Remove SPM folder.

Revert "Remove SPM folder." This reverts commit 3aeb39e. PR review from Lukas! Delete unnecessary files. Revert "Delete unnecessary files." This reverts commit 317a367. Include the default key attribute on entry and include NXhistory under the NXsample for verbose purpose.
FAIRmat-NFDI · Dec 5, 2024 · f57eee9 · f57eee9
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diff --git a/contributed_definitions/NXafm.nxdl.xml b/contributed_definitions/NXafm.nxdl.xml
@@ -96,7 +96,7 @@
                          Link to the group ENTRY[entry]/experiment_instrument/XY_piezo_sensor.
                     </doc>
                 </group>
-                <group name="tip_temperature" type="NXsensor">
+                <group name="tip_temp_sensor" type="NXsensor">
                     <doc>
                          Link to the group ENTRY[entry]/experiment_instrument/cantilever_temperature.
                     </doc>
@@ -146,7 +146,7 @@
                     </doc>
                 </group>
             </group>
-            <group name="tip_temperature" type="NXsensor" optional="true">
+            <group name="tip_temp_sensor" type="NXsensor" optional="true">
                 <doc>
                      The temperature of the scan environment or tip of the cantilever.
                 </doc>

diff --git a/contributed_definitions/NXbias_spectroscopy.nxdl.xml b/contributed_definitions/NXbias_spectroscopy.nxdl.xml
@@ -168,7 +168,7 @@
                      Speed of the scanner or the probe that moves backward direction.
                 </doc>
             </field>
-            <group name="SCAN_DATA" type="NXdata">
+            <group name="SCAN_data" type="NXdata">
                 <doc>
                      The data that comes from scanning the area.
                 </doc>

diff --git a/contributed_definitions/NXbias_sweep.nxdl.xml b/contributed_definitions/NXbias_sweep.nxdl.xml
@@ -82,7 +82,7 @@
                  value after the sweep is completed.
             </doc>
         </field>
-        <group name="SCAN_DATA" type="NXdata">
+        <group name="SCAN_data" type="NXdata">
             <doc>
                  The scan data is the data collected during the scan.
                  If the scan has several channels or derivatives from the channel data,

diff --git a/contributed_definitions/NXcalibration.nxdl.xml b/contributed_definitions/NXcalibration.nxdl.xml
@@ -89,11 +89,6 @@
              A digital persistent identifier (e.g., DOI, ISO standard) referring to a detailed description of a
              calibration method but no actual calibration data.
         </doc>
-        <field name="calibration_type" type="NX_CHAR">
-            <doc>
-                 The type of calibration.
-            </doc>
-        </field>
     </group>
     <group name="calibration_reference" type="NXidentifier">
         <doc>

diff --git a/contributed_definitions/NXcircuit.nxdl.xml b/contributed_definitions/NXcircuit.nxdl.xml
@@ -25,9 +25,15 @@
     <doc>
          Application definition for circuit devices.
     </doc>
+    <group name="hardware" type="NXfabrication">
+        <doc>
+             Hardware where the circuit is implanted; includes hardware manufacturers and
+             type
+        </doc>
+    </group>
     <field name="components">
         <doc>
-             List of components used in the circuit, e.g., resistors, capacitors, transistors or any 
+             List of components used in the circuit, e.g., resistors, capacitors, transistors or any
              other complex components.
         </doc>
     </field>
@@ -66,7 +72,7 @@
     </field>
     <field name="gain" type="NX_NUMBER" units="NX_UNITLESS">
         <doc>
-             Gain of the circuit, if applicable, usually all instruments have a gain which might be 
+             Gain of the circuit, if applicable, usually all instruments have a gain which might be
              important or not.
         </doc>
     </field>
@@ -122,12 +128,6 @@
              thermal shutdown.
         </doc>
     </field>
-    <group name="hardware" type="NXfabrication">
-        <doc>
-             Hardware where the circuit is implanted; includes hardware manufacturers and
-             type
-        </doc>
-    </group>
     <field name="acquisition_time" type="NX_NUMBER" units="NX_TIME">
         <doc>
              Updated rate for several processes using the input signal, e.g., History Graph, the circuit

diff --git a/contributed_definitions/NXlockin.nxdl.xml b/contributed_definitions/NXlockin.nxdl.xml
@@ -24,6 +24,7 @@
 <definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXlockin" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
     <doc>
          A base class definition for a lock-in amplifier.
+
          The lock-in amplifier information: the device is being used to extract a (potentially)
          very weak input signal buried in the noisy background, where the input signal has
          the same frequency (or its harmonic) as a known reference signal. Additionally,
@@ -60,8 +61,8 @@
     <field name="lockin_current_flip_value" type="NX_NUMBER" optional="true">
         <doc>
              The number that defines the sign of the lock-in current. The calibration procedure
-             with retracted tip is normally performed to compensate for the signal phase delay 
-             in SPM. The procedure yields two possible solutions, this number should be equal 
+             with retracted tip is normally performed to compensate for the signal phase delay
+             in SPM. The procedure yields two possible solutions, this number should be equal
              to 1 or -1 depending on which solution is chosen.
         </doc>
     </field>

diff --git a/contributed_definitions/NXpiezo_config_spm.nxdl.xml b/contributed_definitions/NXpiezo_config_spm.nxdl.xml
@@ -57,7 +57,7 @@ Discussion: No need to create this base class rather we can define in spm applic
                  A specific name of the calibration (e.g. active type with name 'LHe').
             </doc>
         </field>
-        <field name="caliberation_date" type="NX_DATE_TIME">
+        <field name="calibration_date" type="NX_DATE_TIME">
             <doc>
                  The date of the calibration.
             </doc>
@@ -83,7 +83,7 @@ Discussion: No need to create this base class rather we can define in spm applic
                  is the maximum distance the piezo can move.
             </doc>
         </field>
-        <field name="calibration_coeffecient_N" type="NX_NUMBER" units="NX_ANY">
+        <field name="calibration_coefficient_N" type="NX_NUMBER" units="NX_ANY">
             <doc>
                  The calibration coefficient is the ratio of the actual distance moved by the piezo due to
                  the voltage applied to the piezo. It is also called first-order correction.
@@ -95,7 +95,7 @@ Discussion: No need to create this base class rather we can define in spm applic
                  to the actual surface.
             </doc>
         </field>
-        <field name="2nd_order_corr_N" type="NX_NUMBER" units="NX_ANY">
+        <field name="2nd_order_correction_N" type="NX_NUMBER" units="NX_ANY">
             <doc>
                  The N (substring) denotes X and Y directions. If you know them, you can enter the 2nd order piezo
                  characteristics to compensate the error for that axis.

diff --git a/contributed_definitions/NXpositioner_sts.nxdl.xml b/contributed_definitions/NXpositioner_sts.nxdl.xml
@@ -225,7 +225,7 @@
     </field>
     <field name="active_calib" type="NX_CHAR">
         <doc>
-             The name of caliberation type.
+             The name of calibration type.
         </doc>
     </field>
     <field name="calib_N" type="NX_NUMBER"/>

diff --git a/contributed_definitions/NXscan_control.nxdl.xml b/contributed_definitions/NXscan_control.nxdl.xml
@@ -22,9 +22,7 @@
 # For further information, see http://www.nexusformat.org
 -->
 <definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXscan_control" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
-    <!--
-Correction: region (use: phase space)
--->
+    <!--Correction: region (use: phase space)-->
     <doc>
          A scan is performed inside an N-dimensional phase space, where each dimension can correspond not only to real space coordinates (x,y) but also to any other parameter. This class contains detailed information about controlling the scan in such a phase space (or its subspace).
 
@@ -114,7 +112,7 @@ Correction: region (use: phase space)
         <field name="scan_angle_N" type="NX_NUMBER" units="NX_ANGLE">
             <doc>
                  The orientation of the scan region or subspace. Usually, the scan_offset and scan_range are enough
-                 to define the scan region. This field defines how the spatial space is oriented with respect to 
+                 to define the scan region. This field defines how the spatial space is oriented with respect to
                  the frame of reference.
 
                  Rename the field describing the angle with an axis of the spatial space (e.g. scan_angle_x).
@@ -221,7 +219,7 @@ Correction: region (use: phase space)
                  The number of oscillations on each scanning point per second.
             </doc>
         </field>
-        <group name="SCAN_DATA" type="NXdata">
+        <group name="SCAN_data" type="NXdata">
             <field name="data">
                 <doc>
                      The scan data is the data collected during the scan.
@@ -330,7 +328,7 @@ Correction: region (use: phase space)
                  Number of oscillation on each scanning point per second.
             </doc>
         </field>
-        <group name="SCAN_DATA" type="NXdata">
+        <group name="SCAN_data" type="NXdata">
             <doc>
                  The scan data is the data collected during the scan.
                  If the scan has several channels or derivatives from the channel data, please
@@ -422,7 +420,7 @@ Correction: region (use: phase space)
                  The number of oscillations on each scanning point per second.
             </doc>
         </field>
-        <group name="SCAN_DATA" type="NXdata">
+        <group name="SCAN_data" type="NXdata">
             <doc>
                  The scan data is the data collected during the scan.
                  If the scan has several channels or derivatives from the channel data, please
@@ -520,7 +518,7 @@ Correction: region (use: phase space)
                  The number of oscillations on each scanning point per second.
             </doc>
         </field>
-        <group name="SCAN_DATA" type="NXdata">
+        <group name="SCAN_data" type="NXdata">
             <doc>
                  The scan data is the data collected during the scan.
                  If the scan has several channels or derivatives from the channel data, please
@@ -600,7 +598,7 @@ Correction: region (use: phase space)
                  The number of oscillations on each scanning point per second.
             </doc>
         </field>
-        <group name="SCAN_DATA" type="NXdata">
+        <group name="SCAN_data" type="NXdata">
             <doc>
                  The scan data is the data collected during the scan.
                  If the scan has several channels or derivatives from the channel data, please

diff --git a/contributed_definitions/NXspm.nxdl.xml b/contributed_definitions/NXspm.nxdl.xml
@@ -30,6 +30,19 @@
          for specific SPM sub-techniques such as STM, STS, AFM etc.
     </doc>
     <group type="NXentry">
+        <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 visualised upon entry.
+                 See https://www.nexusformat.org/2014_How_to_find_default_data.html
+                 for a summary of the discussion.
+            </doc>
+        </attribute>
         <field name="definition">
             <doc>
                  Name of the definition that is used for the application.
@@ -448,6 +461,11 @@
             <doc>
                  The sample information.
             </doc>
+            <group name="history" type="NXhistory">
+                <doc>
+                     A set of physical processes that occurred to the sample prior/during experiment.
+                </doc>
+            </group>
             <group name="sample_environment" type="NXenvironment" optional="true">
                 <doc>
                      Information of environment around the sample.

diff --git a/contributed_definitions/NXstm.nxdl.xml b/contributed_definitions/NXstm.nxdl.xml
@@ -39,7 +39,7 @@ TODO: Replace rename NXenvironment to experiment_environment in NXstm, NXspm and
         </field>
         <field name="scan_mode">
             <doc>
-                 The mode of the scan that is performed. Two commonly used ones are constant 
+                 The mode of the scan that is performed. Two commonly used ones are constant
                  height mode and constant current mode.
             </doc>
             <enumeration>
@@ -135,43 +135,43 @@ TODO: Replace rename NXenvironment to experiment_environment in NXstm, NXspm and
                                  The N (substring) denotes the backward speed of the scanner.
                             </doc>
                         </field>
-                        <group name="SCAN_DATA" type="NXdata">
+                        <group name="SCAN_data" type="NXdata">
                             <doc>
                                  The data that comes from scanning the area.
                             </doc>
                         </group>
                     </group>
                 </group>
-                <group name="tip_temperature" type="NXsensor" optional="true">
+                <group name="tip_temp_sensor" type="NXsensor" optional="true">
                     <doc>
                          This group stands for the same concept as
                          /ENTRY[entry]/experiment_instrument/tip_temperature
                     </doc>
                 </group>
-                <group name="cryo_temperature" type="NXsensor" optional="true">
+                <group name="cryo_temp_sensor" type="NXsensor" optional="true">
                     <doc>
                          This group stands for the same concept as
                          /ENTRY[entry]/experiment_instrument/cryo_temperature
                     </doc>
                 </group>
-                <group name="cryo_shield_temperature" type="NXsensor" optional="true">
+                <group name="cryo_shield_temp_sensor" type="NXsensor" optional="true">
                     <doc>
                          This group stands for the same concept as
                          /ENTRY[entry]/experiment_instrument/cryo_shield_temperature
                     </doc>
                 </group>
             </group>
-            <group name="tip_temperature" type="NXsensor" optional="true">
+            <group name="tip_temp_sensor" type="NXsensor" optional="true">
                 <doc>
                      The temperature of the tip one of the tip.
                 </doc>
             </group>
-            <group name="cryo_temperature" type="NXsensor" optional="true">
+            <group name="cryo_temp_sensor" type="NXsensor" optional="true">
                 <doc>
                      The temperature of the cryostat.
                 </doc>
             </group>
-            <group name="cryo_shield_temperature" type="NXsensor" optional="true">
+            <group name="cryo_shield_temp_sensor" type="NXsensor" optional="true">
                 <doc>
                      The temperature of the cryo shield.
                 </doc>
@@ -195,7 +195,7 @@ TODO: Replace rename NXenvironment to experiment_environment in NXstm, NXspm and
                     <doc>
                          Calibration of the current measurement.
                     </doc>
-                    <field name="caliberation_time" type="NX_DATE_TIME" optional="true" units="NX_TIME">
+                    <field name="calibration_time" type="NX_DATE_TIME" optional="true" units="NX_TIME">
                         <doc>
                              The time or period is taken by the calibration to setup to acquire the data for
                              the calibration.
@@ -261,7 +261,7 @@ TODO: Replace rename NXenvironment to experiment_environment in NXstm, NXspm and
                         <doc>
                              Calibration of the piezo device.
                         </doc>
-                        <field name="2nd_order_corr_N" type="NX_NUMBER" optional="true" units="NX_ANY">
+                        <field name="2nd_order_correction_N" type="NX_NUMBER" optional="true" units="NX_ANY">
                             <doc>
                                  The N (substring) denotes X and Y directions. The 2nd order piezo
                                  compensate the error for that axis. The following equation shows the
@@ -278,7 +278,7 @@ TODO: Replace rename NXenvironment to experiment_environment in NXstm, NXspm and
                                  e.g active calibration, passive calibration.
                             </doc>
                         </field>
-                        <field name="calibration_coeffecient_N" type="NX_NUMBER" optional="true" units="NX_ANY">
+                        <field name="calibration_coefficient_N" type="NX_NUMBER" optional="true" units="NX_ANY">
                             <doc>
                                  The calibration coefficient is the ratio of the actual distance moved by the piezo to
                                  the voltage applied to the piezo. It is also called first-order correction.

diff --git a/contributed_definitions/nyaml/NXafm.yaml b/contributed_definitions/nyaml/NXafm.yaml
@@ -54,7 +54,7 @@ NXafm(NXspm):
         XY_piezo_sensor(NXsensor):
           doc: |
             Link to the group ENTRY[entry]/experiment_instrument/XY_piezo_sensor.
-        tip_temperature(NXsensor):
+        tip_temp_sensor(NXsensor):
           doc: |
             Link to the group ENTRY[entry]/experiment_instrument/cantilever_temperature.
       height_piezo_sensor(NXsensor):
@@ -89,13 +89,13 @@ NXafm(NXspm):
           doc: |
             The positioner information like the position of the tip, the position of the
             sample, PID loop feedback etc.
-      tip_temperature(NXsensor):
+      tip_temp_sensor(NXsensor):
         exists: optional
         doc: |
           The temperature of the scan environment or tip of the cantilever.
 
 # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++
-# 9a15a1db7f7822d982716a9c177ce05e6afeb165692bf2ac13dbc98aad4809dd
+# fa4fba4dbdb47b6b13313bb2987b9130506b025dac0b45aacd9d586f9e5aa137
 # <?xml version='1.0' encoding='UTF-8'?>
 # <?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
 # <!--
@@ -194,7 +194,7 @@ NXafm(NXspm):
 #                          Link to the group ENTRY[entry]/experiment_instrument/XY_piezo_sensor.
 #                     </doc>
 #                 </group>
-#                 <group name="tip_temperature" type="NXsensor">
+#                 <group name="tip_temp_sensor" type="NXsensor">
 #                     <doc>
 #                          Link to the group ENTRY[entry]/experiment_instrument/cantilever_temperature.
 #                     </doc>
@@ -244,7 +244,7 @@ NXafm(NXspm):
 #                     </doc>
 #                 </group>
 #             </group>
-#             <group name="tip_temperature" type="NXsensor" optional="true">
+#             <group name="tip_temp_sensor" type="NXsensor" optional="true">
 #                 <doc>
 #                      The temperature of the scan environment or tip of the cantilever.
 #                 </doc>

diff --git a/contributed_definitions/nyaml/NXbias_spectroscopy.yaml b/contributed_definitions/nyaml/NXbias_spectroscopy.yaml
@@ -120,12 +120,12 @@ NXbias_spectroscopy(NXobject):
         unit: NX_ANY
         doc: |
           Speed of the scanner or the probe that moves backward direction.
-      SCAN_DATA(NXdata):
+      SCAN_data(NXdata):
         doc: |
           The data that comes from scanning the area.
 
 # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++
-# 3ab25dbd62b7ae483b8ff37724fd4398a7c60454114c12914ccb9144fe3fe5a9
+# 5b57b4e955019fabedb0a7fe4fc70a0626dce64f58aa542d7ab6d4161d0a0bdd
 # <?xml version='1.0' encoding='UTF-8'?>
 # <?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
 # <!--
@@ -296,7 +296,7 @@ NXbias_spectroscopy(NXobject):
 #                      Speed of the scanner or the probe that moves backward direction.
 #                 </doc>
 #             </field>
-#             <group name="SCAN_DATA" type="NXdata">
+#             <group name="SCAN_data" type="NXdata">
 #                 <doc>
 #                      The data that comes from scanning the area.
 #                 </doc>