diff --git a/applications/NXapm.nxdl.xml b/applications/NXapm.nxdl.xml index c2e29fe22a..db2b50c629 100644 --- a/applications/NXapm.nxdl.xml +++ b/applications/NXapm.nxdl.xml @@ -84,7 +84,7 @@ is considered as a narrow synonym for crystal defects. The aim of the NXapm application definition is to provide a general yet specific enough - solution to serialize artifacts for virtually all atom probe and field-ion microcopy experiments. + solution to serialize artifacts for virtually all atom probe and field-ion microscopy experiments. Before summarizing the design of the base classes and the parts of the NXapm application definition, it is worthwhile to recall and distinguish concepts that are related to atom extraction @@ -187,7 +187,7 @@ NXapm defines constraints on the existence and cardinality of concepts and its concept branches but seeks to offer a compromise. The key design pattern followed is that most branches are made optional or at most recommended but their child concepts are conditionally required. Thereby, NXapm can cover a variety of simple but also complex - use cases. An example of this parent-optional-but-childs-stronger-restricted design is the combination of the + use cases. An example of this parent-optional-but-children-stronger-restricted design is the combination of the optional group ``measurement`` with its required child ``measurement/instrument``: Users which report simulations are not forced to document the instrument but users which have characterized a specimen are motivated to report about the instrument. They are though not necessarily required to report all @@ -203,7 +203,7 @@ events that can be time-stamped individually. Each instance of a group ``measurement/eventID`` contains ``measurement/instrument`` whose purpose is to store those specific state and settings of the instrument that was present during the collection of the event. - Thereby, changing conditions such as compaigns with different target detection rate can be stored. + Thereby, changing conditions such as campaigns with different target detection rate can be stored. Noteworthy, such an approach of the atom probe detecting groups of events and storing these as groups has also been in use in the proprietary software via CamecaRoot, a set of customized data structures and file formats that use @@ -215,7 +215,7 @@ considered best practice by AMETEK/Cameca, ``raw_data`` for delay-line timing data, ``hit_finding`` for details of the hit finding algorithm, ``hit_spatial_filtering`` a process that filters hits of too low quality and those laying outside the about to be computed reconstruction volume. Furthermore, group ``voltage_and_bowl`` offers a place for documenting calibrations - and processing non-linearities. Group ``mass_to_charge_conversion`` is used to document the mass calibration and the + and processing nonlinearities. Group ``mass_to_charge_conversion`` is used to document the mass calibration and the conversion from time-of-flight to mass-to-charge-state-ratio values. Finally, the groups ``reconstruction`` and ``ranging`` were designed to match and document the classical approaches how @@ -979,7 +979,7 @@ In the case of an open-source instrument, like P. Felfer's Oxcart or G. Schmitz's M-TAP instruments, also use program1, program2, ... with program1 representing - the control software e.g. `M. Monajem and P. Felfer pyCCAPT <https://pyccapt.readthedocs.io/en/latest/>`_. + the control software e.g. `M. Monajem and P. Felfer PYCCAPT <https://pyccapt.readthedocs.io/en/latest/>`_. Further instances (program2, ...) can be used to list the dependencies, the python virtual environment. diff --git a/applications/NXarchive.nxdl.xml b/applications/NXarchive.nxdl.xml index b017e1a38b..fecdc99852 100644 --- a/applications/NXarchive.nxdl.xml +++ b/applications/NXarchive.nxdl.xml @@ -3,7 +3,7 @@ diff --git a/base_classes/NXcomponent.nxdl.xml b/base_classes/NXcomponent.nxdl.xml index 324f55b4a8..c01336f044 100644 --- a/base_classes/NXcomponent.nxdl.xml +++ b/base_classes/NXcomponent.nxdl.xml @@ -74,7 +74,7 @@ via the NXtransformations group. NeXus positions components by applying a set of translations and rotations - to the component starting from 0, 0, 0. The order of these operations + to apply to the component starting from 0, 0, 0. The order of these operations is critical and forms what NeXus calls a dependency chain. The depends_on field defines the path to the top most operation of the dependency chain or the string "." if located in the origin. Usually these operations are stored in a diff --git a/base_classes/NXelectromagnetic_lens.nxdl.xml b/base_classes/NXelectromagnetic_lens.nxdl.xml index 3cf9ed46d3..a13375ce71 100644 --- a/base_classes/NXelectromagnetic_lens.nxdl.xml +++ b/base_classes/NXelectromagnetic_lens.nxdl.xml @@ -26,7 +26,7 @@ Base class for an electro-magnetic lens or a compound lens. For :ref:`NXtransformations` the origin of the coordinate system is placed - in the center of the lens its polepiece, pinhole, or another point of reference. + in the center of the lens its pole piece, pinhole, or another point of reference. The origin should be specified in the :ref:`NXtransformations`. For details of electro-magnetic lenses in the literature see e.g. diff --git a/base_classes/NXem_ebsd.nxdl.xml b/base_classes/NXem_ebsd.nxdl.xml index c8959b455d..b24d271d3c 100644 --- a/base_classes/NXem_ebsd.nxdl.xml +++ b/base_classes/NXem_ebsd.nxdl.xml @@ -78,7 +78,7 @@ From this point onwards typically the microscope runs automatically. Diffraction pattern get collected until the queue finishes or gets interrupted by - either errors or arrival at the end of the users' allocated timeslot at the instrument. + either errors or arrival at the end of the users' allocated time slot at the instrument. Kikuchi pattern (EBSP) are usually indexed on-the-fly. These patterns are the raw data. Once indexed, these patterns are often not stored. diff --git a/base_classes/NXfit.nxdl.xml b/base_classes/NXfit.nxdl.xml index fce599395f..0d0bcf13a0 100644 --- a/base_classes/NXfit.nxdl.xml +++ b/base_classes/NXfit.nxdl.xml @@ -164,9 +164,9 @@ Description of the method used to optimize the parameters during peak fitting. Examples: - + - least squares - - non-linear least squares + - nonlinear least squares - Levenberg-Marquardt algorithm (damped least-squares) - linear regression - Bayesian linear regression @@ -181,7 +181,7 @@ :math:`min(\chi^2)`, where :math:`\chi^2` is the sum of squared residuals between the model and the observed data: :math:`min(\chi^2) = \sum_{i=1}^{N} \left( y_i - \left( \text{peak}_1(p_1, x_i) + \text{peak}_2(p_2, x_i) + \text{backgr}(p_3, x_i) \right) \right)^2` - + It is however also possible to supply more involved formulas (e.g., in the case of constrained fits). @@ -197,7 +197,7 @@ Metric used to determine the goodness of fit. Examples include: - + - :math:`\chi^2`, the squared sum of the sigma-weighted residuals - reduced :math:`\chi^2`:, :math:`\chi^2`: per degree of freedom - :math:`R^2`, the coefficient of determination diff --git a/base_classes/NXpid_controller.nxdl.xml b/base_classes/NXpid_controller.nxdl.xml index 86222bae47..6a194420b4 100644 --- a/base_classes/NXpid_controller.nxdl.xml +++ b/base_classes/NXpid_controller.nxdl.xml @@ -44,7 +44,7 @@ * K_ff A classic PID controller only implements the P, I and D terms and the values of the K_p, K_i and K_d constants are sufficient to fully - describe the behaviour of the feedback system implemented by such a PID controller. The inclusion of a Feed Forward term in a feedback system + describe the behavior of the feedback system implemented by such a PID controller. The inclusion of a Feed Forward term in a feedback system is a modern adaptation that aids optimization of the automated control. It is not present in all PID controllers, but it is also not uncommon. Note that the ``NXpid_controller`` is designed to be a child object of the actuator that its output is connected to. The parent object @@ -130,7 +130,7 @@ the Process Variable that is lower than the Setpoint results in a positive Error Value and a generally positive control output that tells the actuator to push the value of the Process Variable upwards. In some implementations, the actuator will respond to a more positive control output by pushing the Process Variable towards lower values (e.g. - a Peltier cooler) and so the output of the feedback system must be reversed to match the behaviour of the physical system. + a Peltier cooler) and so the output of the feedback system must be reversed to match the behavior of the physical system. A feedback system may also be implemented with reverse action in order to ensure that failures (e.g. disconnected sensor output or actuator input) result in a safe state (e.g. a valve should be left open to release pressure). diff --git a/contributed_definitions/NXapm_composition_space_results.nxdl.xml b/contributed_definitions/NXapm_composition_space_results.nxdl.xml index 15c107dc48..0c6403690a 100644 --- a/contributed_definitions/NXapm_composition_space_results.nxdl.xml +++ b/contributed_definitions/NXapm_composition_space_results.nxdl.xml @@ -69,7 +69,7 @@ check the respective group in the NXapm_paraprobe_results_nanochem data schema/application definition. - @@ -99,7 +99,7 @@ for if desired all the dependencies and libraries--> - Disencouraged place for free-text for e.g. comments. + Discouraged place for free-text for e.g. comments. @@ -233,7 +233,7 @@ inspect the example of the NXem_ebsd application definition--> - diff --git a/contributed_definitions/NXapm_paraprobe_config_clusterer.nxdl.xml b/contributed_definitions/NXapm_paraprobe_config_clusterer.nxdl.xml index b740203e4f..20afcceeb2 100644 --- a/contributed_definitions/NXapm_paraprobe_config_clusterer.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_config_clusterer.nxdl.xml @@ -48,7 +48,7 @@ n_disjoint_clusters: Number of disjoint cluster.--> Configuration of a paraprobe-clusterer tool run in atom probe microscopy. - @@ -146,7 +146,7 @@ unless it is explicitly specified differently--> - + - The symbols used in the schema to specify e.g. dimensions of arrays. + The symbols used in the schema to specify e.g. dimensions of arrays. - Configuration of a paraprobe-intersector tool run in atom probe microscopy. + Configuration of a paraprobe-intersector tool run in atom probe microscopy. - - Version specifier of this application definition. + Version specifier of this application definition. - Official NeXus NXDL schema with which this file was written. + Official NeXus NXDL schema with which this file was written. @@ -48,86 +48,86 @@ unless it is explicitly specified differently--> - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. + Given name of the program/software/tool with which this NeXus + (configuration) file was generated. - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. + Ideally program version plus build number, or commit hash or description + of ever persistent resources where the source code of the program and + build instructions can be found so that the program can be configured + ideally in such a manner that the result of this computational process + is recreatable in the same deterministic manner. - Ideally, a (globally persistent) unique identifier for referring - to this analysis. + Ideally, a (globally persistent) unique identifier for referring + to this analysis. - Possibility for leaving a free-text description about this analysis. + Possibility for leaving a free-text description about this analysis. - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. + Path to the directory where the tool should store NeXus/HDF5 results + of this analysis. If not specified results will be stored in the + current working directory. - ISO 8601 formatted time code with local time zone offset to - UTC information included when this configuration file was created. + ISO 8601 formatted time code with local time zone offset to + UTC information included when this configuration file was created. - For now a support field for the tool to identify how many individual - analyses the tool should execute as part of the analysis. + For now a support field for the tool to identify how many individual + analyses the tool should execute as part of the analysis. - Tracking volume_volume_spatial_correlation is the process of building logical - relations between volumetric features based on meshes, their proximity and - eventual intersections. Volumetric overlap and proximity of volumetric - features is identified for members of sets of features to members of - other sets of volumetric features. - Specifically, for each time step k pairs of sets are compared: - Members of a so-called current_set to members of a so-called next_set. - Members can be different types of volumetric features. - In the analysis of M. Kuehbach et al. specifically features can be - so-called objects (closed non-degnerated polyhedra representing watertight - parts of an e.g. iso-surface) and/or proxies. Proxies are computed - doppelganger/replacement meshes for parts of an iso-surface which initially - were not resulting in watertight meshes because objects at the edge - of the dataset or incompletely measured or truncated objects. + Tracking volume_volume_spatial_correlation is the process of building logical + relations between volumetric features based on meshes, their proximity and + eventual intersections. Volumetric overlap and proximity of volumetric + features is identified for members of sets of features to members of + other sets of volumetric features. + Specifically, for each time step k pairs of sets are compared: + Members of a so-called current_set to members of a so-called next_set. + Members can be different types of volumetric features. + In the analysis of M. Kühbach et al. specifically features can be + so-called objects (closed non-degenerated polyhedra representing watertight + parts of an e.g. iso-surface) and/or proxies. Proxies are computed + doppelganger/replacement meshes for parts of an iso-surface which initially + were not resulting in watertight meshes because objects at the edge + of the dataset or incompletely measured or truncated objects. - Specifies the method whereby to decide if two objects intersect volumetrically. - For reasons which are detailed in the supplementary material of - `M. Kühbach et al. <https://arxiv.org/abs/2205.13510>`_, the tool by - default assumes that two objects intersect if they share at least one - ion with the same evaporation ID (shared_ion). - Alternatively, with specifying tetrahedra_intersections, - the tool can perform an intersection analysis which attempts to - tetrahedralize first each polyhedron. If successful, the tool then checks - for at least one pair of intersecting tetrahedra to identify if two objects - intersect or not. - - However, we found that these geometrical analyses can result in corner - cases which the currently used library (TetGen) was not unable to - tetrahedralize successfully. These cases were virtually always - associated with complicated non-convex polyhedra which had portions - of the mesh that were connected by almost point like tubes of triangles. - Finding more robust methods for computing intersections between - not necessarily convex polyhedra might improve the situation in the future. + Specifies the method whereby to decide if two objects intersect volumetrically. + For reasons which are detailed in the supplementary material of + `M. Kühbach et al. <https://arxiv.org/abs/2205.13510>`_, the tool by + default assumes that two objects intersect if they share at least one + ion with the same evaporation ID (shared_ion). + Alternatively, with specifying tetrahedra_intersections, + the tool can perform an intersection analysis which attempts to + tetrahedralize first each polyhedron. If successful, the tool then checks + for at least one pair of intersecting tetrahedra to identify if two objects + intersect or not. + + However, we found that these geometrical analyses can result in corner + cases which the currently used library (TetGen) was not unable to + tetrahedralize successfully. These cases were virtually always + associated with complicated non-convex polyhedra which had portions + of the mesh that were connected by almost point like tubes of triangles. + Finding more robust methods for computing intersections between + not necessarily convex polyhedra might improve the situation in the future. @@ -135,89 +135,89 @@ unless it is explicitly specified differently--> - Specifies if the tool evaluates if for each pair the two objects - (and proxies if used) intersect volumetrically. + Specifies if the tool evaluates if for each pair the two objects + (and proxies if used) intersect volumetrically. - Specifies if the tool evaluates if for each pair the two objects - (and proxies if used) lie closer to one another than the - threshold_proximity. + Specifies if the tool evaluates if for each pair the two objects + (and proxies if used) lie closer to one another than the + threshold_proximity. - Specifies if the tool evaluates, ones all tracking tasks were - successfully completed, how intersecting or proximity related - objects build sub-graphs. This is the feature which enabled - M. Kühbach et al. 2022 the high-throughput analyses of how many - objects are coprecipitates in the sense that they are single, - duplet, triplet, or high-order. For these analyses to work - has_object_volume needs to be activated. + Specifies if the tool evaluates, ones all tracking tasks were + successfully completed, how intersecting or proximity related + objects build sub-graphs. This is the feature which enabled + M. Kühbach et al. 2022 the high-throughput analyses of how many + objects are coprecipitates in the sense that they are single, + duplet, triplet, or high-order. For these analyses to work + has_object_volume needs to be activated. - The maximum Euclidean distance between two objects below which - both objects are still considered within proximity. + The maximum Euclidean distance between two objects below which + both objects are still considered within proximity. - Specifies if the tool stores the so-called forward relations between - nodes representing members of the current_set to nodes representing - members of the next_set. + Specifies if the tool stores the so-called forward relations between + nodes representing members of the current_set to nodes representing + members of the next_set. - Specifies if the tool stores the so-called backward relations between - nodes representing members of the next_set to nodes representing - members of the current_set. + Specifies if the tool stores the so-called backward relations between + nodes representing members of the next_set to nodes representing + members of the current_set. - Current set stores a set of members, meshes of volumetric features, - which will be checked for proximity and/or volumetric intersection, - to members of the current_set. - The meshes were generated as a result of some other meshing process. + Current set stores a set of members, meshes of volumetric features, + which will be checked for proximity and/or volumetric intersection, + to members of the current_set. + The meshes were generated as a result of some other meshing process. - This identifier can be used to label the current set. The label - effectively represents (can be interpreted as) the time/iteration - step when the current set was taken. As it is detailed in `M. Kühbach - et al. 2022 <https://arxiv.org/abs/2205.13510>`_, this identifier - takes the role of the time variable :math:`k`. + This identifier can be used to label the current set. The label + effectively represents (can be interpreted as) the time/iteration + step when the current set was taken. As it is detailed in `M. Kühbach + et al. 2022 <https://arxiv.org/abs/2205.13510>`_, this identifier + takes the role of the time variable :math:`k`. +doc: For now a support field to tell the tool how many objects to load. +unit: NX_UNITLESS--> - The total number of distinguished feature sets FEATURE. - It is assumed that the members within all these FEATURE sets - are representing a set together. As an example this set might represent - all volumetric_features. However, users might have formed - a subset of this set where individuals were regrouped. - For paraprobe-nanochem this is the case for objects and proxies. - Specifically, objects are distinguished further into those far - from and those close to the edge of the dataset. - Similarly, proxies are distinguished further into those far - from and those close to the edge of the dataset. - So while these four sub-sets contain different so-called types of - features key is that they were all generated for one set, here the - current_set. + The total number of distinguished feature sets FEATURE. + It is assumed that the members within all these FEATURE sets + are representing a set together. As an example this set might represent + all volumetric_features. However, users might have formed + a subset of this set where individuals were regrouped. + For paraprobe-nanochem this is the case for objects and proxies. + Specifically, objects are distinguished further into those far + from and those close to the edge of the dataset. + Similarly, proxies are distinguished further into those far + from and those close to the edge of the dataset. + So while these four sub-sets contain different so-called types of + features key is that they were all generated for one set, here the + current_set. - Descriptive category explaining what these features are. + Descriptive category explaining what these features are. @@ -228,29 +228,29 @@ unless it is explicitly specified differently--> - Name of the (NeXus)/HDF5 file which contains triangulated - surface meshes of the members of the set as instances of - NXcg_polyhedron_set. + Name of the (NeXus)/HDF5 file which contains triangulated + surface meshes of the members of the set as instances of + NXcg_polyhedron_set. - Version identifier of the file such as a secure hash which documents - the binary state of the file to add an additional layer of - reproducibility from which file specifically contains these data. + Version identifier of the file such as a secure hash which documents + the binary state of the file to add an additional layer of + reproducibility from which file specifically contains these data. - String whereby the path to the geometry data can be interferred automatically. - Currently groupname_geometry_prefix/object<ID>/polyhedron. + String whereby the path to the geometry data can be inferred automatically. + Currently groupname_geometry_prefix/object<ID>/polyhedron. - Array of identifier whereby the path to the geometry data - can be interferred automatically. + Array of identifier whereby the path to the geometry data + can be inferred automatically. @@ -260,44 +260,44 @@ unless it is explicitly specified differently--> - Next set stores a set of members, meshes of volumetric features, - which will be checked for proximity and/or volumetric intersection, - to members of the next_set. - The meshes were generated as a result of some other meshing process. + Next set stores a set of members, meshes of volumetric features, + which will be checked for proximity and/or volumetric intersection, + to members of the next_set. + The meshes were generated as a result of some other meshing process. - This identifier can be used to label the next_set. The label - effectively represents (can be interpreted as) the time/iteration - step when the current set was taken. As it is detailed in `M. Kühbach - et al. 2022 <https://arxiv.org/abs/2205.13510>`_, this identifier - takes the role of the time variable :math:`k + 1`. + This identifier can be used to label the next_set. The label + effectively represents (can be interpreted as) the time/iteration + step when the current set was taken. As it is detailed in `M. Kühbach + et al. 2022 <https://arxiv.org/abs/2205.13510>`_, this identifier + takes the role of the time variable :math:`k + 1`. +doc: For now a support field to tell the tool how many objects to load. +unit: NX_UNITLESS--> - The total number of distinguished feature sets FEATURE. - It is assumed that the members within all these FEATURE sets - are representing a set together. As an example this set might represent - all volumetric_features. However, users might have formed - a subset of this set where individuals were regrouped. - For paraprobe-nanochem this is the case for objects and proxies. - Specifically, objects are distinguished further into those far - from and those close to the edge of the dataset. - Similarly, proxies are distinguished further into those far - from and those close to the edge of the dataset. - So while these four sub-sets contain different so-called types of - features key is that they were all generated for one set, here the - next_set. + The total number of distinguished feature sets FEATURE. + It is assumed that the members within all these FEATURE sets + are representing a set together. As an example this set might represent + all volumetric_features. However, users might have formed + a subset of this set where individuals were regrouped. + For paraprobe-nanochem this is the case for objects and proxies. + Specifically, objects are distinguished further into those far + from and those close to the edge of the dataset. + Similarly, proxies are distinguished further into those far + from and those close to the edge of the dataset. + So while these four sub-sets contain different so-called types of + features key is that they were all generated for one set, here the + next_set. - Descriptive category explaining what these features are. + Descriptive category explaining what these features are. @@ -308,29 +308,29 @@ unless it is explicitly specified differently--> - Name of the (NeXus)/HDF5 file which contains triangulated - surface meshes of the members of the set as instances of - NXcg_polyhedron_set. + Name of the (NeXus)/HDF5 file which contains triangulated + surface meshes of the members of the set as instances of + NXcg_polyhedron_set. - Version identifier of the file such as a secure hash which documents - the binary state of the file to add an additional layer of - reproducibility from which file specifically contains these data. + Version identifier of the file such as a secure hash which documents + the binary state of the file to add an additional layer of + reproducibility from which file specifically contains these data. - String whereby the path to the geometry data can be interferred automatically. - Currently groupname_geometry_prefix/object<ID>/polyhedron. + String whereby the path to the geometry data can be inferred automatically. + Currently groupname_geometry_prefix/object<ID>/polyhedron. - Array of identifier whereby the path to the geometry data - can be interferred automatically. + Array of identifier whereby the path to the geometry data + can be inferred automatically. @@ -339,8 +339,8 @@ unless it is explicitly specified differently--> - + diff --git a/contributed_definitions/NXapm_paraprobe_config_nanochem.nxdl.xml b/contributed_definitions/NXapm_paraprobe_config_nanochem.nxdl.xml index 340c30e093..bc0042d472 100644 --- a/contributed_definitions/NXapm_paraprobe_config_nanochem.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_config_nanochem.nxdl.xml @@ -470,7 +470,7 @@ and this does not work because without a delocalization/field quantity you canno `B. Gault et al. <https://doi.org/10.1017/S1431927621012952>`_ In continuation of these thoughts this applies also to reconstructed objects. A well-known example is the discussion of shape deviations - of Al3Sc precipitates in aluminium alloys which in reconstructions + of Al3Sc precipitates in aluminum alloys which in reconstructions can appear as ellipsoids although they should be almost spherical, depending on their size. diff --git a/contributed_definitions/NXapm_paraprobe_config_ranger.nxdl.xml b/contributed_definitions/NXapm_paraprobe_config_ranger.nxdl.xml index 7fd4937625..e5594b5049 100644 --- a/contributed_definitions/NXapm_paraprobe_config_ranger.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_config_ranger.nxdl.xml @@ -42,7 +42,7 @@ Configuration of a paraprobe-ranger tool run in atom probe microscopy. - @@ -232,7 +232,7 @@ unless it is explicitly specified differently--> Report the accumulated atomic mass from each isotope building the ion. Accounts for each identified ion. - Relatistic effects are not accounted for. + Relativistic effects are not accounted for. @@ -241,7 +241,7 @@ unless it is explicitly specified differently--> the ion. Accounts for each identified ion. The value zero indicates it is not possible to build such molecular ion - from nuclids which are all observationally stable. + from nuclides which are all observationally stable. Very small values can give an idea/about how likely such a molecular ion is expected to form assuming equal probabilities. @@ -267,7 +267,7 @@ store_composition_weighted_product(NX_BOOLEAN): It should not be forgotten though the computation relies on assumptions: * The composition is homogeneous within the virtual specimen. - * It is a priori know which nuclids the specimen is build of. + * It is a priori know which nuclides the specimen is build of. --> diff --git a/contributed_definitions/NXapm_paraprobe_config_selector.nxdl.xml b/contributed_definitions/NXapm_paraprobe_config_selector.nxdl.xml index cdaa32bb64..9663ac34c0 100644 --- a/contributed_definitions/NXapm_paraprobe_config_selector.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_config_selector.nxdl.xml @@ -31,7 +31,7 @@ Configuration of a paraprobe-selector tool run in atom probe microscopy. - diff --git a/contributed_definitions/NXapm_paraprobe_config_spatstat.nxdl.xml b/contributed_definitions/NXapm_paraprobe_config_spatstat.nxdl.xml index 81c175e434..9c4f3854ed 100644 --- a/contributed_definitions/NXapm_paraprobe_config_spatstat.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_config_spatstat.nxdl.xml @@ -46,7 +46,7 @@ Configuration of a paraprobe-spatstat tool run in atom probe microscopy. - diff --git a/contributed_definitions/NXapm_paraprobe_config_surfacer.nxdl.xml b/contributed_definitions/NXapm_paraprobe_config_surfacer.nxdl.xml index 8427d9bb1a..984be5dec6 100644 --- a/contributed_definitions/NXapm_paraprobe_config_surfacer.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_config_surfacer.nxdl.xml @@ -41,8 +41,6 @@ Configuration of a paraprobe-surfacer tool run in atom probe microscopy. - Version specifier of this application definition. @@ -181,8 +179,8 @@ unless it is explicitly specified differently--> interior points for certain alpha-shape constructions. By default no such filtering is used during pre-processing. - By contrast, the option kuehbach activates a preprocessing - during which a Hoshen-Kopelman percolation analysis is used + By contrast, the option percolation activates a preprocessing + step during which a Hoshen-Kopelman percolation analysis is used to identify which points are closer to the edge of the dataset. This can reduce the number of points in the alpha-shape computation and thus improve performance substantially. @@ -191,14 +189,14 @@ unless it is explicitly specified differently--> - + - When using the kuehbach preprocessing, this is the width of the - kernel for identifying which ions are in voxels close to the + When using the option percolation during preprocessing, this is the + width of the kernel for identifying which ions are in voxels close to the edge of the point cloud. diff --git a/contributed_definitions/NXapm_paraprobe_config_tessellator.nxdl.xml b/contributed_definitions/NXapm_paraprobe_config_tessellator.nxdl.xml index e963465431..0bf6e109c5 100644 --- a/contributed_definitions/NXapm_paraprobe_config_tessellator.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_config_tessellator.nxdl.xml @@ -32,7 +32,7 @@ Configuration of a paraprobe-tessellator tool run in atom probe microscopy. - diff --git a/contributed_definitions/NXapm_paraprobe_config_transcoder.nxdl.xml b/contributed_definitions/NXapm_paraprobe_config_transcoder.nxdl.xml index 4d548e5bf7..4dd9de431b 100644 --- a/contributed_definitions/NXapm_paraprobe_config_transcoder.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_config_transcoder.nxdl.xml @@ -31,7 +31,7 @@ Configurations of a paraprobe-transcoder tool run in atom probe microscopy. - diff --git a/contributed_definitions/NXapm_paraprobe_results_clusterer.nxdl.xml b/contributed_definitions/NXapm_paraprobe_results_clusterer.nxdl.xml index eb89794977..db2efc503c 100644 --- a/contributed_definitions/NXapm_paraprobe_results_clusterer.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_results_clusterer.nxdl.xml @@ -40,8 +40,6 @@ Results of a paraprobe-clusterer tool run. - diff --git a/contributed_definitions/NXapm_paraprobe_results_distancer.nxdl.xml b/contributed_definitions/NXapm_paraprobe_results_distancer.nxdl.xml index 54ad4dccaf..1da4549b95 100644 --- a/contributed_definitions/NXapm_paraprobe_results_distancer.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_results_distancer.nxdl.xml @@ -40,7 +40,7 @@ Results of a paraprobe-distancer tool run. - @@ -301,7 +301,7 @@ unless it is explicitly specified differently--> A support field to visualize each ion and with this the distance - informations using XDMF and e.g. Paraview. + information using XDMF and e.g. Paraview. diff --git a/contributed_definitions/NXapm_paraprobe_results_intersector.nxdl.xml b/contributed_definitions/NXapm_paraprobe_results_intersector.nxdl.xml index 1c60505c7e..140c1baf5b 100644 --- a/contributed_definitions/NXapm_paraprobe_results_intersector.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_results_intersector.nxdl.xml @@ -61,7 +61,7 @@ Results of a paraprobe-intersector tool run. - @@ -252,7 +252,7 @@ unless it is explicitly specified differently--> chemical composition that were characterized in the same material volume representing a snapshot of an e.g. microstructure at the same point in time. Researchers may have performed two analyses, one to - characterize precipitates A and another one to characterize percipitates + characterize precipitates A and another one to characterize precipitates B. Coprecipitation analysis now logically connects these independent characterization results to establish spatial correlations of e.g. precipitates spatial arrangement. diff --git a/contributed_definitions/NXapm_paraprobe_results_nanochem.nxdl.xml b/contributed_definitions/NXapm_paraprobe_results_nanochem.nxdl.xml index ea636969ae..bf2f7afa02 100644 --- a/contributed_definitions/NXapm_paraprobe_results_nanochem.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_results_nanochem.nxdl.xml @@ -72,7 +72,7 @@ Results of a paraprobe-nanochem tool run. - @@ -311,7 +311,7 @@ if weighting_model == isotopic_decomposition needs isotopic_decomposition_rule-- A list of isotopes (via proton and neutron number) to consider for the isotopic_decomposition weighting model. - Isotopes must exist in the nuclid table. + Isotopes must exist in the nuclide table. Values in match are isotope hash values using the following hashing rule $H = Z + 256*N$ with $Z$ the number of protons and $N$ the number of neutrons of the isotope. @@ -630,7 +630,7 @@ for XDMF in ParaView ?--> XDMF topology for rendering in combination with - xdmf_xyz the scalar field via XDFM in e.g. Paraview. + xdmf_xyz the scalar field via XDMF in e.g. Paraview. @@ -707,7 +707,7 @@ for XDMF in ParaView ?--> XDMF topology for rendering in combination with - xdmf_xyz the scalar field via XDFM in e.g. Paraview. + xdmf_xyz the scalar field via XDMF in e.g. Paraview. @@ -1175,7 +1175,7 @@ details about specific features--> - + Count or weight which, when divided by total, @@ -1263,7 +1263,7 @@ face_identifier_offset(NX_UINT):--> - + Count or weight which, when divided by total @@ -1884,9 +1884,6 @@ face_identifier_offset(NX_UINT):--> - diff --git a/contributed_definitions/NXapm_paraprobe_results_ranger.nxdl.xml b/contributed_definitions/NXapm_paraprobe_results_ranger.nxdl.xml index 52e41fca56..9a56d796e1 100644 --- a/contributed_definitions/NXapm_paraprobe_results_ranger.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_results_ranger.nxdl.xml @@ -41,7 +41,7 @@ Results of a paraprobe-ranger tool run. - @@ -187,7 +187,7 @@ unless it is explicitly specified differently--> - + @@ -245,7 +245,7 @@ unless it is explicitly specified differently--> Paraprobe-ranger performs a combinatorial search over - all possible or a reduced set of nuclids to identify + all possible or a reduced set of nuclides to identify into which ions these can be composed. @@ -306,17 +306,17 @@ unless it is explicitly specified differently--> - + - The number of disjoint nuclids for each molecular ion. + The number of disjoint nuclides for each molecular ion. - + - The number of nuclids for each molecular ion. + The number of nuclides for each molecular ion. @@ -340,7 +340,7 @@ unless it is explicitly specified differently--> - + diff --git a/contributed_definitions/NXapm_paraprobe_results_selector.nxdl.xml b/contributed_definitions/NXapm_paraprobe_results_selector.nxdl.xml index 38fac70961..61f42450d5 100644 --- a/contributed_definitions/NXapm_paraprobe_results_selector.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_results_selector.nxdl.xml @@ -35,8 +35,6 @@ Results of a paraprobe-selector tool run. - diff --git a/contributed_definitions/NXapm_paraprobe_results_spatstat.nxdl.xml b/contributed_definitions/NXapm_paraprobe_results_spatstat.nxdl.xml index d87d2f50ff..46faf02652 100644 --- a/contributed_definitions/NXapm_paraprobe_results_spatstat.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_results_spatstat.nxdl.xml @@ -35,8 +35,6 @@ Results of a paraprobe-spatstat tool run. - diff --git a/contributed_definitions/NXapm_paraprobe_results_surfacer.nxdl.xml b/contributed_definitions/NXapm_paraprobe_results_surfacer.nxdl.xml index 5c5220f2a8..2edb334304 100644 --- a/contributed_definitions/NXapm_paraprobe_results_surfacer.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_results_surfacer.nxdl.xml @@ -55,8 +55,6 @@ Results of a paraprobe-surfacer tool run. - @@ -372,8 +370,8 @@ for eventually performed preprocessing--> - Integer which specifies the first index to be used for distin- - guishing tetrahedra. Identifiers are defined either implicitly + Integer which specifies the first index to be used for distinguishing + tetrahedra. Identifiers are defined either implicitly or explicitly. For implicit indexing the identifiers are defined on the interval [identifier_offset, identifier_offset+c-1]. For explicit indexing the identifier array has to be defined. diff --git a/contributed_definitions/NXapm_paraprobe_results_tessellator.nxdl.xml b/contributed_definitions/NXapm_paraprobe_results_tessellator.nxdl.xml index c6081efe77..ba60544672 100644 --- a/contributed_definitions/NXapm_paraprobe_results_tessellator.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_results_tessellator.nxdl.xml @@ -40,8 +40,6 @@ Results of a paraprobe-tessellator tool run. - diff --git a/contributed_definitions/NXapm_paraprobe_results_transcoder.nxdl.xml b/contributed_definitions/NXapm_paraprobe_results_transcoder.nxdl.xml index f7e0f3433e..e2020b0006 100644 --- a/contributed_definitions/NXapm_paraprobe_results_transcoder.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_results_transcoder.nxdl.xml @@ -57,8 +57,6 @@ Results of a paraprobe-transcoder tool run. - @@ -201,7 +199,7 @@ unless it is explicitly specified differently--> Remote Tools Hub (NORTH) the topic of interoperability became more important and eventually the NXapm application definition was proposed. NORTH is a GUI and related service in a NOMAD OASIS instance which allows - to spawn preconfigured docker containers via JupyterHub. + to spawn pre-configured docker containers via JupyterHub. Currently, NORTH includes the so-called apm container. A container with tools specific for analyzing data from atom probe microscopy as well as processing of point cloud and mesh data. @@ -355,7 +353,7 @@ alternatively:--> paraprobe. Furthermore, this summarizes also why the fundamental design of splitting an analysis always into steps of configuration (with parmsetup), task execution (with the respective C/C++ or Python tool of the toolbox), - and post-processing (e.g. with autoreporter) is useful because it offers + and post-processing (e.g. with auto-reporter) is useful because it offers a clear description of provenance tracking. This is a necessary step to make atom probe microscopy data at all better aligned with the aims of the FAIR principles. @@ -403,7 +401,7 @@ alternatively:--> - + diff --git a/contributed_definitions/NXbeam_splitter.nxdl.xml b/contributed_definitions/NXbeam_splitter.nxdl.xml index e4b2d38e4d..3043820693 100644 --- a/contributed_definitions/NXbeam_splitter.nxdl.xml +++ b/contributed_definitions/NXbeam_splitter.nxdl.xml @@ -38,7 +38,7 @@ - Number of parameters needed do descripe the shape of the beam splitter. + Number of parameters needed do describe the shape of the beam splitter. @@ -111,7 +111,7 @@ @@ -227,7 +227,7 @@ length(NX_FLOAT): Thickness of the beam splitter substrate. Define the minimum and - maximum thickness (for a wedged geomtry). For a homogeneous thickness + maximum thickness (for a wedged geometry). For a homogeneous thickness (e.g. as in plate beam splitters) the minimum and maximum values are equal. @@ -235,7 +235,7 @@ length(NX_FLOAT): - + Complex index of refraction of the beam splitter substrate. Specify at given spectral values (e.g. wavelength, energy, wavenumber etc.). @@ -338,7 +338,7 @@ length(NX_FLOAT): use dim: [[1,N_angles]], N_angles being the number of angles for which the beam splitter can be operated? If this is the case for some devices, we might also have to define a field -for the corresponding defelction angles...--> +for the corresponding deflection angles...--> Reflectance of the beam splitter at given spectral values. diff --git a/contributed_definitions/NXcoordinate_system_set.nxdl.xml b/contributed_definitions/NXcoordinate_system_set.nxdl.xml index 120caa7390..ce437ec7d6 100644 --- a/contributed_definitions/NXcoordinate_system_set.nxdl.xml +++ b/contributed_definitions/NXcoordinate_system_set.nxdl.xml @@ -176,7 +176,7 @@ use depends_on field - not attribute - to point to conventions used--> Which sign convention is followed when converting orientations - between different parameterizations/representations according + between different parametrizations/representations according to convention 6 of DOI: 10.1088/0965-0393/23/8/083501. diff --git a/contributed_definitions/NXdelocalization.nxdl.xml b/contributed_definitions/NXdelocalization.nxdl.xml index f061f7f583..2fa42210a7 100644 --- a/contributed_definitions/NXdelocalization.nxdl.xml +++ b/contributed_definitions/NXdelocalization.nxdl.xml @@ -65,7 +65,7 @@ Reference or link to the points which are delocalized on the grid. - A list of isotopes to consider for the isotope_decomposition weighting model. - Isotopes must exist in the nuclid table. Entries in the fastest changing + Isotopes must exist in the nuclide table. Entries in the fastest changing dimension should be the pair of proton (first entry) and neutron number (second entry). diff --git a/contributed_definitions/NXdispersion_function.nxdl.xml b/contributed_definitions/NXdispersion_function.nxdl.xml index 4aac709e9f..9fd6025168 100644 --- a/contributed_definitions/NXdispersion_function.nxdl.xml +++ b/contributed_definitions/NXdispersion_function.nxdl.xml @@ -73,13 +73,13 @@ The energy unit used in the formula. The field value is a scaling factor for the units attribute. - It is recommeded to set the field value to 1 and carry all the unit + It is recommended to set the field value to 1 and carry all the unit scaling information in the units attribute. - The identifier useed to represent wavelength + The identifier used to represent wavelength in the formula. It is recommended to use `lambda`. @@ -87,7 +87,7 @@ The wavelength unit used in the formula. The field value is a scaling factor for the units attribute. - It is recommeded to set the field value to 1 and carry all the unit + It is recommended to set the field value to 1 and carry all the unit scaling information in the units attribute. diff --git a/contributed_definitions/NXdispersion_repeated_parameter.nxdl.xml b/contributed_definitions/NXdispersion_repeated_parameter.nxdl.xml index 871ff09f36..3d1c92c98c 100644 --- a/contributed_definitions/NXdispersion_repeated_parameter.nxdl.xml +++ b/contributed_definitions/NXdispersion_repeated_parameter.nxdl.xml @@ -47,7 +47,7 @@ A unit array associating a unit with each parameter. The first element should be equal to values/@unit. The values should be SI interpretable standard units - with common prefixes (e.g. mikro, nano etc.) or their + with common prefixes (e.g. micro, nano etc.) or their short-hand notation (e.g. nm, mm, kHz etc.). diff --git a/contributed_definitions/NXdispersive_material.nxdl.xml b/contributed_definitions/NXdispersive_material.nxdl.xml index e4e4118b68..eae5f4d05d 100644 --- a/contributed_definitions/NXdispersive_material.nxdl.xml +++ b/contributed_definitions/NXdispersive_material.nxdl.xml @@ -90,7 +90,7 @@ This field may be used to denote additional phase information, - such as crystalin phase of a crystal (e.g. 4H or 6H for SiC) or + such as crystalline phase of a crystal (e.g. 4H or 6H for SiC) or if a measurement was done on a thin film or bulk material. @@ -196,7 +196,7 @@ This should only be filled for uniaxial or biaxial materials. For uniaxial materials this denotes the extraordinary axis. For biaxial materials this denotes the epsilon 33 tensor element - of the diagionalized perimittivty tensor. + of the diagionalized permittivity tensor. diff --git a/contributed_definitions/NXelectrostatic_kicker.nxdl.xml b/contributed_definitions/NXelectrostatic_kicker.nxdl.xml index 16d9bfeab8..039fa24e78 100644 --- a/contributed_definitions/NXelectrostatic_kicker.nxdl.xml +++ b/contributed_definitions/NXelectrostatic_kicker.nxdl.xml @@ -50,7 +50,7 @@ -volage set on supply. +voltage set on supply. diff --git a/contributed_definitions/NXion.nxdl.xml b/contributed_definitions/NXion.nxdl.xml index 99a19f2e3c..0874421ece 100644 --- a/contributed_definitions/NXion.nxdl.xml +++ b/contributed_definitions/NXion.nxdl.xml @@ -79,10 +79,10 @@ - + A supplementary row vector which decodes the isotope_vector into - a human-readable matrix of nuclids with the following formatting: + a human-readable matrix of nuclides with the following formatting: The first row specifies the isotope mass number, i.e. using the hashvalues from the isotope_vector this is :math:`Z + N`. As an example for a diff --git a/contributed_definitions/NXlab_electro_chemo_mechanical_preparation.nxdl.xml b/contributed_definitions/NXlab_electro_chemo_mechanical_preparation.nxdl.xml index 8bb1e4f93e..798424f5d4 100644 --- a/contributed_definitions/NXlab_electro_chemo_mechanical_preparation.nxdl.xml +++ b/contributed_definitions/NXlab_electro_chemo_mechanical_preparation.nxdl.xml @@ -32,7 +32,6 @@ Manual procedures, electro-chemical, vibropolishing. - Version specifier of this application definition. @@ -74,8 +73,8 @@ one person or not each person performs all polishing steps--> controlled vocabulary items--> - Medium on the abrasive_medium_carrier (cloth or grinding plate) - whereby material is abrasively weared. + Medium on the ``abrasive_medium_carrier`` (cloth or grinding plate) + whereby material is removed. Version specifier of this application definition. diff --git a/contributed_definitions/NXms.nxdl.xml b/contributed_definitions/NXms.nxdl.xml index 08a9f790a5..fbd6aed5d6 100644 --- a/contributed_definitions/NXms.nxdl.xml +++ b/contributed_definitions/NXms.nxdl.xml @@ -36,7 +36,7 @@ so-called microstructural features of interest for which we may store also therm also different scales one would like to distinguish as this is relevant when defects couple/show spatiotemporal correlations to specific mechanisms (e.g. phonons) or when defect affect the properties of other defects ambiguous choices: is the grain boundary part of the grain or is it an own defect? - i.e. can/should we store grains as childs of their grain boundary set vs the interface the childs of the grains? + i.e. can/should we store grains as children of their grain boundary set vs the interface the children of the grains? Depending on the use case we need to have a flexible description which can address a continuum of descriptors: important is that one can logically map different features Length scale of homogeneity: With the reality of a multi-parameter space of all possible methods and effects and @@ -48,7 +48,7 @@ so-called microstructural features of interest for which we may store also therm RVE annealing phenomena at the micrometer scale (pressure, temperature, length scale, interactions considered or not) Some regions are well separated spatially (although it can be non-trivial to quantify the distance in a multi-dim parameter space) Some simulations are cross-scale (classical MD at the cutting edge with micrometer crystal plasticity microsecond and/or annealing at - ns time scale) MD with classical vs abinitio-informed potential for studying evolution of mechanisms and phenomena at different length scales--> + ns time scale) MD with classical vs ab initio-informed potential for studying evolution of mechanisms and phenomena at different length scales--> @@ -386,7 +386,7 @@ snapshots--> constituent: constitutive: ROI(NXcg_roi_set): #multiple rois, for each geometry, connectivity/topology, cellType... -see that the materialpoint that is tracked conceptually in tools like DAMASK is a ROI (which is currently scale-invariant), isnt a coarse-graining of atom configurations a homogenization +see that the material point that is tracked conceptually in tools like DAMASK is a ROI (which is currently scale-invariant), is not a coarse-graining of atom configurations a homogenization several "results" homogenized quantities at (eventually different length scales continuum-scale view thermodynamic(NXview) mechanical @@ -496,8 +496,6 @@ specialize--> - Details about the disorientation distribution function diff --git a/contributed_definitions/NXms_feature_set.nxdl.xml b/contributed_definitions/NXms_feature_set.nxdl.xml index f8a8c90ff0..3b39927959 100644 --- a/contributed_definitions/NXms_feature_set.nxdl.xml +++ b/contributed_definitions/NXms_feature_set.nxdl.xml @@ -22,10 +22,9 @@ # For further information, see http://www.nexusformat.org --> - @@ -55,14 +54,14 @@ which is the parent group that has all these NXms_snapshot instances as childs Set of topological/spatial features in materials build from other features. - + - + Name (or link?) to another NXms_feature_set which defines features what are assumed as the parents/super_features of all members in this feature set. @@ -71,20 +70,8 @@ TJLD: however the here proposed design generalizes the arbitrary (microstructura represents the root feature_set of the feature tree/graph. - - + What is the best matching description how dimensional the feature is. @@ -96,16 +83,16 @@ their group e.g. grains(NXms_feature_set) and use in the application definition - + How many features/members are in this set? - + The keywords of the dictionary of human-readable types of features. Using terms from a community-agreed upon controlled vocabulary, e.g. @@ -120,7 +107,7 @@ TJLD: inherits from NXms_feature_set but would need to have no dimensionality--> - + The integer identifier used to resolve of which type each feature is, i.e. the values of the dictionary of human-readable types of features. @@ -179,12 +166,6 @@ end up as links--> - Assumptions and parameter to arrive at geometric primitives to locate zero-dimensional/point-(like) features which are @@ -199,7 +180,7 @@ but here NXms_feature_set instances--> - + Assumptions and parameters to arrive at geometric primitives to locate one-dimensional/line-like features which are @@ -244,10 +225,7 @@ but here NXms_feature_set instances--> - - diff --git a/contributed_definitions/NXorientation_set.nxdl.xml b/contributed_definitions/NXorientation_set.nxdl.xml index 73f5e3ca0c..196f0f3a34 100644 --- a/contributed_definitions/NXorientation_set.nxdl.xml +++ b/contributed_definitions/NXorientation_set.nxdl.xml @@ -48,7 +48,7 @@ we should offer here support for d==2, d==3--> Details about individual orientations of a set of objects. - For a more detailed insight into the discussion of parameterizing + For a more detailed insight into the discussion of parametrizing orientations in materials science see: * https://doi.org/10.1016/j.matchar.2016.04.008 @@ -129,5 +129,5 @@ therefore the idea to specify if we use implicit or explicit indexing and listin - + diff --git a/contributed_definitions/NXpolarizer_opt.nxdl.xml b/contributed_definitions/NXpolarizer_opt.nxdl.xml index 9142ae4817..47a6560c21 100644 --- a/contributed_definitions/NXpolarizer_opt.nxdl.xml +++ b/contributed_definitions/NXpolarizer_opt.nxdl.xml @@ -112,7 +112,7 @@ - Sketch of thedevice showing its geometry. The paths of the + Sketch of the device showing its geometry. The paths of the incoming and outgoing beam should be illustrated and labelled (0 for the incoming beam, and 1, 2,..., N_outputs for the outputs). @@ -180,7 +180,7 @@ - If the device has a coating describe the material and its properties. diff --git a/contributed_definitions/NXsensor_scan.nxdl.xml b/contributed_definitions/NXsensor_scan.nxdl.xml index afa6a1f27f..3f9b7c5922 100644 --- a/contributed_definitions/NXsensor_scan.nxdl.xml +++ b/contributed_definitions/NXsensor_scan.nxdl.xml @@ -120,7 +120,7 @@ Describes an environment setup for the experiment. All the setting values of the independently scanned controllers are listed under corresponding - NXsensor groups. Similarly, seperate NXsensor groups are used to store the readings from each + NXsensor groups. Similarly, separate NXsensor groups are used to store the readings from each measurement sensor. For example, in a temperature-dependent IV measurement, the temperature and voltage must be diff --git a/contributed_definitions/NXsubstance.nxdl.xml b/contributed_definitions/NXsubstance.nxdl.xml index 6c18182fc3..7d2328c81c 100644 --- a/contributed_definitions/NXsubstance.nxdl.xml +++ b/contributed_definitions/NXsubstance.nxdl.xml @@ -25,7 +25,7 @@ A form of matter with a constant, definite chemical composition. - Examples can be single chemical elements, chemical compunds, or alloys. + Examples can be single chemical elements, chemical compounds, or alloys. For further information, see https://en.wikipedia.org/wiki/Chemical_substance. diff --git a/contributed_definitions/NXtransmission.nxdl.xml b/contributed_definitions/NXtransmission.nxdl.xml index 1fb2d51d46..88eb632614 100644 --- a/contributed_definitions/NXtransmission.nxdl.xml +++ b/contributed_definitions/NXtransmission.nxdl.xml @@ -21,45 +21,46 @@ # # For further information, see http://www.nexusformat.org --> - - + - Variables used throughout the experiment + Variables used throughout the experiment - Number of wavelength points + Number of wavelength points - Number of scans + Number of scans - Application definition for transmission experiments + Application definition for transmission experiments - This application definition + This application definition - An application definition for transmission. + An application definition for transmission. - Version number to identify which definition of this application definition was - used for this entry/data. + Version number to identify which definition of this application definition was + used for this entry/data. - URL where to find further material (documentation, examples) relevant to the - application definition. + URL where to find further material (documentation, examples) relevant to the + application definition. @@ -68,24 +69,24 @@ Draft NeXus application definition for transmission experiments--> - Start time of the experiment. + Start time of the experiment. - Unique identifier of the experiment, such as a (globally persistent) - unique identifier. - - * The identifier is usually defined by the facility or principle - investigator. - * The identifier enables to link experiments to e.g. proposals. + Unique identifier of the experiment, such as a (globally persistent) + unique identifier. + + * The identifier is usually defined by the facility or principle + investigator. + * The identifier enables to link experiments to e.g. proposals. - An optional free-text description of the experiment. However, details of the - experiment should be defined in the specific fields of this application - definition rather than in this experiment description. + An optional free-text description of the experiment. However, details of the + experiment should be defined in the specific fields of this application + definition rather than in this experiment description. - Commercial or otherwise defined given name to the program that was - used to generate the result file(s) with measured data and metadata. + Commercial or otherwise defined given name to the program that was + used to generate the result file(s) with measured data and metadata. - Version number of the program that was used to generate the result - file(s) with measured data and metadata. + Version number of the program that was used to generate the result + file(s) with measured data and metadata. - Website of the software + Website of the software - Contact information of at least the user of the instrument or the investigator - who performed this experiment. Adding multiple users if relevant is recommended. + Contact information of at least the user of the instrument or the investigator + who performed this experiment. Adding multiple users if relevant is recommended. - Name of the user. + Name of the user. - Name of the affiliation of the user at the point in time when the experiment was - performed. + Name of the affiliation of the user at the point in time when the experiment was + performed. - Street address of the user's affiliation. + Street address of the user's affiliation. - Email address of the user. + Email address of the user. - Author ID defined by reasearch id services, e.g. orcid (https://orcid.org/). + Author ID defined by research ID services, e.g. orcid (https://orcid.org/). - Telephone number of the user. + Telephone number of the user. - Manufacturer of the instrument. + Manufacturer of the instrument. - Common beam mask to shape the incident beam + Common beam mask to shape the incident beam - The height of the common beam in percentage of the beam + The height of the common beam in percentage of the beam - If true, the incident beam is depolarized. + If true, the incident beam is depolarized. - Polarizer value inside the beam path + Polarizer value inside the beam path - Attenuator in the reference beam + Attenuator in the reference beam - Attenuator in the sample beam + Attenuator in the sample beam - Wavelength value(s) used for the measurement. - An array of 1 or more elements. Length defines N_wavelenghts + Wavelength value(s) used for the measurement. + An array of 1 or more elements. Length defines N_wavelengths @@ -198,40 +199,40 @@ of instrument.--> - Overall spectral resolution of this spectrometer. - If several gratings are employed the spectral resoultion - should rather be specified for each grating inside the - NXgrating group of this spectrometer. + Overall spectral resolution of this spectrometer. + If several gratings are employed the spectral resolution + should rather be specified for each grating inside the + NXgrating group of this spectrometer. - Diffraction grating, as could be used in a monochromator. - If two or more gratings were used, define the angular - dispersion and the wavelength range (min/max wavelength) - for each grating and make sure that the wavelength ranges - do not overlap. The dispersion should be defined for the - entire wavelength range of the experiment. + Diffraction grating, as could be used in a monochromator. + If two or more gratings were used, define the angular + dispersion and the wavelength range (min/max wavelength) + for each grating and make sure that the wavelength ranges + do not overlap. The dispersion should be defined for the + entire wavelength range of the experiment. - Dispersion of the grating in nm/mm used. + Dispersion of the grating in nm/mm used. - The blaze wavelength of the grating used. + The blaze wavelength of the grating used. - Overall spectral resolution of the instrument - when this grating is used. + Overall spectral resolution of the instrument + when this grating is used. - Wavelength range in which this grating was used + Wavelength range in which this grating was used @@ -242,7 +243,7 @@ of instrument.--> - Wavelength range in which this detector was used + Wavelength range in which this detector was used @@ -250,7 +251,7 @@ of instrument.--> - Detector type + Detector type @@ -260,17 +261,17 @@ of instrument.--> - Response time of the detector + Response time of the detector - Detector gain + Detector gain - Slit setting used for measurement with this detector + Slit setting used for measurement with this detector @@ -282,7 +283,7 @@ of instrument.--> - An array of relative scan start time points. + An array of relative scan start time points. @@ -290,11 +291,11 @@ of instrument.--> - Resulting data from the measurement. - The length of the 2nd dimension is - the number of time points. - If it has length one the time_points - may be empty. + Resulting data from the measurement. + The length of the 2nd dimension is + the number of time points. + If it has length one the time_points + may be empty. @@ -303,11 +304,11 @@ of instrument.--> - The lamp used for illumination + The lamp used for illumination - The type of lamp, e.g. halogen, D2 etc. + The type of lamp, e.g. halogen, D2 etc. @@ -316,7 +317,7 @@ of instrument.--> - The spectrum of the lamp used + The spectrum of the lamp used @@ -324,7 +325,7 @@ of instrument.--> - Wavelength range in which the lamp was used + Wavelength range in which the lamp was used @@ -336,19 +337,19 @@ of instrument.--> - Properties of the sample measured + Properties of the sample measured - A default view of the data emitted intensity vs. wavelength. - From measured_data plot intensity and wavelength. + A default view of the data emitted intensity vs. wavelength. + From measured_data plot intensity and wavelength. - We recommend to use wavelength as a default attribute, but it can be - replaced by any suitable parameter along the X-axis. + We recommend to use wavelength as a default attribute, but it can be + replaced by any suitable parameter along the X-axis. diff --git a/contributed_definitions/NXxpcs.nxdl.xml b/contributed_definitions/NXxpcs.nxdl.xml index 6d3c14d106..f7e112b83a 100644 --- a/contributed_definitions/NXxpcs.nxdl.xml +++ b/contributed_definitions/NXxpcs.nxdl.xml @@ -253,7 +253,7 @@ storage_mode describes the format of the data to be loaded - We encourage the documention of other formats represented here. + We encourage the documentation of other formats represented here. @@ -419,7 +419,7 @@ Size (2-D) of the beam at this position. - @@ -523,7 +523,7 @@ The only requirement for the list is that it may be iterable. Some expected formats are: * iterable list of floats (i.e., :math:`Q(r)`) - * iterable list of tuples (i.e., :math:`Q(r)`, :math:`\varphi`), but preferable use the seperate :math:`\varphi` field below + * iterable list of tuples (i.e., :math:`Q(r)`, :math:`\varphi`), but preferable use the separate :math:`\varphi` field below * iterable list of tuples (e.g., (H, K, L); (qx, qy, qz); (horizontal_pixel, vertical_pixel)) * iterable list of integers (for Nth roi_map value) or strings @@ -565,7 +565,7 @@ dynamics from XPCS analysis). For non-equilibrium sample conditions (i.e., changing sample or process conditions - during the XPCS measurement) will require either a new entry or an additional atttribute. + during the XPCS measurement) will require either a new entry or an additional attribute. -->