Mailman 3 February 2014 - yt-users

Fisheye camera problems
by Munier Azzam Salem 06 Feb '14

06 Feb '14

Hey Guys, I'm trying to run the FisheyeCamera, and got an error that the class cannot be found: * File "fisheye.py", line 28, in <module>* * cam = FisheyeCamera(c, radius, fov, N,* *NameError: name 'FisheyeCamera' is not defined* I thought this might be because it was not added to the data_object_registry, so I tried adding it and rebuilding: *data_object_registry["FisheyeCamera"] = FisheyeCamera* but still no dice :/ Any insights here? I also noticed the MosaicFishEye (which I'm guessing helps you render on multiple projectors?), while properly linked up, throws an error, because it calls the function VectorPlane(), in the amr_utils module, which appears to no longer exist in the dev repo. My script's up here <http://pastebin.com/PK0djMtG>. thanks! Munier -- Munier A. Salem // 845.489.6450

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very quick colormap question
by Stephanie Tonnesen 06 Feb '14

06 Feb '14

Can someone tell me which colormap is the default (Seems to be the same for SlicePlot, ProjectionPlot, and PhasePlot)? I want to change the colormap and be clever about it rather than just making the figure in every single option, but for that I need to know my starting point! Thanks, Stephanie

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phase plot png
by Yi Feng 06 Feb '14

06 Feb '14

Hi, I save the phase plot as png file, but the plot in the png file is small and there is large blank region. How to remove the blank region when I save? Or how to save it as pdf file so that I can use pdfcrop? Thanks! -- Sincerely Yi Feng Department of Astronomy&Astrophysics,UC Santa Cruz

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xlim of phase plot
by Yi Feng 04 Feb '14

04 Feb '14

Hi, I have a phase plot, but the lower limit of x-axis is too low and I want to make it larger? So how to change xlim of a phase plot? Thanks! -- Sincerely Yi Feng Department of Astronomy&Astrophysics,UC Santa Cruz

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velocity vectors on a projection
by Mike Butler 04 Feb '14

04 Feb '14

Hello, I was wondering if there is any way in yt to display the weighted average velocity vectors onto a mass-weighted density projection of a small region from one of my Enzo simulations. As far as I can tell, annotate_velocity only works on slices. Is there some other way to do it? Thanks, Mike

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installing YT without internet connection
by Philipp Girichidis 04 Feb '14

04 Feb '14

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phase plot
by Yi Feng 04 Feb '14

04 Feb '14

Hi, I am using the following to get a phase plot: from yt.mods import * pf1 = load("data.0070.3d.hdf5") my_sphere = pf1.h.sphere("c", (10.0, "pc")) plot = PhasePlot(my_sphere, "tracerdensity", "tracerratio", "CellMassMsun", weight_field=None) plot.save("phase.png") But it says: NameError: name 'PhasePlot' is not defined What is wrong? Thanks! -- Sincerely Yi Feng Department of Astronomy&Astrophysics,UC Santa Cruz

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Computing the surface area of an iso-quantity surface
by trobolo dinni 04 Feb '14

04 Feb '14

Dear yt users, I am trying to use the pf.h.surface routine, for example on density: *surface=pf.h.surface(primary,"Density",external_density)* and then using the sum of the triangles area (via surface.triangles) as an estimate of the surface area. But this method is giving me a wrong value in a test dataset, where I already know the right value for the surface area. I would like hence to ask if there is a better way to estimate the surface area of an iso-quantity surface, or if the process I am following is wrong. Below are the commands I am using to estimate the surface: * #computes the surface of the equidensity surface at the desired density* * #obtains the vertices of the triangles composing the surface tassellation approximation* * surface=pf.h.surface(primary,"Density",density)* * surface_density = surface['Density']* * surface_trg_vertices = surface.triangles* * #rearranges the arrays with the vertex of the triangles (coordinates names: a, b, c) to simplify the vectorial computation* * a_x = surface_trg_vertices[:,0][:,0]* * a_y = surface_trg_vertices[:,0][:,1]* * a_z = surface_trg_vertices[:,0][:,2]* * b_x = surface_trg_vertices[:,1][:,0]* * b_y = surface_trg_vertices[:,1][:,1]* * b_z = surface_trg_vertices[:,1][:,2]* * c_x = surface_trg_vertices[:,2][:,0]* * c_y = surface_trg_vertices[:,2][:,1]* * c_z = surface_trg_vertices[:,2][:,2]* * #finds the sides lengths of the triangles (an array for each set of side)* * side_ab = ((a_x - b_x)**2.0 + (a_y - b_y)**2.0 + (a_z - b_z)**2.0)**0.5* * side_bc = ((b_x - c_x)**2.0 + (b_y - c_y)**2.0 + (b_z - c_z)**2.0)**0.5* * side_ca = ((c_x - a_x)**2.0 + (c_y - a_y)**2.0 + (c_z - a_z)**2.0)**0.5* * #computes the altitude of the triangles wrt the ab side* * s = 0.5 * (side_ab + side_bc + side_ca) #semiperimeter* * altitude_side_ab = (2.0 * (s * (s - side_ab) * (s - side_bc) * (s - side_ca))**0.5) / side_ab* * #computes the area of the triangles using ab sides and altitudes * * trg_surface_area = (side_ab * altitude_side_ab) / 2.0* * #computes the total surface area* * total_surface_area = np.sum(trg_surface_area)* Thanks, Roberto

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yet another plot problem!
by Kathy Eastwood 03 Feb '14

03 Feb '14

Dear yt folks.... This is probably a straightup matplotlib question and not a yt question, but....it was working until I got to the colorbar, and I am now confused. Thanks for any help... kathy here is the code: from yt.imods import * import matplotlib as mpl import matplotlib.pyplot as plt #import matplotlib.colorbar as cb from matplotlib.colors import LogNorm #import numpy as np ts = TimeSeriesData.from_filenames("Strat_Box_hdf5_plt_cnt_01*") padding = 0.05 nx = 5 #number of time series images, plus will need space for vertical colorbar ny = 1 #might want to change this later! #Assuming that all images are the same shape and size width = nx +1 #I think this is inches, not sure height = 4 fig = plt.figure(figsize=(width,height),frameon=False) #Trying to save 0.91 to 0.95 horizontally for the colorbar sizex = 0.85/nx sizey = 0.90/ny haxes = [] for j in range(ny): haxes.append([]) for i in range(nx): left = padding + i*sizex bottom = padding + j*sizey ax = fig.add_axes([left, bottom, sizex, sizey],frameon=False) ax.xaxis.set_visible(False) ax.yaxis.set_visible(False) haxes[-1].append(ax) cax = fig.add_axes([0.9, 0.05, 0.04, sizey],frameon=False) cax.xaxis.set_visible(False) cax.yaxis.set_visible(False) for i, pf in enumerate(ts): sl = pf.h.slice(0, pf.domain_center[0],fields=["Density","Temperature"] ) frb = sl.to_frb( (1.0, 'kpc'), (4096,1024),height=(4.0, 'kpc')) dens_axes = [haxes[0][i]] plots = [dens_axes[0].imshow(frb["Density"], origin='lower', norm=LogNorm())] title=[r'$\mathrm{Density}\ (\mathrm{g\ cm^{-3}})$'] orient = 'vertical' cbar = fig.colorbar(plots,cax=cax, orientation=orient) cbar.set_label(title) fig.savefig('ts_test') Here are the errors: --------------------------------------------------------------------------AttributeError Traceback (most recent call last)<ipython-input-7-e0dcab3d98fe> in <module>() 2 orient = 'vertical' 3 ----> 4 cbar = fig.colorbar(plots,cax=cax, orientation=orient) 5 cbar.set_label(title) 6 /Users/kde/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-macosx-10.4-x86_64.egg/matplotlib/figure.pyc in colorbar(self, mappable, cax, ax, use_gridspec, **kw) 1449 cax, kw = cbar.make_axes(ax, **kw) 1450 cax.hold(True)-> 1451 cb = cbar.colorbar_factory(cax, mappable, **kw) 1452 1453 self.sca(current_ax) /Users/kde/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-macosx-10.4-x86_64.egg/matplotlib/colorbar.pyc in colorbar_factory(cax, mappable, **kwargs) 1272 cb = ColorbarPatch(cax, mappable, **kwargs) 1273 else:-> 1274 cb = Colorbar(cax, mappable, **kwargs) 1275 1276 mappable.callbacksSM.connect('changed', cb.on_mappable_changed) /Users/kde/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-macosx-10.4-x86_64.egg/matplotlib/colorbar.pyc in __init__(self, ax, mappable, **kw) 850 # Ensure the given mappable's norm has appropriate vmin and vmax set 851 # even if mappable.draw has not yet been called.--> 852 mappable.autoscale_None() 853 854 self.mappable = mappable AttributeError: 'list' object has no attribute 'autoscale_None' -- Kathy DeGioia Eastwood, Ph.D. Professor of Physics and Astronomy Northern Arizona University Flagstaff, AZ 86011-6010 Ph: 928-523-7159 FX: 928-523-1371 Kathy.Eastwood(a)nau.edu deliveries: 602 S. Humphreys St., Bldg 19 Rm 2

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Error in TotalMass in RAMSES
by Sam Geen 03 Feb '14

03 Feb '14

Hi, I'm trying to find the total energy (kinetic and thermal) in grid cells in a gas-only simulation in RAMSES. I was playing with the functions in the documentation when I ran into an error "YTCouldNotGenerateField: Could field '('all', 'particle_mass')' in info_00014 could not be generated." (full log below) I'm unsure if this is a problem with the RAMSES frontend throwing an error if there are no particles present, or something else (e.g. whether it's not supposed to work with gas-only simulations). I'm sure there's probably a better way to achieve what I was trying to do, but I thought I'd post this up here in case it's a bug. Incidentally - would it be a problem if the RAMSES accepted "output_XXXXX" rather than just "output_XXXXX/info_XXXXX.txt"? The latter is more cumbersome, but I suppose the former might cause problems if another code also uses the format "output_XXXXX". Cheers, Sam --- (c.f. http://yt-project.org/docs/dev/analyzing/objects.html#processing-objects-de…) In [18]: dd.quantities["TotalMass"]() yt : [DEBUG ] 2014-02-03 12:42:12,067 Filling Density with 174760 (2.287e-02 9.034e+01) (174760 zones) --------------------------------------------------------------------------- YTCouldNotGenerateField Traceback (most recent call last) <ipython-input-18-7ea9fe75efad> in <module>() ----> 1 dd.quantities["TotalMass"]() /home/samgeen/Programming/yt/yt/yt/data_objects/derived_quantities.pyc in __call__(self, *args, **kwargs) 63 chunks = self._data_source.chunks([], chunking_style="io") 64 for ds in parallel_objects(chunks, -1): ---> 65 rv = self.func(ds, *args, **kwargs) 66 if not iterable(rv): rv = (rv,) 67 for i in range(self.n_ret): retvals[i].append(rv[i]) /home/samgeen/Programming/yt/yt/yt/data_objects/derived_quantities.pyc in _TotalMass(data) 119 cell_mass = 0.0 120 try: --> 121 particle_mass = _TotalQuantity(data,["ParticleMassMsun"]) 122 except KeyError: 123 particle_mass = 0.0 /home/samgeen/Programming/yt/yt/yt/data_objects/derived_quantities.pyc in _TotalQuantity(data, fields) 697 totals = [] 698 for field in fields: --> 699 if data[field].size < 1: 700 totals.append(np.zeros(1,dtype=prec_accum[data[field].dtype])[0]) 701 continue /home/samgeen/Programming/yt/yt/yt/data_objects/data_containers.pyc in __getitem__(self, key) 189 return self.field_data[f] 190 else: --> 191 self.get_data(f) 192 # Note that this is less succinct so that we can account for the case 193 # when there are, for example, no elements in the object. /home/samgeen/Programming/yt/yt/yt/data_objects/data_containers.pyc in get_data(self, fields) 580 self.field_data.update(read_particles) 581 fields_to_generate += gen_fluids + gen_particles --> 582 self._generate_fields(fields_to_generate) 583 584 def _generate_fields(self, fields_to_generate): /home/samgeen/Programming/yt/yt/yt/data_objects/data_containers.pyc in _generate_fields(self, fields_to_generate) 596 if field in self.field_data: continue 597 try: --> 598 self.field_data[field] = self._generate_field(field) 599 except GenerationInProgress as gip: 600 for f in gip.fields: /home/samgeen/Programming/yt/yt/yt/data_objects/data_containers.pyc in _generate_field(self, field) 221 tr = self._generate_fluid_field(field) 222 if tr is None: --> 223 raise YTCouldNotGenerateField(field, self.pf) 224 return tr 225 YTCouldNotGenerateField: Could field '('all', 'particle_mass')' in info_00014 could not be generated.

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