# Mars Raw Image Utilities [![Rust](https://github.com/kmgill/mars-raw-utils/actions/workflows/rust.yml/badge.svg)](https://github.com/kmgill/mars-raw-utils/actions/workflows/rust.yml) A set of utilities for processing and calibration of imagery from either the Curiosity or Perseverance rovers. Meant to be used on publicly available images. Implemented calibration steps include (varying per instrument): | Mission | Camera | Decompand | Debayer | Inpaint | Flats | HPC* | | ---------- |:-----------:|:---------:|:-------:|:------------:|:------:|:------:| | MSL | MastCam | ☑ | ☑ | | | | | MSL | MAHLI | ☑ | | ☑ | ☑| ☑| | MSL | NavCam | | | ☑ | ☑| ☑| | MSL | Rear Haz | | | ☑ | ☑| ☑| | MSL | Front Haz | | | ☑ | ☑| ☑| | MSL | ChemCam RMI | | | | ☑| | | Mars2020 | Mastcam-Z | ☑ | ☑ | ☑ | | | | Mars2020 | NavCam | | ☑ | | | | | Mars2020 | Rear Haz | | ☑ | | | | | Mars2020 | Front Haz | | ☑ | | | | | Mars2020 | Watson | ☑ | ☑ | ☑ | | | | Mars2020 | SuperCam | | ☑ | | ☑| | | Ingenuity | Nav | | | | ☑| | | Ingenuity | Color | | | | ☑| | | InSight | IDC | ☑ | | | ☑| | | InSight | ICC | ☑ | | | ☑| | \* Hot pixel detection and correction Additional instruments will be implemented more or less whenever I get to them... ## Building from source: A working Rust (https://www.rust-lang.org/) installation is required for building. So far I've only tested building on Ubuntu 21.10, natively and within the Windows Subsystem for Linux on Windows 10, and on MacOSX Catalina. Within the project folder, the software can be built for testing via `cargo build` and individual binaries can be run in debug mode via, for example, `cargo run --bin m20_fetch_raw -- -i` To build successfully on Linux, you'll likely need the following packages installed via apt: * libssl-dev (Ubuntu) * openssl-devel (RHEL, CentOS, Fedora) ### Clone from git: ``` git clone git@github.com:kmgill/mars-raw-utils.git cd mars-raw-utils/ git submodule init git submodule update ``` ### Install via cargo: This is the easiest installation method for *nix-based systems. It has not been tested in Windows. ``` cargo install --path . mkdir ~/.marsdata cp mars-raw-utils-data/caldata/* ~/.marsdata ``` NOTE: You can set $MARS_RAW_DATA in ~/.bash_profile if a custom data directory is required. ### Install via apt (Debian, Ubuntu, ...): ``` cargo install cargo-deb cargo deb sudo apt install ./target/debian/mars_raw_utils_0.1.3_amd64.deb ``` NOTE: Adjust the output debian package filename to what is outputted by build. ### Install via rpm (RHEL, CentOS, Fedora, ...) ``` cargo install cargo-rpm cp -v mars-raw-utils-data/caldata/* .rpm/ cargo rpm build -v rpm -ivh target/release/rpmbuild/RPMS/x86_64/mars_raw_utils-0.1.3-1.el8.x86_64.rpm ``` NOTE: Adjust the output rpm package filename to what is created by build. ### Docker: The dockerfile demonstrates a method for building an installable debian package, or you can use the container itself: ``` docker build -t mars_raw_utils . docker run --name mars_raw_utils -dit mars_raw_utils docker exec -it mars_raw_utils bash ``` Builds for MacOSX (maybe via Homebrew?) and Windows are in the plan. Though the project has built and run from MacOSX and Windows, I haven't worked out the installation method in a way that handles the calibration data. ### Building RPMs using Docker CentOS targetted RPMs can be built using `dockerbuild.sh` which will result in the build artifacts being placed into the `target` directory. ## Specifying Calibration Data Location: By default, if the software is installed using the .deb file in Debian/Ubuntu, the calibration files will be located in `/usr/share/mars_raw_utils/data/`. In Homebrew on MacOS, they will be located in `/usr/local/share/mars_raw_utils/data/`. For installations using `cargo install --path .` or custom installations, you can use the default `~/.marsdata` or set the calibration file directory by using the `MARS_RAW_DATA` environment variable. The variable will override the default locations (if installed via apt or rpm), as well. ## Calibration Profiles Calibration files are used to specify commonly used parameters for the various instruments and output product types. The files are in toml format and if not specified by their absolute path, need to be discoverable in a known calibration folder. An example profile ``` apply_ilt = true red_scalar = 1.16 green_scalar = 1.0 blue_scalar = 1.05 color_noise_reduction = false color_noise_reduction_amount = 0 hot_pixel_detection_threshold = 0 filename_suffix = "rjcal-rad" ``` ## Mars Science Laboratory (Curiosity): ### Fetch Raws: ``` USAGE: msl_fetch_raw [FLAGS] [OPTIONS] FLAGS: -h, --help Prints help information -l, --list Don't download, only list results -t, --thumbnails Download thumbnails in the results -v Show verbose output -V, --version Prints version information OPTIONS: -c, --camera ... M20 Camera Instrument(s) -M, --maxsol Ending Mission Sol -m, --minsol Starting Mission Sol -n, --num Max number of results -p, --page Results page (starts at 1) -S, --seqid Specific sequence id or substring -s, --sol Mission Sol ``` #### Examples: Show available instruments: ``` msl_fetch_raw -i ``` List what's available for Mastcam on sol 3113: (remove the `-l` to download the images) ``` msl_fetch_raw -c MASTCAM -s 3113 -l ``` List what's available for NAV_RIGHT between sols 3110 and 3112: (remove the `-l` to download the images) ``` msl_fetch_raw -c NAV_RIGHT -m 3110 -M 3112 -l ``` Download NAV_RIGHT during sols 3110 through 3112, filtering for sequence id NCAM00595: ``` msl_fetch_raw -c NAV_RIGHT -m 3110 -M 3112 -S NCAM00595 ``` ### MAHLI Calibration: ``` USAGE: msl_mahli_calibrate [FLAGS] [OPTIONS] --inputs ... FLAGS: -h, --help Prints help information -n Only new images. Skipped processed images. -r, --raw Raw color, skip ILT -v Show verbose output -V, --version Prints version information OPTIONS: -B, --blue Blue weight -G, --green Green weight -i, --inputs ... Input -P, --profile Calibration profile file path -R, --red Red weight ``` #### Common Color Correction Multiples: * RED: 1.16 * GREEN: 1.00 * BLUE: 1.05 #### Common Color Correction Multiples (White Balanced): * RED: 0.8 * GREEN: 1.0 * BLUE: 1.543 #### Examples: Calibrate a directory of JPEGs, applying color correction values: ``` msl_mahli_calibrate -i *jpg -v -R 1.16 -G 1.00 -B 1.05 ``` ### MastCam: ``` USAGE: msl_mcam_calibrate [FLAGS] [OPTIONS] --inputs ... FLAGS: -h, --help Prints help information -n Only new images. Skipped processed images. -r, --raw Raw color, skip ILT -v Show verbose output -V, --version Prints version information OPTIONS: -B, --blue Blue weight -c, --color_noise_reduction Color noise reduction amount in pixels -G, --green Green weight -i, --inputs ... Input -P, --profile Calibration profile file path -R, --red Red weight ``` #### Recommended Color Correction Multiples: * RED: 0.965 * GREEN: 0.985 * BLUE: 1.155 #### Examples: Calibrate a directory of JPEGs, applying color correction values: ``` msl_mcam_calibrate -i *jpg -v -R 0.965 -G 0.985 -B 1.155 ``` Calibrate a directory of JPEGs, skipping ILT conversion (decompanding): ``` msl_mcam_calibrate -i *jpg -v -r ``` Calibrate a directory of JPEGs, applying color noise reduction with a chroma blur radius of 21 pixels: ``` msl_mcam_calibrate -i *jpg -v -c 21 ``` ### Engineering Cameras (Navcam, FHAZ, RHAZ): ``` USAGE: msl_ecam_calibrate [FLAGS] [OPTIONS] --inputs ... FLAGS: -h, --help Prints help information -n Only new images. Skipped processed images. -r, --raw Raw color, skip ILT (not currently used) -v Show verbose output -V, --version Prints version information OPTIONS: -B, --blue Blue weight -G, --green Green weight -t, --hpc_threshold Hot pixel correction variance threshold -i, --inputs ... Input -P, --profile Calibration profile file path -R, --red Red weight ``` #### Examples: Calibrate a directory of JPEGs: ``` msl_ecam_calibrate -i *jpg -v ``` Calibrate a directory of JPEGs, apply a hot pixel detection with a threshold of 2.5 standard deviations: ``` msl_ecam_calibrate -i *jpg -v -t 2.5 ``` ### ChemCam RMI: ``` USAGE: msl_ccam_calibrate [FLAGS] --inputs ... FLAGS: -h, --help Prints help information -n Only new images. Skipped processed images. -v Show verbose output -V, --version Prints version information OPTIONS: -i, --inputs ... Input ``` ## Mars 2020 (Perseverance): ### Fetch Raws: ``` USAGE: m20_fetch_raw [FLAGS] [OPTIONS] FLAGS: -h, --help Prints help information -l, --list Don't download, only list results -t, --thumbnails Download thumbnails in the results -v Show verbose output -V, --version Prints version information OPTIONS: -c, --camera ... M20 Camera Instrument(s) -M, --maxsol Ending Mission Sol -m, --minsol Starting Mission Sol -n, --num Max number of results -p, --page Results page (starts at 1) -S, --seqid Specific sequence id or substring -s, --sol Mission Sol ``` ### MastCam-Z: ``` USAGE: m20_zcam_calibrate [FLAGS] [OPTIONS] --inputs ... FLAGS: -h, --help Prints help information -n Only new images. Skipped processed images. -r, --raw Raw color, skip ILT -v Show verbose output -V, --version Prints version information OPTIONS: -B, --blue Blue weight -G, --green Green weight -i, --inputs ... Input -P, --profile Calibration profile file path -R, --red Red weight ``` ### Watson: ``` USAGE: m20_watson_calibrate [FLAGS] [OPTIONS] --inputs ... FLAGS: -h, --help Prints help information -n Only new images. Skipped processed images. -r, --raw Raw color, skip ILT -v Show verbose output -V, --version Prints version information OPTIONS: -B, --blue Blue weight -G, --green Green weight -i, --inputs ... Input -P, --profile Calibration profile file path -R, --red Red weight ``` ### Engineering Cameras (Navcam, FHAZ, RHAZ): ``` SAGE: m20_ecam_calibrate [FLAGS] [OPTIONS] --inputs ... FLAGS: -h, --help Prints help information -n Only new images. Skipped processed images. -r, --raw Raw color, skip ILT -v Show verbose output -V, --version Prints version information OPTIONS: -B, --blue Blue weight -G, --green Green weight -i, --inputs ... Input -P, --profile Calibration profile file path -R, --red Red weight ``` ### SuperCam ``` USAGE: m20_scam_calibrate [FLAGS] [OPTIONS] --inputs ... FLAGS: -h, --help Prints help information -n Only new images. Skipped processed images. -r, --raw Raw color, skip ILT -v Show verbose output -V, --version Prints version information OPTIONS: -B, --blue Blue weight -G, --green Green weight -i, --inputs ... Input -P, --profile Calibration profile file path -R, --red Red weight ``` ### Ingenuity Nav Camera: ``` USAGE: m20_hnav_calibrate [FLAGS] --inputs ... FLAGS: -h, --help Prints help information -n Only new images. Skipped processed images. -v Show verbose output -V, --version Prints version information OPTIONS: -i, --inputs ... Input ``` ### Ingenuity Color Camera (RTE): ``` USAGE: m20_hrte_calibrate [FLAGS] [OPTIONS] --inputs ... FLAGS: -h, --help Prints help information -n Only new images. Skipped processed images. -v Show verbose output -V, --version Prints version information OPTIONS: -B, --blue Blue weight -G, --green Green weight -i, --inputs ... Input -P, --profile Calibration profile file path -R, --red Red weight ``` ## InSight ### Fetch Raws: ... ### Instrument Context Camera (ICC): ``` USAGE: nsyt_icc_calibrate [FLAGS] [OPTIONS] --inputs ... FLAGS: -h, --help Prints help information -n Only new images. Skipped processed images. -r, --raw Raw color, skip ILT -v Show verbose output -V, --version Prints version information OPTIONS: -B, --blue Blue weight -G, --green Green weight -i, --inputs ... Input -P, --profile Calibration profile file path -R, --red Red weight ``` ### Instrument Deployment Camera (IDC): ``` USAGE: nsyt_idc_calibrate [FLAGS] [OPTIONS] --inputs ... FLAGS: -h, --help Prints help information -n Only new images. Skipped processed images. -r, --raw Raw color, skip ILT -v Show verbose output -V, --version Prints version information OPTIONS: -B, --blue Blue weight -G, --green Green weight -i, --inputs ... Input -P, --profile Calibration profile file path -R, --red Red weight ``` ## Hot Pixel Correction Filter Attempt at hot pixel detection and removal. Method: For each pixel (excluding image border pixels): 1. Compute the standard deviation of a window of pixels (3x3, say) 1. Compute the z-score for the target pixel 1. If the z-score exceeds a threshold variance (example: 2.5) from the mean we replace the pixel value with a median filter ``` USAGE: hpc_filter [FLAGS] [OPTIONS] --inputs ... FLAGS: -h, --help Prints help information -v Show verbose output -V, --version Prints version information OPTIONS: -t, --hpc_threshold Hot pixel correction variance threshold -w, --hpc_window Hot pixel correction window size -i, --inputs ... Input ``` ## Inpainting Filter Applies a basic inpainting filter on a set of input images. Inpainting regions need to be marked in red (rgb 255, 0, 0). ``` USAGE: inpaint_filter [FLAGS] --inputs ... FLAGS: -h, --help Prints help information -v Show verbose output -V, --version Prints version information OPTIONS: -i, --inputs ... Input ``` ## Upscale Experiment (Deprecated) An experiment in smooth image upscaling using the median-based inpainting algorithm. ``` USAGE: upscale [FLAGS] --factor --inputs ... FLAGS: -h, --help Prints help information -v Show verbose output -V, --version Prints version information OPTIONS: -f, --factor Scale factor -i, --inputs ... Input ``` ## Crop ``` USAGE: crop [FLAGS] --crop --inputs ... FLAGS: -h, --help Prints help information -v Show verbose output -V, --version Prints version information OPTIONS: -c, --crop Crop as x,y,width,height -i, --inputs ... Input ``` ## Debayer Apply Malvar Demosaicking (Debayer) on a grayscale bayer-pattern image. Optionally apply a color noise reduction. ``` USAGE: debayer [FLAGS] [OPTIONS] --inputs ... FLAGS: -h, --help Prints help information -v Show verbose output -V, --version Prints version information OPTIONS: -c, --color_noise_reduction Color noise reduction amount in pixels -i, --inputs ... Input ``` ## Levels Apply levels adjustments to an image. Analogous to 'Levels' in Photoshop or GIMP. ``` USAGE: levels [FLAGS] [OPTIONS] --inputs ... FLAGS: -h, --help Prints help information -v Show verbose output -V, --version Prints version information OPTIONS: -b, --blacklevel Black level -g, --gamma Gamma -i, --inputs ... Input -w, --whitelevel White level ``` ## Change Detection (Dust devils, clouds) Calculates a per-frame differential from a mean across a series of images. Intended for use with MSL and Mars2020 dust devil movies and sky surveys. Optional options are for contrast enhancement through Photoshop-like black level, white level, and gamma. ``` USAGE: diffgif [FLAGS] [OPTIONS] --inputs ... --output FLAGS: -h, --help Prints help information -v Show verbose output -V, --version Prints version information OPTIONS: -b, --blacklevel Black level -d, --delay Interframe delay in increments of 10ms -g, --gamma Gamma -i, --inputs ... Input -l, --lowpass Lowpass window size -o, --output Output -p, --prodtype Product type (std, diff, stacked) -w, --whitelevel White level ``` ### Examples #### Dust Devils, MSL Sol 3372, Seq id NCAM00595: ``` msl_fetch_raw -c NAV_RIGHT_B -s 3372 -S NCAM00595 msl_ecam_calibrate -i *JPG -v -t 2.0 diffgif -i *NCAM00595*-rjcal.png -o DustDevilMovie_Sol3372.gif -v -b 0 -w 2.0 -g 2.5 -l 5 -d 20 ``` #### Cloud motion and shadows, MSL Sol 3325, Seq id NCAM00556: ``` msl_fetch_raw -c NAV_RIGHT -s 3325 msl_ecam_calibrate -i *JPG -v -t 2.0 diffgif -i *NCAM00556*-rjcal.png -o CloudShadow_3325.gif -v -b 0 -w 1.0 -g 2.5 -l 5 -d 20 ``` #### Clouds, zenith movie, MSL Sol 3325, Seq id NCAM00551: ``` msl_fetch_raw -c NAV_RIGHT -s 3325 msl_ecam_calibrate -i *JPG -v -t 2.0 diffgif -i *NCAM00551*-rjcal.png -o CloudZenith_3325.gif -v -b 0 -w 3.0 -g 1.0 -l 5 -d 20 ``` ## Data Update Checks Fetches information as to the latest updated sols. Example Output: ``` $ msl_latest Latest data: 2022-02-23T18:30:03Z Latest sol: 3395 Latest sols: [3365, 3374, 3376, 3378, 3390, 3393, 3394, 3395] New Count: 364 Sol Count: 225 Total: 894201 $ m20_latest Latest data: 2022-02-23T10:22:33Z Latest sol: 359 Latest sols: [349] New Count: 270 Sol Count: 99 Total: 217981 $ nsyt_latest Latest data: 2022-02-14T15:11:15Z Latest sol: 1144 Latest sols: [1144] New Count: 2 Sol Count: 2 Total: 6353 ``` ## Mission Dates Mission time and sol are available for MSL, Mars2020, and InSight via `msl_date`, `m20_date`, and `nsyt_date`, respectively. Currently, the output provides valules for the Mars Sol Date, coordinated Mars time, mission sol, mission time (LMST), local true color time, and areocentric solar longitude. The algorithm used for the calculation is based on James Tauber's marsclock.com and is exposed via `time::get_lmst()`. Example Output: ``` $ msl_date Mars Sol Date: 52391.26879394437 Coordinated Mars Time: 06:27:03.797 Mission Sol: 3122 Mission Time: 15:36:49.805 LMST Local True Solar Time: 15:29:37.673 LTST Solar Longitude: 47.04093399663567 $ m20_date Mars Sol Date: 52391.270293050664 Coordinated Mars Time: 06:29:13.320 Mission Sol: 87 Mission Time: 11:38:56.520 LMST Local True Solar Time: 11:31:44.417 LTST Solar Longitude: 47.04161842268443 $ nsyt_date Mars Sol Date: 52391.27048977531 Coordinated Mars Time: 06:29:30.317 Mission Sol: 880 Mission Time: 15:31:59.933 LMST Local True Solar Time: 15:24:47.833 LTST Solar Longitude: 47.041708238462114 ``` ## References: Bell, J. F. et al. (2017), The Mars Science Laboratory Curiosity rover Mastcam instruments: Preflight and in‐flight calibration, validation, and data archiving, Earth and Space Science, 4, 396– 452, doi:10.1002/2016EA000219. https://doi.org/10.1002/2016EA000219 Hayes, A.G., Corlies, P., Tate, C. et al. 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