phcorr

phcorr applies gain, bias, dark and flat corrections to science frames and converts them to electrons.

Any master you leave out is simply skipped. The masters must match the frame size, and the flat must be positive everywhere. The masters come from bias, dark and flat.

Usage

munipack phcorr [options] file(s)

Options

Corrections

Option	Default	Description
-gain	header GAIN, else 1	Gain [e⁻/ADU]; without one, values stay in ADU.
-bias	—	Master bias.
-dark	—	Master dark.
-xdark	exposure-time ratio	Dark scaling factor t (1 when exposure times are unknown).
-flat	—	Master flat.
--normalise-flat	off	Divide the flat by its mean first; use for flats not normalised to 1.

Masking

Option	Default	Description
-bitmask	—	Mask frame; pixels with value 0 are replaced (e.g. hot pixels, bad columns).
-xbitmask	MEAN	Replacement value: ZERO, MEAN (frame mean) or MEDIAN (local mean in a box).
-box	5	Box size for MEDIAN; use 3 for isolated pixels.

Output

Option	Default	Description
-t, --target-directory	—	Write outputs to this (existing) directory.
--enable-overwrite	off	Allow replacing existing files, including the inputs.
-O	off	Enable custom output names (--pattern, --mask, --format).
--pattern	(.+)\.(.+)	Regular expression matched against input names (for -O).
--mask	—	Output name built from the pattern groups, e.g. '\1_c.\2' (for -O).
--format	—	Numbered output names, e.g. 'cal_%03d.fits' (for -O).
-B, --bitpix	−32	Output type; keep −32 for frames in electrons.
--verbose	off	Print the corrections applied to each frame.
-h, --help	—	Show the help.

Output

One calibrated frame per input. Each gets a STDERR extension with the error of every pixel, and its header carries the noise model in electrons. find, aphot and psfphot pick this up automatically.

By default the output keeps the input’s name and goes to the current directory. phcorr refuses to overwrite an existing file, so when the inputs are in the current directory use -t, -O --mask … or --enable-overwrite.

Examples

# full correction, outputs in cal/ with the same names
munipack phcorr -bias bias.fits -dark dark300.fits -flat flat_V.fits \
    -t cal object_V_*.fits

# outputs next to the inputs with a suffix: m51_001.fits -> m51_001_c.fits
munipack phcorr -bias bias.fits -dark dark.fits -flat flat_V.fits \
    -O --mask '\1_c.\2' m51_*.fits

# replace hot pixels by the local mean, correcting in place
munipack phcorr -bias bias.fits -flat flat_V.fits -bitmask hot.fits \
    -xbitmask MEDIAN -box 3 --enable-overwrite frame_*.fits

Typical calibration sequence

The four routines turn raw CCD or CMOS exposures into calibrated frames in electrons, ready for find, aphot, psfphot and astrometry.

# 1. master bias (more than 10 frames is better)
munipack bias -o bias.fits bias_*.fits

# 2. master dark with the bias removed, so it can be scaled to any exposure time
munipack dark -bias bias.fits -o dark120.fits dark120_*.fits

# 3. one master flat per filter
munipack flat -bias bias.fits -dark dark120.fits -o flat_V.fits flat_V_*.fits

# 4. calibrate the science frames into cal/, leaving the originals untouched
mkdir -p cal
munipack phcorr -bias bias.fits -dark dark120.fits -flat flat_V.fits \
    -t cal object_V_*.fits

For every pixel, phcorr computes C = g (S − t D − B) / F: the raw frame S minus the bias B and the dark D (scaled by the exposure-time ratio t), divided by the flat F and multiplied by the gain g.

You can work in one of two ways:

• Darks of the same exposure time as your science frames, no bias. Run dark and phcorr without -bias. The dark then includes the bias. This is the simplest choice when all frames share one exposure time.

• Bias plus scaled darks. Make the dark with -bias and give the same bias to flat and phcorr. One long dark then serves every exposure time.

Warning

Do not scale a dark that still contains the bias: the bias would be scaled too. Use such a dark only for frames of its own exposure time.

Notes

• Output names can also be set explicitly with an @list file of two names per line (input output).

• With -O, the outputs are written to the current directory; -t does not apply.

• Input lists, header keywords (FITS_KEY_*) and Docker use work as for the masters: see Common to bias, dark and flat.

• Frames calibrated with older Munipack versions carry a wrong noise model. Calibrate the raw frames again with the current version before photometry.