Mailman 3 July 2014 - yt-users

Active Particles
by John Regan 24 Jul '14

24 Jul '14

Hi All, I'm having trouble reading Active Particle data from Enzo-3.0 outputs. . . . dd = pf.h.all_data() print dd["RadiationParticle", "particle_position_x"] . . gives File "PrintActiveParticleInfo.py", line 18, in <module> print dd["RadiationParticle", "particle_position_x"] File "/homeappl/home/regan/appl_taito/YT/Dev/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 325, in __getitem__ self.get_data(key) File "/homeappl/home/regan/appl_taito/YT/Dev/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 2627, in get_data if self._generate_field(field): File "/homeappl/home/regan/appl_taito/YT/Dev/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 358, in _generate_field raise KeyError(field) KeyError: ('RadiationParticle', 'particle_position_x') >From dumping the hdf5 file the dataset (particle_position_x) exists in the group RadiationParticle. I'm probably missing something simple.... but any hints would be appreciated! Oh I'm using yt-2.7.dev John P.S. Is there documentation on the yt website for reading Enzo-3.0 outputs? (yt-x86_64)[regan@taito-login3 GeneralRoutines]$ yt version yt module located at: /homeappl/home/regan/appl_taito/YT/Dev/yt-x86_64/src/yt-hg The supplemental repositories are located at: /homeappl/home/regan/appl_taito/YT/Dev/yt-x86_64/src/yt-supplemental The current version and changeset for the code is: --- Version = 2.7-dev Changeset = e89295c7393d --- This installation CAN be automatically updated. yt dependencies were last updated on Tue Dec 3 18:24:50 EET 2013 To update all dependencies, run "yt update --all". (yt-x86_64)[regan@taito-login3 GeneralRoutines]$

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doc bug?
by Michael Zingale 24 Jul '14

24 Jul '14

Looking at the documentation for the PhasePlot here: http://yt-project.org/docs/dev-3.0/visualizing/plots.html#d-phase-plots both of the examples use "weight_field=None", but I think that for the second case, we really want to omit that argument to get an average. Looking at that plot, if we say that is an average, is seems strange to have an H fraction of 100. Am I missing something? -- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale(a)stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale

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ortho_ray question
by Michael Zingale 24 Jul '14

24 Jul '14

I am trying to use ortho_ray. If I do: c = ds.find_max("temperature") coords = c[1] ray = ds.ortho_ray(0, (coords[1], coords[2])) and then plot ray["density"] vs. ray["x"] , I get a jumbled mess. Printing ray["x"], I see that it is not monotonic -- should I expect it to be? The docs seem to suggest that it would be sorted properly. -- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale(a)stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale

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volume rendering handedness
by Michael Zingale 23 Jul '14

23 Jul '14

I've been having trouble understanding the parameters that specify the orientation of the camera for volume rendering. To help, I made a test dataset. On [-1,1]^3, there is a sphere at the origin, a single cube on the +x axis, two cubes on the +y axis, and three cubes on the +z axis. When I do a simple volume-render, I see this: http://bender.astro.sunysb.edu/random/yt-test.png Note that it looks left-handed. I've attached my script. There are a few hacks that I needed to do that I don't completely understand. In particular, if I turn on the coordinate_vectors, the image is blank. I've seen this a lot. Also, I had to make the north vector negative of what I would think. Mike -- #!/usr/bin/env python import matplotlib matplotlib.use('agg') # this example comes from # http://yt-project.org/doc/visualizing/volume_rendering.html import math import sys import pylab from yt.mods import * import yt.visualization.volume_rendering.api as vr def doit(plotfile): ds = load(plotfile) cm = "gist_rainbow" field = ('gas', 'density') use_log = False vals = [0.1, 1] sigma = 0.1 dd = ds.h.all_data() ds.field_info[field].take_log = use_log mi = min(vals) ma = max(vals) if use_log: mi, ma = np.log10(mi), np.log10(ma) # Instantiate the ColorTransferfunction. tf = vr.ColorTransferFunction((mi, ma)) # 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: if (use_log): tf.sample_colormap(math.log10(v), sigma**2, colormap=cm) #, alpha=0.2) else: 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, no_ghost=False, #data_source=reg, north_vector=north, fields = [field], log_fields = [use_log]) #cam.rotate(3.0*np.pi/2., rot_vector=rot_vector) # 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("yt-test.png", nim, 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) -- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale(a)stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale

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TotalMass
by Yong Zheng 22 Jul '14

22 Jul '14

Hi, I am trying to calculate the total mass of an object, but found the result slightly different when I use different methods. To explain the question, I use the test data set in $YT_DEST/src/yt-hg/tests: pf = load("DD0010/moving7_0010") dd = pf.h.all_data() then dd["TotalMassMsun"].sum() returns 1.25198e12 Msun, but dd.quantities["TotalMass"]() returns 1.22517e12 Msun The document says that the first method returns the total mass of baryon and dark matter, while the second returns the total mass of baryon and particles. I wonder what is the difference here? In this data, there is only type of particle (particle_type = 1), so supposedly particle mass should represent the dark matter mass, right? Thanks for your help! Yong

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Long live "Dataset"
by Matthew Turk 19 Jul '14

19 Jul '14

Hi all, A big pull request, pushed by Nathan and accepted by Britton, has globally changed "pf" (an enzo-ism for "parameter file") to "ds" (for "dataset") everywhere in the code base. Fortunately, there's a backcompat layer, but from here on out, long live "ds"! -Matt

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text onto 3D image
by Stephanie Tonnesen 19 Jul '14

19 Jul '14

Hi yt-ers, I am making individual snapshots of a simulation, using: >from yt.visualization.volume_rendering.api import ColorTransferFunction >tf = ColorTransferFunction((-29,-24)) >tf.add_layers(8,w=0.05,colormap="Hue Sat Value 2") >tf.sample_colormap(-26.5,w=0.02,colormap="Hue Sat Value 2") >cam = pf.h.camera([0.0,0.0,1.8],[0.0,-1.0,-0.2],4.4,1024,tf) >im = cam.snapshot('rpsdip_'+sys.argv[1]+'_volumeall.png') I would like to add a timestamp to the frame (and possibly my name while I'm at it!). I know how to add text to a plot, but am not sure how to do it here. Any help is most appreciated! Thanks, Stephanie

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Particle filters and subsequent particle deposition
by Cameron Hummels 19 Jul '14

19 Jul '14

I'm playing with the new particle filter functionality in yt-3.0, but I'm running into some problems. I can successfully create a particle filter, but how do I get those fields to be subsequently deposited on the grid (like the other fields in the "deposit" namespace)? Is there a command for forcing a particle field deposition on to the grid? Thanks! Cameron -- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org

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Coexistence of positive and negative values on a SlicePlot in log scale
by Suoqing JI 17 Jul '14

17 Jul '14

Hi, I understand that typically the negative values would appear as white color on a log slice plot. However, if I directly plot the fields that are generically defined in FLASH, the negative values DO appear correctly. For example, the velx field: http://pbrd.co/1jz3iqR. But for any derived fields, for example, defining velx1 = 1.*velx, the negative values appear white again: http://pbrd.co/1jz4oD8. So, is there anyway to show both positive and negative values on a log slice plot for derived fields (I’m using YT2)? Thanks! Best wishes, -- Suoqing JI Ph.D Student Department of Physics University of California, Santa Barbara CA 93106, USA

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cut_region index error with Tipsy
by Samantha Benincasa 17 Jul '14

17 Jul '14

Hi everyone, I'm working with a Gasoline dataset. I'm trying to create a cut region and then image/analyze just the particles in that set. I'm able to successfully create the region using: cr = ad.cut_region(["obj['Gas','Temperature'] < 1000"]) However, when I try to image that region: proj = ProjectionPlot(pf, "z", ('Gas','Density'),weight_field=('Gas','Density'),data_source=cr) I get the following error: --------------------------------------------------------------------------- IndexError Traceback (most recent call last) <ipython-input-14-4d67ba49bdf1> in <module>() ----> 1 proj = ProjectionPlot(pf, "z", ('Gas','Density'),weight_field=('Gas','Density'),data_source=cr) /1/home/benincsm/yt/yt-3.0-test/yt/yt/visualization/plot_window.pyc in __init__(self, pf, axis, fields, center, width, axes_unit, weight_field, max_level, origin, fontsize, field_parameters, data_source, proj_style, window_size, aspect) 1217 proj = pf.proj(fields, axis, weight_field=weight_field, 1218 center=center, data_source=data_source, -> 1219 field_parameters = field_parameters, style = proj_style) 1220 PWViewerMPL.__init__(self, proj, bounds, fields=fields, origin=origin, 1221 fontsize=fontsize, window_size=window_size, aspect=aspect) /1/home/benincsm/yt/yt-3.0-test/yt/yt/data_objects/construction_data_containers.pyc in __init__(self, field, axis, weight_field, center, pf, data_source, style, field_parameters) 226 self.data_source = data_source 227 self.weight_field = weight_field --> 228 self.get_data(field) 229 230 @property /1/home/benincsm/yt/yt-3.0-test/yt/yt/data_objects/construction_data_containers.pyc in get_data(self, fields) 266 # We do this once 267 for chunk in self.data_source.chunks([], "io", local_only = False): --> 268 self._initialize_chunk(chunk, tree) 269 # This needs to be parallel_objects-ified 270 with self.data_source._field_parameter_state(self.field_parameters): /1/home/benincsm/yt/yt-3.0-test/yt/yt/data_objects/construction_data_containers.pyc in _initialize_chunk(self, chunk, tree) 342 343 def _initialize_chunk(self, chunk, tree): --> 344 icoords = chunk.icoords 345 xax = self.pf.coordinates.x_axis[self.axis] 346 yax = self.pf.coordinates.y_axis[self.axis] /1/home/benincsm/yt/yt-3.0-test/yt/yt/data_objects/selection_data_containers.pyc in icoords(self) 733 @property 734 def icoords(self): --> 735 return self.base_object.icoords[self._cond_ind,:] 736 737 @property IndexError: index 9025361 is out of bounds for axis 0 with size 9025360 Is the imaging step not yet supported in yt-3.0? Thanks, Sam

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