aiCreateTiltSeries creates a tilt series from templates at different locations in space. This tool is mainly used to test geometric parameters in the Artiatomi package and doesn’t aim a direct scientific use case, but it might be usefull for someone…
aiCreateTiltSeries 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
ExtraShifts
The file name for additional particle shifts.
Argument for command line: -o or –ExtraShifts
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
AddTiltAngle
Amount of degrees to add to the tilt angles to rotate the reconstruction in the volume around the tilt or y-axis.
Type: float
Option is mandatory: false
Default value if not set: 0
AddTiltXAngle
Amount of degrees to to rotate the reconstruction in the volume around the X-axis.
Type: float
Option is mandatory: false
Default value if not set: 0
CtfCorrectionType
The type of CTF correction to perform.
Type: one of [NONE, PHASE_FLIP, WIENER_FILTER]
Option is mandatory: true
Possible notations:
- NONE: NONE, None, none, FALSE, false, False, NO, No, no
- PHASE_FLIP: PHASEFLIP, PhaseFlip, phaseflip, PHASE_FLIP, Phase_Flip, phase_flip
- WIENER_FILTER: WIENERFILTER, WienerFilter, wienerfilter, WIENER_FILTER, Wiener_Filter, wiener_filter
CTFSliceThickness
The thickness of a CTF slice for 3D-CTF-Correction in nanometer.
Type: float
Option is mandatory: true
Only applicable if
- CtfCorrectionType = PHASE_FLIP or
- CtfCorrectionType = WIENER_FILTER
SwitchCTFDirection
Inverses the defocus offset value (experimental, do not use).
Type: bool
Option is mandatory: false
Default value if not set: false
Only applicable if
- CtfCorrectionType = PHASE_FLIP or
- CtfCorrectionType = WIENER_FILTER
IgnoreZShiftForCTF
Ignore possible Z-Shift of the reconstruction volume for defocus offset.
Type: bool
Option is mandatory: false
Default value if not set: true
Only applicable if
- CtfCorrectionType = PHASE_FLIP or
- CtfCorrectionType = WIENER_FILTER
VolumeShift
Shift the reconstruction, in unbinned pixel units.
Type: float3, three float values
Option is mandatory: true
Only applicable if IgnoreZShiftForCTF = true.
ProjectionNormalization
Projection normalization method to use before reconstruction.
Type: one of [MEAN, NONE, STANDARD_DEV]
Option is mandatory: true
Possible notations:
- MEAN: MEAN, Mean, mean
- NONE: NONE, none, None
- STANDARD_DEV: STD, std, StandardDeviation, STANDARD_DEV
DebugImages
Save temporary images to disk for debugging.
Type: bool
Option is mandatory: false
Default value if not set: false
Binning
Bin the tilt series images prior to reconstruction.
Type: float
Option is mandatory: false
Default value if not set: 1
CompensateImageRotation
Rotate the image before applying the WBP filter so that the WBP is not interpolated.
Type: bool
Option is mandatory: false
Default value if not set: false
MotiveList
The motive list with alignment information for each particle.
Type: string
Option is mandatory: true
References
File base name for the references.
Type: string
Option is mandatory: true
Masks
File base name for the masks.
Type: string
Option is mandatory: true
ImageSize
Projection image size.
Type: int2, two integer values
Option is mandatory: true
TiltCount
Number of tilts to create.
Type: int
Option is mandatory: true
StartTiltAngle
Start tilt angle value
Type: float
Option is mandatory: true
TiltIncrement
Tilt angle increment
Type: float
Option is mandatory: true
Metadata
Filename for metadata to copy initial values from.
Type: string
Option is mandatory: false
Default value if not set: ’’
OutputDataType
The datatype of the new tilt series.
Argument for command line: -dt or –OutputDataType
Type: one of [CHAR, FLOAT, SHORT, UCHAR, USHORT]
Option is mandatory: false
Default value if not set: FLOAT
Possible notations:
- CHAR: CHAR, char, Char
- FLOAT: FLOAT, float, Float
- SHORT: SHORT, short, Short
- UCHAR: UCHAR, uchar, Uchar, UChar
- USHORT: USHORT, ushort, Ushort, UShort
Scale
Scale the resulting projection image by this factor before conversion to output datatype.
Type: float
Option is mandatory: false
Default value if not set: 1
Offset
Offset to apply to the final projection image before conversion to output datatype.
Type: float
Option is mandatory: false
Default value if not set: 0