Adding PSF content and structure

environment.yml

@@ -7,5 +7,6 @@ dependencies:
   - matplotlib
   - numpy
   - scipy
+  - galsim
   - pip:
     - jupyter-book

shearbook/_bibliography/z_psf_models.bib

@@ -0,0 +1,128 @@
+---
+---
+
+@inproceedings{krist2011,
+	author = {John E. Krist and Richard N. Hook and Felix Stoehr},
+	booktitle = {Optical Modeling and Performance Predictions V},
+	date-added = {2021-02-16 21:32:03 +0100},
+	date-modified = {2021-02-16 21:32:12 +0100},
+	doi = {10.1117/12.892762},
+	editor = {Mark A. Kahan},
+	keywords = {Hubble Space Telescope, point spread function},
+	organization = {International Society for Optics and Photonics},
+	pages = {166 -- 181},
+	publisher = {SPIE},
+	title = {{20 years of Hubble Space Telescope optical modeling using Tiny Tim}},
+	url = {https://doi.org/10.1117/12.892762},
+	volume = {8127},
+	year = {2011},
+	Bdsk-Url-1 = {https://doi.org/10.1117/12.892762}}
+
+@inproceedings{krist1995c,
+	author = {Krist, J. E.},
+	booktitle = {Calibrating Hubble Space Telescope. Post Servicing Mission. Proceedings of a Workshop held at the Space Telescope Science Institute, in Baltimore, Maryland},
+	date-added = {2021-02-18 15:44:16 +0100},
+	date-modified = {2021-02-18 15:45:14 +0100},
+	editor = {Anuradha Koratkar and Claus Leitherer},
+	month = {May},
+	title = {WFPC2 Ghosts, Scatter and PSF Field Dependence},
+	year = {1995}}
+
+@article{massey2009,
+	abstract = {{Charge Transfer Inefficiency (CTI) due to radiation damage above the Earth's atmosphere creates spurious trailing in Hubble Space Telescope (HST) images. Radiation damage also creates unrelated warm pixels -- but these happen to be perfect for measuring CTI. We model CTI in the Advanced Camera for Surveys (ACS)/Wide Field Channel and construct a physically motivated correction scheme. This operates on raw data, rather than secondary science products, by returning individual electrons to pixels from which they were unintentionally dragged during readout. We apply our correction to images from the HST Cosmic Evolution Survey (COSMOS), successfully reducing the CTI trails by a factor of ∼30 everywhere in the CCD and at all flux levels. We quantify changes in galaxy photometry, astrometry and shape. The remarkable 97 per cent level of correction is more than sufficient to enable a (forthcoming) reanalysis of downstream science products and the collection of larger surveys.}},
+	author = {Massey, Richard and Stoughton, Chris and Leauthaud, Alexie and Rhodes, Jason and Koekemoer, Anton and Ellis, Richard and Shaghoulian, Edgar},
+	date-added = {2021-02-18 16:28:45 +0100},
+	date-modified = {2021-02-18 16:28:59 +0100},
+	doi = {10.1111/j.1365-2966.2009.15638.x},
+	eprint = {https://academic.oup.com/mnras/article-pdf/401/1/371/18581537/mnras0401-0371.pdf},
+	issn = {0035-8711},
+	journal = {Monthly Notices of the Royal Astronomical Society},
+	month = {12},
+	number = {1},
+	pages = {371-384},
+	title = {{Pixel-based correction for Charge Transfer Inefficiency in the Hubble Space Telescope Advanced Camera for Surveys}},
+	url = {https://doi.org/10.1111/j.1365-2966.2009.15638.x},
+	volume = {401},
+	year = {2009},
+	Bdsk-Url-1 = {https://doi.org/10.1111/j.1365-2966.2009.15638.x}}
+
+@article{rhodes2010,
+	abstract = {We examine the effects of charge transfer inefficiency (CTI) during CCD readout on the demanding galaxy shape measurements required by studies of weak gravitational lensing. We simulate a CCD readout with CTI such as that caused by charged particle radiation damage in space-based detectors. We verify our simulations on real data from fully depleted p-channel CCDs that have been deliberately irradiated in a laboratory. We show that only charge traps with time constants of the same order as the time between row transfers during readout affect galaxy shape measurements. We simulate deep astronomical images and the process of CCD readout, characterizing the effects of CTI on various galaxy populations. Our code and methods are general and can be applied to any CCDs, once the density and characteristic release times of their charge trap species are known. We baseline our study around p-channel CCDs that have been shown to have charge transfer efficiency up to an order of magnitude better than several models of n-channel CCDs designed for space applications. We predict that for galaxies furthest from the readout registers, bias in the measurement of galaxy shapes, Δe, will increase at a rate of (2.65 $\pm$ 0.02) × 10-4 yr-1 at L2 for accumulated radiation exposure averaged over the solar cycle. If uncorrected, this will consume the entire shape measurement error budget of a dark energy mission surveying the entire extragalactic sky within about 4 yr of accumulated radiation damage. However, software mitigation techniques demonstrated elsewhere can reduce this by a factor of ∼10, bringing the effect well below mission requirements. This conclusion is valid only for the p-channel CCDs we have modeled; CCDs with higher CTI will fare worse and may not meet the requirements of future dark energy missions. We also discuss additional ways in which hardware could be designed to further minimize the impact of CTI.},
+	author = {Jason Rhodes and Alexie Leauthaud and Chris Stoughton and Richard Massey and Kyle Dawson and William Kolbe and Natalie Roe},
+	date-added = {2021-02-18 16:22:18 +0100},
+	date-modified = {2021-02-18 16:22:27 +0100},
+	doi = {10.1086/651675},
+	journal = {Publications of the Astronomical Society of the Pacific},
+	month = {apr},
+	number = {890},
+	pages = {439--450},
+	publisher = {{IOP} Publishing},
+	title = {The Effects of Charge Transfer Inefficiency ({CTI}) on Galaxy Shape Measurements},
+	url = {https://doi.org/10.1086/651675},
+	volume = {122},
+	year = 2010,
+	Bdsk-Url-1 = {https://doi.org/10.1086/651675}}
+
+@article{guyonnet2015,
+	author = {Guyonnet, A. and Astier, P. and Antilogus, P. and Regnault, N. and Doherty, P.},
+	date-added = {2021-02-18 16:03:44 +0100},
+	date-modified = {2021-02-18 16:03:51 +0100},
+	doi = {10.1051/0004-6361/201424897},
+	issn = {1432-0746},
+	journal = {Astronomy & Astrophysics},
+	month = {Feb},
+	pages = {A41},
+	publisher = {EDP Sciences},
+	title = {Evidence for self-interaction of charge distribution in charge-coupled devices},
+	url = {http://dx.doi.org/10.1051/0004-6361/201424897},
+	volume = {575},
+	year = {2015},
+	Bdsk-Url-1 = {http://dx.doi.org/10.1051/0004-6361/201424897}}
+
+@article{krist2003,
+	author = {J. Krist},
+	date-added = {2021-02-18 15:59:27 +0100},
+	date-modified = {2021-02-18 15:59:35 +0100},
+	journal = {Applied Categorical Structures},
+	pages = {6},
+	title = {ACS WFC & HRC field- dependent PSF variations due to optical and charge diffusion effects},
+	year = {2003}}
+
+@article{nino2007,
+	author = {Nino, Daiana and Makidon, R. and Lallo, M. and Sahu, Kailash and Sirianni, M. and Casertano, S.},
+	date-added = {2021-02-18 15:56:11 +0100},
+	date-modified = {2021-02-18 17:20:01 +0100},
+	journal = {Instrument Science Report ACS 2008-03},
+	month = {12},
+	title = {HST Focus Variations with Temperatures},
+	year = {2007}}
+
+@article{jee2011,
+	abstract = {The weak-lensing science of the Large Synoptic Survey Telescope (LSST) project drives the need to carefully model and separate the instrumental artifacts from the intrinsic shear signal caused by gravitational lensing. The dominant source of the systematics for all ground-based telescopes is the spatial correlation of the point-spread function (PSF) modulated by both atmospheric turbulence and optical aberrations in the telescope and camera system. In this article, we present a full field-of-view simulation of the LSST images by modeling both the atmosphere and the system optics with the most current data for the telescope and camera specifications and the environment. To simulate the effects of atmospheric turbulence, we generated six-layer Kolmogorov/von K{\'a}rm{\'a}n phase screens with the parameters estimated from the on-site measurements. LSST will continuously sample the wavefront, correcting the optics alignment and focus. For the optics, we combined the ray-tracing tool ZEMAX and our simulated focal-plane data to introduce realistic residual aberrations and focal-plane height variations. Although this expected focal-plane flatness deviation for LSST is small compared with that of other existing cameras, the fast focal ratio of the LSST optics cause this focal-plane flatness variation and the resulting PSF discontinuities across the CCD boundaries to be significant challenges in our removal of the PSF-induced systematics. We resolve this complication by performing principal component analysis (PCA) CCD by CCD and by interpolating the basis functions derived from the analysis using conventional polynomials. We demonstrate that this PSF correction scheme reduces the residual PSF ellipticity correlation below 10-7 over the cosmologically interesting (dark-matter-dominated) scale 10′--3$\,^{\circ}$. From a null test using the Hubble Space Telescope (HST) Ultra Deep Field (UDF) galaxy images without input shear, we verify that the amplitude of the galaxy ellipticity correlation function, after the PSF correction, is consistent with the shot noise set by the finite number of objects. We conclude that the current optical design and specification for the accuracy in the focal-plane assembly are sufficient to enable the control of the PSF systematics required for weak-lensing science with LSST.},
+	author = {M. James Jee and J. Anthony Tyson},
+	date-added = {2021-02-18 15:48:14 +0100},
+	date-modified = {2021-02-18 15:48:21 +0100},
+	doi = {10.1086/660137},
+	journal = {Publications of the Astronomical Society of the Pacific},
+	month = {may},
+	number = {903},
+	pages = {596--614},
+	publisher = {{IOP} Publishing},
+	title = {Toward Precision {LSST} Weak-Lensing Measurement. I. Impacts of Atmospheric Turbulence and Optical Aberration},
+	url = {https://doi.org/10.1086/660137},
+	volume = {123},
+	year = 2011,
+	Bdsk-Url-1 = {https://doi.org/10.1086/660137}}
+
+@article{LSST2009,
+	adsnote = {Provided by the SAO/NASA Astrophysics Data System},
+	adsurl = {http://adsabs.harvard.edu/abs/2009arXiv0912.0201L},
+	archiveprefix = {arXiv},
+	author = {{LSST Science Collaboration} and {Abell}, P.~A. and {Allison}, J. and {Anderson}, S.~F. and {Andrew}, J.~R. and {Angel}, J.~R.~P. and {Armus}, L. and {Arnett}, D. and {Asztalos}, S.~J. and {Axelrod}, T.~S. and et al.},
+	eprint = {0912.0201},
+	journal = {arXiv e-prints},
+	keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Cosmology and Extragalactic Astrophysics, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Galaxy Astrophysics, Astrophysics - Solar and Stellar Astrophysics},
+	month = dec,
+	primaryclass = {astro-ph.IM},
+	title = {{LSST Science Book, Version 2.0}},
+	year = 2009}

shearbook/_toc.yml

@@ -6,6 +6,17 @@
     - file: intro/about
     - file: intro/run_code
 
+- part: Point Spread Function
+  chapters:
+    - file: psf/psf-intro
+      sections:
+        - file: psf/psf-origins-nb
+    - file: psf/psf-modelling
+      sections:
+        - file: psf/non-parametric-model
+        - file: psf/parametric-model
+        - file: psf/psf-models-ref
+
 - part: Shape Measurement
   chapters:
     - file: moments/moments-intro

shearbook/psf/non-parametric-model.md

@@ -0,0 +1,15 @@
+# Non-parametric
+
+```{warning}
+In progress!
+```
+
+Describe the PSF modelling problem. Use stars to build a model and try to recover the PSF at galaxy positions.
+
+Describe the main idea of a non-parametric model of the PSF.
+
+Give an example, PSFEx (and MCCD maybe?).
+
+_(Note) Should I give a more mathematical description of how one of the models (PSFEx for example) is build?_
+
+_Maybe I can add some figures from the MCCD paper. Showing some of the eigenPSFs learned. Also, some observed CFIS star and the estimated PSF model._

shearbook/psf/parametric-model.md

@@ -0,0 +1,13 @@
+# Parametric
+
+```{warning}
+In progress!
+```
+
+Describe the PSF modelling problem. Characterise the model as much as possible and try to fit the reduced number of parameters with observed stars. Then use the model to recover PSFs at galaxy positions.
+
+Describe the main idea of a parametric model of the PSF.
+
+Give an example, TinyTim.
+
+_(Note) Should I give an example like of how the PSF is generated following an optic model? _

shearbook/psf/psf-intro.md

@@ -0,0 +1,8 @@
+# Introduction to the PSF
+
+In this section we will..
+
+**Contents**
+
+```{tableofcontents}
+```

shearbook/psf/psf-modelling.md

@@ -0,0 +1,8 @@
+# PSF Modelling
+
+In this section we will go through the two main families of Point Spread Function modelling methods.
+
+**Contents**
+
+```{tableofcontents}
+```

shearbook/psf/psf-models-ref.md

@@ -0,0 +1,5 @@
+# References
+
+```{bibliography} ../_bibliography/z_psf_models.bib
+:all:
+```