79]
plt.scatter(X, Y, s=75, zorder=10,
edgecolor="black", facecolor="white", linewidth=1)
plt.scatter(X, Y, s=20, zorder=10,
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Why change the size?

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The size of the figures were reduced to match \columnwidth in cheatsheets.tex; so, the marker sizes were reduced accordingly.

edgecolor="black", facecolor="white")


# Window size extension
X, Y = [0, 0], [0, -8]
plt.plot(X, Y, color="black", linestyle=":", linewidth=1, clip_on=False)
plt.plot(X, Y, color="black", linestyle=":", clip_on=False)

X, Y = [100, 100], [0, -8]
plt.plot(X, Y, color="black", linestyle=":", linewidth=1, clip_on=False)
plt.plot(X, Y, color="black", linestyle=":", clip_on=False)

X, Y = [100, 108], [0, 0]
plt.plot(X, Y, color="black", linestyle=":", linewidth=1, clip_on=False)
plt.plot(X, Y, color="black", linestyle=":", clip_on=False)

X, Y = [100, 108], [75, 75]
plt.plot(X, Y, color="black", linestyle=":", linewidth=1, clip_on=False)
plt.plot(X, Y, color="black", linestyle=":", clip_on=False)


def ext_arrow(p0, p1, p2, p3):
Expand All @@ -69,7 +89,7 @@ def ext_arrow(p0, p1, p2, p3):
ax.arrow(*p3, *(p2-p3), zorder=20, linewidth=0,
length_includes_head=True, width=.4,
head_width=2, head_length=2, color="black")
plt.plot([p1[0], p2[0]], [p1[1], p2[1]], linewidth=.9, color="black")
plt.plot([p1[0], p2[0]], [p1[1], p2[1]], linewidth=.5, color="black")


def int_arrow(p0, p1):
Expand All @@ -85,45 +105,44 @@ def int_arrow(p0, p1):
x = 0
y = 10
ext_arrow( (x-4, y), (x, y), (x+5, y), (x+9, y) )
ax.text(x+9.5, y, "left", ha="left", va="center", size="x-small", zorder=20)
ax.text(x+9.5, y, "left", ha="left", va="center", zorder=20)
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Why did you remove the text size?

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The font size is configured with mpl.rc.


x += 50
ext_arrow( (x-4, y), (x, y), (x+5, y), (x+9, y) )
ax.text(x-4.5, y, "wspace", ha="right", va="center", size="x-small", zorder=20)
ax.text(x-4.5, y, "wspace", ha="right", va="center", zorder=20)

x += 45
ext_arrow( (x-4, y), (x, y), (x+5, y), (x+9, y) )
ax.text(x-4.5, y, "right", ha="right", va="center", size="x-small", zorder=20)
ax.text(x-4.5, y, "right", ha="right", va="center", zorder=20)

y = 0
x = 25
ext_arrow( (x, y-4), (x, y), (x, y+5), (x, y+9) )
ax.text(x, y+9.5, "bottom", ha="center", va="bottom", size="x-small", zorder=20)
ax.text(x, y+9.5, "bottom", ha="center", va="bottom", zorder=20)

y += 35
ext_arrow( (x, y-4), (x, y), (x, y+5), (x, y+9) )
ax.text(x, y-4.5, "hspace", ha="center", va="top", size="x-small", zorder=20)
ax.text(x, y-4.5, "hspace", ha="center", va="top", zorder=20)

y += 35
ext_arrow( (x, y-4), (x, y), (x, y+5), (x, y+9) )
ax.text(x, y-4.5, "top", ha="center", va="top", size="x-small", zorder=20)
ax.text(x, y-4.5, "top", ha="center", va="top", zorder=20)

int_arrow((0, -5), (100, -5))
ax.text(50, -5, "figure width", backgroundcolor="white", zorder=30,
ha="center", va="center", size="x-small")
ha="center", va="center")

int_arrow((105, 0), (105, 75))
ax.text(105, 75/2, "figure height", backgroundcolor="white", zorder=30,
rotation="vertical", ha="center", va="center", size="x-small")
rotation="vertical", ha="center", va="center")

int_arrow((55, 62.5), (95, 62.5))
ax.text(75, 62.5, "axes width", backgroundcolor="white", zorder=30,
ha="center", va="center", size="x-small")
ha="center", va="center")

int_arrow((62.5, 5), (62.5, 70))
ax.text(62.5, 35, "axes height", backgroundcolor="white", zorder=30,
rotation="vertical", ha="center", va="center", size="x-small")
rotation="vertical", ha="center", va="center")


plt.savefig("../figures/adjustments.pdf")
# plt.show()
92 changes: 42 additions & 50 deletions scripts/advanced-plots.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,47 +3,51 @@
# Released under the BSD License
# -----------------------------------------------------------------------------

# Scripts to generate all the basic plots
# Script to generate all the advanced plots
import pathlib

import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt

fig = plt.figure(figsize=(0.4, 0.4))
mpl.rcParams['axes.linewidth'] = 0.5
mpl.rcParams['xtick.major.size'] = 0.0
mpl.rcParams['ytick.major.size'] = 0.0
d = 0.01
ax = fig.add_axes([d, d, 1-2*d, 1-2*d])
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This ax is to make sure we have enough space for the frame lines. If set exactly to 0,0,1,1, then the outer lines are clipped and are not anti-aliased. Not sure the replacement code take care of that

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Yes, the constrained_layout parameters in base.mplstyle include padding around the frame so that it is not clipped.


mpl.style.use([
pathlib.Path(__file__).parent/'../styles/base.mplstyle',
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pathlib.Path(__file__).parent/'../styles/plotlet.mplstyle',
])


subplot_kw = dict(
xlim=(0, 8), xticks=np.arange(1, 8),
ylim=(0, 8), yticks=np.arange(1, 8),
)

# Step plot
# -----------------------------------------------------------------------------
(fig, ax) = plt.subplots(subplot_kw=subplot_kw)
X = np.linspace(0, 10, 16)
Y = 4 + 2*np.sin(2*X)
ax.step(X, Y, color="C1", linewidth=0.75)
ax.set_xlim(0, 8), ax.set_xticks(np.arange(1, 8))
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Is this set somewhere else ?

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Yes, that is set in the plotlet.mplstyle style sheet.

ax.set_ylim(0, 8), ax.set_yticks(np.arange(1, 8))
ax.grid(linewidth=0.125)
plt.savefig("../figures/advanced-step.pdf")
ax.clear()
ax.step(X, Y, color="C1")
ax.grid()
fig.savefig("../figures/advanced-step.pdf")

# Violin plot
# -----------------------------------------------------------------------------
(fig, ax) = plt.subplots(subplot_kw=subplot_kw)
np.random.seed(10)
D = np.random.normal((3, 5, 4), (0.75, 1.00, 0.75), (200, 3))
VP = ax.violinplot(D, [2, 4, 6], widths=1.5,
showmeans=False, showmedians=False, showextrema=False)
for body in VP['bodies']:
body.set_facecolor('C1')
body.set_alpha(1)
ax.set_xlim(0, 8), ax.set_xticks(np.arange(1, 8))
ax.set_ylim(0, 8), ax.set_yticks(np.arange(1, 8))
ax.set_axisbelow(True)
ax.grid(linewidth=0.125)
plt.savefig("../figures/advanced-violin.pdf")
ax.clear()
ax.grid()
fig.savefig("../figures/advanced-violin.pdf")

# Boxplot
# -----------------------------------------------------------------------------
(fig, ax) = plt.subplots(subplot_kw=subplot_kw)
np.random.seed(10)
D = np.random.normal((3, 5, 4), (1.25, 1.00, 1.25), (100, 3))
VP = ax.boxplot(D, positions=[2, 4, 6], widths=1.5, patch_artist=True,
Expand All @@ -57,85 +61,74 @@
"linewidth": 0.75},
capprops={"color": "C1",
"linewidth": 0.75})
ax.set_xlim(0, 8), ax.set_xticks(np.arange(1, 8))
ax.set_ylim(0, 8), ax.set_yticks(np.arange(1, 8))
ax.set_axisbelow(True)
ax.grid(linewidth=0.125)
plt.savefig("../figures/advanced-boxplot.pdf")
ax.clear()
ax.grid()
fig.savefig("../figures/advanced-boxplot.pdf")

# Barbs plot
# -----------------------------------------------------------------------------
(fig, ax) = plt.subplots(subplot_kw=subplot_kw)
np.random.seed(1)
X = [[2, 4, 6]]
Y = [[1.5, 3, 2]]
U = -np.ones((1, 3)) * 0
V = -np.ones((1, 3)) * np.linspace(50, 100, 3)
ax.barbs(X, Y, U, V, barbcolor="C1", flagcolor="C1", length=5, linewidth=0.5)
ax.set_xlim(0, 8), ax.set_xticks(np.arange(1, 8))
ax.set_ylim(0, 8), ax.set_yticks(np.arange(1, 8))
ax.set_axisbelow(True)
ax.grid(linewidth=0.125)
plt.savefig("../figures/advanced-barbs.pdf")
ax.clear()
ax.grid()
fig.savefig("../figures/advanced-barbs.pdf")

# Event plot
# -----------------------------------------------------------------------------
(fig, ax) = plt.subplots(subplot_kw=subplot_kw)
np.random.seed(1)
X = [2, 4, 6]
D = np.random.gamma(4, size=(3, 50))
ax.eventplot(D, colors="C1", orientation="vertical", lineoffsets=X,
linewidth=0.25)
ax.set_xlim(0, 8), ax.set_xticks(np.arange(1, 8))
ax.set_ylim(0, 8), ax.set_yticks(np.arange(1, 8))
ax.set_axisbelow(True)
ax.grid(linewidth=0.125)
plt.savefig("../figures/advanced-event.pdf")
ax.clear()
ax.grid()
fig.savefig("../figures/advanced-event.pdf")

# Errorbar plot
# -----------------------------------------------------------------------------
(fig, ax) = plt.subplots(subplot_kw=subplot_kw)
np.random.seed(1)
X = [2, 4, 6]
Y = [4, 5, 4]
E = np.random.uniform(0.5, 1.5, 3)
ax.errorbar(X, Y, E, color="C1", linewidth=0.75, capsize=1)
ax.set_xlim(0, 8), ax.set_xticks(np.arange(1, 8))
ax.set_ylim(0, 8), ax.set_yticks(np.arange(1, 8))
ax.set_axisbelow(True)
ax.grid(linewidth=0.125)
plt.savefig("../figures/advanced-errorbar.pdf")
ax.clear()
ax.grid()
fig.savefig("../figures/advanced-errorbar.pdf")

# Hexbin plot
# -----------------------------------------------------------------------------
(fig, ax) = plt.subplots(subplot_kw=subplot_kw)
np.random.seed(1)
X = np.random.uniform(1.5, 6.5, 100)
Y = np.random.uniform(1.5, 6.5, 100)
C = np.random.uniform(0, 1, 10000)
ax.hexbin(X, Y, C, gridsize=4, linewidth=0.25, edgecolor="white",
cmap=plt.get_cmap("Wistia"), alpha=1.0)
ax.set_xlim(0, 8), ax.set_xticks(np.arange(1, 8))
ax.set_ylim(0, 8), ax.set_yticks(np.arange(1, 8))
ax.set_axisbelow(True)
ax.grid(linewidth=0.125)
plt.savefig("../figures/advanced-hexbin.pdf")
ax.clear()
ax.grid()
fig.savefig("../figures/advanced-hexbin.pdf")

# Hist plot
# -----------------------------------------------------------------------------
(fig, ax) = plt.subplots(subplot_kw=subplot_kw)
np.random.seed(1)
X = 4 + np.random.normal(0, 1.5, 200)
ax.hist(X, bins=8, facecolor="C1", linewidth=0.25, edgecolor="white")
ax.set_xlim(0, 8), ax.set_xticks(np.arange(1, 8))
ax.set_ylim(0, 80), ax.set_yticks(np.arange(1, 80, 10))
ax.set_axisbelow(True)
ax.grid(linewidth=0.125)
plt.savefig("../figures/advanced-hist.pdf")
ax.clear()
ax.grid()
fig.savefig("../figures/advanced-hist.pdf")

# Xcorr plot
# -----------------------------------------------------------------------------
(fig, ax) = plt.subplots(subplot_kw=subplot_kw)
np.random.seed(3)
Y = np.random.uniform(-4, 4, 250)
X = np.random.uniform(-4, 4, 250)
Expand All @@ -144,6 +137,5 @@
ax.set_xlim(-8, 8), ax.set_xticks(np.arange(-8, 8, 2))
ax.set_ylim(-.25, .25), ax.set_yticks(np.linspace(-.25, .25, 9))
ax.set_axisbelow(True)
ax.grid(linewidth=0.125)
plt.savefig("../figures/advanced-xcorr.pdf")
ax.clear()
ax.grid()
fig.savefig("../figures/advanced-xcorr.pdf")
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