This looks like a bug to me, it would be great if you could file a bug on github along with a script we can use to reproduce the issue. On Thu, Oct 4, 2018 at 11:45 AM Stephanie Tonnesen <stonnes@gmail.com> wrote:
Okay, so I was trying to figure out why I am getting strange results and went back to the IsolatedGalaxies cookbook case. I am attaching the cut_region verion here. This may be a cut_region problem, not a clump problem, though!
First, I ran the plain old cookbook case and got the same very lovely clumps.
[image: clumps_reloaded_Projection_z_density_cookbook.png]
Then I changed c_max to 2e-24 based on some of the density values I was getting, and got this:
[image: clumps_reloaded_Projection_z_density_max2en24.png] Okay, fine, I just didn't set my limit high enough. So when I run with max = 7e-24:
[image: clumps_reloaded_Projection_z_density_max7en24.png] But, when I select the same (or slightly larger) region with cut_region and the same c_min and c_max (or just using the standard max and min definitions) I cannot find any clumps!
[image: clumps_reloaded_Projection_z_density.png]
Do you think this is a cut_region or a clump_finder problem?
Thanks! Stephanie
-- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY
stonnes@gmail.com
On Wed, Oct 3, 2018 at 3:29 PM Britton Smith <brittonsmith@gmail.com> wrote:
It's my fault. I forgot to remove the imports from ./yt/analysis_modules/level_sets/api.py. If you change the import to "from yt.data_objects.level_sets.api import ..." then it will work. I'll update the PR now.
On Wed, Oct 3, 2018 at 12:10 PM Stephanie Tonnesen <stonnes@gmail.com> wrote:
Okay, my git skills are not so good, so definitely not *sure*. Just tried to check by doing this:
cd yt-conda/yt (root) -bash-4.2$ git pull https://github.com/brittonsmith/yt.git clurmps From https://github.com/brittonsmith/yt * branch clurmps -> FETCH_HEAD Already up-to-date.
so...I think yes? I also just did the same thing in my script and got the same output. -- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY
stonnes@gmail.com
On Wed, Oct 3, 2018 at 2:56 PM Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Stephanie,
Are you *sure* you pulled britton's pull request? He deleted that entry in yt/analysis_modules/level_sets/api.py, so it looks like you're using a version of that file from before his pull request.
-Nathan
On Wed, Oct 3, 2018 at 1:44 PM Stephanie Tonnesen <stonnes@gmail.com> wrote:
Go it, thanks!
I think I have pulled your update, Britton, and now my code crashes almost immediately with this error.
yt_clump_fingert.py:4: VisibleDeprecationWarning: The level_sets module has been moved to yt.data_objects.level_sets.This import is deprecated and will be removed in a future release.Please, change the import in your scripts from 'from yt.analysis_modules.level_sets' to 'from yt.data_objects.level_sets.'. from yt.analysis_modules.level_sets.api import * Traceback (most recent call last): File "yt_clump_fingert.py", line 4, in <module> from yt.analysis_modules.level_sets.api import * File "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/api.py", line 28, in <module> from yt.data_objects.level_sets.clump_handling import \ ImportError: cannot import name 'write_clump_index'
I am running: yt version
yt module located at: /mnt/home/stonnesen/yt-conda/yt
The current version of yt is:
--- Version = 3.5.dev0 Changeset = ff956e8708c5 --- This installation CAN be automatically updated.
I am guessing that maybe I didn't include some other necessary update?
Thanks!! Stephanie -- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY
stonnes@gmail.com
On Tue, Oct 2, 2018 at 6:54 PM Britton Smith <brittonsmith@gmail.com> wrote:
Hi Stephanie,
While looking into this issue, I found some low hanging refactoring fruit, so I've issued a pull request that cleans things up and takes care of this as well. You can have a look here: https://github.com/yt-project/yt/pull/2045
In running the example you attached, I found that the calculation resulted in a single clump comprised of the entire domain, so the clump annotation may be effectively invisible as it will draw a box around the entire figure. If I used a slightly smaller smaller data container, I was able to see the annotation, so I think things are ok. Let me know if it still doesn't seem right.
Britton
On Tue, Oct 2, 2018 at 1:05 PM Stephanie Tonnesen <stonnes@gmail.com> wrote:
> Hi John, > > Thanks! I *think* it works--here is my only confusion. If I set > c_max to some value less than the max density (say, 1e-24 in the code I > attached previously), it doesn't crash anymore but it doesn't actually plot > a clump contour either. If I set c_max to the max density setting (or I > guess a bit above, 10**np.floor(np.log10(data_source[field]).max()+1) ), > then I get a contour plotted. Does this seem right to you? > > Also, they both give me this message > "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/contour.py:1180: > UserWarning: No contour levels w > ere found within the data range. > warnings.warn("No contour levels were found" > " > Even though I seem to have one central contour in the c_max = > 10**np.floor(np.log10(data_source[field]).max()+1) case. > > Thanks! > Stephanie > > -- > Dr. Stephanie Tonnesen > Associate Research Scientist > CCA, Flatiron Institute > New York, NY > > stonnes@gmail.com > > > On Tue, Oct 2, 2018 at 7:38 AM Wise, John H < > jwise@physics.gatech.edu> wrote: > >> Hi Stephanie, >> >> I actually ran into this bug in the past week. I fixed in for my >> case >> by making this change in clump_handling.py >> >> - elif (child._validate()): >> + elif ((child.children is not None) and >> child._validate()): >> >> I haven't had the time to submit a PR. If this works for you, let >> me >> know, and I can I create one this week. >> >> Thanks, >> John >> >> >> On 10/01/2018 09:48 PM, Stephanie Tonnesen wrote: >> > Hi, >> > >> > Sorry about the crazy delay, here is a script that reproduces the >> error >> > with the IsolatedGalaxy dataset! >> > >> > The script is attached. I am happy to help someone look into it, >> or >> > look more myself with a bit of extra guidance. >> > >> > Thanks!! >> > >> > Stephanie >> > >> > -- >> > Dr. Stephanie Tonnesen >> > Associate Research Scientist >> > CCA, Flatiron Institute >> > New York, NY >> > >> > stonnes@gmail.com <mailto:stonnes@gmail.com> >> > >> > >> > On Fri, Sep 14, 2018 at 6:51 AM Stephanie Tonnesen < >> stonnes@gmail.com >> > <mailto:stonnes@gmail.com>> wrote: >> > >> > Hi Britton! >> > >> > No, I have not resolved the issue, unfortunately. I will try >> and >> > get a script that reproduces the problem up soon. >> > >> > Best, >> > Stephanie >> > >> > On Thu, Sep 13, 2018 at 7:45 PM Britton Smith >> > <brittonsmith@gmail.com <mailto:brittonsmith@gmail.com>> >> wrote: >> > >> > HI Stephanie, >> > >> > Have you managed to resolve this issue? If so, would you >> be >> > willing to submit a pull request to get this fix in the >> main >> > repo? If not, could you post a script that could be used >> to >> > reproduce this error with some of the public data? >> > >> > Britton >> > >> > On Fri, Sep 7, 2018 at 1:05 PM Nathan Goldbaum >> > <nathan12343@gmail.com <mailto:nathan12343@gmail.com>> >> wrote: >> > >> > Generally an error like this is due to a bug in yt. I >> don't >> > know enough about the code you're using to provide >> useful >> > advice, but perhaps we should be checking if >> `children` is >> > `None` and doing something else. The "workaround" is >> likely >> > to fix whatever bug you've run into. >> > >> > On Fri, Sep 7, 2018 at 2:56 PM, Stephanie Tonnesen >> > <stonnes@gmail.com <mailto:stonnes@gmail.com>> wrote: >> > >> > Hi yt-users! >> > >> > I have been fiddling some more with yt's clump >> finder >> > and have another question. I want to use density >> to >> > find clumps, but want my maximum threshold value >> to be >> > below the fiducial setting--instead of above the >> maximum >> > possible density in the code I just want the >> finder to >> > stop searching at, say 3.2e-24. >> > >> > The code was working but running out of memory >> until I >> > set the max threshold, and I now get this error: >> > >> > ....lots of pleasant looking output messages.... >> > Updating joins ... : 0%| | 0/7 >> [00:00<?, ?it/s] >> > Updating joins ... : 100%|██████████| 7/7 >> [00:00<00:00, >> > 48933.55it/s] >> > yt : [INFO ] 2018-09-07 14:08:55,007 >> Investigating 2 >> > children. >> > yt : [INFO ] 2018-09-07 14:08:55,007 Finding >> clumps: >> > min: 3.200000e-24, max: 3.200000e-24, step: >> 2.000000 >> > yt : [INFO ] 2018-09-07 14:08:55,041 Finding >> clumps: >> > min: 3.200000e-24, max: 3.200000e-24, step: >> 2.000000 >> > yt : [INFO ] 2018-09-07 14:08:55,042 >> Eliminating >> > invalid, childless clump with 2 cells. >> > yt : [INFO ] 2018-09-07 14:08:55,042 1 of 2 >> children >> > survived, linking its children to parent. >> > Traceback (most recent call last): >> > File "yt_clump_fingert.py", line 59, in >> <module> >> > find_clumps(master_clump, c_min, c_max, step) >> > File >> > >> "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py", >> > line 444, in find_clumps >> > find_clumps(child, min_val*d_clump, max_val, >> d_clump) >> > File >> > >> "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py", >> > line 438, in find_clumps >> > find_clumps(clump, min_val*d_clump, max_val, >> d_clump) >> > File >> > >> "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py", >> > line 438, in find_clumps >> > find_clumps(clump, min_val*d_clump, max_val, >> d_clump) >> > File >> > >> "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py", >> > line 438, in find_clumps >> > find_clumps(clump, min_val*d_clump, max_val, >> d_clump) >> > File >> > >> "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py", >> > line 461, in find_clumps >> > for child in clump.children: >> > TypeError: 'NoneType' object is not iterable >> > >> > I tried to circumvent this error by changing my >> max to >> > 2e-24 (not a multiple of 2 of 1e-25), and got the >> same >> > error when the min was 3.2e-24 and the max was >> 2e-24 (!). >> > >> > Is there any way I can get around this error and >> have >> > the clumpfinder stop looking once it has clump >> edges at >> > my maximum density? >> > >> > Thanks! >> > Stephanie >> > -- >> > Dr. Stephanie Tonnesen >> > Associate Research Scientist >> > CCA, Flatiron Institute >> > New York, NY >> > >> > stonnes@gmail.com <mailto:stonnes@gmail.com> >> > >> > _______________________________________________ >> > yt-users mailing list -- yt-users@python.org >> > <mailto:yt-users@python.org> >> > To unsubscribe send an email to >> > yt-users-leave@python.org <mailto: >> yt-users-leave@python.org> >> > >> > >> > _______________________________________________ >> > yt-users mailing list -- yt-users@python.org >> > <mailto:yt-users@python.org> >> > To unsubscribe send an email to >> yt-users-leave@python.org >> > <mailto:yt-users-leave@python.org> >> > >> > _______________________________________________ >> > yt-users mailing list -- yt-users@python.org >> > <mailto:yt-users@python.org> >> > To unsubscribe send an email to yt-users-leave@python.org >> > <mailto:yt-users-leave@python.org> >> > >> > -- >> > -- >> > Dr. Stephanie Tonnesen >> > Associate Research Scientist >> > CCA, Flatiron Institute >> > New York, NY >> > >> > stonnes@gmail.com <mailto:stonnes@gmail.com> >> > >> > >> > >> > _______________________________________________ >> > yt-users mailing list -- yt-users@python.org >> > To unsubscribe send an email to yt-users-leave@python.org >> > >> >> -- >> John Wise >> Associate Professor of Physics >> Center for Relativistic Astrophysics, Georgia Tech >> http://cosmo.gatech.edu >> _______________________________________________ >> yt-users mailing list -- yt-users@python.org >> To unsubscribe send an email to yt-users-leave@python.org >> > _______________________________________________ > yt-users mailing list -- yt-users@python.org > To unsubscribe send an email to yt-users-leave@python.org > _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
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