7.7. rejectCosmicRays

7.7.1. Purpose

This primitive will mask cosmic rays in a GHOST data frame by updating the data mask.

Warning

The algorithm seems to work, but isn’t managing to update the DQ plane. I’m working on the issue. -MCW

7.7.2. Inputs and Outputs

The following options can be passed to rejectCosmicRays via the RecipeSystem, or overridden with a user configuration file, as marked:

Parameter	Type	Default	Override?		Description
			Recipe	User
suffix	str	_cosmicRaysRejected	Y	Y	Suffix affixed to modified file.
subsampling	int	2	Y	Y	The number of pixels to subsample in each direction of each pixel.
sigma_lim	float	5.0	Y	Y	Sigma clipping value.
f_lim	float	6.0	Y	Y	Fine-structure clipping limit.
n_passes	int	2	Y	Y	Number of iterations to perform.

7.7.3. Algorithm

This primitive is a first-principles implementation of the LACosmic algorithm. NumPy array operations are used for maximum efficiency. For a full-discussion of the algorithm, see van Dokkum 2001, PASP 113, 1420-1427 (ADS). In summary (where the symbol

System Message: WARNING/2 (\ast)

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denotes convolution):

1. Create a Laplacian,

   System Message: WARNING/2 (\mathcal{L}^+)

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   , of the input data frame,

   System Message: WARNING/2 (I)

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   .
   • Subsample the image by a factor of subsampling and apply the Laplacian transformation;
   • Set any negative sub-pixels to have value 0 instead;
   • Re-sample the image back to its original resolution.
2. Generate the ‘sigma map’,

   System Message: WARNING/2 (S)

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   , of the frame.
   • Form a ‘noise image’ of the data,

     System Message: WARNING/2 (N=g^{-1}\sqrt{g(M_5\ast I)+\sigma_{rn}^2})

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     , where

     System Message: WARNING/2 (g)

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     and

     System Message: WARNING/2 (\sigma_{rn})

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     are the data gain and read noise respectively.

     System Message: WARNING/2 (M_5)

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     is a

     System Message: WARNING/2 (5\times 5)

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     median filter used to smooth the data.
   • The sigma map is then generated as

     System Message: WARNING/2 (S=\mathcal{L}^+ /f_S N)

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     , where

     System Message: WARNING/2 (f_S)

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     is the subsampling factor used.
   • Smooth the sigma map to help remove sampling flux, resulting in

     System Message: WARNING/2 (S^\prime = S - (S\ast M_5))

     latex exited with error [stdout] This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) %&-line parsing enabled. entering extended mode (./math.tex LaTeX2e <2005/12/01> Babel <v3.8h> and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, arabic, basque, bulgarian, coptic, welsh, czech, slovak, german, ng erman, danish, esperanto, spanish, catalan, galician, estonian, farsi, finnish, french, greek, monogreek, ancientgreek, croatian, hungarian, interlingua, ibyc us, indonesian, icelandic, italian, latin, mongolian, dutch, norsk, polish, por tuguese, pinyin, romanian, russian, slovenian, uppersorbian, serbian, swedish, turkish, ukenglish, ukrainian, loaded. (/usr/share/texmf/tex/latex/base/article.cls Document Class: article 2005/09/16 v1.4f Standard LaTeX document class (/usr/share/texmf/tex/latex/base/size12.clo)) (/usr/share/texmf/tex/latex/base/inputenc.sty (/usr/share/texmf/tex/latex/ucs/utf8x.def)) (/usr/share/texmf/tex/latex/ucs/ucs.sty (/usr/share/texmf/tex/latex/ucs/data/uni-global.def)) (/usr/share/texmf/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?’ option. (/usr/share/texmf/tex/latex/amsmath/amstext.sty (/usr/share/texmf/tex/latex/amsmath/amsgen.sty)) (/usr/share/texmf/tex/latex/amsmath/amsbsy.sty) (/usr/share/texmf/tex/latex/amsmath/amsopn.sty)) (/usr/share/texmf/tex/latex/amscls/amsthm.sty) (/usr/share/texmf/tex/latex/amsfonts/amssymb.sty (/usr/share/texmf/tex/latex/amsfonts/amsfonts.sty)) ! LaTeX Error: File `anyfontsize.sty’ not found. Type X to quit or <RETURN> to proceed, or enter new name. (Default extension: sty) Enter file name: ! Emergency stop. <read *> l.9 \usepackage {bm}^^M No pages of output. Transcript written on math.log.
     .
3. Generate the ‘fine-structure image’ of the frame,

   System Message: WARNING/2 (\mathcal{F}=(M_3\ast I) - ((M_3\ast I) \ast M_7))

   latex exited with error [stdout] This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) %&-line parsing enabled. entering extended mode (./math.tex LaTeX2e <2005/12/01> Babel <v3.8h> and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, arabic, basque, bulgarian, coptic, welsh, czech, slovak, german, ng erman, danish, esperanto, spanish, catalan, galician, estonian, farsi, finnish, french, greek, monogreek, ancientgreek, croatian, hungarian, interlingua, ibyc us, indonesian, icelandic, italian, latin, mongolian, dutch, norsk, polish, por tuguese, pinyin, romanian, russian, slovenian, uppersorbian, serbian, swedish, turkish, ukenglish, ukrainian, loaded. (/usr/share/texmf/tex/latex/base/article.cls Document Class: article 2005/09/16 v1.4f Standard LaTeX document class (/usr/share/texmf/tex/latex/base/size12.clo)) (/usr/share/texmf/tex/latex/base/inputenc.sty (/usr/share/texmf/tex/latex/ucs/utf8x.def)) (/usr/share/texmf/tex/latex/ucs/ucs.sty (/usr/share/texmf/tex/latex/ucs/data/uni-global.def)) (/usr/share/texmf/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?’ option. (/usr/share/texmf/tex/latex/amsmath/amstext.sty (/usr/share/texmf/tex/latex/amsmath/amsgen.sty)) (/usr/share/texmf/tex/latex/amsmath/amsbsy.sty) (/usr/share/texmf/tex/latex/amsmath/amsopn.sty)) (/usr/share/texmf/tex/latex/amscls/amsthm.sty) (/usr/share/texmf/tex/latex/amsfonts/amssymb.sty (/usr/share/texmf/tex/latex/amsfonts/amsfonts.sty)) ! LaTeX Error: File `anyfontsize.sty’ not found. Type X to quit or <RETURN> to proceed, or enter new name. (Default extension: sty) Enter file name: ! Emergency stop. <read *> l.9 \usepackage {bm}^^M No pages of output. Transcript written on math.log.
   , where

   System Message: WARNING/2 (M_3)

   latex exited with error [stdout] This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) %&-line parsing enabled. entering extended mode (./math.tex LaTeX2e <2005/12/01> Babel <v3.8h> and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, arabic, basque, bulgarian, coptic, welsh, czech, slovak, german, ng erman, danish, esperanto, spanish, catalan, galician, estonian, farsi, finnish, french, greek, monogreek, ancientgreek, croatian, hungarian, interlingua, ibyc us, indonesian, icelandic, italian, latin, mongolian, dutch, norsk, polish, por tuguese, pinyin, romanian, russian, slovenian, uppersorbian, serbian, swedish, turkish, ukenglish, ukrainian, loaded. (/usr/share/texmf/tex/latex/base/article.cls Document Class: article 2005/09/16 v1.4f Standard LaTeX document class (/usr/share/texmf/tex/latex/base/size12.clo)) (/usr/share/texmf/tex/latex/base/inputenc.sty (/usr/share/texmf/tex/latex/ucs/utf8x.def)) (/usr/share/texmf/tex/latex/ucs/ucs.sty (/usr/share/texmf/tex/latex/ucs/data/uni-global.def)) (/usr/share/texmf/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?’ option. (/usr/share/texmf/tex/latex/amsmath/amstext.sty (/usr/share/texmf/tex/latex/amsmath/amsgen.sty)) (/usr/share/texmf/tex/latex/amsmath/amsbsy.sty) (/usr/share/texmf/tex/latex/amsmath/amsopn.sty)) (/usr/share/texmf/tex/latex/amscls/amsthm.sty) (/usr/share/texmf/tex/latex/amsfonts/amssymb.sty (/usr/share/texmf/tex/latex/amsfonts/amsfonts.sty)) ! LaTeX Error: File `anyfontsize.sty’ not found. Type X to quit or <RETURN> to proceed, or enter new name. (Default extension: sty) Enter file name: ! Emergency stop. <read *> l.9 \usepackage {bm}^^M No pages of output. Transcript written on math.log.
   and

   System Message: WARNING/2 (M_7)

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   are

   System Message: WARNING/2 (3\times 3)

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   and

   System Message: WARNING/2 (7\times 7)

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   median filters,
4. Mark pixels as cosmic rays (via the image quality plane) if:

   • System Message: WARNING/2 (S^\prime >)

     latex exited with error [stdout] This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) %&-line parsing enabled. entering extended mode (./math.tex LaTeX2e <2005/12/01> Babel <v3.8h> and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, arabic, basque, bulgarian, coptic, welsh, czech, slovak, german, ng erman, danish, esperanto, spanish, catalan, galician, estonian, farsi, finnish, french, greek, monogreek, ancientgreek, croatian, hungarian, interlingua, ibyc us, indonesian, icelandic, italian, latin, mongolian, dutch, norsk, polish, por tuguese, pinyin, romanian, russian, slovenian, uppersorbian, serbian, swedish, turkish, ukenglish, ukrainian, loaded. (/usr/share/texmf/tex/latex/base/article.cls Document Class: article 2005/09/16 v1.4f Standard LaTeX document class (/usr/share/texmf/tex/latex/base/size12.clo)) (/usr/share/texmf/tex/latex/base/inputenc.sty (/usr/share/texmf/tex/latex/ucs/utf8x.def)) (/usr/share/texmf/tex/latex/ucs/ucs.sty (/usr/share/texmf/tex/latex/ucs/data/uni-global.def)) (/usr/share/texmf/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?’ option. (/usr/share/texmf/tex/latex/amsmath/amstext.sty (/usr/share/texmf/tex/latex/amsmath/amsgen.sty)) (/usr/share/texmf/tex/latex/amsmath/amsbsy.sty) (/usr/share/texmf/tex/latex/amsmath/amsopn.sty)) (/usr/share/texmf/tex/latex/amscls/amsthm.sty) (/usr/share/texmf/tex/latex/amsfonts/amssymb.sty (/usr/share/texmf/tex/latex/amsfonts/amsfonts.sty)) ! LaTeX Error: File `anyfontsize.sty’ not found. Type X to quit or <RETURN> to proceed, or enter new name. (Default extension: sty) Enter file name: ! Emergency stop. <read *> l.9 \usepackage {bm}^^M No pages of output. Transcript written on math.log.
     sigma_lim, and

   • System Message: WARNING/2 (\mathcal{L}^+ /\mathcal{F} >)

     latex exited with error [stdout] This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) %&-line parsing enabled. entering extended mode (./math.tex LaTeX2e <2005/12/01> Babel <v3.8h> and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, arabic, basque, bulgarian, coptic, welsh, czech, slovak, german, ng erman, danish, esperanto, spanish, catalan, galician, estonian, farsi, finnish, french, greek, monogreek, ancientgreek, croatian, hungarian, interlingua, ibyc us, indonesian, icelandic, italian, latin, mongolian, dutch, norsk, polish, por tuguese, pinyin, romanian, russian, slovenian, uppersorbian, serbian, swedish, turkish, ukenglish, ukrainian, loaded. (/usr/share/texmf/tex/latex/base/article.cls Document Class: article 2005/09/16 v1.4f Standard LaTeX document class (/usr/share/texmf/tex/latex/base/size12.clo)) (/usr/share/texmf/tex/latex/base/inputenc.sty (/usr/share/texmf/tex/latex/ucs/utf8x.def)) (/usr/share/texmf/tex/latex/ucs/ucs.sty (/usr/share/texmf/tex/latex/ucs/data/uni-global.def)) (/usr/share/texmf/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?’ option. (/usr/share/texmf/tex/latex/amsmath/amstext.sty (/usr/share/texmf/tex/latex/amsmath/amsgen.sty)) (/usr/share/texmf/tex/latex/amsmath/amsbsy.sty) (/usr/share/texmf/tex/latex/amsmath/amsopn.sty)) (/usr/share/texmf/tex/latex/amscls/amsthm.sty) (/usr/share/texmf/tex/latex/amsfonts/amssymb.sty (/usr/share/texmf/tex/latex/amsfonts/amsfonts.sty)) ! LaTeX Error: File `anyfontsize.sty’ not found. Type X to quit or <RETURN> to proceed, or enter new name. (Default extension: sty) Enter file name: ! Emergency stop. <read *> l.9 \usepackage {bm}^^M No pages of output. Transcript written on math.log.
     f_lim.
5. For the purposes of the algorithm (i.e. not in the data to be returned), replace cosmic rays pixels with the median value of surrounding pixels.
6. Iterate over steps 1-5 until n_passes is reached, or the number of cosmic rays detected falls to 0.

7.7.4. Issues and Limitations

Both strong spectral features and, in high-resolution mode, the ThXe calibration output may be incorrectly flagged as cosmic rays. Therefore, this primitive will trigger a call to need to add more here once this actually works

Note

The current preset values of sigma_lim (15.0, 5.0), f_lim (5.0) and n_passes (5) are a first-pass guess at what seems to flag roughly the correct number of cosmic rays. More complete testing, and the possible implementation of a table of preset values on a case-by-case basis, will need to wait until the findApertures routine (and related routines) are finalized and mixed in with the cosmic ray finding.