Test Data¶

emwrap ships small, real tilt-series datasets used by its automated tests and by the tutorials in this documentation. Datasets are no longer configured through EMWRAP_CONFIG: each named dataset is expected under $ROOT/testdata/<NAME>/ (ROOT is the installation folder, i.e. the directory containing emwrap.bashrc), and emwrap can download the known datasets there for you.

Downloading a Dataset¶

Datasets are downloaded with the data action of the same ./emh-tomo --test entry point used to run the tests (see Running Tests):

# List available datasets
./emh-tomo --test data --list

# Download to $ROOT/testdata/<NAME>/
./emh-tomo --test data --download <NAME>

# Or download to a custom location (PATH/<NAME>)
./emh-tomo --test data --download <NAME> /path/to/testdata

If a dataset’s folder does not exist on disk when a test or job that needs it runs, it fails immediately with a message explaining how to download it.

Available Datasets¶

--list currently reports two known datasets:

Name	Source	Tilt Series	Used by
`WarpApofTutorial`	EMPIAR-10491, EMD-15854	TS_1, TS_11, TS_17, TS_23, TS_32	`apof_warp`, `apof_aretomo3`, Warp ApoF Tutorial
`RelionTomoTutorial`	EMPIAR-10164	TS_01, TS_03, TS_43, TS_45, TS_54	(not yet used by any test or tutorial)

WarpApofTutorial¶

5 apoferritin (ApoF) tilt series from EMPIAR-10491, the same dataset used by Warp’s own WarpTools tilt series quick start guide. This is the dataset used by the apof_warp and apof_aretomo3 automated tests (see Running Tests), and by the Warp ApoF Tutorial walkthrough.

./emh-tomo --test data --download WarpApofTutorial

Once downloaded, $ROOT/testdata/WarpApofTutorial/ should look like this:

testdata/WarpApofTutorial/
├── gain_ref.mrc
├── emd_15854.map
├── mdoc/
│   ├── TS_1.mrc.mdoc
│   ├── TS_11.mrc.mdoc
│   └── ...
└── frames/
    ├── 2Dvs3D_53-1_00001_...tif
    └── ...

This layout matches what the emw-import-ts job expects (gain_ref.mrc, mdoc/*.mdoc, frames/), and reflects the dataset’s own acquisition parameters, used when importing the tilt series: a pixel size of 0.789 Å, 300 kV, Cs 2.7 mm, a per-tilt dose of 2.64 e⁻/Å², and a tilt-axis angle of -85.6°.

emd_15854.map is the apoferritin reference map from EMD-15854 (384³ voxels at 0.729 Å/px). It is not part of EMPIAR-10491: it is downloaded separately from EMDB and used by the emw-pytom-create_template job to build the template and mask for template matching. EMDB serves its maps gzipped, so it is decompressed after downloading (23 MB compressed, 216 MB on disk).

RelionTomoTutorial¶

5 tilt series (TS_01, TS_03, TS_43, TS_45, TS_54) from EMPIAR-10164, the dataset used by Relion’s own subtomogram averaging tutorial. Not yet used by any automated test or tutorial in this documentation.

./emh-tomo --test data --download RelionTomoTutorial