napari-slstr

This repo provides tools for using napari to work with remote sensing data files:

• image_labeller: Launch the napari image viewer/labelling tool on an Sentinel 3 / SLSTR scene or slsitr-lite scene
• netcdf_viewer: Launch napari to view 2D gridded data from any netcdf4 file

For more information on napari see: https://napari.org/

Installation Prerequisites

• conda or miniconda (recommended)
• git
• Napari
  • On Mac, ensure you have XCode installed.

Installation

Installing napari and its dependencies

Install napari, preferably into a new conda environment (see https://napari.org/stable/tutorials/fundamentals/installation.html for instructions for your platform)

Important Note - this software has been tested with napari versions 0.4.18 and 0.5.3 on linux. You can install a specific version of napari using the following example syntax python -m pip install "napari[all]==0.4.18"

Check the version of napari that has been installed

$ napari --version
napari version 0.5.3

Installing image_labeller and netcdf_viewer

Create a new folder and clone this repo into it

mkdir napari_slstr_install
cd napari_slstr_install
git clone https://github.com/surftemp/napari-slstr.git

Install napari-slstr image_labeller and netcdf_viewer commands from the repo:

cd napari-slstr
pip install -e .

Check that the image_labeller tool will open, requires an unzipped Sentinel3 SLSTR scene, eg

image_labeller ~/Projects/napari/S3A_SL_1_RBT____20170122T094902_20170122T095202_20181004T064548_0179_013_264______LR1_R_NT_003.SEN3 ./resources/example.cfg

Install updates

To install updates to the image_labeller and netcdf_viewer tools:

cd napari_slstr_install
git pull

Using image_labeller

Defaults

In the resources/example.cfg configuration file, all channels are shown, with nadir and oblique views, plus a false colour view constructed from bands S3 (red), S2(green) and S1(blue).

image_labeller <path-to-SLSTR-scene-folder> ./resources/example.cfg

When viewing an slstr-lite scene, use configuration file (or one based on) ./resources/example_slstr_lite.cfg

updated label files are written into the scene folder when the user closes Napari (select Exit from the File menu).

It is recommended to periodically back up label files.

Using netcdf_viewer

The netcdf_viewer tool uses command line options to control which files and variables are to be displayed, and how to display them. For example:

netcdf_viewer.py [-h] [--x-dim X_DIM] [--y-dim Y_DIM] path layer [layer...] 

netcdf_viewer LC08_L1TP_205025_20230420_20230429_02_T1.nc rgb(B4:B3:B2) B11:275:295:coolwarm --y-dim=nj

• the netcdf file is LC08_L1TP_205025_20230420_20230429_02_T1.nc
• two layers are requested:
  • the first layer is a rgb false colour composed from r=B4,g=B3,b=B2
  • the second layer displays B11 using the coolwarm colour map between 275K and 295K
• use dimension nj as the y axis

Viewing multiple files

Specify multiple paths and their layers using:

netcdf_viewer.py [-h] [--x-dim X_DIM] [--y-dim Y_DIM] path layer [layer...] path layer [layer...]

Notes

--x-dim and --y-dim specify the data dimensions to display on x and y axes. Prefix the dimension name with a minus sign to flip the axes.

Layers are specified using the following (hopefully self-explanatory) notation:

Use rgb(r-var-name:g-var-name:b-var-name) to specify 3 bands to compose a false colour layer

or

Use var-name[:min-value:max-value[:colour-map]] to plot a single band, with optional min/max and colour map.

The following colour maps are available:

"GrBu", "GrBu_d", "PiYG", "PuGr", "RdBu", "RdYeBuCy", "autumn", "blues", "cool", "coolwarm", "cubehelix", "diverging", "fire", "gist_earth", "gray", "gray_r", "grays", "greens", "hot", "hsl", "hsv", "husl", "ice", "inferno", "light_blues", "magma", "orange", "plasma", "reds", "single_hue", "spring", "summer", "turbo", "twilight", "twilight_shifted", "viridis", "winter"