Photometry Parameters File

Create a photometry parameters file like the example on the Example Photometric Parameters Page. You will need to specify a list of files, source name and a list of source coordinates in pixels [x,y]. The first source should be the target and the rest will be reference stars. The jdRef parameter specifies a reference epoch for time series plots.

Source Aperture Photometry Geometry

Specify the aperture geometry, aperture sizes, and the box finding size for locating sources. The options for geometry srcGeometry are “Circular”, “Rectangular”, and “CircularAnnulus”. If using CircularAnnulus, the inner and outer radii are set by the srcStart and the srcEnd keywords while ignoring apRadius, apHeight and apWidth. If using Rectangular, the apHeight and apWidth keywords are used to define the source aperture size while ignoring apRadius, srcStart and srcEnd.

Background Aperture Photometry Geometry

Specify the background aperture geometry (bkgGeometry). You can use either CircularAnnulus or Rectangle. If using CircularAnnulus, the inner and outer radii are set by the backStart and the backEnd keywords, while ignoring backHeight and backWidth. If using Rectangular, the backHeight and backWidth keywords are used to define the background aperture size. Regardless of the geometry, the background aperture is always centered relative to the source aperture. The offset between background aperture and the source aperture is set by backOffset, which is a 2 element list in the form of [DX, DY], where DX and DY are the offset in number of pixels.

Background Subtraction Methods

Specify the background method (bkgMethod). The options are

  • “mean” (default). This calculates the mean background value per pixel and subtracts this from all source pixels

  • “median”. This calculates the median background value value per pixel and subtracts this from all source pixels

  • “robust mean”. This calculates the robust mean background value value per pixel and subtracts this from all source pixels.

  • “colrow”. This calculates a column-by-colum and/or row-by-row fit to the background. The parameters are similar to the Spec Background Parameters. Specify the bkgOrderX, bkgOrderY for the polynomial orders of the fits. For example bkgOrderX: 1 for a linear fit. The order and which directions to be specified are in the backsub_directions parameter. To do backsub_directions: ['Y','X'] would do the Y direction (column-by-column) first and then the X direction (row-by-row). backsub_directions: ['X'] would only do row-by-row subtraction.

  • “rowAmp”. This is a somewhat JWST-specific code that will do row-by-row subtraction of the whole array (masking out sources) but treats each column individually. The sources are masked by making all pixels with a circle with radius backStart from the source Nan and then using numpy.nanmedian() to calculate the median of each row within a given amplifier. Mileage may vary if sources extend over an entire amplifier (512 pixels for JWST Stripe mode, also called 4 output amplifier mode).

Fixed Aperture Sizes

For the circular aperture, apRadius gives the source radius, and backStart and backEnd give the inner and outer radii of the background annulus. For a rectangular aperture, the apHeight and apWidth describe the height and width of the source, and backHeight and backWidth describe the height and width of the background. These units are in pixels.

Scaled Aperture Sizes

The apertures can be fixed for all images or be scaled with the FWHM using either scaleAperture: True or scaleAperture: False. If true, specify the scaling factor. The source aperture will be the FWHM multiplied by the scaling factor

\[r_src = FWHM * apScale.\]

The background start will be calculated as

\[r_in = backStart - apRadius + r_src.\]

The background end will be calculated as

\[r_out = backEnd - backStart + r_in\]

where the apScale, backStart, apRadius and backEnd keywords are specified in the parameter file. You can also specify an apRange parameter which sets the minimum and maximum allowed FWHM. This adds some robustness in the case the FWHM found is wacky - for example if clouds go over.

Timing Method

The phot_pipeline will automatically find the JD time from the DATE-OBS and TIME-OBS keywords. However, if using JWST data, all the integrations are packed into a singel fits file with one DATE-OBS and TIME-OBS. In this case, the data must be split into individual integrations, which are assigned an ON_INT keyword. If timineMethod is set to JWSTint, then phot_pipeline will use the calculate integration times using TFRAME and INTTIME in the header.

The parameter dateKeyword will tell tshirt to look for a specific FITS keyword for the date. Otherwise it searches common ones like DATE-OBS or DATE_OBS.

Star Positions

:code`refStarPos` [[X1,Y1],[X2,Y2]]. A list of star positions will be found in pixels from . This will be the starting guess if centroiding is being used. The first position will be the target star, and the remaining positions will be assumed to be reference stars. skyPositions. Positions on the Sky in RA degrees, DEC degrees. If None, it will be ignored

downselectImgWithCoord

If True, down-select only images where the source is present and ignore ones where the source is missing