here's my script (also here: http://bender.astro.sunysb.edu/random/slice3plot.py ) #!/bin/env python import argparse import yt import matplotlib import matplotlib.pyplot as plt from mpl_toolkits.axes_grid1 import AxesGrid def doit(file, var, log): # load the data ds = yt.load(file) dd = ds.all_data() center = 0.5*(ds.domain_left_edge + ds.domain_right_edge) # see http://yt-project.org/docs/3.0/cookbook/complex_plots.html#multipanel-with-a... fig = plt.figure() grid = AxesGrid(fig, (0.1, 0.1, 0.85, 0.85), nrows_ncols = (1, 3), axes_pad = 1.1, label_mode = "all", share_all = False, cbar_location = "right", cbar_mode = "each", cbar_size = "3%", cbar_pad = "0%") formatter = matplotlib.ticker.ScalarFormatter(useMathText=True) formatter.set_powerlimits((-3,3)) for i, d in enumerate(["x", "y", "z"]): p = yt.SlicePlot(ds, d, var, center=(center[0], center[1], center[2]), origin="native", fontsize=10) p.set_log(var, log) plot = p.plots[var] plot.figure = fig plot.axes = grid[i].axes plot.cax = grid.cbar_axes[i] #cb.formatter.set_scientific(True) #cb.formatter.set_powerlimits((-3,3)) #plot.cax.yaxis.set_major_formatter(formatter) cb = plot.cb cb.formatter = formatter cb.update_ticks() p._setup_plots() ax = plot.axes ax.xaxis.set_major_formatter(formatter) ax.yaxis.set_major_formatter(formatter) ax.xaxis.offsetText.set_fontsize("small") ax.yaxis.offsetText.set_fontsize("small") fig.set_size_inches(12.80, 7.20) plt.savefig("test.png") if __name__ == "__main__": parser = argparse.ArgumentParser() parser.add_argument("--log", help="plot the log of the variable", action="store_true") parser.add_argument("file", help="the name of the file to read", type=str) parser.add_argument("var", help="the name of the variable to plot", type=str) args = parser.parse_args() doit(args.file, args.var, args.log) On Wed, Aug 20, 2014 at 11:34 AM, Michael Zingale < michael.zingale@stonybrook.edu> wrote:

yeah, I was doing that -- it doesn't have an effect.

On Wed, Aug 20, 2014 at 11:33 AM, Chris Malone <chris.m.malone@gmail.com> wrote:

...

Hey Mike,

I'm not sure if this is the issue or not, but after you apply your formatter to the colorbar, you need to call cbar.update_ticks() for them to actually change.

Chris

On Wed, Aug 20, 2014 at 9:12 AM, Michael Zingale < michael.zingale@stonybrook.edu> wrote:

...

Does anyone know how to make a SlicePlot colorbar from yt use mathtext in the tick labels? I am doing the following in a loop over x, y, z planes:

p = yt.SlicePlot(ds, d, var, center=(center[0], center[1], center[2]), origin="native", fontsize=10) p.set_log(var, log)

plot = p.plots[var] plot.figure = fig plot.axes = grid[i].axes plot.cax = grid.cbar_axes[i]

I can get at the colorbar object via cb = plot.cb, but I can't seem to turn on mathtext. I can modify the axes to use my formatter so they look pretty, but I've tried to set a colorbar formatter with no success.

Here's my image:

http://bender.astro.sunysb.edu/random/test.png

Notice that the offset text for the colorbar is "1.e6" instead of in latex (I still have to remove the offset text for the two rightmost y-axes later, but I know how to do that).

Mike

-- Michael Zingale Associate Professor

Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale@stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

-- Michael Zingale Associate Professor

Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale@stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale

-- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale@stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Hi Nathan, the issue is getting it to be 10^6 instead of 1.e6 for the offset text in the colorbar. This just works usually in matplotlib, so yt is doing something to turn it off, but I don't know what. I think I'll just get the fixed-resolution buffers from the slice object and then just use matplotlib to plot it, since I can make it look right there. I poked around yt quite a bit, but I don't see what's wrong. On Wed, Aug 20, 2014 at 1:16 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:

Hi Mike,

It will use MathText if you ask for a logarithmically scaled colorbar.

There's probably a way to do it by spelunking a bit inside the matplotlib API, but I don't know of an easy way to do it off-hand.

If all you care about is the font, you can also use the 'stixgeneral' font family, which is actually the font that matplotlib uses internally to display mathtext. You can change the font globally by updating your matplotlibrc or changing your matplotlib configuration at the top of your script.

Sorry I can't be more helpful. Let us know if you come up with a solution here.

-Nathan

On Wed, Aug 20, 2014 at 8:38 AM, Michael Zingale < michael.zingale@stonybrook.edu> wrote:

...

here's my script (also here: http://bender.astro.sunysb.edu/random/slice3plot.py )

#!/bin/env python

import argparse

import yt

import matplotlib import matplotlib.pyplot as plt from mpl_toolkits.axes_grid1 import AxesGrid

def doit(file, var, log):

# load the data ds = yt.load(file) dd = ds.all_data()

center = 0.5*(ds.domain_left_edge + ds.domain_right_edge)

# see http://yt-project.org/docs/3.0/cookbook/complex_plots.html#multipanel-with-a...

fig = plt.figure()

grid = AxesGrid(fig, (0.1, 0.1, 0.85, 0.85), nrows_ncols = (1, 3), axes_pad = 1.1, label_mode = "all", share_all = False, cbar_location = "right", cbar_mode = "each", cbar_size = "3%", cbar_pad = "0%")

formatter = matplotlib.ticker.ScalarFormatter(useMathText=True) formatter.set_powerlimits((-3,3))

for i, d in enumerate(["x", "y", "z"]):

p = yt.SlicePlot(ds, d, var, center=(center[0], center[1], center[2]), origin="native", fontsize=10) p.set_log(var, log)

plot = p.plots[var] plot.figure = fig plot.axes = grid[i].axes plot.cax = grid.cbar_axes[i]

#cb.formatter.set_scientific(True) #cb.formatter.set_powerlimits((-3,3)) #plot.cax.yaxis.set_major_formatter(formatter)

cb = plot.cb cb.formatter = formatter cb.update_ticks()

p._setup_plots()

ax = plot.axes ax.xaxis.set_major_formatter(formatter) ax.yaxis.set_major_formatter(formatter)

ax.xaxis.offsetText.set_fontsize("small") ax.yaxis.offsetText.set_fontsize("small")

fig.set_size_inches(12.80, 7.20)

plt.savefig("test.png")

if __name__ == "__main__":

parser = argparse.ArgumentParser()

parser.add_argument("--log", help="plot the log of the variable", action="store_true")

parser.add_argument("file", help="the name of the file to read", type=str) parser.add_argument("var", help="the name of the variable to plot", type=str)

args = parser.parse_args()

doit(args.file, args.var, args.log)

On Wed, Aug 20, 2014 at 11:34 AM, Michael Zingale < michael.zingale@stonybrook.edu> wrote:

...

yeah, I was doing that -- it doesn't have an effect.

On Wed, Aug 20, 2014 at 11:33 AM, Chris Malone <chris.m.malone@gmail.com

...

wrote:

...

Hey Mike,

I'm not sure if this is the issue or not, but after you apply your formatter to the colorbar, you need to call cbar.update_ticks() for them to actually change.

Chris

On Wed, Aug 20, 2014 at 9:12 AM, Michael Zingale < michael.zingale@stonybrook.edu> wrote:

...

Does anyone know how to make a SlicePlot colorbar from yt use mathtext in the tick labels? I am doing the following in a loop over x, y, z planes:

p = yt.SlicePlot(ds, d, var, center=(center[0], center[1], center[2]), origin="native", fontsize=10) p.set_log(var, log)

plot = p.plots[var] plot.figure = fig plot.axes = grid[i].axes plot.cax = grid.cbar_axes[i]

I can get at the colorbar object via cb = plot.cb, but I can't seem to turn on mathtext. I can modify the axes to use my formatter so they look pretty, but I've tried to set a colorbar formatter with no success.

Here's my image:

http://bender.astro.sunysb.edu/random/test.png

Notice that the offset text for the colorbar is "1.e6" instead of in latex (I still have to remove the offset text for the two rightmost y-axes later, but I know how to do that).

Mike

-- Michael Zingale Associate Professor

Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale@stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

-- Michael Zingale Associate Professor

Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale@stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale

-- Michael Zingale Associate Professor

Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale@stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

-- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale@stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org