Preparation for SPM proposal to NIAC goes to FAIRmat (#401)

* Fix NXobject issue scan_control with new classes NXspm_scan_region, NXspm_scan_pattern.

* fix generic volatage sensor in spm and the corresponding usages of it.

* Rename the SPM related base classes according NXspm_... .

* Remove duplicate file NXscan_control.yaml

* fix partial name in scan control, scan reagion, scan pattern

* STM and slight SPM

* STS

* AFM

* Afm and cantilever.

* Resolve comments from Tamash!

* New base class for piezo_sensor. remove frequency positioner, bring piezo_sensor for common xyz and X, Y and Z separately.

* Fix comments for PR-407: NXafm, NXspm, NXspm_bias_spectrocopy.

* Include spm_lockin and spm_cantilever

* Remove test NXspm_phse_lock_loop

* include phase lock loop.

* Update phase lock loop.

* Slight modification.

* Reviews from SPM community (#405)

* Review to SPM App. Def. (#408)

---------

Co-authored-by: ca-palma <124777158+ca-palma@users.noreply.github.com>


* Rename NXspm_lockin to NXlockin.

* Rename NXlockin

* Rename Phase lock loop

* update manual.

* minor fixes and updates that come through the review comments.

* fix some requirements of fields and groups.

* fix calibration coffecient.

* A few changes in response to the PR comments.

* consider the PR review comments.

* nameType in afm.

* Update according to the  PR comments.

* Tiny modification.

* Resolve PR comments and tiny modification while fixing test cases in pynxtools-spm.

* some fixes while fixing readers.

* cleaning up the NXamplifier.nxdl.xml

* tiny fix of nameType.

* Unit fix for PLL/Ko_coefficient

---------

Co-authored-by: ca-palma <124777158+ca-palma@users.noreply.github.com>
Co-authored-by: T. Haraszti <haraszti@dwi.rwth-aachen.de>

Author: 3 people

.cspell/custom-dictionary.txt

@@ -505,6 +505,9 @@ xdmf
 ydim
 zener
 zoneplate
+XYZpiezo
+XYpiezo
+transimpedance
 
 # Names used for publications, places, companies, etc.
 Acta

contributed_definitions/NXafm.nxdl.xml

@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
 <?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
 <!--
 # NeXus - Neutron and X-ray Common Data Format
@@ -25,6 +25,45 @@
     <doc>
         Base classed definition for amplifier devices.
     </doc>
+    <field name="classification">
+        <doc>
+            Type of the amplifier base on the response on frequency.
+        </doc>
+        <enumeration open="true">
+            <item value="low-pass">
+                <doc>
+                    A low-pass filter is a filter that passes signals
+                    with a frequency lower than a certain cutoff frequency and 
+                    attenuates signals with frequencies higher than the cutoff frequency.
+                </doc>
+            </item>
+            <item value="high-pass">
+                <doc>
+                    A high-pass filter is a filter that passes signals
+                    with a frequency higher than a certain cutoff frequency and
+                    attenuates signals with frequencies lower than the cutoff frequency.
+                </doc>
+            </item>
+            <item value="band-pass">
+                <doc>
+                    A band-pass filter is a filter that passes signals
+                    within a certain frequency range and attenuates signals outside that range.
+                </doc>
+            </item>
+            <item value="band-stop">
+                <doc>
+                    A band-stop filter is a filter (opposite to the band-pass) that attenuates signals
+                    within a certain frequency range and passes signals outside that range.
+                </doc>
+            </item>
+            <item value="broadband">
+                <doc>
+                    A broadband filter is a filter that passes signals
+                    over a wide range of frequencies with minimal attenuation.
+                </doc>
+            </item>
+        </enumeration>
+    </field>
     <group name="hardware" type="NXfabrication">
         <doc>
             (IC, device) (NXmanufacturer?)
@@ -37,7 +76,7 @@
     </field>
     <field name="active_channels" type="NX_NUMBER">
         <doc>
-            The number of preamplifier channels are ready tp to be used. (array for active
+            The number of preamplifier channels are ready to be used. (array for active
             channels)
         </doc>
     </field>
@@ -51,41 +90,52 @@
 doc: !!! The ratio of the amplitude of the output signal to the amplitude of the input signal. (array for active channels) # From google.-->
     <field name="signal_over_noise" type="NX_NUMBER">
         <doc>
-            The ratio of the amplitude of the useful signal to the amplitude of the noise in
+            The ratio of the amplitude of the target signal to the amplitude of the noise in
             the output signal of the amplifier. S/N=V_signal/V_noise. (array for active
             channels)
         </doc>
     </field>
-    <field name="crosstalk_factor" type="NX_NUMBER">
+    <field name="crosstalk_factor" type="NX_NUMBER" units="db">
         <doc>
-            (if active &gt;1)
+            The unwanted coupling between different channels (if active &gt;1).
+            In ideal amplifier, channels are independent of each other, But due to different resources
+            sharing (e.g., same power supply, electromagnetic interference), there may have some 
+            unwanted coupling between different channels, which is called crosstalk.
         </doc>
     </field>
     <field name="crosstalk_compensation" type="NX_BOOLEAN">
         <doc>
-            for reducing interferences between different signalling pathways
+            If measures are taken for reducing interferences between different signalling
+            pathways.
         </doc>
     </field>
     <field name="bandwidth" type="NX_NUMBER" units="NX_FREQUENCY">
         <doc>
             The spectrum of frequency it can amplify, from its lowest to highest frequency
-            limits.
+            limits. If it is difference of the frequencies, please also provide :ref: 
+            `center_frequency &lt;/NXamplifier/center_frequency-field&gt;`.
+        </doc>
+    </field>
+    <field name="center_frequency" type="NX_NUMBER" units="NX_FREQUENCY">
+        <doc>
+            The frequency in the middle of the bandwidth.
+        </doc>
+    </field>
+    <field name="lower_cutoff_frequency" type="NX_NUMBER" units="NX_FREQUENCY">
+        <doc>
+            The lower frequency point of the bandwidth where gain drops significantly (e.g.,
+            -3dB point).
         </doc>
     </field>
-    <field name="low_pass" type="NX_NUMBER" units="NX_FREQUENCY">
+    <field name="upper_cutoff_frequency" type="NX_NUMBER" units="NX_FREQUENCY">
         <doc>
-            Order and cut-off frequency of the low-pass filter applied on the demodulated
-            signals (X,Y). Cut-off frq (low pass filter) (foreach DemodulatorChannels)
+            The upper frequency point of the bandwidth where gain drops significantly (e.g.,
+            -3dB point).
         </doc>
     </field>
-    <field name="hi_pass" type="NX_NUMBER" units="NX_FREQUENCY">
+    <field name="gain" type="NX_NUMBER">
         <doc>
-            Order and cut-off frequency of the high-pass filter applied on the demodulation
-            signal. Cut-off frq (hi pass filter) (foreach DemodulatorChannels)
+            The ratio of the output signal to the input signal of the amplifier.
         </doc>
     </field>
-    <!--voltage_amplifier_factor(NX_NUMBER):
-doc: !!! Current Amplifier Factor typically refers to the gain of the probe current amplifier. (V/V)
-current_amplifier_capacitive_cross_talk_compensation(NX_CHAR):
-doc: !!! Reduces the effect of capacitive crosstalk in the circuit on experimental results.-->
 </definition>