Mailman 3 July 2013 - yt-users

Unexpected behavior with camera.draw_domain and camera.draw_grids
by Noel Scudder July 10, 2013

July 10, 2013

Hi yt users, I'm having a lot of trouble recreating a volume rendering I did a couple of weeks ago. Specifically, when I try to add a boundary box to my snapshot through draw_domain() or grids through draw_grids(), the transfer function rendering fades very significantly, regardless of alpha value, and it did not behave this way before. However, it does not fade for cam.draw_box(... , ... , np.array([0.1, 0.1, 0.1, 0.2]) . Since draw_domain is basically just a call to draw_box, I took a look in camera.py and did a bit of testing, and the only difference is that the color array is np.array([1.0,1.0,1.0,alpha]) (where alpha=0.2) for draw_domain, and that is what seemed to be causing so much fade in the case of draw_domain. I didn't experience this problem before. Also, I don't know much about how this color stuff works, but I was under the impression that only the alpha value determined how bright the box is compared to the rendering underneath. Furthermore, when I decrease the alpha value, the box fades, but so does the rendering underneath, which should not be the case (?). I see the same behavior when doing draw_grids. Here is the image I created a couple of weeks ago: http://i.imgur.com/R0uhz2D.png And here is the image that the same script (very nearly) creates now: http://i.imgur.com/xcTmCMC.png The rendering underneath the grids is nearly invisible in the second one. If I stack another draw_grids onto the image after this, for a different level range, the rendering goes completely invisible, and the first set of grids almost does-- again, even with alpha values of ~0.05. For reference, here is the script I'm using: ----------------------- from yt.mods import * pf = load("plt_derr_perr_grav_00020") field = "pressure" [variable definitions, cut out for clarity] pf.h pf.field_info[field].take_log=True tf = ColorTransferFunction((mi-1, ma+1), nbins=1.0e6) tf.sample_colormap(np.log10(2.0e21), 0.006, col_bounds=[mi,ma], alpha=[55.0], colormap="RdBu_r") tf.add_layers(6, mi=di, ma=da, col_bounds=[pu,da], alpha=26*na.ones(6,dtype='float64'), colormap="RdBu_r") [more layers, cut out for clarity] tf.grey_opacity=True c = [5.0e9, 5.0e9, 5.0e9] L = [0.15, 1.0, 0.4] W = (pf.domain_right_edge - pf.domain_left_edge)*1.25 Nvec = 768 cam = pf.h.camera(c, L, W, (Nvec,Nvec), transfer_function = tf, fields=[field], pf=pf, no_ghost=False) im = cam.snapshot(clip_ratio=6.0) im.add_background_color('black', inline=True) cam.draw_box(im, np.array([3.0e9, 4.0e9, 4.0e9]), np.array([7.0e9, 6.0e9, 6.0e9]), np.array([0.1, 0.1, 0.1, 0.2])) nim = cam.draw_grids(im, alpha=0.08, min_level=1) nim.write_png('v1.png') ----------------------- Am I doing something wrong or missing something obvious? Was the behavior of draw_grids and draw_domain changed with the new update? Thanks for your help! -Noel Scudder

2 2

Enzo 2.3 and Method Paper released.
by David Collins July 10, 2013

July 10, 2013

Dear Colleague-- We are pleased to announce the joint release of Enzo 2.3 and the Enzo method paper, entitled "Enzo: An Adaptive Mesh Refinement Code for Astrophysics." Enzo 2.3 brings some new physics packages, improvements to the code, and some needed bug fixes. The method paper describes in detail the algorithms used for every physics package presented in this release, along with test problems and a description of the community development practices that have made the code so successful. The new physics modules in Enzo 2.3 include a constrained transport MHD method (MHDCT) and a new radiation background described by Haardt & Madau 2012, a PPM implementation for CUDA, and improvements to the CUDA MHD solver. Code improvements include MPI performance timers and improvements to the inline interface between Enzo and the analysis package yt, and several new problem types, including a cluster potential problem, a magnetic reconnection problem that utilizes the new MHDCT solver, and a particle orbit problem. Bug fixes to the gravity, chemistry, and radiation solvers are also included. The components of this release can be found by following these links: - The paper can be found here <http://arxiv.org/abs/1307.2265> - The code to reproduce the tests can be found at here<http://enzo-project.org/ReleaseNotes.html> - Enzo 2.3 can be found here <https://bitbucket.org/enzo/enzo-stable> - The continually updated development branch can be found here<https://bitbucket.org/enzo/enzo-dev> - A full list of changes can be found here<http://enzo-project.org/ReleaseNotes.html> - Documentation can be found at enzo-project.org <http://enzo-project.org/enzo-project.org>, along with links to the above. Sincerely, David Collins, on behalf of the Enzo Collaboration.

1 0

Enzo Fields Definition -- regarding
by Reju Sam John July 9, 2013

July 9, 2013

Dear all, In yt distribution where I can find the definition of Enzo Fields that YT knows (like TotalEnergy, GasEnergy, etc. ). Please help me. -- Reju Sam John

4 4

radial profile algorithm
by Reju Sam John July 9, 2013

July 9, 2013

Dear all, How radial profile calculation is defined in yt. Please tell me where i can find the source code of radial profile plotter in the yt distribution. ThankYou -- Reju Sam John

2 2

data_source with SlicePlot
by Elizabeth Tasker July 9, 2013

July 9, 2013

Hi everyone, I seem to have to make sad choice when creating slices or projections: I can't seem to both use a region as the data source for my slice/projection and also specify a font size for the legend / axis labels. With SlicePlot, I can use "fontsize" but there is no data_source argument. With add_projection (which isn't quite a slice but close enough), I have a data_source argument but "fontsize" isn't recognised (I also tried "p.set_font({"size": 30})" but to no avail). Is it possible to have a slice (or projection) with both these options available without resorting to creating frbs? Thanks! Elizabeth

2 7

installation error
by Latif July 9, 2013

July 9, 2013

Hi all, I am trying to install stable release (even tried developement fork) of yt and gettinge the follwing error. Any ideas what is going wrong here. Installing distribute ******************************************** FAILURE REPORT: ******************************************** response = self._open(req, data) File "/usr/users/mlatif/ytnew/yt-x86_64/lib/python2.7/urllib2.py", line 422, in _open '_open', req) File "/usr/users/mlatif/ytnew/yt-x86_64/lib/python2.7/urllib2.py", line 382, in _call_chain result = func(*args) File "/usr/users/mlatif/ytnew/yt-x86_64/lib/python2.7/urllib2.py", line 1222, in https_open return self.do_open(httplib.HTTPSConnection, req) File "/usr/users/mlatif/ytnew/yt-x86_64/lib/python2.7/urllib2.py", line 1184, in do_open raise URLError(err) urllib2.URLError: <urlopen error [Errno 110] Connection timed out> Cheers Latif

2 2

Is there any methods to make peculiar velocity plots?
by Reju Sam John July 8, 2013

July 8, 2013

Dear All, Is there any methods to make peculiar velocity plots in yt? or any methods to plot or calculate mean (and mass weighted among all constituents) velocity of a halo, averaged within the virial radius? Thank you for any help you can provide and for considering my request.. -- Reju Sam John

2 1

saving a plot from a plotcollection object
by mohammad safarzadeh July 8, 2013

July 8, 2013

Hi, When I want to save a plot collection object. I get this error and I would like to know how to resolve this. In [3]: pc=pc=PlotCollection(pf,[ 0.5808,0.5398, 0.4504 ]) yt : [INFO ] 2013-07-07 18:02:49,267 Created plot collection with default plot-center = [0.58079999999999998, 0.53979999999999995, 0.45040000000000002] In [4]: pc.add_thin_projection("particle_density",0,0.1) yt : [INFO ] 2013-07-07 18:03:19,026 Getting the binary hierarchy yt : [INFO ] 2013-07-07 18:03:19,032 Finished with binary hierarchy reading yt : [INFO ] 2013-07-07 18:03:38,125 Projection completed Out[4]: <yt.visualization.plot_types.PCProjectionPlot at 0x3876550> In [20]: pc.save() --------------------------------------------------------------------------- ParseFatalException Traceback (most recent call last) <ipython-input-20-aabd56408a20> in <module>() ----> 1 pc.save() /home/safarzadeh/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.pyc in save(self, basename, format, override, force_save) 181 for plot in self.plots: 182 fn.append(plot.save_image(basename, format=format, --> 183 override=override, force_save=force_save)) 184 mylog.info("Saved %s", fn[-1]) 185 if ytcfg.getboolean("yt", "__withinreason"): /home/safarzadeh/yt-x86_64/src/yt-hg/yt/visualization/plot_types.pyc in save_image(self, prefix, format, override, force_save, figure_canvas) 120 canvas.print_figure(fn) 121 else: --> 122 only_on_root(canvas.print_figure, fn) 123 self["Type"] = self._type_name 124 self["GeneratedAt"] = self.data.pf.unique_identifier /home/safarzadeh/yt-x86_64/src/yt-hg/yt/funcs.pyc in only_on_root(func, *args, **kwargs) 366 cfg_option = "__topcomm_parallel_rank" 367 if not ytcfg.getboolean("yt","__parallel"): --> 368 return func(*args,**kwargs) 369 if ytcfg.getint("yt", cfg_option) > 0: return 370 return func(*args, **kwargs) /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/backend_bases.pyc in print_figure(self, filename, dpi, facecolor, edgecolor, orientation, format, **kwargs) 2015 orientation=orientation, 2016 bbox_inches_restore=_bbox_inches_restore, -> 2017 **kwargs) 2018 finally: 2019 if bbox_inches and restore_bbox: /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/backends/backend_agg.pyc in print_png(self, filename_or_obj, *args, **kwargs) 443 444 def print_png(self, filename_or_obj, *args, **kwargs): --> 445 FigureCanvasAgg.draw(self) 446 renderer = self.get_renderer() 447 original_dpi = renderer.dpi /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/backends/backend_agg.pyc in draw(self) 399 400 self.renderer = self.get_renderer() --> 401 self.figure.draw(self.renderer) 402 403 def get_renderer(self): /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/artist.pyc in draw_wrapper(artist, renderer, *args, **kwargs) 53 def draw_wrapper(artist, renderer, *args, **kwargs): 54 before(artist, renderer) ---> 55 draw(artist, renderer, *args, **kwargs) 56 after(artist, renderer) 57 /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/figure.pyc in draw(self, renderer) 882 dsu.sort(key=itemgetter(0)) 883 for zorder, func, args in dsu: --> 884 func(*args) 885 886 renderer.close_group('figure') /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/artist.pyc in draw_wrapper(artist, renderer, *args, **kwargs) 53 def draw_wrapper(artist, renderer, *args, **kwargs): 54 before(artist, renderer) ---> 55 draw(artist, renderer, *args, **kwargs) 56 after(artist, renderer) 57 /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/axes.pyc in draw(self, renderer, inframe) 1981 1982 for zorder, a in dsu: -> 1983 a.draw(renderer) 1984 1985 renderer.close_group('axes') /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/artist.pyc in draw_wrapper(artist, renderer, *args, **kwargs) 53 def draw_wrapper(artist, renderer, *args, **kwargs): 54 before(artist, renderer) ---> 55 draw(artist, renderer, *args, **kwargs) 56 after(artist, renderer) 57 /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/axis.pyc in draw(self, renderer, *args, **kwargs) 1047 self._update_label_position(ticklabelBoxes, ticklabelBoxes2) 1048 -> 1049 self.label.draw(renderer) 1050 1051 self._update_offset_text_position(ticklabelBoxes, ticklabelBoxes2) /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/artist.pyc in draw_wrapper(artist, renderer, *args, **kwargs) 53 def draw_wrapper(artist, renderer, *args, **kwargs): 54 before(artist, renderer) ---> 55 draw(artist, renderer, *args, **kwargs) 56 after(artist, renderer) 57 /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/text.pyc in draw(self, renderer) 524 renderer.open_group('text', self.get_gid()) 525 --> 526 bbox, info = self._get_layout(renderer) 527 trans = self.get_transform() 528 /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/text.pyc in _get_layout(self, renderer) 307 w, h, d = get_text_width_height_descent(clean_line, 308 self._fontproperties, --> 309 ismath=ismath) 310 else: 311 w, h, d = 0, 0, 0 /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/backends/backend_agg.pyc in get_text_width_height_descent(self, s, prop, ismath) 177 if ismath: 178 ox, oy, width, height, descent, fonts, used_characters = \ --> 179 self.mathtext_parser.parse(s, self.dpi, prop) 180 return width, height, descent 181 /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/mathtext.pyc in parse(self, s, dpi, prop) 2972 self.__class__._parser = Parser() 2973 -> 2974 box = self._parser.parse(s, font_output, fontsize, dpi) 2975 font_output.set_canvas_size(box.width, box.height, box.depth) 2976 result = font_output.get_results(box) /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/mathtext.pyc in parse(self, s, fonts_object, fontsize, dpi) 2350 self._state_stack = [self.State(fonts_object, 'default', 'rm', fontsize, dpi)] 2351 try: -> 2352 self._expression.parseString(s) 2353 except ParseException, err: 2354 raise ValueError("\n".join([ /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc in parseString(self, instring, parseAll) 1046 if not self.keepTabs: 1047 instring = instring.expandtabs() -> 1048 loc, tokens = self._parse( instring, 0 ) 1049 if parseAll: 1050 StringEnd()._parse( instring, loc ) /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc in _parseCache(self, instring, loc, doActions, callPreParse) 979 else: 980 try: --> 981 value = self._parseNoCache( instring, loc, doActions, callPreParse ) 982 ParserElement._exprArgCache[ lookup ] = (value[0],value[1].copy()) 983 return value /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc in _parseNoCache(self, instring, loc, doActions, callPreParse) 922 if self.mayIndexError or loc >= len(instring): 923 try: --> 924 loc,tokens = self.parseImpl( instring, preloc, doActions ) 925 except IndexError: 926 raise ParseException( instring, len(instring), self.errmsg, self ) /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc in parseImpl(self, instring, loc, doActions) 2557 def parseImpl( self, instring, loc, doActions=True ): 2558 if self.expr is not None: -> 2559 return self.expr._parse( instring, loc, doActions, callPreParse=False ) 2560 else: 2561 raise ParseException("",loc,self.errmsg,self) /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc in _parseCache(self, instring, loc, doActions, callPreParse) 979 else: 980 try: --> 981 value = self._parseNoCache( instring, loc, doActions, callPreParse ) 982 ParserElement._exprArgCache[ lookup ] = (value[0],value[1].copy()) 983 return value /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc in _parseNoCache(self, instring, loc, doActions, callPreParse) 922 if self.mayIndexError or loc >= len(instring): 923 try: --> 924 loc,tokens = self.parseImpl( instring, preloc, doActions ) 925 except IndexError: 926 raise ParseException( instring, len(instring), self.errmsg, self ) /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc in parseImpl(self, instring, loc, doActions) 2305 raise ParseSyntaxException( ParseException(instring, len(instring), self.errmsg, self) ) 2306 else: -> 2307 loc, exprtokens = e._parse( instring, loc, doActions ) 2308 if exprtokens or exprtokens.keys(): 2309 resultlist += exprtokens /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc in _parseCache(self, instring, loc, doActions, callPreParse) 979 else: 980 try: --> 981 value = self._parseNoCache( instring, loc, doActions, callPreParse ) 982 ParserElement._exprArgCache[ lookup ] = (value[0],value[1].copy()) 983 return value /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc in _parseNoCache(self, instring, loc, doActions, callPreParse) 922 if self.mayIndexError or loc >= len(instring): 923 try: --> 924 loc,tokens = self.parseImpl( instring, preloc, doActions ) 925 except IndexError: 926 raise ParseException( instring, len(instring), self.errmsg, self ) /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc in parseImpl(self, instring, loc, doActions) 2670 tokens = [] 2671 try: -> 2672 loc, tokens = self.expr._parse( instring, loc, doActions, callPreParse=False ) 2673 hasIgnoreExprs = ( len(self.ignoreExprs) > 0 ) 2674 while 1: /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc in _parseCache(self, instring, loc, doActions, callPreParse) 979 else: 980 try: --> 981 value = self._parseNoCache( instring, loc, doActions, callPreParse ) 982 ParserElement._exprArgCache[ lookup ] = (value[0],value[1].copy()) 983 return value /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc in _parseNoCache(self, instring, loc, doActions, callPreParse) 922 if self.mayIndexError or loc >= len(instring): 923 try: --> 924 loc,tokens = self.parseImpl( instring, preloc, doActions ) 925 except IndexError: 926 raise ParseException( instring, len(instring), self.errmsg, self ) /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc in parseImpl(self, instring, loc, doActions) 2305 raise ParseSyntaxException( ParseException(instring, len(instring), self.errmsg, self) ) 2306 else: -> 2307 loc, exprtokens = e._parse( instring, loc, doActions ) 2308 if exprtokens or exprtokens.keys(): 2309 resultlist += exprtokens /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc in _parseCache(self, instring, loc, doActions, callPreParse) 979 else: 980 try: --> 981 value = self._parseNoCache( instring, loc, doActions, callPreParse ) 982 ParserElement._exprArgCache[ lookup ] = (value[0],value[1].copy()) 983 return value /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc in _parseNoCache(self, instring, loc, doActions, callPreParse) 922 if self.mayIndexError or loc >= len(instring): 923 try: --> 924 loc,tokens = self.parseImpl( instring, preloc, doActions ) 925 except IndexError: 926 raise ParseException( instring, len(instring), self.errmsg, self ) /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc in parseImpl(self, instring, loc, doActions) 2414 for e in self.exprs: 2415 try: -> 2416 ret = e._parse( instring, loc, doActions ) 2417 return ret 2418 except ParseException, err: /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc in _parseCache(self, instring, loc, doActions, callPreParse) 979 else: 980 try: --> 981 value = self._parseNoCache( instring, loc, doActions, callPreParse ) 982 ParserElement._exprArgCache[ lookup ] = (value[0],value[1].copy()) 983 return value /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc in _parseNoCache(self, instring, loc, doActions, callPreParse) 948 else: 949 for fn in self.parseAction: --> 950 tokens = fn( instring, tokensStart, retTokens ) 951 if tokens is not None: 952 retTokens = ParseResults( tokens, /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/mathtext.pyc in raise_error(s, loc, toks) 2047 """ 2048 def raise_error(s, loc, toks): -> 2049 raise ParseFatalException(msg + "\n" + s) 2050 2051 empty = Empty() ParseFatalException: Expected end of math '$' $\rm{$\mathrm{Particle}\/\mathrm{Density}$}$ (at char 0), (line:1, col:1)

2 1

Command line rendering error
by Noel Scudder July 3, 2013

July 3, 2013

Hi yt users, I'm having a problem volume rendering through the command line. I've been playing around with the yt command, and I noticed that when I do $ yt plot --field density plt_def_00020 I will get plots for my axes just as I would expect. However, if I do $ yt render --field density plt_def_00020 I get the following error: Traceback (most recent call last): File "/home/noel/shocks/yt-x86_64/bin/yt", line 9, in <module> load_entry_point('yt==2.5.4', 'console_scripts', 'yt')() File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 1691, in run_main args.func(args) File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 97, in run self(args) File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 1404, in __call__ cam = pf.h.camera(center, L, width, (N,N), transfer_function=tf) File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 225, in __init__ self.log_fields = [self.pf.field_info[f].take_log for f in self.fields] File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 131, in __missing__ return self.fallback[key] File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 131, in __missing__ return self.fallback[key] File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 130, in __missing__ raise KeyError("No field named %s" % key) KeyError: 'No field named Density' It looks to me like the Camera function isn't being called with a specific field, and is defaulting to "Density", which is not a field for Castro data. I took a stab at fixing this by editing the camera line to cam = pf.h.camera(center, L, width, (N,N), transfer_function=tf, fields=field) But then my command yields the following error: Traceback (most recent call last): File "/home/noel/shocks/yt-x86_64/bin/yt", line 9, in <module> load_entry_point('yt==2.5.4', 'console_scripts', 'yt')() File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 1691, in run_main args.func(args) File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 97, in run self(args) File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 1404, in __call__ cam = pf.h.camera(center, L, width, (N,N), transfer_function=tf, fields=field) File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 225, in __init__ self.log_fields = [self.pf.field_info[f].take_log for f in self.fields] File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 131, in __missing__ return self.fallback[key] File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 131, in __missing__ return self.fallback[key] File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 130, in __missing__ raise KeyError("No field named %s" % key) KeyError: 'No field named d' I tried to delve a little deeper, but couldn't make any more headway. Does anyone know how to fix these errors? Thanks in advance. Cheers, Noel Scudder

2 1

No 'astype' attribute error - clump finding, volume rendering
by Noel Scudder July 2, 2013

July 2, 2013

Hi yt users, I have a (hopefully) simple question I'm hoping to get cleared up. I've run into the same error both in clump finding and volume rendering: AttributeError: 'list' object has no attribute 'astype'. My volume rendering script: ---------------------- from yt.mods import * pf = load("plt_derr_perr_grav_00020") field = "pressure" pf.h #color transfer function/layer creation I'll leave out for clarity c = [5.0e9, 5.0e9, 5.0e9] L = [0.15, 1.0, 0.20] W = (pf.domain_right_edge - pf.domain_left_edge)*0.5 Nvec = 768 cam = pf.h.camera(c, L, W, (Nvec,Nvec), transfer_function = tf, fields=[field], pf=pf, no_ghost=False) im = cam.snapshot(clip_ratio=6.0) ... ---------------------- Without "no_ghost=False", the script runs as it's supposed to. If it's included, I get the following message: File "<stdin>", line 1, in <module> File "volume.py", line 17, in <module> cam.snapshot("v1.png") File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 684, in snapshot self.initialize_source() File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 636, in initialize_source return self.volume.initialize_source() File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.py", line 200, in initialize_source for b in self.traverse(): File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.py", line 210, in traverse yield self.get_brick_data(node) File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.py", line 284, in get_brick_data vcd = grid.get_vertex_centered_data(field,smoothed=True,no_ghost=self.no_ghost).astype('float64') File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 510, in get_vertex_centered_data cg = self.retrieve_ghost_zones(1, field, smoothed=smoothed) File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 477, in retrieve_ghost_zones level, new_left_edge, **kwargs) File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 3867, in __init__ self.pf.domain_dimensions.astype("float64")) AttributeError: 'list' object has no attribute 'astype' My clump-finding script closely follows the "Identifying Clumps" recipe in the cookbook: ---------------------- from yt.mods import * from yt.analysis_modules.level_sets.api import * field = "density" step = 2.0 pf = load("plt_derr_perr_grav_00020") pf.h data_source = pf.h.all_data() c_min = 10**na.floor(na.log10(data_source[field]).min() ) c_max = 10**na.floor(na.log10(data_source[field]).max()+1) function = 'self.data[\'%s\'].size > 8' %field master_clump = Clump(data_source, None, field, function=function) find_clumps(master_clump, c_min, c_max, step) ... ---------------------- An error will occur occur at find_clumps: Finding clumps: min: 1.500000e-04, max: 1.500000e+07, step: 2.000000 First pass100% |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 Traceback (most recent call last): | ETA: --:--:-- File "<stdin>", line 1, in <module> File "clumps.py", line 30, in <module> find_clumps(master_clump, c_min, c_max, step) File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 179, in find_clumps clump.find_children(min_val) File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 120, in find_children self.cached_fields) File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/contour_finder.py", line 107, in identify_contours cg = grid.retrieve_ghost_zones(1, "tempContours", smoothed=False) File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 479, in retrieve_ghost_zones cube = self.hierarchy.covering_grid(level, new_left_edge, **kwargs) File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 3706, in __init__ self.dds = self.pf.domain_width/rdx.astype("float64") AttributeError: 'list' object has no attribute 'astype' Can anyone tell me why I am getting this error in both cases? I've been doing my utmost, but I'm not familiar enough with python nor yt yet.Thanks for your help! Cheers, Noel Scudder

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