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THEMIS Science Software Training Software − 1 UCLA, July 25, 2007
Science Software – v2.00 TrainingUCB, UCLA and Colorado
July 23 – July 27, 2007
THEMIS Science Software Training Software − 2 UCLA, July 25, 2007
Agenda
Agenda09:00 Welcome and Logistics D. King09:15 Probe and Science Status V. Angelopoulos 09:30 Web Site Review
All Except Software and Help V. Angelopoulos Software and Help D. King
10:00 Themis Data Analysis Software K. Bromund10:45 Graphical User Interface (GUI) J. McTiernan11:15 V2.00 Software Status Report V. Angelopoulos 11:25 Summary and Action Items D. King
------- Break for Lunch ---------
1:00 Software / IDL Setup Team Software / IDL Command Line Demo K. Bromund
Software / IDL GUI Demo J. McTiernan 3:45 Wrap-up D. King
THEMIS Science Software Training Software − 3 UCLA, July 25, 2007
Welcome
Welcome and Logistics• Morning and Afternoon Sessions
• THEMIS Beta and Official Web Sites• Initial Release – v2.00
• Scientists Enhancing Software
• Action Items and Summary
• Your Feedback and Suggestions
THEMIS Science Software Training Software − 4 UCLA, July 25, 2007
THEMIS Data Analysis Software
K Bromund
SP Systems Inc./NASA/GSFC
M Davis, D Larson, H Frey, J Bonnell, J McTiernan, J Lewis, D King, V Angelopoulos – UC Berkeley
K Ramer, P Cruce, H Schwarzl – UCLA
E Georgescu – MPE
P Robert, O LeContel– CETP
B Jackel, E Donovan – Calgary
THEMIS Science Software Training Software − 5 UCLA, July 25, 2007
Overview• Software Objectives
– Powerful, Flexible Command Line Interface– GUI to provide Easy Access to Key Features
• Software Installation• Data Distribution• Key Routines, crib sheets.• Examples
Overview
THEMIS Science Software Training Software − 6 UCLA, July 25, 2007
Software Objectives
• Code is available to everyone, but not required to analyze data.
• IDL based (library of routines –but no main program!).• Command driven.• Separates the tasks of:
• Reading files.• Manipulating data• Plotting
• Platform independent. Works on:• Solaris• Linux• Windows• MacOSx
THEMIS Science Software Training Software − 7 UCLA, July 25, 2007
Software Design• Implements automatic file retrieval
• Given time interval and data type as input • Relies on well defined directory structure. • Automatic WEB download to local directory cache.
• All data is easily “loaded”, “manipulated” and “plotted”.• Level 2 Data Loaded by default• Option to Load Level 1 data
• Can be loaded directly in 'raw' or 'calibrated' format.• Calibration routines can be called separately from Load
routines.• Able to compare calibrated with raw data.• Goal: keywords to load routines control processing
parameters.• Software maintains variables (data quantities) and associated
metadata.• Command line interface commands are building blocks usable
for batch mode processing and/or GUIs.
THEMIS Science Software Training Software − 8 UCLA, July 25, 2007
System Requirements
IDL Patch Recommended• http://cdf.gsfc.nasa.gov/html/cdf_patch_for_idl6x_new.html• Required for IDL 6.2 and below• Required for Intel Mac, regardless of IDL version
For Mac, system configurations are required to run IDL• X11 – may need to be installed.• mouse click-through
– one-time X11 configuration necessary for proper operation:
defaults write com.apple.x11 wm_click_through -bool true
– see User's Guide for full instructions.
THEMIS Science Software Training Software − 9 UCLA, July 25, 2007
Configuring the Software
Set up the IDL path • Windows and IDLDE on any platform:
File->Preferences Path TabPress InsertBrowse to find your installation and then select the ‘idl’ directoryCheck the box preceding the path to 'search subdirectories'
• UNIX-like systems (Mac OS X, Linux, Solaris)setenv IDL_BASE_DIR /path/to/tdas_2_00da0/idlsource $IDL_BASE_DIR/themis/setup_themis
Download the User's Guide For More Information: ftp://apollo.ssl.berkeley.edu/pub/THEMIS/3 Ground Systems/3.2 Science Operations/Science Operations Documents/Software Users Guides/
THEMIS Science Software Training Software − 10 UCLA, July 25, 2007
Data Definitions
The software operates on Level 1 and Level 2 data.
Data Level Definitions:
Level 0 Data – • Raw files (*.pkt) one per APID.
• Only used for loading ESA data.
Level 1 Data -• CDF (Common Data Files) files (*.cdf)
• Contain raw, uncalibrated data. i.e. counts, DAC units.
• Used primarily by instrument scientists.
• Typically requires software to interpret.
Level 2 Data• CDF files – contain physical quantities
• Available for most instruments/data quantities
THEMIS Science Software Training Software − 11 UCLA, July 25, 2007
Data / Directory structure
• Data Directory structure is large! (scores of files per day)• Directory hierarchy keeps directory sizes manageable• Software performs automatic file retrieval.• Software maintains directory hierarchy.
• Behavior of Automatic File Retrieval is configurable• Can be set to ‘No Download’ or ‘No Update’ mode
• Root directory of local copy of hierarchy determined automatically, but configurable.
• GUI and Command Line share same local file cache and configurations.– thm_ui_config IDL widget – 'Config' button in the thm_gui IDL widget. – Environment variables
THEMIS Science Software Training Software − 12 UCLA, July 25, 2007
Primary RoutinesLoad Routine SummaryName Description L0 L1
raw calibratedL2
thm_load_asi All-Sky Imager. * -thm_load_ask All Sky Keogram * -thm_load_efi Electric Fields Instrument waveforms * (*)thm_load_esa ElectroStatic Analyzer *thm_load_esa_pkt ElectroStatic Analyzer *thm_load_fbk Fields Filter Bank * * *thm_load_fft On-board Fields Fast Fourier Transform. * *thm_load_fgm Flux Gate Magnetometer waveforms * * *thm_load_fit On-Board Fields Spin-Fit * * -thm_load_gmag Ground Magnetometer *thm_load_hsk Housekeeping *thm_load_mom On-board Particle Moments * (*)thm_load_scm Search Coil Magnetometer waveform * (*)thm_load_sst Solid State Telescope * - *thm_load_state Orbit and Attitude v2
Notes:(*) calibration routine available but still under development- data reduction and analysis routines available: see crib sheet
THEMIS Science Software Training Software − 13 UCLA, July 25, 2007
Primary Routines
Usage Conventions:Use keywords to determine functionality
calibrationcoordinate transformation
datatype and probe keywords determine what data is loaded and/or created through calibration process
/get_support_data keyword to load support data required by thm_cal* and thm_cotrans routines.
Examplethm_load_state, probe = 'a', /get_support_datathm_load_fgm, probe='a', coord='gsm', datatype='fgl',
type='calibrated'
THEMIS Science Software Training Software − 14 UCLA, July 25, 2007
Primary Routines
Calibration Routines• thm_cal_efi• thm_cal_fbk• thm_cal_fit• thm_cal_fgm• thm_cal_scm• thm_cal_mom
• Calibration can be called separately from thm_load routine when raw data is loaded
• for other instruments, see examples in crib sheet.
THEMIS Science Software Training Software − 15 UCLA, July 25, 2007
Primary Routines
Coordinate Transformations• thm_cotrans
– transforms to/from any of the following coordinate systems in a single call
– updates metadata in output.– knows coordinate system of input from metadata
• Currently Supported Coordinate Systems– SPG Spinning Probe Geometric– SSLSpinning SunSensor L-vectorZ– DSLDespun SunSensor L-vectorZ– GEI Geocentric Equatorial Inertal– GSE Geocentric Solar Ecliptic– GSM Geocentric Solar
• Example– thm_load_state, /get_support_data– thm_cotrans, 'th?_fg?', out_coord='gsm'
THEMIS Science Software Training Software − 16 UCLA, July 25, 2007
Primary Routines
Plotting• tplot• tplot_names• tlimit• tlimit, /full• tlimit, /last• ctime, t• get_data• store_data• tr = timerange(/current)• etc.
Data Processing– tdegap– tdeflag– wav_data – dpwrspec– etc.
Exporting– tplot_ascii– makepng– makegif– tplot_save– tplot_restore
THEMIS Science Software Training Software − 17 UCLA, July 25, 2007
Variable Names
Probe specification. Example: tha• a – can be one of [a-e] specifies probe
Particle data. Example: tha_peif• p – particles• e – ESA s – SST• f – full, r – reduced, m – moments (slow survey), b – burst
FGM data. Example: tha_fgl• l – low telemetry rate, h – high telemetry rate, e – engineering
decimated high rate, s – slow survey spin fit.Electric Fields and SCM. Example: tha_efs
• ef - efi, sc – scm, fb – fbk, ff – fft• s – slow survey spin fit, f – fast survey, p – particle burst, w –
waves burst.Wildcards accepted in names when plotting and data
processing:• th?_fg?• th[ab]_fg[lh]• th?_state*
THEMIS Science Software Training Software − 18 UCLA, July 25, 2007
Crib Sheets
thm_crib_asi
thm_crib_efi
thm_crib_esa_da
thm_crib_esa_moments
thm_crib_export
thm_crib_fbk
thm_crib_fft
thm_crib_fgm
thm_crib_fitthm_crib_gmagthm_crib_momthm_crib_scmthm_crib_sstthm_crib_statethm_crib_tplotthm_map_examples
Crib Sheets for Loading, Processing and Plotting
.run thm_crib_asior cut and pasteor copy and modify for your own use
THEMIS Science Software Training Software − 19 UCLA, July 25, 2007
Command Line Example 1
– To load data:» timespan,'6-10-2',2,/days
» thm_load_gmag,site=’ccnv’
– To plot data:» tplot,’thg_mag_ccnv’
THEMIS Science Software Training Software − 20 UCLA, July 25, 2007
Command Line Example 2
– Wavelet transform on an interval of interest
– Define and display the interval» Tr = ['2006-10-2/16:00','2006-10-3/05']
» timebar,tr
– Split the 3-vector into components:» split_vec,'thg_mag_ccnv'
– Compute transform of one component» wav_data,'thg_mag_ccnv_x',/kol
$ ,trange=tr ,maxpoints=24l*3600*2
– Set color limits (log scale)» zlim,'*pow', .0001,.01,1
– Plot it.» tplot,'*ccnv_x*',trange=tr
THEMIS Science Software Training Software − 21 UCLA, July 25, 2007
Command Line Example 3
thm_crib_esa_da
data analysisof ESA electronspectra and distributions:
THEMIS Science Software Training Software − 22 UCLA, July 25, 2007
Graphical User Interface
The GUI is an IDL command you can run from the IDL command line:
IDL> thm_gui
Can select data for loading, calibration, processing, and plotting.Can save the history of processing.
Data loaded with GUI can be manipulated from command line, and vice versa
THEMIS Science Software Training Software − 23 UCLA, July 25, 2007
The THEMIS Graphical User Interface
J. McTiernan23-Jul-2007
http://ssl.berkeley.edu/~jimm/themis/thm_gui.ppt
THEMIS Science Software Training Software − 24 UCLA, July 25, 2007
IDL> thm_gui
Called from IDL command line.
Gives the ability to load and plot data, and also some data processing tasks.
Calls various TPLOT routines
IDL functions are available from command line when widget is up.
Find this document: http://ssl.berkeley.edu/~jimm/themis/thm_gui.ppt
THEMIS Science Software Training Software − 25 UCLA, July 25, 2007
Main Widget:
THEMIS Science Software Training Software − 26 UCLA, July 25, 2007
Choose Data to Load:
Click here for FGM dataClick here for FGM data
THEMIS Science Software Training Software − 27 UCLA, July 25, 2007
Data choice window:
Nothing will happen Nothing will happen until you click hereuntil you click here
THEMIS Science Software Training Software − 28 UCLA, July 25, 2007
Choices show up in History Window:
Click here to clear choices.Click here to clear choices.
THEMIS Science Software Training Software − 29 UCLA, July 25, 2007
Load Data:
Click here to load.Click here to load.
THEMIS Science Software Training Software − 30 UCLA, July 25, 2007
Oops, Nothing happens unless you choose a time rangeOops, Nothing happens unless you choose a time range
Click Here to choose times.Click Here to choose times.
THEMIS Science Software Training Software − 31 UCLA, July 25, 2007
Time Range Window:
You can type here. You can type here.
Initially times are set to Initially times are set to
1970-01-01/00:00:001970-01-01/00:00:00
Times show up in history as you type.Times show up in history as you type.Click here for a time selection Click here for a time selection widgetwidget
THEMIS Science Software Training Software − 32 UCLA, July 25, 2007
Time selection widget:
THEMIS Science Software Training Software − 33 UCLA, July 25, 2007
Selection shows up in the History:
Now you can load data.Now you can load data.
THEMIS Science Software Training Software − 34 UCLA, July 25, 2007
After loading, All data is “active”.After loading, All data is “active”.
State data has been loaded automatically for FGM.State data has been loaded automatically for FGM.
THEMIS Science Software Training Software − 35 UCLA, July 25, 2007
Setting Active Data:
Type a string, or click to set data to “active”Type a string, or click to set data to “active”
THEMIS Science Software Training Software − 36 UCLA, July 25, 2007
What next?
Coordinate transformCoordinate transform Data ProcessingData Processing Plotting.Plotting.
THEMIS Science Software Training Software − 37 UCLA, July 25, 2007
Coordinate Transform:Click one of these to choose Click one of these to choose output coordinates.output coordinates.
Shows current transformShows current transform
Click here to do the Click here to do the deed.deed.
Message window: this will show Message window: this will show warnings, errors, and progress.warnings, errors, and progress.
THEMIS Science Software Training Software − 38 UCLA, July 25, 2007
Clicked on GEI, and Transform Button:
THEMIS Science Software Training Software − 39 UCLA, July 25, 2007
Back on the main widget:
New “active” data. Remember – only active data is processed.New “active” data. Remember – only active data is processed.
THEMIS Science Software Training Software − 40 UCLA, July 25, 2007
Plot Widget: If there is active data, plot pops up first.
THEMIS Science Software Training Software − 41 UCLA, July 25, 2007
Plot Widget: Setting “PNG”
Click hereClick here
Click hereClick here
File shows up in File shows up in working dir.working dir.
Remember to click on SCREEN to return to screen plots
THEMIS Science Software Training Software − 42 UCLA, July 25, 2007
Check History:
These are the IDL commands used.These are the IDL commands used.
THEMIS Science Software Training Software − 43 UCLA, July 25, 2007
Data Processing (dproc) widget:
THEMIS Science Software Training Software − 44 UCLA, July 25, 2007
Data Processing (dproc) widget:
Deletes Deletes Active Data.Active Data.
THEMIS Science Software Training Software − 45 UCLA, July 25, 2007
After dpwrspec button: (and time limits button)
*For some time ranges, this crashes in the IDL POLY_FIT routine, due to a singular matrix detected.
THEMIS Science Software Training Software − 46 UCLA, July 25, 2007
Note new “active” data:
These processes reset the “active” data.These processes reset the “active” data.
THEMIS Science Software Training Software − 47 UCLA, July 25, 2007
Other Stuff:
Click here for an overview plot:Click here for an overview plot:
THEMIS Science Software Training Software − 48 UCLA, July 25, 2007
Sample Overview Plot:
THEMIS Science Software Training Software − 49 UCLA, July 25, 2007
Other Stuff:
Click here to save history. Here to clear historyClick here to save history. Here to clear history
THEMIS Science Software Training Software − 50 UCLA, July 25, 2007
HELP Widget:
This has descriptions of This has descriptions of all of the buttons and all of the buttons and windows in the widgets.windows in the widgets.
THEMIS Science Software Training Software − 51 UCLA, July 25, 2007
Error Widget:
This should pop up This should pop up automatically if there is a crash. automatically if there is a crash. Also you can get this by Also you can get this by clicking the ERROR button on clicking the ERROR button on the main widget. the main widget.
You can edit this form, and You can edit this form, and please save this and email it to: please save this and email it to: [email protected]
Also email a saved history file Also email a saved history file and any other pertinent and any other pertinent information that can be cut and information that can be cut and pasted from the IDL window.pasted from the IDL window.
THEMIS Science Software Training Software − 52 UCLA, July 25, 2007
Configuration Widget: Allows configuration to be changed, saved.
Saves in a file. Saves in a file. Input into every Input into every session session
Resets to Resets to initial state.initial state.
Resets to default state in distribution, deletes Resets to default state in distribution, deletes any saved files.any saved files.
Messages:Messages:
You need to be able to You need to be able to write to this directory if write to this directory if you download data.you download data.
THEMIS Science Software Training Software − 53 UCLA, July 25, 2007
Exit Button:
Click here to exit GUI. Popups are dismissed, except for Help, Error or Config. Loaded data is not Click here to exit GUI. Popups are dismissed, except for Help, Error or Config. Loaded data is not deleted – will show up in Loaded Data window on restart (but not in Active Data).deleted – will show up in Loaded Data window on restart (but not in Active Data).
THEMIS Science Software Training Software − 54 UCLA, July 25, 2007
THM_GUI Tips:
Remember to save and email your history file if you have a bug. Also feel free to include any other output messages that show up in the IDL command line.
Always choose a time range before loading data. Don't load more than a couple of days at a time, or a couple of hours if you are loading full resolution all-sky imager (asf) data.
The choice of "probe" in the data loading widgets is global, that is, all of the selected data will be loaded for the probe(s) chosen most recently. If, for example, you want to load EFI data from probe "A" and FGM data from probe "B", you will need to load these separately. When choosing multiple probes, data types, or whatever, hold the "control" key, and click more than one. Also, you can click on an option, then hold "shift" and the left mouse button, and drag the cursor over the others.
The data names are kind of cryptic, there is a table in the User's Guide and also at the end of the text in the help widget for guidance.
THEMIS Science Software Training Software − 55 UCLA, July 25, 2007
THM_GUI Tips:
Once you've chosen data, hit the "Clear Load Queue" to clear it out if you don't want to load it. If a load fails (for a reason other than "the data isn't there"), then the data are still waiting to be loaded. Clear the load queue.
Remember that all loaded data are set to "active" immediately upon loading. If you don't want all of that data to be active, then click on what you want in the Loaded Data window.
If you want to delete all data, type "*" window below the Loaded Data window, click "Set Active Data to String", call up the Data Processing widget, and click "Delete".
For coordinate transforms, data that have "Unknown" for a coordinate system will not be transformed. Multiple data sets with different input coordinates *can* be transformed. Data Processing and Plotting tasks are only possible when there is "active" data.
THEMIS Science Software Training Software − 56 UCLA, July 25, 2007
THM_GUI Tips:
When typing in strings for numerical input -- be careful. Strings that aren't numbers are interpreted as 0 by IDL, but strings that aren't numbers, but start with a number are set to the number, e.g., 'a14' is set to 0, but '1a4' is set to 1. When in doubt, look in the History.
Sometimes data is inappropriate for a given operation (especially wavelet transforms, and power spectra). We have tried to catch as many of these situations as we can, but there probably will be more as more types of data are imported. If something looks weird, save your history, and email us.
Some processes can take a while (e.g., calibrating SCM data, wavelet transforms of whole days). Currently there is no good way to stop a process except for the standard IDL "control-C" on the IDL window. This doesn't always work...
For some time ranges, the "dpwrspec" button crashes in the IDL POLY_FIT routine. We have no clue why this happens. Try changing the input time range.
THEMIS Science Software Training Software − 57 UCLA, July 25, 2007
THM_GUI Tips:
The Plot Data button first issues a "tplot" call when the widget pops up.
If you create a "PNG" plot, remember to reset to "SCREEN" for screen plotting.
Don't try to plot more than about 10 quantities at a time, if there is spectrogram data, there will be a crash.
There will undoubtedly be more of these…