Checked Sandors comments for apm, em, matwerk and consolidated with l…

…atest fixes needed for apm, em_om, and em_spctrscpy readers

contributed_definitions/NXapm.nxdl.xml

@@ -104,8 +104,11 @@ to describe also the upcoming technique of atomic scale analytical tomography ht
          of reconstructed positions of certain ions. During ranging time-of-flight data
          are identified as representing specific ions to annotate each ion with a label.
 
-         Commercial software used in atom probe research is designed as an integrated acquisition and instrument control software. For AMETEK/Cameca local electrode
-         atom probe (LEAP) instruments the least processed (rawest) numerical results and metadata are stored in so-called STR, RRAW, RHIT, and HITS files, which are proprietary and their file format specifications not publicly documented.
+         Commercial software used in atom probe research is designed as an integrated
+         acquisition and instrument control software. For AMETEK/Cameca local electrode
+         atom probe (LEAP) instruments the least processed (rawest) numerical results
+         and metadata are stored in so-called STR, RRAW, RHIT, and HITS files, which
+         are proprietary and their file format specifications not publicly documented.
 
          Supplementary metadata are kept in a database (formerly known as the ISDb)
          which is connected to the instrument control software and synced with the
@@ -147,8 +150,9 @@ to describe also the upcoming technique of atomic scale analytical tomography ht
          key post-processing steps which transform the proprietary data into a
          tomographic reconstruction with ranging definitions.
 
-         Future guidance by the technology partners like AMETEK/Cameca could improve this description to cover a substantial larger number of eventually metadata that
-         so far are neither publicly documented nor accessible.
+         Future guidance by the technology partners like AMETEK/Cameca could improve
+         this description to cover a substantial larger number of eventually metadata
+         that so far are neither publicly documented nor accessible.
     </doc>
     <group type="NXentry" minOccurs="1" maxOccurs="unbounded">
         <attribute name="version">
@@ -703,7 +707,7 @@ NEW ISSUE: see in WO2016171675A1 Invizo 6000 patent from AMETEK-->
                 <field name="pulsed_voltage" type="NX_FLOAT" recommended="true"/>
                 <field name="standing_voltage" type="NX_FLOAT" recommended="true"/>
                 <group type="NXcsg" optional="true"/>
-                <group name="LASER_SOURCE" type="NXsource" minOccurs="0" maxOccurs="2">
+                <group name="SOURCE" type="NXsource" minOccurs="0" maxOccurs="2">
                     <!--INVIZO 6000 instrument have two symmetric lasers! so for these
 laser_gun and laser_beam exists: [min, 0, max, 2]-->
                     <doc>
@@ -1213,7 +1217,7 @@ numerically the same voltage-and-bowl correction results are obtained
                     <doc>
                          Mass-to-charge-state ratio values.
                     </doc>
-                    <!--\@units: Da-->
+                    <!--\@units: Da / a unitless quantity because it is the charge state and not the charge-->
                     <dimensions rank="1">
                         <dim index="1" value="n_ions"/>
                     </dimensions>
@@ -1297,7 +1301,10 @@ these methods are de facto application definitions.-->
                     <field name="xdmf_topology" type="NX_UINT" units="NX_UNITLESS">
                         <doc>
                              An array of triplets of integers which can serve as a supplementary
-                             array for Paraview to display the reconstructed dataset. The XDMF primitive type is here 1, the number of primitives 1 per triplet, the last integer in each triplet is the identifier of each point starting from zero.
+                             array for Paraview to display the reconstructed dataset.
+                             The XDMF primitive type is here 1, the number of primitives 1 per
+                             triplet, the last integer in each triplet is the identifier of
+                             each point starting from zero.
                         </doc>
                         <dimensions rank="1">
                             <dim index="1" value="n_topology"/>
@@ -1465,6 +1472,7 @@ NEW ISSUE: unit must match with range, is Da-->
                             <doc>
                                  Right boundary of each mass-to-charge-state ratio value bin.
                             </doc>
+                            <!--\@units: Da-->
                             <dimensions rank="1">
                                 <dim index="1" value="n_bins"/>
                             </dimensions>
@@ -1522,7 +1530,7 @@ eventually processed via deconvolution methods-->
                         <field name="charge_state" type="NX_INT"/>
                         <field name="mass_to_charge_range" type="NX_FLOAT"/>
                         <field name="nuclid_list" type="NX_UINT" recommended="true"/>
-                        <field name="name" recommended="true"/>
+                        <field name="name"/>
                     </group>
                 </group>
             </group>

contributed_definitions/NXem.nxdl.xml

@@ -1145,7 +1145,11 @@ is needed, will the rest be inferred automatically?-->
                      Different technologies are in use like CCD, scintillator, 
                      direct electron, CMOS, or image plate to name but a few.
                 </doc>
-                <field name="local_name"/>
+                <field name="local_name">
+                    <doc>
+                         Instrument-specific alias/name
+                    </doc>
+                </field>
                 <!--it is unfortunate that for NXdetector there are already many places
 how one can specify details which could equally end up in fabrications
 we should give better guidance which option to use-->

contributed_definitions/NXem_ebsd.nxdl.xml

@@ -241,7 +241,7 @@ enumeration: [sha_256_hash]-->
                  Program which was used for creating the file instance which is
                  formatted according to the NXem_ebsd application definition.
             </doc>
-            <field name="program_name">
+            <field name="program">
                 <attribute name="version"/>
             </field>
         </group>
@@ -382,7 +382,7 @@ in every case data are Kikuchi diffraction pattern and their metadata-->
             </doc>
             <field name="sequence_index" type="NX_POSINT"/>
             <group type="NXprogram" minOccurs="0" maxOccurs="unbounded">
-                <field name="program_name">
+                <field name="program">
                     <attribute name="version"/>
                 </field>
             </group>
@@ -689,7 +689,7 @@ rank: 1
                              production workflow how EBSD data are collected in
                              materials engineering, in industry, and academia.
                         </doc>
-                        <field name="program_name">
+                        <field name="program">
                             <attribute name="version"/>
                         </field>
                     </group>
@@ -1233,7 +1233,7 @@ is somehow connected to pyxem. NEED TO TALK TO DEVELOPERS HERE!-->
                              which can be for some use cases the parser.
                              Consider the explanations in the docstring of the ipf_mapID group.
                         </doc>
-                        <field name="program_name">
+                        <field name="program">
                             <attribute name="version"/>
                         </field>
                     </group>
@@ -1631,7 +1631,7 @@ while for _indices fastest to fast-->
                          which can be for some use cases the parser.
                          Consider the explanations in the docstring of the ipf_mapID group.
                     </doc>
-                    <field name="program_name">
+                    <field name="program">
                         <attribute name="version"/>
                     </field>
                 </group>
@@ -1921,6 +1921,5 @@ acquisition_speed(NX_FLOAT):
      Average number of patterns taken per second averaged over entire set.
    unit: NX_FREQUENCY
 acquisition_time(NX_FLOAT):
-  doc: Wall-clock time the acquisition took.
-  unit: NX_TIME-->
+  doc: Wall-clock time the acquisition took.-->
 </definition>