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Index
A
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B
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C
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D
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E
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F
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G
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H
|
I
|
L
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M
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N
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O
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P
|
R
|
S
|
T
|
U
|
V
|
W
A
Affine Transform
Axis scaling
Input co-ord's file
Output co-ord's file
Rotation
Translation
Array Start
Input file
Array to Memory
,
[1]
Input file
,
[1]
Output File
,
[1]
Array to VTK
Input file
Output File
Type
Auto Centre
Input file
Output File
B
Bin
Bin dimensions
Input file
Output File
Blank Line Fill
Input file
Output File
bonsu.phasing.abstract
module
bonsu.phasing.CSHIO
module
bonsu.phasing.ER
module
bonsu.phasing.HIO
module
bonsu.phasing.HPR
module
bonsu.phasing.RAAR
module
bonsu.phasing.ShrinkWrap
module
bonsu.phasing.SO2D
module
C
Centred Resize
Input file
Output File
Co-ordinate Transformation
2theta
Arm length (m)
Array binning
CCD x-axis flip
d phi
d theta
Input data
Output amp file
Output phase file
phi
Pixel {x,y} (microns)
Rocking curve type
Transform from
Transform type
wavelength (nm)
Comments
Input file
Output File
Compressed Sensing HIO (CSHIO)
Beta
Divisor
Epsilon
Epsilon min
Eta
Exp amp
Iterations
Mask
p-norm
Relax modulus constraint
Square root exp amp
Support
Conjugate Reflect
Input file
Output File
Convolve
First Input file
Output File
Second Input file
Crop Pad
Crop dimensions: End
Crop dimensions: Start
Input file
Output File
Pad dimensions: End
Pad dimensions: Start
CSHIO (class in bonsu.phasing.CSHIO)
Cuboid Support
(xyz) from array
(xyz) from dimensions
Support file
Support size
D
Dock Visualisation
E
Empty Array
(xyz) from array
(xyz) from dimensions
Output file
ER (class in bonsu.phasing.ER)
ER Mask
Exp amp
Iterations
Mask
Square root exp amp
Support
ER Mask with Partial Coherence Optimisation (ER Mask PC)
Beta
Exp amp
Initial PSF HWHM
Interval between R-L optimisation
Iterations
Iterations preceding R-L optimisation
Mask
R-L iterations
Reset PSF
Square root exp amp
Support
Zero fill end dimensions of PSF
ERMask (class in bonsu.phasing.ER)
ERMaskPC (class in bonsu.phasing.ER)
Error Reduction (ER)
Exp amp
Iterations
Square root exp amp
Support
F
Fourier Transform
Direction
Input file
Output File
G
Gaussian Fill
Input file
Output File
Sigma
GetBeta() (bonsu.phasing.abstract.PhaseAbstract method)
GetDivisor() (bonsu.phasing.CSHIO.CSHIO method)
GetDtaumax() (bonsu.phasing.SO2D.SO2D method)
GetDtaumin() (bonsu.phasing.SO2D.SO2D method)
GetEpsilon() (bonsu.phasing.CSHIO.CSHIO method)
GetEpsilonmin() (bonsu.phasing.CSHIO.CSHIO method)
GetEta() (bonsu.phasing.CSHIO.CSHIO method)
GetExpdata() (bonsu.phasing.abstract.PhaseAbstract method)
GetGammaHWHM() (bonsu.phasing.abstract.PhaseAbstractPC method)
GetMask() (bonsu.phasing.abstract.PhaseAbstract method)
GetMaxphase() (bonsu.phasing.HIO.PCHIO method)
(bonsu.phasing.HIO.PGCHIO method)
GetMinphase() (bonsu.phasing.HIO.PCHIO method)
(bonsu.phasing.HIO.PGCHIO method)
GetNumiterRL() (bonsu.phasing.abstract.PhaseAbstractPC method)
GetNumiterRLinterval() (bonsu.phasing.abstract.PhaseAbstractPC method)
GetNumiterRLpre() (bonsu.phasing.abstract.PhaseAbstractPC method)
GetNumsoiter() (bonsu.phasing.SO2D.SO2D method)
GetPnorm() (bonsu.phasing.CSHIO.CSHIO method)
GetPSF() (bonsu.phasing.abstract.PhaseAbstractPC method)
GetPSFZeroEnd() (bonsu.phasing.abstract.PhaseAbstractPC method)
GetPsiexiterror() (bonsu.phasing.SO2D.SO2D method)
GetPsiexitratio() (bonsu.phasing.SO2D.SO2D method)
GetPsiresetratio() (bonsu.phasing.SO2D.SO2D method)
GetQ() (bonsu.phasing.HIO.PGCHIO method)
GetReweightiter() (bonsu.phasing.SO2D.SO2D method)
GetSeqdata() (bonsu.phasing.abstract.PhaseAbstract method)
GetSOS() (bonsu.phasing.abstract.PhaseAbstract method)
GetSupport() (bonsu.phasing.abstract.PhaseAbstract method)
GetSWCyclelength() (bonsu.phasing.ShrinkWrap.ShrinkWrap method)
GetSWSigma() (bonsu.phasing.ShrinkWrap.ShrinkWrap method)
GetSWThreshold() (bonsu.phasing.ShrinkWrap.ShrinkWrap method)
GetTaumax() (bonsu.phasing.SO2D.SO2D method)
H
HDF5 to Numpy
HDF key path
Input HDF file
Output File
HIO (class in bonsu.phasing.HIO)
HIO Mask
Beta
Exp amp
Iterations
Mask
Square root exp amp
Support
HIO Mask with Partial Coherence Optimisation (HIO Mask PC)
Beta
Exp amp
Initial PSF HWHM
Interval between R-L optimisation
Iterations
Iterations preceding R-L optimisation
Mask
R-L iterations
Reset PSF
Square root exp amp
Support
Zero fill end dimensions of PSF
HIO Plus
Beta
Exp amp
Iterations
Mask
Square root exp amp
Support
HIOMask (class in bonsu.phasing.HIO)
HIOMaskPC (class in bonsu.phasing.HIO)
HIOPlus (class in bonsu.phasing.HIO)
HPR (class in bonsu.phasing.HPR)
HPR Mask with Partial Coherence Optimisation (HPR Mask PC)
Beta
Exp amp
Initial PSF HWHM
Interval between R-L optimisation
Iterations
Iterations preceding R-L optimisation
Mask
R-L iterations
Reset PSF
Square root exp amp
Support
Zero fill end dimensions of PSF
HPRPC (class in bonsu.phasing.HPR)
Hybrid Input-Output (HIO)
Beta
Exp amp
Iterations
Square root exp amp
Support
Hybrid Projection Reflection (HPR)
Beta
Exp amp
Iterations
Mask
Square root exp amp
Support
I
Image to Numpy
Input Image file
Output File
Interpolate Object
Array Bounds: End
Array Bounds: Start
Array grid size
Co-ord's File
Input file
Interpolation range
Output File
L
Laxarus Viewer
Load Co-ordinates
Input file
Load PSF
Input file
LorentzFillPSF() (bonsu.phasing.abstract.PhaseAbstractPC method)
M
Mask
Input file
Maximum Value
Minimum Value
Output File
Median Filter
Input file
Output File
Memory Arrays
Array Creation
module
bonsu.phasing.abstract
bonsu.phasing.CSHIO
bonsu.phasing.ER
bonsu.phasing.HIO
bonsu.phasing.HPR
bonsu.phasing.RAAR
bonsu.phasing.ShrinkWrap
bonsu.phasing.SO2D
N
Nexus Viewer I16
O
Object to VTK
Co-ord's File
Input file
Output File
Type
P
Pause() (bonsu.phasing.abstract.PhaseAbstract method)
PCHIO (class in bonsu.phasing.HIO)
PGCHIO (class in bonsu.phasing.HIO)
Phase Constrained HIO
Beta
Exp amp
Iterations
Mask
Phase Max
Phase Min
Square root exp amp
Support
Phase Gradient Constrained HIO
Beta
Exp amp
Iterations
Mask
Phase Max
Phase Min
Square root exp amp
Support
Phase Only ER (POER)
Exp amp
Iterations
Mask
Square root exp amp
Support
PhaseAbstract (class in bonsu.phasing.abstract)
PhaseAbstractPC (class in bonsu.phasing.abstract)
POER (class in bonsu.phasing.ER)
Polyhedron Support
(xyz) from array
(xyz) from dimensions
Initial Point Coordinates
Support file
Terminal Point Coordinates
PrepareCustom() (bonsu.phasing.abstract.PhaseAbstract method)
Python Script
Input file
Output File
R
RAAR (class in bonsu.phasing.RAAR)
RAAR Mask with Partial Coherence Optimisation (RAAR Mask PC)
Beta
Exp amp
Initial PSF HWHM
Interval between R-L optimisation
Iterations
Iterations preceding R-L optimisation
Mask
R-L iterations
Reset PSF
Square root exp amp
Support
Zero fill end dimensions of PSF
RAARPC (class in bonsu.phasing.RAAR)
Random Start
Amp max
Relaxed Average Alternating Reflection (RAAR)
Beta
Exp amp
Iterations
Mask
Square root exp amp
Support
Resume() (bonsu.phasing.abstract.PhaseAbstract method)
Reweighted 2D Saddle Point Optimisation (SO2D)
Exit Error
Exit Ratio
Exp amp
Initial beta
Iterations
Mask
Max step increment
Max step size
Min step increment
Reset Ratio
Square root exp amp
Step optimisation iterations
Support
Rotate Support
Angle
Axis
Input file
Output File
S
Save Co-ordinates
Output file
Save PSF
Input file
Save Residual
Output file
Save Sequence
Output file
Save Support
Output file
Scale Array
Input file
Output File
Scale factor
Scale Array Dims
Input file
Output File
Scale dimensions
sequence data
SetBeta() (bonsu.phasing.abstract.PhaseAbstract method)
SetDivisor() (bonsu.phasing.CSHIO.CSHIO method)
SetDtaumax() (bonsu.phasing.SO2D.SO2D method)
SetDtaumin() (bonsu.phasing.SO2D.SO2D method)
SetEpsilon() (bonsu.phasing.CSHIO.CSHIO method)
SetEpsilonmin() (bonsu.phasing.CSHIO.CSHIO method)
SetEta() (bonsu.phasing.CSHIO.CSHIO method)
SetExpdata() (bonsu.phasing.abstract.PhaseAbstract method)
SetGammaHWHM() (bonsu.phasing.abstract.PhaseAbstractPC method)
SetMask() (bonsu.phasing.abstract.PhaseAbstract method)
SetMaxphase() (bonsu.phasing.HIO.PCHIO method)
(bonsu.phasing.HIO.PGCHIO method)
SetMinphase() (bonsu.phasing.HIO.PCHIO method)
(bonsu.phasing.HIO.PGCHIO method)
SetNumiter() (bonsu.phasing.abstract.PhaseAbstract method)
SetNumiterRL() (bonsu.phasing.abstract.PhaseAbstractPC method)
SetNumiterRLinterval() (bonsu.phasing.abstract.PhaseAbstractPC method)
SetNumiterRLpre() (bonsu.phasing.abstract.PhaseAbstractPC method)
SetNumsoiter() (bonsu.phasing.SO2D.SO2D method)
SetNumthreads() (bonsu.phasing.abstract.PhaseAbstract method)
SetPnorm() (bonsu.phasing.CSHIO.CSHIO method)
SetPSF() (bonsu.phasing.abstract.PhaseAbstractPC method)
SetPSFZeroEnd() (bonsu.phasing.abstract.PhaseAbstractPC method)
SetPsiexiterror() (bonsu.phasing.SO2D.SO2D method)
SetPsiexitratio() (bonsu.phasing.SO2D.SO2D method)
SetPsiresetratio() (bonsu.phasing.SO2D.SO2D method)
SetQ() (bonsu.phasing.HIO.PGCHIO method)
SetReweightiter() (bonsu.phasing.SO2D.SO2D method)
SetSeqdata() (bonsu.phasing.abstract.PhaseAbstract method)
SetSOS() (bonsu.phasing.abstract.PhaseAbstract method)
SetStartiter() (bonsu.phasing.abstract.PhaseAbstract method)
SetSupport() (bonsu.phasing.abstract.PhaseAbstract method)
SetSWCyclelength() (bonsu.phasing.ShrinkWrap.ShrinkWrap method)
SetSWSigma() (bonsu.phasing.ShrinkWrap.ShrinkWrap method)
SetSWThreshold() (bonsu.phasing.ShrinkWrap.ShrinkWrap method)
SetTaumax() (bonsu.phasing.SO2D.SO2D method)
Shrink Wrap
Algorithm
Beta
Cycle length
Exp amp
Iterations
Mask
Sigma
Square root exp amp
Support
Threshold
ShrinkWrap (class in bonsu.phasing.ShrinkWrap)
SO2D (class in bonsu.phasing.SO2D)
SPE to Numpy
Input SPE file
Output File
Start() (bonsu.phasing.abstract.PhaseAbstract method)
(bonsu.phasing.ER.SWERMaskPC method)
(bonsu.phasing.HIO.SWHIOMaskPC method)
(bonsu.phasing.HPR.SWHPRPC method)
(bonsu.phasing.RAAR.SWRAARPC method)
Stop() (bonsu.phasing.abstract.PhaseAbstract method)
Sum or Subtract Array
Add or Subtract
Input file
Output File
support
SWCSHIO (class in bonsu.phasing.CSHIO)
SWER (class in bonsu.phasing.ER)
SWERMask (class in bonsu.phasing.ER)
SWERMaskPC (class in bonsu.phasing.ER)
SWHIO (class in bonsu.phasing.HIO)
SWHIOMask (class in bonsu.phasing.HIO)
SWHIOMaskPC (class in bonsu.phasing.HIO)
SWHIOPlus (class in bonsu.phasing.HIO)
SWHPR (class in bonsu.phasing.HPR)
SWHPRPC (class in bonsu.phasing.HPR)
SWPCHIO (class in bonsu.phasing.HIO)
SWPGCHIO (class in bonsu.phasing.HIO)
SWPrepare() (bonsu.phasing.ShrinkWrap.ShrinkWrap method)
SWRAAR (class in bonsu.phasing.RAAR)
SWRAARPC (class in bonsu.phasing.RAAR)
SWSO2D (class in bonsu.phasing.SO2D)
SWStart() (bonsu.phasing.ShrinkWrap.ShrinkWrap method)
T
Threshold Data
Input file
Maximum Value
Minimum Value
Output File
Transpose Array
Input file
Output File
U
Undock Visualisation
V
View Array
Amplitude options
Array spacing
Axes
,
[1]
Cut plane normal
Cut plane origin
Input file
Isosurface options
Phase options
Type
View Object
Amplitude options
Axes
Co-ord's File
Cut plane normal
Cut plane origin
Input file
Phase options
Type
View Support
Data array file
Support file
View VTK Array
Amplitude options
Axes
Cut plane normal
Cut plane origin
Input file
Phase options
Type
Voxel Replace
Complex Value
End dimensions
Input file
Output File
Start dimensions
W
Wrap Data
Input file
Output File
Wrap Direction