Plugins and formats

Formats Glimt reads itself

JPEG, PNG, WebP, GIF, WebP and PNG (APNG) animations, TIFF (every page, and grey TIFFs of floats from science stretched to show), BMP, ICO, QOI, PNM, Radiance HDR (tone-mapped), Zeiss LSM and .gel scans, camera RAW files through their embedded preview, and HEIC, AVIF and video through ffmpeg, JPEG XL and SVG, as the packages are built.

Two kinds of plugins

Both are small desktop files in a folder of your own, which name a program. Glimt runs it directly, never through a shell, with each file as an argument of its own, so a file named $(rm -rf ~).jpg stays a name.

Plugins (~/.local/share/glimt/plugins) run a program on the selected files from Edit → Plugins: rotate them, send them somewhere, or describe them with a model on your own computer.
Decoder plugins (~/.local/share/glimt/decoders, Glimt 0.24.0 or newer) teach Glimt a format it does not read itself. The program gets a file and writes the image to its standard output; Glimt then lists, shows and makes thumbnails of such files as of any other.

The decoders that come with Glimt

They are in examples/decoders in Glimt's source, and each is tested in Glimt's release tests.

Decoder	Formats	Field	Needs
`dicom.desktop`	DICOM (`.dcm`), also compressed, in the window the file names	medicine, dentistry	python3-pydicom, python3-gdcm
`nifti.desktop`	NIfTI (`.nii`, `.nii.gz`): the middle axial slice	brain MRI, fMRI	python3-nibabel
`openslide.desktop`	Whole-slide images (`.svs`, `.ndpi`, `.mrxs`, `.scn` …)	pathology	python3-openslide
`bioformats.desktop`	Zeiss `.czi`, Leica `.lif`, Nikon `.nd2`, Olympus `.oib`/`.oir` and more (ICS once added)	microscopy	Java and Bio-Formats' bftools
`mrc.desktop`	MRC (`.mrc`, `.map`, `.rec` …): a micrograph or the middle section	cryo-EM, structural biology	python3-mrcfile
`fits.desktop`	FITS (also `.fits.fz`), with astronomers' zscale stretch	astronomy, solar physics	python3-astropy
`hdf5.desktop`	HDF5, NetCDF-4, NeXus (`.h5`, `.nc`, `.nxs`): the largest dataset of two or more dimensions	climate, physics, satellites	python3-h5py
`jpeg2000.desktop`	JPEG 2000 (`.jp2`, `.j2k`, `.jpf`, `.jpx`)	archives, libraries	ffmpeg
`photoshop.desktop`	Photoshop (`.psd`, `.psb`) as saved	design, architecture	ImageMagick
`tga.desktop`, `exr.desktop`	TGA, OpenEXR renderings	games, 3D	ImageMagick
`xcf.desktop`	GIMP's own files, their layers put together	design	ImageMagick
`imagemagick-fits.desktop`, `imagemagick-dicom.desktop`	FITS and DICOM through ImageMagick alone	astronomy, medicine	ImageMagick

To use them, copy those you need with the script a desktop file names (glimt-fits for fits.desktop). Take one of each pair: fits.desktop or imagemagick-fits.desktop, dicom.desktop or imagemagick-dicom.desktop. With both, the first by name takes the files, also on a computer without the Python modules it needs.

git clone https://github.com/thornbux/glimt
mkdir -p ~/.local/share/glimt/decoders
cd glimt/examples/decoders
cp jpeg2000.desktop fits.desktop glimt-fits ~/.local/share/glimt/decoders/

Restart Glimt, and those files show in the list as images do. A decoder whose program is missing shows its error where the image would be.

They are for a quick look, not for measuring: the values are stretched to grey (between the 1st and 99th percentile, or zscale for FITS), and the scripts read only the slice or level they show. DICOM and NIfTI files can hold patient data: Glimt and its decoders only show the picture, print or keep no name, ID or other field, and send nothing anywhere.

Writing a decoder

[Glimt Decoder]
Name=JPEG 2000
Extensions=jp2;j2k;j2c;jpf;jpx
Exec=ffmpeg -v error -protocol_whitelist file -format_whitelist j2k_pipe -f j2k_pipe -i %f -frames:v 1 -f image2pipe -vcodec ppm -

Extensions: the file endings it takes, separated by ;; an ending may have two parts, as nii.gz. A format Glimt reads itself is never given to a plugin, and when two decoders take the same ending, the one whose file comes first by name does.
Exec: the command. %f is the file's absolute path, as one argument; it may stand inside a word, as ImageMagick's %f[0] for a file's first frame. A program next to the desktop file is found there, so a decoder can bring its own script.
The program writes the image to its standard output, as PNM, PNG, TIFF or any other format Glimt reads. It has 30 seconds and may write at most 512 MB; it is stopped after that, with everything it started.
New decoders are seen after a restart. In a Flatpak they run on the host.

Which formats go into Glimt, and which into plugins

A format is built into Glimt when the image library Glimt already uses reads it, with no new dependency: BMP, ICO, QOI and PNM came in that way, with a few lines each. A format that needs a large library, a library in C, or a program of its own becomes a decoder plugin, so Glimt stays small and fast for everyone, and those who need FITS or DICOM add one file. A decoder that works well is welcome in Glimt's examples/decoders: send a pull request with the desktop file, a line on what it needs, and a test in tools/release-tests/tests.sh.