2.3.3.1.10. NXapm_reconstruction¶
Status:
base class, extends NXprocess
Description:
Base class for the configuration and results of a reconstruction algorithm. ...
Base class for the configuration and results of a 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 evaporation_id, which must not be confused with the pulse_id!
- Groups cited:
NXcollection, NXdata, NXnote, NXparameters, NXprocess, NXprogram
Structure:
reconstructed_positions: (optional) NX_FLOAT (Rank: 2, Dimensions: [n, 3]) {units=NX_LENGTH}
Three-dimensional positions of the ions in the reconstructed volume.
@depends_on: (optional) NX_CHAR
The instance of NXcoordinate_system in which the positions are defined.
volume: (optional) NX_FLOAT {units=NX_VOLUME}
Sum of ion volumes ...
Sum of ion volumes
The value can be extracted from the CAnalysis.CSpatial.fRecoVolume field of a CamecaRoot ROOT file.
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.
PROGRAM: (optional) NXprogram
config: (optional) NXparameters ⤆
Parameters that configure a reconstruction algorithm which takes ...
Parameters that configure a reconstruction algorithm which takes hit data and mass-to-charge-state ratio values to construct a model of the evaporated specimen. This model is called the reconstructed volume. Researchers in the field of atom probe call these algorithms reconstruction protocols.
Different such protocols exist. Although these are qualitatively similar, each protocol uses and interprets the parameters slightly differently.
The majority of reconstructions is performed with the proprietary software APSuite / IVAS, the source code for the reconstruction protocols that this software implements in detail is not open but the parameters and their qualitative effect on the reconstructed volume follows the protocols that are discussed in the atom probe literature. This group allows to document these parameters in a standardized manner.
voltage_filter_initial: (optional) NX_FLOAT {units=NX_VOLTAGE}
Lowest voltage at which an ion that is considered in the reconstructed ...
Lowest voltage at which an ion that is considered in the reconstructed volume has been extracted from the specimen.
voltage_filter_final: (optional) NX_FLOAT {units=NX_VOLTAGE}
Highest voltage at which an ion that is considered in the reconstructed ...
Highest voltage at which an ion that is considered in the reconstructed volume has been extracted from the specimen.
protocol_name: (optional) NX_CHAR
Qualitative statement about which reconstruction protocol was used. ...
Qualitative statement about which reconstruction protocol was used.
For reconstructions performed with APSuite / IVAS the value “cameca” should be used.
Any of these values or a custom value (if you use a custom value, also set @custom=True):
bas|geiser|gault|camecaprimary_element: (optional) NX_CHAR
Assumed primary element based on which the reconstruction is calibrated. ...
Assumed primary element based on which the reconstruction is calibrated.
The value can be extracted from the CAnalysis.CSpatial.fPrimaryElement field of a CamecaRoot ROOT file.
efficiency: (optional) NX_FLOAT {units=NX_DIMENSIONLESS}
Assumed detection efficiency ...
Assumed detection efficiency
The value can be extracted from the CAnalysis.CSpatial.fEfficiency field of a CamecaRoot ROOT file.
flight_path: (optional) NX_FLOAT {units=NX_LENGTH}
Nominal flight path ...
Nominal flight path
The value can be extracted from the CAnalysis.CSpatial.fFlightPath field of a CamecaRoot ROOT file.
evaporation_field: (optional) NX_FLOAT {units=NX_ANY}
Assumed evaporation electric field ...
Assumed evaporation electric field
The value can be extracted from the CAnalysis.CSpatial.fEvaporationField field of a CamecaRoot ROOT file.
image_compression: (optional) NX_FLOAT {units=NX_UNITLESS}
Image compression factor (ICF) ...
Image compression factor (ICF)
The value can be extracted from the CAnalysis.CSpatial.fImageCompression field of a CamecaRoot ROOT file.
kfactor: (optional) NX_FLOAT {units=NX_VOLUME}
Sum of ion volumes ...
Sum of ion volumes
The value can be extracted from the CAnalysis.CSpatial.fKfactor field of a CamecaRoot ROOT file.
shank_angle: (optional) NX_FLOAT {units=NX_ANGLE}
Shank angle ...
Shank angle
The value can be extracted from the CAnalysis.CSpatial.fShankAngle field of a CamecaRoot ROOT file.
ion_volume: (optional) NX_FLOAT {units=NX_VOLUME}
Assumed atomic volume
tip_radius: (optional) NX_FLOAT {units=NX_LENGTH}
The value can be extracted from the CAnalysis.CSpatial.fTipRadius ...
The value can be extracted from the CAnalysis.CSpatial.fTipRadius field of a CamecaRoot ROOT file.
tip_radius_zero: (optional) NX_FLOAT {units=NX_LENGTH}
The value can be extracted from the CAnalysis.CSpatial.fTipRadius0 ...
The value can be extracted from the CAnalysis.CSpatial.fTipRadius0 field of a CamecaRoot ROOT file.
voltage_zero: (optional) NX_FLOAT {units=NX_VOLTAGE}
The value can be extracted from the CAnalysis.CSpatial.fVoltage0 ...
The value can be extracted from the CAnalysis.CSpatial.fVoltage0 field of a CamecaRoot ROOT file.
crystallographic_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.
comment: (optional) NX_CHAR
Possibility of a free text field that allows to report additional details re ...
Possibility of a free text field that allows to report additional details related to the reconstruction protocol. For LEAP systems and reconstructions that are performed with APSuite / IVAS see also B. Gault et al. <https://doi.org/10.1093/mam/ozae081>_ and T. Blum et al. (page 371). for best practices on the reporting of metadata in atom probe tomography.
naive_discretization: (optional) NXprocess
PROGRAM: (optional) NXprogram
Visual overview of the reconstructed dataset via a three-dimensional ...
Visual overview of the reconstructed dataset via a three-dimensional histogram of ion counts. Ion counts are characterized using one nanometer cubic bins without applying any smoothening of reconstructed positions during the histogram computation.
Such preview is useful to get an impression of the macroscopic shape of the reconstructed volume. Visualizing by ion counts highlights density variations the reconstructed volume that are signatures of features such as poles, interfaces or irregularities of the specimen shape.
obb: (optional) NXcollection ⤆
Tight, axis-aligned bounding box about the point cloud of the reconstruction.
xmin: (optional) NX_FLOAT {units=NX_LENGTH}
Minimum coordinate value along the x-direction
xmax: (optional) NX_FLOAT {units=NX_LENGTH}
Maximum coordinate value along the x-direction
ymin: (optional) NX_FLOAT {units=NX_LENGTH}
Minimum coordinate value along the y-direction
ymax: (optional) NX_FLOAT {units=NX_LENGTH}
Maximum coordinate value along the y-direction
zmin: (optional) NX_FLOAT {units=NX_LENGTH}
Minimum coordinate value along the z-direction
zmax: (optional) NX_FLOAT {units=NX_LENGTH}
Maximum coordinate value along the z-direction
Hypertext Anchors¶
List of hypertext anchors for all groups, fields, attributes, and links defined in this class.
