Mailman 3 January 2011 - yt-users

'figure' parameter in add_profile_sphere
by Nicholas Earl Jan. 6, 2011

Jan. 6, 2011

Hey all, Do do I use the figure function in add_profile_sphere. Specifically, I wish to use the figsize matplotlib function, but I just can't seem to get it to work. Thanks, Nick Earl

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Normalize in BinnedProfile1D
by Nicholas Earl Jan. 6, 2011

Jan. 6, 2011

Hey there, Is there perhaps a quick way to normalize the output of the BinnedProfile1D function? I have this: pf = load("DD%04i/DD%04i" % (n,n)) # opens and loads dataset dd = pf.h.all_data() # selects the entire dataset (for phase plots) bp = BinnedProfile1D(dd, 100, "Metal_Fraction", 1e-11, 1e-3, log_space=True) Is there something like a 'normed=True' parameter? Thanks! Nick

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python error on ncsa-ember
by Agarwal, Shankar Jan. 6, 2011

Jan. 6, 2011

Hi, Problem 1: I recently installed enzo1.5 + YT on NCSA-Ember with the help of Enzo community. I am able to successfully use iyt and ipython. However if I try to execute the following command, i get an error: [sagarwal@ember RD0001]$ python hop_mass_sum.py Traceback (most recent call last): File "hop_mass_sum.py", line 1, in <module> from yt.mods import * ImportError: No module named yt.mods Here is the hop_mass_sum.py script: from yt.mods import * fn = "RedshiftOutput0001" … [View More]

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Colorbar and labels on volume rendered images
by Elizabeth Harper-Clark Jan. 6, 2011

Jan. 6, 2011

Good morning everyone, I was wondering how to add colorbars and text labels (e.g. with the time) to images produced through volume rendering. I am unsure of how to adapt all the usual techniques I know for projections etc. gievn the different technique for drawing the images. I am using a constant colorbar so if anyone can suggest a post-processing way of adding to created images that would work too! I am using the following to create my volume rendered images: for i, snapshot in … [View More]

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Odd path issue
by david collins Jan. 5, 2011

Jan. 5, 2011

Hi there-- I have this odd problem when trying to save a projection. I do pc.add_projection(field,axis) pc.save(name) on newly made projection (not one taken from the cache in X.yt file) and it gives me the following mess: <errstack> print self.pc.save(frame_template%(frame), format = self.format) File "/nics/b/home/collins/local_xt5/src/yt-hg/yt/yt/visualization/plot_collection.py", line 153, in save override=override, force_save=force_save)) File "/nics/b/home/collins/… [View More]local_xt5/src/yt-hg/yt/yt/visualization/plot_types.py", line 121, in save_image only_on_root(canvas.print_figure, fn) File "/nics/b/home/collins/local_xt5/src/yt-hg/yt/yt/funcs.py", line 347, in only_on_root return func(*args,**kwargs) File "/nics/b/home/collins/local_xt5/lib/python2.6/site-packages/matplotlib/backend_bases.py", line 1419, in print_figure **kwargs) File "/nics/b/home/collins/local_xt5/lib/python2.6/site-packages/matplotlib/backend_bases.py", line 1308, in print_eps return ps.print_eps(*args, **kwargs) File "/nics/b/home/collins/local_xt5/lib/python2.6/site-packages/matplotlib/backends/backend_ps.py", line 869, in print_eps return self._print_ps(outfile, 'eps', *args, **kwargs) File "/nics/b/home/collins/local_xt5/lib/python2.6/site-packages/matplotlib/backends/backend_ps.py", line 895, in _print_ps orientation, isLandscape, papertype) File "/nics/b/home/collins/local_xt5/lib/python2.6/site-packages/matplotlib/backends/backend_ps.py", line 969, in _print_figure self.figure.draw(renderer) File "/nics/b/home/collins/local_xt5/lib/python2.6/site-packages/matplotlib/figure.py", line 772, in draw for a in self.axes: a.draw(renderer) File "/nics/b/home/collins/local_xt5/lib/python2.6/site-packages/matplotlib/axes.py", line 1601, in draw a.draw(renderer) File "/nics/b/home/collins/local_xt5/lib/python2.6/site-packages/matplotlib/text.py", line 452, in draw bbox, info = self._get_layout(renderer) File "/nics/b/home/collins/local_xt5/lib/python2.6/site-packages/matplotlib/text.py", line 253, in _get_layout clean_line, self._fontproperties, ismath=ismath) File "/nics/b/home/collins/local_xt5/lib/python2.6/site-packages/matplotlib/backends/backend_ps.py", line 308, in get_text_width_height_descent self.mathtext_parser.parse(s, 72, prop) File "/nics/b/home/collins/local_xt5/lib/python2.6/site-packages/matplotlib/mathtext.py", line 2795, in parse font_output = fontset_class(prop, backend) File "/nics/b/home/collins/local_xt5/lib/python2.6/site-packages/matplotlib/mathtext.py", line 658, in __init__ self._stix_fallback = StixFonts(*args, **kwargs) File "/nics/b/home/collins/local_xt5/lib/python2.6/site-packages/matplotlib/mathtext.py", line 902, in __init__ fullpath = findfont(name) File "/nics/b/home/collins/local_xt5/lib/python2.6/site-packages/matplotlib/font_manager.py", line 1307, in findfont if not os.path.exists(font): File "/nics/b/home/collins/local_xt5/lib/python2.6/genericpath.py", line 18, in exists st = os.stat(path) TypeError: coercing to Unicode: need string or buffer, dict found </errstack> pdb shows that (Pdb) path {'afm': None, 'ttf': '/nics/b/home/collins/local_nautalus/src/yt-x86_64/lib/python2.6/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf'} which isn't a path. I just built from changeset 3628:da3894bf42a5. If I then re-do the plot commands (so it reads the cached projection off disk) it works fine. Has anyone seen this problem? Thanks, d. -- Sent from my Stone Tablet and carried by my Pterodactyl. [View Less]

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Volume rendering error: "No module named extensions.volume_rendering"
by Elizabeth Harper-Clark Jan. 4, 2011

Jan. 4, 2011

Hi guys, I think I am doing something stupid. I have just returned to try to do some volume rendering and I now get the following error (Script at end of email) (please note: I have no problems with any of my other yt scripts): *[h-clark@tpb4 my_scripts]$ python2.6 VolumeRunNew.py GMCidresbig128a yt INFO 2011-01-04 15:32:52,325 Loading plugins from /home/h-clark/.yt/my_plugins.py /home/h-clark/YT/lib/python2.6/site-packages/matplotlib/__init__.py:833: UserWarning: This call to … [View More]matplotlib.use() has no effect because the the backend has already been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot, or matplotlib.backends is imported for the first time. if warn: warnings.warn(_use_error_msg) Traceback (most recent call last): File "VolumeRunNew.py", line 2, in <module> import yt.extensions.volume_rendering as vr ImportError: No module named extensions.volume_rendering * I tried with the simple volume rendering code in the cookbook too and get the same error. I tried updating yt: *[h-clark@tpb4 yt-hg]$ hg pull pulling from http://hg.enzotools.org/yt/ searching for changes adding changesets adding manifests adding file changes added 134 changesets with 198 changes to 91 files (-1 heads) (run 'hg update' to get a working copy) [h-clark@tpb4 yt-hg]$ hg update 75 files updated, 0 files merged, 3 files removed, 0 files unresolved [h-clark@tpb4 yt-hg]$ hg identify 4db47be8e251 (yt) tip* but still get the same error. What am I doing wrong? Thanks, Libby Script: from yt.mods import * import yt.extensions.volume_rendering as vr import numpy as na import yt.amr_utils as au import yt.extensions.image_writer as iw N = 1024 pi = 3.1415926535897932384626433832795028841971693993751058209749445923078164062862089986280348253421170679 frame_template = "aaSN/%s/3D3_%04i_%02i.png" #frame_template = "aaWoC/%s/3D3_%04i_%02i.png" alpha_channel = 255*na.ones((N,N,1), dtype='uint8') def save(arr, fn, norm = 0.5): arr = arr / (norm*arr.max()) # assume min = 0 arr = na.clip( arr*255, 0, 255).astype("uint8") arr = na.concatenate( [arr, alpha_channel], axis=-1) au.write_png(arr.copy(), fn) for numb in range(50,51): print "Numb = ",numb pf = load(os.path.expanduser("/home/h-clark/my_scripts/SciNet/%s/DD%04i/data%04i" % (sys.argv[-1],numb, numb))) #pf = load(os.path.expanduser("/home/h-clark/my_scripts/WOCOUT/%s/DD%04i/data%04i" % (sys.argv[-1],numb, numb))) #c = pf.h.find_max("Density")[1] c = [0.5,0.5,0.5] W = 1.0 tf = vr.ColorTransferFunction((-24, -20.0)) dd = pf.h.sphere(c, 0.1) print dd.quantities["Extrema"]("Density") hv = vr.HomogenizedVolume(fields = ["Density"], pf = pf) h5fn = "%s_partitioned.h5" % pf if not os.path.exists(h5fn): hv.initialize_source() hv.store_bricks(h5fn) else: hv.load_bricks(h5fn) tf.add_layers(10, colormap='hot', w=0.03) for theta in range (0,1): zeta = 0.8 epz = 0.5 athe = 0.5*pi aphi = 0.62 + 2*pi*theta/100 #2*pi*phi/20 print athe,aphi lx = na.sin(athe)*na.cos(aphi) ly = na.sin(athe)*na.sin(aphi) lz = na.cos(athe) print lx,ly,lz mx = lx*na.cos(zeta) + ly*na.sin(zeta) my = ly*na.cos(zeta) - lx*na.sin(zeta) mz = lz ny = my*na.cos(epz) + mz*na.sin(epz) nz = mz*na.cos(epz) - my*na.sin(epz) nx = mx print "vector:",nx,ny,nz L = [nx, ny, nz] cam = vr.Camera(c, L, W, (N,N), transfer_function = tf, pf = pf, volume = hv, sub_samples=10) frame = cam.snapshot() save(frame, frame_template % (sys.argv[-1],numb,theta), norm = 0.5) [View Less]

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Re: [yt-users] yt-users Digest, Vol 35, Issue 2
by Wolfram Schmidt Jan. 4, 2011

Jan. 4, 2011

On 01/03/2011 07:33 PM, yt-users-request(a)lists.spacepope.org wrote: Hi John, thanks for your suggestions! Unfortunately, the first option doesn't seem to work for multi plots, and I am not sure how option 2 can be carried over to multi plots. Cheers, Wolfram > ------------------------------ > > Message: 2 > Date: Mon, 3 Jan 2011 10:22:21 -0500 > From: John Wise <jwise(a)astro.princeton.edu> > To: Discussion of the yt analysis package > <yt-users(a)lists.… [View More]

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pixel resolution of plots
by Wolfram Schmidt Jan. 3, 2011

Jan. 3, 2011

Hi, is it possible to change the pixel resolution of the plots produced by yt? For printed documents, the default resolution appears to be rather low. Wolfram

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