aiPatchTracker performs tilt series alignment by tracking patches from one tilt to the other.
It is important for aiPatchTracker to rely on the initial coarse alignments. The more precise image shifts and image rotation are determined before hand, the better are the results of aiPatchTracker. In case that patches in higher tilt angles are not well tracked, check for the image rotation value which should be known +/- 1 degree.
aiPatchTracker can be used without a configuration file and all parameters can be provided by command line arguments. For convenience, parameters can also be given using a configuration file with the -u command line argument. Note: If a parameter is passed by file and by command line, the command line overrides the file.
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
Input
The file to process.
Argument for command line: -i or –Input
Type: string
Option is mandatory: true
AlignBeamDeclination
Align for beam declination.
Argument for command line: -aligBeamDecl or –AlignBeamDeclination
Type: bool
Option is mandatory: false
Default value if not set: true
AlignInPlaneRotation
Align for in plane rotation.
Argument for command line: -aligInPlaneRot or –AlignInPlaneRotation
Type: bool
Option is mandatory: false
Default value if not set: true
AlignFixedInPlaneRotation
Align for a fixed / constant in plane rotation.
Argument for command line: -aligFixedInPlaneRot or –AlignFixedInPlaneRotation
Type: bool
Option is mandatory: false
Default value if not set: false
Only applicable if AlignInPlaneRotation = true.
AlignTilt
Align for tilt angles
Argument for command line: -aligTilt or –AlignTilt
Type: bool
Option is mandatory: false
Default value if not set: true
AlignMagnification
Align for magnification change.
Argument for command line: -aligMag or –AlignMagnification
Type: bool
Option is mandatory: false
Default value if not set: true
FixMagnificationOnFirstTilt
Ensures that the magnification change on the first recorded tilt is 1.
Argument for command line: -fixMagInFirstTilt or –FixMagnificationOnFirstTilt
Type: bool
Option is mandatory: false
Default value if not set: true
Only applicable if AlignMagnification = true.
AlignMaxIterations
Maximum number of optimization iterations to perform.
Argument for command line: -aligIter or –AlignMaxIterations
Type: int
Option is mandatory: false
Default value if not set: 10000
AlignZShift
Z shift to apply during marker alignment.
Argument for command line: -aligZ or –AlignZShift
Type: float
Option is mandatory: false
Default value if not set: 0
FixLowerTiltAngles
Increases the costs for modifying lower tilt angles and avoids changes in these lower tilts.
Argument for command line: -fixTilt or –FixLowerTiltAngles
Type: bool
Option is mandatory: false
Default value if not set: false
PatchSize
The patch size the algorithm tries to track.
Argument for command line: -size or –PatchSize
Type: int
Option is mandatory: true
PatchDistance
The distance in between two neighboring patches (center-to-center).
Argument for command line: -dist or –PatchDistance
Type: int
Option is mandatory: false
Default value if not set: 256
MaxDistance
The maximum distance a cross-check is allowed to diverge.
Argument for command line: -maxDist or –MaxDistance
Type: float
Option is mandatory: false
Default value if not set: 5
MinTrackLength
The minimum number of tilts on which a patch must have been successfully tracked for beeing accepted.
Argument for command line: -trackLength or –MinTrackLength
Type: int
Option is mandatory: false
Default value if not set: 10
LowPassLow
The lower low-pass filter limit.
Argument for command line: -lplow or –LowPassLow
Type: float
Option is mandatory: true
LowPassHigh
The higher low-pass filter limit.
Argument for command line: -lphigh or –LowPassHigh
Type: float
Option is mandatory: true
LowPassSteps
The number of low-pass filter steps in the range [LowPassLow:LowPassHigh].
Argument for command line: -lpsteps or –LowPassSteps
Type: int
Option is mandatory: false
Default value if not set: 5
SeedTilts
Tilt indices that are used as seeds for patch tracking.
Argument for command line: -seeds or –SeedTilts
Type: List<int>, a list of integer values
Option is mandatory: false
Default value if not set: []
AlignmentFile
Save the tracked markers in a seperate file. If empty, markers are stored directly inside tilt series metadata.
Argument for command line: -aligFile or –AlignmentFile
Type: string
Option is mandatory: false
Default value if not set: ‘patchAlignment’
AlignMarkers
Run marker alignment and filtering after marker/patch detection.
Argument for command line: -align or –AlignMarkers
Type: bool
Option is mandatory: false
Default value if not set: false
FilterLimit
The maximum reprojection error allowed per patch for final alignment.
Argument for command line: -filter or –FilterLimit
Type: float
Option is mandatory: false
Default value if not set: 10