aiCoarseTiltSeriesAlignator determines the shifts from one tilt series image to another based on crossed correlation and tilt angle dependent cosine stretching.
The more precise initial image rotation is determined before hand, the better are the results of aiCoarseTiltSeriesAlignator. Intial roation angles should be known +/- 1 degree.
aiCoarseTiltSeriesAlignator 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
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
MaxTiltDifference
The maximum tilt angle difference allowed in between projections for beeing incorporated in shift determination.
Argument for command line: -maxTilt or –MaxTiltDifference
Type: float
Option is mandatory: true
MaxShift
Maximum allowed shift.
Argument for command line: -m or –MaxShift
Type: int
Option is mandatory: false
Default value if not set: 0
ImageRotation
Overwrites the image rotation given in tilt series metadata.
Argument for command line: -r or –ImageRotation
Type: float
Option is mandatory: false
Default value if not set: -360
DisableFailedFrames
Sets the ‘IgnoreFrame’ flag if a frame cannot be tracked (enables all frames before execution).
Argument for command line: -fail or –DisableFailedFrames
Type: bool
Option is mandatory: false
Default value if not set: true