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--- data:data_analysis_manual [2021/06/30 19:04]
Peter Young [Reference data-sets]
+++ data:data_analysis_manual [2023/07/28 18:19] (current)
Peter Young [Line fitting]
@@ Line 11: / Line 11: @@
 SPICE papers:
   * Instrument paper: //Astron. Astrophys.//, **642**, A14, 2020. [[https://doi.org/10.1051/0004-6361/201935574|DOI]], [[https://ui.adsabs.harvard.edu/abs/2020A%26A...642A..14S|ADS]]
-  * First results: Submitted
+  * First results: //Astron. Astrophys.//, **656**, A38, 2021. [[https://doi.org/10.1051/0004-6361/202141221|DOI]], [[https://ui.adsabs.harvard.edu/abs/2021A%26A...656A..38F/abstract|ADS]]
   * In-flight calibration: Not available yet
   * Other papers can be found in the [[https://ui.adsabs.harvard.edu/public-libraries/rIi8Zx4zTg2stP5nTojx2Q|SPICE ADS library]]
@@ Line 22: / Line 22: @@
 The data levels, FITS files, and headers are described in
-  * The [[https://spice.ias.u-psud.fr/spice-data/documents/SPICE-UIO-DPDD-0002-1.4-Data_Product_Description_Document.pdf|Data Products Description Document]] (DPDD)
+  * The [[https://spice-wiki.ias.u-psud.fr/lib/exe/fetch.php/documents_public:spice-uio-dpdd-0002-1.7-data_product_description_document_spicefits_.pdf|Data Products Description Document]] (DPDD)
   * The LLDPDD for the Low-Latency (LL) files
 The full SPICE data set (to be cited in papers) has a DOI: [[https://doi.org/10.5270/esa-lbmdy7c|doi:10.5270/esa-lbmdy7c]]. DOIs will also be attributed to each data release.
+When browsing the SPICE catalog and archive you will see the following codes:
+**n-ras**: a raster scan with one of the narrow slits (2", 4" or 6")\\
+**w-ras**: a raster scan with the wide slit (30")\\
+**n-sit**: a sit-and-stare study with one of the narrow slits\\
+**w-sit**: a sit-and-stare study with the wide slit\\
+**n-exp**: a single exposure with a narrow slit that yields the entire spectrum\\
+**w-exp**: a single exposure with the wide slit that yields the entire spectrum
+For the "ras" data, the FITS file contains a single raster scan. If the raster is repeated, then each repeat goes in a new file.
+Rasters can be performed in the "exp" mode, but each exposure will end up in a different FITS file.
 ===== Find data =====
 UiO catalogue:
   * Can be generated with IDL/SolarSoft (SSW) from a local data tree:
-    - Make sure ''$SPICE_DATA'' points to the data tree you want to have catalogued
+    - Make sure ''$SPICE\_DATA'' points to the data tree you want to have catalogued
-    - Run SPICE_GEN_CAT. The catalogue file will be written to the data tree root directory (you need to have write access)
+    - Run SPICE\_GEN\_CAT. The catalogue file will be written to the data tree root directory (you need to have write access)
-    - Run SPICE_CAT
+    - Run SPICE\_CAT
-  * The catalogue file generated from all SPICE files is accessible [[http://astro-sdc-db.uio.no/vol/spice/fits/spice_catalog.txt|through the UiO website]] (restricted to SPICE team)
+  * The catalogue file generated from all SPICE files is accessible [[http://astro-sdc-db.uio.no/vol/spice/fits/spice_catalog.csv|through the UiO website]] (restricted to SPICE team)
   * How to use it in [[data:data_analysis_manual:read_catalog_python|Python]]
-  * A CSV export of the part of the catalogue corresponding to each release is provided with the release.
+  * How to use it in IDL: [[data:data_analysis_manual#the_spice_catalog|see below]]
+  * A CSV export of the part of the catalogue corresponding to each release is provided with the data releases. This export is completed with additional columns for the list of windows, the file size, and a reference to the dark used for on-ground dark subtraction.
+Data releases:
+  * All L1+ files with their latest versions (at a given date) are collected in a data release
+  * The releases are provided under https://spice.osups.universite-paris-saclay.fr/spice-data/
+  * The latest release is updated with new data as they arrive (and after a superficial validation step).
+  * Each release includes release notes, and a CSV catalog of the files in the release.
+  * The SPICE data used in a publication have to be cited properly. How to do this is explained in the release notes.
-SOAR (and institute mirrors):
+SOAR:
   * [[https://soar.esac.esa.int/|SOAR]] ([[https://issues.cosmos.esa.int/solarorbiterwiki/display/SOSP/SOAR+(Solar+Orbiter+Archive)+-+How+to+Use|how to use it]])
+  * SOAR has a TAP interface that can be used for automated queries ([[https://www.cosmos.esa.int/web/soar/tables-views-and-columns|documentation of available tables]])
+  * The ''sunpy-soar'' [[https://github.com/sunpy/sunpy-soar/|Python module]] uses this TAP interface for queries through SunPy/Fido
+    * Only queries by instrument / time / level / product [[https://github.com/sunpy/sunpy-soar/issues/46|at the moment]]
 Quicklooks:
   * Quicklook archive (to be developed)
   * [[https://github.com/ITA-Solar/solo-spice-ql/wiki/spice_xfiles|Quicklooks in SSW]]
+  * [[https://git.ias.u-psud.fr/spice/pre-analysis/|Pre-analysis]] (per STP)
-In the future: VSO. VSO through SSW or sunpy. Sunpy/Fido
+VSO:
+  * (in the near future)
+  * Accessible through IDL/SSW and Python/Fido
+===== Tips and Advice on Analyzing SPICE Data =====
+==== Doppler Maps ====
+WARNING: Doppler maps created from SPICE lines show unusual patterns that we believe are due to the point spread function of the instrument. Work is underway on a deconvolution procedure that will correct for this effect. If you need advice on features you see in a Doppler map, please contact the SPICE PI at frederic.auchere -at- universite-paris-saclay.fr or another member of the SPICE team.
+==== Burn-in Effects ====
+The SPICE detectors have microchannel plates (MCPs). Over time, the sensitivity of MCPs decreases at the locations of strong emission lines. This effect is referred to as "burn-in" and results in a flat-top or "self-reversal" to the line profile. This has already been noticed for the C III 977 line. The SPICE team plans to provide a correction to this effect once it is fully characterized.
+==== Flare lines ====
+The two key flare lines for SPICE are:
+  * Fe XVIII 974.86Å, formed around 7MK. It is located between the stronger H I 972.54Å (Lyman-gamma) and C III 977.02Å lines, but measurements are possible in flares, and are probably also possible in bright active region cores.
+  * Fe XX 721.56Å, formed around 10MK. It lies close to Fe VIII 721.26Å. One can estimate the strength of this line by comparing with Mg IX 706.06Å. The latter will be about a factor 10 stronger.
+To determine if a flare is occurring at the time of a SPICE observation, please check [[https://datacenter.stix.i4ds.net/view/plot/lightcurves|the STIX Data Browser]].
 ===== Access data =====
@@ Line 60: / Line 105: @@
 ===== Read and display data (IDL) =====
-External links:
+Detailed information about the IDL data analysis software is available at [[https://github.com/ITA-Solar/solo-spice-ql/wiki|https://github.com/ITA-Solar/solo-spice-ql/wiki]].
-  * Oslo's quicklook tools [[https://github.com/ITA-Solar/solo-spice-ql/wiki|spice_data, spice_object...]]
-  * Peter Young's [[https://pyoung.org/spice/analysis_guide.html|SPICE Analysis Guide]]
+Some additional information is given below.
 ==== Environment variables ====
-Choose a location to store your SPICE data (e.g., '/my_data/spice') and then point the environment variable ''$SPICE_DATA'' to it:
+Choose a location to store your SPICE data (e.g., '/my_data/spice') and then point the environment variable ''$SPICE\_DATA'' to it:
-''setenv,'SPICE_DATA=/my_data/spice'
+''setenv,'SPICE\_DATA=/my\_data/spice'
 ''
-This line should be added to your IDL_STARTUP file.
+This line should be added to your IDL\_STARTUP file.
-Data are organized under ''$SPICE_DATA'' with a year/month/day subdirectory structure. See the "Ingesting downloaded data" section below.
+Data are organized under ''$SPICE\_DATA'' with a year/month/day subdirectory structure. See the "Ingesting downloaded data" section below.
@@ Line 81: / Line 124: @@
 The SPICE catalog can be accessed by doing:
-''IDL> spice_cat''
+''IDL> spice\_cat''
-Use the "SPICE_GEN_CAT" button to make sure you have the most up-to-date list.
+Use the "SPICE\_GEN\_CAT" button to make sure you have the most up-to-date list.
 ==== Reference data-sets ====
@@ Line 97: / Line 140: @@
 The first true science observations were obtained during 18 to 22 November 2020. For example, an active region can be seen in the raster beginning 19:57 UT on 18-Nov-2020.
+An M-class flare was captured with SPICE during observations on 2 April 2022 [[https://ui.adsabs.harvard.edu/abs/2023arXiv230702396J/abstract|(Janvier et al., 2023, A&A)]]. A sequence of 15-min cadence large rasters was run for most of the day and the flare can be seen in the raster beginning 13:15.The same active region complex produced a number of other, smaller flares during 1-4 April.
 ==== Ingesting downloaded data ====
-After you have downloaded some SPICE FITS files, you can ingest them into your data directory with spice_ingest:
+After you have downloaded some SPICE FITS files, you can ingest them into your data directory with spice\_ingest:
-''IDL> spice_ingest, files''
+''IDL> spice\_ingest, files''
-This routine automatically creates the sub-directory structure (year/month/day) within $SPICE_DATA for the files.
+This routine automatically creates the sub-directory structure (year/month/day) within $SPICE\_DATA for the files.
 ==== Finding and reading a FITS file ====
-Once a file has been ingested, then you can find it with spice_find_file using the observation time:
+Once a file has been ingested, then you can find it with spice\_find\_file using the observation time:
-''IDL> file=spice_find_file('28-may-2020 16:05')''
+''IDL> file=spice\_find\_file('28-may-2020 16:05')''
 A file can be read into an IDL object with:
-''IDL> d=spice_object(file)''
+''IDL> d=spice\_data(file)''
+==== Extracting information from the data object ====
+The table below gives some methods for extracting information out of the data object. Where "i" is given, it means the index of a wavelength window should be specified (indices begin at 0).
+You can get a list of all methods by doing:
+IDL> d->help
+^ Command                        ^ Function                               ^
+| d->get\_number\_windows()      | No. of spectral windows                |
+| d->get\_window\_data(i,/load)  | Extract a data window                  |
+| d->get\_lambda\_vector(i)      | Get wavelength vector for the window                  |
+| d->get\_header(i)              | Extract a data window header           |
+| d->get\_window\_id(i)          | Get the data window ID                 |
+| d->get\_start\_time()          | Start time of observation              |
+| d->get\_end\_time()            | End time of observation                |
+| d->get\_sit\_and\_stare()      | Set to 1 if sit-and-stare observation  |
+| d->get\_number\_exposures()    | Number of exposures in raster          |
+| d->get\_xcen(i)                | Get the X-center for the window        |
+| d->get\_ycen(i)                | Get the Y-center for the window        |
+==== Quicklook tools ====
+A set of five widget-based tools are available for browsing SPICE data, and these can be accessed through spice\_xfiles:
+'' IDL> spice\_xfiles''
+This allows you to select a FITS file from your SPICE data directory. A new widget appears from which you can then select one of the five quicklook tools: Detector, Raster Browser, Raster, Whisker and Intensity map. These tools mimic software that were available for EIS and IRIS.
+For further details, please visit the [[https://github.com/ITA-Solar/solo-spice-ql/wiki|SPICE Quicklook and Data Analysis Software Page]].
+=== Raster Browser ===
+This is useful for browsing the 3D data cubes from SPICE rasters. In addition to being called from spice\_xfiles (see above), it can also be called directly from the command line:
+''IDL> spice\_raster\_browser,file''
+Use a 3-button mouse to browse the images and spectra: the middle button allows you to select a new pixel, the left button zooms in and the right button zooms out.
+===== Ephemeris information =====
+You can access ephemeris information from the SPICE headers. For example, the keywords:
+DSUN\_AU - distance of the spacecraft from the Sun in AU\\
+EAR\_TDEL - light travel time from the spacecraft to Earth (seconds)
+The full list of keywords is given in the [[https://spice.ias.u-psud.fr/spice-data/documents/SPICE-UIO-DPDD-0002-1.4-Data_Product_Description_Document.pdf|DPDD]] - search for "Solar ephemeris keywords".
+Users should make sure to correct the SPICE observing times for EAR\_TDEL in order to compare with observations from Earth-orbiting spacecraft. This is especially important for highly-dynamic structures such as flares or CMEs.
 ===== Read and display data (Python) =====
@@ Line 130: / Line 228: @@
 Known instrumental artefacts: see release notes.
+==== Change of radiometric calibration with time ====
+The SPICE calibration pipeline applies the same radiometric calibration to all of the SPICE data, irrespective of the time it was taken. However, the SPICE team has found that the instrument sensitivity decreased by a factor 2-3 in the first two years of the mission and has remained constant since then. The SPICE team is characterizing these changes and they will be incorporated into the SPICE pipeline. Until then, users should be careful about comparing emission line radiances at different times during the mission.
+==== Units and uncertainties ====
+The data cube (returned by the object method get\_window\_data) of the SPICE level-2 files contains spectral radiances in units of W/m^2/s/sr/nm. The wavelength vector has units of nm. To convert a radiance in W/m^2/s/sr to erg/cm^2/s/sr, it is necessary to multiply by 1000.
+Uncertainties on the spectral radiances are not provided directly but will be obtained through an IDL procedure. This is not currently available (as of July 2023). However, Appendix B of [[https://ui.adsabs.harvard.edu/abs/2023A%26A...673A..82H/abstract|Huang et al. (2023, A&A, 673, A82)]] gives a method for deriving uncertainties using information in the level-2 file header and this is  recommended for SPICE users.
 ==== Line fitting ====
-TBW
+=== Using EIS fitting software for SPICE ===
+The routine spice\_getwindata returns a "windata" structure in a form compatible with the eis\_auto\_fit suite of routines for Hinode/EIS. Further information on these routines is given in [[https://doi.org/10.5281/zenodo.6339584
+|EIS Software Note 15]]. The mask spectra fitting routines (Case 2 in the document) do not currently work with SPICE, however.
+The EIS software enable a number of operations to be performed on windata structures, as described in [[https://sohoftp.nascom.nasa.gov/solarsoft/hinode/eis/doc/eis_notes/21_WINDATA/eis_swnote_21.pdf|EIS Software Note 21]]. For example, eis\_bin\_windata allows spatial binning of the rasters.
+If you have problems running the EIS software on SPICE data, please contact [[https://science.gsfc.nasa.gov/sed/bio/peter.r.young|Dr. Peter Young]].
+=== Line window width and spectral tilt ===
+The SPICE slits are tilted with respect to the detector axes, an effect that is corrected in the level-2 SPICE files. That is, the emission line is aligned to the detector y-axis in the level-2 data, but the image of the window is seen to be tilted (see images below). The maximum window width for unbinned data is 32 wavelength pixels. The spectrum tilt is about 10 pixels from bottom-to-top for the SW data and about 5 pixels for the LW data. In the corrected data, the wavelength window is tilted to the right (going from bottom to top) for the LW channel, and to the left for the SW channel.
+{{ :data:plot_tilt_example.png?500 |}}
+A consequence of the tilt is that the amount of continuum on the sides of an isolated emission line varies along the slit. For, e.g., Ne VIII 770 in the SW channel, there is relatively little continuum on the right side of the profile at the top of the slit, and relatively little on the left side at the bottom of the slit. If you use an automatic fitting routine for a SPICE raster, you may find bad fits at the top and bottom of the slit because of this effect. The routine will struggle to find a good continuum measurement. Forcing the continuum to be uniform can be a good solution.
+A further problem is when a window contains more than one line, which makes  it more difficult to estimate a continuum level. For example, N IV 765.15 has a weak blend on the short-wavelength side (N III 764.35). At the top of the slit there may not be enough continuum for a good fit, while at the bottom of the slit there may not be enough pixels to accurately fit the blending line.

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