aiDoseBoosterTraining trains a neural network to be used later on in aiDoseBooster. Based on the Noise2Noise idea where noisy movie stack images are used for training.
aiDoseBoosterTraining 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
DeadPixelRemoval
Enables removal of dead pixels based on thresholding. If set to ‘relative’, the threshold is X times the STD + MEAN of the image.
Argument for command line: -deadPixel or –DeadPixelRemoval
Type: one of [ABSOLUTE, NONE, RELATIVE]
Option is mandatory: false
Default value if not set: NONE
Possible notations:
- ABSOLUTE: ABSOLUTE, Absolute, absolute
- NONE: NONE, None, none
- RELATIVE: RELATIVE, Relative, relative
DeadPixelThreshold
Threshold above which a pixel is considered invalid.
Argument for command line: -threshold or –DeadPixelThreshold
Type: float
Option is mandatory: true
Only applicable if
- DeadPixelRemoval = ABSOLUTE or
- DeadPixelRemoval = RELATIVE
Network
The file to store the trained network configuration.
Argument for command line: -n or –Network
Type: string
Option is mandatory: true
NetworkIn
If given, the training refines the provided network configuration.
Argument for command line: -ni or –NetworkIn
Type: string
Option is mandatory: false
Default value if not set: ’’
Iterations
The number of iterations to train the network.
Argument for command line: -iter or –Iterations
Type: int
Option is mandatory: true
ResetIterations
When refining an existing network, this parameter allows to reset the iteration counter in order to put more weight on the new dataset.
Argument for command line: -resetIter or –ResetIterations
Type: bool
Option is mandatory: false
Default value if not set: false
DeadPixelMap
An image indicating defective pixels (same size as movie frames).
Argument for command line: -deadPixelMap or –DeadPixelMap
Type: string
Option is mandatory: false
Default value if not set: ’’
GainReference
An image for gain reference (same size as movie frames).
Argument for command line: -gainRef or –GainReference
Type: string
Option is mandatory: false
Default value if not set: ’’
Skip
Skip the X first frames of a stack.
Argument for command line: -skip or –Skip
Type: int
Option is mandatory: false
Default value if not set: 0
FlipYAxis
Flip all images on Y axis before any processing.
Argument for command line: -flip or –FlipYAxis
Type: bool
Option is mandatory: false
Default value if not set: false