aiTemplateMatching

aiTemplateMatching determines the positions and orientations of a template given as a small volume in a larger volume.

aiTemplateMatching needs a configuration file provided by the -u argument. Some options can be overwritten using command line arguments.

Options are:

CudaDeviceIDs

The deviceIDs of the GPUs to use.
Argument for command line: -d or –CudaDeviceIDs
Type: List<int>, a list of integer values
Option is mandatory: true

Input

The file to process.
Argument for command line: -i or –Input
Type: string
Option is mandatory: true

LP

Low pass filter value.
Argument for command line: -lp or –LP
Type: float
Option is mandatory: true

LPS

Low pass filter sigma value.
Argument for command line: -lps or –LPS
Type: float
Option is mandatory: true

HP

High pass filter value.
Argument for command line: -hp or –HP
Type: float
Option is mandatory: false
Default value if not set: 0

HPS

High pass filter sigma value.
Argument for command line: -hps or –HPS
Type: float
Option is mandatory: false
Default value if not set: 0

MotiveList

The list of particles to save the result to.
Type: string
Option is mandatory: true

Reference

Reference filename.
Type: string
Option is mandatory: true

ReferenceNr

Reference number (for a final motive list with multiple references).
Type: int
Option is mandatory: false
Default value if not set: 0

Mask

Mask filename.
Type: string
Option is mandatory: true

AngIter

Number of angular search increments.
Type: int
Option is mandatory: true

AngIncr

Angular search increment.
Type: float
Option is mandatory: true

PhiAngIter

Number of angular search increments for phi angle.
Type: int
Option is mandatory: true

PhiAngIncr

Angular search increment for phi angle.
Type: float
Option is mandatory: true

CouplePhiToPsi

Indicates if the phi angle is coupled to psi (can be necessary for restricted search ranges).
Type: bool
Option is mandatory: true

Threshold

Only include matches with a correlation score above threshold.
Type: float
Option is mandatory: true

MaxParticleCount

Limit the number of detected particles, such that only the particles with best correlation values remain (applied before final distance filter).
Type: int
Option is mandatory: true

MinDist

Minimum distance in between two particles (in unbinned pixels).
Type: float
Option is mandatory: true

Fragments

The number of fragments the tomogram is split into on each GPU (0 for automatic).
Type: int
Option is mandatory: true

ExtendedStatistics

Computes extended statistics of the CC value over the scanned rotations and stores them in the free value section of the motive list (needs more GPU memory though).
Type: bool
Option is mandatory: false
Default value if not set: false

CorrelationMethod

Defines the correlation method to use: ‘Cross-Correlation’ or ‘Phase-Correlation’.
Type: one of [CROSSCORRELATION, PHASECORRELATION]
Option is mandatory: true
Possible notations:

• CROSSCORRELATION: CROSSCORRELATION, CROSS-CORRELATION, CROSS_CORRELATION, CrossCorrelation, Cross-Correlation, Cross_Correlation, crosscorrelation, cross-correlation, cross_correlation
• PHASECORRELATION: PHASECORRELATION, PHASE-CORRELATION, PHASE_CORRELATION, PhaseCorrelation, Phase-Correlation, Phase_Correlation, phasecorrelation, phase-correlation, phase_correlation