aiVolumeMatching finds the best possible orientation of one volume relative to a reference.
aiVolumeMatching needs a configuration file provided by the -u argument. Some options can be overwritten using command line arguments.
Options are:
CudaDeviceID
The deviceID of the GPU to use.
Argument for command line: -d or –CudaDeviceID
Type: int
Option is mandatory: false
Default value if not set: 0
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
If a motive list is provided, the found displacement can be stored there as reference displacement.
Type: string
Option is mandatory: false
Default value if not set: ’’
FixedReference
The filename of the volume that is used as reference.
Type: string
Option is mandatory: true
MovingVolume
If no motive list is provided, the filename of the volume that needs to oriented on the reference. If a motive list is provided, the reference index of the reference to align.
Type: string
Option is mandatory: true
OutputVolume
If provided, the best displacement is stored in this file.
Type: string
Option is mandatory: false
Default value if not set: ’’
Mask
Mask filename.
Type: string
Option is mandatory: false
Default value if not set: ’’
RotateMask
Indicates if the reference mask has to be rotated with the particle orientation.
Type: bool
Option is mandatory: true
MaxShift
Maximum allowed shift (or set MaskCC filename)
Type: int
Option is mandatory: false
Default value if not set: 0
MaskCC
MaskCC filename. Naming convention: filename.em/mrc.
Type: string
Option is mandatory: true
Only applicable if MaxShift = -1.
RotateMaskCC
Indicates if the CC-Mask has to be rotated with the particle orientation.
Type: bool
Option is mandatory: true
Only applicable if MaxShift = -1.
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
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
SubPixelRatio
For values > 1, the shift is determined with sub-pixel precission. 2=0.5 pixel shift, 4=0.25 pixel shift, etc.
Type: int
Option is mandatory: false
Default value if not set: 1
Symmetry
If provided, the found displacement is added to the symmetry file as an additional symmetry displacement.
Type: string
Option is mandatory: false
Default value if not set: ’’
RigidScan
Scan Psi angles with fixed angular distance (equal to PhiAngIncr).
Type: bool
Option is mandatory: false
Default value if not set: false
PreRotation
Apply a fixed rotation to the moving volume before scanning rotations. Values are for (phi, psi, theta).
Type: float3, three float values
Option is mandatory: false
Default value if not set: (0, 0, 0)
CCFile
If provided, the CC value for all scanned angles is stored in a pseudo motive list (one entry per scanned rotation).
Type: string
Option is mandatory: false
Default value if not set: ’’