chore(rebuild): Merge pull request #110 from sbesson/json_snippets_la…

…test Extract specification snippets as standalone JSON files (latest) SHA: caa7e8e Reason: push, by @joshmoore Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
ome · Apr 8, 2022 · a87990d · a87990d
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diff --git a/0.1/index.html b/0.1/index.html
@@ -1489,7 +1489,7 @@
 </style>
   <meta content="Bikeshed version fb1e763a4, updated Tue Mar 1 13:13:50 2022 -0800" name="generator">
   <link href="https://ngff.openmicroscopy.org/0.1/" rel="canonical">
-  <meta content="8dec6918ee6630f43f339b281b66043e0a797ca4" name="document-revision">
+  <meta content="caa7e8eb83291947e4168539d30a7afc967f6f4f" name="document-revision">
 <style>/* style-autolinks */
 
 .css.css, .property.property, .descriptor.descriptor {
@@ -1825,7 +1825,7 @@
   <div class="head">
     <img alt="OME logo (6 circles in a hexagon)" src="http://www.openmicroscopy.org/img/logos/ome-logomark.svg" style="float:right;width:42px;height:42px;"> 
    <h1 class="p-name no-ref" id="title">Next-generation file formats (NGFF)</h1>
-   <h2 class="no-num no-toc no-ref heading settled" id="subtitle"><span class="content">Final Community Group Report, <time class="dt-updated" datetime="2022-03-18">18 March 2022</time></span></h2>
+   <h2 class="no-num no-toc no-ref heading settled" id="subtitle"><span class="content">Final Community Group Report, <time class="dt-updated" datetime="2022-04-08">8 April 2022</time></span></h2>
    <div data-fill-with="spec-metadata">
     <dl>
      <dt>This version:

diff --git a/0.2/index.html b/0.2/index.html
@@ -1489,7 +1489,7 @@
 </style>
   <meta content="Bikeshed version fb1e763a4, updated Tue Mar 1 13:13:50 2022 -0800" name="generator">
   <link href="https://ngff.openmicroscopy.org/0.2/" rel="canonical">
-  <meta content="8dec6918ee6630f43f339b281b66043e0a797ca4" name="document-revision">
+  <meta content="caa7e8eb83291947e4168539d30a7afc967f6f4f" name="document-revision">
 <style>/* style-autolinks */
 
 .css.css, .property.property, .descriptor.descriptor {
@@ -1825,7 +1825,7 @@
   <div class="head">
     <img alt="OME logo (6 circles in a hexagon)" src="http://www.openmicroscopy.org/img/logos/ome-logomark.svg" style="float:right;width:42px;height:42px;"> 
    <h1 class="p-name no-ref" id="title">Next-generation file formats (NGFF)</h1>
-   <h2 class="no-num no-toc no-ref heading settled" id="subtitle"><span class="content">Final Community Group Report, <time class="dt-updated" datetime="2022-03-18">18 March 2022</time></span></h2>
+   <h2 class="no-num no-toc no-ref heading settled" id="subtitle"><span class="content">Final Community Group Report, <time class="dt-updated" datetime="2022-04-08">8 April 2022</time></span></h2>
    <div data-fill-with="spec-metadata">
     <dl>
      <dt>This version:

diff --git a/0.3/index.html b/0.3/index.html
@@ -8,7 +8,7 @@
   <link href="https://www.w3.org/2008/site/images/favicon.ico" rel="icon">
   <meta content="Bikeshed version fb1e763a4, updated Tue Mar 1 13:13:50 2022 -0800" name="generator">
   <link href="https://ngff.openmicroscopy.org/0.3/" rel="canonical">
-  <meta content="8dec6918ee6630f43f339b281b66043e0a797ca4" name="document-revision">
+  <meta content="caa7e8eb83291947e4168539d30a7afc967f6f4f" name="document-revision">
 <style>/* style-autolinks */
 
 .css.css, .property.property, .descriptor.descriptor {
@@ -344,7 +344,7 @@
   <div class="head">
    <p data-fill-with="logo"><a class="logo" href="https://www.w3.org/"> <img alt="W3C" height="48" src="https://www.w3.org/StyleSheets/TR/2021/logos/W3C" width="72"> </a> </p>
    <h1 class="p-name no-ref" id="title">Next-generation file formats (NGFF)</h1>
-   <p id="w3c-state"><a href="https://www.w3.org/standards/types#CG-FINAL">Final Community Group Report</a>, <time class="dt-updated" datetime="2022-03-18">18 March 2022</time></p>
+   <p id="w3c-state"><a href="https://www.w3.org/standards/types#CG-FINAL">Final Community Group Report</a>, <time class="dt-updated" datetime="2022-04-08">8 April 2022</time></p>
    <details open>
     <summary>More details about this document</summary>
     <div data-fill-with="spec-metadata">

diff --git a/0.4/index.html b/0.4/index.html
@@ -8,7 +8,7 @@
   <link href="https://www.w3.org/2008/site/images/favicon.ico" rel="icon">
   <meta content="Bikeshed version fb1e763a4, updated Tue Mar 1 13:13:50 2022 -0800" name="generator">
   <link href="https://ngff.openmicroscopy.org/0.4/" rel="canonical">
-  <meta content="8dec6918ee6630f43f339b281b66043e0a797ca4" name="document-revision">
+  <meta content="caa7e8eb83291947e4168539d30a7afc967f6f4f" name="document-revision">
 <style>/* style-autolinks */
 
 .css.css, .property.property, .descriptor.descriptor {
@@ -344,7 +344,7 @@
   <div class="head">
    <p data-fill-with="logo"><a class="logo" href="https://www.w3.org/"> <img alt="W3C" height="48" src="https://www.w3.org/StyleSheets/TR/2021/logos/W3C" width="72"> </a> </p>
    <h1 class="p-name no-ref" id="title">Next-generation file formats (NGFF)</h1>
-   <p id="w3c-state"><a href="https://www.w3.org/standards/types#CG-FINAL">Final Community Group Report</a>, <time class="dt-updated" datetime="2022-03-18">18 March 2022</time></p>
+   <p id="w3c-state"><a href="https://www.w3.org/standards/types#CG-FINAL">Final Community Group Report</a>, <time class="dt-updated" datetime="2022-04-08">8 April 2022</time></p>
    <details open>
     <summary>More details about this document</summary>
     <div data-fill-with="spec-metadata">

diff --git a/latest/index.html b/latest/index.html
@@ -1489,7 +1489,7 @@
 </style>
   <meta content="Bikeshed version fb1e763a4, updated Tue Mar 1 13:13:50 2022 -0800" name="generator">
   <link href="https://ngff.openmicroscopy.org/latest/" rel="canonical">
-  <meta content="8dec6918ee6630f43f339b281b66043e0a797ca4" name="document-revision">
+  <meta content="caa7e8eb83291947e4168539d30a7afc967f6f4f" name="document-revision">
 <style>/* style-autolinks */
 
 .css.css, .property.property, .descriptor.descriptor {
@@ -1825,7 +1825,7 @@
   <div class="head">
     <img alt="OME logo (6 circles in a hexagon)" src="http://www.openmicroscopy.org/img/logos/ome-logomark.svg" style="float:right;width:42px;height:42px;"> 
    <h1 class="p-name no-ref" id="title">Next-generation file formats (NGFF)</h1>
-   <h2 class="no-num no-toc no-ref heading settled" id="subtitle"><span class="content">Editor’s Draft, <time class="dt-updated" datetime="2022-03-18">18 March 2022</time></span></h2>
+   <h2 class="no-num no-toc no-ref heading settled" id="subtitle"><span class="content">Editor’s Draft, <time class="dt-updated" datetime="2022-04-08">8 April 2022</time></span></h2>
    <div data-fill-with="spec-metadata">
     <dl>
      <dt>This version:
@@ -1867,6 +1867,7 @@ <h2 class="no-num no-toc no-ref" id="contents">Table of Contents</h2>
      <ol class="toc">
       <li><a href="#why-ngff"><span class="secno">1.1</span> <span class="content">Why "<span><abbr title="Next-generation file-format">NGFF</abbr></span>"?</span></a>
       <li><a href="#ome-ngff"><span class="secno">1.2</span> <span class="content">OME-NGFF</span></a>
+      <li><a href="#document-conventions"><span class="secno">1.3</span> <span class="content">Document conventions</span></a>
      </ol>
     <li>
      <a href="#on-disk"><span class="secno">2</span> <span class="content">On-disk (or in-cloud) layout</span></a>
@@ -1959,6 +1960,11 @@ <h3 class="heading settled" data-level="1.2" id="ome-ngff"><span class="secno">1
 of bioimaging data, whether during acquisition or sharing in the cloud.</p>
    <p class="note" role="note"><span>Note:</span> The following text makes use of OME-Zarr <a data-link-type="biblio" href="#biblio-ome-zarr-py">[ome-zarr-py]</a>, the current prototype implementation,
 for all examples.</p>
+   <h3 class="heading settled" data-level="1.3" id="document-conventions"><span class="secno">1.3. </span><span class="content">Document conventions</span><a class="self-link" href="#document-conventions"></a></h3>
+   <p>The key words “MUST”, “MUST NOT”, “REQUIRED”, “SHALL”, “SHALL NOT”, “SHOULD”, “SHOULD NOT”,
+“RECOMMENDED”, “MAY”, and “OPTIONAL” are to be interpreted as described in <a href="https://tools.ietf.org/html/rfc2119">RFC 2119</a>.</p>
+   <p>Some of the JSON examples in this document include commments. However, these are only for
+clarity purposes and comments MUST NOT be included in JSON objects.</p>
    <h2 class="heading settled" data-level="2" id="on-disk"><span class="secno">2. </span><span class="content">On-disk (or in-cloud) layout</span><a class="self-link" href="#on-disk"></a></h2>
    <p>An overview of the layout of an OME-Zarr fileset should make
 understanding the following metadata sections easier. The hierarchy
@@ -2130,47 +2136,63 @@ <h3 class="heading settled" data-level="3.3" id="multiscale-md"><span class="sec
    <p>Each "multiscales" dictionary MAY contain the field "coordinateTransformations", describing transformations that are applied to all resolution levels in the same manner.
 The transformations MUST follow the same rules about allowed types, order, etc. as in "datasets:coordinateTransformations" and are applied after them.
 They can for example be used to specify the <code>scale</code> for a dimension that is the same for all resolutions.</p>
-   <p>Each "multiscales" dictionary SHOULD contain the field "name". It SHOULD contain the field "version", which indicates the version of the multiscale metadata of this image (current version is 0.4).</p>
+   <p>Each "multiscales" dictionary SHOULD contain the field "name". It SHOULD contain the field "version", which indicates the version of the multiscale metadata of this image (current version is 0.5-dev).</p>
    <p>Each "multiscales" dictionary SHOULD contain the field "type", which gives the type of downscaling method used to generate the multiscale image pyramid.
 It SHOULD contain the field "metadata", which contains a dictionary with additional information about the downscaling method.</p>
-<pre>{
-    "multiscales": [
-        {
-            "version": "0.4",
-            "name": "example",
-            "axes": [
-                {"name": "t", "type": "time", "unit": "millisecond"},
-                {"name": "c", "type": "channel"},
-                {"name": "z", "type": "space", "unit": "micrometer"},
-                {"name": "y", "type": "space", "unit": "micrometer"},
-                {"name": "x", "type": "space", "unit": "micrometer"}
-            ],
-            "datasets": [
-                {
-                    "path": "0",
-                    "coordinateTransformations": [{"type": "scale", "scale": [1.0, 1.0, 0.5, 0.5, 0.5]}]  # the voxel size for the first scale level (0.5 micrometer)
-                }
-                {
-                    "path": "1",
-                    "coordinateTransformations": [{"type": "scale", "scale": [1.0, 1.0, 1.0, 1.0, 1.0]}]  # the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer)
-                },
-                {
-                    "path": "2",
-                    "coordinateTransformations": [{"type": "scale", "scale": [1.0, 1.0, 2.0, 2.0, 2.0]}]  # the voxel size for the second scale level (downscaled by a factor of 4 -> 2 micrometer)
-                }
-            ],
-            "coordinateTransformations": [{"type": "scale", "scale": [0.1, 1.0, 1.0, 1.0, 1.0]],  # the time unit (0.1 milliseconds), which is the same for each scale level
-            "type": "gaussian",
-            "metadata": {                                       # the fields in metadata depend on the downscaling implementation
-                "method": "skimage.transform.pyramid_gaussian", # here, the paramters passed to the skimage function are given
-                "version": "0.16.1",
-                "args": "[true]",
-                "kwargs": {"multichannel": true}
-            }
-        }
-    ]
-}
-</pre>
+<pre class="include-code highlight"><c- p>{</c->
+    <c- f>"multiscales"</c-><c- p>:</c-> <c- p>[</c->
+        <c- p>{</c->
+            <c- f>"version"</c-><c- p>:</c-> <c- u>"0.5-dev"</c-><c- p>,</c->
+            <c- f>"name"</c-><c- p>:</c-> <c- u>"example"</c-><c- p>,</c->
+            <c- f>"axes"</c-><c- p>:</c-> <c- p>[</c->
+                <c- p>{</c-><c- f>"name"</c-><c- p>:</c-> <c- u>"t"</c-><c- p>,</c-> <c- f>"type"</c-><c- p>:</c-> <c- u>"time"</c-><c- p>,</c-> <c- f>"unit"</c-><c- p>:</c-> <c- u>"millisecond"</c-><c- p>},</c->
+                <c- p>{</c-><c- f>"name"</c-><c- p>:</c-> <c- u>"c"</c-><c- p>,</c-> <c- f>"type"</c-><c- p>:</c-> <c- u>"channel"</c-><c- p>},</c->
+                <c- p>{</c-><c- f>"name"</c-><c- p>:</c-> <c- u>"z"</c-><c- p>,</c-> <c- f>"type"</c-><c- p>:</c-> <c- u>"space"</c-><c- p>,</c-> <c- f>"unit"</c-><c- p>:</c-> <c- u>"micrometer"</c-><c- p>},</c->
+                <c- p>{</c-><c- f>"name"</c-><c- p>:</c-> <c- u>"y"</c-><c- p>,</c-> <c- f>"type"</c-><c- p>:</c-> <c- u>"space"</c-><c- p>,</c-> <c- f>"unit"</c-><c- p>:</c-> <c- u>"micrometer"</c-><c- p>},</c->
+                <c- p>{</c-><c- f>"name"</c-><c- p>:</c-> <c- u>"x"</c-><c- p>,</c-> <c- f>"type"</c-><c- p>:</c-> <c- u>"space"</c-><c- p>,</c-> <c- f>"unit"</c-><c- p>:</c-> <c- u>"micrometer"</c-><c- p>}</c->
+            <c- p>],</c->
+            <c- f>"datasets"</c-><c- p>:</c-> <c- p>[</c->
+                <c- p>{</c->
+                    <c- f>"path"</c-><c- p>:</c-> <c- u>"0"</c-><c- p>,</c->
+                    <c- f>"coordinateTransformations"</c-><c- p>:</c-> <c- p>[{</c->
+                        // <c- kc>t</c->he voxel size <c- kc>f</c->or <c- kc>t</c->he <c- kc>f</c->irs<c- kc>t</c-> scale level (<c- mf>0.5</c-> microme<c- kc>ter</c->)
+                        <c- f>"type"</c-><c- p>:</c-> <c- u>"scale"</c-><c- p>,</c->
+                        <c- f>"scale"</c-><c- p>:</c-> <c- p>[</c-><c- mf>1.0</c-><c- p>,</c-> <c- mf>1.0</c-><c- p>,</c-> <c- mf>0.5</c-><c- p>,</c-> <c- mf>0.5</c-><c- p>,</c-> <c- mf>0.5</c-><c- p>]</c->
+                    <c- p>}]</c->
+                <c- p>},</c->
+                <c- p>{</c->
+                    <c- f>"path"</c-><c- p>:</c-> <c- u>"1"</c-><c- p>,</c->
+                    <c- f>"coordinateTransformations"</c-><c- p>:</c-> <c- p>[{</c->
+                        // <c- kc>t</c->he voxel size <c- kc>f</c->or <c- kc>t</c->he seco<c- kc>n</c->d scale level (dow<c- kc>ns</c->caled by a <c- kc>fa</c->c<c- kc>t</c->or o<c- kc>f</c-> <c- mi>2</c-> <c- mi>-</c->> <c- mi>1</c-> microme<c- kc>ter</c->)
+                        <c- f>"type"</c-><c- p>:</c-> <c- u>"scale"</c-><c- p>,</c->
+                        <c- f>"scale"</c-><c- p>:</c-> <c- p>[</c-><c- mf>1.0</c-><c- p>,</c-> <c- mf>1.0</c-><c- p>,</c-> <c- mf>1.0</c-><c- p>,</c-> <c- mf>1.0</c-><c- p>,</c-> <c- mf>1.0</c-><c- p>]</c->
+                    <c- p>}]</c->
+                <c- p>},</c->
+                <c- p>{</c->
+                    <c- f>"path"</c-><c- p>:</c-> <c- u>"2"</c-><c- p>,</c->
+                    <c- f>"coordinateTransformations"</c-><c- p>:</c-> <c- p>[{</c->
+                        // <c- kc>t</c->he voxel size <c- kc>f</c->or <c- kc>t</c->he <c- kc>t</c->hird scale level (dow<c- kc>ns</c->caled by a <c- kc>fa</c->c<c- kc>t</c->or o<c- kc>f</c-> <c- mi>4</c-> <c- mi>-</c->> <c- mi>2</c-> microme<c- kc>ter</c->)
+                        <c- f>"type"</c-><c- p>:</c-> <c- u>"scale"</c-><c- p>,</c->
+                        <c- f>"scale"</c-><c- p>:</c-> <c- p>[</c-><c- mf>1.0</c-><c- p>,</c-> <c- mf>1.0</c-><c- p>,</c-> <c- mf>2.0</c-><c- p>,</c-> <c- mf>2.0</c-><c- p>,</c-> <c- mf>2.0</c-><c- p>]</c->
+                    <c- p>}]</c->
+                <c- p>}</c->
+            <c- p>],</c->
+            <c- f>"coordinateTransformations"</c-><c- p>:</c-> <c- p>[{</c->
+                // <c- kc>t</c->he <c- kc>t</c->ime u<c- kc>n</c->i<c- kc>t</c-> (<c- mf>0.1</c-> milliseco<c- kc>n</c->ds)<c- p>,</c-> which is <c- kc>t</c->he same <c- kc>f</c->or each scale level
+                <c- f>"type"</c-><c- p>:</c-> <c- u>"scale"</c-><c- p>,</c->
+                <c- f>"scale"</c-><c- p>:</c-> <c- p>[</c-><c- mf>0.1</c-><c- p>,</c-> <c- mf>1.0</c-><c- p>,</c-> <c- mf>1.0</c-><c- p>,</c-> <c- mf>1.0</c-><c- p>,</c-> <c- mf>1.0</c-><c- p>]</c->
+            <c- p>}],</c->
+            <c- f>"type"</c-><c- p>:</c-> <c- u>"gaussian"</c-><c- p>,</c->
+            <c- f>"metadata"</c-><c- p>:</c-> <c- p>{</c->
+                <c- f>"description"</c-><c- p>:</c-> <c- u>"the fields in metadata depend on the downscaling implementation. Here, the parameters passed to the skimage function are given"</c-><c- p>,</c->
+                <c- f>"method"</c-><c- p>:</c-> <c- u>"skimage.transform.pyramid_gaussian"</c-><c- p>,</c->
+                <c- f>"version"</c-><c- p>:</c-> <c- u>"0.16.1"</c-><c- p>,</c->
+                <c- f>"args"</c-><c- p>:</c-> <c- u>"[true]"</c-><c- p>,</c->
+                <c- f>"kwargs"</c-><c- p>:</c-> <c- p>{</c-><c- f>"multichannel"</c-><c- p>:</c-> <c- kc>true</c-><c- p>}</c->
+            <c- p>}</c->
+        <c- p>}</c->
+    <c- p>]</c->
+<c- p>}</c-></pre>
    <p>If only one multiscale is provided, use it. Otherwise, the user can choose by
 name, using the first multiscale as a fallback:</p>
 <pre class="language-python highlight"><c- n>datasets</c-> <c- o>=</c-> <c- p>[]</c->
@@ -2187,7 +2209,7 @@ <h3 class="heading settled" data-level="3.4" id="omero-md"><span class="secno">3
 can be found under the "omero" key in the group-level metadata:</p>
 <pre class="language-json highlight"><c- f>"id"</c-><c- p>:</c-> <c- mi>1</c-><c- p>,</c->                              # ID i<c- kc>n</c-> OMERO
 <c- f>"name"</c-><c- p>:</c-> <c- u>"example.tif"</c-><c- p>,</c->                # Name as show<c- kc>n</c-> i<c- kc>n</c-> <c- kc>t</c->he UI
-<c- f>"version"</c-><c- p>:</c-> <c- u>"0.4"</c-><c- p>,</c->                     # Curre<c- kc>nt</c-> versio<c- kc>n</c->
+<c- f>"version"</c-><c- p>:</c-> <c- u>"0.5-dev"</c-><c- p>,</c->                 # Curre<c- kc>nt</c-> versio<c- kc>n</c->
 <c- f>"channels"</c-><c- p>:</c-> <c- p>[</c->                         # Array ma<c- kc>t</c->chi<c- kc>n</c->g <c- kc>t</c->he c dime<c- kc>ns</c->io<c- kc>n</c-> size
     <c- p>{</c->
         <c- f>"active"</c-><c- p>:</c-> <c- kc>true</c-><c- p>,</c->
@@ -2244,7 +2266,7 @@ <h3 class="heading settled" data-level="3.6" id="label-md"><span class="secno">3
 above).</p>
 <pre class="language-json highlight"><c- f>"image-label"</c-><c- p>:</c->
   <c- p>{</c->
-    <c- f>"version"</c-><c- p>:</c-> <c- u>"0.4"</c-><c- p>,</c->
+    <c- f>"version"</c-><c- p>:</c-> <c- u>"0.5-dev"</c-><c- p>,</c->
     <c- f>"colors"</c-><c- p>:</c-> <c- p>[</c->
       <c- p>{</c->
         <c- f>"label-value"</c-><c- p>:</c-> <c- mi>1</c-><c- p>,</c->
@@ -2366,7 +2388,7 @@ <h3 class="heading settled" data-level="3.7" id="plate-md"><span class="secno">3
             <c- f>"name"</c-><c- p>:</c-> <c- u>"B"</c->
         <c- p>}</c->
     <c- p>],</c->
-    <c- f>"version"</c-><c- p>:</c-> <c- u>"0.4"</c-><c- p>,</c->
+    <c- f>"version"</c-><c- p>:</c-> <c- u>"0.5-dev"</c-><c- p>,</c->
     <c- f>"wells"</c-><c- p>:</c-> <c- p>[</c->
         <c- p>{</c->
             <c- f>"path"</c-><c- p>:</c-> <c- u>"A/1"</c-><c- p>,</c->
@@ -2530,7 +2552,7 @@ <h3 class="heading settled" data-level="3.8" id="well-md"><span class="secno">3.
             <c- f>"path"</c-><c- p>:</c-> <c- u>"3"</c->
         <c- p>}</c->
     <c- p>],</c->
-    <c- f>"version"</c-><c- p>:</c-> <c- u>"0.4"</c->
+    <c- f>"version"</c-><c- p>:</c-> <c- u>"0.5-dev"</c->
   <c- p>}</c->
 </pre>
    <p>The following JSON object defines a well with two fields of view in a plate with