Mailman 3 September 2015 - yt-users

Re: [yt-users] yt-users Digest, Vol 91, Issue 23
by Barbara Ramirez Sept. 16, 2015

Sept. 16, 2015

Hello John! Thanks for your fast answer 1) Ok, here is the script I'm using (sorry for the mess): http://paste.yt-project.org/show/5881/ 2) It is indeed a big cosmological simulation. so temperatures range between 10^4 - 10^8 3) It was done in FLASH 4 (but I'm switching to ENZO for future simulations) Let's hope is doable! thanks for your help! -- Barbara L. Ramirez MSc. Institut für Astro- und Teilchenphysik University of Innsbruck

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PHOX mock observation errors
by Barbara Ramirez Sept. 15, 2015

Sept. 15, 2015

Hello! I have written before about trying to implement the xray photon generator. This time I've updated all the libraries, YT, Heasoft... etc. I'm just trying to generate a photon list for the moment but I'm getting two sorts of errors: 1) / //---------------------------------------------------------------------------// //RuntimeError Traceback (most recent call last)// ///home/barbara/hires_final/photon_trial.py in <module>()// // 90 cosmo = Cosmology()// // 91 // //---> 92 photons = PhotonList.from_scratch(Roi, redshift, A, exp_time,thermal_model,center="center",cosmology=cosmo)// // 93 photons.write_h5_file("my_photons.h5")// // 94 // // ///home/barbara/yt-x86_64/src/yt-hg/yt/analysis_modules/photon_simulator/photon_simulator.pyc in from_scratch(cls, data_source, redshift, area, exp_time, photon_model, parameters, center, dist, cosmology)// // 329 parameters["Width"] = 2.*width.in_units("kpc")// // 330 // //--> 331 photons = photon_model(data_source, parameters)// // 332 // // 333 mylog.info("Finished generating photons.")// // ///home/barbara/yt-x86_64/src/yt-hg/yt/analysis_modules/photon_simulator/photon_models.pyc in __call__(self, data_source, parameters)// // 188 raise RuntimeError("Number of photons generated for this chunk "+// // 189 "exceeds photons_per_chunk (%d)! " % self.photons_per_chunk +// //--> 190 "Increase photons_per_chunk!")// // 191 // // 192 if self.method == "invert_cdf":// // //RuntimeError: Number of photons generated for this chunk exceeds photons_per_chunk (1000000000)! Increase photons_per_chunk!/ Ok, so I increase the number of photons per chunk and I get: 2) /---------------------------------------------------------------------------// //MemoryError Traceback (most recent call last)// ///home/barbara/hires_final/photon_trial.py in <module>()// // 90 cosmo = Cosmology()// // 91 // //---> 92 photons = PhotonList.from_scratch(Roi, redshift, A, exp_time,thermal_model,center="center",cosmology=cosmo)// // 93 photons.write_h5_file("my_photons.h5")// // 94 // // ///home/barbara/yt-x86_64/src/yt-hg/yt/analysis_modules/photon_simulator/photon_simulator.pyc in from_scratch(cls, data_source, redshift, area, exp_time, photon_model, parameters, center, dist, cosmology)// // 329 parameters["Width"] = 2.*width.in_units("kpc")// // 330 // //--> 331 photons = photon_model(data_source, parameters)// // 332 // // 333 mylog.info("Finished generating photons.")// // ///home/barbara/yt-x86_64/src/yt-hg/yt/analysis_modules/photon_simulator/photon_models.pyc in __call__(self, data_source, parameters)// // 156 // // 157 number_of_photons = np.zeros(num_cells, dtype="uint64")// //--> 158 energies = np.zeros(self.photons_per_chunk)// // 159 // // 160 start_e = 0// // //MemoryError: / This is just a trial, so I'm using almost a copy of the code that's on the documentation: Roi = ds.sphere("center",radius=width_half) apec_model = TableApecModel("/home/barbara/yt-x86_64/atomdb_v2.0.2",0.5,10.0,100,thermal_broad=False,apec_vers="2.0.2") thermal_model = ThermalPhotonModel(apec_model, X_H=0.75,photons_per_chunk=1000000000, Zmet=0.3,method="invert_cdf") A = 6000. exp_time = 100.0e3 redshift = 0.05 cosmo = Cosmology() photons = PhotonList.from_scratch(Roi, redshift, A, exp_time,thermal_model,center="center",cosmology=cosmo) photons.write_h5_file("my_photons.h5") My snapshot information: length unit 0.999752515846 cm time unit 1.0 s mass unit 1.0 g velocity unit 1.0 cm/s Enter total Width of plot in Mpccm: 0.5 smallest cell: 14.6469091426 kpccm/h minima and maxima 1.04339659244e-29 g/cm**3 1.5187912088e-24 g/cm**3 The simulation is [ 89.40546647 89.40546647 89.40546647] Mpccm Centering region in:, [ 44.58268195 44.53902694 44.51719943] Mpccm yt : [INFO ] 2015-09-15 16:49:43,219 Cosmology: h = 0.71, omega_matter = 0.27, omega_lambda = 0.73 Am I just using wrong parameters to try to simulate the Xray emission of this simulated cluster? Thanks beforehand for the help! -- Barbara L. Ramirez MSc. Institut für Astro- und Teilchenphysik University of Innsbruck

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Re: [yt-users] yt-users Digest, Vol 91, Issue 18
by Guido granda muñoz Sept. 14, 2015

Sept. 14, 2015

Hello Nathan, I updated yt an the problem was solved, thank you. Regards, 2015-09-13 14:56 GMT-03:00 <yt-users-request(a)lists.spacepope.org>: > 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: multi projection plots with title and annotations > (Nathan Goldbaum) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 12 Sep 2015 18:46:25 -0500 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] multi projection plots with title and > annotations > Message-ID: > <CAJXewOni8_yTvGo9e+PezJfvQqfO5EcHdpMKkcw+prTX3uSw= > w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Just in case you haven't updated in a while, I would do so since there was > a fix included in yt 3.2.1 that might solve your problem. > > > https://bitbucket.org/yt_analysis/yt/pull-requests/1698/ensure-the-frb-is-v… > > If you're already on yt 3.2.1 I'll take a closer look at this soon. > > Nathan > > On Saturday, September 12, 2015, Guido granda mu?oz <guidogranda(a)gmail.com > > > wrote: > > > Hello there, > > > > I'm trying to do a multipanel plot of projected density with titles in > > each axis and annotations but I couldn't figure out how to do it, could > you > > please help me. > > > > I'm using AxesGrid as in your example( > > > http://yt-project.org/doc/cookbook/complex_plots.html#multipanel-with-axes-… > ) > > however > > something is wrong. I'm sending my output image as a attached file. > > > > My code is the following: > > > > > > > > > > import yt > > import matplotlib.pyplot as plt > > import sys > > import numpy as np > > from mpl_toolkits.axes_grid1 import AxesGrid > > import matplotlib.colorbar as cb > > from matplotlib.colors import LogNorm > > > > data=[] > > data.append(sys.argv[1]) > > data.append(sys.argv[2]) > > data.append(sys.argv[3]) > > data.append(sys.argv[4]) > > > > pf1=yt.load(data[0]) > > pf2=yt.load(data[1]) > > pf3=yt.load(data[2]) > > pf4=yt.load(data[3]) > > > > pfs=[] > > pfs.append(pf1) > > pfs.append(pf2) > > pfs.append(pf3) > > pfs.append(pf4) > > > > > > fig=plt.figure() > > grid = AxesGrid(fig, (0.075,0.075,0.85,0.85),nrows_ncols = (2, > 2),axes_pad > > = 1.0,label_mode = "all",share_all = > > > True,cbar_location="right",cbar_mode="single",cbar_size="5%",cbar_pad="5%",cbar_set_cax=True) > > > > > > axe=['y','y','y','y'] > > field=['density','density','density','density'] > > colors=[] > > title=['100 Mpc/h box size', '75 Mpc/h box size','100 Mpc/h box size','50 > > Mpc/h box size'] > > > > for i in range(len(data)): > > p > > =yt.ProjectionPlot(pfs[i],axe[i],field[i],center='c',width=(25,'Mpc/h')) > > p.set_zlim('density',4.4601764879407653e-5,5.0e-2) > > p.annotate_timestamp(corner='upper_left', > > redshift=True,draw_inset_box=True) > > p.annotate_title(title[i]) > > plot=p.plots[field] > > plot.figure=fig > > plot.axes=grid[i].axes > > plot.cax=grid.cbar_axes[i] > > p._setup_plots() > > > > > > fig.savefig('plot1_f.png',pdi=300) > > > > > > > > > > Kind regards, > > -- > > Guido > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > 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 91, Issue 18 > **************************************** > -- Guido

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ANN: yt-3.2.1 release
by Nathan Goldbaum Sept. 10, 2015

Sept. 10, 2015

We are proud to announce the release of yt 3.2.1! yt (http://yt-project.org) is an open-source, community-developed toolkit for analysis and visualization of volumetric data of all types, with a particular emphasis on astrophysical and nuclear engineering simulations. Version 3.2.1 is a regularly scheduled bugfix release including fixes for a number of issues reported since the release of yt 3.2. These changes are summarized below and include a number of bugfixes, performance improvements, and documentation improvements. We urge all users of version 3.2 to upgrade to yt 3.2.1 immediately. Summary of changes ------------------ * Fixed an issue with reading ORION2 star particle data * The "particle_velocity_cylindrical_radius" field now uses the correct field definition. * Prevent unit test failure from occuring if scipy or astropy is not installed * Present better error messages when trying to load empty files or directories * Add support for the fabs ufunc to YTArray * Remove enzo installation option from the install script * Fixed issue with the EPS writer when it is supplied a ProfilePlot * Fixed reading of the NMSU-ART star particle creation time field * Use a stronger hashing algorithm for calculating selection hashes to fix issues with data object selection in Python 3 * Fix an error in the docstrings of Cosmology.t_from_z() * Fix python3 answer test failure for Enzo species field names * Fix incorrect use of "normal" instead of "center" in spherical coordinate fields. * Avoid NameError when comparing temperature units with offsets * Avoid creating YTQuantity instances with more than one value * Include requirements files and cuda sources in source distribution. Avoid including a full docs build. * Add search bar to main docs page * Add canonical link for documentation to improve google search results for yt documentation * Use nice latex representation for unit labels returned by DerivedField.get_label() * Add assert_allclose_units to avoid test failures in Numpy 1.10 and newer * Avoid unsafe casting error in Numpy 1.10 or newer * Fix incorrect plots created by scripts that call PlotContainer._setup_plots() directly. * Allow the creation of gradient fields based on fields with dimensionless units * Correct two incorrect paths in the documentation on loading data * The MaxLocation and MinLocation derived quantities now work correctly with non-cartesian data and particle fields. * Use OrderedDict in PlotWindow answer tests to avoid unstable test names in Python 3 * Speed improvements for the absorption_spectrum analysis module * Speed improvements for smoothed covering grids * Fixed a small CSS issue in the main docs page * Fix incorrect velocity and time units for Gadget cosmological datasets * Use truediv operator in unit object tests for Python 3 compatibility * Fix several bugs in the photon simulator analysis module. * Ensure camera width and center are in code units before rendering, avoiding a possible segmentation fault. * Ensure fields passed to process_octree during smoothing are contiguous. Fixes a regression in the values of smoothed SPH fields. Coming Soon! ------------ The next major release of yt will be version 3.3, which is slated to include an overhaul of the volume rendering system and support for analyzing and visualizing unstructured mesh data. Standard Installation Methods ----------------------------- As with previous releases, you can install yt from source using one of the following methods. 1) From the install script (http://yt-project.org/#getyt ): If you previously installed yt from the install script, you can update your installation in-place using the following command: # Update $ yt update If you are on the “stable” branch, updating will bring you from yt 3.2 to 3.2.1, incorporating all changes since 3.2, whereas if you are on the development “yt” branch, only the changes since your last update should be incorporated. To install from scratch, do the following: # Installation $ wget http://bitbucket.org/yt_analysis/yt/raw/stable/doc/install_script.sh $ bash install_script.sh 2) From pip (source or binary wheel, see below for more details): # Installation $ pip install yt # Update $ pip install -U yt 3) From the Anaconda Python Distribution (https://store.continuum.io/cshop/anaconda/): # Installation $ conda install yt # Update $ conda update yt Note that it might take up to a week for the conda package built by Continuum Analytics to be updated for yt 3.2.1. Installing Binary Packages via pip If you do not have compilers available, it is also possible to install binary packages (“wheels”) using pip on Windows and Mac OS X (64-bit only for both). This has the advantage of not needing to install yt from source using a proper compiler setup, which has caused occasional problems on both of these platforms and prevented us from installing yt easily on other Python distributions. Note that it may take several days for binary wheels for yt 3.2.1 to be uploaded. We have so far been able to install and run the binary distribution via pip on the following platforms and Python stacks: Note that it might take a day or two for the pip wheels to be updated. Windows x86_64: Enthought Canopy Python (https://www.enthought.com/products/canopy/) WinPython (http://winpython.sourceforge.net/) Mac OS X x86_64: Enthought Canopy Python (https://www.enthought.com/products/canopy/) Homebrew Python (http://brew.sh/) Python.org Python Mac OS X’s system Python MacPorts Python (https://www.macports.org/) This is somewhat experimental, so other distributions may work (or not), please submit bug reports or successes to the mailing list or to the Bitbucket issues page (http://bitbucket.org/yt_analysis/yt/issues). Both Python 2.7 and Python 3.4 are supported. The dependencies for installing yt via this method are the same as from source: NumPy h5py HDF5 SymPy Matplotlib IPython (not required, but strongly recommended) To install a new version of yt on one of these platforms, simply do $ pip install yt and you should get the binary distribution automatically. Also, if your python installation is system-wide (e.g., the Mac system Python) you might need to run pip with administrator privileges. For more information, including more installation instructions, links to community resources, and information on contributing to yt’s development, please see the yt homepage at http://yt-project.org and the documentation for yt-3.2 at http://yt-project.org/docs/3.2. yt is the product of a large community of developers and users and we are extraordinarily grateful for and proud of their contributions. Please forward this announcement on to any interested parties. As always, if you have any questions, concerns, or run into any trouble updating please don't hesitate to send a message to the mailing list or stop by our IRC channel. All the best, Nathan Goldbaum, on behalf of the yt development team

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HOP and FOF for filtered particles
by José Utreras Sept. 8, 2015

Sept. 8, 2015

Hi everyone I'm working with Enzo and I'm trying to identify groups of stars particles. Now I wanted to create groups but only of young stars. I thought using HOP but I don't see how to filter particles before crating the groups. Thanks! Jose

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draw_ids
by David Collins Sept. 4, 2015

Sept. 4, 2015

Hi, Everybody-- I'm trying to sort out some funny issues with a run, and I'm using the draw_ids flag to annotate_grids. I'm noticing that the same IDs are used in wildly different grids. Where do the ids used for this flag come from, and how can I relate them to the grids in index.grids? d. -- -- Sent from a computer.

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stitching data sets together
by Jonah Miller Sept. 3, 2015

Sept. 3, 2015

Hi Everyone, I have data for a simulation in spherical coordinates that I wish to input into yt and visualize using the generic reader tools. However, the simulation is broken up into six volumes, each of which is a solid angle that makes up part of a sphere. Unfortunately, stitching together the arrays of data produces a lot of redundancies, there's no easy way to include all of it in a single array without including the same data points several times. So what I'd like is a way to feed in each solid angle as an individual data set, but visualize all six datasets on a single plot. Is this possible? Thanks in advance for your help! Best, Jonah MIller

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problem with units
by alex volioths Sept. 3, 2015

Sept. 3, 2015

Hello everyone, I've been practicing with the example "Creating a X-ray observation from an in-memory dataset" from here http://yt-project.org/doc/analyzing/analysis_modules/photon_simulator.html However even with simple copy and paste after defining the photons I get this error message: File "/usr/local/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 685, in runfile execfile(filename, namespace) File "/usr/local/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 78, in execfile builtins.execfile(filename, *where) File "/home/afi/Documents/X_ray_sim/X_mock.py", line 75, in <module> exp_time, thermal_model, center="c") File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/analysis_modules/photon_simulator/photon_simulator.py", line 330, in from_scratch photons = photon_model(data_source, parameters) File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/analysis_modules/photon_simulator/photon_models.py", line 140, in __call__ kT_bins = np.linspace(kT_min, max(my_kT_max, kT_max), num=n_kT+1) File "/usr/lib/python2.7/dist-packages/numpy/core/function_base.py", line 87, in linspace step = (stop-start)/float((num-1)) File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/units/yt_array.py", line 745, in __sub__ ro = sanitize_units_add(self, right_object, "subtraction") File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/units/yt_array.py", line 134, in sanitize_units_add raise YTUnitOperationError(op_string, inp.units, dimensionless) YTUnitOperationError: The subtraction operator for YTArrays with units (keV) and (1) is not well defined. Any ideas? I am new to yt and i can't see something wrong. Thnak you Alex Creating a X-ray observation from an in-memory datasetCreating a X-ray observation from an in-memory dataset

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pastebin downtime
by Matthew Turk Sept. 1, 2015

Sept. 1, 2015

Hey all, we're moving the pastebin to a different server. Might be some downtime in the next day or two.

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