Fairmat 2024: changes to contributed definitions

contributed_definitions/NXamplifier.nxdl.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
+<!--
+# NeXus - Neutron and X-ray Common Data Format
+# 
+# Copyright (C) 2014-2022 NeXus International Advisory Committee (NIAC)
+# 
+# This library is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License as published by the Free Software Foundation; either
+# version 2 of the License, or (at your option) any later version.
+#
+# This library is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this library; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+# 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" name="NXamplifier" extends="NXobject" type="group" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
+    <doc>
+         Base classed definition for amplifier devices.
+    </doc>
+    <group name="hardware" type="NXfabrication">
+        <doc>
+             (IC, device) (NXmanufacturer?)
+        </doc>
+    </group>
+    <field name="num_of_channels" type="NX_NUMBER">
+        <doc>
+             The number of preamplifier channels are assgined.
+        </doc>
+    </field>
+    <field name="active_channels" type="NX_NUMBER">
+        <doc>
+             The number of preamplifier channels are ready tp to be used. (array for active
+             channels)
+        </doc>
+    </field>
+    <field name="openloop_amplification" type="NX_NUMBER">
+        <doc>
+             The output signal does not go through a feedback loop to adjust the
+             amplification of the amplifier. (array for active channels)
+        </doc>
+    </field>
+    <!--amplification(NX_NUMBER):
+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 amplitue of the useful 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">
+        <doc>
+             (if active &gt;1)
+        </doc>
+    </field>
+    <field name="crosstalk_compensation" type="NX_BOOLEAN">
+        <doc>
+             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.
+        </doc>
+    </field>
+    <field name="low_pass" 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)
+        </doc>
+    </field>
+    <field name="hi_pass" type="NX_NUMBER" units="NX_FREQUENCY">
+        <doc>
+             Order and cut-off frequency of the high-pass filter applied on the demodulation
+             signal. Cut-off frq (hi pass filter) (foreach DemodulatorChannels)
+        </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>

contributed_definitions/NXapm_compositionspace_config.nxdl.xml

@@ -0,0 +1,191 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
+<!--
+# NeXus - Neutron and X-ray Common Data Format
+#
+# Copyright (C) 2014-2024 NeXus International Advisory Committee (NIAC)
+#
+# This library is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License as published by the Free Software Foundation; either
+# version 3 of the License, or (at your option) any later version.
+#
+# This library is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this library; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+# 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="application" type="group" name="NXapm_compositionspace_config" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
+    <doc>
+         Application definition for a configuration of the CompositionSpace tool used in atom probe.
+
+         * `A. Saxena et al. &lt;https://www.github.com/eisenforschung/CompositionSpace.git&gt;`_
+
+         This is an application definition for the common NFDI-MatWerk/FAIRmat infrastructure
+         use case IUC09 that explores how to improve the organization and results storage of the
+         CompositionSpace software using NeXus.
+    </doc>
+    <!--by default for appdefs the value of the exists keyword is required unless it is explicitly specified differently-->
+    <group type="NXentry" minOccurs="1" maxOccurs="1">
+        <field name="definition" type="NX_CHAR">
+            <attribute name="version" type="NX_CHAR" optional="true"/>
+            <enumeration>
+                <item value="NXapm_compositionspace_config"/>
+            </enumeration>
+        </field>
+        <group name="config" type="NXobject">
+            <group type="NXidentifier" optional="true"/>
+            <field name="analysis_identifier" type="NX_UINT" recommended="true"/>
+            <group name="reconstruction" type="NXserialized">
+                <doc>
+                     Specification of the tomographic reconstruction used for this analysis.
+                     Typically, reconstructions in the field of atom probe tomography are communicated via
+                     files which store at least reconstructed ion positions and mass-to-charge-state-ratio
+                     values. Container files like HDF5 though can store multiple reconstructions.
+                     Therefore, the position and mass_to_charge concepts point to specific instances
+                     to use for this analysis.
+                </doc>
+                <field name="type" type="NX_CHAR" optional="true"/>
+                <field name="path" type="NX_CHAR"/>
+                <field name="checksum" type="NX_CHAR" recommended="true"/>
+                <field name="algorithm" type="NX_CHAR" recommended="true"/>
+                <field name="position" type="NX_CHAR">
+                    <doc>
+                         Name of the node which resolves the reconstructed
+                         ion position values to use for this analysis.
+                    </doc>
+                </field>
+                <field name="mass_to_charge" type="NX_CHAR" optional="true">
+                    <doc>
+                         Name of the node which resolves the mass-to-charge-state ratio
+                         values for each reconstructed ion to use for this analysis.
+                    </doc>
+                </field>
+            </group>
+            <group name="ranging" type="NXserialized">
+                <doc>
+                     Specification of the ranging definitions used for this analysis.
+
+                     Indices start from 1. The value 0 is reserved for the null model of unranged positions whose
+                     iontype is unknown_type. The value 0 is also reserved for voxels that lie outside the dataset.
+                </doc>
+                <field name="type" type="NX_CHAR" optional="true"/>
+                <field name="path" type="NX_CHAR"/>
+                <field name="checksum" type="NX_CHAR" recommended="true"/>
+                <field name="algorithm" type="NX_CHAR" recommended="true"/>
+                <field name="ranging_definitions" type="NX_CHAR">
+                    <doc>
+                         Name of the (parent) node directly below which the ranging definitions for
+                         (molecular) ions are stored.
+                    </doc>
+                </field>
+            </group>
+            <group name="voxelization" type="NXprocess">
+                <doc>
+                     Step during which the point cloud is discretized to compute element-specific composition fields.
+                     Iontypes are atomically decomposed to correctly account for the multiplicity of each element that
+                     was ranged for each ion.
+                </doc>
+                <field name="edge_length" type="NX_NUMBER" units="NX_LENGTH">
+                    <doc>
+                         Edge length of cubic voxels building the 3D grid that is used for discretizing
+                         the point cloud.
+                    </doc>
+                </field>
+            </group>
+            <group name="autophase" type="NXprocess">
+                <doc>
+                     Optional step during which the subsequent segmentation step is prepared with the aim to eventually
+                     reduce the dimensionality of the chemical space in which the machine learning model works.
+
+                     In this step a supervised reduction of the dimensionality of the chemical space is quantified using
+                     the (Gini) feature importance of each element to suggest which columns of the composition matrix
+                     should be taken for the subsequent segmentation step.
+                </doc>
+                <field name="use" type="NX_BOOLEAN">
+                    <doc>
+                         Was the automated phase assignment used?
+                    </doc>
+                </field>
+                <field name="initial_guess" type="NX_POSINT" units="NX_UNITLESS">
+                    <doc>
+                         Estimated guess for which a Gaussian mixture model is evaluted to preprocess a result that
+                         is subsequenty post-processed with a random_forest_classifier to lower the number of
+                         dimensions in the chemical space to the subset of trunc_species many elements with the
+                         highest feature importance.
+                    </doc>
+                </field>
+                <field name="trunc_species" type="NX_POSINT" units="NX_UNITLESS">
+                    <doc>
+                         The number of elements to use for reducing the dimensionality.
+                    </doc>
+                </field>
+                <group name="random_forest_classifier" type="NXprocess" optional="true">
+                    <doc>
+                         Configuration for the random forest classification model.
+                    </doc>
+                </group>
+            </group>
+            <group name="segmentation" type="NXprocess">
+                <doc>
+                     Step during which the voxel set is segmented into voxel sets with different
+                     chemical composition.
+                </doc>
+                <group name="pca" type="NXprocess" optional="true">
+                    <doc>
+                         A principal component analysis of the chemical space to guide a decision into how many sets of voxels
+                         with different chemical composition the machine learning algorithm suggests to split the voxel set.
+                    </doc>
+                </group>
+                <group name="ic_opt" type="NXprocess">
+                    <doc>
+                         The decision is guided through the evalution of the information criterion
+                         minimization.
+                    </doc>
+                    <field name="n_max_ic_cluster" type="NX_POSINT" units="NX_UNITLESS">
+                        <doc>
+                             The maximum number of chemical classes to probe with the Gaussian mixture model
+                             with which the voxel set is segmented into a mixture of voxels with that many different
+                             chemical compositions.
+                        </doc>
+                    </field>
+                    <group name="gaussian_mixture" type="NXprocess" optional="true">
+                        <doc>
+                             Configuration for the Gaussian mixture model that is used in the segmentation
+                             step.
+                        </doc>
+                    </group>
+                </group>
+            </group>
+            <group name="clustering" type="NXprocess">
+                <doc>
+                     Step during which the chemically segmented voxel sets are analyzed for their
+                     spatial organization.
+                </doc>
+                <group name="dbscan" type="NXobject">
+                    <doc>
+                         Configuration for the DBScan algorithm that is used in the clustering step.
+                    </doc>
+                    <field name="eps" type="NX_FLOAT" units="NX_LENGTH">
+                        <doc>
+                             The maximum distance between voxel pairs in a neighborhood to be considered
+                             connected.
+                        </doc>
+                    </field>
+                    <field name="min_samples" type="NX_UINT" units="NX_UNITLESS">
+                        <doc>
+                             The number of voxels in a neighborhood for a voxel to be considered as a core
+                             point.
+                        </doc>
+                    </field>
+                </group>
+            </group>
+        </group>
+    </group>
+</definition>