3.3.3.29. NXapm_paraprobe_results_intersector

Status:

application definition (contribution), extends NXobject

Description:

Results of a paraprobe-intersector tool run.

Symbols:

The symbols used in the schema to specify e.g. dimensions of arrays.

n_c2n: The total number of links pointing from current to next.

n_n2c: The total number of links pointing from next to current.

n_features_curr: The total number of members in the current_set.

n_features_next: The total number of members in the next_set.

n_cluster: The total number of cluster found for coprecipitation analysis.

n_total: The number of rows in the table/matrix for coprecipitation stats.

Groups cited:

NXcoordinate_system_set, NXcs_computer, NXcs_cpu, NXcs_gpu, NXcs_io_obj, NXcs_io_sys, NXcs_mm_sys, NXcs_profiling_event, NXcs_profiling, NXentry, NXfabrication, NXprocess, NXtransformations, NXuser

Structure:

ENTRY: (required) NXentry

@version: (required) NX_CHAR

Version specifier of this application definition.

definition: (required) NX_CHAR ⤆

Official NeXus NXDL schema with which this file was written. ...

Official NeXus NXDL schema with which this file was written.

Obligatory value: NXapm_paraprobe_results_intersector

program: (required) NX_CHAR

Given name of the program/software/tool with which this NeXus ...

Given name of the program/software/tool with which this NeXus (configuration) file was generated.

@version: (required) NX_CHAR

Ideally program version plus build number, or commit hash or description ...

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.

analysis_identifier: (required) NX_CHAR

Ideally, a (globally persistent) unique identifier for referring ...

Ideally, a (globally persistent) unique identifier for referring to this analysis.

analysis_description: (optional) NX_CHAR

Possibility for leaving a free-text description about this analysis.

start_time: (required) NX_DATE_TIME ⤆

ISO 8601 formatted time code with local time zone offset to UTC ...

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. the paraprobe-tool executable started as a process.

end_time: (required) NX_DATE_TIME ⤆

ISO 8601 formatted time code with local time zone offset to UTC ...

ISO 8601 formatted time code with local time zone offset to UTC information included when the analysis behind this results file were completed and the paraprobe-tool executable exited as a process.

config_filename: (required) NX_CHAR

The absolute path and name of the config file for this analysis.

@version: (required) NX_CHAR

At least SHA256 strong hash of the specific config_file for ...

At least SHA256 strong hash of the specific config_file for tracking provenance.

results_path: (optional) NX_CHAR

Path to the directory where the tool should store NeXus/HDF5 results ...

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.

USER: (recommended) NXuser ⤆

If used, contact information and eventually details ...

If used, contact information and eventually details of at least the person who performed this analysis.

name: (required) NX_CHAR ⤆

affiliation: (recommended) NX_CHAR ⤆

address: (optional) NX_CHAR ⤆

email: (recommended) NX_CHAR ⤆

orcid: (recommended) NX_CHAR

orcid_platform: (recommended) NX_CHAR

telephone_number: (optional) NX_CHAR ⤆

role: (recommended) NX_CHAR ⤆

social_media_name: (optional) NX_CHAR

social_media_platform: (optional) NX_CHAR

COORDINATE_SYSTEM_SET: (optional) NXcoordinate_system_set

Details about the coordinate system conventions used.

TRANSFORMATIONS: (required) NXtransformations ⤆

The individual coordinate systems which should be used. ...

The individual coordinate systems which should be used. Field names should be prefixed with the following controlled terms indicating which individual coordinate system is described:

  • paraprobe

  • lab

  • specimen

  • laser

  • leap

  • detector

  • recon

PROCESS: (required) NXprocess ⤆

VOLUME_VOLUME_SPATIAL_CORRELATION: (optional) NXprocess

The results of an overlap/intersection analysis.

current_to_next_link: (required) NX_UINT (Rank: 2, Dimensions: [n_c2n, 2]) {units=NX_UNITLESS}

A matrix of feature_identifier which specifies which named features ...

A matrix of feature_identifier which specifies which named features from the current set have directed link(s) pointing to which named feature(s) from the next set.

current_to_next_link_type: (required) NX_UINT (Rank: 1, Dimensions: [n_c2n]) {units=NX_UNITLESS}

For each link/pair in current_to_next a characterization ...

For each link/pair in current_to_next a characterization whether the link is due to a volumetric overlap (0x00 == 0), proximity (0x01 == 1), or something else unknown (0xFF == 255).

next_to_current_link: (optional) NX_UINT (Rank: 2, Dimensions: [n2c, 2]) {units=NX_UNITLESS}

A matrix of feature_identifier which specifies which named feature(s) ...

A matrix of feature_identifier which specifies which named feature(s) from the next set have directed link(s) pointing to which named feature(s) from the current set. Only if the mapping whereby the links is symmetric next_to_current maps the links in current_to_next in the opposite direction.

next_to_current_link_type: (optional) NX_UINT (Rank: 1, Dimensions: [n_n2c]) {units=NX_UNITLESS}

For each link/pair in next_to_current a characterization ...

For each link/pair in next_to_current a characterization whether the link is due to a volumetric overlap (0x00 == 0), proximity (0x01 == 1), or something else unknown (0xFF == 255).

intersection_volume: (optional) NX_FLOAT (Rank: 1, Dimensions: [c2n]) {units=NX_VOLUME}

For each pair of links in current_to_next the volume of the ...

For each pair of links in current_to_next the volume of the intersection, i.e. how much volume do the two features share. If features do not intersect the volume is zero.

coprecipitation_analysis: (optional) NXprocess

During coprecipitation analysis the current and next set are analyzed ...

During coprecipitation analysis the current and next set are analyzed for links in a special way. Three set comparisons are made. Members of the set in each comparison are analyzed for overlap and proximity:

The first comparison is the current_set against the current_set. The second comparison is the next_set against the next_set. The third comparison is the current_set against the next_set.

Once the (forward) links for these comparisons are ready the pair relations are analyzed with respect to which feature identifier cluster in identifier space. Thereby a logical connection (link) is established between the features in the current_set and next_set. Recall that these two set typically represent different features within an observed system for otherwise the same parameterization. Examples include two sets of e.g. precipitates with differing 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 B. Coprecipitation analysis now logically connects these independent characterization results to establish spatial correlations of e.g. precipitates spatial arrangement.

current_set_feature_to_cluster: (required) NX_UINT (Rank: 2, Dimensions: [n_features_curr, 2]) {units=NX_UNITLESS}

Matrix of feature_identifier and cluster_identifier pairs which ...

Matrix of feature_identifier and cluster_identifier pairs which encodes the cluster to which each feature_identifier was assigned. Here for features of the current_set.

next_set_feature_to_cluster: (required) NX_UINT (Rank: 2, Dimensions: [n_features_next, 2]) {units=NX_UNITLESS}

Matrix of feature_identifier and cluster_identifier pairs which ...

Matrix of feature_identifier and cluster_identifier pairs which encodes the cluster to which each feature_identifier was assigned. Here for features of the next_set.

cluster_identifier: (required) NX_UINT (Rank: 1, Dimensions: [n_cluster]) {units=NX_UNITLESS}

The identifier (names) of the cluster.

cluster_composition: (required) NX_UINT (Rank: 2, Dimensions: [n_cluster, 3]) {units=NX_UNITLESS}

Pivot table as a matrix. The first column encodes how many ...

Pivot table as a matrix. The first column encodes how many members from the current_set are in each cluster, one row per cluster. The second column encodes how many members from the next_set are in each cluster, in the same row per cluster respectively. The last column encodes the total number of members in the cluster.

cluster_statistics: (required) NX_UINT (Rank: 2, Dimensions: [n_total, 2]) {units=NX_UNITLESS}

Pivot table as a matrix. The first column encodes the different ...

Pivot table as a matrix. The first column encodes the different types of clusters based on their number of members in the sub-graph. The second column encodes how many clusters with as many members exist.

performance: (recommended) NXcs_profiling

current_working_directory: (required) NX_CHAR ⤆

command_line_call: (optional) NX_CHAR ⤆

start_time: (recommended) NX_DATE_TIME ⤆

end_time: (recommended) NX_DATE_TIME ⤆

total_elapsed_time: (required) NX_NUMBER ⤆

number_of_processes: (required) NX_POSINT ⤆

number_of_threads: (required) NX_POSINT ⤆

number_of_gpus: (required) NX_POSINT ⤆

CS_COMPUTER: (recommended) NXcs_computer ⤆

name: (recommended) NX_CHAR ⤆

operating_system: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

uuid: (optional) NX_CHAR ⤆

CS_CPU: (optional) NXcs_cpu ⤆

name: (optional) NX_CHAR ⤆

FABRICATION: (recommended) NXfabrication ⤆

identifier: (optional) NX_CHAR ⤆

capabilities: (optional) NX_CHAR

CS_GPU: (optional) NXcs_gpu ⤆

name: (optional) NX_CHAR ⤆

FABRICATION: (recommended) NXfabrication ⤆

identifier: (optional) NX_CHAR ⤆

capabilities: (optional) NX_CHAR

CS_MM_SYS: (optional) NXcs_mm_sys ⤆

total_physical_memory: (required) NX_NUMBER ⤆

CS_IO_SYS: (optional) NXcs_io_sys ⤆

CS_IO_OBJ: (required) NXcs_io_obj ⤆

technology: (required) NX_CHAR ⤆

max_physical_capacity: (required) NX_NUMBER ⤆

name: (optional) NX_CHAR ⤆

FABRICATION: (recommended) NXfabrication ⤆

identifier: (optional) NX_CHAR ⤆

capabilities: (optional) NX_CHAR

CS_PROFILING_EVENT: (required) NXcs_profiling_event

start_time: (optional) NX_DATE_TIME ⤆

end_time: (optional) NX_DATE_TIME ⤆

description: (required) NX_CHAR ⤆

elapsed_time: (required) NX_NUMBER ⤆

number_of_processes: (required) NX_POSINT ⤆

Specify if it was different from the number_of_processes ...

Specify if it was different from the number_of_processes in the NXcs_profiling super class.

number_of_threads: (required) NX_POSINT ⤆

Specify if it was different from the number_of_threads ...

Specify if it was different from the number_of_threads in the NXcs_profiling super class.

number_of_gpus: (required) NX_POSINT ⤆

Specify if it was different from the number_of_threads ...

Specify if it was different from the number_of_threads in the NXcs_profiling super class.

max_virtual_memory_snapshot: (recommended) NX_NUMBER ⤆

max_resident_memory_snapshot: (recommended) NX_NUMBER ⤆

Hypertext Anchors

List of hypertext anchors for all groups, fields, attributes, and links defined in this class.

NXDL Source:

https://github.com/nexusformat/definitions/blob/main/contributed_definitions/NXapm_paraprobe_results_intersector.nxdl.xml