From d7a616ad45d4c84c65b1748c505205b297346d98 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Wed, 1 Mar 2023 11:18:15 -0500 Subject: [PATCH 01/10] unit -> units --- latest/index.bs | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/latest/index.bs b/latest/index.bs index aa5feb95..ac836b3a 100644 --- a/latest/index.bs +++ b/latest/index.bs @@ -242,9 +242,9 @@ keys as specified below for discovering certain types of data, especially images -------------------------- "axes" describes the dimensions of a physical coordinate space. It is a list of dictionaries, where each dictionary describes a dimension (axis) and: -- MUST contain the field "name" that gives the name for this dimension. The values MUST be unique across all "name" fields. -- SHOULD contain the field "type". It SHOULD be one of "space", "time" or "channel", but MAY take other values for custom axis types that are not part of this specification yet. -- SHOULD contain the field "unit" to specify the physical unit of this dimension. The value SHOULD be one of the following strings, which are valid units according to UDUNITS-2. +- MUST contain the field "name" that gives the name for this dimension. The value MUST be a string. The values MUST be unique across all "name" fields. +- SHOULD contain the field "type". It SHOULD be one of strings "space", "time" or "channel", but MAY take other string values for custom axis types that are not part of this specification yet. +- SHOULD contain the field "units" to specify the physical units associated with this dimension. The value SHOULD be one of the following strings, which are valid units according to UDUNITS-2. - Units for "space" axes: 'angstrom', 'attometer', 'centimeter', 'decimeter', 'exameter', 'femtometer', 'foot', 'gigameter', 'hectometer', 'inch', 'kilometer', 'megameter', 'meter', 'micrometer', 'mile', 'millimeter', 'nanometer', 'parsec', 'petameter', 'picometer', 'terameter', 'yard', 'yoctometer', 'yottameter', 'zeptometer', 'zettameter' - Units for "time" axes: 'attosecond', 'centisecond', 'day', 'decisecond', 'exasecond', 'femtosecond', 'gigasecond', 'hectosecond', 'hour', 'kilosecond', 'megasecond', 'microsecond', 'millisecond', 'minute', 'nanosecond', 'petasecond', 'picosecond', 'second', 'terasecond', 'yoctosecond', 'yottasecond', 'zeptosecond', 'zettasecond' From 1e6b48e3a35c5a3be5995e3af0400c15d9bc2cb3 Mon Sep 17 00:00:00 2001 From: William Moore Date: Wed, 2 Nov 2022 16:56:11 +0000 Subject: [PATCH 02/10] Fix 'units' -> 'unit' in 0.4 and latest schemas, examples and test files --- .../multiscales_transformations.json | 4 +- 0.4/schemas/image.schema | 2 +- 0.4/tests/image_suite.json | 92 +++++++++---------- 0.4/tests/strict_image_suite.json | 18 ++-- .../multiscales_transformations.json | 4 +- latest/schemas/image.schema | 2 +- latest/tests/image_suite.json | 92 +++++++++---------- latest/tests/strict_image_suite.json | 18 ++-- 8 files changed, 116 insertions(+), 116 deletions(-) diff --git a/0.4/examples/multiscales_strict/multiscales_transformations.json b/0.4/examples/multiscales_strict/multiscales_transformations.json index 82836d0f..0097c47c 100644 --- a/0.4/examples/multiscales_strict/multiscales_transformations.json +++ b/0.4/examples/multiscales_strict/multiscales_transformations.json @@ -5,12 +5,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ diff --git a/0.4/schemas/image.schema b/0.4/schemas/image.schema index 59e8e28e..aec5db5f 100644 --- a/0.4/schemas/image.schema +++ b/0.4/schemas/image.schema @@ -124,7 +124,7 @@ "type": "string", "enum": ["space"] }, - "units": { + "unit": { "type": "string" } } diff --git a/0.4/tests/image_suite.json b/0.4/tests/image_suite.json index f22fa67f..42906985 100644 --- a/0.4/tests/image_suite.json +++ b/0.4/tests/image_suite.json @@ -14,17 +14,17 @@ { "name": "t", "type": "time", - "units": "micrometer" + "unit": "micrometer" }, { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -60,12 +60,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -115,12 +115,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ] } @@ -138,12 +138,12 @@ { "name": "y", "type": "space", - "units": "micron" + "unit": "micron" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -204,12 +204,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ] } @@ -231,12 +231,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -270,12 +270,12 @@ { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -344,12 +344,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -382,12 +382,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -476,12 +476,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -530,11 +530,11 @@ "axes": [ { "type": "space", - "units": "micron" + "unit": "micron" }, { "type": "space", - "units": "micron" + "unit": "micron" } ], "datasets": [ @@ -567,7 +567,7 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -641,12 +641,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -679,12 +679,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -725,12 +725,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -754,12 +754,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [], @@ -779,12 +779,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "version": "0.4" @@ -829,12 +829,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -867,12 +867,12 @@ { "name": "y", "type": "invalid", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -905,12 +905,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -1032,12 +1032,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -1087,12 +1087,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -1117,12 +1117,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ diff --git a/0.4/tests/strict_image_suite.json b/0.4/tests/strict_image_suite.json index 22b34c5e..ec6295d3 100644 --- a/0.4/tests/strict_image_suite.json +++ b/0.4/tests/strict_image_suite.json @@ -122,12 +122,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -205,12 +205,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ] } @@ -228,12 +228,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -279,17 +279,17 @@ { "name": "z", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ diff --git a/latest/examples/multiscales_strict/multiscales_transformations.json b/latest/examples/multiscales_strict/multiscales_transformations.json index c99040c2..80dbedab 100644 --- a/latest/examples/multiscales_strict/multiscales_transformations.json +++ b/latest/examples/multiscales_strict/multiscales_transformations.json @@ -5,12 +5,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ diff --git a/latest/schemas/image.schema b/latest/schemas/image.schema index 3926c4f4..055b058a 100644 --- a/latest/schemas/image.schema +++ b/latest/schemas/image.schema @@ -124,7 +124,7 @@ "type": "string", "enum": ["space"] }, - "units": { + "unit": { "type": "string" } } diff --git a/latest/tests/image_suite.json b/latest/tests/image_suite.json index 39cb73d5..7c3300b5 100644 --- a/latest/tests/image_suite.json +++ b/latest/tests/image_suite.json @@ -14,17 +14,17 @@ { "name": "t", "type": "time", - "units": "micrometer" + "unit": "micrometer" }, { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -60,12 +60,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -115,12 +115,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ] } @@ -138,12 +138,12 @@ { "name": "y", "type": "space", - "units": "micron" + "unit": "micron" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -204,12 +204,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ] } @@ -231,12 +231,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -270,12 +270,12 @@ { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -344,12 +344,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -382,12 +382,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -476,12 +476,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -530,11 +530,11 @@ "axes": [ { "type": "space", - "units": "micron" + "unit": "micron" }, { "type": "space", - "units": "micron" + "unit": "micron" } ], "datasets": [ @@ -567,7 +567,7 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -641,12 +641,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -679,12 +679,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -725,12 +725,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -754,12 +754,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [], @@ -779,12 +779,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "version": "0.5-dev" @@ -829,12 +829,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -867,12 +867,12 @@ { "name": "y", "type": "invalid", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -905,12 +905,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -1032,12 +1032,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -1087,12 +1087,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -1117,12 +1117,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ diff --git a/latest/tests/strict_image_suite.json b/latest/tests/strict_image_suite.json index b8aeebe1..7bff90ca 100644 --- a/latest/tests/strict_image_suite.json +++ b/latest/tests/strict_image_suite.json @@ -122,12 +122,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -205,12 +205,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ] } @@ -228,12 +228,12 @@ { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ @@ -279,17 +279,17 @@ { "name": "z", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "y", "type": "space", - "units": "micrometer" + "unit": "micrometer" }, { "name": "x", "type": "space", - "units": "micrometer" + "unit": "micrometer" } ], "datasets": [ From 5a26ac80bc85c261a71441c262b132836abea134 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Thu, 9 Mar 2023 19:25:18 -0500 Subject: [PATCH 03/10] change unit to units in schema --- latest/schemas/image.schema | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/latest/schemas/image.schema b/latest/schemas/image.schema index 055b058a..3926c4f4 100644 --- a/latest/schemas/image.schema +++ b/latest/schemas/image.schema @@ -124,7 +124,7 @@ "type": "string", "enum": ["space"] }, - "unit": { + "units": { "type": "string" } } From 38f2d80b6188853016a80347b060760512db285f Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Thu, 9 Mar 2023 19:27:51 -0500 Subject: [PATCH 04/10] change unit to units in examples --- .../multiscales_strict/multiscales_example.json | 10 +++++----- .../multiscales_transformations.json | 4 ++-- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/latest/examples/multiscales_strict/multiscales_example.json b/latest/examples/multiscales_strict/multiscales_example.json index 73e5286c..3c0f71db 100644 --- a/latest/examples/multiscales_strict/multiscales_example.json +++ b/latest/examples/multiscales_strict/multiscales_example.json @@ -4,11 +4,11 @@ "version": "0.5-dev", "name": "example", "axes": [ - {"name": "t", "type": "time", "unit": "millisecond"}, + {"name": "t", "type": "time", "units": "millisecond"}, {"name": "c", "type": "channel"}, - {"name": "z", "type": "space", "unit": "micrometer"}, - {"name": "y", "type": "space", "unit": "micrometer"}, - {"name": "x", "type": "space", "unit": "micrometer"} + {"name": "z", "type": "space", "units": "micrometer"}, + {"name": "y", "type": "space", "units": "micrometer"}, + {"name": "x", "type": "space", "units": "micrometer"} ], "datasets": [ { @@ -37,7 +37,7 @@ } ], "coordinateTransformations": [{ - // the time unit (0.1 milliseconds), which is the same for each scale level + // the time units (0.1 milliseconds), which is the same for each scale level "type": "scale", "scale": [0.1, 1.0, 1.0, 1.0, 1.0] }], diff --git a/latest/examples/multiscales_strict/multiscales_transformations.json b/latest/examples/multiscales_strict/multiscales_transformations.json index 80dbedab..c99040c2 100644 --- a/latest/examples/multiscales_strict/multiscales_transformations.json +++ b/latest/examples/multiscales_strict/multiscales_transformations.json @@ -5,12 +5,12 @@ { "name": "y", "type": "space", - "unit": "micrometer" + "units": "micrometer" }, { "name": "x", "type": "space", - "unit": "micrometer" + "units": "micrometer" } ], "datasets": [ From 4f5049ece023d44684381ec2ac9ec47bfb5f841b Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Tue, 14 Mar 2023 13:42:01 +0100 Subject: [PATCH 05/10] Fix `` element for newer bikeshed versions MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Apparently a new release of bikeshed is now unhappy with the use of `` and `` is required: ``` $ bikeshed spec "latest/index.bs" "latest/index.out.html" LINE 651:1: Tag wasn't closed at end of file. ✘ Did not generate, due to fatal errors Failed ``` --- 0.1/index.bs | 3 +-- 0.2/index.bs | 3 +-- 0.3/index.bs | 3 +-- 0.4/index.bs | 3 +-- latest/index.bs | 3 +-- 5 files changed, 5 insertions(+), 10 deletions(-) diff --git a/0.1/index.bs b/0.1/index.bs index b60204f1..52a33115 100644 --- a/0.1/index.bs +++ b/0.1/index.bs @@ -501,8 +501,7 @@ Projects which support reading and/or writing OME-NGFF data include: -Diagram of related projects +Diagram of related projects All implementations prevent an equivalent representation of a dataset which can be downloaded or uploaded freely. An interactive version of this diagram is available from the [OME2020 Workshop](https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/). diff --git a/0.2/index.bs b/0.2/index.bs index 4e25ad2c..487f91a3 100644 --- a/0.2/index.bs +++ b/0.2/index.bs @@ -559,8 +559,7 @@ Projects which support reading and/or writing OME-NGFF data include: -Diagram of related projects +Diagram of related projects All implementations prevent an equivalent representation of a dataset which can be downloaded or uploaded freely. An interactive version of this diagram is available from the [OME2020 Workshop](https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/). diff --git a/0.3/index.bs b/0.3/index.bs index 84192b65..47bc2dcf 100644 --- a/0.3/index.bs +++ b/0.3/index.bs @@ -569,8 +569,7 @@ Projects which support reading and/or writing OME-NGFF data include: -Diagram of related projects +Diagram of related projects All implementations prevent an equivalent representation of a dataset which can be downloaded or uploaded freely. An interactive version of this diagram is available from the [OME2020 Workshop](https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/). diff --git a/0.4/index.bs b/0.4/index.bs index d39b2c5f..e2a41769 100644 --- a/0.4/index.bs +++ b/0.4/index.bs @@ -639,8 +639,7 @@ Projects which support reading and/or writing OME-NGFF data include: -Diagram of related projects +Diagram of related projects All implementations prevent an equivalent representation of a dataset which can be downloaded or uploaded freely. An interactive version of this diagram is available from the [OME2020 Workshop](https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/). diff --git a/latest/index.bs b/latest/index.bs index aa5feb95..d0996a9d 100644 --- a/latest/index.bs +++ b/latest/index.bs @@ -648,8 +648,7 @@ Projects which support reading and/or writing OME-NGFF data include: -Diagram of related projects +Diagram of related projects All implementations prevent an equivalent representation of a dataset which can be downloaded or uploaded freely. An interactive version of this diagram is available from the [OME2020 Workshop](https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/). From 1a74291faebce555e8eb93eae45c2f65619d1deb Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Tue, 14 Mar 2023 13:42:01 +0100 Subject: [PATCH 06/10] Fix `` element for newer bikeshed versions MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Apparently a new release of bikeshed is now unhappy with the use of `` and `` is required: ``` $ bikeshed spec "latest/index.bs" "latest/index.out.html" LINE 651:1: Tag wasn't closed at end of file. ✘ Did not generate, due to fatal errors Failed ``` --- 0.1/index.bs | 3 +-- 0.2/index.bs | 3 +-- 0.3/index.bs | 3 +-- 0.4/index.bs | 3 +-- latest/index.bs | 3 +-- 5 files changed, 5 insertions(+), 10 deletions(-) diff --git a/0.1/index.bs b/0.1/index.bs index b60204f1..52a33115 100644 --- a/0.1/index.bs +++ b/0.1/index.bs @@ -501,8 +501,7 @@ Projects which support reading and/or writing OME-NGFF data include: -Diagram of related projects +Diagram of related projects All implementations prevent an equivalent representation of a dataset which can be downloaded or uploaded freely. An interactive version of this diagram is available from the [OME2020 Workshop](https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/). diff --git a/0.2/index.bs b/0.2/index.bs index 4e25ad2c..487f91a3 100644 --- a/0.2/index.bs +++ b/0.2/index.bs @@ -559,8 +559,7 @@ Projects which support reading and/or writing OME-NGFF data include: -Diagram of related projects +Diagram of related projects All implementations prevent an equivalent representation of a dataset which can be downloaded or uploaded freely. An interactive version of this diagram is available from the [OME2020 Workshop](https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/). diff --git a/0.3/index.bs b/0.3/index.bs index 84192b65..47bc2dcf 100644 --- a/0.3/index.bs +++ b/0.3/index.bs @@ -569,8 +569,7 @@ Projects which support reading and/or writing OME-NGFF data include: -Diagram of related projects +Diagram of related projects All implementations prevent an equivalent representation of a dataset which can be downloaded or uploaded freely. An interactive version of this diagram is available from the [OME2020 Workshop](https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/). diff --git a/0.4/index.bs b/0.4/index.bs index d39b2c5f..e2a41769 100644 --- a/0.4/index.bs +++ b/0.4/index.bs @@ -639,8 +639,7 @@ Projects which support reading and/or writing OME-NGFF data include: -Diagram of related projects +Diagram of related projects All implementations prevent an equivalent representation of a dataset which can be downloaded or uploaded freely. An interactive version of this diagram is available from the [OME2020 Workshop](https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/). diff --git a/latest/index.bs b/latest/index.bs index ac836b3a..88da6a6a 100644 --- a/latest/index.bs +++ b/latest/index.bs @@ -648,8 +648,7 @@ Projects which support reading and/or writing OME-NGFF data include: -Diagram of related projects +Diagram of related projects All implementations prevent an equivalent representation of a dataset which can be downloaded or uploaded freely. An interactive version of this diagram is available from the [OME2020 Workshop](https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/). From 859a5c82369858ea51fc998bd63edb7970e60b16 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Fri, 17 Mar 2023 15:44:46 -0400 Subject: [PATCH 07/10] clarify relationship between units and old unit key --- latest/index.bs | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/latest/index.bs b/latest/index.bs index 88da6a6a..de375341 100644 --- a/latest/index.bs +++ b/latest/index.bs @@ -244,7 +244,12 @@ keys as specified below for discovering certain types of data, especially images "axes" describes the dimensions of a physical coordinate space. It is a list of dictionaries, where each dictionary describes a dimension (axis) and: - MUST contain the field "name" that gives the name for this dimension. The value MUST be a string. The values MUST be unique across all "name" fields. - SHOULD contain the field "type". It SHOULD be one of strings "space", "time" or "channel", but MAY take other string values for custom axis types that are not part of this specification yet. -- SHOULD contain the field "units" to specify the physical units associated with this dimension. The value SHOULD be one of the following strings, which are valid units according to UDUNITS-2. +- SHOULD contain the field "units" to specify the physical units associated with this dimension. Previous versions of the specification used the name "unit" for this field. For backwards compatibility, + the field "unit" is also permitted by this specification, but this usage will be forbidden in future versions of the specification. If both "units" and "unit" fields are present, the value associated with "units" should be used. + + Implementation note: if possible, applications implementing this specification SHOULD warn users when consuming "axes" metadata if the "unit" field is present on any elements of "axes". + + The value of "units" SHOULD be one of the following strings, which are valid units according to UDUNITS-2. - Units for "space" axes: 'angstrom', 'attometer', 'centimeter', 'decimeter', 'exameter', 'femtometer', 'foot', 'gigameter', 'hectometer', 'inch', 'kilometer', 'megameter', 'meter', 'micrometer', 'mile', 'millimeter', 'nanometer', 'parsec', 'petameter', 'picometer', 'terameter', 'yard', 'yoctometer', 'yottameter', 'zeptometer', 'zettameter' - Units for "time" axes: 'attosecond', 'centisecond', 'day', 'decisecond', 'exasecond', 'femtosecond', 'gigasecond', 'hectosecond', 'hour', 'kilosecond', 'megasecond', 'microsecond', 'millisecond', 'minute', 'nanosecond', 'petasecond', 'picosecond', 'second', 'terasecond', 'yoctosecond', 'yottasecond', 'zeptosecond', 'zettasecond' From 815d9a4631afd2d6397b0458ca318e29dce68f80 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Fri, 17 Mar 2023 20:21:14 -0400 Subject: [PATCH 08/10] style --- latest/index.bs | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/latest/index.bs b/latest/index.bs index de375341..e2c0e7b2 100644 --- a/latest/index.bs +++ b/latest/index.bs @@ -245,9 +245,9 @@ keys as specified below for discovering certain types of data, especially images - MUST contain the field "name" that gives the name for this dimension. The value MUST be a string. The values MUST be unique across all "name" fields. - SHOULD contain the field "type". It SHOULD be one of strings "space", "time" or "channel", but MAY take other string values for custom axis types that are not part of this specification yet. - SHOULD contain the field "units" to specify the physical units associated with this dimension. Previous versions of the specification used the name "unit" for this field. For backwards compatibility, - the field "unit" is also permitted by this specification, but this usage will be forbidden in future versions of the specification. If both "units" and "unit" fields are present, the value associated with "units" should be used. + the field "unit" is also permitted, but this usage will not be supported by future versions of the specification. If both "units" and "unit" fields are present, the value associated with "units" should be used. - Implementation note: if possible, applications implementing this specification SHOULD warn users when consuming "axes" metadata if the "unit" field is present on any elements of "axes". + Implementation note: wherever possible, applications implementing this specification SHOULD give users a deprecation warning when consuming "axes" metadata if the "unit" field is present on any elements of "axes". The value of "units" SHOULD be one of the following strings, which are valid units according to UDUNITS-2. - Units for "space" axes: 'angstrom', 'attometer', 'centimeter', 'decimeter', 'exameter', 'femtometer', 'foot', 'gigameter', 'hectometer', 'inch', 'kilometer', 'megameter', 'meter', 'micrometer', 'mile', 'millimeter', 'nanometer', 'parsec', 'petameter', 'picometer', 'terameter', 'yard', 'yoctometer', 'yottameter', 'zeptometer', 'zettameter' From 5a59d3fc6567e7b4c1dc65eaea6b199ee1e2e87a Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Mar 2023 09:38:17 -0400 Subject: [PATCH 09/10] add units to schema --- latest/schemas/image.schema | 3 +++ 1 file changed, 3 insertions(+) diff --git a/latest/schemas/image.schema b/latest/schemas/image.schema index 055b058a..45eaf823 100644 --- a/latest/schemas/image.schema +++ b/latest/schemas/image.schema @@ -126,6 +126,9 @@ }, "unit": { "type": "string" + }, + "units": { + "type": "string" } } }, From e3bba84ff075b56c9ef9fed5e9461fc12006de91 Mon Sep 17 00:00:00 2001 From: Davis Vann Bennett Date: Tue, 21 Mar 2023 10:28:34 -0400 Subject: [PATCH 10/10] style tweaks --- latest/index.bs | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/latest/index.bs b/latest/index.bs index e2c0e7b2..b92bc586 100644 --- a/latest/index.bs +++ b/latest/index.bs @@ -245,9 +245,9 @@ keys as specified below for discovering certain types of data, especially images - MUST contain the field "name" that gives the name for this dimension. The value MUST be a string. The values MUST be unique across all "name" fields. - SHOULD contain the field "type". It SHOULD be one of strings "space", "time" or "channel", but MAY take other string values for custom axis types that are not part of this specification yet. - SHOULD contain the field "units" to specify the physical units associated with this dimension. Previous versions of the specification used the name "unit" for this field. For backwards compatibility, - the field "unit" is also permitted, but this usage will not be supported by future versions of the specification. If both "units" and "unit" fields are present, the value associated with "units" should be used. + the field "unit" is permitted, but this usage will not be supported by future versions of the specification. If both "units" and "unit" fields are present, the value associated with "units" should be used. - Implementation note: wherever possible, applications implementing this specification SHOULD give users a deprecation warning when consuming "axes" metadata if the "unit" field is present on any elements of "axes". + Implementation note: wherever possible, applications implementing this specification SHOULD issue a deprecation warning if the "unit" field is present on any elements of "axes". Users should be notified that the "unit" field is being deprecated and replaced by "units". The value of "units" SHOULD be one of the following strings, which are valid units according to UDUNITS-2. - Units for "space" axes: 'angstrom', 'attometer', 'centimeter', 'decimeter', 'exameter', 'femtometer', 'foot', 'gigameter', 'hectometer', 'inch', 'kilometer', 'megameter', 'meter', 'micrometer', 'mile', 'millimeter', 'nanometer', 'parsec', 'petameter', 'picometer', 'terameter', 'yard', 'yoctometer', 'yottameter', 'zeptometer', 'zettameter'