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
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