Mailman 3 April 2014 - yt-users

Porting .ply files to Blender with colors?
by Jill P. Naiman 15 Aug '22

15 Aug '22

Hi All, I was curious if anyone has had any luck porting .ply files generated with yt into Blender with colors? It seems to port in the surfaces just fine, but they are a uniform color. From what I can gather, Blender imports .ply files with face color instead of vertex so I tried the surf.export_ply routine with "face" instead of "vertex" for sample_type, but no luck ("vertex" doesn't work either). Let me know if I can provide any more useful info. Thanks for any help, -J

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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.

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Freeprocessing
by tom fogal 01 May '14

01 May '14

Hi all, I'm Tom; new here, but I've been lurking on #yt (and #enzo) for a while now. My group and I created an in situ visualization tool that we're calling "Freeprocessing", and a few of you helped me hook it up to yt for a publication. Thanks for all your help---that paper was recently accepted! :-) Now that the edits are in, I'd like to delve into the problem deeper and hopefully expand on the 'proof of concept' we had used in the paper. If you could give it a try, I'd love to get people's thoughts on future directions, or even just issues we could address. More info on the website: https://tfogal.github.io/freeprocessing/ I'm "tfogal" on freenode/#yt and would love to chat with some of you there, but email works if you're not the IRC type. Thanks! -tom

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yt confusion
by Kathy Eastwood 30 Apr '14

30 Apr '14

Dear yt folks, I am sorry to keep bothering you, but I have once again confused myself. Below I reference two bits of yt documentation and one yt cookbook example. http://yt-project.org/docs/2.6/reference/api/generated/yt.data_objects.data… This is a function that returns the vertices of marching cube triangles http://yt-project.org/docs/2.5/api/generated/yt.data_objects.data_container… This creates a surface object which also returns vertices of same marching cubes triangles. (Note that there is an error in the Examples section; the text there actually refers to the script shown on the previous extract_isocontours page.) http://yt-project.org/docs/2.5/cookbook/complex_plots.html#plotting-isocont… This is an example which uses the output triangles of the surface object to make an isocontour plot So now I am rather confused. If I want to make an isocontour plot, using the vertices of the triangles resulting from the marching cubes method, what is the difference between these two? In particular, I have decided that I would like to output the vertices to a file and then read them in to some other plotting program. Are the two ways shown exactly equivalent? Is one to be preferred over the other, particularly if I want to use a sphere data container as my source? I have not been able to get the .surface to work with just a sphere data container. 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

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Best way to create radial bins
by Thomas Hansen 28 Apr '14

28 Apr '14

Hi everyone, I'm kind of new to yt and am currently working on creating a set of graphs but am having a bit of difficulty. My goal is to take a list of central points (a set of x,y,z coordinates) and then look at a set of 30 spherical "shells" which surround the central points. So I want to be able to know how much mass is between, say 30 and 60 parsecs away from a certain point (along with 60-90, 90-120, etc.). The problem is, the number of points is absolutely massive, so I need a fairly quick way of finding these values for all the points I'm interested in. I've tried a few tactics already. First I tried going to each point, creating a sphere with that center and the maximum radius. Then I used the center location to set a field parameter, then created a BinnedProfile1D using a "radius" field and the sphere I created, but that seemed to be impractically slow. Next, I tried the somewhat hackish method of for each point, creating a series of 30 spheres with radii corresponding with the boundaries I wanted between the shells. I then used the boolean("NOT") command to construct a series of shells by finding the part of each sphere not in the smaller one. I could then sum over the values in each shell. This seemed to go a bit faster, but I feel like this could use an absolutely massive amount of computation, if I understand how yt works properly. Is there a better way of doing this? Thank you so much for your time, Thomas

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Problem with covering grid
by Elizabeth Tasker 25 Apr '14

25 Apr '14

Hi, I've hit a problem with the latest version of yt and covering grid that is linked with the number of ghostzones. My code looked like: for dim in range(3): left.append(cloud_position[c][dim] - 0.5*width[dim]) right.append(cloud_position[c][dim] + 0.5*width[dim]) dims.append(int(round((right[dim]-left[dim])/cellsize))) cgrid = pf.h.covering_grid(level, left_edge = left, dims=dims, num_ghost_zones=2) but gives me: TypeError Traceback (most recent call last) /home/tasker/yt-new2/src/yt-hg/scripts/iyt in <module>() ----> 1 execfile("export_hdf5_cube.py") /home/tasker/yt-new2/src/yt-hg/scripts/iyt in <module>() 51 left_edge = left, 52 dims=dims, ---> 53 num_ghost_zones=2) 54 55 /home/tasker/yt-new2/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, level, left_edge, dims, fields, pf, num_ghost_zones, use_pbar, **kwargs) 3689 self.level = level 3690 rdx = self.pf.domain_dimensions*self.pf.refine_by**level -> 3691 rdx[np.where(dims - 2 * num_ghost_zones <= 1)] = 1 # issue 602 3692 self.dds = self.pf.domain_width / rdx.astype("float64") 3693 self.ActiveDimensions = np.array(dims, dtype='int32') TypeError: unsupported operand type(s) for -: 'list' and 'int' This happens regardless of whether I use num_ghost_zones or not. If I don't have ghost_zones set, the error occurs at line 52, but still points to line 3691. Dims and left look fine: In [9]: dims Out[9]: [64, 64, 64] In [10]: left Out[10]: [20.424700000000001, 11.512700000000001, 15.7158] In [11]: level Out[11]: 5 In [14]: rdx = pf.domain_dimensions*pf.refine_by**level In [15]: rdx Out[15]: array([4096, 4096, 4096]) If I set num_ghost_zones = na.array([0,0,0]) then it runs. However, if I then try cgrid["x"] I hit more problems circulating around the same area: ValueError Traceback (most recent call last) /home/tasker/yt-new2/src/yt-hg/scripts/iyt in <module>() ----> 1 cgrid["y"] /home/tasker/yt-new2/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key) 316 if key not in self.fields: 317 self.fields.append(key) --> 318 self.get_data(key) 319 return self.field_data[key] 320 /home/tasker/yt-new2/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields) 3733 try: 3734 #print "Generating", field -> 3735 self._generate_field(field) 3736 continue 3737 except NeedsOriginalGrid, ngt_exception: /home/tasker/yt-new2/src/yt-hg/yt/data_objects/data_containers.pyc in _generate_field(self, field) 3764 if self.pf.field_info.has_key(field): 3765 # First we check the validator; this might even raise! -> 3766 self.pf.field_info[field].check_available(self) 3767 self[field] = self.pf.field_info[field](self) 3768 else: # Can't find the field, try as it might /home/tasker/yt-new2/src/yt-hg/yt/data_objects/field_info_container.pyc in check_available(self, data) 354 """ 355 for validator in self.validators: --> 356 validator(data) 357 # If we don't get an exception, we're good to go 358 return True /home/tasker/yt-new2/src/yt-hg/yt/data_objects/field_info_container.pyc in __call__(self, data) 482 if not data._spatial: 483 raise NeedsGridType(self.ghost_zones,self.fields) --> 484 if self.ghost_zones <= data._num_ghost_zones: 485 return True 486 raise NeedsGridType(self.ghost_zones,self.fields) ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() cgrid["Density"] and the velocities are fine. I'm suspecting this is because the position calculation in the code is not expecting an array for the ghost zone number? Oddly, I see from the mailing list is this reminiscent of a problem nyx was having. Elizabeth

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mayavi
by Kathy Eastwood 25 Apr '14

25 Apr '14

Hi, everyone Has anyone tried using mayavi inside yt? I see that it can be called inside an ipynb.... Just curious...I'm getting kind of frustrated with the 3d aspects of matplotlib. 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

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Re: [yt-users] yt-users Digest, Vol 74, Issue 30
by Yong Zheng 23 Apr '14

23 Apr '14

Hi John, Greg and Cameron, Thank you so much for such detail instructions! I've gotten it back. Many many thanks! -Yong On Tue, Apr 22, 2014 at 2:05 PM, <yt-users-request(a)lists.spacepope.org>wrote: > 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. Reverse yt back to v2.5 (Yong Zheng) > 2. Re: Reverse yt back to v2.5 (John Wise) > 3. Re: Reverse yt back to v2.5 (Greg Meece) > 4. Re: Reverse yt back to v2.5 (Cameron Hummels) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 22 Apr 2014 10:07:15 -0400 > From: Yong Zheng <yz2505(a)columbia.edu> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] Reverse yt back to v2.5 > Message-ID: > <CACvSp01XjHW_uGuydBbi2YbMzJdTrsnkan= > e+KSHeNa0LiUg_A(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi everyone, > > I recently updated the yt, then realized there is a license issue with > HEALPix in the new version... Is there a way that I can reverse back to my > previous version (yt2.5)? > > Thanks! > Yong > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 2 > Date: Tue, 22 Apr 2014 10:54:30 -0400 > From: John Wise <jwise(a)physics.gatech.edu> > To: yt-users(a)lists.spacepope.org > Subject: Re: [yt-users] Reverse yt back to v2.5 > Message-ID: <535682A6.4060007(a)physics.gatech.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Yong, > > If you issue the command "hg up yt-2.5.5" inside the yt source > directory, this will bring the source back to v2.5. Then you will > compile and install yt as usual. > > Thanks, > John > > On 04/22/2014 10:07 AM, Yong Zheng wrote: > > Hi everyone, > > > > I recently updated the yt, then realized there is a license issue with > > HEALPix in the new version... Is there a way that I can reverse back to > > my previous version (yt2.5)? > > > > Thanks! > > Yong > > > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > -- > John Wise > Assistant Professor of Physics > Center for Relativistic Astrophysics, Georgia Tech > http://cosmo.gatech.edu > > > ------------------------------ > > Message: 3 > Date: Tue, 22 Apr 2014 10:57:03 -0400 > From: Greg Meece <meecegre(a)msu.edu> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Reverse yt back to v2.5 > Message-ID: > < > CADDDyPCqQzr2h73O4_kfZy3FrJR4GJfQSb_LXx9GtTTv9uV8cg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Mercurial contains all of the past changes to yt. In your yt directory, go > into src/yt-hg and then type 'hg tags' to list all of the tagged changsets. > You can update to any of theses (e.g., 'hg update yt-2.5') and then install > using the setup.py script in that directory. > > --Greg > > > On Tue, Apr 22, 2014 at 10:07 AM, Yong Zheng <yz2505(a)columbia.edu> wrote: > > > Hi everyone, > > > > I recently updated the yt, then realized there is a license issue with > > HEALPix in the new version... Is there a way that I can reverse back to > my > > previous version (yt2.5)? > > > > Thanks! > > Yong > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 4 > Date: Tue, 22 Apr 2014 08:05:37 -0700 > From: Cameron Hummels <chummels(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Reverse yt back to v2.5 > Message-ID: > < > CACyTu7Gn3CKDp4WkZSC5zTx18ebRLTuDSwkNrxXxgXwHO17n4A(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > And just for reference, when Greg and John refer to "installing yt as > usual" (after switching to the desired changeset in mercurial), they mean, > go to the yt-hg directory (e.g. yt-i386/src/yt-hg or yt-x86_64/src/yt-hg) > and then type: > > python setup.py develop > > This should set you up to go. Good luck! > > Cameron > > > On Tue, Apr 22, 2014 at 7:57 AM, Greg Meece <meecegre(a)msu.edu> wrote: > > > Mercurial contains all of the past changes to yt. In your yt directory, > go > > into src/yt-hg and then type 'hg tags' to list all of the tagged > changsets. > > You can update to any of theses (e.g., 'hg update yt-2.5') and then > install > > using the setup.py script in that directory. > > > > --Greg > > > > > > On Tue, Apr 22, 2014 at 10:07 AM, Yong Zheng <yz2505(a)columbia.edu> > wrote: > > > >> Hi everyone, > >> > >> I recently updated the yt, then realized there is a license issue with > >> HEALPix in the new version... Is there a way that I can reverse back to > my > >> previous version (yt2.5)? > >> > >> Thanks! > >> Yong > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > > > -- > Cameron Hummels > Postdoctoral Researcher > Steward Observatory > University of Arizona > http://chummels.org > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > _______________________________________________ > 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 74, Issue 30 > **************************************** >

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Volume renderings that are too dark
by Cameron Hummels 23 Apr '14

23 Apr '14

Hello, I'm having some issues with volume renderings being too dark in yt 2.x. I know that in the past, people have recommended using the "clip_ratio" argument in the various Camera methods in order to enhance the output image by clipping the values at some multiple of the standard deviation of the array. Unfortunately, I'm having trouble getting it to actually do anything recently. I slightly modified the notebook from the yt docs cookbook entry on the TransferFunctionHelper to demonstrate this issue. If you scroll down to the bottom of the notebook to the bold text, you'll see what I mean. Perhaps I'm misusing this infrastructure, but I figured I'd check with people here to set me straight. http://nbviewer.ipython.org/gist/anonymous/11196301 Oh, and note that this is simply an example--I don't think *this* VR is too dark in the notebook, but many of the ones that I generate are too dark, and I'd like to brighten them. Thanks for the help! Cameron -- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org

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