# Reference File¶

The `pathloss`

correction step uses a PATHLOSS reference file.

## PATHLOSS Reference File¶

- REFTYPE:
PATHLOSS

- Data model:

The PATHLOSS reference file contains correction factors as functions of source position in the aperture and wavelength.

### Reference Selection Keywords for PATHLOSS¶

CRDS selects appropriate PATHLOSS references based on the following keywords.
PATHLOSS is not applicable for instruments not in the table.
All keywords used for file selection are *required*.

Instrument |
Keywords |
---|---|

MIRI |
INSTRUME, EXP_TYPE, DATE-OBS, TIME-OBS |

NIRISS |
INSTRUME, EXP_TYPE, DATE-OBS, TIME-OBS |

NIRSpec |
INSTRUME, EXP_TYPE, DATE-OBS, TIME-OBS |

### Standard Keywords¶

The following table lists the keywords that are *required* to be present in all
reference files. The first column gives the FITS keyword names.
The second column gives the jwst data model name for each keyword, which is
useful when using data models in creating and populating a new reference file.
The third column gives the equivalent meta tag in ASDF reference file headers,
which is the same as the name within the data model meta tree (second column).

FITS Keyword |
Data Model Name |
ASDF meta tag |
---|---|---|

AUTHOR |
model.meta.author |
author |

DATAMODL |
model.meta.model_type |
model_type |

DATE |
model.meta.date |
date |

DESCRIP |
model.meta.description |
description |

FILENAME |
model.meta.filename |
N/A |

INSTRUME |
model.meta.instrument.name |
instrument: {name} |

PEDIGREE |
model.meta.pedigree |
pedigree |

REFTYPE |
model.meta.reftype |
reftype |

TELESCOP |
model.meta.telescope |
telescope |

USEAFTER |
model.meta.useafter |
useafter |

**NOTE:** More information on standard required keywords can be found here:
Standard Required Keywords

### Type Specific Keywords for PATHLOSS¶

In addition to the standard reference file keywords listed above,
the following keywords are *required* in PATHLOSS reference files,
because they are used as CRDS selectors
(see Reference Selection Keywords for PATHLOSS):

Keyword |
Data Model Name |
---|---|

EXP_TYPE |
model.meta.exposure.type |

### Reference File Format¶

The PATHLOSS reference files are FITS files with extensions for each of the aperture types. The FITS primary HDU does not contain a data array.

#### MIRI LRS Fixed Slit¶

The MIRI LRS Fixed Slit reference file has the following FITS structure:

HDU |
EXTNAME |
XTENSION |
NAXIS |
Dimensions |
---|---|---|---|---|

1 |
PATHLOSS |
BinTable |
2 |
3 columns x 388 rows |

The PATHLOSS extension contains wavelength, pathloss correction, and pathloss uncertainty data. The table has the following format:

Column Name |
Data Type |
Units |
Dimensions |
---|---|---|---|

WAVELENGTH |
float32 |
microns |
388 |

PATHLOSS |
float32 |
N/A |
388 x 50 x 20 |

PATHLOSS_ERR |
float32 |
N/A |
388 x 50 x 20 |

The pathloss data in each table row are stored as a 2-D array, containing correction factors as a function of source position (relative to the LRS slit reference point) in the spatial and spectral directions, respectively. Wavelength dependence runs along the row axis of the table. The correction factors are multiplicative and hence get multiplied into the science data being corrected.

#### NIRSpec IFU¶

The NIRSpec IFU PATHLOSS reference file just four extensions: one pair for point sources and one pair for uniform sources. In each pair, there are either 3-D arrays for point sources, because the pathloss correction depends on the position of the source in the aperture, or 1-D arrays for uniform sources. The pair of arrays are the pathloss correction itself as a function of decenter in the aperture (pointsource only) and wavelength, and the variance on this measurement (currently estimated). The data apply equally to all IFU slices. The structure of the FITS file is as follows:

HDU |
EXTNAME |
XTENSION |
Dimensions |
Data type |
---|---|---|---|---|

1 |
PS |
ImageHDU |
21 x 21 x 21 |
float64 |

2 |
PSVAR |
ImageHDU |
21 x 21 x 21 |
float64 |

3 |
UNI |
ImageHDU |
21 |
float64 |

4 |
UNIVAR |
ImageHDU |
21 |
float64 |

#### NIRSpec Fixed Slit¶

The NIRSpec Fixed Slit reference file has the following FITS structure:

HDU |
EXTNAME |
EXTVER |
XTENSION |
Dimensions |
Data type |
---|---|---|---|---|---|

1 |
PS |
1 |
ImageHDU |
21 x 21 x 21 |
float64 |

2 |
PSVAR |
1 |
ImageHDU |
21 x 21 x 21 |
float64 |

3 |
UNI |
1 |
ImageHDU |
21 |
float64 |

4 |
UNIVAR |
1 |
ImageHDU |
21 |
float64 |

5 |
PS |
2 |
ImageHDU |
21 x 21 x 21 |
float64 |

6 |
PSVAR |
2 |
ImageHDU |
21 x 21 x 21 |
float64 |

7 |
UNI |
2 |
ImageHDU |
21 |
float64 |

8 |
UNIVAR |
2 |
ImageHDU |
21 |
float64 |

9 |
PS |
3 |
ImageHDU |
21 x 21 x 21 |
float64 |

10 |
PSVAR |
3 |
ImageHDU |
21 x 21 x 21 |
float64 |

11 |
UNI |
3 |
ImageHDU |
21 |
float64 |

12 |
UNIVAR |
3 |
ImageHDU |
21 |
float64 |

13 |
PS |
4 |
ImageHDU |
21 x 21 x 21 |
float64 |

14 |
PSVAR |
4 |
ImageHDU |
21 x 21 x 21 |
float64 |

15 |
UNI |
4 |
ImageHDU |
21 |
float64 |

16 |
UNIVAR |
4 |
ImageHDU |
21 |
float64 |

HDU’s 1–4 are for the S200A1 aperture, 5–8 are for S200A2, 9–12 are for S200B1, and 13–16 are for S1600A1. Currently there is no reference data for the S400A1 aperture.

#### NIRSpec MSASPEC¶

The NIRSpec MSASPEC reference file has 2 sets of 4 extensions: one set for the 1x1 aperture (slitlet) size and one set for the 1x3 aperture (slitlet) size. Currently there is not any reference data for other aperture sizes. The FITS file has the following structure:

HDU |
EXTNAME |
EXTVER |
XTENSION |
Dimensions |
Data type |
---|---|---|---|---|---|

1 |
PS |
1 |
ImageHDU |
21 x 63 x 21 |
float64 |

2 |
PSVAR |
1 |
ImageHDU |
21 x 63 x 21 |
float64 |

3 |
UNI |
1 |
ImageHDU |
21 |
float64 |

4 |
UNIVAR |
1 |
ImageHDU |
21 |
float64 |

5 |
PS |
2 |
ImageHDU |
21 x 63 x 21 |
float64 |

6 |
PSVAR |
2 |
ImageHDU |
21 x 63 x 21 |
float64 |

7 |
UNI |
2 |
ImageHDU |
21 |
float64 |

8 |
UNIVAR |
2 |
ImageHDU |
21 |
float64 |

#### NIRISS SOSS¶

The NIRISS SOSS reference file has just 1 extension HDU. The structure of the FITS file is as follows:

HDU |
EXTNAME |
XTENSION |
Dimensions |
Data type |
---|---|---|---|---|

1 |
PS |
ImageHDU |
17 x 2040 x 1 |
float32 |

The PS extension contains a 3-D array of correction values. The third dimension (length = 1) is a dummy to force the array dimensionality to be the same as the NIRSpec reference file arrays. The other 2 dimensions refer to the number of columns in the correction (the same as the number of columns in the science data) and the range of values for the Pupil Wheel position (PWCPOS).

### WCS Header Keywords¶

The headers of the pathloss extensions in all of the above reference files should contain WCS information that describes what variables the correction depends on and how they relate to the dimensions of the correction array.

#### NIRSpec¶

For the NIRSpec reference files (IFU, Fixed Slit, and MSASPEC), the WCS keywords should have the values shown in the tables below. Dimension 1 expresses the decenter along the dispersion direction for a point source:

Keyword |
Value |
Comment |
---|---|---|

CRPIX1 |
1.0 |
Reference pixel in fastest dimension |

CRVAL1 |
-0.5 |
Coordinate value at this reference pixel |

CDELT1 |
0.05 |
Change in coordinate value for unit change in index |

CTYPE1 |
‘UNITLESS’ |
Type of physical coordinate in this dimension |

Dimension 2 expresses the decenter along the direction perpendicular to the dispersion for a point source:

CRPIX2 |
1.0 |
Reference pixel in fastest dimension |

CRVAL2 |
-0.5 |
Coordinate value at this reference pixel |

CDELT2 |
0.05 |
Change in coordinate value for unit change in index |

CTYPE2 |
‘UNITLESS’ |
Type of physical coordinate in this dimension |

Dimension 3 expresses the change of correction as a function of wavelength:

CRPIX3 |
1.0 |
Reference pixel in fastest dimension |

CRVAL3 |
6.0E-7 |
Coordinate value at this reference pixel |

CDELT3 |
2.35E-7 |
Change in coordinate value for unit change in index |

CTYPE3 |
‘METER’ |
Type of physical coordinate in this dimension |

#### NIRISS SOSS¶

The NIRISS SOSS reference file should also have WCS components, but their interpretation is different from those in the NIRSpec reference file. Dimension 1 expresses the column number in the science data:

Keyword |
Value |
Comment |
---|---|---|

CRPIX1 |
5.0 |
Reference pixel in fastest dimension |

CRVAL1 |
5.0 |
Coordinate value at this reference pixel |

CDELT1 |
1.0 |
Change in coordinate value for unit change in index |

CTYPE1 |
‘PIXEL’ |
Type of physical coordinate in this dimension |

Dimension 2 expresses the value of the PWCPOS keyword:

CRPIX2 |
9.0 |
Reference pixel in fastest dimension |

CRVAL2 |
245.304 |
Coordinate value at this reference pixel |

CDELT2 |
0.1 |
Change in coordinate value for unit change in index |

CTYPE2 |
‘Pupil Wheel Setting’ |
Type of physical coordinate in this dimension |

Dimension 3 is a dummy axis for the NIRISS SOSS reference file:

CRPIX3 |
1.0 |
Reference pixel in fastest dimension |

CRVAL3 |
1.0 |
Coordinate value at this reference pixel |

CDELT3 |
1.0 |
Change in coordinate value for unit change in index |

CTYPE3 |
‘Dummy’ |
Type of physical coordinate in this dimension |

#### MIRI LRS¶

For the MIRI LRS reference file, the WCS keywords should have the values shown in the tables below. Dimension 1 expresses the decenter of a point source in the spatial direction (perpendicular to dispersion):

Keyword |
Value |
Comment |
---|---|---|

CRPIX1 |
1.0 |
Reference pixel in the spatial direction |

CRVAL1 |
-25.0 |
Coordinate value at this reference pixel |

CDELT1 |
1.0 |
Change in coordinate value for unit change in index |

CTYPE1 |
‘UNITLESS’ |
Type of physical coordinate in this dimension |

Dimension 2 expresses the decenter along the dispersion for a point source:

CRPIX2 |
1.0 |
Reference pixel in dispersion direction |

CRVAL2 |
-5.0 |
Coordinate value at this reference pixel |

CDELT2 |
0.5 |
Change in coordinate value for unit change in index |

CTYPE2 |
‘UNITLESS’ |
Type of physical coordinate in this dimension |

Note that WCS keywords related to wavelength are not needed for the MIRI LRS reference file, because an array of wavelength values is included in the table of reference data.