yt-users September 2017

yt-users@python.org

12 participants
13 discussions

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

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Variance in phase/profiles
by david collins 11 Apr '20

11 Apr '20

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

6 8

3-D Mass power spectra
by 梁家豪 03 Jun '19

03 Jun '19

Dear yt Can current yt calculate 3-D Mass power spectra? I checked the website but I didn't find any information. I think calculating 3-D Mass power spectra is a very useful for cosmological simulations. So I guess maybe yt supports this function now....? Thanks in advance

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Digital NEST - Data Visualization Project
by Frederick Bogert 15 Oct '17

15 Oct '17

Hello Everyone, I am a volunteer at Digital NEST, a non-profit high-tech training and collaboration space for young people. We have been exploring the idea of using yt as the main focus of a course that will introduce young students to data visualization, python programming and open source software. One of our ideas is to contribute to the open issues marked "new-contributor-friendly" on the yt github. However, we were hoping to find someone who has a visualization project in mind and would want to collaborate with us. Maybe you have a data set and want visualizations produced and don't have the time to create them. We are open to discuss other projects that are more in-depth and are still focused on data visualization. You can find out more about Digital NEST here : http://digitalnest.org/about / Thanks, Alex

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Plotting SFRs
by Ashley Jarvis 05 Oct '17

05 Oct '17

Hi all, I’m attempting to adapt the example script for plotting star formation rates (found at http://yt-project.org/doc/analyzing/analysis_modules/star_analysis.html#sta… <http://yt-project.org/doc/analyzing/analysis_modules/star_analysis.html#sta…>) to work with output data from a simulation run using Enzo. However, when I attempt to run the script, I get the following error: ——————————————————— File "PlotSFR.py", line 26, in <module> sfr = StarFormationRate(data, star_mass=mass_old, star_creation_time=ct_old, volume=sp.volume()) File "/usr/local/anaconda/lib/python2.7/site-packages/yt/analysis_modules/star_analysis/sfr_spectrum.py", line 115, in __init__ self._ds.quan(1.0, 'Mpccm**3').units File "/usr/local/anaconda/lib/python2.7/site-packages/yt/units/yt_array.py", line 1355, in __new__ dtype=dtype, bypass_validation=bypass_validation) File "/usr/local/anaconda/lib/python2.7/site-packages/yt/units/yt_array.py", line 430, in __new__ units = Unit(input_units, registry=registry) File "/usr/local/anaconda/lib/python2.7/site-packages/yt/units/unit_object.py", line 257, in __new__ unit_data = _get_unit_data_from_expr(unit_expr, registry.lut) File "/usr/local/anaconda/lib/python2.7/site-packages/yt/units/unit_object.py", line 572, in _get_unit_data_from_expr unit_data = _get_unit_data_from_expr(unit_expr.args[0], unit_symbol_lut) File "/usr/local/anaconda/lib/python2.7/site-packages/yt/units/unit_object.py", line 566, in _get_unit_data_from_expr return _lookup_unit_symbol(str(unit_expr), unit_symbol_lut) File "/usr/local/anaconda/lib/python2.7/site-packages/yt/units/unit_object.py", line 657, in _lookup_unit_symbol "symbols." % symbol_str) yt.units.unit_registry.UnitParseError: Could not find unit symbol 'Mpccm' in the provided symbols. ——————————————————— I am using version 3.3.5 of yt. Does anyone know how I can resolve this? Any suggestions would be greatly appreciated. Thanks, Ashley

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Saving clump data
by José Mauricio Utreras 27 Sep '17

27 Sep '17

Hello yt users, I have tried to save a clump dataset but I'm getting the following error: *Code:* *...* *find_clumps(master_clump, cmin, cmax, step)* *fn=master_clump.save_as_dataset(fields=["cell_mass", "total","x","y","z","velocity_x","velocity_y","velocity_z"])* *print(fn)* *...* *Error* *yt : [INFO ] 2017-09-22 10:34:12,164 Saving field data to yt dataset: G-0001_clump_0.h5.* *Traceback (most recent call last):* * File "Save_Clumps.py", line 43, in <module>* * master_clump.save_as_dataset(fields=["cell_mass", "total","x","y","z","velocity_x","velocity_y","velocity_z"])* * File "/home/jutreras/miniconda3/lib/python3.6/site-packages/yt/analysis_modules/level_sets/clump_handling.py", line 365, in save_as_dataset* * extra_attrs=extra_attrs)* * File "/home/jutreras/miniconda3/lib/python3.6/site-packages/yt/frontends/ytdata/utilities.py", line 149, in save_as_dataset* * _yt_array_hdf5(fh[field_type], field_name, data[field])* * File "/home/jutreras/miniconda3/lib/python3.6/site-packages/yt/frontends/ytdata/utilities.py", line 208, in _yt_array_hdf5* * dataset = fh.create_dataset(str(field), data=data)* * File "/home/jutreras/miniconda3/lib/python3.6/site-packages/h5py/_hl/group.py", line 111, in create_dataset* * self[name] = dset* * File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/h5py_1496889914775/work/h5py/_objects.c:2846)* * File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/h5py_1496889914775/work/h5py/_objects.c:2804)* * File "/home/jutreras/miniconda3/lib/python3.6/site-packages/h5py/_hl/group.py", line 276, in __setitem__* * h5o.link(obj.id <http://obj.id>, self.id <http://self.id>, name, lcpl=lcpl, lapl=self._lapl)* * File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/h5py_1496889914775/work/h5py/_objects.c:2846)* * File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/h5py_1496889914775/work/h5py/_objects.c:2804)* * File "h5py/h5o.pyx", line 202, in h5py.h5o.link (/home/ilan/minonda/conda-bld/h5py_1496889914775/work/h5py/h5o.c:3901)* *RuntimeError: Unable to create link (Name already exists)* A file G-0001_clump_0.h5 is created but when I try to load the data I get another error *----> 1 ds_clumps = yt.load('CLUMPS/G-0001_clump_0.h5')* *~/miniconda3/lib/python3.6/site-packages/yt/convenience.py in load(*args, **kwargs)* * 96 return output_type_registry[n](fn)* * 97 mylog.error("Couldn't figure out output type for %s", args[0])* *---> 98 raise YTOutputNotIdentified(args, kwargs)* * 99 * * 100 mylog.error("Multiple output type candidates for %s:", args[0])* *YTOutputNotIdentified: Supplied ('CLUMPS/G-0001_clump_0.h5',) {}, but could not load!* Cheers! José Utreras

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Reading in arrays from Active Particles
by John Regan 22 Sep '17

22 Sep '17

Hi All, I'm hoping to modify YT to read in arrays from ActiveParticle fields. I have an array which is part of the AP data structure. At the moment YT sees the field but only reads the first element which kinda makes sense. Just wondering how I can modify the source code so that YT realised that a field is in fact an array and to read in all the values? At the moment YT is also complaining with the message: yt/yt/frontends/enzo/io.py:140: VisibleDeprecationWarning: boolean index did not match indexed array along dimension 0; dimension is 20 but corresponding boolean dimension is 1 which is because of course the field is an array of length 20 rather than a scalar. Any tips on what is required? I am looking on io.py at the _read_particle_fields function and I imagine it is this function that needs modification? Cheers, John

2 3

Parallel data reading and covering grid
by Yingchao Lu 20 Sep '17

20 Sep '17

Dear yt users, I am trying to read some AMR data and convert them into 3D array. The test code: ######################### BEGIN ######################### import yt from time import time yt.enable_parallelism() ds = yt.load("flash_hdf5_plt_cnt_0000") tstart = time() cg = ds.covering_grid(level=ds.max_level, left_edge=ds.domain_left_edge, dims=ds.domain_dimensions*2**ds.max_level) cg['dens'] if yt_isroot(): print "It takes {0}s".format(time()-tstart) ######################### END ######################### I tried to run to serial or parallel on an interactive session on stampede: ######################### BEGIN ######################### [yclu@ test]$ ls flash_hdf5_plt_cnt_0000 test.py [yclu@ test]$ python test.py It takes 34.0571820736s [yclu@ test]$ export OMP_NUM_THREADS=68 [yclu@ test]$ python test.py It takes 33.1969199181s [yclu@ test]$ export OMP_NUM_THREADS=1 [yclu@ test]$ mpirun -np 68 python test.py It takes 58.0391800404s ######################### END ######################### The time does not seem to be reduced by parallelism. And multi-process seem to have huge communication overhead. Is there a way to increase the speed by parallelism? Thanks, Yingchao

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Creating image from FITS data
by tazkera haque 20 Sep '17

20 Sep '17

Hi People, I am trying to play around with FITS file format. I want to create an image from this file which will include data from center to 20 arc minutes. each pixel is 3x3 arc sec. *import yt* *ds = yt.load("signal_wfilt_sn.fits")* *ds.print_stats()* *ds.field_list* *ds.domain_width* *ds.derived_field_list* *dd = ds.all_data()* *dd* *sp = ds.sphere(ds.domain_center, (400, 'code_length')) # create sphere of 20 arcminutes with 3x3 pixel size* *sp[("fits", "image_0")] # check array of data within the sphere* *#plot 1D histogram of data over pixel* *pplot = yt.ProfilePlot(sp, "image_0", ["pixel"], weight_field=None, n_bins=1024, * *plot_spec=dict(color='red', linestyle="--"), y_log={'pixel':False})* *pplot.show()* *# convert data to numpy array* *import numpy as np* *image = np.array(sp['image_0'])* *# create image?* *imgplot = plt.imshow(image)* *imgplot* *plt.show()* *image* *The code is failing at this point with error:* ---------------------------------------------------------------------------TypeError Traceback (most recent call last)<ipython-input-21-6a83e68fbbf2> in <module>()----> 1 imgplot = plt.imshow(image) 2 3 imgplot 4 plt.show() /home/trina/anaconda2/lib/python2.7/site-packages/matplotlib/pyplot.pyc in imshow(X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, resample, url, hold, data, **kwargs) 3155 filternorm=filternorm, filterrad=filterrad, 3156 imlim=imlim, resample=resample, url=url, data=data,-> 3157 **kwargs) 3158 finally: 3159 ax._hold = washold /home/trina/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.pyc in inner(ax, *args, **kwargs) 1896 warnings.warn(msg % (label_namer, func.__name__), 1897 RuntimeWarning, stacklevel=2)-> 1898 return func(ax, *args, **kwargs) 1899 pre_doc = inner.__doc__ 1900 if pre_doc is None: /home/trina/anaconda2/lib/python2.7/site-packages/matplotlib/axes/_axes.pyc in imshow(self, X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, resample, url, **kwargs) 5122 resample=resample, **kwargs) 5123 -> 5124 im.set_data(X) 5125 im.set_alpha(alpha) 5126 if im.get_clip_path() is None: /home/trina/anaconda2/lib/python2.7/site-packages/matplotlib/image.pyc in set_data(self, A) 598 if (self._A.ndim not in (2, 3) or 599 (self._A.ndim == 3 and self._A.shape[-1] not in (3, 4))):--> 600 raise TypeError("Invalid dimensions for image data") 601 602 self._imcache = None TypeError: Invalid dimensions for image data I am completely new to image processing, so I am interested to know how you create image for this type of data in yt. Your help is very appreciated. I also provided a link to the dataset: https://www.dropbox.com/s/bftuihqcoun8tny/signal_wfilt_sn.fits?dl=0 Thanks a lot Tazkera haque

2 4

Creating image from FITS data
by tazkera haque 20 Sep '17

20 Sep '17

Hi People, I am trying to play around with FITS file format. I want to create an image from this file which will include data from center to 20 arc minutes. each pixel is 3x3 arc sec. *import yt* *ds = yt.load("signal_wfilt_sn.fits")* *ds.print_stats()* *ds.field_list* *ds.domain_width* *ds.derived_field_list* *dd = ds.all_data()* *dd* *sp = ds.sphere(ds.domain_center, (400, 'code_length')) # create sphere of 20 arcminutes with 3x3 pixel size* *sp[("fits", "image_0")] # check array of data within the sphere* *#plot 1D histogram of data over pixel* *pplot = yt.ProfilePlot(sp, "image_0", ["pixel"], weight_field=None, n_bins=1024, * *plot_spec=dict(color='red', linestyle="--"), y_log={'pixel':False})* *pplot.show()* *# convert data to numpy array* *import numpy as np* *image = np.array(sp['image_0'])* *# create image?* *imgplot = plt.imshow(image)* *imgplot* *plt.show()* *image* *The code is failing at this point with error:* ---------------------------------------------------------------------------TypeError Traceback (most recent call last)<ipython-input-21-6a83e68fbbf2> in <module>()----> 1 imgplot = plt.imshow(image) 2 3 imgplot 4 plt.show() /home/trina/anaconda2/lib/python2.7/site-packages/matplotlib/pyplot.pyc in imshow(X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, resample, url, hold, data, **kwargs) 3155 filternorm=filternorm, filterrad=filterrad, 3156 imlim=imlim, resample=resample, url=url, data=data,-> 3157 **kwargs) 3158 finally: 3159 ax._hold = washold /home/trina/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.pyc in inner(ax, *args, **kwargs) 1896 warnings.warn(msg % (label_namer, func.__name__), 1897 RuntimeWarning, stacklevel=2)-> 1898 return func(ax, *args, **kwargs) 1899 pre_doc = inner.__doc__ 1900 if pre_doc is None: /home/trina/anaconda2/lib/python2.7/site-packages/matplotlib/axes/_axes.pyc in imshow(self, X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, resample, url, **kwargs) 5122 resample=resample, **kwargs) 5123 -> 5124 im.set_data(X) 5125 im.set_alpha(alpha) 5126 if im.get_clip_path() is None: /home/trina/anaconda2/lib/python2.7/site-packages/matplotlib/image.pyc in set_data(self, A) 598 if (self._A.ndim not in (2, 3) or 599 (self._A.ndim == 3 and self._A.shape[-1] not in (3, 4))):--> 600 raise TypeError("Invalid dimensions for image data") 601 602 self._imcache = None TypeError: Invalid dimensions for image data I am completely new to image processing, so I am interested to know how you create image for this type of data in yt. Your help is very appreciated. I have also attached the jupyter notebook and the actual data I am using for the processing. Thanks a lot Tazkera Haque

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yt-users September 2017