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Merged
mkuehbach merged 3 commits into from
Jul 30, 2025
Merged

Ray's suggestions added to FIRmat-NFDI nexus_definitions PR #402 (how FAIRmat sees it) #403

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6fac725
Integrate Rays comments FAIRmat-NFDI nexus_definitions PR #402
atomprobe-tc Jul 29, 2025
8a36199
Whitespace fixing
atomprobe-tc Jul 29, 2025
f19afcf
Updated yaml file
atomprobe-tc Jul 29, 2025
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12 changes: 6 additions & 6 deletions applications/NXapm.nxdl.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@
<symbol name="p">
<doc>
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.
</doc>
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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.
</doc>
</field>
<field name="end_time" type="NX_DATE_TIME" recommended="true">
Expand Down Expand Up @@ -740,7 +740,7 @@
<group name="measurement" type="NXapm_measurement" optional="true">
<field name="status" type="NX_CHAR" recommended="true"/>
<field name="quality" type="NX_CHAR" recommended="true"/>
<group name="instrument" type="NXinstrument_apm">
<group name="instrument" type="NXapm_instrument">
<field name="type" type="NX_CHAR" recommended="true"/>
<field name="location" type="NX_CHAR" recommended="true"/>
<field name="flight_path" type="NX_FLOAT" recommended="true"/>
Expand Down Expand Up @@ -832,10 +832,10 @@
</group>
</group>
</group>
<group name="eventID" type="NXevent_data_apm" nameType="partial" minOccurs="0" maxOccurs="unbounded">
<group name="eventID" type="NXapm_event_data" nameType="partial" minOccurs="0" maxOccurs="unbounded">
<field name="start_time" type="NX_DATE_TIME" recommended="true"/>
<field name="end_time" type="NX_DATE_TIME" recommended="true"/>
<group name="instrument" type="NXinstrument_apm" recommended="true">
<group name="instrument" type="NXapm_instrument" recommended="true">
<group name="reflectron" type="NXcomponent" recommended="true">
<field name="voltage" type="NX_FLOAT"/>
</group>
Expand Down
17 changes: 9 additions & 8 deletions applications/NXem.nxdl.xml
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Expand Up @@ -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.
</doc>
</field>
<field name="end_time" type="NX_DATE_TIME" recommended="true">
Expand Down Expand Up @@ -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.
</doc>
</field>
Expand Down Expand Up @@ -747,8 +747,8 @@
</field>
</group>
<group name="measurement" type="NXem_measurement" optional="true">
<!--voltage like all other dynamic quantities should better be placed in instances of NXevent_data_em-->
<group name="instrument" type="NXinstrument_em">
<!--voltage like all other dynamic quantities should better be placed in instances of NXem_event_data-->
<group name="instrument" type="NXem_instrument">
<field name="name" type="NX_CHAR" recommended="true"/>
<field name="location" type="NX_CHAR" recommended="true"/>
<field name="type" type="NX_CHAR" recommended="true"/>
Expand Down Expand Up @@ -976,7 +976,7 @@
<group name="sensorID" type="NXsensor" nameType="partial" minOccurs="0" maxOccurs="unbounded"/>
<group name="actuatorID" type="NXactuator" nameType="partial" minOccurs="0" maxOccurs="unbounded"/>
</group>
<group name="eventID" type="NXevent_data_em" nameType="partial" minOccurs="0" maxOccurs="unbounded">
<group name="eventID" type="NXem_event_data" nameType="partial" minOccurs="0" maxOccurs="unbounded">
<field name="start_time" type="NX_DATE_TIME" recommended="true"/>
<field name="end_time" type="NX_DATE_TIME" recommended="true"/>
<field name="identifier_sample" type="NX_CHAR" recommended="true"/>
Expand Down Expand Up @@ -1341,7 +1341,7 @@
</field>
</group>
</group>
<group name="instrument" type="NXinstrument_em" recommended="true">
<group name="instrument" type="NXem_instrument" recommended="true">
<group name="ebeam_column" type="NXebeam_column">
<field name="operation_mode" type="NX_CHAR" recommended="true"/>
<group name="electron_source" type="NXsource" optional="true">
Expand Down Expand Up @@ -1640,7 +1640,6 @@ is required to provide such information in this way!-->
<group name="microstructureID" type="NXmicrostructure" nameType="partial" minOccurs="0" maxOccurs="unbounded"/>
</group>
</group>
<!--exists: optional-->
<group name="ebsd" type="NXem_ebsd" optional="true">
<group name="gnomonic_reference_frame" type="NXcoordinate_system" recommended="true">
<field name="alias" type="NX_CHAR" optional="true"/>
Expand Down Expand Up @@ -1786,7 +1785,9 @@ not wish to duplicate all payload data-->
<attribute name="axes" type="NX_CHAR"/>
<attribute name="AXISNAME_indices" type="NX_UINT" nameType="partial"/>
<field name="title" type="NX_CHAR" recommended="true"/>
<field name="intensity" type="NX_NUMBER"/>
<field name="intensity" type="NX_NUMBER">
<attribute name="long_name" type="NX_CHAR"/>
</field>
<field name="axis_i" type="NX_NUMBER">
<attribute name="long_name" type="NX_CHAR"/>
</field>
Expand Down
26 changes: 13 additions & 13 deletions applications/nyaml/NXapm.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down Expand Up @@ -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: |
Expand Down Expand Up @@ -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: |
Expand Down Expand Up @@ -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):
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -1531,7 +1531,7 @@ NXapm(NXobject):
dim: (n,)

# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++
# 1b00d2191b69e2bfe0c99007cdf2cd0e6215b63bf90f5f7f4940d5651953763a
# 7bec46bfcbbb372ad9c37859e21fe81ecdd1e4ca1c8502c0fdcbf71e757f898c
# <?xml version="1.0" encoding="UTF-8"?>
# <?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
# <!--
Expand Down Expand Up @@ -1578,7 +1578,7 @@ NXapm(NXobject):
# <symbol name="p">
# <doc>
# 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.
# </doc>
Expand Down Expand Up @@ -1683,7 +1683,7 @@ NXapm(NXobject):
# 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,
Expand Down Expand Up @@ -1874,7 +1874,7 @@ 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.
# </doc>
# </field>
# <field name="end_time" type="NX_DATE_TIME" recommended="true">
Expand Down Expand Up @@ -2274,7 +2274,7 @@ NXapm(NXobject):
# <group name="measurement" type="NXapm_measurement" optional="true">
# <field name="status" type="NX_CHAR" recommended="true"/>
# <field name="quality" type="NX_CHAR" recommended="true"/>
# <group name="instrument" type="NXinstrument_apm">
# <group name="instrument" type="NXapm_instrument">
# <field name="type" type="NX_CHAR" recommended="true"/>
# <field name="location" type="NX_CHAR" recommended="true"/>
# <field name="flight_path" type="NX_FLOAT" recommended="true"/>
Expand Down Expand Up @@ -2366,10 +2366,10 @@ NXapm(NXobject):
# </group>
# </group>
# </group>
# <group name="eventID" type="NXevent_data_apm" nameType="partial" minOccurs="0" maxOccurs="unbounded">
# <group name="eventID" type="NXapm_event_data" nameType="partial" minOccurs="0" maxOccurs="unbounded">
# <field name="start_time" type="NX_DATE_TIME" recommended="true"/>
# <field name="end_time" type="NX_DATE_TIME" recommended="true"/>
# <group name="instrument" type="NXinstrument_apm" recommended="true">
# <group name="instrument" type="NXapm_instrument" recommended="true">
# <group name="reflectron" type="NXcomponent" recommended="true">
# <field name="voltage" type="NX_FLOAT"/>
# </group>
Expand Down
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