Mailman 3 July 2012 - yt-users

Plot collections on non-square slices
by Mark Krumholz 24 Jul '12

24 Jul '12

Hi YT Users, I have a computational domain that is not cubical, and I want to plot a slice through it that is rectangular rather than square. I can make a slice with PlotCollection, but when I write the image to a file using save, I find that it has been padded with whitesapce on the left and right to make it square. I would like the image to have the same aspect ratio as the data, not be white-padded. Is there a way to do this with PlotCollection, or should I just give up and use FixedResolutionBuffer to extract the data and construct the image myself? Thanks. -- Mark Krumholz krumholz(a)ucolick.org

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Slices from Flash data
by Alice Coucke 23 Jul '12

23 Jul '12

Good morning, I am currently working on visualization from Flash Data. I am using Slices of the internal energy along the x-axis. I have a weird line at the top of the slice (see attachment). That looks like a periodic boundary conditions problem. The thing is, I don't know whether it is a problem in my code or that I am using yt wrong. I feel like is a plot problem, I looked at the data with another visualization tool (Visit) and it doesn't seem to have this line ... Thank you for your help and have a great day, Alice [cid:AC8237E3-8ABE-47F3-9F64-9E5B7F633DCC@internal.amnh.org]

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Xray luminosity in yt
by Yuan Li 19 Jul '12

19 Jul '12

Dear all, I am trying to calculate the x-ray luminosity of my cool core cluster. I know that there is XRayEmissivity in yt but it is bremsstrahlung radiation only. I am trying to get the X-ray luminosity or emissivity from cooler gas as well. If anyone has a routine that can do this, please let me know. Thank you! Yuan

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Calculation of enclosed mass for a given radius
by Latif 19 Jul '12

19 Jul '12

Hi Guys, I want to compute the enclosed mass for a given radius to make use of it for computing other quantities. I would like to define a new field like EnclosedMass. How can i use accumulation flag in combination with new defined field to compute the enclosed mass(like in prof.add_fields case). Unfortunately, add_field does not accept it. May be there be there is another way to do this. Any help in this regard will appreciated. prof.add_fields("CellMass",weight=None,accumulation=True) def EnclosedMass(field,data): return data["Density"]*data["CellVolume"] add_field("EnclosedMass", function=EnclosedMass,weight=None,accumulation=True) Thanks in advance! Cheers Latif

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Re: [yt-users] Luminosity within r
by Massimo Gaspari 18 Jul '12

18 Jul '12

Matt, Sam, Eric, Britton, Thank you for all the previous infos (projections and 2D profiles). Now I have a clearer vision of these features. Sam, you are right, the derived field is created before the radial binning.I will let you know if I have further doubts (for sure). As I said to Matt previously, I want to extend my congratulations to all the YT developers.You are doing a great job. Cheers, Max

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Installation error lib64
by Carolyn Peruta 18 Jul '12

18 Jul '12

Hello all, I tried to update yt on my mac (10.7.4) and I'm running into errors with lib64. I took Sam's advice and created a symbolic link from $(YT_DEST)/lib64 to /usr/local/lib/x86_64 but I am still getting errors like this: ld: warning: directory not found for option '-L/Users/cperuta/yt-x86_64/lib64/' I've attached the logfile Ideas?

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title of PlotCollection
by Pengfei Chen 17 Jul '12

17 Jul '12

Hi, I'm trying to add a title for the picture, but I can't find the right command to do so. Here is the code: pf = load(fn) halos = HaloFinder(pf) pc = PlotCollection(pf, [pos_x, pos_y, pos_z]) p = pc.add_slice("Density", 0) pc.set_width(3*rad, '1') p.modify["hop_particles"](halos, max_number=100, alpha=0.3) p.modify["title"](halos, text='z=%.2f'%z) And there is some error reported for the last line. The meaning of the error is more than one name is given to the title. Then I replace it with: p.modify["text"](halos, pos=(0.02, 0.98), text='z=%.2f'%z) But it still has error. Could someone please help me about it? Pengfei

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clobbering projection field data
by Elizabeth Tasker 14 Jul '12

14 Jul '12

Hi, I'm creating a series of projections in a loop, where the conditions for the projection change with each iteration: for v in range(resolution[2]): projection = pf.h.proj(2, 'LOSVelocityRangeDensity') I can't seem to persuade yt to delete the old projection and make a fresh one each sweep. I've tried: if projection.has_key("LOSVelocityRangeDensity"): del projection["LOSVelocityRangeDensity"] and for g in pf.h.grids: if g.has_key("LOSVelocityRangeDensity"): del g["LOSVelocityRangeDensity"] But it's clearly not re-making the projection. Is there a better way to make it ever forget it has ever produced a projection of this field before and start from scratch with the new loop parameters? Elizabeth

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install error
by Elizabeth Tasker 13 Jul '12

13 Jul '12

Hi, We've had some problems installing yt via the install script. Initially it did not download distribute, which we did by hand. Then, it couldn't get pip, so I commented that line out and now it's died on cython with: cythonc:> yt/utilities/lib/PointsInVolume.c building extension "yt.utilities.lib.QuadTree" sources cythonc:> yt/utilities/lib/QuadTree.c building extension "yt.utilities.lib.RayIntegrators" sources cythonc:> yt/utilities/lib/RayIntegrators.c building extension "yt.utilities.lib.VolumeIntegrator" sources cythonc:> yt/utilities/lib/VolumeIntegrator.c building extension "yt.utilities.lib.grid_traversal" sources cythonc:> yt/utilities/lib/grid_traversal.c Error compiling Cython file: ------------------------------------------------------------ ... if im.vd_strides[0] == -1: with nogil, parallel(num_threads = num_threads): idata = <ImageAccumulator *> malloc(sizeof(ImageAccumulator)) idata.supp_data = self.supp_data v_pos = <np.float64_t *> malloc(3 * sizeof(np.float64_t)) for j in prange(size, schedule="static",chunksize=1): ^ ------------------------------------------------------------ yt/utilities/lib/grid_traversal.pyx:368:31: Invalid keyword argument: chunksize Error compiling Cython file: ------------------------------------------------------------ ... idata.supp_data = self.supp_data v_pos = <np.float64_t *> malloc(3 * sizeof(np.float64_t)) v_dir = <np.float64_t *> malloc(3 * sizeof(np.float64_t)) # If we do not have a simple image plane, we have to cast all # our rays for j in prange(size, schedule="dynamic", chunksize=100): ^ ------------------------------------------------------------ yt/utilities/lib/grid_traversal.pyx:393:31: Invalid keyword argument: chunksize Error compiling Cython file: ------------------------------------------------------------ ... cdef np.float64_t px, py cdef np.float64_t width[3] for i in range(3): width[i] = self.width[i] if im.vd_strides[0] == -1: with nogil, parallel(num_threads = num_threads): ^ ------------------------------------------------------------ yt/utilities/lib/grid_traversal.pyx:364:32: Invalid value for num_threads argument, expected an int error: 3 errors while compiling 'yt/utilities/lib/grid_traversal.pyx' with Cython Has anyone had a similar experience? Elizabeth

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Error on loading clumps
by Eve Lee 12 Jul '12

12 Jul '12

Hello, I'm trying to load clumps that I have saved using pf.h.save_object but I seem to get some error as attached below. I had no trouble loading these clumps with older version of yt (last year's) so I'm not sure what's going on... Thanks in advance! Best Regards, Eve Error: -------------------------------------------------------------------------- ValueError Traceback (most recent call last) /mnt/raid-project/murray/elee/enzo/ic_pn/res_128/v2.0/gravon_staron/short_dt/<ipython-input-4-dfa9a6552cd3> in <module>() ----> 1 clump = pf.h.load_object("Clump") /opt/python/2.7.1-mkl/lib/python2.7/site-packages/yt-2.3-py2.7-linux-x86_64.egg/yt/data_objects/hierarchy.pyc in load_object(self, name) 285 under the name *name* on the node /Objects. 286 """ --> 287 obj = self.get_data("/Objects", name) 288 if obj is None: 289 return /opt/python/2.7.1-mkl/lib/python2.7/site-packages/yt-2.3-py2.7-linux-x86_64.egg/yt/data_objects/hierarchy.pyc in get_data(self, node, name) 314 full_name = "%s/%s" % (node, name) 315 try: --> 316 return self._data_file[full_name][:] 317 except TypeError: 318 return self._data_file[full_name] /opt/python/2.7.1-mkl/lib/python2.7/site-packages/h5py-2.0.1-py2.7-linux-x86_64.egg/h5py/_hl/dataset.pyc in __getitem__(self, args) 301 if self.shape == (): 302 fspace = self.id.get_space() --> 303 selection = sel2.select_read(fspace, args) 304 arr = numpy.ndarray(selection.mshape, dtype=new_dtype) 305 for mspace, fspace in selection: /opt/python/2.7.1-mkl/lib/python2.7/site-packages/h5py-2.0.1-py2.7-linux-x86_64.egg/h5py/_hl/selections2.pyc in select_read(fspace, args) 22 23 if fspace.shape == (): ---> 24 return ScalarReadSelection(fspace, args) 25 26 raise NotImplementedError() /opt/python/2.7.1-mkl/lib/python2.7/site-packages/h5py-2.0.1-py2.7-linux-x86_64.egg/h5py/_hl/selections2.pyc in __init__(self, fspace, args) 10 self.mshape = () 11 else: ---> 12 raise ValueError("Illegal slicing argument for scalar dataspace") 13 14 self.mspace = h5s.create(h5s.SCALAR) ValueError: Illegal slicing argument for scalar dataspace

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