Unit support (#1136)

* Support new properties.json format with unit.

* Implement requested changes.

* Added newlines in datasource-properties.json.

* Update changelog.

* Add conversion hook for Unit.

* Rename unit to length_unit.

* Fix naming issues, and add unit to CLI

* Set default in CLI to string instead of LengthUnit

There seems to be an typer issue, that a LengthUnit is not recognized.

* Create constants for default unit and default unit str.

CONTRIBUTING.md

@@ -140,7 +140,7 @@ The `webknossos` folder contains examples, which are not part of the package, bu
 The tests also contain functionality for the WEBKNOSSOS client. There a two modes to run the tests:
 
 1. `./test.sh --refresh-snapshots`, sending network requests to a WEBKNOSSOS instance:
- This expects a local WEBKNOSSOS setup with specific test data, which is shipped with WEBKNOSSOS. If you're starting and running WEBKNOSSOS manually, please use port 9000 (the default) and run the `tools/postgres/prepareTestDb.sh` script in the WEBKNOSSOS repository (⚠️ this overwrites your local WEBKNOSSOS database). Alternatively, a docker-compose setup is started automatically for the tests, see `./test.sh` and `tests/docker-compose.yml` for details. The network requests & response are recorded as "cassettes" by [vcr.py](https://vcrpy.readthedocs.io), see next point:
+ This expects a local WEBKNOSSOS setup with specific test data, which is shipped with WEBKNOSSOS. If you're starting and running WEBKNOSSOS manually, please use port 9000 (the default) and run the `tools/postgres/dbtool.js prepare-test-db` script in the WEBKNOSSOS repository (⚠️ this overwrites your local WEBKNOSSOS database). Alternatively, a docker-compose setup is started automatically for the tests, see `./test.sh` and `tests/docker-compose.yml` for details. The network requests & response are recorded as "cassettes" by [vcr.py](https://vcrpy.readthedocs.io), see next point:
 2. `./test.sh` replays responses from previous network snapshots using [vcr.py](https://vcrpy.readthedocs.io) via [pytest-recording](https://github.com/kiwicom/pytest-recording). No additional network requests are allowed in this mode.
 
 `./test.sh --store-durations` updates the durations for

webknossos/Changelog.md

@@ -15,6 +15,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 ### Breaking Changes
 
 ### Added
+- Added support for new voxel size that stores unit and updated to WEBKNOSSOS API version 7. [#1136](https://github.com/scalableminds/webknossos-libs/pull/1136)
 
 ### Changed
 

webknossos/local_wk_setup.sh

@@ -1,7 +1,7 @@
 function export_vars {
  export WK_TOKEN=1b88db86331a38c21a0b235794b9e459856490d70408bcffb767f64ade0f83d2bdb4c4e181b9a9a30cdece7cb7c65208cc43b6c1bb5987f5ece00d348b1a905502a266f8fc64f0371cd6559393d72e031d0c2d0cabad58cccf957bb258bc86f05b5dc3d4fff3d5e3d9c0389a6027d861a21e78e3222fb6c5b7944520ef21761e
  export WK_URL=http://localhost:9000
- export DOCKER_TAG=master__27071
+ export DOCKER_TAG=master__28678
 }
 
 function ensure_local_test_wk {

webknossos/testdata/complex_property_ds/datasource-properties.json

@@ -8,34 +8,62 @@
  "name": "color",
  "category": "color",
  "boundingBox": {
- "topLeft": [0, 0, 0],
+ "topLeft": [
+ 0,
+ 0,
+ 0
+ ],
  "width": 1024,
  "height": 1024,
  "depth": 1024
  },
  "wkwResolutions": [
  {
- "resolution": [1, 1, 1],
+ "resolution": [
+ 1,
+ 1,
+ 1
+ ],
  "cubeLength": 1024
  },
  {
- "resolution": [16, 16, 16],
+ "resolution": [
+ 16,
+ 16,
+ 16
+ ],
  "cubeLength": 64
  },
  {
- "resolution": [2, 2, 2],
+ "resolution": [
+ 2,
+ 2,
+ 2
+ ],
  "cubeLength": 512
  },
  {
- "resolution": [32, 32, 32],
+ "resolution": [
+ 32,
+ 32,
+ 32
+ ],
  "cubeLength": 32
  },
  {
- "resolution": [4, 4, 4],
+ "resolution": [
+ 4,
+ 4,
+ 4
+ ],
  "cubeLength": 256
  },
  {
- "resolution": [8, 8, 8],
+ "resolution": [
+ 8,
+ 8,
+ 8
+ ],
  "cubeLength": 128
  }
  ],
@@ -45,34 +73,62 @@
  {
  "name": "segmentation",
  "boundingBox": {
- "topLeft": [0, 0, 0],
+ "topLeft": [
+ 0,
+ 0,
+ 0
+ ],
  "width": 1024,
  "height": 1024,
  "depth": 1024
  },
  "wkwResolutions": [
  {
- "resolution": [1, 1, 1],
+ "resolution": [
+ 1,
+ 1,
+ 1
+ ],
  "cubeLength": 1024
  },
  {
- "resolution": [16, 16, 16],
+ "resolution": [
+ 16,
+ 16,
+ 16
+ ],
  "cubeLength": 64
  },
  {
- "resolution": [2, 2, 2],
+ "resolution": [
+ 2,
+ 2,
+ 2
+ ],
  "cubeLength": 512
  },
  {
- "resolution": [32, 32, 32],
+ "resolution": [
+ 32,
+ 32,
+ 32
+ ],
  "cubeLength": 32
  },
  {
- "resolution": [4, 4, 4],
+ "resolution": [
+ 4,
+ 4,
+ 4
+ ],
  "cubeLength": 256
  },
  {
- "resolution": [8, 8, 8],
+ "resolution": [
+ 8,
+ 8,
+ 8
+ ],
  "cubeLength": 128
  }
  ],
@@ -90,5 +146,12 @@
  "dataFormat": "wkw"
  }
  ],
- "scale": [11.239999771118164, 11.239999771118164, 28]
+ "scale": {
+ "unit": "nanometer",
+ "factor": [
+ 11.239999771118164,
+ 11.239999771118164,
+ 28
+ ]
+ }
 }

webknossos/testdata/tiff/datasource-properties.wkw-fixture.json

@@ -11,18 +11,33 @@
  "elementClass": "uint8",
  "wkwResolutions": [
  {
- "resolution": [1, 1, 1],
+ "resolution": [
+ 1,
+ 1,
+ 1
+ ],
  "cubeLength": 1024
  }
  ],
  "numChannels": 1,
  "boundingBox": {
- "topLeft": [0, 0, 0],
+ "topLeft": [
+ 0,
+ 0,
+ 0
+ ],
  "width": 265,
  "height": 265,
  "depth": 257
  }
  }
  ],
- "scale": [11.24, 11.24, 25.0]
+ "scale": {
+ "unit": "nanometer",
+ "factor": [
+ 11.24,
+ 11.24,
+ 25.0
+ ]
+ }
 }

webknossos/testdata/tiff/datasource-properties.zarr-fixture.json

@@ -3,11 +3,14 @@
  "name": "test_dataset",
  "team": "<unknown>"
  },
- "scale": [
- 11.24,
- 11.24,
- 25.0
- ],
+ "scale": {
+ "unit": "nanometer",
+ "factor": [
+ 11.24,
+ 11.24,
+ 25.0
+ ]
+ },
  "dataLayers": [
  {
  "name": "tiff",
@@ -43,4 +46,4 @@
  "largestSegmentId": 255
  }
  ]
-}
+}