Mailman 3 August 2015 - yt-users

custom axes tickmarks projection plot
by Gabriel Goodwin Aug. 10, 2015

Aug. 10, 2015

Hello All, Does know how to specify custom tickmark locations for the y axis of a projection plot in the 3.2 release? I was able to do it in 3.1 using the following code: p = yt.ProjectionPlot(ds,2,string,center=[cent,height,0],width=(wide,height),origin="native",data_source=cut,method='integrate',weight_field='temperature') ax = p.plots[string].axes ax.yaxis.set_ticks([0.00, 0.15, 0.30]) This would place tickmarks and their labels on the y axis at 0, 0.15, and 0.3. When I try and do this using yt 3.2 I get the following error: AttributeError Traceback (most recent call last)<ipython-input-76-6e901a613181> in <module>() 16 ax = p.plots[string].axes---> 17 ax.yaxis.set_ticks([0.00, 0.15, 0.30]) AttributeError: 'NoneType' object has no attribute 'yaxis' It appears that we can no longer manipulate the axes object like we were able to in 3.1. Thank you!

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annotate_grids() not working (Enzo)
by bh11e Aug. 10, 2015

Aug. 10, 2015

Hello, yt users! I visualize Enzo output with yt (version = 3.1-dev, Changeset = f6379bbc462b+ (yt) tip). Sometimes annotate_grids() doesn't work neither for slice plots nor for projection plots. This affects all data sets from a given simulation. At the same time other annotations like annotate_line() display correctly. Had anyone gad a similar problem before? Many thanks, --Boyan Hristov

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data_source=region
by Shankar Agarwal Aug. 6, 2015

Aug. 6, 2015

Hi, http://yt-project.org/doc/cookbook/complex_plots.html#thin-slice-projections Is it possible to create a thin slice projection of particles (instead of density)? I tried the following three methods but get errors: 1. p = yt.ParticlePlot(ds, 2, ['particle_mass'], data_source=region) TypeError: __init__() got multiple values for keyword argument 'data_source' 2. p = yt.ParticleProjectionPlot(ds, 2, ['particle_mass'], data_source=region) finfo = self.ds._get_field_info("unknown", fname) 3. p = yt.ProjectionPlot(ds, 2, ['particle_mass'], data_source=region) File "/home/sagarwal/codes/yt/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 1429, in __init__ field_parameters = field_parameters, method = method) File "/home/sagarwal/codes/yt/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 253, in __init__ field = self._determine_fields(ensure_list(field)) File "/home/sagarwal/codes/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 518, in _determine_fields finfo = self.ds._get_field_info("unknown", fname) Shankar

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Custom Colorbar Axis
by Gabriel Goodwin Aug. 5, 2015

Aug. 5, 2015

Hello All, Does anyone know how to specify the tickmark locations on the colorbar axis? I am able to do this on the plot axes without issue, but have not been able to successfully do the same with the colorbar. Attached is a pic of one of my plots using default colorbar axis ticks. I have tried to use the following code (and many variants of it I have found in the python/matplotlib documentation) to specify the location of the tickmarks, but they don't place the ticks accurately. My data is temperature plotted over the range of 300K to 5500K and I want to have tickmarks at 300K, 800K, 3500K, and 4500K. Also attached is pic of my plot showing an attempted custom colorbar axis. I'm not sure if it makes a difference, but I made the colormap in matplotlib. colorbar_axes = p.plots[string].cax colorbar_axes.yaxis.set_ticks([0, 0.1, 0.8]) Thanks for the help!

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Interesting crash when using ("deposit", "all_cic")
by Brian O'Shea Aug. 4, 2015

Aug. 4, 2015

Hi folks, I have been trying to make some dark matter density movies using the "all_cic" field, and have discovered that using "all_cic" can reliably cause yt to seg fault on the supercomputer I'm using (x86_64 linux cluster with kernel 2.6.32-504.8.1.el6.x86_64) using the tip of yt-dev (changeset fa08e386d0da). The script that causes the crash is here: http://paste.yt-project.org/show/5774/ After I turned up the log level and started using pdb to debug, I discovered that the line in the script that causes the seg fault is line 88: dm_dens_x = my_reg[("deposit", "all_cic")].value where my_reg is defined as (on line 82): my_reg = ds.arbitrary_grid(left, right, dims=[1,800, 800]) After stepping through with pdb, it seems that the code dies in this function: /mnt/home/oshea/yt-3/lib/python2.7/site-packages/sympy/core/basic.py(83)__new__() with the traceback shown here: http://paste.yt-project.org/show/5775/ Based on this traceback, it seems that there are problems with the unit system. Interestingly enough, though, this does not happen on every dataset - it seems to happen occasionally, but predictably. For example, I can generate two images using this script, but it will seg fault on the third. On a different dataset in the time series, it will produce one image and then seg fault on the second. If I run the script over and over, it will eventually produce quite a few images, until it runs into a situation where it seg faults on the first image I produce (at which point I went to the debugger). I don't have enough experience with the guts of yt - and the units section of yt in particular - to have a sense of what might be happening here based on the traceback. Does anybody have any suggestions? Thank you! --Brian

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overplotting halos gives different results ??
by Shankar Agarwal Aug. 4, 2015

Aug. 4, 2015

Hi, When I try to overplot halos I see that some of the circles go missing, depending on what "center" is use for the density projection. The following two attempts gave me different number of circles. Cheers, Shankar ______________________________________________________________ Try 1: sim_ds = yt.load('Enzo_64/RD0006/RedshiftOutput0006') halos_ds = yt.load('halo_catalog/halo_catalog.0.h5') hc = HaloCatalog(data_ds=sim_ds, halos_ds=halos_ds) hc.load() p = yt.ProjectionPlot(sim_ds, "x", "density", center=(0.5,0.5,0.5)) p.annotate_halos(hc) ______________________________________________________________ ______________________________________________________________ Try 2: p = yt.ProjectionPlot(sim_ds, "x", "density", center=(0.5,0.3,0.3)) p.annotate_halos(hc) ______________________________________________________________

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Why individual plots have to be saved before being handed to eps_writer?
by Anni Järvenpää Aug. 4, 2015

Aug. 4, 2015

Hi All, I have been updating the eps_writer to handle a mixture of profiles, slices and projections that can be displayed in a single plot (multiple panels). eps_writer with my edits can be reviewed at http://paste.yt-project.org/show/5773/. However, in order to get the plot axes to work correctly I need to save the individual plots as well before passing them to the eps_writer. Here is an example script: http://paste.yt-project.org/show/5772/. It works correctly as is, but uncommenting the changes in plots causes weird results if I don't also save the individual plots. The result of saving and not-saving are below (as you can see the plot doesn't change but the axes/colorbar does). http://www.mv.helsinki.fi/home/aajarven/yt/noedit.png http://www.mv.helsinki.fi/home/aajarven/yt/edits-nosave.png http://www.mv.helsinki.fi/home/aajarven/yt/edits-save.png Does anyone know why the plots must be saved before being handed to the eps_writer api? I'd like to push these changes to the eps_writer and could possibly raise the save as a bug? Let me know. Anni

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multipanel plot resolution
by Shankar Agarwal Aug. 1, 2015

Aug. 1, 2015

Hi, When making a typical 1x1 plot, I see that the final image has 800x800 pixels. I then used the following script to make a 2x2 multipanel plot, with each panel showing the projected density: http://yt-project.org/doc/cookbook/complex_plots.html#time-series-multipanel However, I see that each of the four panels is not 800x800. It is about 388x388. As such, some of the details in each panel is lost (which I can see if I plot the four panels separately on 1x1 plots). Is there an easy way to tell the above script that each panel be 800x800 pixel? By the way, I see there is a statement Npixels = 512 in http://yt-project.org/doc/cookbook/complex_plots.html#off-axis-projection-a… Cheers, Shankar

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