2.3.3.3.41. NXapm_reconstruction¶
Status:
base class (contribution), extends NXprocess
Description:
Base class for the configuration and results of a (static) reconstruction algori ...
Base class for the configuration and results of a (static) reconstruction algorithm.
Generating a tomographic reconstruction of the specimen uses selected and calibrated ion hit positions, the evaporation sequence, and voltage curve data. Very often scientists use own software scripts according to published procedures, so-called reconstruction protocols.
Symbols:
The symbols used in the schema to specify e.g. dimensions of arrays.
n: Number of ions spatially filtered from results of the hit_finding algorithm from which an instance of a reconstructed volume has been generated. These ions get new identifier assigned in the process - the so-called identifier_evaporation, which must not be confused with the identifier_pulse!
Structure:
parameter: (optional) NX_CHAR
Different reconstruction protocols exist. Although these approaches ...
Different reconstruction protocols exist. Although these approaches are qualitatively similar, each protocol uses different parameters (and interprets these differently). The source code to IVAS/APSuite is not open. For now users should store reconstruction parameter in this free-text field to guide how to parameterize this better in the future. For LEAP systems and reconstructions performed with IVAS/APSuite see T. Blum et al. (page 371).
primary_element: (optional) NX_CHAR
CAnalysis.CSpatial.fPrimaryElement
efficiency: (optional) NX_FLOAT {units=NX_DIMENSIONLESS}
CAnalysis.CSpatial.fEfficiency
flight_path: (optional) NX_FLOAT {units=NX_LENGTH}
CAnalysis.CSpatial.fFlightPath
evaporation_field: (optional) NX_FLOAT {units=NX_ANY}
CAnalysis.CSpatial.fEvaporationField
image_compression: (optional) NX_FLOAT {units=NX_UNITLESS}
CAnalysis.CSpatial.fImageCompression ...
CAnalysis.CSpatial.fImageCompression
Image compression factor (ICF)
kfactor: (optional) NX_FLOAT {units=NX_UNITLESS}
CAnalysis.CSpatial.fKfactor ...
CAnalysis.CSpatial.fKfactor
k factor
volume: (optional) NX_FLOAT {units=NX_VOLUME}
CAnalysis.CSpatial.fRecoVolume ...
CAnalysis.CSpatial.fRecoVolume
Sum of ion volumes
shank_angle: (optional) NX_FLOAT {units=NX_ANGLE}
CAnalysis.CSpatial.fShankAngle ...
CAnalysis.CSpatial.fShankAngle
Shank angle
tip_radius: (optional) NX_FLOAT {units=NX_LENGTH}
CAnalysis.CSpatial.fTipRadius
tip_radius_zero: (optional) NX_FLOAT {units=NX_LENGTH}
CAnalysis.CSpatial.fTipRadius0
voltage_zero: (optional) NX_FLOAT {units=NX_VOLTAGE}
CAnalysis.CSpatial.fVoltage0
protocol_name: (optional) NX_CHAR
Qualitative statement about which reconstruction protocol was used. ...
Qualitative statement about which reconstruction protocol was used.
Any of these values or a custom value (if you use a custom value, also set @custom=True):
bas|geiser|gault|camecacrystallographic_calibration: (optional) NX_CHAR
Different strategies for crystallographic calibration of the ...
Different strategies for crystallographic calibration of the reconstruction are possible. Therefore, we collect first such feedback before parametrizing this further.
If no crystallographic calibration was performed, the field should be filled with the n/a, meaning not applied.
field_of_view: (optional) NX_FLOAT {units=NX_LENGTH}
The nominal diameter of the specimen ROI which is measured in the ...
The nominal diameter of the specimen ROI which is measured in the experiment. The physical specimen cannot be measured completely because ions may launch but hit in locations other than the detector.
reconstructed_positions: (optional) NX_FLOAT (Rank: 2, Dimensions: [n, 3]) {units=NX_LENGTH}
Three-dimensional reconstructed positions of the ions.
@depends_on: (optional) NX_CHAR
The instance of :ref:`NXcoordinate_system` ...
The instance of NXcoordinate_system in which the positions are defined.
PROGRAM: (optional) NXprogram
obb: (optional) NXobject
Tight, axis-aligned bounding box about the point cloud of the reconstruction.
xmin: (optional) NX_FLOAT {units=NX_LENGTH}
TODO
xmax: (optional) NX_FLOAT {units=NX_LENGTH}
TODO
ymin: (optional) NX_FLOAT {units=NX_LENGTH}
TODO
ymax: (optional) NX_FLOAT {units=NX_LENGTH}
TODO
zmin: (optional) NX_FLOAT {units=NX_LENGTH}
TODO
zmax: (optional) NX_FLOAT {units=NX_LENGTH}
TODO
naive_discretization: (optional) NXprocess
PROGRAM: (optional) NXprogram
To get a first visual overview of the reconstructed dataset, ...
To get a first visual overview of the reconstructed dataset, here a 3d histogram of the ion is stored. Ion counts are characterized using one nanometer cubic bins without applying position smoothening algorithms during the histogram computation.
Hypertext Anchors¶
List of hypertext anchors for all groups, fields, attributes, and links defined in this class.
