Mailman 3 November 2014 - yt-dev

Issue #942: volume rendering blank if draw_coordinate_vectors() is on but draw_domain() is not used. (yt_analysis/yt)
by Michael Zingale Nov. 21, 2014

Nov. 21, 2014

New issue 942: volume rendering blank if draw_coordinate_vectors() is on but draw_domain() is not used. https://bitbucket.org/yt_analysis/yt/issue/942/volume-rendering-blank-if Michael Zingale: If I do a volume rendering with the draw_coordinate_vectors() on, but not the draw_domain(), we don't get any image. Here's a sample script that can be used with the maestro_subCh_plt00248.tgz file on the data page: ``` #!/usr/bin/env python # this is for the wdconvect problem import matplotlib matplotlib.use('agg') # this example comes from # http://yt-project.org/doc/visualizing/volume_rendering.html import math import sys import numpy as np import os import pylab import yt import yt.visualization.volume_rendering.api as vr def doit(plotfile): ds = yt.load(plotfile) cm = "coolwarm" field = ('boxlib', 'radial_velocity') vals = [-5.e6, -2.5e6, -1.25e6, 1.25e6, 2.5e6, 5.e6] sigma = 1.e5 # select a sphere center = (0, 0, 0) R = (5.e8, 'cm') dd = ds.sphere(center, R) # Instantiate the ColorTransferfunction. tf = vr.ColorTransferFunction((min(vals), max(vals))) # Set up the camera parameters: center, looking direction, width, resolution c = np.array([0.0, 0.0, 0.0]) L = np.array([1.0, 1.0, 1.0]) L = np.array([1.0, 1.0, 1.2]) W = 1.5*ds.domain_width N = 720 north=[0.0,0.0,1.0] for v in vals: tf.sample_colormap(v, sigma**2, colormap=cm) #, alpha=0.2) # alternate attempt ds.periodicity = (True, True, True) # Create a camera object cam = vr.Camera(c, L, W, N, transfer_function=tf, ds=ds, data_source=dd, no_ghost=False, north_vector=north, fields = [field], log_fields = [False]) #cam.zoom(3) # make an image im = cam.snapshot() # add an axes triad -- note if we do this, we HAVE to do draw # domain, otherwise the image is blank (likely a bug) cam.draw_coordinate_vectors(im) # add the domain box to the image: #nim = cam.draw_domain(im) # increase the contrast -- for some reason, the enhance default # to save_annotated doesn't do the trick (likely a bug) #max_val = im[:,:,:3].std() * 4.0 #nim[:,:,:3] /= max_val f = pylab.figure() pylab.text(0.2, 0.85, "{:.3g} s".format(float(ds.current_time.d)), transform=f.transFigure, color="white") cam._render_figure = f # save annotated -- this added the transfer function values, # but this messes up our image size defined above cam.save_annotated("{}.png".format(os.path.normpath(plotfile)), im, dpi=145, clear_fig=False) if __name__ == "__main__": # Choose a field plotfile = "" try: plotfile = sys.argv[1] except: sys.exit("ERROR: no plotfile specified") doit(plotfile) ```

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Issue #940: Projection Warning: invalid value encountered in divide (yt_analysis/yt)
by Cameron Hummels Nov. 20, 2014

Nov. 20, 2014

New issue 940: Projection Warning: invalid value encountered in divide https://bitbucket.org/yt_analysis/yt/issue/940/projection-warning-invalid-v… Cameron Hummels: I oftentimes get the following warning when I generate projections in 3.0: ``` #!python /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/construction_data_containers.py:320: RuntimeWarning: invalid value encountered in divide np.divide(nvals, nwvals[:,None], nvals) ``` In fact, this error and a few other related errors show up on one of the notebooks in the docs: http://yt-project.org/docs/dev/analyzing/filtering.html It appears that sometimes the weight field in a projection has zeros in it, so that dividing by the weight field results in this error. I don't think it is a big deal, because in the end, we mask out the `nan`s that are created by such an operation, but to a new user, it might set off red alerts that something major is wrong. Responsible: chummels

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Reviewing PRs
by Nathan Goldbaum Nov. 19, 2014

Nov. 19, 2014

Hi all, If anyone has some free time in the next couple of days, I would really appreciate it if you could look over the PR backlog. Given that we'd like to release yt 3.1 on Dec. 1, I think it would be nice to get some of the pending PRs in the backlog in before the release. Looking at the list, I think the following need reviews: https://bitbucket.org/yt_analysis/yt/pull-request/1310/data_source-for-slic… https://bitbucket.org/yt_analysis/yt/pull-request/1309/apply-yt-font-proper… https://bitbucket.org/yt_analysis/yt/pull-request/1304/improving-memory-man… https://bitbucket.org/yt_analysis/yt/pull-request/1308/particle_cylindrical… https://bitbucket.org/yt_analysis/yt/pull-request/1300/fix-issues-with-dime… https://bitbucket.org/yt_analysis/yt/pull-request/1299/sphericalcamera-and-… https://bitbucket.org/yt_analysis/yt/pull-request/1307/explicitly-use-path-… Thanks for your help! -Nathan

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A sketch for a cut_region selector
by Nathan Goldbaum Nov. 19, 2014

Nov. 19, 2014

Hi all, I spent some time tonight thinking of a way to supply a cut_region as a data_source for a SlicePlot. Right now this will raise a NotImplementedError, since cut_regions don't work using selectors. Instead, they override data selection at the level of the chunking system. This is a problem for a SlicePlot, since a slice is really a 2D selection object and makes use of a selector object to decide whether or not data should be included in the slice. Cut regions technically could be implemented using selectors, but they don't lend themselves to the geometrically focused selector API. One way around this is to eat some memory and pass the positions of cells that pass the cut_region selection criteria down to the cython selector. Lo and behold, it actually works! Kind of. I've pasted the necessary diff here: http://paste.yt-project.org/show/5210/ Here's an example script: http://paste.yt-project.org/show/5211/ After much gnashing of teeth (about 20 minutes worth on my laptop), this should produce the following image: http://imgur.com/DlHruOi The way I've done this is really bad: not only am I re-aquiring the GIL and messing with python objects inside a tight cython function, but I'm also using the python objects to do an O(N^2) search algorithm! I think it's possible to speed this up significantly by using a smarter search algorithm implemented in C. Before I spend effort on that, I wanted to send this e-mail out to summarize my thoughts and check to see if this is a crazy approach. If this is a worthy approach, does anyone know of an O(logN) search algorithm I could use to find a 3D position in a list of 3D positions? Thanks for taking a look :) -Nathan

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Issue #939: Units error in RAMSES frontend (yt_analysis/yt)
by samgeen Nov. 17, 2014

Nov. 17, 2014

New issue 939: Units error in RAMSES frontend https://bitbucket.org/yt_analysis/yt/issue/939/units-error-in-ramses-fronte… samgeen: There appear to a problem with the units in the RAMSES frontend. I've attached a comparison of pymses and yt slice outputs. I've plotted the pymses density with hydrogen atoms/cm^3, but multiplying by 1.67e-24 should convert to g/cm^3 The box length is 0.0012554779, if this helps (the setup script is in the zip file). I'll try to take a poke at the frontend at some point to see if I can see some bugs.

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convert_to_cgs
by Matthew Turk Nov. 16, 2014

Nov. 16, 2014

Hi all, Would it be feasible (I am volunteering to do this if so) to change instances of convert_to_cgs to something like convert_to_native, and then adding a new set of unit collections? This would basically mean if we wanted units to be in 10^10MSun + Mpc + GYr, it would convert to that, rather than cgs. My naive assumption is that if we had string keys for unit collections, this would be simple, and the unit object would simply check the string key, get the units, and go. -Matt

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yt Developers Hangout
by Hilary Egan Nov. 9, 2014

Nov. 9, 2014

Hi all, We'll be having a yt developers meeting at 2pm EST on Friday, November 14th. Reply to me directly if you'd like an invite to the google hangout. We'll also be recording the meeting as sending out notes in case you are interested, but aren't able to make it. -Hilary

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Issue #938: Units error with creating light ray from single dataset (yt_analysis/yt)
by Devin Silvia Nov. 8, 2014

Nov. 8, 2014

New issue 938: Units error with creating light ray from single dataset https://bitbucket.org/yt_analysis/yt/issue/938/units-error-with-creating-li… Devin Silvia: When I try to generated a light ray from a single dataset, I get a YTUfuncUnitError message. Here's the script: http://paste.yt-project.org/show/5197/ And here is the output: http://paste.yt-project.org/show/5198/ I'd try to troubleshoot this a bit, but all of my attempts just seemed to push the error off to a different piece of the code base, so I think perhaps something more fundamental might be the culprit. Responsible: ngoldbaum

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Issue #937: to_pw silently drops some fields (yt_analysis/yt)
by Douglas Rudd Nov. 7, 2014

Nov. 7, 2014

New issue 937: to_pw silently drops some fields https://bitbucket.org/yt_analysis/yt/issue/937/to_pw-silently-drops-some-fi… Douglas Rudd: to_pw silently drops fields from frb._exclude_fields and _key_fields without notifying the user. ``` #!python >> ds = yt.load("outputs/sedov_000960.art") >> fields = ["density","temperature","dx"] >> plot = ds.slice(2, ds.domain_center[2]).to_pw(fields) >> print plot.fields ['density', 'temperature'] ``` In this case ('index', 'dx') is in both exclusion lists. Any reason I can't plot a slice of my resolution?

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Issue #936: No tests for owls_subfind (yt_analysis/yt)
by Kacper Kowalik Nov. 6, 2014

Nov. 6, 2014

New issue 936: No tests for owls_subfind https://bitbucket.org/yt_analysis/yt/issue/936/no-tests-for-owls_subfind Kacper Kowalik: pull request 1247 Responsible: xarthisius

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