Mailman 3 March 2019 - yt-users

by Stephanie Tonnesen

Hi yt-users, This is actually a bit directed at the developers of the clump finder. I would like to know if including a validator speeds up the clump finder routine. Basically, if I say via validator that I only want clumps whose minimum temperature is below some value, will that help me speed things up by tossing out clumps that don’t fulfill that criteria early on in the process? Or does it only validate after having gone through the entire clump finding routine (after it has looked for children a bunch of times and reached the max density or variable value)? Thanks! Stephanie -- -- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY stonnes(a)gmail.com

4 weeks

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Changing units in image creation

by Andrew Cook

Hello, I'm looking at changing the units for my density field from g/cm^2 to solar masses/pc^3. I tried using set_unit but that gave me an error saying it couldn't change from one to the other. I'm using Enzo 2.5 and yt 3.5.0 for visualisation. Many thanks Andy

1 month

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halos and particles question

by Dave Semeraro

Hi there, I was wondering what is the correct way to obtain a list of particles that lie inside each halo in a catalog. I think I can figure out how to brute force this but I was wondering if there was a YT way to do it. In the end I would like particle positions (x,y,z) for particles grouped by which halo they are in. <disclaimer> I am not an astrophysicist and did not stay in a holiday inn express last night. I don’t even know what a halo is really for. I just need to get disjoint sets of particles that are grouped together for some work I am doing with tessellation. </disclaimer> I was thinking halos calculate a position and center for clumps of particles. I would like separate lists of particle positions for each of those clumps. So far I can generate the halos (cut and paste from the docs). I just don’t know the next step. I am working with the enzo_cosmology_plus dataset as an example. Thanks, Dave Semeraro Visualization Group Texas Advanced Computing Center University of Texas Austin

1 month

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yt halo finding

by Salome Mtchedlidze

Hello, I am trying to become familiar with yt halo finding. I have already created halo catalog and with Jupiter notebook I could see what was the number of halos (when it creates halo catalog it also writes what is the number of halos). I am trying to plot number of halos dependence on their masses and for this I need to have number of halos (with certain masses) as an output. I was trying to use callbacks and quantities but failed. Do you know what will be the best solution to get number of halos as an output? Thanks, Salome

1 month

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Create_profile error with yt 3.5

by Lu, Yinghe

Hello, I recently updated yt from 3.2.1 to 3.5.1 and I am receiving Segmentation Fault error when running yt.data_objects.profiles.create_profile. A good way to reproduce the error would be when running the test code in the documentation radial_profiles_styles.py. I can't seem to find anywhere in the documentation what has changed regarding this function during the updates. Would appreciate if anyone can take a look into this!

1 month

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Removing a source from a scene and keyname references

by Steiner, Andrew (Andrew W. Steiner)

Hello all, What I'm trying to figure out is the best way to remove a source from a scene, if possible doing it by keyname (or is there some other unique identifier?). I know that the scene add_source method has a keyword argument for add_source, but there isn't a remove_source function yet. I can directly access 'sources' in the scene object, but I haven't yet figured out a good way to manipulate that. I have a few volume, line, and point sources, but I would like to remove some of them and add them back in as I rotate my camera. Take care, Andrew -- Andrew W. Steiner Joint Faculty Asst. Prof. at UTK/ORNL https://neutronstars.utk.edu/

1 month

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2019 John Hunter Excellence in Plotting Contest

by Madicken Munk

In memory of John Hunter, we are pleased to be reviving the SciPy John Hunter Excellence in Plotting Competition for 2019. This open competition aims to highlight the importance of data visualization to scientific progress and showcase the capabilities of open source software. Participants are invited to submit scientific plots to be judged by a panel. The winning entries will be announced and displayed at the conference. John Hunter’s family and NumFocus are graciously sponsoring cash prizes for the winners in the following amounts: - 1st prize: $1000 - 2nd prize: $750 - 3rd prize: $500 - Entries must be submitted by June, 8th to the form at https://goo.gl/forms/cFTB3FUBrMPfQ7Vz1 - Winners will be announced at Scipy 2019 in Austin, TX. - Participants do not need to attend the Scipy conference. - Entries may take the definition of “visualization” rather broadly. Entries may be, for example, a traditional printed plot, an interactive visualization for the web, or an animation. - Source code for the plot must be provided, in the form of Python code and/or a Jupyter notebook, along with a rendering of the plot in a widely used format. This may be, for example, PDF for print, standalone HTML and Javascript for an interactive plot, or MPEG-4 for a video. If the original data can not be shared for reasons of size or licensing, "fake" data may be substituted, along with an image of the plot using real data. - Each entry must include a 300-500 word abstract describing the plot and its importance for a general scientific audience. - Entries will be judged on their clarity, innovation and aesthetics, but most importantly for their effectiveness in communicating a real-world problem. Entrants are encouraged to submit plots that were used during the course of research or work, rather than merely being hypothetical. - SciPy reserves the right to display any and all entries, whether prize-winning or not, at the conference, use in any materials or on its website, with attribution to the original author(s). SciPy John Hunter Excellence in Plotting Competition Co-Chairs Hannah Aizenman Thomas Caswell Madicken Munk Nelle Varoquaux

1 month, 1 week

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yt streamlines and periodic boundaries

by Yann Pfau-Kempf

Hello, I am a new user of yt and I am specifically trying to use its streamline capabilities. My script essentially does the same as the example below, i.e. I load some data from numpy arrays and trace streamlines from a set of seeds. It turns out that despite being set to being fully periodic (the only option, otherwise yt tries to access data outside of the box) the streamlines stop at the box edges. Is there a trick to get actually periodic streamlines? Or should I work around, replicate my array N times in each direction and fold the coordinates to the original range afterwards by hand? Thanks in advance for your help, Best regards, Yann Pfau-Kempf University of Helsinki ------------------------------------------------------------------------ streamlength=30 Bx=np.ones((10,10,10)) By=np.ones((10,10,10)) Bz=np.ones((10,10,10)) data=dict(Bx=Bx,By=By,Bz=Bz) streamline_seeds = np.array([0,0,0]) yt_dataset = yt.frontends.stream.load_uniform_grid( data, [10, 10, 10], bbox=np.array([[0,10], [0, 10], [0, 10]]), periodicity=[True, True, True]) streamlines_pos = yt.visualization.api.Streamlines(yt_dataset, streamline_seeds, "Bx", "By", "Bz", length=streamlength, direction=1) streamlines_neg = yt.visualization.api.Streamlines(yt_dataset, streamline_seeds, "Bx", "By", "Bz", length=streamlength, direction=-1) print streamlines_pos.streamlines[0], streamlines_neg.streamlines[0] Output: [[ 0. 0. 0. ] [ 0.55872607 0.55872607 0.55872607] [ 1.11745213 1.11745213 1.11745213] [ 1.6761782 1.6761782 1.6761782 ] [ 2.23490427 2.23490427 2.23490427] [ 2.79363033 2.79363033 2.79363033] [ 3.3523564 3.3523564 3.3523564 ] [ 3.91108247 3.91108247 3.91108247] [ 4.46980854 4.46980854 4.46980854] [ 5.0285346 5.0285346 5.0285346 ] [ 5.58726067 5.58726067 5.58726067] [ 6.14598674 6.14598674 6.14598674] [ 6.7047128 6.7047128 6.7047128 ] [ 7.26343887 7.26343887 7.26343887] [ 7.82216494 7.82216494 7.82216494] [ 8.380891 8.380891 8.380891 ] [ 8.93961707 8.93961707 8.93961707] [ 9.49834314 9.49834314 9.49834314] [10.05706921 10.05706921 10.05706921] [ 0. 0. 0. ] [ 0. 0. 0. ] [ 0. 0. 0. ] [ 0. 0. 0. ] [ 0. 0. 0. ] [ 0. 0. 0. ] [ 0. 0. 0. ] [ 0. 0. 0. ] [ 0. 0. 0. ] [ 0. 0. 0. ] [ 0. 0. 0. ] [ 0. 0. 0. ]] code_length [[ 0. 0. 0. ]

1 month, 1 week

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Creating a 3D image of a cosmological box

by Andrew Cook

Hello, This is a slightly big ask but I'm trying to get an image of one of my simulations with the full box in view with all halos visible. I'm not sure if something needs to be specifically set up with Enzo or MUSIC but hopefully this is just a yt thing. Many thanks Andy

1 month, 1 week

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Proper way to set units when using Scene() and VolumeSource()

by Steiner, Andrew (Andrew W. Steiner)

Hello all, I'm having trouble figuring out how to set the units with a generic data set. See the code below. It complains that: Traceback (most recent call last): File "post2.py", line 36, in <module> cam.width=1.5*ds.domain_width[0] ... more traceback info ... File "/usr/lib/python3/dist-packages/yt/units/unit_object.py", line 664, in _lookup_unit_symbol "Code units have not been defined. \n" yt.units.unit_registry.UnitParseError: Code units have not been defined. Try creating the array or quantity using ds.arr or ds.quan instead. Code for the simplified test case is given below. I'm just trying to find the simple addition which fixes my units to something so it will proceed with the rendering. Thank you, Andrew -- Andrew W. Steiner Joint Faculty Asst. Prof. at UTK/ORNL https://neutronstars.utk.edu/ --------------------------------------- import yt import numpy as np import h5py import math from yt.visualization.volume_rendering.api import Scene, \ VolumeSource, LineSource, PointSource from yt.visualization.volume_rendering.transfer_function_helper \ import TransferFunctionHelper # Generate the data, a sum of two Gaussians centered at (0.4,0.3,0.2) # and (0.4,0.3,0.8). grid=128 arr=np.zeros(shape=(grid,grid,grid)) width=0.3 for i in range(0,grid): x=i/127 for j in range(0,grid): y=j/127 for k in range(0,grid): z=k/127 arr[i][j][k]=(math.exp(-(x-0.4)**2/width**2-(y-0.3)**2/width**2- (z-0.2)**2/width**2)+ math.exp(-(x-0.4)**2/width**2-(y-0.3)**2/width**2- (z-0.8)**2/width**2)) # Load the data into yt ds=yt.load_uniform_grid(dict(density=arr),arr.shape,nprocs=4, bbox=np.array([[0.0,1.0],[0.0,1.0],[0.0,1.0]])) # Create the scene sc=Scene() # Create the camera cam=sc.add_camera() cam.width=1.5*ds.domain_width[0] cam.position=[1.5,0.6,0.7] cam.focus=ds.domain_center cam.north_vector=[0.0,0.0,1.0] cam.switch_orientation() # Create the volume source vol=VolumeSource(ds,field='density') # Setup the transfer function tfh=TransferFunctionHelper(ds) tfh.set_field('density') tfh.set_log(False) tfh.set_bounds() tfh.build_transfer_function() tfh.tf.add_layers(5) tfh.plot('tf.png') vol.set_transfer_function(tfh.tf) # Add the volume source to the scene sc.add_source(vol) sc.save('post2.png',sigma_clip=1.0)

1 month, 1 week

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yt-users March 2019