MarsSI Tutorial
Contents
I.
Introduction .............................................................................................................. 1
1. MarsSI presentation .............................................................................................. 1
2. Important information............................................................................................. 1
II. Adopting MarsSI....................................................................................................... 2
1. Connection to MarsSI ............................................................................................ 2
2. MarsSI home page ................................................................................................ 2
2.1.
“Maps” tab ................................................................................................... 3
2.2.
“Workspace” tab .......................................................................................... 4
2.3.
“About” tab ................................................................................................... 5
2.4.
Exit .............................................................................................................. 5
III.
Data description .................................................................................................... 6
1. On-board the Mars Reconnaissance Orbiter spacecraft........................................ 6
1.1.
CTX images and stereos ............................................................................. 6
1.2.
HiRISE images and stereos......................................................................... 6
1.3.
CRISM observations .................................................................................... 7
2. On-board the Mars Express spacecraft ................................................................. 9
2.1.
HRSC observations ..................................................................................... 9
2.2.
OMEGA observations ................................................................................ 10
3. On-board the Mars Odyssey spacecraft .............................................................. 11
3.1.
THEMIS observations ................................................................................ 11
IV.
Proposed processing ........................................................................................... 13
1. Process a CTX image and stereos ...................................................................... 13
2. Process a HiRISE image and stereos ................................................................. 16
3. Process a CRISM observation ............................................................................ 19
MarsSI tutorial
I.
Introduction
1.
MarsSI presentation
MarsSI (Acronym for MARS System Information) is a web Geographic Information
System application which allows the managing and processing of Martian orbital data.
From this application, the users will be able to easily and rapidly select observations, to
process raw data via proposed automatic pipelines and to get back final products which
can be visualized under Geographic Information Systems like ARCGIS and QGIS.
Moreover MarsSI also proposes an automatic stereo-restitution pipeline in order to
produce Digital Terrain Models (DTM). This application is part of the ERC project eMars funded by the European Union’s Seventh Framework Programme (FP7/20072013) (ERC Grant Agreement No. 280168).
By using MarsSI, you agree to acknowledge the use of this application while publishing
results. The acknowledgement sentence has to be as follow: “Data have been
processed with the MarsSI (emars.univ-lyon1.fr) application, funded by the European
Union’s Seventh Framework Programme (FP7/2007-2013) (ERC Grant Agreement No.
280168)”.
2.
Important information
Where can I find MarsSI: emars.univ-lyon1.fr.
How can I have an account: send an email to [email protected]
I need help: send an email to [email protected]
Where can I find tutorials (e.g., available observations, proposed processing pipelines):
https://www.youtube.com/channel/UCAn2ZPUPJ6g-ZaJkiOhue7A
The acknowledgement sentence to use: Data have been processed with the MarsSI
(emars.univ-lyon1.fr) application, funded by the European Union’s Seventh Framework
Programme (FP7/2007-2013) (ERC Grant Agreement No. 280168).
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MarsSI tutorial
II.
Adopting MarsSI
1.
Connection to MarsSI
The application is opened to the scientific community via the website: emars.univlyon1.fr.
A login and a password are required. To create an account, a request has to be made
by email to Loïc Lozac’h ([email protected]).We will create for you both a
personal account on MarsSI and an FTP account to retrieve your products. A login and
a password will be emailed back to you and they are the same for the access to the
MarsSI application and to the ftp account.
Figure 1 : Connexion page
2.
MarsSI home page
There are 3 tabs corresponding to 3 environments:
● the “Maps” tab for data visualization and selection,
● the “Workspace” tab for data processing and
● the “About” tab to have more information about the application and the products.
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Figure 2 : MarsSI interface
2.1.
“Maps” tab
The “Maps tab” is composed of four windows: “Layers”, “Map tools”, “Map”, and “Cart”.
It will help you to select the observation you desire and add them to your cart for further
processing.
Figure 3 : “Maps tab” interface
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MarsSI tutorial
In the “Layers” window, you can manage all the available layers to be displayed in the
“Map” window. The first layer corresponds to the Mars Orbiter Laser Altimeter (MOLA)
global map (topography) and the second one to the THermal EMIssion Spectrometer
(THEMIS) day infrared global map. The “eye” icon enables to display the layer in the
“Map” window. The next layers correspond to the image footprints for each available
instrument from different missions including Mars Reconnaissance Orbiter (MRO), Mars
Express (MEx) and Mars Odyssey (MO). See the Section IV to have details about the
data types.
In the “Map” tool, you can manage the maps. You can zoom-in using a rectangular
feature or by clicking on an area on the “Map” window and and zoom-out. You can also
get information about the selected images by using the “Show features” button. If you
want to select an observation for your cart, you have to use the “Select” button and click
on the desired observation or click and drag on a group of observations.
If you want to search through observations based on geographic information or
attributes click on “Search”. You have different options. The first option is by geographic
information. You can draw an area using a point, line or polygon or you can zoom-in the
current selection. The second option is by attributes. Select the type of
layers/observations, an attribute which can be the target name, the id, the latitude, the
longitude, the geometric angles etc., then theoperator “contains”,“equal to” or “not equal
to” and finally the value. You can add several attributes by clicking on the plus button.
To process one or several images, you have to add them into the “Cart” window by
selecting the observation and clicking on the “Add” button. You can remove one or
several observation(s) just by clicking on it in the “Cart” window and on the “Remove”
button.
2.2. “Workspace” tab
When you are ready to process the data, click on the “Workspace” tab. The selected
footprint(s) is (are) again visible on the map window on the left and listed underneath.
On the right, there are three windows addressed for the data processing:
● the “Data to process” window,
● the “Data under processing” window and
● the “Data processed” window, from where you can copy your processed data to
your FTP.
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MarsSI tutorial
Figure 4 : “Workspace tab” interface
Choose the data which have to be processed in the “Data to process” window and click
on the “Process” button. Then the data will be visible on the “Data under processing”
window, that means that the data is processing.
Then, when the data is processed, it will be visible on the “Data processed” window. Do
not hesitate to click on the “Refresh” button to refresh the windows.
To save your final products on your FTP account when the data processing is done,
click on the “Copy” button Then you can retrieve your products via ftp://emars.univlyon1.fr.
Again, enter your name and password (same as your account to connect to MarsSI)
and download your final products. Find the right repertory corresponding to the selected
data type and download the derived products on your hard-disk.
2.3. “About” tab
In the About tab, you can find more information about MarsSI, a description of each
available data and the processing pipelines that are used by MarsSI.
2.4. Exit
To exit your session click on the “log out” button under your name on the top left side of
the screen. In any case, your MarsSI session will close automatically after some time
without activity.
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MarsSI tutorial
III.
Data description
1.
On-board the Mars Reconnaissance Orbiter spacecraft
1.1.
CTX images and stereos
The Context Camera (CTX) is a camera on board the Mars Reconnaissance Orbiter
(MRO) acquiring grayscale images at 6 meters per pixel scale over a swath 30
kilometers wide. CTX provides context images for the MRO HiRISE and CRISM
observations, is used to monitor changes occurring on the planet, and acquires
stereopairs of selected, critical science targets.
Data name example: P16_007430_1783_XN_01S083W
These raw data can be calibrated and map-projected thanks to MarsSI (see further
section).
References:
●
●
1.2.
CTX instrument description website: http://www.msss.com/all_projects/mro-ctx.php
CTX instrument description paper: Malin et al., (2007), Context Camera Investigation on board
the Mars Reconnaissance Orbiter, Journal of Geophysical Research, 112, E05S04, doi:
10.1029/2006JE002808.
HiRISE images and stereos
The High Resolution Imaging Science Experiment (HiRISE) is a telescope working in
orbit in the visible wavelengths and producing high resolution images resolving surface
details down to 1-meter size (0.25 to 1.3 m/px). The images enable to study for instance
the martian geomorphology but also seasonal surface changes.
The HiRISE camera has 3 different color filtered CCDs: red (“RED”) from 570-830 nm,
blue-green (“BG”) less than 580 nm and near-infrared (“IR”) greater than 790 nm. The
high-resolution color images enable to distinguish the composition and albedo
heterogeneities directly correlated to the geomorphology, complementary to the
mineralogic results from the CRISM, HRSC, OMEGA and THEMIS instruments. The
RED detectors provide a wide image used for geomorphologic analysis and for
stereoanalysis, while the additional detectors are used to create false-color imaging of
the central of the swath only (20% of the RED swath width).
The pipeline for the topographic mapping derived from HiRISE images uses both the
USGS ISIS system (the ISIS 3 system) and the commercial stereogrammetric software
SOCET SET. The DTMs have a 1-meter spatial resolution and 25 cm vertical precision.
For more details about the process used to create HiRISE DTMs, see Kirk, R.L. et al.
(2008).
[http://onlinelibrary.wiley.com/wol1/doi/10.1029/2007JE003000/full ].
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Data names:
❖ PSP_005000_1000_RED.JP2: grayscale mosaic of all RED-filter channels
❖ PSP_005000_1000_COLOR.JP2 IR, RED, BG 3-color product over center 20%
of the RED swath width.
Each JP2 image also has a PDS label (.lbl) providing useful information about the
observation such as map projection and viewing information.
References:
●
●
●
●
1.3.
HiRISE instrument and data website: http://hirise.lpl.arizona.edu
HiRISE DTM creation explanation: http://www.uahirise.org/dtm/about.php
HiRISE instrument description paper: McEwen, A. et al. (2007). J. Geophys. Res., 112, E05S02,
doi:10.1029/2005JE002605.
HiRISE DTM description paper: Kirk, R.L. et al. (2008). J. Geophys. Res., 113, E00A24,
doi:10.1029/2007JE003000.
CRISM observations
The Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) is a visible and
infrared hyperspectral imager, built and tested by the Johns Hopkins University Applied
Physics Laboratory under the supervision of principal investigator Scott Murchie. The
observations enable to have mineralogy information of the martian surface at a spatial
resolution of ~20 m/px.
It is composed of two spectrometers, one ranging from 362 to 1053 nm corresponding
to the visible near infrared (VNIR) range, and another from 1002 to 3920 nm
corresponding to the infrared (IR) range. In both VNIR and IR channels the
electromagnetic spectrum is sampled with a step of 6.55 nm. Each detector is a matrix
(from the focal plane) of 640x480 (spatial and spectral) elements giving acquisition scan
lines one-pixel high and 640-column wide. Each element of this line contains a data
spectrum. Because the CRISM instrument is a pushbroom scanner the hyperspectral
image is built by stacking multiple scan lines as the MRO spacecraft flies over the
target. At an altitude of 300 km, each scan line of the martian surface is about 18 m long
(the highest spatial resolution) and about 10 km across.
The CRISM instrument has two acquisition modes:
● the multispectral untargeted mode (nadir pointing). The instrument acquires
multi-spectral images using fixed pointing where the emission angle is set at 0°
(with 72 bands chosen over the 544 spectral bands, in order to identify principal
minerals). There are two types of observations using this acquisition mode
available in MarsSI depending on the spatial resolution: “Multispectral Survey”
(MSP) with 200 m/px and “Multispectral window” (MSW) with 100 m/px.
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● the hyperspectral targeted mode (multiangular pointing). The instrument tracks
the targets and takes 11 hyperspectral images (544 bands from 362 to 3920 nm)
at different emission angles due to the rotation of the detector at +- 70°: 10
hyperspectral images taken at different emission angles before and after the
central image corresponding to the close nadir image (image #07). The 10
hyperspectral multi-angular observations are reduced to a factor 10 compared to
the spatial resolution of the central image. According to the spatial resolution of
the central image, four product types are associated to this acquisition mode. If
the central image is sampled at 20 m/px, the associated product is a Full
Resolution Targeted observation (FRT). By reducing the spatial resolution of the
central image by a factor 2, the spatial resolution is set at 40 m/px and the
associated products are “Half Resolution Short” (HRS) and “Half Resolution
Long” (HRL) observations. An HRL sampled surface is twice as long as an HRS
observation. Only the central image #07 is processed by MarsSI for the
mineralogy identification.
Data names:
❖ FRT000A82E_07_DE164S_DDR1.IMG: data cube containing the ancillary data
(e.g. latitude, longitude, incidence, emission, phase angles) of the central image
(corresponding to the image “07” of the targeted sequence) of an FRT
observation in the VNIR range (from 362 to 1053 nm)
❖ FRT000A82E_07_IF164S_TRR3.IMG: calibrated data cube containing the
reflectance data (I/F unit) in the VNIR range (from 362 to 1053 nm) of the central
image (corresponding to the “07” image of the targeted sequence) of an FRT
observation
❖ FRT000A82E_07_DE164L_DDR1.IMG: data cube containing the ancillary data
(e.g. latitude, longitude, incidence, emission, phase angles) of the central image
(corresponding to the “07” image of the targeted sequence) of an FRT
observation in the IR range (from 1002 to 3920 nm)
❖ FRT000A82E_07_IF164L_TRR3.IMG: calibrated data cube containing the
reflectance data (I/F unit) in the IR range (from 1002 to 3920 nm) of the central
image (corresponding to the “07” image of the targeted sequence) of an FRT
observation
Each IMG image also has a PDS label (.lbl) providing useful information about the
observation.
Important: Since September, 2010, the inbound segment in CRISM targeted mode is
absent due to problems of the gimbal instrument. After this date, the targeted
observations with 11 eleven multiangular images are not available. Only the central
image is given.
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References:
●
●
CRISM instrument description website: http://crism.jhuapl.edu/instrument/design/overview.php
CRISM instrument description paper: Murchie, S., et al. (2007), J. Geophys. Res., 112, E05S03,
doi:10.1029/2006JE002682.
2.
On-board the Mars Express spacecraft
2.1.
HRSC observations
The High Resolution Stereo Camera (HRSC) onboard the Mars Express spacecraft is a
multi-channel stereo color camera, with the purpose of completing global imagery of
Mars in panchromatic and color images, and of providing systematic stereo-imagery for
DTM production. The HRSC camera produces multiple data products for each
observation: 5 panchromatic images taken at 5 different emergence angles, upon which
the nadir channel, and 4 images taken with 4 color filters taken at 4 different emergence
angles. The nadir image has in general a higher resolution than the other images.
This multiple data enables to produce color images and DTMs through stereorestitution
using the different viewing angles. MarsSI proposes the highest data level (level 4)
when available, and level 2 otherwize, all processed by the HRSC team. Level 4
includes DTM products and orthorectified images.
There is no proposed processing of HRSC images in MarsSI except their download.
Data names:
❖ H1950_0000_ND4.IMG: Level 4 nadir panchromatic image taken during orbit
#1950 of Mars Express.
❖ H1950_0000_IR4.IMG: Level 4 image taken with the IR channel
❖ H1950_0000_RE4.IMG: Level 4 image taken with the red channel
❖ H1950_0000_GR4.IMG: Level 4 image taken with the green channel
❖ H1950_0000_BL4.IMG: Level 4 image taken with the blue channel
❖ H1950_0000_DT4.IMG: DTM using a spherical areoid as reference
❖ H1950_0000_DA4.IMG: DTM using an ellipsoidal areoid as reference
The four non-nadir panchromatic images are also available as level 2 products.
References:
●
●
HRSC instrument description website: http://sci.esa.int/mars-express/34826design/?fbodylongid=1597
HRSC instrument description papers:
- G. Neukum, R. Jaumann, and the HRSC Co-Investigator and Experiment Team, HRSC: The
High Resolution Stereo Camera of Mars Express, in Mars Express: The scientific payload, edited
by A. Wilson, pp. 17-35, ESA, Noordwijk, The Netherlands, 2004.
- R. Jaumann et al.: The High Resolution Stereo Camera (HRSC) Experiment on Mars Express:
Instrument Aspects and Experiment Conduct from Interplanetary Cruise through Nominal
Mission, Planetary and Space Science, 55, 928-952, 2007.
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2.2.
OMEGA observations
OMEGA, the Observatoire pour la Minéralogie, l’Eau, les Glaces et l’Activité (Bibring et
al., 2004), is a visible and near-infrared imaging spectrometer onboard ESA’s Mars
Express (MEx) spacecraft, which has been operating in Mars orbit since 12/2003.
OMEGA covers the wavelengths 0.38-5.1 µm with 352 spectral channels, 7 to 20 nm
wide. Spatial resolution varies from ~300 m to 5 km per pixel depending on the
spacecraft altitude at the time of acquisition. OMEGA’s Signal-to-Noise ratio (or ‘S/N’) is
better than 100 over the whole spectral range (and can reach 1000 for some spectels),
allowing detection of absorption bands as shallow as ~1 %.
The OMEGA instrument actually consists of two co-aligned grating spectrometers, one
working in the visible and near infrared (VNIR) in the range 038-1,05 µm, the other in
the short wavelength infrared (SWIR) in the range 0.93-5.1 µm. The VNIR spectrometer
builds images in a “pushbroom” mode with a two-dimensional detector, with 96
elements in the spectral dimension. The SWIR spectrograph builds images in a
“whiskbroom” mode with two 128-element line detectors over the wavelength ranges
0.93-2.73 µm (SWIR-C) and 2.55-5.1 µm (SWIR-L). A moving mirror generates images
either 16, 32, 64 or 128 pixels wide depending on the altitude and speed of the
spacecraft relative to Mars: the lower the altitude, the faster the spacecraft and the
narrower the images in order to yield contiguous pixels with a sufficient integration time
on each of them. MEx orbit is indeed highly elliptical, which yields various observation
conditions, with wide coverage at coarse spatial resolution from high altitude or finer
spatial resolution but narrow coverage from low altitude, closer to periapsis. The secular
precession of MEx orbit since mission start has allowed observation of most of the
planet from various altitudes and at various local times. As a consequence, OMEGA
observations have various spatial resolutions, various widths and have been obtained
under various incidence and emission conditions. This particularity, notably with respect
to most other datasets from spacecraft in heliosynchronous low mars orbit, has to be
taken into account.
The first hierarchical sorting of the OMEGA data archive is the splitting in various
‘missions’ corresponding to the nominal science phase of MEx (Nom) and to 4
successive mission extensions (Ext1 to Ext4). In each ‘mission’, OMEGA data are
sorted by MEx orbit number and observation number in each orbit. Each observation is
archived as 2 binary files with plain-text headers at file beginning: a ORBNN/
ORBNNYY_X.QUB file with raw science data at the so-called ‘Level-1B’
(uncompressed, uncalibrated raw digital numbers issued from the detectors), and a
GEMNN/ORBNNYY_X.NAV file holding geometrical observation parameters such as
incidence angle, latitude and longitude, etc. (NNYY is orbit number, in decimal format
up to 9999, then NN in hexadecimal format and YY in decimal format, eg. ‘BA32’; and X
is observation number of orbit NNYY). A sequence of observations from one orbit
typically starts (resp. ends) with a wide image at low spatial resolution taken from high
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altitude toward (resp. from) narrower images at higher spatial resolution taken closer to
periapsis, ie. from low altitude.
Before OMEGA data can be used for science it must be processed to the so-called
‘Level-2’, which is calibrated radiance (in physical units: W.m -2.sr-1.µm-1) or reflectance
(‘I/F’), which is radiance divided by the solar irradiance at Mars at the time of
observation. Reflectance SWIR-C data to be used for spectral analysis of the surface
can further be processed to remove (most of) the atmospheric CO 2 absorptions using
the so-called ‘volcano-scan’ correction (eg. Bibring et al., 1989; Mustard et al., 2005).
One final caveat to consider in using OMEGA data is the evolution of the instrument
during the course of the nominal and successive extended missions. Several issues
incrementally arose during the life of the instrument, mostly in the SWIR-C channel: the
sensitivity of some spectels increased or decreased (‘hot’ and ‘cold’ spectels), which
was mitigated by modifying their transfer function in the calibration, but some of those
spectels eventually failed, resulting in an incremental loss of exploitable channels with
time, mostly in the SWIR-C channel. Eventually the whole SWIR-C channel failed in
~2010. These artifacts, along with others, which arose in some observation modes,
were mitigated by a continuously evolving pipeline of calibration from Level-1B to Level2 data. The calibration pipeline from Level-1B data to Level-2 is not yet available in
MarsSI but will eventually be implemented when confidence in the product quality is
deemed sufficient.
Important: please be advised that without the proper calibration routine to Level-2
(available from IAS) OMEGA data as available in ESA’s PSA or in MarsSI cannot
readily be used.
For more information on OMEGA instrument and data, check-out the OMEGA
Experiment Archive Interface Control Document available from ESA’s Planetary
Science Archive (http://www.sciops.esa.int/index.php?project=PSA&page=mex):
ftp://psa.esac.esa.int/pub/mirror/MARS-EXPRESS/OMEGA/MEX-M-OMEGA-2-EDRFLIGHT-V1.0/DOCUMENT/EAICD_OMEGA.PDF
References:
●
●
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Bibring, J.-P., et al. (2004), OMEGA: Observatoire pour la Minéralogie, l'Eau, les Glaces et
l'Activité, in Mars Express - The Scientific Payload, European Space Agency Special Publication,
SP-1240, edited, pp. 37-49, ESA.
Bibring, J. P., et al. (1989), Results from the Ism Experiment, Nature, 341(6243), 591-593.
Mustard, J. F., et al. (2005), Olivine and pyroxene, diversity in the crust of Mars, Science,
307(5715), 1594-1597.
3.
On-board the Mars Odyssey spacecraft
3.1.
THEMIS observations
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THEMIS (THermal Emission Imaging System) is a multispectral imager allowing the
analysis of the morphology, the composition and the physical properties of the Martian
surface. It has 9 channels in the thermal infrared between 6.78µm and 14.88µm and 5
channels in the visible and near-infrared between 0.42µm and 0.86µm.
There are 3 types of THEMIS data: the infrared data, at 100 m/pixel, acquired by day
and night, and the visible images, from 18 to 35 m/pixel (Christensen et al, 2004). The
infrared images are approximately 30 km large and more than 100 km long on the
surface and reached global coverage of the planet.
Data types
Spatial Res.
Number of Band Spectral Range
(TIR) THEMIS InfraRed Day
100 m/pixel
10
6.78–14.88 μm
(TIR) THEMIS InfraRed Night
100 m/pixel
10
6.78–14.88 μm
(VNIR) THEMIS visible
18-35 m/pixel
5
0.42–0.86 μm
Figure 5 : THEMIS sensors features
The nighttime’s images of THEMIS allow constraining the thermal inertia of the surface.
Those images have a higher resolution than the TES pixels (100 m/pixel versus 3
km/pixel). It allows a more local analysis than with the TES dataset. The global
coverage of the THEMIS dataset allows also a regional study at high resolution. Global
maps acquired by night and day are available.
Only Infrared THEMIS data are available for download on MarsSI. The calibration
pipeline is not yet available in MarsSI but will eventually be implemented when
confidence in the product quality is deemed sufficient. For viewing convenience, the
footprints coverage has been splitted in 4 categories:
❖ THEMIS IR Day L: Long ground track during day time for infrared sensor
❖ THEMIS IR Day S: Short ground track during day time for infrared sensor
❖ THEMIS IR Night L: Long ground track during night time for infrared sensor
❖ THEMIS IR Night S: Short ground track during night time for infrared sensor
References:
● THEMIS instrument description website:
●
http://ode.rsl.wustl.edu/moon/pagehelp/quickstartguide/index.html?themis.htm
THEMIS instrument description paper: CHRISTENSEN, Philip R., JAKOSKY, Bruce M.,
KIEFFER, Hugh H., et al.The thermal emission imaging system (THEMIS) for the Mars 2001
Odyssey Mission. Space Science Reviews, 2004, vol. 110, no 1-2, p. 85-130.
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IV.
Proposed processing
In this section, we give you an overview of proposed pipelines used for the treatment of
the CTX, HiRISE, CRISM and THEMIS observations and the procedures to generate
the derived data.
Figure 6 : Scheme representing data available on MarsSI and their derived data and processing
1.
Process a CTX image and stereos
CTX image processing: from the download, the calibration to the projection
The pipelines used for the data calibration and projection are those proposed by ISIS3
(https://isis.astrogeology.usgs.gov/index.html).
From the “Maps” tab, zoom-in on your region of interest, you can display the THEMIS
mosaic for more precision, and then display the CTX layer. You get all CTX stamps that
appear in green. The stamps are regularly updated to take into account new data. You
can use the “Select” button to choose the stamp you desire. You can choose several
stamps by clicking several stamps, or by dragging your mouse to select adjacent
stamps. You can also use the “Search” button for more options.
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To add your desired stamps to your cart click on “Add” in the “Cart” window, and go to
the “Workspace” tab. Your CTX image appears in the window “Data to process”. If not,
you may already have processed it yourself, or someone else may have processed it,
then it may already be in the “Data processed” window. If the image has not been
processed, you will have to go through several steps (cf. Figure 6):
1. Download the CTX EDR image (raw data) to the MarsSI server by clicking on the
EDR image and the “Process” button in the “Data to process” window. This will
take a few minutes.
2. When the first step is done, you can create a calibrated RDR image: click on the
proposed RDR image in the “Data to process” window and on the “Process”
button. This will take another few minutes, depending on the length of the CTX
observation.
3. Project the CTX image by processing the proposed MRDR image in the “Data to
process” window. This will take more time than the previous processes, another
few minutes.
When these different steps are done, the MRDR image is waiting for you in the “Data
processed” window and you can copy it to your FTP partition.
Data type (cf. Figure 6):
❖ EDR image: Raw image in a standard format called the Experiment Data Record
❖ RDR image: Converted raw image into reflectance (irradiance/solar flux or I/F)
called Radiometric Data Record
❖ MRDR image: Projected image from RDR image
See the tutorial here: https://www.youtube.com/watch?v=5jg_40AUFro
Output data example:
❖ EDR image file:
P16_007430_1783_XN_01S083W.IMG : NASA PDS archive file
❖ RDR image file:
P16_007430_1783_XN_01S083W _RDR.cub : ISIS3 processing file
❖ MRDR image file:
P16_007430_1783_XN_01S083W _MRDR.tif : Standard compressed Geotiff
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CTX DTMs processing: from the download to the DTM creation
The CTX DTM images created by MarsSI are generated using the NASA AMES Stereo
Pipeline (http://ti.arc.nasa.gov/tech/asr/intelligent-robotics/ngt/stereo/).
References:
●
●
Moratto, Z. M., M. J. Broxton, R. A. Beyer, M. Lundy, and K. Husmann. 2010. Ames Stereo
Pipeline, NASA's Open Source Automated Stereogrammetry Software. Lunar and Planetary
Science Conference 41, abstract #2364. [ADS Abstract].
Broxton, M. J. and L. J. Edwards. 2008. The Ames Stereo Pipeline: Automated 3D Surface
Reconstruction from Orbital Imagery. Lunar and Planetary Science Conference 39, abstract
#2419. [ADS Abstract].
From the “Maps” tab, zoom-in on your region of interest, you can display the THEMIS
mosaic for more precision, and then display the CTX stereo layer. You get all areas
where MarsSI proposes to compute a CTX DTM, appearing in yellow. The stamps are
regularly updated to take into account new data. You can use for example the select
button to choose the stamp you desire.
To add your desired stamps to your cart click on “Add” in the “Cart” window: you can
notice in the “Cart” window that three data were added, the two overlapping EDR
images that will be used, and the EDTM file that will be computed. Then go to the
“Workspace” tab.
Important: The EDTM stamps have been created automatically based on the
percentage of intersection and the difference in emission angle between the two EDR
images. Please be advised that EDTM stamps mean only possible DTMs: a viewing
validation of the EDR images should be performed from the PDS’s link available in the
footprint attribute. Atmospheric clouds for example can prevent the DTM calculation.
Your CTX images and DTM appear in the window “Data to process”. If not, you may
already have processed it yourself, or someone else may have processed it, then it may
already be in the “Data processed” window. If the images have not been processed, you
will have to go through several steps (cf. Figure 6):
1. Download the CTX EDR image (raw data) to the MarsSI server and create a
calibrated RDR image as described previously.
2. Create the DTM by processing the proposed EDTM data in the “Data to process”
window which may take few hours, depending on the length of the overlapping
images.
3. Process the proposed ALEDTM data in the “Data to process” window to align the
CTX DTM to the MOLA data. This last step should only take few minutes.
When these different steps are done, the ALEDTM is waiting for you in the “Data
processed” window and you can copy it to your FTP partition.
Data type (cf. Figure 6):
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MarsSI tutorial
❖ EDR image: Raw image in a standard format called the Experiment Data Record
❖ RDR image: Converted raw image into reflectance (irradiance/solar flux or I/F)
called Radiometric Data Record
❖ EDTM image: CTX DTM not aligned to MOLA data
❖ ALEDTM image: CTX DTM aligned to MOLA data
See the tutorial here: https://www.youtube.com/watch?v=C4PYUIKg77c
Output data example:
❖ EDTM image file:
CTX_003605_1712_035502_1679-DTM.tif (Geotiff file format)
CTX_003605_1712_035502_1679-DRG.tif (Orthoimage Geotiff file format)
❖ ALEDTM image file:
CTX_003605_1712_035502_1679-ALIGN-DTM.tif (Geotiff file format)
Additional information about AMES Stereo Pipeline products can be found in:
http://byss.ndc.nasa.gov/stereopipeline/binaries/asp_book-2.5.0.pdf
2.
Process a HiRISE image and stereos
HiRISE image processing: from the download, the calibration to the projection
The pipelines used for the data calibration and projection are those proposed by ISIS3
(https://isis.astrogeology.usgs.gov/index.html).
From the “Maps” tab, zoom in on your region of interest, you can display the THEMIS
mosaic for more precision, and then display the HiRISE layer. You get all HiRISE
stamps that appear in dark blue. The stamps are regularly updated to take into account
new data. You can use the “Select” button to choose the stamp you desire. You can
choose several stamps by clicking several stamps, or by dragging your mouse to select
adjacent stamps. You can also use the “Search” button for more options.
To add your desired stamps to your cart click on “Add” in the “Cart” window, and go to
the “Workspace” tab.
HiRISE Red and Color (RDRV11 files) projected images can be directly download to the
MarsSI server by clicking on the “Process” button in the “Data to process” window. If
you want to calibrate and project from the raw data with MarsSI and the image has not
been processed yet, follow the following steps (same as for CTX images) (cf. Figure 6):
1. Download the HiRISE EDR image (raw data) to the MarsSI server by clicking on
the proposed EDR image and on the “Process” button in the “Data to process”
window. This will take a few minutes.
2. Process the proposed RDR image in the “Data to process” window
corresponding to the calibrated image. This may take several tens of minutes.
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MarsSI tutorial
3. Project the HiRISE image by processing the proposed MRDR image in the “Data
to process” window. This may take more than an hour.
When these different steps are done, the MRDR image is waiting for you in the “Data
processed” window and you can copy it to your FTP partition.
Data type (cf. Figure 6):
❖ EDR image: Raw image in a standard format called the Experiment Data Record
❖ RDR image: Converted raw image into reflectance (irradiance/solar flux or I/F)
called Radiometric Data Record
❖ MRDR image: Projected image from RDR image
❖ RDRV11 Red and Color images : HiRISE Team calibrated and projected product
images
❖ DTM image: HiRISE Team stereo-rectified product image
Output data example:
❖ EDR image file:
PSP_005000_1000_RED[0-9]_[0-1].IMG (NASA PDS archive file format)
PSP_005000_1000_[IR/BG][10-13]_[0-1].IMG
❖ RDR image file:
PSP_005000_1000_RED_RDR.cub (ISIS3 file format)
❖ MRDR image file:
PSP_005000_1000_RED_MRDR.tif (Geotiff file format)
❖ RDRV11 image file:
PSP_005000_1000_[RED/COLOR].JP2 (JPEG2000 file format, comes with .prj
and .j2w header files)
❖ DTM image file:
DTEEC_00500_1000_00600_1000_U01.tif (Geotiff file format)
Additional information about HiRISE products can be found in:
http://hirise.lpl.arizona.edu/pdf/HiRISE_EDR_SIS_2007_03_15.pdf
http://hirise.lpl.arizona.edu/pdf/HiRISE_RDR_v12_DTM_11_25_2009.pdf
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MarsSI tutorial
HiRISE DTMs processing: from the download to the DTM creation
Some HiRISE DTMs have been generated by the HiRISE team and can be directly
downloaded to MarsSI (Layer: HiRISE team DTM - red color footprint). If not, you can
use MarsSI to generate your own HiRISE DTM image that uses the NASA AMES
Stereo Pipeline (http://ti.arc.nasa.gov/tech/asr/intelligent-robotics/ngt/stereo/). Only the
HiRISE Red image can be processed for the DTM creation.
From the “Maps” tab, zoom-in on your region of interest, you can display the THEMIS
mosaic for more precision, and then display the HiRISE stereo layer. You get all areas
where MarsSI proposes to compute a HiRISE DTM, appearing in cyan. The stamps are
regularly updated to take into account new data. You can use for example the select
button to choose the stamp you desire.
To add your desired stamps to your cart click on “Add” in the “Cart” window: you can
notice in the “Cart” window that three data were added, the two overlapping EDR
images that will be used, and the EDTM file that will be computed. Then go to the
“Workspace” tab.
Important: The EDTM stamps have been created automatically based on the
percentage of from the intersection and the difference in emission angle betweenof the
two EDR images. Please be advised that EDTM stamps meanare only possible DTMs:
images. aA viewing validation of the EDR images should be performed from the PDS’s
link available in the footprint attribute. Atmospheric clouds for example can prevent the
DTM calculation.
Your HiRISE images and DTM appear in the window “Data to process”. If not, you may
already have processed it yourself, or someone else may have processed it, then it may
be in the “Data processed” window. If the images have not been processed yet, you will
have to go through several steps (cf. Figure 6):
1. Download the CTX EDR image (raw data) to the MarsSI server and create a
calibrated RDR image as described previously.
2. Create the DTM by processing the proposed EDTM data in the “Data to process”
window.
3. Process the proposed ALEDTM data in the “Data to process” window to align the
HiRISE DTM to the MOLA data. [available soon]
When these different steps are done, the EDTM is waiting for you in the “Data
processed” window and you can copy it to your FTP partition.
Data type (cf. Figure 6):
❖ EDR image: Raw image in a standard format called the Experiment Data Record
❖ RDR image: Converted raw image into reflectance (irradiance/solar flux or I/F)
called Radiometric Data Record
❖ EDTM image: HiRISE DTM not aligned to MOLA data
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MarsSI tutorial
❖ ALEDTM image: HiRISE DTM aligned to MOLA data [available soon]
Output data example:
❖ EDTM image file:
HI_005000_1000_006000_1000-DEM.tif (Geotiff file format)
HI_005000_1000_006000_1000-DRG.tif (Orthoimage Geotiff file format)
❖ ALEDTM image file:
HI_005000_1000_006000_1000-ALIGN-DTM.tif (Geotiff file format)
Additional information about AMES Stereo Pipeline products can be found in:
http://byss.ndc.nasa.gov/stereopipeline/binaries/asp_book-2.5.0.pdf
3.
Process a CRISM observation
From the “Maps” tab, zoom-in on your region of interest, you can display the THEMIS
mosaic for more precision, and then display the CRISM FRTHRLHRS07 layer
corresponding to the central image of the targeted sequence. You get all CRISM
stamps that appear in red. You can use the “Select” button to choose the stamp you
desire. You can choose several stamps by clicking on several stamps, or by dragging
your mouse to select adjacent stamps. You can also use the “Search” button for more
options.
To add your desired stamps to your cart click on “Add” in the “Cart” window: you can
notice in the “Cart” window that different data were added: the TRDR files and the DDR
files in Short (VNIR) and Long (IR) wavelength ranges, “S” and “L”. Only the “L” cubes
are used in the CRISM processing and are needed for further processing in MarsSI, but
you can also download the “S” cubes for your own use. Then, go to the “Workspace”
tab.
Your CRISM TRDR and DDR “L” files appear in the window “Data to process”. If not,
you may already have processed them yourself, or someone else may have processed
them, then they may already be in the “Data processed” window. If the data have not
been processed, you will have to go download and process the TRDR and DDR cubes
by clicking on the “Process” button in the “Data to process” button.
The TRDR cube containing the reflectance values in the infrared range will be
processed using an implementation of the CAT pipeline (CRISM Analysis Tools, an
add-on to IDL/ENVI available from the CRISM team (Murchie et al., 2007; Pelkey et al.,
2007)). The cube will be corrected for the observation geometry (reflectance divided by
the cosine of the incidence angle, available in the associated DDR cube) and for
absorptions due to atmospheric CO2 using the CAT algorithm developed for CRISM
based on the ‘volcano-scan’ approach (McGuire et al., 2009).
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MarsSI tutorial
The TRDR cube corrected for atmospheric absorption and incidence angle will then be
processed through a custom pipeline to remove column-dependant noise and enhance
spectral features of small spatial extent: this pipeline basically divides the whole spectral
data in the cube by a median spectrum computed from half of the lines (those in the
middle) of the cube, on a column-by-column basis: a procedure we dub ‘ratioing’. The
output ratioed cube is dubbed ‘medianratio’. A by-product of the procedure is the
creation of a transposed cube where columns and lines are switched, but which is only
saved for the pipeline processing and should not be used as a standalone product.
This procedure dramatically reduces detector noise (mostly column-dependant),
corrects for most residual atmospheric absorptions (CO2 gas and/or water vapor/ice)
and enhances small spectral features in ratioed spectra. However, there are also
caveats to this ratioing procedure, such as the risk to introduce artifacts in ratioed
spectra if the median spectra used for division itself was not blank but had spectral
features: in such cases, the ratioed spectra will show inverted spectral features (eg., an
absorption in median spectra will yield a positive peak in ratioed spectra) which will be
artifacts and must not be interpreted as meaningful data. Still, for typical CRISM data,
acquired over terrain with spectral features of low spatial extent (a few times smaller
than the cube spatial extent), the median spectra will be nearly featureless and allow for
reasonably straightforward detection of meaningful spectral features in ratioed spectra.
The penultimate step of the pipeline computes so-called ‘spectral parameters’ or
‘spectral criteria’ such as band depths or combination of band depths, as initially
implemented in the CAT for multispectral CRISM data (Pelkey et al., 2007), or other
parameters based on analysis of the shape of the spectra. We take advantage of the
higher number of spectral channels in hyperspectral targeted CRISM observations
compared to original CAT multispectral parameters: signal-to-noise is improved by
using medians of spectral channels and specificity of criteria is improved by combining
two or more criteria. The definition of a subset of the custom criteria available in MarsSI
is given in Thollot et al. (2012) and the remaining can be made available on request
(pending publication in a future paper). The resulting data cube, dubbed ‘hyparam’ (for
hyperspectral parameters), has the same spatial dimensions as the TRDR but each
band in the spectral dimension contains the result of the computing of a spectral
criterion designed for detection of one or several spectral features from the ‘medianratio’
cube resulting from the previous step. The ‘hyparam’ cube can be used in parallel with
spectral data in IDL/ENVI to compare the spatial mapping of spectral criterion with
actual spectra.
Finally, the pipeline projects the ‘hyparam’ cube (adding the ‘_p’ suffix) for use in a GIS
in combination with other datasets (DTMs, CTX or HiRISE, etc.).
References on CRISM processing:
●
●
McGuire, P. C., et al. (2009), An improvement to the volcano-scan algorithm for atmospheric
correction of CRISM and OMEGA spectral data, Planet. Space Sci., 57(7), 809-815.
Murchie, S., et al. (2007), Compact reconnaissance Imaging Spectrometer for Mars (CRISM) on
Mars Reconnaissance Orbiter (MRO), J. Geophys. Res., 112(E5).
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MarsSI tutorial
●
●
Pelkey, S. M., et al. (2007), CRISM multispectral summary products: Parameterizing mineral
diversity on Mars from reflectance, J. Geophys. Res., 112(E8).
Thollot, P., et al. (2012), Most Mars minerals in a nutshell: Various alteration phases formed in a
single environment in Noctis Labyrinthus, J. Geophys. Res., 117, E00J06.
When the processing through the full pipeline is done, the CATRDR “L” data will be
waiting for you in the “Data processed” window and you will be able to copy it to your
FTP directory.
Data type (cf. Figure 6):
❖ TRDR cube: hyperspectral data calibrated to I/F unit called Targeted Reduced
Data Records
❖ DDR cube: information about observation conditions (e.g., geographic
coordinates (latitude and longitude), geometric angles (incidence, emission and
phase))
❖ CATRDR cube: projected images containing the mineralogic identification
derived from a TRDR cube (IR range) corrected for the atmospheric (only CO 2
gas) and photometric effects
Output data example:
❖ FRT000A82E_07_DE164S_DDR1.IMG: data cube containing the ancillary data
(e.g. latitude, longitude, incidence, emission, phase angles) of the central image
(corresponding to the “07” image of the targeted sequence) of a FRT observation
in the VNIR range (from 362 to 1053 nm) + a label (.lbl) and a header files (.hdr)
❖ FRT000A82E_07_IF164S_TRR3.IMG: calibrated data cube containing the
reflectance data (I/F unit) in the VNIR range (from 362 to 1053 nm) of the central
image (corresponding to the “07” image of the targeted sequence) of a FRT
observation + a label (.lbl) and a header files (.hdr)
❖ FRT000A82E_07_DE164L_DDR1.IMG: data cube containing the ancillary data
(e.g. latitude, longitude, incidence, emission, phase angles) of the central image
(corresponding to the “07” image of the targeted sequence) of a FRT observation
in the IR range (from 1002 to 3920 nm) + a label (.lbl) and a header files (.hdr)
❖ FRT000A82E_07_IF164L_TRR3.IMG: calibrated data cube containing the
reflectance data (I/F unit) in the IR range (from 1002 to 3920 nm) of the central
image (corresponding to the “07” image of the targeted sequence) of a FRT
observation + a label (.lbl) and a header files (.hdr)
Nota: in all subsequent file types, some parameters used in the CAT-based pipeline at
some steps can be traced at the ‘cat history’ line in the header (.hdr) file, with the
volcano-scan used for atmospheric correction and lines used to compute the median
with which spectra have been divided in the ratioing step.
❖ FRT000A82E_07_IF164L_TRR3_CAT.img: calibrated data cube containing the
reflectance data (I/F unit) in the IR range (from 1002 to 3920 nm) of the central
image of a FRT observation converted in CAT format + a header file (.hdr)
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MarsSI tutorial
❖ FRT000A82E_07_IF164L_TRR3_CAT_corr.img: calibrated data cube containing
the reflectance data (I/F unit) in the IR range (from 1002 to 3920 nm) of the
central image of a FRT observation converted in CAT format and corrected for
the incidence angle and for atmospheric CO2 absorptions using the volcano-scan
algorithm + a header file (.hdr)
❖ FRT000A82E_07_IF164L_TRR3_CAT_corr_transposed.img:
transposed
calibrated and incidence/atmosphere-corrected data cube.
❖ FRT000A82E_07_IF164L_TRR3_CAT_corr_medianratio.img: calibrated data
cube in I/F, incidence and atmosphere-corrected, in which every spectrum has
been divided, on a column-by-column basis, by a column-wise median over the
central half of the cube (eg., lines 121 to 361 for a 480-lines cube), thus
mitigating detector noise and removing residual atmospheric absorptions + a
header file (.hdr) CAUTION: as explained above the ratioing procedure may
introduce artifacts (which can be detected by a trained spectroscopist).
❖ FRT000A82E_07_IF164L_TRR3_CAT_corr_medianratioline.img: cube with only
1 (one) line, holding for each column the median spectrum used in the ratioing
procedure: this cube might be looked at to check for possible positive spectral
features if inverted features are suspected to show-up as artifacts in the
medianratio data + a header file (.hdr)
❖ FRT000A82E_07_IF164L_TRR3_CAT_corr_medianratio_hyparam.img: higherlevel data cube in which each band of the spectral dimensions contains the result
of the computing of a so-called ‘spectral parameter’ (or ‘criterion’) designed for
detection of one or several spectral features in the ‘medianratio’ cube + a header
file (.hdr). CAUTION: depending on multiple parameters, even spectral criteria
dubbed with a mineral name may or may not pick-up spectral features exclusive
to this mineral: thus, actual spectra (ratioed or not) must be checked by a trained
spectroscopist before concluding to any mineralogical identification.
❖ FRT000A82E_07_IF164L_TRR3_CAT_corr_medianratio_hyparam_p.img: same
as above but projected in equirectangular, sphere-based (radius 3396190 m)
projection + a header file (.hdr)
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