NXapm_paraprobe_results_ranger¶
Status:
application definition, extends NXobject
Description:
Results of a paraprobe-ranger tool run in atom probe microscopy.
Symbols:
The symbols used in the schema to specify e.g. dimensions of arrays.
n_ions: The total number of ions in the reconstruction.
n_ivec: The maximum number of atoms per molecular ion type.
- 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, NXion, 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.
Obligatory value:
NXapm_paraprobe_results_ranger
program: (required) NX_CHAR
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 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: (optional) NX_CHAR
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.
time_stamp: (required) NX_DATE_TIME
ISO 8601 formatted time code with local time zone offset to UTC information included when this configuration file was created.
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 tracking provenance.
USER: (recommended) NXuser
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 used. fields should be prefixed with a prefix taken from an enumeration which details the individual coordinate systems:
lab
specimen
laser
leap
detector
recon
PROCESS: (optional) NXprocess
use_existent_ranging: (optional) NXprocess
Paraprobe-ranger loads the iontypes and evaluates for each ion on which iontype it matches. If it matches on none, the ion is considered of the default unknown type with a 0 as its respective value in the iontypes array.
iontypes: (required) NX_UINT (Rank: 1, Dimensions: [n_ions]) {units=NX_UNITLESS}
The iontype ID for each ion that was best matching, stored in the order of the evaporation sequence ID.
ION: (required) NXion
molecular_ion_search: (optional) NXprocess
Paraprobe-ranger performs a combinatorial search over all possible or a reduced set of nuclids to identify into which ions these can be composed.
isotope_vector_matrix: (required) NX_UINT (Rank: 2, Dimensions: [i, 32]) {units=NX_UNITLESS}
The main result is the list of molecular ions, here formatted according to the definitions of a set of isotope_vectors as detailed in NXion.
mass_to_charge_state_ratio: (required) NX_FLOAT (Rank: 1, Dimensions: [i]) {units=NX_ANY}
The mass-to-charge-state ratio of each molecular ion without considering relativistic or quantum effects.
mass: (optional) NX_FLOAT (Rank: 1, Dimensions: [i]) {units=NX_ANY}
The mass of each molecular ion without considering relativistic or quantum effects.
charge_state: (required) NX_UINT (Rank: 1, Dimensions: [i]) {units=NX_CHARGE}
The charge_state of each molecular ion.
natural_abundance_product: (optional) NX_FLOAT (Rank: 1, Dimensions: [i]) {units=NX_DIMENSIONLESS}
The product of the natural abundance of the isotopes building each molecular ion. Further details are available in NXapm_paraprobe_config_ranger.
composition_product: (optional) NX_FLOAT (Rank: 1, Dimensions: [i]) {units=NX_DIMENSIONLESS}
The product of the natural abundance of the isotopes building each molecular ion. Further details are available in NXapm_paraprobe_config_ranger.
number_of_disjoint_nuclids: (optional) NX_POSINT (Rank: 1, Dimensions: [i]) {units=NX_UNITLESS}
The number of disjoint nuclids for each molecular ion.
number_of_nuclids: (optional) NX_POSINT (Rank: 1, Dimensions: [i]) {units=NX_UNITLESS}
The number of nuclids for each molecular ion.
performance: (recommended) NXcs_profiling
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
CS_GPU: (optional) NXcs_gpu
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
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 in the NXcs_profiling super class.
number_of_threads: (required) NX_POSINT
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 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.
/NXapm_paraprobe_results_ranger/ENTRY/analysis_description-field
/NXapm_paraprobe_results_ranger/ENTRY/analysis_identifier-field
/NXapm_paraprobe_results_ranger/ENTRY/config_filename@version-attribute
/NXapm_paraprobe_results_ranger/ENTRY/COORDINATE_SYSTEM_SET-group
/NXapm_paraprobe_results_ranger/ENTRY/COORDINATE_SYSTEM_SET/TRANSFORMATIONS-group
/NXapm_paraprobe_results_ranger/ENTRY/performance/command_line_call-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER-group
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_CPU-group
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_CPU/FABRICATION-group
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_CPU/FABRICATION/capabilities-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_CPU/FABRICATION/identifier-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_CPU/name-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_GPU-group
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_GPU/FABRICATION-group
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_GPU/FABRICATION/capabilities-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_GPU/FABRICATION/identifier-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_GPU/name-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_IO_SYS-group
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_IO_SYS/CS_IO_OBJ-group
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_IO_SYS/CS_IO_OBJ/FABRICATION-group
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_IO_SYS/CS_IO_OBJ/name-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_IO_SYS/CS_IO_OBJ/technology-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_MM_SYS-group
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_MM_SYS/total_physical_memory-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_PROFILING_EVENT-group
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_PROFILING_EVENT/description-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_PROFILING_EVENT/elapsed_time-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_PROFILING_EVENT/end_time-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/CS_PROFILING_EVENT/start_time-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/name-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/operating_system-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/operating_system@version-attribute
/NXapm_paraprobe_results_ranger/ENTRY/performance/CS_COMPUTER/uuid-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/end_time-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/number_of_gpus-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/number_of_processes-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/number_of_threads-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/start_time-field
/NXapm_paraprobe_results_ranger/ENTRY/performance/total_elapsed_time-field
/NXapm_paraprobe_results_ranger/ENTRY/PROCESS/molecular_ion_search-group
/NXapm_paraprobe_results_ranger/ENTRY/PROCESS/molecular_ion_search/charge_state-field
/NXapm_paraprobe_results_ranger/ENTRY/PROCESS/molecular_ion_search/composition_product-field
/NXapm_paraprobe_results_ranger/ENTRY/PROCESS/molecular_ion_search/isotope_vector_matrix-field
/NXapm_paraprobe_results_ranger/ENTRY/PROCESS/molecular_ion_search/mass-field
/NXapm_paraprobe_results_ranger/ENTRY/PROCESS/molecular_ion_search/mass_to_charge_state_ratio-field
/NXapm_paraprobe_results_ranger/ENTRY/PROCESS/molecular_ion_search/natural_abundance_product-field
/NXapm_paraprobe_results_ranger/ENTRY/PROCESS/molecular_ion_search/number_of_disjoint_nuclids-field
/NXapm_paraprobe_results_ranger/ENTRY/PROCESS/molecular_ion_search/number_of_nuclids-field
/NXapm_paraprobe_results_ranger/ENTRY/PROCESS/use_existent_ranging-group
/NXapm_paraprobe_results_ranger/ENTRY/PROCESS/use_existent_ranging/ION-group
/NXapm_paraprobe_results_ranger/ENTRY/PROCESS/use_existent_ranging/ION/charge_state-field
/NXapm_paraprobe_results_ranger/ENTRY/PROCESS/use_existent_ranging/ION/isotope_vector-field
/NXapm_paraprobe_results_ranger/ENTRY/PROCESS/use_existent_ranging/ION/mass_to_charge_range-field
/NXapm_paraprobe_results_ranger/ENTRY/PROCESS/use_existent_ranging/ION/nuclid_list-field
/NXapm_paraprobe_results_ranger/ENTRY/PROCESS/use_existent_ranging/iontypes-field
/NXapm_paraprobe_results_ranger/ENTRY/program@version-attribute
/NXapm_paraprobe_results_ranger/ENTRY/USER/affiliation-field
/NXapm_paraprobe_results_ranger/ENTRY/USER/orcid_platform-field
/NXapm_paraprobe_results_ranger/ENTRY/USER/social_media_name-field
/NXapm_paraprobe_results_ranger/ENTRY/USER/social_media_platform-field
/NXapm_paraprobe_results_ranger/ENTRY/USER/telephone_number-field