SPIM 微珠注册（已弃用）

<VariablesAssignment.txt>

###
### Section: General Parameters
###

Time Point Pattern = "18"
Acquisition Angle Pattern = "0-270:45"
# The input files can be in any format that Fiji can read.
# They need to be 3D stacks with correct calibration, though.
Input File Pattern = "spim_TL{t}_Angle{a}.lsm"
Input Directory = "F:\Stephan\dros\"
Output Directory = "F:\Stephan\dros\output"
Registration File Directory = "F:\Stephan\dros\registration\"
Debug Level = "DEBUG_MAIN"
Show ImageJ Window = true

###
### Section: Time Lapse 
###

Time Lapse Registration = false
Reference Time Point = 1

###
### Section: Data Structures, Access and Paging
###

Factory for Images during Segmentation = ArrayContainerFactory()
Factory for Recursive Gauss = ArrayContainerFactory()
Factory for Images during Fusion = ArrayContainerFactory()
#Factory for Output Images = ArrayContainerFactory()
Factory for Entropy = ArrayContainerFactory()
Factory for Scale Space = ArrayContainerFactory()

#Factory for Images during Segmentation = CubeContainerFactory(16)
#Factory for Recursive Gauss = CubeContainerFactory(16)
#Factory for Images during Fusion = CubeContainerFactory(16)
Factory for Output Images = CubeContainerFactory( 256 )
#Factory for Entropy = CubeContainerFactory(16)
#Factory for Scale Space = CubeContainerFactory(35)

Paging Temporary Directory = null

Out of Bounds Strategy for Fusion = OutsideStrategyValueFactory(0)
Out of Bounds Strategy for Gauss = OutsideStrategyMirrorFactory()
Interpolator for Output Image = LinearInterpolatorFactory()

###
### Section: Main Switches
###

Write Output Image = true
Show Output Image = true
Segmentation Use Scale Space = true
Fusion Use Entropy = false
Fusion Use Gauss = false
Fusion Use Blending = false

Fuse all Images at once = false
Fuse Images sequentially = false
Number of Paralell Views = 4
Create multiple registered Output Images = true    

Register Only = false
Display Registration = false
Read Segmentation = true
Write Segmentation = true
Read Registration = false
Write Registration = true

###
### Section: Image Parameters
###

Override Z-Stretching of Image = true

# 20x, 2um z spacing ( 2.0 / 0.73 )
Image Z-Stretching = 2.739726027397260273972602739726

Image Background = 0

###
### Section: Threshold Bead Segmentation
###

Bead Segmentation Threshold = 0.9
Bead Segmentation Fixed Threshold = 0.02
Bead Segmentation Use Fixed Threshold = true 
Bead Segmentation Circularity Factor = 0.5
Bead Segmentation Minimum Black Border around Bead = 1
Bead Segmentation Minimum Bead Size = 10
Bead Segmentation Maximum Bead Size = 13375
Bead Segmentation Use Center of Mass = false

###
### Section: Scale Space Bead Segmentation
###

Bead Scale Space Minimum Peak Value = 0.01
Bead Scale Space Minimum Initial Peak Value = 0.005
Bead Scale Space Identity Radius = 3.0
Bead Scale Space Maxima Tolerance = 0.01
Bead Scale Space Image Sigma = 0.5
Bead Scale Space Initial Sigma = 1.4
Bead Scale Space Steps per Octave = 4
Bead Scale Space Steps = 3
Bead Scale Space Number of Threads = 0

###
### Section: Point Descriptor and Global Optimization
###

Point Descriptor Difference Threshold = 50
Point Descriptor Ratio of Distance = 10
Point Descriptor Number of Neighbors = 3
Point Descriptor Use Associated Beads = false   
Point Descriptor Use RANSAC = true

RANSAC Maximum Epsilon = 5
RANSAC Minimum Inlier Ratio = 0.1  
RANSAC Number of Iterations = 1000

# p__ = ( 1 - r^n ) ^ k
# k = log(p__) / log ( 1 - r^n )

# p__ ... probability that ransac fails
# r   ... min inlier ratio
# n   ... minimal number of points needed to create model
# k   ... number of iterations 

###
### Section: Output Image
###

Output Image Scale = 1

Output Image Crop Offset X = 0
Output Image Crop Offset Y = 0
Output Image Crop Offset Z = 0
Output Image Crop Size X = 0
Output Image Crop Size Y = 0
Output Image Crop Size Z = 0


Output Image Number of Threads = 0

###
### Section: Volume Injection
###

Volume Injection Sigma = 0.25
Volume Injection Cut Off Radius = 2

###
### Section: Entropy
###

Entropy Histogram Bins = 256
Entropy Window Size X = 25
Entropy Window Size Y = 25

###
### Section: Blending
###

Blending Alpha = 1.5

###
### Section: Gauss Fusion
###

Gauss Fusion Sigma 1 = 20
Gauss Fusion Sigma 2 = 40 ### 变量分配.txt
Input File Pattern = String inputFilePattern
Time Point Pattern = String timepointPattern 
Acquisition Angle Pattern = String anglePattern
Input Directory = String inputdirectory 
Output Directory = String outputdirectory
Registration File Directory = String registrationFiledirectory
Debug Level = String debugLevel
Show ImageJ Window = boolean showImageJWindow

Time Lapse Registration = boolean timeLapseRegistration
Reference Time Point = int referenceTimePoint

Factory for Images during Segmentation = ContainerFactory imageFactory
Factory for Recursive Gauss = ContainerFactory recursiveGaussFactory
Factory for Images during Fusion = ContainerFactory imageFactoryFusion
Factory for Output Images = ContainerFactory outputImageFactory
Factory for Entropy = ContainerFactory entropyFactory
Factory for Scale Space = ContainerFactory scaleSpaceFactory

Paging Temporary Directory = String tempDir

Out of Bounds Strategy for Fusion = OutsideStrategyFactory strategyFactoryOutput    
Out of Bounds Strategy for Gauss = OutsideStrategyFactory strategyFactoryGauss
Interpolator for Output Image = InterpolatorFactory interpolatorFactorOutput

Write Output Image = boolean writeOutputImage
Show Output Image = boolean showOutputImage
Segmentation Use Scale Space = boolean useScaleSpace
Fusion Use Entropy = boolean useEntropy
Fusion Use Gauss = boolean useGauss
Fusion Use Blending = boolean useLinearBlening

Fuse all Images at once = boolean paralellFusion    
Fuse Images sequentially = boolean sequentialFusion
Number of Paralell Views = int numParalellViews  
Create multiple registered Output Images = boolean multipleImageFusion    

Register Only = boolean registerOnly
Display Registration = boolean displayRegistration
Read Segmentation = boolean readSegmentation
Write Segmentation =  boolean writeSegmentation
Read Registration = boolean readRegistration
Write Registration = boolean writeRegistration   

Override Z-Stretching of Image = boolean overrideImageZStretching
Image Z-Stretching = double zStretching
Image Background = int background
    
Bead Segmentation Threshold = float threshold
Bead Segmentation Fixed Threshold = float fixedThreshold
Bead Segmentation Use Fixed Threshold = boolean useFixedThreshold 
Bead Segmentation Circularity Factor = double circularityFactor
Bead Segmentation Minimum Black Border around Bead = int minBlackBorder
Bead Segmentation Minimum Bead Size = int minSize
Bead Segmentation Maximum Bead Size = int maxSize
Bead Segmentation Use Center of Mass = boolean useCenterOfMass

Bead Scale Space Minimum Peak Value = float minPeakValue
Bead Scale Space Minimum Initial Peak Value = float minInitialPeakValue
Bead Scale Space Identity Radius = float identityRadius
Bead Scale Space Maxima Tolerance = float maximaTolerance
Bead Scale Space Image Sigma = float imageSigma
Bead Scale Space Initial Sigma = float initialSigma
Bead Scale Space Steps per Octave = int stepsPerOctave
Bead Scale Space Steps = int steps
Bead Scale Space Number of Threads = int scaleSpaceNumberOfThreads

Point Descriptor Difference Threshold = double differenceThreshold
Point Descriptor Ratio of Distance = double ratioOfDistance
Point Descriptor Number of Neighbors = int neighbors
Point Descriptor Use Associated Beads = boolean useAssociatedBeads    
Point Descriptor Use RANSAC = boolean useRANSAC

RANSAC Maximum Epsilon = float max_epsilon
RANSAC Minimum Inlier Ratio = float min_inlier_ratio   
RANSAC Number of Iterations = int numIterations

Output Image Scale = int scale
Output Image Crop Offset X = int cropOffsetX
Output Image Crop Offset Y = int cropOffsetY
Output Image Crop Offset Z = int cropOffsetZ
Output Image Crop Size X = int cropSizeX
Output Image Crop Size Y = int cropSizeY
Output Image Crop Size Z = int cropSizeZ
Output Image Number of Threads = int numberOfThreads

Volume Injection Sigma = float sigma
Volume Injection Cut Off Radius = int cutOffRadiusGauss

Entropy Histogram Bins = int histogramBins
Entropy Window Size X = int windowSizeX
Entropy Window Size Y = int windowSizeY

Blending Alpha = float alpha

Gauss Fusion Sigma 1 = float fusionSigma1
Gauss Fusion Sigma 2 = float fusionSigma2