Merge branch 'master' into 791-field-naming

nexusformat · Nov 3, 2020 · b4982f6 · b4982f6
2 parents b961d10 + 98a25a5
commit b4982f6
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diff --git a/.gitignore b/.gitignore
@@ -16,7 +16,5 @@ impatient-guide/_build
 .DS_Store
 __github_creds__.txt
 
-launch.json
-
-# Microsoft VSCode editor
+# Microsoft VSCode editor configuration
 .vscode
diff --git a/applications/NXarpes.nxdl.xml b/applications/NXarpes.nxdl.xml
@@ -104,16 +104,22 @@
           </doc>
         </field>
         <field name="sensor_size" type="NX_INT">
-          <doc>number of raw active elements in fast and slow pixel dimension direction</doc>
-          <dimensions rank="2" />
+          <doc>number of raw active elements in each dimension</doc>
+          <dimensions rank="1">
+          	<dim index="1" value="2" />
+          </dimensions>
         </field>
         <field name="region_origin" type="NX_INT">
           <doc>origin of rectangular region selected for readout</doc>
-          <dimensions rank="2" />
+          <dimensions rank="1">
+          	<dim index="1" value="2" />
+          </dimensions>
         </field>
         <field name="region_size" type="NX_INT">
           <doc>size of rectangular region selected for readout</doc>
-          <dimensions rank="2" />
+          <dimensions rank="1" >
+          	<dim index="1" value="2" />
+          </dimensions>
         </field>
       </group>
     </group>

diff --git a/applications/NXmx.nxdl.xml b/applications/NXmx.nxdl.xml
@@ -469,7 +469,7 @@
 							detector. The length can be in physical units or pixels as
 							documented by the units attribute.  Normally, this should
 							be derived from the axis chain, but the direct specification
-							may take precendence if it is not a derived quantity.
+							may take precedence if it is not a derived quantity.
 						</doc>
 					</field>
 
@@ -481,7 +481,7 @@
 							detector. The length can be in physical units or pixels as
 							documented by the units attribute.  Normally, this should
 							be derived from the axis chain, but the direct specification
-							may take precendence if it is not a derived quantity.
+							may take precedence if it is not a derived quantity.
 						</doc>
 					</field>
 
@@ -571,8 +571,7 @@
 								* bit 3: over-responding
 								* bit 4: noisy
 								* bit 5: -undefined-
-								* bit 6: pixel is part of a cluster of 
-									problematic pixels (bit set in addition to others)
+								* bit 6: pixel is part of a cluster of problematic pixels (bit set in addition to others)
 								* bit 7: -undefined-
 								* bit 8: user defined mask (e.g. around beamstop)
 								* bits 9-30: -undefined-
@@ -711,21 +710,21 @@
 
 							In the case of a polychromatic beam this is an array of
 							length **m** of wavelengths, with the relative weights
-							in incident_wavelength_weight.
+							in ``incident_wavelength_weights``.
 
 							In the case of a monochromatic beam that varies shot-
 							to-shot, this is an array of wavelengths, one for each
-							recorded shot. Here, incident_wavelength_weight and 
+							recorded shot. Here, ``incident_wavelength_weights`` and 
 							incident_wavelength_spread are not set.
 
 							In the case of a polychromatic beam that varies shot-to-
 							shot, this is an array of length **m** with the relative
-							weights in incident_wavelength_weight as a 2D array.
+							weights in ``incident_wavelength_weights`` as a 2D array.
 
 							In the case of a polychromatic beam that varies shot-to-
 							shot and where the channels also vary, this is a 2D array
 							of dimensions **np** by **m** (slow to fast) with the
-							relative weights in incident_wavelength_weight as a 2D
+							relative weights in ``incident_wavelength_weights`` as a 2D
 							array.
 
 							Note, :ref:`variants &lt;Design-Variants&gt;` are a good way
@@ -736,7 +735,8 @@
 						</doc>
 					</field>
 
-					<field name="incident_wavelength_weight" type="NX_FLOAT" minOccurs="0" >
+					<field name="incident_wavelength_weight" type="NX_FLOAT" minOccurs="0" 
+						deprecated="use incident_wavelength_weights, see https://github.com/nexusformat/definitions/issues/837">
 						<doc>
 							In the case of a polychromatic beam this is an array of 
 							length **m** of the relative weights of the corresponding
@@ -748,6 +748,18 @@
 							corresponding wavelengths in incident_wavelength.
 						</doc>
 					</field>
+					<field name="incident_wavelength_weights" type="NX_FLOAT" minOccurs="0" >
+						<doc>
+							In the case of a polychromatic beam this is an array of 
+							length **m** of the relative weights of the corresponding
+							wavelengths in ``incident_wavelength``.
+
+							In the case of a polychromatic beam that varies shot-to-
+							shot, this is a 2D array of dimensions **np** by **m** 
+							(slow to fast) of the relative weights of the
+							corresponding wavelengths in ``incident_wavelength``.
+						</doc>
+					</field>
 
 					<field name="incident_wavelength_spread" type="NX_FLOAT" units="NX_WAVELENGTH"
 						minOccurs="0" >

diff --git a/base_classes/NXaperture.nxdl.xml b/base_classes/NXaperture.nxdl.xml
@@ -53,4 +53,17 @@
         <doc>Description of aperture</doc>
     </field>
     <group type="NXnote"><doc>describe any additional information in a note*</doc></group>
+    <attribute name="default">
+        <doc>
+            .. index:: plotting
+
+            Declares which child group contains a path leading 
+            to a :ref:`NXdata` group.
+
+            It is recommended (as of NIAC2014) to use this attribute
+            to help define the path to the default dataset to be plotted.
+            See https://www.nexusformat.org/2014_How_to_find_default_data.html
+            for a summary of the discussion.
+        </doc>
+    </attribute>
 </definition>
diff --git a/base_classes/NXattenuator.nxdl.xml b/base_classes/NXattenuator.nxdl.xml
@@ -75,4 +75,17 @@
             <item value="moving" />
         </enumeration>
     </field>
+    <attribute name="default">
+        <doc>
+            .. index:: plotting
+
+            Declares which child group contains a path leading 
+            to a :ref:`NXdata` group.
+
+            It is recommended (as of NIAC2014) to use this attribute
+            to help define the path to the default dataset to be plotted.
+            See https://www.nexusformat.org/2014_How_to_find_default_data.html
+            for a summary of the discussion.
+        </doc>
+    </attribute>
 </definition>
diff --git a/base_classes/NXbeam.nxdl.xml b/base_classes/NXbeam.nxdl.xml
@@ -129,4 +129,17 @@
             useful for simulations which need to store plottable information at each beamline
             component.</doc>
     </group>
+    <attribute name="default">
+        <doc>
+            .. index:: plotting
+
+            Declares which child group contains a path leading 
+            to a :ref:`NXdata` group.
+
+            It is recommended (as of NIAC2014) to use this attribute
+            to help define the path to the default dataset to be plotted.
+            See https://www.nexusformat.org/2014_How_to_find_default_data.html
+            for a summary of the discussion.
+        </doc>
+    </attribute>
 </definition>
diff --git a/base_classes/NXbeam_stop.nxdl.xml b/base_classes/NXbeam_stop.nxdl.xml
@@ -61,4 +61,17 @@
             <item value="out"/>
         </enumeration>
     </field>
+    <attribute name="default">
+        <doc>
+            .. index:: plotting
+
+            Declares which child group contains a path leading 
+            to a :ref:`NXdata` group.
+
+            It is recommended (as of NIAC2014) to use this attribute
+            to help define the path to the default dataset to be plotted.
+            See https://www.nexusformat.org/2014_How_to_find_default_data.html
+            for a summary of the discussion.
+        </doc>
+    </attribute>
 </definition>
diff --git a/base_classes/NXbending_magnet.nxdl.xml b/base_classes/NXbending_magnet.nxdl.xml
@@ -74,5 +74,18 @@
   </field>
 	<group name="spectrum" type="NXdata"><doc>bending magnet spectrum</doc></group>
   <group type="NXgeometry"><doc>"Engineering" position of bending magnet</doc></group>
+  <attribute name="default">
+      <doc>
+          .. index:: plotting
+
+          Declares which child group contains a path leading 
+          to a :ref:`NXdata` group.
+
+          It is recommended (as of NIAC2014) to use this attribute
+          to help define the path to the default dataset to be plotted.
+          See https://www.nexusformat.org/2014_How_to_find_default_data.html
+          for a summary of the discussion.
+      </doc>
+  </attribute>
 
 </definition>
diff --git a/base_classes/NXcapillary.nxdl.xml b/base_classes/NXcapillary.nxdl.xml
@@ -64,4 +64,17 @@
         The focal size in FWHM
       </doc>
     </field>
+    <attribute name="default">
+        <doc>
+            .. index:: plotting
+
+            Declares which child group contains a path leading 
+            to a :ref:`NXdata` group.
+
+            It is recommended (as of NIAC2014) to use this attribute
+            to help define the path to the default dataset to be plotted.
+            See https://www.nexusformat.org/2014_How_to_find_default_data.html
+            for a summary of the discussion.
+        </doc>
+    </attribute>
 </definition>
diff --git a/base_classes/NXcite.nxdl.xml b/base_classes/NXcite.nxdl.xml
@@ -54,4 +54,17 @@
 	<field name="bibtex" type="NX_CHAR">
 		<doc>Bibliographic reference data in BibTeX format.</doc>
 	</field>
+    <attribute name="default">
+        <doc>
+            .. index:: plotting
+
+            Declares which child group contains a path leading 
+            to a :ref:`NXdata` group.
+
+            It is recommended (as of NIAC2014) to use this attribute
+            to help define the path to the default dataset to be plotted.
+            See https://www.nexusformat.org/2014_How_to_find_default_data.html
+            for a summary of the discussion.
+        </doc>
+    </attribute>
 </definition>
diff --git a/base_classes/NXcollimator.nxdl.xml b/base_classes/NXcollimator.nxdl.xml
@@ -66,4 +66,17 @@
     <field name="transmitting_material">
         <doc>name of transmitting material</doc>
     </field>
+    <attribute name="default">
+        <doc>
+            .. index:: plotting
+
+            Declares which child group contains a path leading 
+            to a :ref:`NXdata` group.
+
+            It is recommended (as of NIAC2014) to use this attribute
+            to help define the path to the default dataset to be plotted.
+            See https://www.nexusformat.org/2014_How_to_find_default_data.html
+            for a summary of the discussion.
+        </doc>
+    </attribute>
 </definition>
diff --git a/base_classes/NXcrystal.nxdl.xml b/base_classes/NXcrystal.nxdl.xml
@@ -258,6 +258,19 @@
   <group type="NXshape" name="shape">
     <doc>A NXshape group describing the shape of the crystal arrangement</doc>
   </group>
+  <attribute name="default">
+      <doc>
+          .. index:: plotting
+
+          Declares which child group contains a path leading 
+          to a :ref:`NXdata` group.
+
+          It is recommended (as of NIAC2014) to use this attribute
+          to help define the path to the default dataset to be plotted.
+          See https://www.nexusformat.org/2014_How_to_find_default_data.html
+          for a summary of the discussion.
+      </doc>
+  </attribute>
   <!-- TODO need more parameters here, such as ...
        list from Rainer Gehrke, DESY (some items may already be present)
 

diff --git a/base_classes/NXcylindrical_geometry.nxdl.xml b/base_classes/NXcylindrical_geometry.nxdl.xml
@@ -91,5 +91,18 @@
     </dimensions>
 
   </field>
+    <attribute name="default">
+        <doc>
+            .. index:: plotting
+
+            Declares which child group contains a path leading 
+            to a :ref:`NXdata` group.
+
+            It is recommended (as of NIAC2014) to use this attribute
+            to help define the path to the default dataset to be plotted.
+            See https://www.nexusformat.org/2014_How_to_find_default_data.html
+            for a summary of the discussion.
+        </doc>
+    </attribute>
 
 </definition>
diff --git a/base_classes/NXdata.nxdl.xml b/base_classes/NXdata.nxdl.xml
@@ -49,6 +49,19 @@
 		<symbol name="nz"><doc>length of the ``z`` field</doc></symbol>
 	</symbols>
 
+	<attribute name="auxiliary_signals">
+		<doc>
+			.. index:: plotting
+
+			Array of strings holding the names of additional signals to
+			be plotted with the default signal (specified by the
+			``signal`` attribute).  Each auxiliary signal needs to be of
+			the same shape as the default signal.
+
+			..  NIAC2018:
+			    https://www.nexusformat.org/NIAC2018Minutes.html
+		</doc>
+	</attribute>
 	<attribute name="signal">
 		<doc>
 			.. index:: plotting
@@ -60,12 +73,11 @@
 
 			It is recommended (as of NIAC2014) to use this attribute
 			rather than adding a signal attribute to the dataset.
-			See http://wiki.nexusformat.org/2014_How_to_find_default_data
+			See https://www.nexusformat.org/2014_How_to_find_default_data.html
 			for a summary of the discussion.
 		</doc>
 	</attribute>
 	<attribute name="axes">
-		<!-- http://www.nexusformat.org/2014_axes_and_uncertainties -->
 		<doc>
 			.. index:: plotting
 
@@ -92,7 +104,7 @@
 			while the other two dimensions have no fields to be used as dimension scales.
 
 			See examples provided on the NeXus wiki:
-			http://www.nexusformat.org/2014_axes_and_uncertainties
+			https://www.nexusformat.org/2014_axes_and_uncertainties.html
 
 			If there are no axes at all (such as with a stack of images), 
 			the axes attribute can be omitted.

diff --git a/base_classes/NXdetector.nxdl.xml b/base_classes/NXdetector.nxdl.xml
@@ -799,4 +799,17 @@
       </doc>
     </group>
   </choice>
+  <attribute name="default">
+      <doc>
+          .. index:: plotting
+
+          Declares which child group contains a path leading 
+          to a :ref:`NXdata` group.
+
+          It is recommended (as of NIAC2014) to use this attribute
+          to help define the path to the default dataset to be plotted.
+          See https://www.nexusformat.org/2014_How_to_find_default_data.html
+          for a summary of the discussion.
+      </doc>
+  </attribute>
 </definition>
diff --git a/base_classes/NXdetector_group.nxdl.xml b/base_classes/NXdetector_group.nxdl.xml
@@ -87,4 +87,17 @@
 	    <doc>Code number for group type, e.g. bank=1, tube=2 etc.</doc>
 	    <dimensions><dim index="1" ref="group_index"/></dimensions>
 	</field>
+    <attribute name="default">
+        <doc>
+            .. index:: plotting
+
+            Declares which child group contains a path leading 
+            to a :ref:`NXdata` group.
+
+            It is recommended (as of NIAC2014) to use this attribute
+            to help define the path to the default dataset to be plotted.
+            See https://www.nexusformat.org/2014_How_to_find_default_data.html
+            for a summary of the discussion.
+        </doc>
+    </attribute>
 </definition>
diff --git a/base_classes/NXdetector_module.nxdl.xml b/base_classes/NXdetector_module.nxdl.xml
@@ -159,4 +159,17 @@
 			</doc>
 		</attribute>
 	</field>
+    <attribute name="default">
+        <doc>
+            .. index:: plotting
+
+            Declares which child group contains a path leading 
+            to a :ref:`NXdata` group.
+
+            It is recommended (as of NIAC2014) to use this attribute
+            to help define the path to the default dataset to be plotted.
+            See https://www.nexusformat.org/2014_How_to_find_default_data.html
+            for a summary of the discussion.
+        </doc>
+    </attribute>
 </definition>