diff --git a/base_classes/NXlens_em.nxdl.xml b/base_classes/NXlens_em.nxdl.xml index 88dbc1e624..675a1b1ef4 100644 --- a/base_classes/NXlens_em.nxdl.xml +++ b/base_classes/NXlens_em.nxdl.xml @@ -87,18 +87,18 @@ with other research fields (MPES, XPS, OPT) could be useful--> - This field should be used when the exact voltage or current of the lens - is not directly controllable as the control software of the microscope - does not enable or was not configured to display these values. + This field should be used when the exact voltage or current of the lens is not + directly controllable as the control software of the microscope does not enable + or was not configured to display these values (for end users). In this case this value field should be used and the value from the control software stored as is. Although this value does not document the exact physical voltage or excitation, it can still give useful context to reproduce the lens setting, - which, provided a properly working instrument and software sets the lens - into a similar state to the technical level possible when no more information - is available physically or accessible legally. + provided a properly working instrument and software sets the lens + into a similar state to the technical level possible when no more + information is available physically or accessible legally. diff --git a/contributed_definitions/NXapm_compositionspace_config.nxdl.xml b/contributed_definitions/NXapm_compositionspace_config.nxdl.xml new file mode 100644 index 0000000000..ca8bb05171 --- /dev/null +++ b/contributed_definitions/NXapm_compositionspace_config.nxdl.xml @@ -0,0 +1,73 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + Number of voxel of discretized domain for analyzed part of the dataset. + + + + + The dimensionality of the grid. + + + + + The cardinality or total number of cells/grid points. + + + + + Number of terms in the composition clustering dictionary + + + + + Number of terms in the position clustering dictionary + + + + + Config for a run with Alaukik Saxena's composition space tool. + + This is an initial draft application definition for the common NFDI-MatWerk, + FAIRmat infrastructure use case IUC09 how to improve the organization and + results storage of the composition space tool and make these data at the + same time directly understandable for research data management systems + like NOMAD Oasis. + + + + + + + + + + + diff --git a/contributed_definitions/NXapm_compositionspace_results.nxdl.xml b/contributed_definitions/NXapm_compositionspace_results.nxdl.xml new file mode 100644 index 0000000000..b3d0fcd2ab --- /dev/null +++ b/contributed_definitions/NXapm_compositionspace_results.nxdl.xml @@ -0,0 +1,473 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + Number of voxel of discretized domain for analyzed part of the dataset. + + + + + The dimensionality of the grid. + + + + + The cardinality or total number of cells/grid points. + + + + + Number of terms in the composition clustering dictionary + + + + + Number of terms in the position clustering dictionary + + + + + Results of a run with Alaukik Saxena's composition space tool. + + This is an initial draft application definition for the common NFDI-MatWerk, + FAIRmat infrastructure use case IUC09 how to improve the organization and + results storage of the composition space tool and make these data at the + same time directly understandable for research data management systems + like NOMAD Oasis. + + + + + + + + + + + + + + + + + + TBD, maybe how to link between pyiron state tracking and app state tracking. + + + + + Disencouraged place for free-text for e.g. comments. + + + + + ISO 8601 formatted time code with local time zone offset to UTC + information included when the analysis behind this results file + was started, i.e. when composition space tool was started as a process. + + + + + ISO 8601 formatted time code with local time zone offset to UTC + information included when the analysis behind this results file + were completed and composition space tool exited as a process. + + + + + + The path and name of the config file that was used for this analysis. + TBD, this can be e.g. Alaukik's YAML file for composition space. + + + + + + + + + Details about the file (technology partner or community format) + from which reconstructed ion positions were loaded. + + + + + + + + + Details about the file (technology partner or community format) + from which ranging definitions were loaded which detail how to + map mass-to-charge-state ratios on iontypes. + + + + + + + + + + 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. + + + + + A statement whether the executable managed to process the analysis + or failed prematurely. This status is written to the results file after the + end_time at which point the executable must not compute any analysis. + Only when this status message is present and shows `success`, the + user should consider the results. In all other cases it might be + that the executable has terminated prematurely or another error + occurred. + + + + + + + + + If used, contact information and eventually details + of at least the person who performed this analysis. + + + + + + + + + Details about coordinate systems (reference frames) used. In atom probe several coordinate + systems have to be distinguished. Names of instances of such :ref:`NXcoordinate_system` + should be documented explicitly and doing so by picking from the + following controlled set of names: + + * composition_space + * lab + * specimen + * laser + * instrument + * detector + * recon + + The aim of this convention is to support users with contextualizing which reference + frame each instance (coordinate system) is. If needed, instances of :ref:`NXtransformations` + are used to detail the explicit affine transformations whereby one can convert + representations between different reference frames. + Inspect :ref:`NXtransformations` for further details. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Reference to or definition of a coordinate system with + which the positions and directions are interpretable. + + + + + + + + + + Position of each cell in Euclidean space. + + + + + + + + + + + + + + + + For each ion, the identifier of the voxel in which the ion is located. + + + + + + + + + + + + + + + + + + In Alaukik's tool the GMM step. + + + + + + + + + The keywords of the dictionary of distinguished compositionally- + defined cluster, e.g. the phases. Examples for keywords could be + phase1, phase2, and so one and so forth. + + + + + + + + Resolves for each keyword in cluster_dict which integer is used to + label something that it belongs or is assumed to represent this + cluster. + + + + + + + + + For example if the voxel grid is used to report that there + are voxels which are assumed to represent volume of either phase1 + or phase2, the cluster_dict_keyword would be a list with two names + phase1 and phase2, respectively. The cluster_dict_value would be a + list of e.g. integers 1 and 2. These could be used to build an + array with as many entries as there are voxel and store in this array + the respective value to encode which phase is assumed for each voxel. + + + + + + + + + + In Alaukik's tool the DBScan step after the GMM step. + + + + + + + + + The keywords of the dictionary of distinguished spatially-contiguous + clusters. Examples for keywords could be precipitate1, precipitate2, + and so one and so forth. + + + + + + + + Resolves for each keyword in cluster_dict which integer is used to + label something that it belongs or is assumed to represent this + cluster. + + + + + + + + + For example if the voxel grid is used to report that there + are voxels which are assumed to represent volume of certain precipitates, + say we found ten precipitates and consider the rest as matrix. + We could make a list of say matrix, precipitate1, precipitate2, ..., + precipitate10. With cluster_dict_value then running from 0 to 10, + i.e. matrix is flagged special as 0 and the remaining particles + are indexed conveniently as 1, 2, ..., 10 like end users expect. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Specify if it was different from the number_of_processes + in the NXcs_profiling super class. + + + + + + Specify if it was different from the number_of_threads + in the NXcs_profiling super class. + + + + + + Specify if it was different from the number_of_threads + in the NXcs_profiling super class. + + + + + + + + + diff --git a/contributed_definitions/NXebeam_column.nxdl.xml b/contributed_definitions/NXebeam_column.nxdl.xml index e31f22fbcc..03b54b7792 100644 --- a/contributed_definitions/NXebeam_column.nxdl.xml +++ b/contributed_definitions/NXebeam_column.nxdl.xml @@ -2,9 +2,9 @@ - Citing the JEOL TEM glosssary this is the value *when a cone shaped, + Citing the JEOL TEM glossary this is the value *when a cone shaped, convergent electron beam illuminates a specimen, the semi-angle of the cone is termed convergence angle.* diff --git a/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml b/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml new file mode 100644 index 0000000000..9cd6d87515 --- /dev/null +++ b/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml @@ -0,0 +1,30 @@ +category: application +doc: | + Config for a run with Alaukik Saxena's composition space tool. + + This is an initial draft application definition for the common NFDI-MatWerk, + FAIRmat infrastructure use case IUC09 how to improve the organization and + results storage of the composition space tool and make these data at the + same time directly understandable for research data management systems + like NOMAD Oasis. +symbols: + doc: | + The symbols used in the schema to specify e.g. dimensions of arrays. + n_voxel: | + Number of voxel of discretized domain for analyzed part of the dataset. + d: | + The dimensionality of the grid. + c: | + The cardinality or total number of cells/grid points. + n_clst_dict: | + Number of terms in the composition clustering dictionary + n_spat_dict: | + Number of terms in the position clustering dictionary +type: group +NXapm_compositionspace_config(NXobject): + # by default for appdefs the value of the exists keyword is required unless it is explicitly specified differently + (NXentry): + exists: [min, 1, max, 1] + definition(NX_CHAR): + \@version(NX_CHAR): + enumeration: [NXapm_compositionspace_config]