2.3.3.1.5. NXapm_charge_state_analysis¶
Status:
base class, extends NXprocess
Description:
Base class to document the parameters, configuration, and results of a processin ...
Base class to document the parameters, configuration, and results of a processing for recovering the charge state and nuclide composition of an ion from ranging definitions as used in the research field of atom probe microscopy.
A ranging definition classically reports only the mass-to-charge-state-ratio interval plus the elemental composition, but not necessarily the nuclide that compose the ion.
As the mass-resolving-power in an atom probe instrument is finite and typically lower than for cutting edge tandem mass spectrometry it is possible that different combinations of nuclides are indistinguishable and thus multiple ions in eventually even different charge states can be valid labels for a given mass-to-charge-state-ratio peak. Enumerating the possible combinations is a programmatic approach that can help with peak identification.
Symbols:
The symbols used in the schema to specify e.g. dimensions of arrays.
n_cand: The number of ion candidates.
n_ivec_max: Maximum number of allowed atoms per ion.
n_variable: Number of entries
- Groups cited:
Structure:
charge_state: (optional) NX_INT (Rank: 1, Dimensions: [n_cand]) {units=NX_UNITLESS}
Signed charge, i.e. integer multiple of the elementary ...
Signed charge, i.e. integer multiple of the elementary charge of each candidate.
nuclide_hash: (optional) NX_UINT (Rank: 2, Dimensions: [n_cand, n_ivec_max]) {units=NX_UNITLESS}
Table of nuclide instances of which each candidate is composed. ...
Table of nuclide instances of which each candidate is composed. Each row vector is sorted in descending order. Unused entries in the matrix should be set to 0. Use the hashing rule that is defined in nuclide_hash of NXatom.
mass: (optional) NX_FLOAT (Rank: 1, Dimensions: [n_cand]) {units=NX_MASS}
Accumulated mass of the nuclides in each candidate. ...
Accumulated mass of the nuclides in each candidate. Not corrected for quantum effects.
natural_abundance_product: (optional) NX_FLOAT (Rank: 1, Dimensions: [n_cand]) {units=NX_DIMENSIONLESS}
The product of the natural abundances of the nuclides for each candidate.
shortest_half_life: (optional) NX_FLOAT (Rank: 1, Dimensions: [n_cand]) {units=NX_TIME}
For each candidate the half life of the nuclide that has the ...
For each candidate the half life of the nuclide that has the shortest half life.
config: (optional) NXparameters ⤆
Parameters for the algorithm used to recover which combinations of nuclides ...
Parameters for the algorithm used to recover which combinations of nuclides have a mass and charge that matches a set of constraints.
Each parameter in this group is defines one constraint.
nuclides: (optional) NX_UINT (Rank: 1, Dimensions: [n_variable]) {units=NX_UNITLESS}
Parameter that defines the elements considered in the combinatorial search. ...
Parameter that defines the elements considered in the combinatorial search. The array contains nuclides as many times as their multiplicity and must not be empty. Nuclides are encoded using the hashing rule that is defined in by nuclide_hash of NXatom.
Constraining the elements or nuclides instead of providing all nuclides reduces the time to perform an exhaustive combinatorial search.
mass_to_charge_range: (optional) NX_FLOAT (Rank: 1, Dimensions: [2]) {units=NX_ANY}
Parameter that defines the interval :math:`[{\frac{m}{q}}_{min}, {\frac{m}{q ...
Parameter that defines the interval \([{\frac{m}{q}}_{min}, {\frac{m}{q}}_{max}]\) within which ions with given mass-to-charge-state-ratio qualify as candidates.
min_half_life: (optional) NX_FLOAT {units=NX_TIME}
Parameter that defines the minimum half life for how long each nuclide of ea ...
Parameter that defines the minimum half life for how long each nuclide of each ion needs to be stable such that the ion qualifies as a candidate.
min_abundance: (optional) NX_FLOAT {units=NX_DIMENSIONLESS}
Parameter that defines the minimum natural abundance of each nuclide of each ...
Parameter that defines the minimum natural abundance of each nuclide of each ion such that the ion qualifies as a candidate.
sacrifice_isotopic_uniqueness: (optional) NX_BOOLEAN
If the value is false, it means that non-unique solutions are accepted. ...
If the value is false, it means that non-unique solutions are accepted. These are solutions where multiple candidates have been built from different nuclide instances but the charge_state of all the ions is the same.
Hypertext Anchors¶
List of hypertext anchors for all groups, fields, attributes, and links defined in this class.
