# Mars Raw Image Utilities
[](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 <camera>... M20 Camera Instrument(s)
-M, --maxsol <maxsol> Ending Mission Sol
-m, --minsol <minsol> Starting Mission Sol
-n, --num <num> Max number of results
-p, --page <page> Results page (starts at 1)
-S, --seqid <seqid> Specific sequence id or substring
-s, --sol <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 <INPUT>...
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> Blue weight
-G, --green <GREEN> Green weight
-i, --inputs <INPUT>... Input
-P, --profile <PARAM_CAL_PROFILE> Calibration profile file path
-R, --red <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 <INPUT>...
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> Blue weight
-c, --color_noise_reduction <COLOR_NOISE_REDUCTION> Color noise reduction amount in pixels
-G, --green <GREEN> Green weight
-i, --inputs <INPUT>... Input
-P, --profile <PARAM_CAL_PROFILE> Calibration profile file path
-R, --red <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 <INPUT>...
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> Blue weight
-G, --green <GREEN> Green weight
-t, --hpc_threshold <THRESHOLD> Hot pixel correction variance threshold
-i, --inputs <INPUT>... Input
-P, --profile <PARAM_CAL_PROFILE> Calibration profile file path
-R, --red <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 <INPUT>...
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>... 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 <camera>... M20 Camera Instrument(s)
-M, --maxsol <maxsol> Ending Mission Sol
-m, --minsol <minsol> Starting Mission Sol
-n, --num <num> Max number of results
-p, --page <page> Results page (starts at 1)
-S, --seqid <seqid> Specific sequence id or substring
-s, --sol <sol> Mission Sol
```
### MastCam-Z:
```
USAGE:
m20_zcam_calibrate [FLAGS] [OPTIONS] --inputs <INPUT>...
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> Blue weight
-G, --green <GREEN> Green weight
-i, --inputs <INPUT>... Input
-P, --profile <PARAM_CAL_PROFILE> Calibration profile file path
-R, --red <RED> Red weight
```
### Watson:
```
USAGE:
m20_watson_calibrate [FLAGS] [OPTIONS] --inputs <INPUT>...
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> Blue weight
-G, --green <GREEN> Green weight
-i, --inputs <INPUT>... Input
-P, --profile <PARAM_CAL_PROFILE> Calibration profile file path
-R, --red <RED> Red weight
```
### Engineering Cameras (Navcam, FHAZ, RHAZ):
```
SAGE:
m20_ecam_calibrate [FLAGS] [OPTIONS] --inputs <INPUT>...
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> Blue weight
-G, --green <GREEN> Green weight
-i, --inputs <INPUT>... Input
-P, --profile <PARAM_CAL_PROFILE> Calibration profile file path
-R, --red <RED> Red weight
```
### SuperCam
```
USAGE:
m20_scam_calibrate [FLAGS] [OPTIONS] --inputs <INPUT>...
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> Blue weight
-G, --green <GREEN> Green weight
-i, --inputs <INPUT>... Input
-P, --profile <PARAM_CAL_PROFILE> Calibration profile file path
-R, --red <RED> Red weight
```
### Ingenuity Nav Camera:
```
USAGE:
m20_hnav_calibrate [FLAGS] --inputs <INPUT>...
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>... Input
```
### Ingenuity Color Camera (RTE):
```
USAGE:
m20_hrte_calibrate [FLAGS] [OPTIONS] --inputs <INPUT>...
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> Blue weight
-G, --green <GREEN> Green weight
-i, --inputs <INPUT>... Input
-P, --profile <PARAM_CAL_PROFILE> Calibration profile file path
-R, --red <RED> Red weight
```
## InSight
### Fetch Raws:
...
### Instrument Context Camera (ICC):
```
USAGE:
nsyt_icc_calibrate [FLAGS] [OPTIONS] --inputs <INPUT>...
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> Blue weight
-G, --green <GREEN> Green weight
-i, --inputs <INPUT>... Input
-P, --profile <PARAM_CAL_PROFILE> Calibration profile file path
-R, --red <RED> Red weight
```
### Instrument Deployment Camera (IDC):
```
USAGE:
nsyt_idc_calibrate [FLAGS] [OPTIONS] --inputs <INPUT>...
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> Blue weight
-G, --green <GREEN> Green weight
-i, --inputs <INPUT>... Input
-P, --profile <PARAM_CAL_PROFILE> Calibration profile file path
-R, --red <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 <INPUT>...
FLAGS:
-h, --help Prints help information
-v Show verbose output
-V, --version Prints version information
OPTIONS:
-t, --hpc_threshold <THRESHOLD> Hot pixel correction variance threshold
-w, --hpc_window <WINDOW_SIZE> Hot pixel correction window size
-i, --inputs <INPUT>... 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 <INPUT>...
FLAGS:
-h, --help Prints help information
-v Show verbose output
-V, --version Prints version information
OPTIONS:
-i, --inputs <INPUT>... Input
```
## Upscale Experiment (Deprecated)
An experiment in smooth image upscaling using the median-based inpainting algorithm.
```
USAGE:
upscale [FLAGS] --factor <FACTOR> --inputs <INPUT>...
FLAGS:
-h, --help Prints help information
-v Show verbose output
-V, --version Prints version information
OPTIONS:
-f, --factor <FACTOR> Scale factor
-i, --inputs <INPUT>... Input
```
## Crop
```
USAGE:
crop [FLAGS] --crop <WINDOW_SIZE> --inputs <INPUT>...
FLAGS:
-h, --help Prints help information
-v Show verbose output
-V, --version Prints version information
OPTIONS:
-c, --crop <WINDOW_SIZE> Crop as x,y,width,height
-i, --inputs <INPUT>... Input
```
## Debayer
Apply Malvar Demosaicking (Debayer) on a grayscale bayer-pattern image. Optionally apply a color noise reduction.
```
USAGE:
debayer [FLAGS] [OPTIONS] --inputs <INPUT>...
FLAGS:
-h, --help Prints help information
-v Show verbose output
-V, --version Prints version information
OPTIONS:
-c, --color_noise_reduction <COLOR_NOISE_REDUCTION> Color noise reduction amount in pixels
-i, --inputs <INPUT>... Input
```
## Levels
Apply levels adjustments to an image. Analogous to 'Levels' in Photoshop or GIMP.
```
USAGE:
levels [FLAGS] [OPTIONS] --inputs <INPUT>...
FLAGS:
-h, --help Prints help information
-v Show verbose output
-V, --version Prints version information
OPTIONS:
-b, --blacklevel <BLACK_LEVEL> Black level
-g, --gamma <PARAM_GAMMA> Gamma
-i, --inputs <INPUT>... Input
-w, --whitelevel <WHITE_LEVEL> 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 <INPUT>... --output <OUTPUT>
FLAGS:
-h, --help Prints help information
-v Show verbose output
-V, --version Prints version information
OPTIONS:
-b, --blacklevel <BLACK_LEVEL> Black level
-d, --delay <PARAM_DELAY> Interframe delay in increments of 10ms
-g, --gamma <PARAM_GAMMA> Gamma
-i, --inputs <INPUT>... Input
-l, --lowpass <PARAM_LOWPASS> Lowpass window size
-o, --output <OUTPUT> Output
-p, --prodtype <PARAM_PRODUCT_TYPE> Product type (std, diff, stacked)
-w, --whitelevel <WHITE_LEVEL> 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
```
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