I was under the impression that these things used the values of take_log that from FieldInfo, which is False for the velocity components. Using Density instead of x-velocity still throws the same error. d. On Fri, Apr 26, 2013 at 5:11 PM, Geoffrey So wrote:

Could it also be trying to take log of negative values in the velocity? If so changing x-velcity to another positive field would not end in error.

From G.S.

On Fri, Apr 26, 2013 at 4:06 PM, David Collins wrote:

...

Hi, all--

I'm running into problems making phase objects. It looks like the error is in the color bar, and is similar to other errors I get when trying to use PlotCollections. The hash I'm on is 34b95297062b. I'm trying:

pf = load(fname) pc = PlotCollection(pf,'c') phase=pc.add_phase_object(pf.h.all_data(),['CellMass', 'x-velocity','CellVolume'],weight=None)

min/max are as follows: CellMass: [4.1e-12,1.5e-03] (30631133,) x-velocity: [-7.2e+01,5.5e+01] CellVolume: [1.45e-11,6.0e-08]

Is there a more up-to-date manner to do this that doesn't use PlotCollection? Or is there something obvious that I'm missing?

It seems to be choking in plot_types.py/__init_colorbar

def __init_colorbar(self): temparray = np.ones((self.x_bins.size, self.y_bins.size)) self.norm = matplotlib.colors.Normalize() self.image = self._axes.pcolormesh(self.x_bins, self.y_bins, temparray, shading='flat', norm=self.norm, cmap=self.cmap, rasterized=True) self.colorbar = self._figure.colorbar(self.image, extend='neither', shrink=0.95, format="%0.2e" )

It looks like what's happening is figure.colorbar chokes on the fact that temparray is "ones", so the spacing between elements is zero. This is outside of my yt knowledge, though.

Traceback (most recent call last): File "<stdin>", line 1, in <module> File "p14_phase_test.py", line 4, in <module>

phase=pc.add_phase_object(pf.h.all_data(),['CellMass','x-velocity','CellVolume']) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_collection.py", line 1184, in add_phase_object figure=figure, axes=axes)) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_types.py", line 815, in __init__ self.__init_colorbar() File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_types.py", line 834, in __init_colorbar format="%0.2e" ) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/figure.py", line 1387, in colorbar cb = cbar.colorbar_factory(cax, mappable, **kw) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 1173, in colorbar_factory cb = Colorbar(cax, mappable, **kwargs) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 854, in __init__ ColorbarBase.__init__(self, ax, **kw) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 298, in __init__ self.draw_all() File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 323, in draw_all self._config_axes(X, Y) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 409, in _config_axes self.update_ticks() File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 345, in update_ticks ticks, ticklabels, offset_string = self._ticker() File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 560, in _ticker ticks = self._locate(b) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 808, in _locate z = np.take(y, i0) + (xn-np.take(b,i0))*dy/db FloatingPointError: invalid value encountered in divide

_______________________________________________ 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

As Geoffrey mentioned, you can manually construct the histogram using BinnedProfile1D or BinnedProfile2D and then plot it up yourself using e.g. matplotlib's pyplot. It's on my radar to finish up Matt's improved profile plotting interface but for right now the only way to do this is via PlotCollection. On Fri, Apr 26, 2013 at 4:38 PM, Geoffrey So wrote:

I think another way of doing similar things is using BinnedProfile2D, or if the dataset is small matplotlib has a histogram2d which I sometimes use.

From G.S.

On Fri, Apr 26, 2013 at 4:15 PM, David Collins wrote:

...

I was under the impression that these things used the values of take_log that from FieldInfo, which is False for the velocity components.

Using Density instead of x-velocity still throws the same error.

d.

On Fri, Apr 26, 2013 at 5:11 PM, Geoffrey So wrote:

...

Could it also be trying to take log of negative values in the velocity? If so changing x-velcity to another positive field would not end in error.

From G.S.

On Fri, Apr 26, 2013 at 4:06 PM, David Collins wrote:

...

Hi, all--

I'm running into problems making phase objects. It looks like the error is in the color bar, and is similar to other errors I get when trying to use PlotCollections. The hash I'm on is 34b95297062b. I'm trying:

pf = load(fname) pc = PlotCollection(pf,'c') phase=pc.add_phase_object(pf.h.all_data(),['CellMass', 'x-velocity','CellVolume'],weight=None)

min/max are as follows: CellMass: [4.1e-12,1.5e-03] (30631133,) x-velocity: [-7.2e+01,5.5e+01] CellVolume: [1.45e-11,6.0e-08]

Is there a more up-to-date manner to do this that doesn't use PlotCollection? Or is there something obvious that I'm missing?

It seems to be choking in plot_types.py/__init_colorbar

def __init_colorbar(self): temparray = np.ones((self.x_bins.size, self.y_bins.size)) self.norm = matplotlib.colors.Normalize() self.image = self._axes.pcolormesh(self.x_bins, self.y_bins, temparray, shading='flat', norm=self.norm, cmap=self.cmap, rasterized=True) self.colorbar = self._figure.colorbar(self.image, extend='neither', shrink=0.95, format="%0.2e" )

It looks like what's happening is figure.colorbar chokes on the fact that temparray is "ones", so the spacing between elements is zero. This is outside of my yt knowledge, though.

Traceback (most recent call last): File "<stdin>", line 1, in <module> File "p14_phase_test.py", line 4, in <module>

phase=pc.add_phase_object(pf.h.all_data(),['CellMass','x-velocity','CellVolume']) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_collection.py", line 1184, in add_phase_object figure=figure, axes=axes)) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_types.py", line 815, in __init__ self.__init_colorbar() File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_types.py", line 834, in __init_colorbar format="%0.2e" ) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/figure.py", line 1387, in colorbar cb = cbar.colorbar_factory(cax, mappable, **kw) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 1173, in colorbar_factory cb = Colorbar(cax, mappable, **kwargs) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 854, in __init__ ColorbarBase.__init__(self, ax, **kw) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 298, in __init__ self.draw_all() File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 323, in draw_all self._config_axes(X, Y) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 409, in _config_axes self.update_ticks() File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 345, in update_ticks ticks, ticklabels, offset_string = self._ticker() File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 560, in _ticker ticks = self._locate(b) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 808, in _locate z = np.take(y, i0) + (xn-np.take(b,i0))*dy/db FloatingPointError: invalid value encountered in divide

_______________________________________________ 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

_______________________________________________ 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

Aha, found it. I apologize, my mistake again. I had numpy.seterr(invalid='raise') set in my startup script, for reasons that made sense at one point, but no longer do. That causes the action that I described to raise an error, rather than being quietly ignored. For whatever reason it's an issue with this combination of things where it wasn't before, but it's my own issue. Sorry for the bother! d. On Fri, Apr 26, 2013 at 6:20 PM, Matthew Turk wrote:

I don't think there should be any issues with the existing plot collection. This is the first I have seen of it, and I am keen to fix it. I rely on this functionality for my own work as well; any regressions here are bugs.

Which version of matplotlib are you on? And, can you replicate this using the DD0010 that comes with yt, or any of the workshop data sets? On Apr 26, 2013 7:40 PM, "Nathan Goldbaum" wrote:

...

As Geoffrey mentioned, you can manually construct the histogram using BinnedProfile1D or BinnedProfile2D and then plot it up yourself using e.g. matplotlib's pyplot.

It's on my radar to finish up Matt's improved profile plotting interface but for right now the only way to do this is via PlotCollection.

On Fri, Apr 26, 2013 at 4:38 PM, Geoffrey So wrote:

...

I think another way of doing similar things is using BinnedProfile2D, or if the dataset is small matplotlib has a histogram2d which I sometimes use.

From G.S.

On Fri, Apr 26, 2013 at 4:15 PM, David Collins wrote:

...

I was under the impression that these things used the values of take_log that from FieldInfo, which is False for the velocity components.

Using Density instead of x-velocity still throws the same error.

d.

On Fri, Apr 26, 2013 at 5:11 PM, Geoffrey So wrote:

...

Could it also be trying to take log of negative values in the velocity? If so changing x-velcity to another positive field would not end in error.

From G.S.

On Fri, Apr 26, 2013 at 4:06 PM, David Collins

...

wrote:

...

Hi, all--

I'm running into problems making phase objects. It looks like the error is in the color bar, and is similar to other errors I get when trying to use PlotCollections. The hash I'm on is 34b95297062b. I'm trying:

pf = load(fname) pc = PlotCollection(pf,'c') phase=pc.add_phase_object(pf.h.all_data(),['CellMass', 'x-velocity','CellVolume'],weight=None)

min/max are as follows: CellMass: [4.1e-12,1.5e-03] (30631133,) x-velocity: [-7.2e+01,5.5e+01] CellVolume: [1.45e-11,6.0e-08]

Is there a more up-to-date manner to do this that doesn't use PlotCollection? Or is there something obvious that I'm missing?

It seems to be choking in plot_types.py/__init_colorbar

def __init_colorbar(self): temparray = np.ones((self.x_bins.size, self.y_bins.size)) self.norm = matplotlib.colors.Normalize() self.image = self._axes.pcolormesh(self.x_bins, self.y_bins, temparray, shading='flat', norm=self.norm, cmap=self.cmap, rasterized=True) self.colorbar = self._figure.colorbar(self.image, extend='neither', shrink=0.95, format="%0.2e" )

It looks like what's happening is figure.colorbar chokes on the fact that temparray is "ones", so the spacing between elements is zero. This is outside of my yt knowledge, though.

Traceback (most recent call last): File "<stdin>", line 1, in <module> File "p14_phase_test.py", line 4, in <module>

phase=pc.add_phase_object(pf.h.all_data(),['CellMass','x-velocity','CellVolume']) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_collection.py", line 1184, in add_phase_object figure=figure, axes=axes)) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_types.py", line 815, in __init__ self.__init_colorbar() File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_types.py", line 834, in __init_colorbar format="%0.2e" ) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/figure.py", line 1387, in colorbar cb = cbar.colorbar_factory(cax, mappable, **kw) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 1173, in colorbar_factory cb = Colorbar(cax, mappable, **kwargs) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 854, in __init__ ColorbarBase.__init__(self, ax, **kw) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 298, in __init__ self.draw_all() File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 323, in draw_all self._config_axes(X, Y) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 409, in _config_axes self.update_ticks() File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 345, in update_ticks ticks, ticklabels, offset_string = self._ticker() File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 560, in _ticker ticks = self._locate(b) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 808, in _locate z = np.take(y, i0) + (xn-np.take(b,i0))*dy/db FloatingPointError: invalid value encountered in divide

_______________________________________________ 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

_______________________________________________ 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

_______________________________________________ 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