Mailman 3 February 2014 - yt-users

seg fault in Quadtree
by Britton Smith 28 Feb '14

28 Feb '14

Hi all, I'm trying to make projections of a rather large Enzo dataset and getting a segfault somewhere in Quadtree.so. This dataset is ~230 GB in size with 27 levels of AMR. As far as I can tell, the only hard coded limit I could find in QuadTree.pyx is for 80 levels, which I am clearly below. Does anyone familiar with this part of the code have any idea if there are any other hard-coded limits in here that I might be exceeding? If not, does anyone have any advice for how I might debug this? I'm seeing this behavior in both yt-2.x and yt-3.0, so it does seem to be something intrinsic to the quadtree code. Thanks! Britton

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Issues Installing yt
by Alex Bogert 26 Feb '14

26 Feb '14

Hi all, I am trying to install yt using pip in an anaconda environment I just setup. I am running into an issue with freetype. I installed freetype from this location: http://download.savannah.gnu.org/releases/freetype and I created the freetype.cfg file as shown in the example. Yet, installing with pip produces the same error that it cannot read the FTYPE location from freetype.cfg . Thanks, Alex Install Log : Downloading/unpacking yt Downloading yt-2.6.1.tar.gz (2.3MB): 2.3MB downloaded Running setup.py (path:/global/scratch2/sd/bogert/pip_build_bogert/yt/setup.py) egg_info for package yt non-existing path in 'yt/utilities/spatial': 'tests' PNG_LOCATION: PNG found via ctypes in: /usr/include, /usr/lib64 Reading FTYPE location from freetype.cfg failed. Please place the base directory of your FTYPE install in freetype.cfg and restart. (ex: "echo '/usr/local/' > freetype.cfg" ) You can locate the path by looking for ft2build.h Complete output from command python setup.py egg_info: non-existing path in 'yt/utilities/spatial': 'tests' PNG_LOCATION: PNG found via ctypes in: /usr/include, /usr/lib64 Reading FTYPE location from freetype.cfg failed. Please place the base directory of your FTYPE install in freetype.cfg and restart. (ex: "echo '/usr/local/' > freetype.cfg" ) You can locate the path by looking for ft2build.h

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FixedResolutionBuffer problem
by Mike Butler 26 Feb '14

26 Feb '14

Hello, I am trying to make a fixed resolution buffer of a projection of a region in one of my simulations. Here is the relevant part of the script: size=0.025 center=[0.48,0.545,1.003] right0=[center[0]+size,center[1]+size,center[2]+size] left0=[center[0]-size,center[1]-size,center[2]-size] region=pf.h.region(center,left0,right0) p=pf.h.proj(0,"Density",data_source=region) test=FixedResolutionBuffer(p,[0.52,0.57,0.978,1.028],(512,512)) f=h5py.File("test.h5","w") f.create_dataset("/density",data=test["Density"]) f.close When I write the buffer to a h5 file, it seems to be projecting through the whole domain, instead of only the 0.05x0.05x0.05 region I specify. Any ideas what I am doing wrong? Thanks, Mike

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ProjectionPlot of a new field
by Geoffrey So 25 Feb '14

25 Feb '14

Hi all, Will I be saving computation time by multiplying some constant conversion factors on the projection object instead of creating a derived field with an existing field multiplied by the factors? And how would I go about multiplying the projection by some factors? If there's no significant saving I'll just do the derived field. From G.S.

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Problem with volume rendering
by Joshua G. Albert 25 Feb '14

25 Feb '14

Hello, Attn: Sam Skillman (Matthew thinks you might know a solution) I'm attempting to follow the Simple Volume Rendering recipe given in the cookbook (http://yt-project.org/doc/cookbook/simple_plots.html#Simple_Volume_Rendering). I'm using Ramses simulation output and after consulting Matthew Turk it should be fine, using the bleeding edge version, which I am. My code that fails is: pf = load(header) dd = pf.h.all_data() mi,ma = dd.quantities['Extrema']('Density')[0] tf = ColorTransferFunction((np.log10(mi)+1,np.log10(ma))) tf.add_layers(5,w=0.02) center=pf.domain_center look = [0.0,0.0,-1.0] width = 1.0 res = 512 cam = pf.h.camera(center,look,width,res,tf) cam.snapshot("%s_test_snap.png" % pf, clip_ratio=8.0) #Something fails in the progressbar of all places! I get a series of "Failed to split grids." It fails at snapshot, and at the end of the traceback I find: /data2/albert/ramses/yt-x86_64/src/yt-hg/yt/extern/progressbar/widgets.pyc in update_js(self, pbar) 344 $myPB.progressbar({{value: 0, max: {pbar.maxval:d}}}); 345 }} --> 346 """.format(divid=self.uuid, pbar=pbar) 347 348 ValueError: Unknown format code 'd' for object of type 'float' Any idea how to solve this easily? Possibly a good idea to optionally remove the progressbar in the future? -- Best Regards, Joshua G. Albert

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yt for PLUTO
by Varadarajan Parthasarathy 20 Feb '14

20 Feb '14

Hi, I read through the webpages of yt-project and came to know that PLUTO is partly supported for yt and there is still a scope for creating a new code front end. To that extent, I would like to inform with how much I could get into this: import h5py from yt.mods import * f = h5py.File("/.../.../testproblem/data.nnnn.dbl.h5", "r") print f.items() [(u'cell_coords', <HDF5 group "/cell_coords" (3 members)>), (u'node_coords', <HDF5 group "/node_coords" (3 members)>), (u'vars', <HDF5 group "/vars" (5 members)>)] print f.keys() [u'cell_coords', u'node_coords', u'vars'] where cell_coords and node_coords are X, Y, Z cell and node contain different values. 'vars' are 'prs', 'rho', 'vx1', 'vx2', 'vx3'. But after this I am not able to get the data into the dictionary and hence unable to produce plots. I did see through the PLUTO specified field list, but I am not able to make the way out. Also, the simulation was not run with Chombo refinement, but I hope it may not be a serious issue. Moreover, the procedure given in loading a generic array data for HDF5 files was a bit confusing with regard to, data_dir = ytcfg.get('yt','test_data_dir') f = h5py.File(data_dir+"/Unigriddata/....h5", "r") can anyone explain if this 'test_data_dir' is just the working directory and then 'f' consists of the file, else the procedure that I have followed directly is still correct. I will be really glad if I can get to do data analysis and other such stuff with yt. I hope to hear soon. Regards., Varadarajan

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ANN: SciPy 2014 Conference, July 6th - 12th, Austin, TX!
by Matthew Turk 20 Feb '14

20 Feb '14

Hello All! I am pleased to announce that SciPy 2014, the thirteenth annual Scientific Computing with Python conference, will be held this July 6th-12th in Austin, Texas. SciPy is a community dedicated to the advancement of scientific computing through open source Python software for mathematics, science, and engineering. The annual SciPy Conference allows participants from all types of organizations to showcase their latest projects, learn from skilled users and developers, and collaborate on code development. For more information please visit our website: https://conference.scipy.org/scipy2014/ This year the conference has been extended to include an additional day of presentations. During the presentation days SciPy is proud to host the following event and talk types: Keynotes Expert Panels Short Talks Poster Presentations Birds of a Feather Sessions The full program will consist of two days of tutorials by followed by three days of presentations, and concludes with two days of developer sprints on projects of interest to attendees. This year, we are excited to present a job fair for the first time! Specialized Tracks This year we are happy to announce two specialized tracks that run in parallel to the general conference: Scientific Computing in Education Thanks to efforts such as Software Carpentry, the Hacker Within and grassroots Python Bootcamps, teaching scientific computing as a discipline is becoming more widely accepted and recognized as a crucial task in developing scientific literacy. This special track will focus on efforts to promote and develop scientific computing education, as well as related topics such as reproducibility and best practices for scientific computing. Geospatial Data in Science Python has become a core component of organiziing, understanding, and visualizing geospatial data. This track will focus on libraries, tools and techniques for processing Geospatial data of all types and for all purposes -- from low-volume to high-volume, local and global. Domain-specific Mini-symposia Introduced in 2012, mini-symposia are held to discuss scientific computing applied to a specific scientific domain/industry during a half afternoon after the general conference. Their goal is to promote industry specific libraries and tools, and gather people with similar interests for discussions. Mini-symposia on the following topics will take place this year: Astronomy and astrophysics Bioinformatics Geophysics Vision, Visualization, and Imaging Computational Social Science and Digital Humanities Engineering Tutorials Multiple interactive half-day tutorials will be taught by community experts. The tutorials provide conceptual and practical coverage of tools that have broad interest at both an introductory or advanced level. This year, a third track will be added, which target specifically programmers with no prior knowledge of scientific python. Developer Sprints A hackathon environment is setup for attendees to work on the core SciPy packages or their own personal projects. Theconference is an opportunity for developers that are usually physically separated to come together and engage in highly productive sessions. It is also an occasion for new community members to introduce themselves and receive tips from community experts. This year, some of the sprints will be scheduled and announced ahead of the conference. Birds-of-a-Feather (BOF) Sessions Birds-of-a-Feather sessions are self-organized discussions that run parallel to the main conference. The BOFs sessions cover primary, tangential, or unrelated topics in an interactive, discussion setting. This year, some of the BOF sessions will be scheduled and announced ahead of the conference. Important Dates March 14th: Presentation abstracts, poster, tutorial submission deadline. Application for sponsorship deadline. April 17th: Speakers selected April 22nd: Sponsorship acceptance deadline May 1st: Speaker schedule announced May 6th, or 150 registrants: Early-bird registration ends July 6-12th: 2 days of tutorials, 3 days of conference, 2 days of sprints We look forward to a very exciting conference and hope to see you all in Austin this summer! The SciPy2014 Organizers

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text inside figure window?
by Stephanie Tonnesen 19 Feb '14

19 Feb '14

Hi users, I am still fiddling with PhasePlot, and would now like to be able to have some text inside the window. I am *not* looking for a legend box or anything, just text. If I were writing this on a plot in python I would just be looking to use p.text(x,y,'text'). I will paste the section of code writing the PhasePlot below. Thanks! Stephanie profile = Profile2D(tracerp25, x_field='zkpc', x_n=36, x_min=-6., x_max=0.,x_log=False,y_field='BMagnitude',y_n=40,y_min=1e-8,y_max=1e-4,y_log=True,weight_field=None) profile.add_fields(['CellMassMsun']) plot = PhasePlot(tracerp25,"zkpc","BMagnitude",["CellMassMsun"],profile=profile,fontsize=21) plot.set_log("totPressure",True) plot.set_log("z-velocity",False) plot.set_log("zvelocity8",False) plot.set_zlim("CellMassMsun",9e3,1e8) plot.set_figure_size(4.5) plot.set_cmap(field="CellMassMsun",cmap='Eos B') plot.plots['CellMassMsun'].hide_colorbar() ax = plot.plots['CellMassMsun'].axes ax.set_ylabel(r'|B| (Gauss)',fontsize=18) #ax.set_xlabel('z dist from disk plane (kpc)',fontsize=27) #ax.set_ylabel(r' ',fontsize=27) #ax.set_xlabel('dist below disk plane (kpc)',fontsize=18) ax.set_xlabel(r' ',fontsize=18) for label in ax.xaxis.get_ticklabels(): label.set_rotation(35) label.set_fontsize(18) label.set_visible(False) for label in ax.yaxis.get_ticklabels(): label.set_fontsize(18) # label.set_visible(False) ax.xaxis.set_ticks([-6,-5,-4,-3,-2,-1,0]) plot.save()

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strange error with StarMassMsun
by Geoffrey So 18 Feb '14

18 Feb '14

I'm getting a strange error when executing the command starmass = ell.quantities['TotalQuantity']('StarMassMsun')[0] This is on Stampede, and on my laptop running OSX I did not get the same error. Has anyone else seen something similar? From G.S. In [100]: ell.quantities['TotalQuantity']('StarMassMsun') --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /home1/01041/tg802953/dev-yt/src/yt-hg/scripts/iyt in <module>() ----> 1 ell.quantities['TotalQuantity']('StarMassMsun') /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/derived_quantities.pyc in __call__(self, *args, **kwargs) 80 self._data_source.pf.h.io) 81 if lazy_reader and not self.force_unlazy: ---> 82 return self._call_func_lazy(args, kwargs) 83 else: 84 return self._call_func_unlazy(args, kwargs) /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/derived_quantities.pyc in _call_func_lazy(self, args, kwargs) 87 self.retvals = [ [] for i in range(self.n_ret)] 88 for gi,g in enumerate(self._get_grids()): ---> 89 rv = self.func(GridChildMaskWrapper(g, self._data_source), *args, **kwargs) 90 if not iterable(rv): rv = (rv,) 91 for i in range(self.n_ret): self.retvals[i].append(rv[i]) /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/derived_quantities.pyc in _TotalQuantity(data, fields) 703 totals = [] 704 for field in fields: --> 705 if data[field].size < 1: 706 totals.append(0.0) 707 continue /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/derived_quantities.pyc in __getitem__(self, item) 48 def __getitem__(self, item): 49 if item not in self.local_cache: ---> 50 data = self.data_source._get_data_from_grid(self.grid, item) 51 self.local_cache[item] = data 52 return self.local_cache[item] /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 79 old_keys = grid.field_data.keys() 80 grid.field_parameters = self.field_parameters ---> 81 tr = func(self, grid, field, *args, **kwargs) 82 grid.field_parameters = old_params 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] ) /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 2644 return np.array([f[i,:][pointI] for i in range(3)]) 2645 else: -> 2646 tr = grid[field] 2647 if tr.size == 1: # dx, dy, dz, cellvolume 2648 tr = tr * np.ones(grid.ActiveDimensions, dtype='float64') /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/grid_patch.pyc in __getitem__(self, key) 145 """ 146 if key not in self.field_data: --> 147 self.get_data(key) 148 return self.field_data[key] 149 /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/grid_patch.pyc in get_data(self, field, convert) 188 else: raise 189 else: --> 190 self._generate_field(field) 191 return self.field_data[field] 192 /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/grid_patch.pyc in _generate_field(self, field) 133 self[field] = temp_array[sl] 134 else: --> 135 self[field] = self.pf.field_info[field](self) 136 else: # Can't find the field, try as it might 137 raise exceptions.KeyError(field) /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/field_info_container.pyc in __call__(self, data) 383 ii = self.check_available(data) 384 original_fields = data.keys() # Copy --> 385 dd = self._function(self, data) 386 dd *= self._convert_function(data) 387 for field_name in data.keys(): /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/universal_fields.pyc in _StarMass(field, data) 439 440 def _StarMass(field,data): --> 441 return data["star_density"] * data["CellVolume"] 442 add_field("StarMassMsun", units=r"M_{\odot}", 443 function=_StarMass, /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/grid_patch.pyc in __getitem__(self, key) 145 """ 146 if key not in self.field_data: --> 147 self.get_data(key) 148 return self.field_data[key] 149 /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/grid_patch.pyc in get_data(self, field, convert) 188 else: raise 189 else: --> 190 self._generate_field(field) 191 return self.field_data[field] 192 /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/grid_patch.pyc in _generate_field(self, field) 133 self[field] = temp_array[sl] 134 else: --> 135 self[field] = self.pf.field_info[field](self) 136 else: # Can't find the field, try as it might 137 raise exceptions.KeyError(field) /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/field_info_container.pyc in __call__(self, data) 383 ii = self.check_available(data) 384 original_fields = data.keys() # Copy --> 385 dd = self._function(self, data) 386 dd *= self._convert_function(data) 387 for field_name in data.keys(): /home1/01041/tg802953/dev-yt/src/yt-hg/yt/frontends/enzo/fields.pyc in _spdensity(field, data) 360 blank, np.array(data.LeftEdge).astype(np.float64), 361 np.array(data.ActiveDimensions).astype(np.int32), --> 362 np.float64(data['dx'])) 363 return blank 364 /home1/01041/tg802953/dev-yt/src/yt-hg/yt/utilities/lib/CICDeposit.so in yt.utilities.lib.CICDeposit.CICDeposit_3 (yt/utilities/lib/CICDeposit.c:1643)() ValueError: Buffer dtype mismatch, expected 'float64_t' but got 'float'

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Re: [yt-users] yt-users Digest, Vol 72, Issue 26
by Varadarajan Parthasarathy 18 Feb '14

18 Feb '14

Hi, pf = load("/../../testproblem/data.nnnn.dbl.h5"), as well as pf = load("/../../testproblem/data.nnnn.dbl.h5", "r") gave- File "<stdin>", line 1, in <module> File "/usr/local/lib/python2.7/dist-packages/yt/convenience.py", line 78, in load return output_type_registry[candidates[0]](*args, **kwargs) File "/usr/local/lib/python2.7/dist-packages/yt/frontends/pluto/data_structures.py", line 182, in __init__ self.current_time = self._handle.attrs['time'] File "/usr/lib/python2.7/dist-packages/h5py/_hl/attrs.py", line 36, in __getitem__ attr = h5a.open(self._id, self._e(name)) File "h5a.pyx", line 77, in h5py.h5a.open (h5py/h5a.c:1945) KeyError: "can't open attribute (Attribute: Can't open object)" the h5 files produced from PLUTO are having cell_coords (group), node_coords(group) and vars(group), and this vars contain prs, rho, vx1, vx2 and vx3, which are the data sets, but their attributes are not clear. Cheers, V. On Tue, Feb 18, 2014 at 5:19 PM, <yt-users-request(a)lists.spacepope.org>wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. Re: strange error with StarMassMsun (Geoffrey So) > 2. yt for PLUTO (Varadarajan Parthasarathy) > 3. rainbow+white? (Stephanie Tonnesen) > 4. Re: yt for PLUTO (Kacper Kowalik) > 5. Re: rainbow+white? (Sam Skillman) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 17 Feb 2014 12:38:47 -0800 > From: Geoffrey So <gsiisg(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] strange error with StarMassMsun > Message-ID: <C72AB831-6629-41B4-ADE4-2A9479CA96EA(a)gmail.com> > Content-Type: text/plain; charset=us-ascii > > Thanks, will give it a try and let you know. > > From > G.S. > > Sent from my iPhone > > > On Feb 17, 2014, at 5:01 AM, John Wise <jwise(a)physics.gatech.edu> wrote: > > > > Hi Geoffrey, > > > > This pull request has been merged, so all you have to do is update your > yt installation on Stampede now. > > > > Thanks, > > John > > > >> On 02/16/2014 08:00 PM, John Wise wrote: > >> Hi Geoffrey, > >> > >> This will happen if you're running with 32-bit precision in Enzo, and > >> the particle fields except for position will be in 32-bit. However, the > >> CICDeposit3 routine expects 64-bit floats as input. I've created a pull > >> request that fixes this bug. > >> > >> > https://bitbucket.org/yt_analysis/yt/pull-request/706/input-enzo-deposited-… > >> > >> > >> You can go ahead and test it by pulling my changeset and recompiling. > >> > >> hg pull -r f9127d6 https://bitbucket.org/jwise77/yt > >> hg up > >> > >> Please see if this works for you and comment on the PR page. > >> > >> Cheers, > >> John > >> > >>> On 02/14/2014 05:12 PM, Geoffrey So wrote: > >>> I'm getting a strange error when executing the command > >>> > >>> starmass = ell.quantities['TotalQuantity']('StarMassMsun')[0] > >>> > >>> This is on Stampede, and on my laptop running OSX I did not get the > same > >>> error. Has anyone else seen something similar? > >>> > >>> From > >>> G.S. > >>> > >>> In [100]: ell.quantities['TotalQuantity']('StarMassMsun') > >>> > --------------------------------------------------------------------------- > >>> > >>> ValueError Traceback (most recent call > >>> last) > >>> /home1/01041/tg802953/dev-yt/src/yt-hg/scripts/iyt in <module>() > >>> ----> 1 ell.quantities['TotalQuantity']('StarMassMsun') > >>> > >>> > /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/derived_quantities.pyc > >>> > >>> in __call__(self, *args, **kwargs) > >>> 80 self._data_source.pf.h.io > >>> <http://data_source.pf.h.io>) > >>> 81 if lazy_reader and not self.force_unlazy: > >>> ---> 82 return self._call_func_lazy(args, kwargs) > >>> 83 else: > >>> 84 return self._call_func_unlazy(args, kwargs) > >>> > >>> > /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/derived_quantities.pyc > >>> > >>> in _call_func_lazy(self, args, kwargs) > >>> 87 self.retvals = [ [] for i in range(self.n_ret)] > >>> 88 for gi,g in enumerate(self._get_grids()): > >>> ---> 89 rv = self.func(GridChildMaskWrapper(g, > >>> self._data_source), *args, **kwargs) > >>> 90 if not iterable(rv): rv = (rv,) > >>> 91 for i in range(self.n_ret): > >>> self.retvals[i].append(rv[i]) > >>> > >>> > /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/derived_quantities.pyc > >>> > >>> in _TotalQuantity(data, fields) > >>> 703 totals = [] > >>> 704 for field in fields: > >>> --> 705 if data[field].size < 1: > >>> 706 totals.append(0.0) > >>> 707 continue > >>> > >>> > /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/derived_quantities.pyc > >>> > >>> in __getitem__(self, item) > >>> 48 def __getitem__(self, item): > >>> 49 if item not in self.local_cache: > >>> ---> 50 data = > >>> self.data_source._get_data_from_grid(self.grid, item) > >>> 51 self.local_cache[item] = data > >>> 52 return self.local_cache[item] > >>> > >>> > /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/data_containers.pyc > >>> > >>> in save_state(self, grid, field, *args, **kwargs) > >>> 79 old_keys = grid.field_data.keys() > >>> 80 grid.field_parameters = self.field_parameters > >>> ---> 81 tr = func(self, grid, field, *args, **kwargs) > >>> 82 grid.field_parameters = old_params > >>> 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) > >>> for k in old_keys] ) > >>> > >>> > /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/data_containers.pyc > >>> > >>> in _get_data_from_grid(self, grid, field) > >>> 2644 return np.array([f[i,:][pointI] for i in range(3)]) > >>> 2645 else: > >>> -> 2646 tr = grid[field] > >>> 2647 if tr.size == 1: # dx, dy, dz, cellvolume > >>> 2648 tr = tr * np.ones(grid.ActiveDimensions, > >>> dtype='float64') > >>> > >>> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/grid_patch.pyc > in > >>> __getitem__(self, key) > >>> 145 """ > >>> 146 if key not in self.field_data: > >>> --> 147 self.get_data(key) > >>> 148 return self.field_data[key] > >>> 149 > >>> > >>> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/grid_patch.pyc > in > >>> get_data(self, field, convert) > >>> 188 else: raise > >>> 189 else: > >>> --> 190 self._generate_field(field) > >>> 191 return self.field_data[field] > >>> 192 > >>> > >>> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/grid_patch.pyc > in > >>> _generate_field(self, field) > >>> 133 self[field] = temp_array[sl] > >>> 134 else: > >>> --> 135 self[field] = self.pf.field_info[field](self) > >>> 136 else: # Can't find the field, try as it might > >>> 137 raise exceptions.KeyError(field) > >>> > >>> > /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/field_info_container.pyc > >>> > >>> in __call__(self, data) > >>> 383 ii = self.check_available(data) > >>> 384 original_fields = data.keys() # Copy > >>> --> 385 dd = self._function(self, data) > >>> 386 dd *= self._convert_function(data) > >>> 387 for field_name in data.keys(): > >>> > >>> > /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/universal_fields.pyc > >>> > >>> in _StarMass(field, data) > >>> 439 > >>> 440 def _StarMass(field,data): > >>> --> 441 return data["star_density"] * data["CellVolume"] > >>> 442 add_field("StarMassMsun", units=r"M_{\odot}", > >>> 443 function=_StarMass, > >>> > >>> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/grid_patch.pyc > in > >>> __getitem__(self, key) > >>> 145 """ > >>> 146 if key not in self.field_data: > >>> --> 147 self.get_data(key) > >>> 148 return self.field_data[key] > >>> 149 > >>> > >>> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/grid_patch.pyc > in > >>> get_data(self, field, convert) > >>> 188 else: raise > >>> 189 else: > >>> --> 190 self._generate_field(field) > >>> 191 return self.field_data[field] > >>> 192 > >>> > >>> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/grid_patch.pyc > in > >>> _generate_field(self, field) > >>> 133 self[field] = temp_array[sl] > >>> 134 else: > >>> --> 135 self[field] = self.pf.field_info[field](self) > >>> 136 else: # Can't find the field, try as it might > >>> 137 raise exceptions.KeyError(field) > >>> > >>> > /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/field_info_container.pyc > >>> > >>> in __call__(self, data) > >>> 383 ii = self.check_available(data) > >>> 384 original_fields = data.keys() # Copy > >>> --> 385 dd = self._function(self, data) > >>> 386 dd *= self._convert_function(data) > >>> 387 for field_name in data.keys(): > >>> > >>> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/frontends/enzo/fields.pyc in > >>> _spdensity(field, data) > >>> 360 blank, > >>> np.array(data.LeftEdge).astype(np.float64), > >>> 361 > >>> np.array(data.ActiveDimensions).astype(np.int32), > >>> --> 362 np.float64(data['dx'])) > >>> 363 return blank > >>> 364 > >>> > >>> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/utilities/lib/CICDeposit.so > in > >>> yt.utilities.lib.CICDeposit.CICDeposit_3 > >>> (yt/utilities/lib/CICDeposit.c:1643)() > >>> > >>> ValueError: Buffer dtype mismatch, expected 'float64_t' but got 'float' > >>> > >>> > >>> _______________________________________________ > >>> yt-users mailing list > >>> yt-users(a)lists.spacepope.org > >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > -- > > John Wise > > Assistant Professor of Physics > > Center for Relativistic Astrophysics, Georgia Tech > > http://cosmo.gatech.edu > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > Message: 2 > Date: Mon, 17 Feb 2014 23:16:37 +0100 > From: Varadarajan Parthasarathy <varada(a)camk.edu.pl> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] yt for PLUTO > Message-ID: > <CAPFsH9fr6qTi5WNqt7wtQy092OapkfA96ZyZBhP1ELdo= > CghxQ(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I read through the webpages of yt-project and came to know that > PLUTO is partly supported for yt and there is still a scope for creating a > new code front end. To that extent, I would like to inform with how much I > could get into this: > > import h5py > from yt.mods import * > > f = h5py.File("/.../.../testproblem/data.nnnn.dbl.h5", "r") > > print f.items() > [(u'cell_coords', <HDF5 group "/cell_coords" (3 members)>), > (u'node_coords', <HDF5 group "/node_coords" (3 members)>), (u'vars', <HDF5 > group "/vars" (5 members)>)] > > print f.keys() > [u'cell_coords', u'node_coords', u'vars'] > > where cell_coords and node_coords are X, Y, Z cell and node contain > different values. 'vars' are 'prs', 'rho', 'vx1', 'vx2', 'vx3'. > > But after this I am not able to get the data into the dictionary and hence > unable to produce plots. I did see through the PLUTO specified field list, > but I am not able to make the way out. Also, the simulation was not run > with Chombo refinement, but I hope it may not be a serious issue. Moreover, > the procedure given in loading a generic array data for HDF5 files was a > bit confusing with regard to, > > data_dir = ytcfg.get('yt','test_data_dir') > f = h5py.File(data_dir+"/Unigriddata/....h5", "r") > > can anyone explain if this 'test_data_dir' is just the working directory > and then 'f' consists of the file, else the procedure that I have followed > directly is still correct. > > I will be really glad if I can get to do data analysis and other such stuff > with yt. > > I hope to hear soon. > > Regards., > Varadarajan > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 3 > Date: Mon, 17 Feb 2014 20:27:07 -0500 > From: Stephanie Tonnesen <stonnes(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: [yt-users] rainbow+white? > Message-ID: > < > CAE4JVxBRAT9ofEJGB0yLaOqRP2OMULrHHA2Y8CWq15JVETp2Rg(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi yt-users, > > I am imagining that this is something silly, but I tried to use rainbow + > white, and it seems to me that it is actually rainbow + black? Certainly > on the colormaps page those two maps look identical: > > http://yt-project.org/docs/dev/visualizing/colormaps/index.html?highlight=c… > Is this actually the case? is there just some simple pointer that is > messed up somewhere? Or can someone point me to the white in > rainbow+white? > > Thanks! > > Stephanie > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 4 > Date: Tue, 18 Feb 2014 09:24:53 +0100 > From: Kacper Kowalik <xarthisius.kk(a)gmail.com> > To: yt-users(a)lists.spacepope.org > Subject: Re: [yt-users] yt for PLUTO > Message-ID: <530318D5.1060103(a)gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > On 02/17/2014 11:16 PM, Varadarajan Parthasarathy wrote: > > Hi, > > > > I read through the webpages of yt-project and came to know that > > PLUTO is partly supported for yt and there is still a scope for creating > a > > new code front end. To that extent, I would like to inform with how much > I > > could get into this: > > > > import h5py > > from yt.mods import * > > > > f = h5py.File("/.../.../testproblem/data.nnnn.dbl.h5", "r") > > Hi Varadarajan, > does yt's load method any sort of error? Could you try the following > script: > > from yt.mods import * > pf = load("/.../.../testproblem/data.nnnn.dbl.h5") > slc = SlicePlot(pf, 'z', 'rho') > slc.save() > > this should create an slice plot of gas density, but the most > interesting part is load(). It should take care of reading and > interpreting all data from hdf5 file. > Best regards, > Kacper > > > > print f.items() > > [(u'cell_coords', <HDF5 group "/cell_coords" (3 members)>), > > (u'node_coords', <HDF5 group "/node_coords" (3 members)>), (u'vars', > <HDF5 > > group "/vars" (5 members)>)] > > > > print f.keys() > > [u'cell_coords', u'node_coords', u'vars'] > > > > where cell_coords and node_coords are X, Y, Z cell and node contain > > different values. 'vars' are 'prs', 'rho', 'vx1', 'vx2', 'vx3'. > > > > But after this I am not able to get the data into the dictionary and > hence > > unable to produce plots. I did see through the PLUTO specified field > list, > > but I am not able to make the way out. Also, the simulation was not run > > with Chombo refinement, but I hope it may not be a serious issue. > Moreover, > > the procedure given in loading a generic array data for HDF5 files was a > > bit confusing with regard to, > > > > data_dir = ytcfg.get('yt','test_data_dir') > > f = h5py.File(data_dir+"/Unigriddata/....h5", "r") > > > > can anyone explain if this 'test_data_dir' is just the working directory > > and then 'f' consists of the file, else the procedure that I have > followed > > directly is still correct. > > > > I will be really glad if I can get to do data analysis and other such > stuff > > with yt. > > > > I hope to hear soon. > > > > Regards., > > Varadarajan > > > > > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: signature.asc > Type: application/pgp-signature > Size: 901 bytes > Desc: OpenPGP digital signature > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 5 > Date: Tue, 18 Feb 2014 08:17:27 -0800 > From: Sam Skillman <samskillman(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] rainbow+white? > Message-ID: > <CAB4=1s15uFHog3=SWXH7mZ+CU0mncpBuXgMKHrNm5oZ02= > SZxg(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Stephanie, > > Hmm, it doesn't look like there is a messed up pointer in the > yt/visualization/_colormap_data.py file to me, and looking at (random site > found searching for idl maps) > http://ham.space.umn.edu/johnd/ct/ct-names.html it seems like they have > qualitatively the same colors for rainbow+white. If you want to try > editing the _colormap_data.py entry for "idl39" you might have some luck. > It seems from > > http://yt-project.org/docs/dev/_images/cmap_images__Projection_Rainbow_+_wh… > the white is being put at the max value (which gets put at the bottom > for the _r) rather than the min value, which is I think what you want. > > Let us know if that helps. > Sam > > > On Mon, Feb 17, 2014 at 5:27 PM, Stephanie Tonnesen <stonnes(a)gmail.com > >wrote: > > > Hi yt-users, > > > > I am imagining that this is something silly, but I tried to use rainbow + > > white, and it seems to me that it is actually rainbow + black? Certainly > > on the colormaps page those two maps look identical: > > > http://yt-project.org/docs/dev/visualizing/colormaps/index.html?highlight=c… > > Is this actually the case? is there just some simple pointer that is > > messed up somewhere? Or can someone point me to the white in > rainbow+white? > > > > Thanks! > > > > Stephanie > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > End of yt-users Digest, Vol 72, Issue 26 > **************************************** > >

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