Utils (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- edu.utexas.clm.reconstructreader.Utils

```
public final class Utils
extends Object
```

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class Utils.ReconstructSectionIndexComparator

Nested Classes
Modifier and Type	Class and Description
`static class`	`Utils.ReconstructSectionIndexComparator`

Field Summary

Fields
Modifier and Type Field and Description

static String DELIM

Fields
Modifier and Type	Field and Description
`static String`	`DELIM`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static void`	`appendBezierPathXML(StringBuilder sb, double[] dpts)`
`static void`	`appendClosedPathXML(StringBuilder sb, double[] pts)`
`static void`	`appendOpenPathXML(StringBuilder sb, double[] dpts)`
`static double[]`	`createNodeValueVector(String val)`
`static float[]`	`doubleToFloat(double[] doubles)`
`static <T extends ContourSet> T`	`findContourByName(List<T> contours, String name)`
`static Element`	`findElementByAttribute(NodeList list, String name, String value)`
`static Element`	`findElementByAttributeRegex(NodeList list, String name, String regex)`
`static Element`	`getFirstImageTransformElement(Document doc)` Finds the first Transform Element with an Image child node.
`static Element`	`getImageDomainContour(Node image)`
`static ArrayList<Element>`	`getImageTransformElements(Document doc)` Finds all Transform Elements with Image children.
`static double`	`getMag(Document d)`
`static double`	`getMag(Node n)`
`static double`	`getMedianMag(List<Document> sectionList)`
`static double[]`	`getPathExtent(double[] pts)`
`static double[]`	`getReconstructBoundingBox(double[] wh, AffineTransform trans)`
`static double[]`	`getReconstructImageWH(Node image)`
`static double[]`	`getReconstructImageWH(Node image, double[] wh)`
`static double[]`	`getReconstructStackSize(List<Document> sections)`
`static ArrayList<String>`	`getSeriesKeys()`
`static double[]`	`getTransformedPoints(Element contour, double stackHeight, double mag)`
`static String`	`hexColor(String inColor)`
`static int`	`nodeValueToVector(String val, double[] matrix)`
`static AffineTransform`	`reconstructTransform(Element trans, double mag, double k)`
`static AffineTransform`	`reconstructTransform(Element trans, double mag, double k, double zoom)`
`static AffineTransform`	`reconstructTransform(Element trans, double mag, double k, double zoom, boolean doFlip)`
`static int`	`sectionIndex(Node n)`
`static void`	`selectElementsByIndex(List<Element> elementList, List<Integer> indexList, List<Element> outputList, int index)`
`static String`	`stackTraceToString(Throwable t)`
`static String`	`transformToString(AffineTransform trans)`
`static String`	`transformToString(double[] matrix)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail
- DELIM
```
public static final String DELIM
```
  See Also:
  
  Constant Field Values

Method Detail

sectionIndex

public static int sectionIndex(Node n)

getReconstructStackSize

public static double[] getReconstructStackSize(List<Document> sections)

reconstructTransform

public static AffineTransform reconstructTransform(Element trans,
                                                   double mag,
                                                   double k)

reconstructTransform

public static AffineTransform reconstructTransform(Element trans,
                                                   double mag,
                                                   double k,
                                                   double zoom)

reconstructTransform

public static AffineTransform reconstructTransform(Element trans,
                                                   double mag,
                                                   double k,
                                                   double zoom,
                                                   boolean doFlip)

transformToString

public static String transformToString(AffineTransform trans)

transformToString

public static String transformToString(double[] matrix)

getReconstructBoundingBox

public static double[] getReconstructBoundingBox(double[] wh,
                                                 AffineTransform trans)

findElementByAttributeRegex

public static Element findElementByAttributeRegex(NodeList list,
                                                  String name,
                                                  String regex)

findElementByAttribute

public static Element findElementByAttribute(NodeList list,
                                             String name,
                                             String value)

createNodeValueVector

public static double[] createNodeValueVector(String val)

nodeValueToVector

public static int nodeValueToVector(String val,
                                    double[] matrix)

getFirstImageTransformElement
```
public static Element getFirstImageTransformElement(Document doc)
```
Finds the first Transform Element with an Image child node.

Parameters:

doc - the section XML Document

Returns:

the first Transform Element with an Image child node.

getImageTransformElements
```
public static ArrayList<Element> getImageTransformElements(Document doc)
```
Finds all Transform Elements with Image children.

Parameters:

doc - the section XML Document

Returns:

an ArrayList containing all Transforms with Image children

getReconstructImageWH

public static double[] getReconstructImageWH(Node image)

getImageDomainContour

public static Element getImageDomainContour(Node image)

getReconstructImageWH

public static double[] getReconstructImageWH(Node image,
                                             double[] wh)

findContourByName

public static <T extends ContourSet> T findContourByName(List<T> contours,
                                                         String name)

selectElementsByIndex

public static void selectElementsByIndex(List<Element> elementList,
                                         List<Integer> indexList,
                                         List<Element> outputList,
                                         int index)

appendOpenPathXML

public static void appendOpenPathXML(StringBuilder sb,
                                     double[] dpts)

appendClosedPathXML

public static void appendClosedPathXML(StringBuilder sb,
                                       double[] pts)

appendBezierPathXML

public static void appendBezierPathXML(StringBuilder sb,
                                       double[] dpts)

hexColor

public static String hexColor(String inColor)

getMag

public static double getMag(Document d)

getMag
```
public static double getMag(Node n)
```

getTransformedPoints

public static double[] getTransformedPoints(Element contour,
                                            double stackHeight,
                                            double mag)

getPathExtent

public static double[] getPathExtent(double[] pts)

getMedianMag

public static double getMedianMag(List<Document> sectionList)

stackTraceToString

public static String stackTraceToString(Throwable t)

doubleToFloat

public static float[] doubleToFloat(double[] doubles)

getSeriesKeys

public static ArrayList<String> getSeriesKeys()

Class Utils

Nested Class Summary

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DELIM

Method Detail

sectionIndex

getReconstructStackSize

reconstructTransform

reconstructTransform

reconstructTransform

transformToString

transformToString

getReconstructBoundingBox

findElementByAttributeRegex

findElementByAttribute

createNodeValueVector

nodeValueToVector

getFirstImageTransformElement

getImageTransformElements

getReconstructImageWH

getImageDomainContour

getReconstructImageWH

findContourByName

selectElementsByIndex

appendOpenPathXML

appendClosedPathXML

appendBezierPathXML

hexColor

getMag

getMag

getTransformedPoints

getPathExtent

getMedianMag

stackTraceToString

doubleToFloat

getSeriesKeys