Mailman 3 January 2014 - yt-users

Trouble with SciPy install
by Nathan Butcher 24 Jan '14

24 Jan '14

Hello, I am trying to install yt with SciPy on Michigan State University's HPCC system and am running into errors that I cannot resolve by following the instructions in the install script. I have tried uncommenting each of the NUMPY_ARGS statements and had no success. I have attached the log file from my most recent installation attempt as the error message is long. My guess is that it has to do with the "recompile with -fPIC" message in lines 75202 and 75205 but I cannot figure out what that means. Can anybody explain what this error message means and how to resolve it. Thank you, Nathan Butcher

1 0

building fKDpy.so manually
by Remudin Mekuria 24 Jan '14

24 Jan '14

Hi all, While trying to run the attached script from "yt-cookbook" to get halo mass function, I am getting NameError: global name 'fKD' is not defined. It looks like I am tied up already, since I can't do "yt update" on the top of my manual installation. If I am not wrong, it looks to me that I have to build fKDpy.so, may you help me on how to do that. Thank you in advance for your kindest help. Cheers, Remudin ==================== yt : [INFO ] 2014-01-24 15:32:41,413 Building kd tree for 2097152 particles... Traceback (most recent call last): File "mass_function.py", line 15, in <module> hp = amods.halo_profiler.HaloProfiler("/home/remudin/gas_plus_dm_uni_adia_simulation/RD0003/RedshiftOutput0003") File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_profiler/multi_halo_profiler.py", line 305, in __init__ self._load_halo_data() File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_profiler/multi_halo_profiler.py", line 983, in _load_halo_data self._run_hop(hop_file) File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_profiler/multi_halo_profiler.py", line 1140, in _run_hop **self.halo_finder_kwargs) File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/halo_objects.py", line 2305, in __init__ premerge=premerge, tree=self.tree) File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/halo_objects.py", line 1670, in __init__ HaloList.__init__(self, data_source, dm_only) File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/halo_objects.py", line 1059, in __init__ self._run_finder() File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/halo_objects.py", line 1698, in _run_finder tree=self.tree) File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py", line 63, in __init__ self._chain_hop() File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py", line 1526, in _chain_hop self._init_kd_tree() File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py", line 341, in _init_kd_tree fKD.dens = np.zeros(self.size, dtype='float64', order='F') NameError: global name 'fKD' is not defined ================================== ................................ ................................. Remudin Reshid; MEKURIA, School of Physics, Wits University, 1 Jan Smuts Ave, Braamfontein, WITS 2050 Johannesburg, South Africa ................................ ................................. <table width="100%" border="0" cellspacing="0" cellpadding="0" style="width:100%;"> <tr> <td align="left" style="text-align:justify;"><font face="arial,sans-serif" size="1" color="#999999"><span style="font-size:11px;">This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorised signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. </span></font></td> </tr> </table

1 0

Release of pywwt 0.1.0, a Python interface to the World Wide Telescope Windows Client
by John ZuHone 23 Jan '14

23 Jan '14

Hi all, Apologies for the spam, but I thought maybe the yt-users list would be good place to find some interest in this new library I wrote, pywwt: http://www.jzuhone.com/pywwt pywwt is a Python interface for the Microsoft World Wide Telescope (WWT, http://www.worldwidetelescope.org) Windows client, using the Layer Control API (LCAPI). The LCAPI provides an interface to WWT’s Layer Manager by sending data and information in the form of strings over HTTP. pywwt provides a straightforward Python interface to make these calls, enabling the control of WWT from scripts or an IPython notebook. Most importantly, it enables the passing of data created within a Python environment to WWT. The upshot of this is that particle data that can be loaded into yt can be passed off to a World Wide Telescope client running on a Windows machine, either the same host or a host on the same network. To see an example IPython notebook (complete with an example video!), visit: http://www.jzuhone.com/pywwt/pywwt_example.html pywwt requires the following packages: • NumPy • Matplotlib • AstroPy • Beautiful Soup 4 • Requests • Dateutil pywwt can be installed from pip: pip install pywwt or download the source from http://github.com/jzuhone/pywwt and install: python setup.py install My use cases are limited, and I'd be interested in what others could do with it, so if you are interested please fork the code and help develop! Best, John Z

2 2

NotImplementedError
by Yong Zheng 22 Jan '14

22 Jan '14

Hi, I newly installed yt in my laptop, but ran into an error call "NotImplementedError" when I tried to use 'pixelize_healpix' which used to work fine in my another computer, the whole message is as followed: img2d,count = pixelize_healpix(NP, img1d, resolution, resolution, rotation) File "grid_traversal.pyx", line 1127, in yt.utilities.lib.grid_traversal.pixelize_healpix (yt/utilities/lib/grid_traversal.c:14555) NotImplementedError Can any of you help to explain why this happens here? How can I fix it? Thanks for your help! Yong

2 1

Surface plot from FITS data cube
by Mairan Teodoro 21 Jan '14

21 Jan '14

Hi yt-users! I'm new to yt and Python (I'm an IDL guy). Currently, I'm using VisIt to visualize my FITS data cube. However, since I'm wandering through the fields of Python, I would really like to use yt as my default visualization tool. Having said that, I would like to ask if somebody out there has some piece of code to read a FITS data cube into a Python array (I know how to do this already) and use yt to visualize it and make iso-surface plots (like the ones I've attached to this message). I went through the yt manual examples (especially the volume plot sections) but all I've got was some kind of blurred blotch (see figure "UniformGridData_volume_rendered.png"). Any help would be very appreciated. Best regards! m. --Dr. Mairan Teodoro NASA Goddard Space Flight Center 8800 Greenbelt Rd. Greenbelt, MD 20771 USA Bldg. 34, Rm. 321 301-286-6321 Code 667 http://asd.gsfc.nasa.gov/Mairan.Teodoro http://etacar2014.wikidot.com

2 1

Another clump finder error
by Caroline Van Borm 21 Jan '14

21 Jan '14

Hi all, Sorry to bother you again, but I have another problem with the clump finder. I have been able to run the script to find the clumps, wrote them to a text file, and saved the clump object using <pf.h.save_object(master_clump, 'myclumps')>. However, when I try to read the object back in and get the lowest clumps using master_clump = pf.h.load_object('myclumps') leaf_clumps = get_lowest_clumps(master_clump) I get an error saying: Traceback (most recent call last): File "./findclumps.py", line 66, in <module> leaf_clumps = get_lowest_clumps(master_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 209, in get_lowest_clumps if clump.children is None or len(clump.children) == 0: AttributeError: 'NoneType' object has no attribute 'children' Does this happen because the clump object didn't actually get saved? And how can I check whether it did or not? Thanks again! Cheers, Caroline

4 4

Setting x and y limits in PhasePlot
by Devin Silvia 20 Jan '14

20 Jan '14

Hi all, I'm currently running into and issue where I can't seem to figure out how to control the x and y limits of my axes in a PhasePlot. Is this possible? Or do I need to go the PlotCollection route? Thanks! Devin -- Devin W. Silvia Research Associate Department of Physics and Astronomy Michigan State University www.devinsilvia.com

2 1

yt-installation failed on getting pip
by Remudin Mekuria 20 Jan '14

20 Jan '14

Dear YT-users, My installation of yt on Ubuntu machine failed up on getting pip. I have tried to test the source of the problem first by installing pip as "sudo apt-get install python-pip". And I have pip installed. It turn out to be the same even when i do again "bash install_script.sh". Then, I also tried to verify these is not a network connection problem as it is saying in the error message"error: Download error for https://pypi.python.org/packages/source/p/pip/pip-1.5.tar.gz: Tunnel connection failed: 407 Proxy Authentication Required". I will be glad to receive your help on these. Cheers, Remudin ################ ################ ################ ################ ...... Installing Python. This may take a while, but don't worry. yt loves you. Installing mercurial-2.8 Setting YT_DIR=/home/remudin/yt-x86_64/src/yt-hg/ Installing distribute Installing pip ******************************************** FAILURE REPORT: ******************************************** Processing dependencies for distribute==0.6.32 Finished processing dependencies for distribute==0.6.32 After install bootstrap. Creating /home/remudin/yt-x86_64/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg-info Creating /home/remudin/yt-x86_64/lib/python2.7/site-packages/setuptools.pth Searching for pip Reading http://pypi.python.org/simple/pip/ Best match: pip 1.5 Downloading https://pypi.python.org/packages/source/p/pip/pip-1.5.tar.gz#md5=6969b8a8ad… error: Download error for https://pypi.python.org/packages/source/p/pip/pip-1.5.tar.gz: Tunnel connection failed: 407 Proxy Authentication Required ******************************************** ******************************************** Failure. Check /home/remudin/yt-x86_64/yt_install.log. The last 10 lines are above. ################ ################ ################ ################ ................................ ................................. Remudin Reshid; MEKURIA, School of Physics, Wits University, 1 Jan Smuts Ave, Braamfontein, WITS 2050 Johannesburg, South Africa ................................ ................................. <table width="100%" border="0" cellspacing="0" cellpadding="0" style="width:100%;"> <tr> <td align="left" style="text-align:justify;"><font face="arial,sans-serif" size="1" color="#999999"><span style="font-size:11px;">This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorised signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. </span></font></td> </tr> </table

2 1

Does anybody have a sample script for plotting a time-series of images from frb's?
by Kathy Eastwood 16 Jan '14

16 Jan '14

Hi, everybody I've been working off the example scripts on the yt website, and can't quite seem to do what I want to do. I want to plot something like 20 tall/skinny images in a horizontal row, and label the time steps below, and put the colorbar vertically. I am constrained to using frb's because my images are not square. I have managed to make a plot with three such images, although I haven't managed to put in the time step labels, and there is white space between the images. But it was very much brute force -- I had to create a separate set of axes for each image. All the example scripts that use frb's use the "get_multi_plot" inside yt, whereas the only example of a time series in the image plots uses the AxesGrid from matplotlib. I have not managed to make the AxesGrid work with an frb. There is also a non-image-plotting example in the bootcamp of using "TimeSeriesData" to go through a lot of files, which would be great, but I have not been able to figure out how to translate that into what I need. If anybody has a sample script of something vaguely similar to this, I would really appreciate it! thanks kathy -- Kathy DeGioia Eastwood, Ph.D. Professor of Physics and Astronomy Northern Arizona University Flagstaff, AZ 86011-6010 Ph: 928-523-7159 FX: 928-523-1371 Kathy.Eastwood(a)nau.edu deliveries: 602 S. Humphreys St., Bldg 19 Rm 209

4 3

Clump finder error
by Caroline Van Borm 16 Jan '14

16 Jan '14

Hi all, I have a problem with the clump finder. When I try to run it on my dataset (Enzo data), using a script that mostly follows the find_clumps.py from the yt docs, I get the following, very long, error: Traceback (most recent call last): File "./findclumps.py", line 44, in <module> find_clumps(master_clump, c_min, c_max, step) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 182, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 191, in find_clumps elif (child._isValid()): File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 145, in _isValid self.function_value = eval(self.function) File "<string>", line 1, in <module> File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 94, in __call__ return self._call_func_unlazy(args, kwargs) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 119, in _call_func_unlazy retval = self.func(self._data_source, *args, **kwargs) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 378, in _IsBound mass_to_use = data["TotalMass"] File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 332, in __getitem__ self.get_data(key) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 2618, in get_data if self._generate_field(field): File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 362, in _generate_field self[field] = self.pf.field_info[field](self) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 395, in __call__ dd = self._function(self, data) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/universal_fields.py", line 444, in _TotalMass return (data["Density"]+data["particle_density"]) * data["CellVolume"] File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 332, in __getitem__ self.get_data(key) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 2618, in get_data if self._generate_field(field): File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 359, in _generate_field self._generate_field_in_grids(field, ngt_exception.ghost_zones) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 369, in _generate_field_in_grids grid[field] = self.__touch_grid_field(grid, field) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 95, in save_state tr = func(self, grid, field, *args, **kwargs) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 373, in __touch_grid_field return grid[field] File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 157, in __getitem__ self.get_data(key) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 200, in get_data self._generate_field(field) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 145, in _generate_field self[field] = self.pf.field_info[field](self) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 395, in __call__ dd = self._function(self, data) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/universal_fields.py", line 998, in _pdensity if data["particle_position_x"].size == 0: return blank File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 157, in __getitem__ self.get_data(key) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 200, in get_data self._generate_field(field) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 145, in _generate_field self[field] = self.pf.field_info[field](self) File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 396, in __call__ dd *= self._convert_function(data) TypeError: unsupported operand type(s) for *=: 'NoneType' and 'float' The main difference is that for the function passed to Clump, I'm using 'self.data.quantities["IsBound"](truncate=True,include_thermal_energy=True) > 1.0' to find gravitationally bound objects. When I run the clump finder on my data with a function that keeps clumps based on the number of cells, it works fine. I also tried running the script on the IsolatedGalaxy dataset as demonstrated in the docs. This works fine too, also when the function is set to the one mentioned above. Anyone knows what's going on here? Btw, my yt version is b118390aa42c. Thanks! Cheers, Caroline

3 5