Closed esheldon closed 8 years ago
I'm willing to do the SExtractor run if anyone can give me an appropriate config file and point me at the recommended version of the code
I'm also willing to help out and run these at SLAC. For SExtractor and PSFEx I also just need the appropriate config files...
I asked a question about config files and code version on the DES balrog slack channel.
Eric Suchyta says:
For Y1 it’s 2.18.10
And config files can be found here
https://desar2.cosmology.illinois.edu/DESFiles/desarchive/OPS/config/20150806/finalcut/
In particular
20150806_sex.nnw
20150806_sex.conv
20150806_sex.config
20150806_sex.param.finalcut.20130702
The exact call used in Y1 by DESDM (note the date prefix has been stripped from the config file names)
/usr/apps/des/stacks/7.2-stacks/7.2.6/des_prereq/bin/sex /projects/des/Archive/OPS/red/20140715085529_20131130/red/DECam_00258910/DECam_00258910_01.fits[0] -c /usr/apps/des/software/7.2-level/7.2.18+1/des_home/etc/sex.config -FILTER_NAME /usr/apps/des/software/7.2-level/7.2.18+1/des_home/etc/sex.conv -STARNNW_NAME /usr/apps/des/software/7.2-level/7.2.18+1/des_home/etc/sex.nnw -INTERP_TYPE VAR_ONLY -WEIGHT_TYPE MAP_WEIGHT -WEIGHT_IMAGE /projects/des/Archive/OPS/red/20140715085529_20131130/red/DECam_00258910/DECam_00258910_01.fits[2],/projects/des/Archive/OPS/red/20140715085529_20131130/red/DECam_00258910/DECam_00258910_01.fits[2] -SEEING_FWHM 1.034 -FLAG_IMAGE /projects/des/Archive/OPS/red/20140715085529_20131130/red/DECam_00258910/DECam_00258910_01.fits[1] -CATALOG_NAME /projects/des/Archive/OPS/red/20140715085529_20131130/red/DECam_00258910/DECam_00258910_01_cat.fits -SATUR_LEVEL 38652.0000 -PARAMETERS_NAME /usr/apps/des/software/7.2-level/7.2.18+1/des_home/etc/sex.param -PSF_NAME /projects/des/Archive/OPS/red/20140715085529_20131130/red/DECam_00258910/DECam_00258910_01_psfcat.psf -CHECKIMAGE_TYPE SEGMENTATION -CHECKIMAGE_NAME /projects/des/Archive/OPS/red/20140715085529_20131130/QA/DECam_00258910/DECam_00258910_01_seg.fits -DETECT_THRESH 3.0 -PARAMETERS_NAME /usr/apps/des/software/7.2-level/7.2.18+1/des_home/etc/sex.param.finalcut.20130702
The simulated images and truth files are here
http://www.cosmo.bnl.gov/Private/gpfs/workarea/esheldon/lensing/des-lensing/psfsim/v006/output/
Or at BNL
/gpfs/mnt/gpfs01/astro/workarea/esheldon/lensing/des-lensing/psfsim/v006/output
You can use the psfsim
package to get filenames if you set the PSFSIM_DIR
environment variable
@cpadavis Can you do the SExtractor run?
@rmjarvis would you be willing to run PSFEx once we get catalogs? I was thinking it might not be too hard for you since you have been running PSFEx on real data
Sure. I'm on vacation for the next 10 days in London with the family, but I'll try to carve out a little time to start that run at BNL.
Should we start with the desdm psfex config file, or the v2 one? (Or maybe modified to have oversampling = 0.6 rather than 0.5.)
I think we should test things we have run on the real data first. y1a-v02 is supposed to give the best rho stats of the ones you tried so far, so let's test that first.
@cpadavis do you have a timescale over which you can run SExtractor on the simulations?
Just finished downloading.
I had to modify the config files you suggested I use because they expect *.psf, flag files, and weight maps. I also could not find SExtractor 2.18.10 on the sextractor website, so I'm just going with the most recent version of sextractor on there for now... (2.19.5)
The two things I am not sure on are:
I'm running sextractor now and should have a run with weight_type as none and seeing_fwhm=1.034 before the end of today
I forget -- for PSFEx, what column parameters do there need to be? I recall needing VIGNET, which I think isn't in the config file
Regarding the SExtractor run: The noise is currently constant for all images and is set in the galsim config file based on a sky level and read noise
https://github.com/esheldon/psfsim_config/blob/master/psfsim-stars-v006.yaml
I don't have any experience running SExtractor so I can't help much more.
As for PSFEx, we had planned to try running with the standard desdm config as well as mike's y1a1-v02
config.
I don't have a copy of that config, but there are notes here describing the changes needed
https://github.com/rmjarvis/DESWL/blob/master/psfex/notes.txt
OK catalogs with vignets done. I feel silly doing this because I don't have BNL access, so with the vignets you have to transfer ~100 gigs.
Config files: http://www.slac.stanford.edu/~cpd/psfsim/20150806_sextractor_configuration_files/
Catalog entries without vignets: http://www.slac.stanford.edu/~cpd/psfsim/catalogs/
catalog entries with vignets: http://www.slac.stanford.edu/~cpd/psfsim/catalogs_psfex/
I can copy them over.
sorry, I'm not that familiar with these codes. How do these pieces fit together? Is this the input Mike needs to run PSFEx?
This should be what Mike needs to run PSFex, unless I messed up.
Here is the sextractor pipeline: You take your image, run sextractor to get a catalog. You can run psfex directly on the catalog and it will try to determine the stars, but iirc Mike has a program that does a better job finding the stars. So Mike will run findstars and then run psfex on that output. Then you can run sextractor again on the base catalog + .psf output to determine the values of columns which depend on the PSF (e.g. MAG_PSF, SPREAD_MODEL)
On Mon, Aug 1, 2016 at 7:29 AM Erin Sheldon notifications@github.com wrote:
I can copy them over.
sorry, I'm not that familiar with these codes. How do these pieces fit together? Is this the input Mike needs to run PSFEx?
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We can run psfEx using LSST wrappers (use a command line driver called processFile or write a simple python wrapper) -- that means that you don't need to separately run SExtractor, and we've separated the star selection from the psf estimation
R
At this stage I don't think we care about the sextractor measured quantities based on the PSF model, so a rerun is not necessary in any case.
It will be good to see the result using the LSST wrapper as well. We have never been quite sure if we are using PSFEx correctly, even after consulting Bertin.
@cpadavis can you post the locations on the slac file system (rather than the web)? It will be more efficient to transfer via rsync.
config files at:
/nfs/slac/g/ki/ki19/des/cpd/20150806_sextractor_configuration_files
sextractor catalogs you can run psfex on at:
/nfs/slac/g/ki/ki19/des/cpd/PSFSIM/v006/output/catalogs_psfex
On Tue, Aug 2, 2016 at 10:52 AM Erin Sheldon notifications@github.com wrote:
@cpadavis https://github.com/cpadavis can you post the locations on the slac file system (rather than the web)? It will be more efficient to transfer via rsync.
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@rmjarvis
Chris' catalogs are here:
/gpfs/mnt/gpfs01/astro/workarea/esheldon/lensing/des-lensing/psfsim/v006-sextractor/output
the files seem to have patterns like this psfsim-stars-v006-003767_cat.fits
so the same as the simulation files but with _cat.fits
OK. I'm back from London now (vacation after the Oxford meeting), but I need to go to California for a funeral this weekend, so it will probably be next week before I get a chance to work on this.
I finished running PSFEx on the sims. The rho stats look much better than what we are getting on the data.
For comparison, here is the y1a1-v02 run on DES Y1 r-band data:
In fact, it's even slightly worse than depicted on the data, since the data run gets to take advantage of overlapping exposures beating down the power by a factor of nexp ~= 3, which I didn't do for the simulation run -- this is just the mean rho1 power averaged over all 20K simulation images.
So I think this means that whatever is causing us problems with PSFEx on the data is something that isn't yet included in the simulations.
Are we modeling inter-ccd correlations in the PSF? Could that cause it in the actual data?
On Wed, Aug 24, 2016 at 6:30 PM Mike Jarvis notifications@github.com wrote:
I finished running PSFEx on the sims. The rho stats look much better than what we are getting on the data. [image: rho1] https://cloud.githubusercontent.com/assets/623887/17953442/523a146c-6a41-11e6-96ab-1d50ace6166a.png
For comparison, here is the y1a1-v02 run on DES Y1 r-band data: [image: rho1_all_r] https://cloud.githubusercontent.com/assets/623887/17953459/762e942e-6a41-11e6-82e8-14961ec75892.png
In fact, it's even slightly worse than depicted on the data, since the data run gets to take advantage of overlapping exposures beating down the power by a factor of nexp ~= 3, which I didn't do for the simulation run -- this is just the mean rho1 power averaged over all 20K simulation images.
So I think this means that whatever is causing us problems with PSFEx on the data is something that isn't yet included in the simulations.
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aaron pointed out our variation across the ccd is too small by a factor of order 5 I recall. Looks like that would still not make up the difference with real data though.
I think the main cause of the rho stats in the real data is from the WCS. PSFEx does things in CCD coordinates, remember, so it has to include the effect of the WCS on the PSF. This was one of the changes we made for Piff -- doing things in sky coordinates means we can remove the effect of the WCS from the PSF profiles before trying to interpolate them.
In these sims, the WCS are all simple Jacobians. We could make that more realistic by copying the WCS from data images, which are 3rd order. (And reality is probably closer to 5th order across the focal plane, but piecewise 3rd order might be an ok approximation to that.)
In these sims I used an example wcs from a des exposure
See https://github.com/esheldon/psfsim_config/blob/master/psfsim-stars-v006.yaml
So, is that actually being used in full? @rmjarvis your comment seems to imply it only takes the jacobian?
No, they use the local WCS at a random location within a DES exposure. They don't use the full WCS solution. That particular wcs class was designed for use with a MEDS sim where we just wanted a local wcs for each galaxy. Here is what we probably want, which takes the full wcs from a DES image:
wcs :
type : Fits
dir:
type: FormattedStr
format: "%s/OPS/red/20140715085838_20131201/red/DECam_00259397"
items:
- *DESDATA
file_name:
type : NumberedFile
root : 'DECam_00154912_'
digits : 2
ext : '.fits'
num :
# Pick a random chip, but not either of our bad chips.
type : ExcludedRandom # This is a custom type defined in exclude_random.py
min: 1
max : 62
exclude: [ 61, 31 ]
You can grab exclude_random.py from the galsim/examples/des directory.
Would we also remove the des_wcs:
entry under input:
?
(or remove input:
altogether?)
Sure. It wouldn't be an error to leave it in, but it's not necessary anymore.
OK, it sounds like we should run a new sim. Should we wait for Aaron's new variation numbers?
Sure. Might as well try to get that right too.
We could also start making some of the other changes we talked about, like doing 62 (or 60) chip exposures and matching the positions/fluxes of objects from the real data catalogs to get more realistic distributions of those quantities. Probably still without galaxies I guess to keep that part simple.
Here are some new numbers for variation of Wavefront terms. All values are in waves at 700nm.
I calculated the Mean and Spread == Max-Min for each Zernike term, spatially, inside each of the 62 CCDs . Note that the variation across each sensor is not very Gaussian - a uniform distribution is closer, thats why I calculated a spread. See plot below for these quantities.
Then to characterize the Means and Spreads, I calculated the width of the Means and range of the Spreads over the 62 CCDs. The Means of the Means are zero. Here are those values:
Zern 4, Stdev of Mean = 0.085, Lo,Hi of Spread = 0.043,0.212 Zern 5, Stdev of Mean = 0.062, Lo,Hi of Spread = 0.018,0.259 Zern 6, Stdev of Mean = 0.054, Lo,Hi of Spread = 0.019,0.165 Zern 7, Stdev of Mean = 0.042, Lo,Hi of Spread = 0.011,0.152 Zern 8, Stdev of Mean = 0.044, Lo,Hi of Spread = 0.011,0.092 Zern 9, Stdev of Mean = 0.144, Lo,Hi of Spread = 0.011,0.236 Zern 10, Stdev of Mean = 0.136, Lo,Hi of Spread = 0.008,0.249 Zern 11, Stdev of Mean = 0.073, Lo,Hi of Spread = 0.015,0.103
So, use the “Stdev of Mean” values to generate a Mean for each term for the CCD, then pick uniformly inside the Lo,Hi to pick a Spread. And then use that Spread to set the range of that term around the Mean.
You see that the Spread can be biggish - at 0.2 waves - which is the thing I was worried about.
Hope that is sorta clear,
Aaron
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On Aug 25, 2016, at 9:03 AM, Erin Sheldon notifications@github.com<mailto:notifications@github.com> wrote:
OK, it sounds like we should run a new sim. Should we wait for Aaron's new variation numbers?
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Prof. Aaron Roodman Chair Dept. of Particle Physics & Astrophysics SLAC National Accelerator Laboratory Stanford University
SLAC National Accelerator Laboratory E-mail: roodman@slac.stanford.edumailto:roodman@slac.stanford.edu 2575 Sand Hill Rd. Phone: 650-926-2705 MS 29 Menlo Park, CA 94025 URL: http://www.slac.stanford.edu/~roodman
Thanks, Aaron!
The image you posted didn't go through. It it was important, maybe try editing the post on GitHub, and dragging the image onto the comment window.
The Means of the Means are zero.
@aaronroodman: Is this really true? This surprises me. I would have thought for at least some of the aberrations, the mean would be non-zero.
@esheldon I think this is an approximate translation of the prescription Aaron gave into the galsim config file. I'm not sure that the way we're doing the polynomials will give exactly the right spreads, but I think it should be close. There might be an extra factor of O(1) that needs to be applied.
eval_variables:
fmean_4: { type: RandomGaussian, sigma: 0.085, index_key: file_num }
fspread_4: { type: Random, min: 0.043, max: 0.212, index_key: file_num }
fmean_5: { type: RandomGaussian, sigma: 0.062, index_key: file_num }
fspread_5: { type: Random, min: 0.018, max: 0.259, index_key: file_num }
fmean_6: { type: RandomGaussian, sigma: 0.054, index_key: file_num }
fspread_6: { type: Random, min: 0.019, max: 0.165, index_key: file_num }
fmean_7: { type: RandomGaussian, sigma: 0.042, index_key: file_num }
fspread_7: { type: Random, min: 0.011, max: 0.152, index_key: file_num }
fmean_8: { type: RandomGaussian, sigma: 0.044, index_key: file_num }
fspread_8: { type: Random, min: 0.011, max: 0.092, index_key: file_num }
fmean_9: { type: RandomGaussian, sigma: 0.144, index_key: file_num }
fspread_9: { type: Random, min: 0.011, max: 0.236, index_key: file_num }
fmean_10: { type: RandomGaussian, sigma: 0.136, index_key: file_num }
fspread_10: { type: Random, min: 0.008, max: 0.249, index_key: file_num }
fmean_11: { type: RandomGaussian, sigma: 0.073, index_key: file_num }
fspread_11: { type: Random, min: 0.015, max: 0.103, index_key: file_num }
psf:
# [ snip... ]
defocus:
type: Eval
str: "mean_4 + a * image_pos.x + b * image_pos.y + c * image_pos.x**2 + d * image_pos.y**2 + e * image_pos.x*image_pos.y"
fa: { type: RandomGaussian, sigma: spread_4/2048., index_key: file_num }
fb: { type: RandomGaussian, sigma: spread_4/4096., index_key: file_num }
fc: { type: RandomGaussian, sigma: spread_4/2048**2, index_key: file_num }
fd: { type: RandomGaussian, sigma: spread_4/2048/4096, index_key: file_num }
fe: { type: RandomGaussian, sigma: spread_4/4096**2, index_key: file_num }
astig1:
type: Eval
str: "mean_5 + a * image_pos.x + b * image_pos.y + c * image_pos.x**2 + d * image_pos.y**2 + e * image_pos.x*image_pos.y"
fa: { type: RandomGaussian, sigma: spread_5/2048., index_key: file_num }
fb: { type: RandomGaussian, sigma: spread_5/4096., index_key: file_num }
fc: { type: RandomGaussian, sigma: spread_5/2048**2, index_key: file_num }
fd: { type: RandomGaussian, sigma: spread_5/2048/4096, index_key: file_num }
fe: { type: RandomGaussian, sigma: spread_5/4096**2, index_key: file_num }
astig2:
type: Eval
str: "mean_6 + a * image_pos.x + b * image_pos.y + c * image_pos.x**2 + d * image_pos.y**2 + e * image_pos.x*image_pos.y"
fa: { type: RandomGaussian, sigma: spread_6/2048., index_key: file_num }
fb: { type: RandomGaussian, sigma: spread_6/4096., index_key: file_num }
fc: { type: RandomGaussian, sigma: spread_6/2048**2, index_key: file_num }
fd: { type: RandomGaussian, sigma: spread_6/2048/4096, index_key: file_num }
fe: { type: RandomGaussian, sigma: spread_6/4096**2, index_key: file_num }
coma1:
type: Eval
str: "mean_7 + a * image_pos.x + b * image_pos.y + c * image_pos.x**2 + d * image_pos.y**2 + e * image_pos.x*image_pos.y"
fa: { type: RandomGaussian, sigma: spread_7/2048., index_key: file_num }
fb: { type: RandomGaussian, sigma: spread_7/4096., index_key: file_num }
fc: { type: RandomGaussian, sigma: spread_7/2048**2, index_key: file_num }
fd: { type: RandomGaussian, sigma: spread_7/2048/4096, index_key: file_num }
fe: { type: RandomGaussian, sigma: spread_7/4096**2, index_key: file_num }
coma2:
type: Eval
str: "mean_8 + a * image_pos.x + b * image_pos.y + c * image_pos.x**2 + d * image_pos.y**2 + e * image_pos.x*image_pos.y"
fa: { type: RandomGaussian, sigma: spread_8/2048., index_key: file_num }
fb: { type: RandomGaussian, sigma: spread_8/4096., index_key: file_num }
fc: { type: RandomGaussian, sigma: spread_8/2048**2, index_key: file_num }
fd: { type: RandomGaussian, sigma: spread_8/2048/4096, index_key: file_num }
fe: { type: RandomGaussian, sigma: spread_8/4096**2, index_key: file_num }
trefoil1:
type: Eval
str: "mean_9 + a * image_pos.x + b * image_pos.y + c * image_pos.x**2 + d * image_pos.y**2 + e * image_pos.x*image_pos.y"
fa: { type: RandomGaussian, sigma: spread_9/2048., index_key: file_num }
fb: { type: RandomGaussian, sigma: spread_9/4096., index_key: file_num }
fc: { type: RandomGaussian, sigma: spread_9/2048**2, index_key: file_num }
fd: { type: RandomGaussian, sigma: spread_9/2048/4096, index_key: file_num }
fe: { type: RandomGaussian, sigma: spread_9/4096**2, index_key: file_num }
trefoil2:
type: Eval
str: "mean_10 + a * image_pos.x + b * image_pos.y + c * image_pos.x**2 + d * image_pos.y**2 + e * image_pos.x*image_pos.y"
fa: { type: RandomGaussian, sigma: spread_10/2048., index_key: file_num }
fb: { type: RandomGaussian, sigma: spread_10/4096., index_key: file_num }
fc: { type: RandomGaussian, sigma: spread_10/2048**2, index_key: file_num }
fd: { type: RandomGaussian, sigma: spread_10/2048/4096, index_key: file_num }
fe: { type: RandomGaussian, sigma: spread_10/4096**2, index_key: file_num }
spher:
type: Eval
str: "mean_11 + a * image_pos.x + b * image_pos.y + c * image_pos.x**2 + d * image_pos.y**2 + e * image_pos.x*image_pos.y"
fa: { type: RandomGaussian, sigma: spread_11/2048., index_key: file_num }
fb: { type: RandomGaussian, sigma: spread_11/4096., index_key: file_num }
fc: { type: RandomGaussian, sigma: spread_11/2048**2, index_key: file_num }
fd: { type: RandomGaussian, sigma: spread_11/2048/4096, index_key: file_num }
fe: { type: RandomGaussian, sigma: spread_11/4096**2, index_key: file_num }
Thanks @aaronroodman and @rmjarvis
Yesterday I ran a version 007
with a full wcs but without the variations from Aaron. I'll run a version 008
today that also includes the above spread.
I'm finding it hard to picture exactly why the values Aaron gave are also consistent with the plain std. dev. that @aaronroodman had given previously. I think the figure would help. Can you please repost the figure? The easiest way is to click under the message "Attach files by selecting them"
@rmjarvis I'm getting an error with this new config.
ValueError: could not convert string to float: spread_5/2048.
Here is the config: https://github.com/esheldon/psfsim_config/blob/master/psfsim-stars-v008.yaml
Sorry. All those sigma
definitions need to be wrapped in "$...". e.g. "$spread_5/2048." They need to be evaluated, and the $ prefix on the string is the thing that instructs GalSim to do so.
Also, I just noticed I got the normalization for the d and e parameters reversed. d is the y^2 coefficient, so should be spread_*/4096**2
. e is the xy coefficient, so it should be spread_*/2048./4096
.
Although it's possible that we don't want to do that. It might be better to have them all use 2048**2 normalization (and have a,b use 2048.) and just let the y direction run a bit more. I'm not sure which is actually more realistic.
Thanks, after those fixes the config runs
ah yes I left something out -
The numbers I sent characterize our “ideal” wavefront, where the means are defined to be zero.
On top of that I should add an additional Gaussian smearing to characterize the variation from image to image. And for that contribution the means have not been zero - although they should be going forward. Year 1 and part of 2 have non-zero mean Coma, and the mean of Astigmatism has been non-zero too.
As of two nights ago, the Blanco primary astigmatism is under active control by the donut system - hurrah!!
I will supply values for this additional smearing.
On Aug 25, 2016, at 9:15 PM, Mike Jarvis notifications@github.com<mailto:notifications@github.com> wrote:
The Means of the Means are zero.
@aaronroodmanhttps://github.com/aaronroodman: Is this really true? This surprises me. I would have thought for at least some of the aberrations, the mean would be non-zero.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/rmjarvis/Piff/issues/33#issuecomment-242626357, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AEEa86hamhPJ_sRrnCMkVoc_YRggC5f8ks5qjmh3gaJpZM4JSwYn.
Prof. Aaron Roodman Chair Dept. of Particle Physics & Astrophysics SLAC National Accelerator Laboratory Stanford University
SLAC National Accelerator Laboratory E-mail: roodman@slac.stanford.edumailto:roodman@slac.stanford.edu 2575 Sand Hill Rd. Phone: 650-926-2705 MS 29 Menlo Park, CA 94025 URL: http://www.slac.stanford.edu/~roodman
I'm running a v008 now based on the current config; we can incorporate more things later but I wanted to get something out before the weekend.
So there is already v007 and now v008 is coming, probably done in a few hours. So @rmjarvis can process these at his leisure.
FYI, I started a Piff run on v009. It's substantially slower than PSFEx (not surprising, since we haven't tried to do any optimization yet), but I figured it was worth trying it to see how it compares to PSFEx.
Here are the rho stats for the best PSFEx result so far.
We have created some PSF simulations to test PIFF and PSFEx. I can give more details as needed, but in brief these are using galsim with
Still TODO
Logical steps in processing
The first step in analysis is running SExtractor or another reduction such as LSST DM stack. This is important since the stars are intentionally placed randomly and thus blended.
I think the next logical step is running PSFEx. This is an interesting test in itself since PSFEx is widely used, including in DES. We will learn something about PSFEx from this, and probably iron out some bugs in the sims.
Last is running PIFF. I don't know the current status, whether this is feasible at a large scale.