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UMLdiagram.uxf
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<diagram program="umlet" version="13.1">
<help_text>// Uncomment the following line to change the fontsize and font:
fontsize=12
// fontfamily=SansSerif //possible: SansSerif,Serif,Monospaced
//////////////////////////////////////////////////////////////////////////////////////////////
// Welcome to UMLet!
//
// Double-click on elements to add them to the diagram, or to copy them
// Edit elements by modifying the text in this panel
// Hold Cmd to select multiple elements
// Use Cmd+mouse to select via lasso
//
// Use +/- or Cmd+mouse wheel to zoom
// Drag a whole relation at its central square icon
//
// Press Cmd+C to copy the whole diagram to the system clipboard (then just paste it to, eg, Word)
// Edit the files in the "palettes" directory to create your own element palettes
//
// Select "Custom Elements > New..." to create new element types
//////////////////////////////////////////////////////////////////////////////////////////////
// This text will be stored with each diagram; use it for notes.</help_text>
<zoom_level>10</zoom_level>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>830</x>
<y>190</y>
<w>150</w>
<h>220</h>
</coordinates>
<panel_attributes>FiniteSet
--
setAccess protected
boundary
stepSize
--
public
makeGrids()
makeHandles()
makeInverseHandles()
getSubsetIndices()
hasSubset( set )
makeIndexSet()
save( docNode )</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>1360</x>
<y>1090</y>
<w>180</w>
<h>350</h>
</coordinates>
<panel_attributes>/SurfaceFitter/
--
setAccess protected
fittedPoints
fitDomain
fitOptions
fittedParam
setAccess prot, Abstract
/ charts /
--
public
/ fitSurface( pointCloud )/
/ normallyEvolve(..) /
/ generateEmbedding(..) /
/ populateSOI(SOI) /
setChartResolution(..)
getChartResolution(..)
setFitOptions(..)
setFittedParameters(..)
setDesiredChart(..)
setFitDomain(..)
inspectQuality(..)
storeQualityInspection(..)</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Package</type>
<coordinates>
<x>820</x>
<y>0</y>
<w>1130</w>
<h>1000</h>
</coordinates>
<panel_attributes>diffgeometry
</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>1520</x>
<y>30</y>
<w>170</w>
<h>330</h>
</coordinates>
<panel_attributes>Map
--
setAccess protected
domain : Set
image : Set
subSampling
ssZero
phi
dependent
representation
phiSize
--
public
Map( .. )
apply(.. )
applyComponent( .. )
compose( mp )
composeInverse( mp )
indexValues( .. )
upsample()
subsample(ssFactor)
XMLnode = save( ... )
</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>1290</x>
<y>1490</y>
<w>140</w>
<h>220</h>
</coordinates>
<panel_attributes>TPSFitter
--
setAccess protected
redPointCloud
charts
--
public
fitSurface( options )
generateSeed()
generateEmbedding(..)
populateSOI(..)
normallyEvolve(..)
zEvolve(..)
inspectTPS(..)</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>1680</x>
<y>560</y>
<w>200</w>
<h>40</h>
</coordinates>
<panel_attributes>lt=-
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<additional_attributes>30;30;190;30</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
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</coordinates>
<panel_attributes>lt=<<-</panel_attributes>
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</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>1580</x>
<y>330</y>
<w>50</w>
<h>70</h>
</coordinates>
<panel_attributes>lt=<<-</panel_attributes>
<additional_attributes>30;30;30;50</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>1340</x>
<y>370</y>
<w>110</w>
<h>70</h>
</coordinates>
<panel_attributes>lt=-
>contains</panel_attributes>
<additional_attributes>30;50;100;50</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>1290</x>
<y>440</y>
<w>110</w>
<h>70</h>
</coordinates>
<panel_attributes>lt=-
>contains</panel_attributes>
<additional_attributes>150;-10;150;-10</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>860</x>
<y>130</y>
<w>50</w>
<h>80</h>
</coordinates>
<panel_attributes>lt=<<-</panel_attributes>
<additional_attributes>30;30;30;60</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>1220</x>
<y>380</y>
<w>150</w>
<h>220</h>
</coordinates>
<panel_attributes>Atlas
--
protected
charts
transitionMaps
topology
--
public
addChart( chart )
addTransitionMap(..)
getChart( imName )
getChartIndex(..)
getTransitionMap(..)
getTMapIndex(..)
XMLnode = save( .. )
</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>1340</x>
<y>130</y>
<w>200</w>
<h>60</h>
</coordinates>
<panel_attributes>lt=-
>contains</panel_attributes>
<additional_attributes>30;40;180;40</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>1470</x>
<y>350</y>
<w>290</w>
<h>50</h>
</coordinates>
<panel_attributes>lt=-
</panel_attributes>
<additional_attributes>30;30;270;30</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>510</x>
<y>1330</y>
<w>410</w>
<h>50</h>
</coordinates>
<panel_attributes>lt=-</panel_attributes>
<additional_attributes>30;30;390;30</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Package</type>
<coordinates>
<x>1280</x>
<y>1060</y>
<w>550</w>
<h>790</h>
</coordinates>
<panel_attributes>surfaceFitting
</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>1680</x>
<y>560</y>
<w>40</w>
<h>60</h>
</coordinates>
<panel_attributes>lt=-
</panel_attributes>
<additional_attributes>30;30;30;50</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>650</x>
<y>1290</y>
<w>50</w>
<h>90</h>
</coordinates>
<panel_attributes>lt=->></panel_attributes>
<additional_attributes>30;70;30;30</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Package</type>
<coordinates>
<x>400</x>
<y>520</y>
<w>370</w>
<h>520</h>
</coordinates>
<panel_attributes>surfaceAnalysis
</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>990</x>
<y>640</y>
<w>660</w>
<h>50</h>
</coordinates>
<panel_attributes>lt=<.</panel_attributes>
<additional_attributes>30;30;640;30</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>1470</x>
<y>350</y>
<w>50</w>
<h>60</h>
</coordinates>
<panel_attributes>lt=-
</panel_attributes>
<additional_attributes>30;30;30;40</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>590</x>
<y>1090</y>
<w>180</w>
<h>230</h>
</coordinates>
<panel_attributes>/SurfaceDetector/
--
setAccess protected
pointCloud
options
Constant, Abstract
defaultOptions
--
public
/ detectSurface( stack )/
setPointCloud(..)
setOptions(..)
inspectQuality(..)
storeQualityInspection(..)</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>1160</x>
<y>200</y>
<w>80</w>
<h>50</h>
</coordinates>
<panel_attributes>lt=.</panel_attributes>
<additional_attributes>60;30;30;30</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>290</x>
<y>1090</y>
<w>190</w>
<h>330</h>
</coordinates>
<panel_attributes>Stack
--
setAccess protected
image
resolution
description
channelColor
Ilim
projectionMask
dependent
aspect
imageSize
--
public
rescaleToUnitAspect()
setResolution(..)
setDescription(..)
setIntensityLimits()
generateProjectionMask()
getSlice( dim , val )
getMask()
setProjectionMask()
</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>1220</x>
<y>140</y>
<w>150</w>
<h>220</h>
</coordinates>
<panel_attributes>Field
--
protected
name
targetSpace : Set
patches : Map
patchClass
topology
--
addPatch( patch )
getPatch( domName )
getPatchIndex(..)
checkDefinition()
setName( name )
XMLnode = save( .. )</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>1670</x>
<y>860</y>
<w>40</w>
<h>70</h>
</coordinates>
<panel_attributes>lt=<<-</panel_attributes>
<additional_attributes>30;30;30;60</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>1780</x>
<y>540</y>
<w>40</w>
<h>60</h>
</coordinates>
<panel_attributes>lt=<<-</panel_attributes>
<additional_attributes>30;30;30;50</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>420</x>
<y>550</y>
<w>160</w>
<h>290</h>
</coordinates>
<panel_attributes>SurfaceOfInterest
--
SetAccess protected
nLayers
dependent
data
--
public
SurfaceOfInterest()
pullbackStack( Stack )
makeIP(..)
properLength(..)
properArea(..)
properAngle(..)
integrate(..)
loadSegmentation(..)
partition(..)
tmapMask(..)
multilayer2stack(..);</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>1440</x>
<y>550</y>
<w>130</w>
<h>80</h>
</coordinates>
<panel_attributes>AffineMap
--
--
public
AffineMap( M )
getInverse()</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>1520</x>
<y>1440</y>
<w>50</w>
<h>70</h>
</coordinates>
<panel_attributes>lt=-
</panel_attributes>
<additional_attributes>30;30;30;50</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>160</x>
<y>30</y>
<w>170</w>
<h>730</h>
</coordinates>
<panel_attributes>Experiment
--
SetAccess protected
fileMeta
expMeta
detectOptions
fitOptions
SOIOptions
fittedParam
ROI
currentTime
stack
detector
fitter
SOI
dependent
metadataFile
nTimePoints
optionIndex
optionLength
currentROI
--
public
initNew()
save()
loadTime( t )
loadStack( justMeta )
rescaleStackToUnitAspect()
fitSurface()
normallyEvolve(..)
zEvolve(..)
setFileMeta(..)
setExpMeta(..)
setDetectOptions(..)
resetDetector()
setFitOptions(..)
resetFitter()
setSOIOptions(..)
determineROIfromFit(..)
updateROI()
jitterCorrectROI(..)
batchProcess( timePts )
generateSOI()
</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>1830</x>
<y>800</y>
<w>40</w>
<h>140</h>
</coordinates>
<panel_attributes>lt=<<-</panel_attributes>
<additional_attributes>30;130;30;30</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>1720</x>
<y>930</y>
<w>150</w>
<h>60</h>
</coordinates>
<panel_attributes>TensorPatch
--
public Sealed
calculateTransform( .. )
</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>870</x>
<y>580</y>
<w>150</w>
<h>410</h>
</coordinates>
<panel_attributes>2DManifold
--
protected
topologicalSpace
atlas
fields : Field
timePoints
dynamic
dependent
embedding
g
nTimePoints
--
public
getField(..)
getFieldIndex( name )
getFieldNames()
createField(..)
removeField(name)
NCalcInducedMetric( .. )
NCalcChristoffel( .. )
NCalcCurvature( .. )
tIdx(t)
save( dir )
load( dir )
protected
getFieldIndex()</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>1320</x>
<y>1440</y>
<w>420</w>
<h>40</h>
</coordinates>
<panel_attributes>lt=-
</panel_attributes>
<additional_attributes>30;30;410;30</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>1320</x>
<y>1440</y>
<w>40</w>
<h>60</h>
</coordinates>
<panel_attributes>lt=-
</panel_attributes>
<additional_attributes>30;30;30;50</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>1010</x>
<y>1090</y>
<w>140</w>
<h>230</h>
</coordinates>
<panel_attributes>PointCloud
--
setAccess protected
points
ROI
dependent
unalingnedPoints
--
public
getMoments()
determineROI()
determineRanges()
setROI( ROI )
setPoints( points )
inspect()</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>1630</x>
<y>610</y>
<w>150</w>
<h>280</h>
</coordinates>
<panel_attributes>/TransformableCP/
--
SetAccess protected
chart
protected
atlas
coordReps
dependent
chartName
availableReps
--
public
compose( mp )
getTransform( chName )
setTransform( ..)
/ calculateTransform( .. )/
XMLnode = save( .. )
protected
getRepIndex( chName )
</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Package</type>
<coordinates>
<x>270</x>
<y>1060</y>
<w>920</w>
<h>760</h>
</coordinates>
<panel_attributes>surfaceDetection
</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>1440</x>
<y>390</y>
<w>130</w>
<h>140</h>
</coordinates>
<panel_attributes>CoordinateMap
--
private
inverse
--
public
getInverse()
setInverse( mInv )
getJacobian( mp )
</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>1460</x>
<y>1490</y>
<w>160</w>
<h>220</h>
</coordinates>
<panel_attributes>SphereLikeFitter
--
setAccess protected
charts
--
public
fitSurface( options )
normallyEvolve(..)
generateEmbedding(..)
populateSOI( SOI )
private
parameterFit();
fitPolynomial(..)
determineZLimits()
</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>1800</x>
<y>610</y>
<w>140</w>
<h>120</h>
</coordinates>
<panel_attributes>SquareMatPatch
--
--
public
multiply( Mp )
inverse()
trace()
determinant()
diagonalize()
</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>630</x>
<y>1490</y>
<w>140</w>
<h>120</h>
</coordinates>
<panel_attributes>fastCylinderDetector
--
Constant
defaultOptions
--
public
detectSurface(..)
inspectQuality(..);</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>550</x>
<y>650</y>
<w>340</w>
<h>50</h>
</coordinates>
<panel_attributes>lt=<<-</panel_attributes>
<additional_attributes>320;30;30;30</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>950</x>
<y>20</y>
<w>580</w>
<h>60</h>
</coordinates>
<panel_attributes>lt=-
< maps from / to</panel_attributes>
<additional_attributes>30;40;570;40</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>1800</x>
<y>800</y>
<w>140</w>
<h>30</h>
</coordinates>
<panel_attributes>SquareTensorPatch
--
--
</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>1050</x>
<y>1290</y>
<w>50</w>
<h>140</h>
</coordinates>
<panel_attributes>lt=.></panel_attributes>
<additional_attributes>30;30;30;120</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>1420</x>
<y>1410</y>
<w>40</w>
<h>70</h>
</coordinates>
<panel_attributes>lt=<<-</panel_attributes>
<additional_attributes>30;30;30;60</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>1740</x>
<y>350</y>
<w>150</w>
<h>220</h>
</coordinates>
<panel_attributes>ComponentPatch
--
SetAccess protected
type
--
public
compose( mp )
cmp( {i, j}, domain )
contract( .. )
contractSelf( .. )
contractOther( .. )
raise( index, g )
lower( index, g )
setImageName( .. )
XMLnode = save( .. )
</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>1090</x>
<y>320</y>
<w>140</w>
<h>120</h>
</coordinates>
<panel_attributes>lt=<.</panel_attributes>
<additional_attributes>30;30;30;110;130;110</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>430</x>
<y>1430</y>
<w>180</w>
<h>230</h>
</coordinates>
<panel_attributes>PlanarDetector
--
setAccess protected
surfaceMatrix
mask
manualMask
maxI
summedI
--
protected
updatePointCloud(..)
public
applyMasks(..)
setManualMask(..)
resetMask(..)
</panel_attributes>
<additional_attributes/>
</element>
<element>
<type>com.baselet.element.old.element.Relation</type>
<coordinates>
<x>510</x>
<y>1330</y>
<w>50</w>
<h>120</h>
</coordinates>
<panel_attributes>lt=-</panel_attributes>
<additional_attributes>30;100;30;30</additional_attributes>
</element>
<element>
<type>com.baselet.element.old.element.Class</type>
<coordinates>
<x>990</x>
<y>1410</y>
<w>180</w>
<h>390</h>
</coordinates>
<panel_attributes>RegionOfInterest
--
setAccess protected
rotation
translation
xpRange