8. The Analysis Utilities

8.1. DS9

This button opens SAOImage DS9 and by default displays the Primary FITS extension of every FITS file selected. The user can display a custom extension using the dedicated pull-down menu. Several files can be displayed in DS9 as different ds9-frames.

Hint

The DS9 launched by SIPGI is an embedded version installed with SIPGI itself. If you have a preferred and different DS9 version installed on your machine, you can configure the First Alternative Fits Viewer (see below) to launch it.

8.2. First Alternative Fits Viewer

It displays the selected file using the external FITS viewer defined in the SIPGI Preferences as first alternative FITS viewer. The viewer name is shown on the button.

8.3. Secondary Alternative Fits Viewer

It displays the selected file using the external FITS viewer defined in the SIPGI Preferences as second alternative FITS viewer. The viewer name is shown on the button.

Hint

We suggest to select as First Alternative Fits Viewer your favorite tool to manage images, and as Second Alternative Fits Viewer your favorite tool to manage tables.

8.4. Show Slit Position

It shows the reference slit positions on the selected frame. SIPGI displays in DS9 the selected frame with green line regions showing the position where the slits are supposed to be according to the Paf file contained in the selected frame. For MOS observations, it shows the SIPGI number of each slit (see Fig. Fig. 8.1 and for more details about mask slit numbering see note below).

_images/slit_positions.png — Fig. 8.1 A MOS frame as shown by the Show Slit Position utility. Green lines indicate the supposed slit position (in case of no distorted frame). The green numbers indicate the slit number.

In case a reduced file is provided, the slit numbering is overlaid on the EXR2D extension,

Note

In MOS data, SIPGI enumerates slits following the slit numbering order in the LMS/MMS file. SIPGI does not enumerate alignment and reference slits (by default square slits are considered reference slits).

SIPGI enumeration starts from #1. The relation between the SIPGI and the LMS/MMS slit numbering is described by the set of keywords: LBT INS SLIT# ID. For example: LBT INS SLIT1 ID = ‘07_M31’ means: the first slit extracted by SIPGI (SLIT1) is the slit number 07 in the LMS/MMS file and its original object name is M31.

EXR2D frames show 2D extracted spectra packed together from bottom to top according to their slit number .

Table 8.1 **The Show Slit Position Utility Summary**. In bold mandatory inputs
	MODS	LUCI
INPUTS	Through-slit flat frame	Through-slit flat frame

8.5. Show Spectra Location

It shows the spectra location and spectral tracing using the solution stored in the Master Flat. The user can use this tool to check the quality of the tracing. A good tracing is necessary to properly follow the traces of the targets and extract them correctly. In fact, 1D spectra are extracted within a region that runs parallel to the pixel rows. This means that if the tracing presents some sort of curvature wrt the real edge of the 2D spectrum (i.e. wrt the pixel rows), the target will go out from the extraction region. The user must select the Master Flat to check and the frame on which this solution must be checked. SIPGI opens the frame in DS9 with superimposed the edges of the spectra (see white vertical “lines” in Fig. 8.2).

The extension of the lines identifies the spectral region fitted by the Master Flat and it is defined by the keywords PIX_LOW and PIX_HIGH contained in the Grism tables.

Black solid lines in the upper and lower part of the frame indicate the expected position of the extraction limits (i.e. WLEN_START and WLEN_END, see Grism tables) according to the solution stored in the Master Flat. These lines should be placed within the tracing region, since SIPGI will perform the wavelength calibration using all the lines included in the [WLEN_START, WLEN_END] range, but in any case never outside the tracing regions.

The utility Show Spectra Location can be used also on science frames. This allows the user to directly check the spectral tracing on science raw frames.

_images/spectra_tracing.png — Fig. 8.2 A MOS frame as shown by the Show Spectra Location utility. White horizontal lines indicate the right and left edges of the slits as estimated by the Create Master Flat recipe.

Table 8.2 **The Show Slit Position Utility Summary**. In bold mandatory inputs
	MODS	LUCI
INPUTS	Through-slit flat frame	Through-slit flat frame
INPUTS	Master Flat	Master Flat

8.6. Show Lambda Calibration

The Master Lamp frame contains the final solution used to obtain rectified 2D spectra linearly calibrated in lambda. For each slit, this solution predicts the wavelength to associate at each pixel in the frame.

This utility takes in input a Master Lamp (or a master Flat if the user wants to check the intermediate solution). In addition to the information shown by Show Spectra Location, it displays the position of the Lines catalog lines appended to the input frames, on the basis of the solution stored in the Master File (see Fig. Fig. 8.3). In case no additional frame is provided the recipe displays the solution directly on the master frame image.

The Lines catalog can be passed as further input. In case no Lines catalog is provided, the recipe will look for a Lines catalog in the input frames. If no catalog is found in the input frames, the utility uses the Master Lamp Lines catalog.

Table 8.3 **The Show Lambda Calibration Utility Summary**. In bold mandatory inputs
	MODS	LUCI
INPUTS	Through-slit flat frame or science (mandatory if Master Flat is provided)	Through-slit flat frame or science (mandatory if Master Flat is provided)
INPUTS	Master Flat or Master Lamp	Master Flat or Master Lamp

_images/show_lambda_cal.png — Fig. 8.3 A MOS frame as shown by the Show Lambda Calibration utility. Black lines show the lines expected positions as estimated by the Create Master Lamp(or Create Master Flat) recipe.

8.7. Check Lambda Calibration

This utility takes in input a Master Lamp and provides a quantitative estimate of the wavelength calibration accuracy.

For each slit it recomputes the real lines positions in the middle of the slit, and estimates the differences between the lines positions expected according to the input Master Lamp and real ones for all the lines in the catalog (DeltaL [Å]). It shows a message like:

Slit 1 - good lines: 20; mean DeltaL=0.018640; DeltaL rms=0.129130,

containing:

slit number;

number of good lines (see Create Master Lamp) used for the fit;

the mean and rms value of these differences.

Together with this, it provides a global information on the wavelength solution giving:

the Median of the “mean DeltaL” over all the slits;

the Median of the “DeltaL rms” over all the slits. A warning is raised when this quantity is greater than 1/5 of the spectral sampling;

the Maximum DeltaL rms over all the slits;

the Minimum DeltaL rms over all the slits.

For each line in the Lines catalog, the recipe provides also the number of slits in which the line is good (see Create Master Lamp), plus the median and std of the differences between the expected and real position of that line in all of the slits.

Table 8.4 **The Check Lambda Calibration Utility Summary**. In bold mandatory inputs
	MODS	LUCI
INPUTS	Master Lamp	Master Lamp

8.8. Plot Lambda Calibration

This utility allows to check the wavelength calibration of the selected Master Lamp with deeper detail wrt the Check Lambda Calibration. The Check Lambda Calibration utility provides information on the quality of the wavelength calibration for each slit and on the global wavelength calibration quality. In both cases, all the information is picked up in the middle of the slit.

The user could be interested to have information on the wavelength calibration quality in the target position, and/or along the dispersion direction.

The Plot Lambda Calibration utility addresses both issues. It is a graphical task which allows:

to have information on the wavelength calibration accuracy in any “slice” of the 2D spectra for all the slits (see Create Master Lamp recipe);

to exclude some lines from the fit and refit the wavelength solution;

to have information on the calibration accuracy for each fitted line.

For more details on its use, see the Plot Lambda Calibration description in the Cookbook section.

Table 8.5 **The Plot Lambda Calibration Utility Summary**. In bold mandatory inputs
	MODS	LUCI
INPUTS	Master Lamp	Master Lamp

8.9. Plot Sensitivity

This utility allows the user to visualize the raw and smoothed selected sensitivity functions (see Create Sensitivity) and to check its quality.

For more details on its use, see the Plot Sensitivity description in the Cookbook section.

Table 8.6 **The Plot Sensitivity Utility Summary**. In bold mandatory inputs
	MODS	LUCI
INPUTS	Sensitivity function	Sensitivity function
INPUTS	Standard reduced frames	Standard reduced frames

8.10. Show Reduced Spectra

This utility offers a wide range of tools to visualize the reduced spectra. It works both on the BFCR (DFCR) frames and on the combined frames.

It allows to:

visualize the 2D and 1D spectra;

visualize the 1D error spectrum;

visualize the 1D sky spectrum at the target position;

visualize the extraction profile and the extraction region;

edit the 1D spectrum;

check the target redshift;

fit the emission/absorption lines;

perform some “simple” statistic (e.g. S/N measurements in a selected region, median, rms).

For more details on its use, see the Show Reduced Spectra description in the Cookbook section.

Table 8.7 **The Show Reduced Utility Summary**. In bold mandatory inputs
	MODS	LUCI
INPUTS	Reduced or combined frame	Reduced or combined frame
INPUTS	Spectro-photometric standars	Stellar template

8.11. Manage Detections

This task allows to manage the objects detections. Both the Reduce Observations and the Combine Observations recipe detect objects as described here. However, the user may want to modify these detections (and update the corresponding 1D spectra), extract new non-detected objects or delete some detections (and their relative 1D spectra). This task allows the user to do all these operations.

It open a new window and shows the selected reduced or combined frame, and for each slit, it shows the extraction profile and a summary of all the objects that have been detected by the recipes in that slit.

For more details on its use, see the Manage Detections description in the Cookbook section.

Table 8.8 **The Manage Detections Utility Summary**. In bold mandatory inputs
	MODS	LUCI
INPUTS	Reduced or combined frame	Reduced or combined frame

8.12. Plot Extraction Profile

This task shows the extraction profiles of the selected frame (see the extraction profile paragraph).

It opens a new window and shows the extraction profile (grey shaded area) of the slit shown at the bottom of the panel. The green solid line is the median value of the profile, the red horizontal line is the (median + rms) and the blue line is the detection threshold. The grey vertical lines indicate the extraction limits of the object shown at the bottom of the panel.

Table 8.9 **The Plot Extraction Profile Utility Summary**. In bold mandatory inputs
	MODS	LUCI
INPUTS	Reduced or combined frame	Reduced or combined frame

8.13. Show Window Table

It shows the window table of the selected file. This table exists only in reduced frames. It stores the information both on EXR2D structure and on the detection of 1D spectra.

All 2D extracted spectra are stacked up in the EXR2D following the order explained in the Show Slit Position Note. Every extracted slit covers the wavelength range from WLEN START to WLEN END with a WLEN INC sampling (see Grism tables keywords or WLEN_START, WLEN_END, and WLEN_INC parameter in Reduce Observations).

The Window Table columns are (see Fig. 8.4):

Slit: sequential SIPGI slit number (always starting from 1)

Obj: sequential number of detected objects within slit

M/LMS Slit: the original slit number as defined in M/LMS

Target Name: the target name as defined in M/LMS

N Pix: the slit dimension in pixels

Sp Start: first row (Y axis) of the slit in EXR2D extension

Sp End: last row (Y axis) of the slit in EXR2D extension

Obj Start: first row (Y axis) of object spectrum, relative to Sp Start

Obj End: last row (Y axis) of object spectrum, relative to Sp Start

Obj Pos: peak position of object in 2D extracted spectrum, relative to Sp Start

Each WIN Table has at least 1 entry for each slit. Multiple entries for the same slit can exist in case more than one object was detected in the same slit.

_images/wintable.png — Fig. 8.4 The figure shows the quantity stored in the WIN table. In this example the slit #7 starting from pixel 329 (330 in DS9) and ends at pixel 401 (402 in DS9). One object as been detected from pixel 360 to pixel 371. The peak of the profile object is at pixel 365.899

Slit	Obj	M/LMS Slit	Target Name	N Pix	Sp Start	Sp End	Obj Start	Obj End	Obj Pos
1	1	1	Obj1	50	0	49	19	27	22.89
…
7	1	4	Obj7	73	329	401	30	41	35.899
…

Table 8.10 **The Show Window Table Utility Summary**. In bold mandatory inputs
	MODS	LUCI
INPUTS	Reduced or combined frame	Reduced or combined frame