diff --git a/applications/NXapm.nxdl.xml b/applications/NXapm.nxdl.xml
index 86c0e50130..9d76fb6ebf 100644
--- a/applications/NXapm.nxdl.xml
+++ b/applications/NXapm.nxdl.xml
@@ -44,7 +44,7 @@
Number of pulses collected in between start_time and end_time resolved by an
- instance of :ref:`NXevent_data_apm`. If this is not defined, p is the number of
+ instance of :ref:`NXapm_event_data`. If this is not defined, p is the number of
ions included in the reconstructed volume if the application definition is used
to store results of an already reconstructed dataset.
@@ -149,7 +149,7 @@
or a new file. Removing the specimen from the instrument is an interruption. Changing evaporation conditions
while the specimen is remains in the analysis_chamber and resuming thereafter the measurement
is not considered as an interruption. It is a common strategy to probe the evaporation process for different
- instrument parameters. Each individual collection should then though be stored in an own NXevent_data_apm
+ instrument parameters. Each individual collection should then though be stored in an own NXapm_event_data
group. Parking the specimen to the buffer_chamber and resuming the measurement at a later stage is an interruption.
During a run, the microscope is used for a certain amount of time to characterize a single specimen.
- The groups ``sample`` and ``specimen`` provide concepts for storing metadata about the sample and the specimen,
@@ -340,7 +340,7 @@
More detailed timing data over the course of the experiment have to be
collected to compute this event chain during the experiment. For this
- purpose the :ref:`NXevent_data_apm` instance should be used.
+ purpose the :ref:`NXapm_event_data` instance should be used.
@@ -740,7 +740,7 @@
-
+
@@ -832,10 +832,10 @@
-
+
-
+
diff --git a/applications/NXem.nxdl.xml b/applications/NXem.nxdl.xml
index ad9fe43f47..1ebf12fdb1 100644
--- a/applications/NXem.nxdl.xml
+++ b/applications/NXem.nxdl.xml
@@ -219,7 +219,7 @@
may not be sufficient to infer how long the experiment took or for how long
data were acquired. To bookkeep more fine-grained timestamps over the
course of the experiment is possible with start_time and end_time fields
- of respective :ref:`NXevent_data_em` instances.
+ of respective :ref:`NXem_event_data` instances.
@@ -422,7 +422,7 @@
For multi-layered specimens this field should only be used to describe
the density of the excited volume. For scanning electron microscopy
the usage of this field is discouraged and instead an instance of a
- region-of-interest connected to individual :ref:`NXevent_data_em`
+ region-of-interest connected to individual :ref:`NXem_event_data`
instances can provide a cleaner description of the relevant details.
@@ -747,8 +747,8 @@
-
-
+
+
@@ -976,7 +976,7 @@
-
+
@@ -1341,7 +1341,7 @@
-
+
@@ -1640,7 +1640,6 @@ is required to provide such information in this way!-->
-
@@ -1786,7 +1785,9 @@ not wish to duplicate all payload data-->
-
+
+
+
diff --git a/applications/nyaml/NXapm.yaml b/applications/nyaml/NXapm.yaml
index 36936ed3ec..400b91a843 100644
--- a/applications/nyaml/NXapm.yaml
+++ b/applications/nyaml/NXapm.yaml
@@ -78,7 +78,7 @@ doc: |
or a new file. Removing the specimen from the instrument is an interruption. Changing evaporation conditions
while the specimen is remains in the analysis_chamber and resuming thereafter the measurement
is not considered as an interruption. It is a common strategy to probe the evaporation process for different
- instrument parameters. Each individual collection should then though be stored in an own NXevent_data_apm
+ instrument parameters. Each individual collection should then though be stored in an own NXapm_event_data
group. Parking the specimen to the buffer_chamber and resuming the measurement at a later stage is an interruption.
During a run, the microscope is used for a certain amount of time to characterize a single specimen.
- The groups ``sample`` and ``specimen`` provide concepts for storing metadata about the sample and the specimen,
@@ -173,7 +173,7 @@ symbols:
Number of bins used in the mass-to-charge-state-ratio spectrum.
p: |
Number of pulses collected in between start_time and end_time resolved by an
- instance of :ref:`NXevent_data_apm`. If this is not defined, p is the number of
+ instance of :ref:`NXapm_event_data`. If this is not defined, p is the number of
ions included in the reconstructed volume if the application definition is used
to store results of an already reconstructed dataset.
p_out: |
@@ -288,7 +288,7 @@ NXapm(NXobject):
More detailed timing data over the course of the experiment have to be
collected to compute this event chain during the experiment. For this
- purpose the :ref:`NXevent_data_apm` instance should be used.
+ purpose the :ref:`NXapm_event_data` instance should be used.
end_time(NX_DATE_TIME):
exists: recommended
doc: |
@@ -651,7 +651,7 @@ NXapm(NXobject):
exists: recommended
quality(NX_CHAR):
exists: recommended
- instrument(NXinstrument_apm):
+ instrument(NXapm_instrument):
type(NX_CHAR):
exists: recommended
location(NX_CHAR):
@@ -759,14 +759,14 @@ NXapm(NXobject):
model(NX_CHAR):
serial_number(NX_CHAR):
exists: recommended
- eventID(NXevent_data_apm):
+ eventID(NXapm_event_data):
nameType: partial
exists: ['min', '0', 'max', 'unbounded']
start_time(NX_DATE_TIME):
exists: recommended
end_time(NX_DATE_TIME):
exists: recommended
- instrument(NXinstrument_apm):
+ instrument(NXapm_instrument):
exists: recommended
reflectron(NXcomponent):
exists: recommended
@@ -1531,7 +1531,7 @@ NXapm(NXobject):
dim: (n,)
# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++
-# 1b00d2191b69e2bfe0c99007cdf2cd0e6215b63bf90f5f7f4940d5651953763a
+# 7bec46bfcbbb372ad9c37859e21fe81ecdd1e4ca1c8502c0fdcbf71e757f898c
#
#
#
-#
+#
+#
#
#
#
@@ -2754,7 +2753,7 @@ NXem(NXobject):
#
#
#
-#
+#
#
#
#
@@ -3119,7 +3118,7 @@ NXem(NXobject):
#
#
#
-#
+#
#
#
#
@@ -3418,7 +3417,6 @@ NXem(NXobject):
#
#
#
-#
#
#
#
@@ -3564,7 +3562,9 @@ NXem(NXobject):
#
#
#
-#
+#
+#
+#
#
#
#
diff --git a/base_classes/NXaberration.nxdl.xml b/base_classes/NXaberration.nxdl.xml
index faca9e7310..fad8ee1961 100644
--- a/base_classes/NXaberration.nxdl.xml
+++ b/base_classes/NXaberration.nxdl.xml
@@ -25,12 +25,14 @@
Quantified aberration coefficient in an aberration_model.
- For an introduction in the aberrations in electron microscopy
+ For an introduction in the details about aberrations with relevance for electron microscopy
see `R. Dunin-Borkowski et al. <https://doi.org/10.1017/9781316337455.022>`_ and
`S. J. Pennycock and P. D. Nellist <https://doi.org/10.1007/978-1-4419-7200-2>`_ (page 44ff, and page 118ff)
for different definitions available and further details.
Table 7-2 of Ibid. publication (page 305ff) documents how to convert from the Nion to the CEOS definitions.
Conversion tables are also summarized by `Y. Liao <https://www.globalsino.com/EM/page3740.html>`_ an introduction.
+
+ The use of the base class is not restricted to electron microscopy but can also be useful for classical optics.
diff --git a/base_classes/NXevent_data_apm.nxdl.xml b/base_classes/NXapm_event_data.nxdl.xml
similarity index 96%
rename from base_classes/NXevent_data_apm.nxdl.xml
rename to base_classes/NXapm_event_data.nxdl.xml
index 820f061d95..162cd3e80e 100644
--- a/base_classes/NXevent_data_apm.nxdl.xml
+++ b/base_classes/NXapm_event_data.nxdl.xml
@@ -21,7 +21,7 @@
#
# For further information, see http://www.nexusformat.org
-->
-
+
The symbols used in the schema to specify e.g. dimensions of arrays.
@@ -37,7 +37,7 @@
Having at least one instance for an instance of NXapm is recommended.
- This base class applies the concept of the :ref:`NXevent_data_em` base class to the specific needs
+ This base class applies the concept of the :ref:`NXem_event_data` base class to the specific needs
of atom probe research. Again static and dynamic quantities are split to avoid a duplication
of information. Specifically, the time interval considered is the entire time
starting at start_time until end_time during which we assume the pulser triggered pulses.
@@ -110,7 +110,7 @@
-
+
Place to store dynamic metadata of the instrument to document as close as possible
the state of the instrument during the event, i.e. in between start_time and end_time.
diff --git a/base_classes/NXinstrument_apm.nxdl.xml b/base_classes/NXapm_instrument.nxdl.xml
similarity index 97%
rename from base_classes/NXinstrument_apm.nxdl.xml
rename to base_classes/NXapm_instrument.nxdl.xml
index 10b76c84e7..0d859aa531 100644
--- a/base_classes/NXinstrument_apm.nxdl.xml
+++ b/base_classes/NXapm_instrument.nxdl.xml
@@ -24,9 +24,9 @@
-
+
The symbols used in the schema to specify e.g. dimensions of arrays.
@@ -34,7 +34,7 @@ or volatile (meta)data.-->
Number of pulses collected in between start_time and end_time
- inside a parent instance of :ref:`NXevent_data_apm`.
+ inside a parent instance of :ref:`NXapm_event_data`.
@@ -44,7 +44,7 @@ or volatile (meta)data.-->
For collecting data and experiments which are simulations of an atom probe
microscope or a session with such instrument use the :ref:`NXapm` application definition
- and the :ref:`NXevent_data_apm` groups it provides.
+ and the :ref:`NXapm_event_data` groups it provides.
This base class implements the concept of :ref:`NXapm` whereby (meta)data are distinguished
whether these typically change during a session, so-called dynamic, or not, so-called static metadata.
@@ -194,7 +194,7 @@ or volatile (meta)data.-->
Laser- and/or voltage-pulsing device to trigger ion removal.
- When the base class NXinstrument_apm is used in the NXapm
+ When the base class NXapm_instrument is used in the NXapm
application definition, the values for the following fields:
* pulse_frequency
@@ -208,7 +208,7 @@ or volatile (meta)data.-->
* spot_position
should be recorded in the order of, and assumed associated,
- with the pulse_id in an instance of :ref:`NXevent_data_apm`.
+ with the pulse_id in an instance of :ref:`NXapm_event_data`.
diff --git a/base_classes/NXapm_measurement.nxdl.xml b/base_classes/NXapm_measurement.nxdl.xml
index c536a2daf1..d4f1f07747 100644
--- a/base_classes/NXapm_measurement.nxdl.xml
+++ b/base_classes/NXapm_measurement.nxdl.xml
@@ -65,6 +65,6 @@
field of a CamecaRoot ROOT file.
-
-
+
+
diff --git a/base_classes/NXcorrector_cs.nxdl.xml b/base_classes/NXcorrector_cs.nxdl.xml
index e79b409d46..2926785690 100644
--- a/base_classes/NXcorrector_cs.nxdl.xml
+++ b/base_classes/NXcorrector_cs.nxdl.xml
@@ -33,15 +33,15 @@
- Base class for a corrector reducing (spherical) aberrations in electron microscopy.
+ Base class for a corrector reducing (spherical) aberrations of an electron optical setup.
Different technology partners use different conventions and
models for quantifying the aberration coefficients.
- Correctors in an electron microscope are composed of multiple lenses
- and multipole stigmators. Their technical details are specific for the
- technology partner as well as microscope. Most technical details are
- proprietary knowledge.
+ Aberration correction components are especially important for (scanning)
+ transmission electron microscopy. Composed of multiple lenses and multipole stigmators,
+ their technical details are specific for the technology partner as well as
+ the microscope and instrument. Most technical details are proprietary knowledge.
If one component corrects for multiple types of aberrations (like it is the case
reported here `CEOS <https://www.ceos-gmbh.de/en/research/electrostat>`_) follow this
@@ -50,6 +50,14 @@
* Use :ref:`NXcorrector_cs` for spherical aberration
* Use :ref:`NXmonochromator` for energy filtering or chromatic aberration
* Use the group corrector_ax in :ref:`NXem` for axial astigmatism aberration
+
+ Although this base class currently provides concepts that are foremost used in
+ the field of electron microscopy using this base class is not restricted to this
+ research field. NXcorrector_cs can also serve as a container to detail, in
+ combination with :ref:`NXaberration`, about measured aberrations in classical optics.
+ In optics, though, the difference is that the design of the :ref:`NXoptical_lens`
+ itself (e.g., using aspheric lenses or combinations of lenses) enables to
+ reduce spherical aberrations.
@@ -63,7 +71,7 @@
the corrector is configured to enable calibrated usage of the instrument.
This :ref:`NXprocess` group should also be used when one describes in a computer
- simulation the specific details about the modelled or assumed aberrations.
+ simulation the specific details about the modeled or assumed aberrations.
@@ -164,6 +172,7 @@
+
diff --git a/base_classes/NXebeam_column.nxdl.xml b/base_classes/NXebeam_column.nxdl.xml
index d27ac26085..36612f877a 100644
--- a/base_classes/NXebeam_column.nxdl.xml
+++ b/base_classes/NXebeam_column.nxdl.xml
@@ -25,8 +25,8 @@
Base class for a set of components providing a controllable electron beam.
- The idea behind defining NXebeam_column as an own base class vs. adding these
- concepts in NXinstrument_em is that the electron beam generating component
+ The idea behind defining :ref:`NXebeam_column` as an own base class vs. adding these
+ concepts in :ref:`NXem_instrument` is that the electron beam generating component
might be worthwhile to use also in other types of experiments.
diff --git a/base_classes/NXevent_data_em.nxdl.xml b/base_classes/NXem_event_data.nxdl.xml
similarity index 97%
rename from base_classes/NXevent_data_em.nxdl.xml
rename to base_classes/NXem_event_data.nxdl.xml
index c26a78a7e6..beb08d404a 100644
--- a/base_classes/NXevent_data_em.nxdl.xml
+++ b/base_classes/NXem_event_data.nxdl.xml
@@ -21,7 +21,7 @@
#
# For further information, see http://www.nexusformat.org
-->
-
+
Base class to store state and (meta)data of events for electron microscopy.
@@ -48,7 +48,7 @@
data of the instrument state can be stored and documented in an representation
that facilitates interoperability. This is the idea behind this base class.
- :ref:`NXevent_data_em` represents an instance to describe and serialize flexibly
+ :ref:`NXem_event_data` represents an instance to describe and serialize flexibly
whatever is considered a time interval during which the instrument is
considered stable enough for allowing any working on tasks with it.
Examples of such tasks are the collecting of data (images and spectra) or
@@ -59,7 +59,7 @@
ROIs on the specimen), or they explore the state of the microscope for
service or maintenance tasks.
- :ref:`NXevent_data_em` serves the harmonization and documentation of these cases:
+ :ref:`NXem_event_data` serves the harmonization and documentation of these cases:
* Firstly, via a header section whose purpose is to contextualize
and identify the event instance in time.
@@ -94,7 +94,7 @@
implemented as time-dependent functional descriptions of e.g. lens excitations,
beam shape functions, trajectories of groups of electrons and ions, or detector noise models.
This also warrants to document the time-dependent details of individual components
- of the microscope via the here implemented class :ref:`NXevent_data_em`.
+ of the microscope via the here implemented class :ref:`NXem_event_data`.
@@ -151,7 +151,7 @@
-
+
diff --git a/base_classes/NXinstrument_em.nxdl.xml b/base_classes/NXem_instrument.nxdl.xml
similarity index 97%
rename from base_classes/NXinstrument_em.nxdl.xml
rename to base_classes/NXem_instrument.nxdl.xml
index 3e4b358e18..80340405a1 100644
--- a/base_classes/NXinstrument_em.nxdl.xml
+++ b/base_classes/NXem_instrument.nxdl.xml
@@ -21,13 +21,13 @@
#
# For further information, see http://www.nexusformat.org
-->
-
+
Base class for instrument-related details of a real or simulated electron microscope.
For collecting data and experiments which are simulations of an electron
microscope (or such session) use the :ref:`NXem` application definition and
- the :ref:`NXevent_data_em` groups it provides.
+ the :ref:`NXem_event_data` groups it provides.
This base class implements the concept of :ref:`NXem` whereby (meta)data are distinguished
whether these typically change during a session (dynamic) or not (static metadata).
@@ -162,7 +162,7 @@ in a particular narrow community which work with that particular microscope-->
attribute. However, it is better to describe the reference frame in which the
tilt is defined explicitly using instances of :ref:`NXtransformations` and
respective instances of :ref:`NXcoordinate_system`. Especially when this
- NXinstrument_em base class is used in an application definition like NXem.
+ NXem_instrument base class is used in an application definition like NXem.
@@ -176,7 +176,7 @@ in a particular narrow community which work with that particular microscope-->
attribute. However, it is better to describe the reference frame in which the
tilt is defined explicitly using instances of :ref:`NXtransformations` and
respective instances of :ref:`NXcoordinate_system`. Especially when this
- NXinstrument_em base class is used in an application definition like NXem.
+ NXem_instrument base class is used in an application definition like NXem.
@@ -190,7 +190,7 @@ in a particular narrow community which work with that particular microscope-->
attribute. However, it is better to describe the reference frame in which the
rotation is defined explicitly using instances of :ref:`NXtransformations` and
respective instances of :ref:`NXcoordinate_system`. Especially when this
- NXinstrument_em base class is used in an application definition like NXem.
+ NXem_instrument base class is used in an application definition like NXem.
@@ -204,7 +204,7 @@ in a particular narrow community which work with that particular microscope-->
attribute. However, it is better to describe the reference frame in which the
position values are defined explicitly using instances of :ref:`NXtransformations`
and respective instances of :ref:`NXcoordinate_system`. Especially when this
- NXinstrument_em base class is used in an application definition like NXem.
+ NXem_instrument base class is used in an application definition like NXem.
diff --git a/base_classes/NXem_measurement.nxdl.xml b/base_classes/NXem_measurement.nxdl.xml
index 4648fe57ac..8dda84b57a 100644
--- a/base_classes/NXem_measurement.nxdl.xml
+++ b/base_classes/NXem_measurement.nxdl.xml
@@ -25,6 +25,6 @@
Base class for documenting a measurement with an electron microscope.
-
-
+
+
diff --git a/base_classes/nyaml/NXaberration.yaml b/base_classes/nyaml/NXaberration.yaml
index 29b1343063..f44b946481 100644
--- a/base_classes/nyaml/NXaberration.yaml
+++ b/base_classes/nyaml/NXaberration.yaml
@@ -2,12 +2,14 @@ category: base
doc: |
Quantified aberration coefficient in an aberration_model.
- For an introduction in the aberrations in electron microscopy
+ For an introduction in the details about aberrations with relevance for electron microscopy
see `R. Dunin-Borkowski et al. `_ and
`S. J. Pennycock and P. D. Nellist `_ (page 44ff, and page 118ff)
for different definitions available and further details.
Table 7-2 of Ibid. publication (page 305ff) documents how to convert from the Nion to the CEOS definitions.
Conversion tables are also summarized by `Y. Liao `_ an introduction.
+
+ The use of the base class is not restricted to electron microscopy but can also be useful for classical optics.
type: group
NXaberration(NXobject):
magnitude(NX_NUMBER):
@@ -43,7 +45,7 @@ NXaberration(NXobject):
Alias to name or refer to this specific type of aberration.
# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++
-# 56e233c76debb9af5eff7325e0624f51d50b71e6153718e5ecd01d30bae025b3
+# a1f4a97012425a049e1c14093a96246f024dda6eaceeecbe877d79a54caa82e1
#
#
#
-#
+#
#
#
# The symbols used in the schema to specify e.g. dimensions of arrays.
@@ -122,7 +122,7 @@ NXevent_data_apm(NXobject):
#
# Having at least one instance for an instance of NXapm is recommended.
#
-# This base class applies the concept of the :ref:`NXevent_data_em` base class to the specific needs
+# This base class applies the concept of the :ref:`NXem_event_data` base class to the specific needs
# of atom probe research. Again static and dynamic quantities are split to avoid a duplication
# of information. Specifically, the time interval considered is the entire time
# starting at start_time until end_time during which we assume the pulser triggered pulses.
@@ -195,7 +195,7 @@ NXevent_data_apm(NXobject):
#
#
#
-#
+#
#
# Place to store dynamic metadata of the instrument to document as close as possible
# the state of the instrument during the event, i.e. in between start_time and end_time.
diff --git a/base_classes/nyaml/NXinstrument_apm.yaml b/base_classes/nyaml/NXapm_instrument.yaml
similarity index 97%
rename from base_classes/nyaml/NXinstrument_apm.yaml
rename to base_classes/nyaml/NXapm_instrument.yaml
index 44dc9d83b2..c023bab8ca 100644
--- a/base_classes/nyaml/NXinstrument_apm.yaml
+++ b/base_classes/nyaml/NXapm_instrument.yaml
@@ -5,7 +5,7 @@ doc: |
For collecting data and experiments which are simulations of an atom probe
microscope or a session with such instrument use the :ref:`NXapm` application definition
- and the :ref:`NXevent_data_apm` groups it provides.
+ and the :ref:`NXapm_event_data` groups it provides.
This base class implements the concept of :ref:`NXapm` whereby (meta)data are distinguished
whether these typically change during a session, so-called dynamic, or not, so-called static metadata.
@@ -16,14 +16,14 @@ symbols:
The symbols used in the schema to specify e.g. dimensions of arrays.
p: |
Number of pulses collected in between start_time and end_time
- inside a parent instance of :ref:`NXevent_data_apm`.
+ inside a parent instance of :ref:`NXapm_event_data`.
# One could use an NXnote or reference to another NeXus file where these static (meta)data
# are stored but then referencing this in an application definition would demand to make such
-# file required, while NXinstrument_apm can be used directly for the static and the dynamic
+# file required, while NXapm_instrument can be used directly for the static and the dynamic
# or volatile (meta)data.
type: group
-NXinstrument_apm(NXinstrument):
+NXapm_instrument(NXinstrument):
type(NX_CHAR):
doc: |
Which type of instrument.
@@ -120,7 +120,7 @@ NXinstrument_apm(NXinstrument):
doc: |
Laser- and/or voltage-pulsing device to trigger ion removal.
- When the base class NXinstrument_apm is used in the NXapm
+ When the base class NXapm_instrument is used in the NXapm
application definition, the values for the following fields:
* pulse_frequency
@@ -134,7 +134,7 @@ NXinstrument_apm(NXinstrument):
* spot_position
should be recorded in the order of, and assumed associated,
- with the pulse_id in an instance of :ref:`NXevent_data_apm`.
+ with the pulse_id in an instance of :ref:`NXapm_event_data`.
# technical design
fabrication(NXfabrication):
@@ -275,7 +275,7 @@ NXinstrument_apm(NXinstrument):
ion influx on the detector to avoid detection losses.
# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++
-# 0ec8c6a09ca271d9161ad9169ff7275817d6470e1471d89b4f2e7ef539fa76cf
+# 00518a52b2aa711a0d4118d218d66634f3679c4ee944463680e8c22db1f7f81e
#
#
#
-#
+#
#
#
# The symbols used in the schema to specify e.g. dimensions of arrays.
@@ -312,7 +312,7 @@ NXinstrument_apm(NXinstrument):
#
#
# Number of pulses collected in between start_time and end_time
-# inside a parent instance of :ref:`NXevent_data_apm`.
+# inside a parent instance of :ref:`NXapm_event_data`.
#
#
#
@@ -322,7 +322,7 @@ NXinstrument_apm(NXinstrument):
#
# For collecting data and experiments which are simulations of an atom probe
# microscope or a session with such instrument use the :ref:`NXapm` application definition
-# and the :ref:`NXevent_data_apm` groups it provides.
+# and the :ref:`NXapm_event_data` groups it provides.
#
# This base class implements the concept of :ref:`NXapm` whereby (meta)data are distinguished
# whether these typically change during a session, so-called dynamic, or not, so-called static metadata.
@@ -472,7 +472,7 @@ NXinstrument_apm(NXinstrument):
#
# Laser- and/or voltage-pulsing device to trigger ion removal.
#
-# When the base class NXinstrument_apm is used in the NXapm
+# When the base class NXapm_instrument is used in the NXapm
# application definition, the values for the following fields:
#
# * pulse_frequency
@@ -486,7 +486,7 @@ NXinstrument_apm(NXinstrument):
# * spot_position
#
# should be recorded in the order of, and assumed associated,
-# with the pulse_id in an instance of :ref:`NXevent_data_apm`.
+# with the pulse_id in an instance of :ref:`NXapm_event_data`.
#
#
#
diff --git a/base_classes/nyaml/NXapm_measurement.yaml b/base_classes/nyaml/NXapm_measurement.yaml
index 11f255a755..5adc2c029d 100644
--- a/base_classes/nyaml/NXapm_measurement.yaml
+++ b/base_classes/nyaml/NXapm_measurement.yaml
@@ -36,11 +36,11 @@ NXapm_measurement(NXobject):
The value can be extracted from the CAnalysis.CResults.fQuality
field of a CamecaRoot ROOT file.
- (NXinstrument_apm):
- (NXevent_data_apm):
+ (NXapm_instrument):
+ (NXapm_event_data):
# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++
-# 85fa0cb41b085e4263ca6a0ddab3aff086d8648f508d16664b4ed50d3ac4c93e
+# e9faeab8da622424796b78d0d80729b7859b197cd4fec4e288968e979d08a831
#
#
#
#
@@ -197,7 +214,7 @@ NXcorrector_cs(NXcomponent):
# the corrector is configured to enable calibrated usage of the instrument.
#
# This :ref:`NXprocess` group should also be used when one describes in a computer
-# simulation the specific details about the modelled or assumed aberrations.
+# simulation the specific details about the modeled or assumed aberrations.
#
#
#
@@ -298,6 +315,7 @@ NXcorrector_cs(NXcomponent):
#
#
#
+#
#
#
#
diff --git a/base_classes/nyaml/NXebeam_column.yaml b/base_classes/nyaml/NXebeam_column.yaml
index 10e2470632..9339274384 100644
--- a/base_classes/nyaml/NXebeam_column.yaml
+++ b/base_classes/nyaml/NXebeam_column.yaml
@@ -2,8 +2,8 @@ category: base
doc: |
Base class for a set of components providing a controllable electron beam.
- The idea behind defining NXebeam_column as an own base class vs. adding these
- concepts in NXinstrument_em is that the electron beam generating component
+ The idea behind defining :ref:`NXebeam_column` as an own base class vs. adding these
+ concepts in :ref:`NXem_instrument` is that the electron beam generating component
might be worthwhile to use also in other types of experiments.
type: group
NXebeam_column(NXcomponent):
@@ -188,7 +188,7 @@ NXebeam_column(NXcomponent):
scan_controller(NXscan_controller):
# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++
-# cbaec8a59a4f6890e012a26be203da955643a842a209386b1e198542eee4b64f
+# 19fbb7dc6ddf8316d8d7fbb2c80394526bee2dc817ff6b0e3a0e6dfc6a5fbb88
#
#
#
-#
+#
#
# Base class to store state and (meta)data of events for electron microscopy.
#
@@ -177,7 +177,7 @@ NXevent_data_em(NXobject):
# data of the instrument state can be stored and documented in an representation
# that facilitates interoperability. This is the idea behind this base class.
#
-# :ref:`NXevent_data_em` represents an instance to describe and serialize flexibly
+# :ref:`NXem_event_data` represents an instance to describe and serialize flexibly
# whatever is considered a time interval during which the instrument is
# considered stable enough for allowing any working on tasks with it.
# Examples of such tasks are the collecting of data (images and spectra) or
@@ -188,7 +188,7 @@ NXevent_data_em(NXobject):
# ROIs on the specimen), or they explore the state of the microscope for
# service or maintenance tasks.
#
-# :ref:`NXevent_data_em` serves the harmonization and documentation of these cases:
+# :ref:`NXem_event_data` serves the harmonization and documentation of these cases:
#
# * Firstly, via a header section whose purpose is to contextualize
# and identify the event instance in time.
@@ -223,7 +223,7 @@ NXevent_data_em(NXobject):
# implemented as time-dependent functional descriptions of e.g. lens excitations,
# beam shape functions, trajectories of groups of electrons and ions, or detector noise models.
# This also warrants to document the time-dependent details of individual components
-# of the microscope via the here implemented class :ref:`NXevent_data_em`.
+# of the microscope via the here implemented class :ref:`NXem_event_data`.
#
#
#
@@ -280,7 +280,7 @@ NXevent_data_em(NXobject):
#
#
#
-#
+#
#
#
#
diff --git a/base_classes/nyaml/NXinstrument_em.yaml b/base_classes/nyaml/NXem_instrument.yaml
similarity index 96%
rename from base_classes/nyaml/NXinstrument_em.yaml
rename to base_classes/nyaml/NXem_instrument.yaml
index 823df9f1dc..1d6be98a0b 100644
--- a/base_classes/nyaml/NXinstrument_em.yaml
+++ b/base_classes/nyaml/NXem_instrument.yaml
@@ -4,14 +4,14 @@ doc: |
For collecting data and experiments which are simulations of an electron
microscope (or such session) use the :ref:`NXem` application definition and
- the :ref:`NXevent_data_em` groups it provides.
+ the :ref:`NXem_event_data` groups it provides.
This base class implements the concept of :ref:`NXem` whereby (meta)data are distinguished
whether these typically change during a session (dynamic) or not (static metadata).
This design allows to store e.g. hardware related concepts only once instead of demanding
that each image or spectrum from the session needs to be stored also with the static metadata.
type: group
-NXinstrument_em(NXinstrument):
+NXem_instrument(NXinstrument):
name(NX_CHAR):
doc: |
Given name of the microscope at the hosting institution.
@@ -129,7 +129,7 @@ NXinstrument_em(NXinstrument):
attribute. However, it is better to describe the reference frame in which the
tilt is defined explicitly using instances of :ref:`NXtransformations` and
respective instances of :ref:`NXcoordinate_system`. Especially when this
- NXinstrument_em base class is used in an application definition like NXem.
+ NXem_instrument base class is used in an application definition like NXem.
\@comment(NX_CHAR):
doc: |
Discouraged free-text field to provide details about how to interpret tilt1.
@@ -140,7 +140,7 @@ NXinstrument_em(NXinstrument):
attribute. However, it is better to describe the reference frame in which the
tilt is defined explicitly using instances of :ref:`NXtransformations` and
respective instances of :ref:`NXcoordinate_system`. Especially when this
- NXinstrument_em base class is used in an application definition like NXem.
+ NXem_instrument base class is used in an application definition like NXem.
\@comment(NX_CHAR):
doc: |
Discouraged free-text field to provide details about how to interpret tilt2.
@@ -151,7 +151,7 @@ NXinstrument_em(NXinstrument):
attribute. However, it is better to describe the reference frame in which the
rotation is defined explicitly using instances of :ref:`NXtransformations` and
respective instances of :ref:`NXcoordinate_system`. Especially when this
- NXinstrument_em base class is used in an application definition like NXem.
+ NXem_instrument base class is used in an application definition like NXem.
\@comment(NX_CHAR):
doc: |
Discouraged free-text field to provide details about how to interpret rotation.
@@ -162,7 +162,7 @@ NXinstrument_em(NXinstrument):
attribute. However, it is better to describe the reference frame in which the
position values are defined explicitly using instances of :ref:`NXtransformations`
and respective instances of :ref:`NXcoordinate_system`. Especially when this
- NXinstrument_em base class is used in an application definition like NXem.
+ NXem_instrument base class is used in an application definition like NXem.
dimensions:
rank: 1
dim: (3,)
@@ -183,7 +183,7 @@ NXinstrument_em(NXinstrument):
(NXactuator):
# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++
-# 4b56a758c2ec8bb62faf19ecb426b97d7b99d1d87f6fa9df5741c32e857b3cf9
+# bced4402af1c0aad3f118b57c4d13a130318c151c544ba05b896f47b6081b924
#
#
#
-#
+#
#
# Base class for instrument-related details of a real or simulated electron microscope.
#
# For collecting data and experiments which are simulations of an electron
# microscope (or such session) use the :ref:`NXem` application definition and
-# the :ref:`NXevent_data_em` groups it provides.
+# the :ref:`NXem_event_data` groups it provides.
#
# This base class implements the concept of :ref:`NXem` whereby (meta)data are distinguished
# whether these typically change during a session (dynamic) or not (static metadata).
@@ -348,7 +348,7 @@ NXinstrument_em(NXinstrument):
# attribute. However, it is better to describe the reference frame in which the
# tilt is defined explicitly using instances of :ref:`NXtransformations` and
# respective instances of :ref:`NXcoordinate_system`. Especially when this
-# NXinstrument_em base class is used in an application definition like NXem.
+# NXem_instrument base class is used in an application definition like NXem.
#
#
#
@@ -362,7 +362,7 @@ NXinstrument_em(NXinstrument):
# attribute. However, it is better to describe the reference frame in which the
# tilt is defined explicitly using instances of :ref:`NXtransformations` and
# respective instances of :ref:`NXcoordinate_system`. Especially when this
-# NXinstrument_em base class is used in an application definition like NXem.
+# NXem_instrument base class is used in an application definition like NXem.
#
#
#
@@ -376,7 +376,7 @@ NXinstrument_em(NXinstrument):
# attribute. However, it is better to describe the reference frame in which the
# rotation is defined explicitly using instances of :ref:`NXtransformations` and
# respective instances of :ref:`NXcoordinate_system`. Especially when this
-# NXinstrument_em base class is used in an application definition like NXem.
+# NXem_instrument base class is used in an application definition like NXem.
#
#
#
@@ -390,7 +390,7 @@ NXinstrument_em(NXinstrument):
# attribute. However, it is better to describe the reference frame in which the
# position values are defined explicitly using instances of :ref:`NXtransformations`
# and respective instances of :ref:`NXcoordinate_system`. Especially when this
-# NXinstrument_em base class is used in an application definition like NXem.
+# NXem_instrument base class is used in an application definition like NXem.
#
#
#
diff --git a/base_classes/nyaml/NXem_measurement.yaml b/base_classes/nyaml/NXem_measurement.yaml
index 48e4dc84a0..b71a354794 100644
--- a/base_classes/nyaml/NXem_measurement.yaml
+++ b/base_classes/nyaml/NXem_measurement.yaml
@@ -3,12 +3,12 @@ doc: |
Base class for documenting a measurement with an electron microscope.
type: group
NXem_measurement(NXobject):
- instrument(NXinstrument_em):
- eventID(NXevent_data_em):
+ instrument(NXem_instrument):
+ eventID(NXem_event_data):
nameType: partial
# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++
-# b316172f1da3439b7e2e8914311c4473c77b211748924007325b78d22ab4bfa2
+# e35bca0f3966d7ba1e2093a64bd3d90479fef1794d86380a0db13003ecb6ccf0
#
#
#