Mailman 3 September 2021 - yt-users

enzo-mrp-music/get_halo_initial_extent.py not working with yt 4.0.1
by C Bernhardt 02 Jun '23

02 Jun '23

Dear yt users, I just updated yt to 4.0.1 and now I get this error message when trying to run enzo-mrp-music.py from John Wise on https://github.com/jwise77/enzo-mrp-music. Traceback (most recent call last): File "enzo-mrp-music/enzo-mrp-music.py", line 264, in <module> params = find_lagrangian_region(params) File "enzo-mrp-music/enzo-mrp-music.py", line 177, in find_lagrangian_region get_center_and_extent(params["halo_info"], File "enzo-mrp-music/get_halo_initial_extent.py", line 147, in get_center_and_extent halo_indices, halo_com, shifted = get_halo_indices(my_halo, final_dataset, File "enzo-mrp-music/get_halo_initial_extent.py", line 119, in get_halo_indices get_halo_sphere_particles(my_halo, dataset, radius_factor=radius_factor) File "enzo-mrp-music/get_halo_initial_extent.py", line 73, in get_halo_sphere_particles my_sphere = pf.h.sphere(my_halo_data['center'], radius_factor * r_200) AttributeError: 'EnzoDataset' object has no attribute 'h' I am honestly not sure what the attribute 'h' does in this case, so I didn't know what to try to adjust. Any suggestions for getting around this? Or how can I go back to yt 3? Kind regards, -- Carla Bernhardt PhD Student Universität Heidelberg ZAH Institut für Theoretische Astrophysik

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Porting .ply files to Blender with colors?
by Jill P. Naiman 14 Aug '22

14 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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Clump Finding for Gadget2 format
by 201s408s＠stu.kobe-u.ac.jp 21 Feb '22

21 Feb '22

Dear all, For my master's research, I installed yt and I want to load my research data converted to gadget2 format with yt. The function I want to use is the clump function, and I want to create a similar figure by performing the same processing as the Clump Finding below. https://yt-project.org/doc/cookbook/constructing_data_objects.html#cookbook… First of all, I tried to test with the gadget data placed in the data index, but neither the default nor the hdf5 format works. Is it possible to do Clump Finding in Gadget2 format?

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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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Error when attempting to call surface object
by Sam Patrick 15 Oct '21

15 Oct '21

Hi all, I've been trying to do some preliminary experimentation with YT's surface object. I have the following snippet of code: sphere = ds.sphere(center, radius) surf = ds.surface(sphere, ('gas', 'density'), 1e-23) ratio = (surf.volume() / surf.surface_area).in_units('pc') However when trying to run the code I get the following error: File "my_analysis.py", line 107, in contours ratio = (surf.volume() / surf.surface_area).in_units('pc') File "/home/brs/stack/yt/yt/data_objects/selection_objects/data_selection_objects.py", line 1394, in volume return self.quantities.total_quantity(("index", "cell_volume")) File "/home/brs/stack/yt/yt/data_objects/derived_quantities.py", line 172, in __call__ rv = super().__call__(fields) File "/home/brs/stack/yt/yt/data_objects/derived_quantities.py", line 55, in __call__ for sto, ds in parallel_objects(chunks, -1, storage=storage): File "/home/brs/stack/yt/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 527, in parallel_objects for result_id, obj in oiter: File "/home/brs/stack/yt/yt/data_objects/selection_objects/data_selection_objects.py", line 94, in chunks for ci, chunk in enumerate(self.index._chunk(self, chunking_style, **kwargs)): File "/home/brs/stack/yt/yt/geometry/geometry_handler.py", line 233, in _chunk self._identify_base_chunk(dobj) File "/home/brs/stack/yt/yt/geometry/grid_geometry_handler.py", line 335, in _identify_base_chunk gi = dobj.selector.select_grids( File "/home/brs/stack/yt/yt/data_objects/selection_objects/data_selection_objects.py", line 73, in selector raise YTDataSelectorNotImplemented(self._type_name) P019 yt : [ERROR ] 2021-09-13 12:14:32,552 YTDataSelectorNotImplemented: Data selector 'surface' not implemented. I was hoping someone could help with this. My yt version is 4.1.dev0 and my Python version is 3.8.5 Many thanks, Sam Patrick

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ImportError when importing HaloCatalog: cannot import name 'ensure_list' from 'yt.funcs'
by Ian Woodward 04 Oct '21

04 Oct '21

I'm running yt 4.0.1 and yt_astro_analysis 1.0.0. I'm trying to import HaloCatalog. I use: from yt_astro_analysis.halo_analysis.api import HaloCatalog but get the error below. On checking funcs.py, it appears that the function 'ensure_list' doesn't exist. Are yt 4.0.1 and yt_astro_analysis 1.0.0 out of sync? I'd be grateful for any suggestions about how to fix this. Cheers Ian ImportError Traceback (most recent call last) /tmp/ipykernel_9530/3924969598.py in <module> 3 import yt 4 import yt_astro_analysis ----> 5 from yt_astro_analysis.halo_analysis.api import HaloCatalog ~/miniconda3/envs/enzo/lib/python3.7/site-packages/yt_astro_analysis/halo_analysis/api.py in <module> 15 16 ---> 17 from yt_astro_analysis.halo_analysis.halo_catalog import \ 18 HaloCatalog 19 ~/miniconda3/envs/enzo/lib/python3.7/site-packages/yt_astro_analysis/halo_analysis/halo_catalog.py in <module> 30 from yt_astro_analysis.halo_analysis.halo_object import \ 31 Halo ---> 32 from yt_astro_analysis.halo_analysis.halo_callbacks import \ 33 callback_registry 34 from yt_astro_analysis.halo_analysis.halo_filters import \ ~/miniconda3/envs/enzo/lib/python3.7/site-packages/yt_astro_analysis/halo_analysis/halo_callbacks.py in <module> 27 from yt.utilities.exceptions import \ 28 YTSphereTooSmall ---> 29 from yt.funcs import \ 30 ensure_list 31 from yt.utilities.logger import ytLogger as mylog ImportError: cannot import name 'ensure_list' from 'yt.funcs' (/home/ian/miniconda3/envs/enzo/lib/python3.7/site-packages/yt/funcs.py)

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Yt will soon drop support for Python 3.6
by Clément Robert 28 Sep '21

28 Sep '21

Dear yt users, As was previously mentionned in yt 4.0.0's release notes, we're planning to drop support for Python 3.6 in our next feature release (4.1.0). The change is set to happen on the dev branch of yt not earlier than October the 20th, this year. This means that if you wish to use our most recent features and bugfixes past this date, you'll need to make sure you're running Python 3.7 or newer. Note that the 4.0.x series will retain compatibility with Python 3.6. The exact method to upgrade your Python runtime depends on what tool(s) you used to install Python or to manage your environments. In general, please lookup the method that applies to your tools. Here is the documentation for some common methods: - using venv (see "--upgrade" flag) https://docs.python.org/3/library/venv.html - using conda https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-pyth… In general, yt is primarily tested with the latest Python versions available, so we recommend upgrading Python to the latest version available to you. There will be a reminder in two weeks from now. Note that we're also planning to officially support Python 3.10 as soon as possible, but likely not earlier than mid-October. Have a great day, Clément Robert, on behalf of the yt dev team

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Yt-colormaps in matplotlib
by adrian.jost＠mail.de 23 Sep '21

23 Sep '21

Hi, I found some cool colormaps in the yt package and I was wondering how to use them for normal plots created via matplotlib (the colormap I'm looking for is not available in matplotlib, at least it is not listed on the matplotlib website). Can anybody help me please?

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LTP in python
by jackyhuynh30＠gmail.com 23 Sep '21

23 Sep '21

Dear sir, I see in scikitimage have LBP in package feature in texture.pyx and texture.py . With LBP is the center pixel's value is greater than the neighbor's value, write "0". Otherwise, write "1". With code as : # signed / thresholded texture for i in range(P): if texture[i] - image[r, c] >= 0: signed_texture[i] = 1 else: signed_texture[i] = 0 Local ternary patterns (LTP) are an extension of Local binary patterns (LBP), Unlike LBP, it does not threshold the pixels into 0 and 1, rather it uses a threshold constant to threshold pixels into three values. Considering k as the threshold constant, c as the value of the center pixel, a neighboring pixel p, the result of threshold is: 1 if p >c+k 0 if p > c-k && p <c+k 1 if p < c-k with my code as : # signed / thresholded texture for i in range(P): if texture[i] - (image[r, c]+T) > 0: signed_texture[i] = 1 elif texture[i] - (image[r, c]-T) < 0: signed_texture[i] = -1 elif texture[i] - (image[r, c]+T) <= 0 && texture[i] - (image[r, c]-T) >= 0: signed_texture[i] = 0 but i not sure this is correct with python , Pls help me In C++ i see code : unsigned short lut[8][3]; int radius; float thresholdPos; float thresholdNeg; FeatureLTP() : radius(1) , thresholdPos( 0.1f) , thresholdNeg(-0.1f) { unsigned short cnt = 0; for (int i = 0; i < 8; i++) { for (int j = 0; j < 3; j++) lut[i][j] = cnt++; cnt++; //we skip the 4th number (only three patterns) } } int operator() (const Mat &I, Mat &fI) const { CV_Assert(I.isContinuous() && (I.channels() == 1)); Mat_<float> m(I); Mat_<ushort> n(m.size()); n = 0; const float *p = (const float*)m.ptr(); for (int r=radius; r<m.rows-radius; r++) { for (int c=radius; c<m.cols-radius; c++) { const float cval = p[r * m.cols + c]; static const int off[8][2] = {-1,-1, -1,0, -1,1, 0,1, 1,1, 1,0, 1,-1, 0,-1}; for (int li=0; li<8; li++) { // walk neighbours: int y = r + off[li][0] * radius; int x = c + off[li][1] * radius; float diff = p[y * m.cols + x] - cval; n(r,c) += (diff > thresholdPos) ? lut[li][0] : (diff < thresholdNeg) ? lut[li][1] : lut[li][2]; } } } fI = n; return 256; } this is difference with python ? Pls help me , I new python and c++ thankyou so much

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Re: Rockstar is not working
by Nick Gnedin 22 Sep '21

22 Sep '21

Britton, I tried your methods 1 and 2 and RS (Rockstar-Galaxies Version: 0.99.9-RC3-newA) runs with both to the end. However, I discovered a weird thing - the actual value for the particle mass has no effect. I ran it both with the default value and with the changed value, both values are correctly listed in corresponding out_0.list files: #Particle mass: 4.22991e+06 Msun/h [default value] #Particle mass: 5.02229e+06 Msun/h [assigned correct value] However, the produced mass functions are the same in both runs, and they differ by the OmegaM/OmegaDM factor (the ratio of 5.02229e+06/4.22991e+06) from the mass function that I consider correct (obtained with the old RS (Rockstar Version: 0.99.9-RC3) as implemented in yt '3.7.dev0' in yt.analysis_modules.halo_finding.rockstar.api, which also agrees with the analytical fit from hmf.py). Perhaps yt sets the RS particle mass correctly but feeds the actual particle data with the default mass? Nick On 9/10/2021 4:51 AM, Britton Smith wrote: > Hi Nick, > > Thanks for sending the script; I can see why my solution didn't work. > The time series object does not have a unit registry like a loaded > dataset. I issued a pull request to yt_astro_analysis which should fix > this by allowing you to do what you should have been able to all along. > https://github.com/yt-project/yt_astro_analysis/pull/84 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_yt-2Dprojec…> > > With this PR, you can now give the particle mass in three ways: > 1. as a regular float. This will assume units of Msun/h. This was the > original way that was broken and should now be fixed again. > 2. as a tuple of (value, unit) for example (5.02229e+06,"Msun/h"). > 3. as a unyt_quantity > > To make the 3rd option work, you would do > ts[0].quan(5.02229e+06,"Msun/h"), since ts[0] will be the first dataset. > The first two should work as is. > > Let me know if this works and I'll get the PR merged. > > Britton > > On Thu, Sep 9, 2021 at 4:25 PM Nick Gnedin <gnedin(a)fnal.gov > <mailto:gnedin@fnal.gov>> wrote: > > > Britton, > > Actually, your suggestion does not work: > > File "rs-hfc.py", line 19, in <module> > ts.unit_registry.add("h", 0.6814, dimensionless) > P010 yt : [ERROR ] 2021-09-09 10:23:11,397 AttributeError: > 'DatasetSeries' object has no attribute 'unit_registry' > > > Here is my script (based on your suggestion from a couple of years > back): > > sets = glob.glob(root+"/"+dir+"/rei20c1_a*/*.art") > sets.sort() > ts = yt.DatasetSeries(sets) > ts.unit_registry.add("h", 0.6814, dimensionless) > rh = HaloCatalog(data_ds=ts, finder_method='rockstar', > finder_kwargs={"num_readers":n, "num_writers":4, > "outbase":root+"/"+dir+"/rstest1", "particle_type":"N-BODY_0", > "particle_mass":yt.YTQuantity(5.02229e+06,"Msun/h")}) > rh.create() > del rh > del ts > > > > > > On 9/9/2021 9:01 AM, Britton Smith wrote: > > Hi Nick, > > > > Rockstar wants particle masses in units of Msun/h, so it's trying > to do > > that conversion. If your dataset doesn't have h defined, you can do > > something like this: > > > > from unyt.dimensions import dimensionless > > > > ds = yt.load(...) > > ds.unit_registry.add("h", VALUE, dimensionless) > > > > Hopefully, that does the trick. > > > > Britton > > > > > > On Tue, Sep 7, 2021 at 8:57 PM Nick Gnedin <gnedin(a)fnal.gov > <mailto:gnedin@fnal.gov> > > <mailto:gnedin@fnal.gov <mailto:gnedin@fnal.gov>>> wrote: > > > > > > Britton, > > > > You were right, when I updated yt and yt_astro_analysis to > the latest > > versions (and downgraded matplotlib to circumvent the > matplotlib._png > > bug), Rockstar now runs, but I encounter a unit error: > > > > File "rs-hfc.py", line 21, in <module> > > rh.create() > > File "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis > > ... > > File > > > "/data/gnedin/soft/anaconda3/envs/yt/lib/python3.8/site-packages/unyt/unit_object.py", > > > > line 972, in _get_unit_data_from_expr > > return _lookup_unit_symbol(unit_expr.name > <https://urldefense.proofpoint.com/v2/url?u=http-3A__unit-5Fexpr.name&d=DwMF…> > > > <https://urldefense.proofpoint.com/v2/url?u=http-3A__unit-5Fexpr.name&d=DwMF… <https://urldefense.proofpoint.com/v2/url?u=http-3A__unit-5Fexpr.name&d=DwMF…>>, > > unit_symbol_lut) > > File > > > "/data/gnedin/soft/anaconda3/envs/yt/lib/python3.8/site-packages/unyt/unit_registry.py", > > > > line 330, in _lookup_unit_symbol > > raise UnitParseError( > > P011 yt : [ERROR ] 2021-09-07 14:39:16,965 UnitParseError: > Could not > > find unit symbol 'h' in the provided symbols. > > > > I removed any reference to h in my script, so I am > flabbergasted by > > that > > error. Here is my script: > > > > import yt, yt.funcs > > import glob, sys, os.path > > yt.enable_parallelism() > > from yt.extensions.astro_analysis.halo_analysis import > HaloCatalog > > > > root = > > > "/data/gnedin/REI/D/Cai.B20.N128L2.sf=1_uv=0.15_bw=10_res=100.WC1" > > n = 16 > > dirs = ( "A", ) > > for dir in dirs: > > sets = glob.glob(root+"/"+dir+"/rei20c1_a*/*.art") > > sets.sort() > > ts = yt.DatasetSeries(sets) > > rh = HaloCatalog(data_ds=ts, finder_method='rockstar', > > finder_kwargs={"num_readers":n, > "num_writers":4, > > "outbase":root+"/"+dir+"/rscor", "particle_type":"N-BODY_0", > > "particle_mass":yt.YTQuantity(5.02229e+06/0.6814,"Msun")}) > > rh.create() > > del rh > > del ts > > ## > > > > > > Nick > > > > > > On 9/6/2021 10:00 AM, Britton Smith wrote: > > > Hi Nick, > > > > > > I was not able to reproduce this error using the latest > dev yt and > > > yt_astro_analysis installed. The call to ytcfg.get looks > > correct to me. > > > The error looks to me like the older yt config parser > syntax, so > > the yt > > > installation may be out of date. > > > > > > Britton > > > > > > On Thu, Sep 2, 2021 at 1:40 AM Nick Gnedin > <gnedin(a)fnal.gov <mailto:gnedin@fnal.gov> > > <mailto:gnedin@fnal.gov <mailto:gnedin@fnal.gov>> > > > <mailto:gnedin@fnal.gov <mailto:gnedin@fnal.gov> > <mailto:gnedin@fnal.gov <mailto:gnedin@fnal.gov>>>> wrote: > > > > > > > > > Folks, > > > > > > I am trying to run rockstar using your instructions on > > > > > > > > > https://yt-astro-analysis.readthedocs.io/en/latest/halo_finding.html#rockst… > <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.…> > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.… <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.…>> > > > > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.… <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.…> <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.… <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.…>>> > > > > > > and I am getting the following error almost immediately: > > > > > > Traceback (most recent call last): > > > File "rs-hfc.py", line 24, in <module> > > > hc.create() > > > File > > > > > > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py", > > > > > > line 333, in create > > > self._run(save_halos, save_output, > > > File > > > > > > "/data/gnedin/soft/anaconda3/lib/python3.8/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", > > > > > > line 301, in barrierize > > > return func(*args, **kwargs) > > > File > > > > > > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py", > > > > > > line 224, in _run > > > self.finder_method(self) > > > File > > > > > > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_finding_methods.py", > > > > > > line 39, in __call__ > > > return self.function(hc, *self.args, **self.kwargs) > > > File > > > > > > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_finding_methods.py", > > > > > > line 87, in _rockstar_method > > > rh = RockstarHaloFinder(ds, **finder_kwargs) > > > File > > > > > > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py", > > > > > > line 214, in __init__ > > > self.runner = InlineRunner() > > > File > > > > > > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py", > > > > > > line 44, in __init__ > > > psize = ytcfg.get("yt", "internals", > > "global_parallel_size") > > > File > > > > > > "/data/gnedin/soft/anaconda3/lib/python3.8/site-packages/yt/config.py", > > > line 137, in get > > > val = super(YTConfigParser, self).get(section, > option, > > *args, > > > **kwargs) > > > TypeError: get() takes 3 positional arguments but 4 > were given > > > > > > Nick Gnedin > > > > > > > > > -- > > > This email has been checked for viruses by AVG. > > > https://www.avg.com > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c…> > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c… <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c…>> > > > > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c… <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c…> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c… <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c…>>> > > > > > > _______________________________________________ > > > yt-users mailing list -- yt-users(a)python.org > <mailto:yt-users@python.org> > > <mailto:yt-users@python.org <mailto:yt-users@python.org>> > > > <mailto:yt-users@python.org > <mailto:yt-users@python.org> <mailto:yt-users@python.org > <mailto:yt-users@python.org>>> > > > To unsubscribe send an email to > yt-users-leave(a)python.org <mailto:yt-users-leave@python.org> > > <mailto:yt-users-leave@python.org > <mailto:yt-users-leave@python.org>> > > > <mailto:yt-users-leave@python.org > <mailto:yt-users-leave@python.org> > > <mailto:yt-users-leave@python.org > <mailto:yt-users-leave@python.org>>> > > > > https://mail.python.org/mailman3/lists/yt-users.python.org/ > <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.python.org_mailma…> > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.python.org_mailma… <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.python.org_mailma…>> > > > > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.python.org_mailma… <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.python.org_mailma…> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.python.org_mailma… <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.python.org_mailma…>>> > > > Member address: brittonsmith(a)gmail.com > <mailto:brittonsmith@gmail.com> > > <mailto:brittonsmith@gmail.com > <mailto:brittonsmith@gmail.com>> <mailto:brittonsmith@gmail.com > <mailto:brittonsmith@gmail.com> > > <mailto:brittonsmith@gmail.com <mailto:brittonsmith@gmail.com>>> > > > > > > > -- > This email has been checked for viruses by AVG. > https://www.avg.com > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c…> >

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