Purpose

This document describes the steps required to acquire, reduce, and analyze DEIMOS throughput measurements.

Directory Structure

The following directories occur in $DEIMOS_THRU_DIR, which is currently set to /s/sdata1001/dmoseng/kroot/throughput:

Directory Subdirectories Title Contents

raw/ YYYYmmmDD Raw data directory Contains dated subdirectories with raw DEIMOS throughput images in .gz format

extract/ log 1200G plots 830G 600ZD 900ZD Mirror None Extracted data directory Includes subdirectories grouped by grating containing extracted DEIMOS throughput data.

calibs/ 1200G/doc 1200G 600ZD/doc 600ZD 830G/doc 830G 900ZD/doc 900ZD Sensitivity data Contains the sensitivity files needed by X

dat/ Data files Contains various data files used in reduction

Directory	Subdirectories	Title	Contents
`raw/`	`YYYYmmmDD`	Raw data directory	Contains dated subdirectories with raw DEIMOS throughput images in `.gz` format
`extract/`	`log 1200G plots 830G 600ZD 900ZD Mirror None`	Extracted data directory	Includes subdirectories grouped by grating containing extracted DEIMOS throughput data.
`calibs/`	`1200G/doc 1200G 600ZD/doc 600ZD 830G/doc 830G 900ZD/doc 900ZD`	Sensitivity data	Contains the sensitivity files needed by X
`dat/`		Data files	Contains various data files used in reduction

Phases

Phase I: Acquire Data

Observations of standard stars are acquired at least once per run using the automated script described in DEIMOS Standard Star Recipes.

Software

Filename	Description
/home/deimos/idl/observe_flux_standard.pro	IDL GUI interface

Inputs

No inputs

Outputs

Filename	Description
`$DEIMOS_THRU_DIR/raw/YYYYmmmDD/dYYMM_NNNN.fits`	Raw spectra of standard star

Phase II: Spectral Extraction

Extraction involved taking the input 2-D image and extracting a 1-D spectrum.

Software

Filename	Description
`/home/dmoseng/bin/do_deimos_throughput`	Shell script to launch IDL
`/home/dmoseng/idl/dmoseng/throughput/run_do_deimos_throughput.pro`	IDL driver script to perform reduction of specific images
`/home/dmoseng/idl/dmoseng/throughput/do_deimos_throughput.pro`	IDL script to define input and output filenames.
`/home/dmoseng/idl/dmoseng/throughput/deimos_throughput.pro`	IDL script to extract spectrum

Inputs

Filename	Description
`$DEIMOS_THRU_DIR/raw/YYYYmmmDD/dYYMM_NNNN.fits`	Raw spectra of standard star

Outputs

Filename	Description
`$DEIMOS_THRU_DIR/extract/<grating>/YYYYmmmDD_dNNNN_NNNN.fits`	FITS binary table with two extensions: (1) METADATA has keyword/value pairs (2) SPECTRUM has wavelength and flux
`$DEIMOS_THRU_DIR/extract/<grating>/YYYYmmmDD_dNNNN_NNNN.sav`	IDL SAVE file with the following structures: (1) meta: metadata (2) spec: spectrum (wavelength, counts) (3) diag0: diagnostics for blue chip (trace, profile, spectrum) (4) diag1: diagnostics for red chip (trace, profile, spectrum)
`$DEIMOS_THRU_DIR/extract/<grating>/YYYYmmmDD_dNNNN_NNNN.ps`	Postscript plot file showing profile, trace and extracted 1-D spectrum for both the red and blue chip, plus combined spectrum
`$DEIMOS_THRU_DIR/extract/<grating>/YYYYmmmDD_dNNNN_NNNN_M_trace.region`	trace listing for chip M
`$DEIMOS_THRU_DIR/extract/log/do_deimos_throughput.YYYY-MMM-DD-HH:MM:SS.log`	logfile from execution of this routine

Procedure

Login to an HQ machine as user dmoseng and launch IDL with appropriate settings via:
```
/home/dmoseng/bin/do_deimos_throughput
```
Extract spectra in IDL via
```
do_deimos_throughput, /VERBOSE, /PSFILE
```
of if you want to overwrite all old extractions you can run
```
do_deimos_throughput, /VERBOSE, /PSFILE, /CLOBBER
```
Resulting extracted spectra will go into the directory
```
/s/sdata1001/dmoseng/kroot/throughput/extract
```
and will be organized into subdirectories by grating.

Phase III: Reviewing

All spectra should be reviewed before being extracted in order to ensure that they are "good". Follow these steps to review spectra:

Build throughput image list

Log into an HQ machine as user dmoseng
Launch idl for throughput annalysis via
```
	~dmoseng/bin/do_deimos_throughput
```
Execute IDL command
```
	build_throughput_file_list
```
Output file is /s/sdata1001/dmoseng/kroot/throughput/dat/input.lst (CSV format)

Generate stats on reductions

Log into an HQ machine as user dmoseng
Launch idl for throughput annalysis via
```
	~dmoseng/bin/do_deimos_throughput
```
Execute IDL command
```
	throughput_file_stats
```
Output file is /s/sdata1001/dmoseng/kroot/throughput/dat/throughput_file_stats.ps, where objects colors are as follows:
- black: unreviewed
- green: good
- red: bad
- cyan: requires further review

Phase IV: Conversion

Follow these steps to convert 1-d spectrum to absolute flux using X's reduction algorithm. See his original doco in ~kics/DEIMOS/README.

Log into an HQ machine as user dmoseng.
Launch IDL with appropriate settings via
```
do_deimos_sensstd
```
In IDL, analyze all new data via:
```
do_deimos_sensstd
```

Phase V: Documentation Phase

Launch IDL with appropriate settings via
```
do_deimos_sensstd
```
In IDL, execute command
```
deimos_sensstd_update_web
```

Data Products

Extraction phase

All files live in the directory /s/sdata1001/dmoseng/throughput/extract and subdirectories.

FITS binary tables

Filename: YYYYmmmDD_dNNNN_NNNN.fits
Contents: FITS binary tables which include 2 extensions, 1 with scalar data and 1 with spectrum in units of counts vs. wavelength.

Postscript file

Filename: YYYYmmmDD_dNNNN_NNNN.ps
Contains up to 5 plots:
1. red trace
2. red spectrum (DN vs. pixel)
3. blue trace
4. blue spectrum (DN vs. pixel)
5. combined spectrum (DN vs. wavelength)

Calibration phase

All files live in the directory /s/sdata1001/dmoseng/throughput/calibs and subdirectories.

FITS binary table

Filename: sens_grating_DDMMMYYYY_NNNN.fits where
- grating is the grating name (600ZD)
- DDMMMYYYY is the date (30DEC2002)
- NNNN is the file number (0112)
Contains 2 extension
1. Scalar data (grating, cenlam, etc.)
2. Spectrum in 4 columns
  1. wavelength
  2. zero point per pixel
  3. zero point per Angstrom
  4. efficiency

Data files and Plots

Location: calibs/grating/THRU_DIR
Files:
- EFF_sens_grating_YYYYMMMDD_0124.pdf: efficiency plot, PDF format
- EFFsens_grating_YYYYMMMDD_0124.dat: efficiency table, ASCII format
- ZPANG_sens_grating_YYYYMMMDD_0124.dat: zero point (per Angstrom), PDF format
- ZPANG_sens_grating_YYYYMMMDD_0124.pdf: zero point (per Angstrom), ASCII format
- ZPPIX_sens_grating_YYYYMMMDD_0124.dat: zero point (per pixel), PDF format
- ZPPIX_sens_grating_YYYYMMMDD_0124.pdf: zero point (per pixel), ASCII format

Action Items

Extraction phase

Allow output of ds9 regions files which show the trace
Troubleshoot instances in which the pipeline fails
Re-run pipeline on these images

Calibration phase

Update calib software to output plots in a browser-friendly format (png, gif, jpg, etc.)
Document the deimos_sensstd routine
Allow that script to reprocess old data
Fix the deimos_sensstd routine to prevent it from continually updating the thru_summ file.
Improve the graphics from deimos_sensstd
Fix filename output by deimos_sensstd function
- old: EFFsens_600ZD_30MAY2003_0124.dat
- new: EFF_sens_600ZD_30MAY2003_0124.dat