| Package | Description |
|---|---|
| woSource | |
| woSource.math |
| Modifier and Type | Field and Description |
|---|---|
protected Rectangle3D |
VesselSegm.bodyRect |
protected Rectangle3D |
humanLungSegm.bodyROI |
Rectangle3D |
DoseReader_Oct2012_oldUR.doseRect |
Rectangle3D |
DoseReader.doseRect |
protected Rectangle3D |
humanLungSegm.innerbodyROI |
protected Rectangle3D |
PulmonaryTrunkSegm.lungRect |
protected Rectangle3D |
AirwaySegm.lungRect |
protected Rectangle3D |
humanLungSegm.lungROI |
protected Rectangle3D |
VesselSegm.vesselRect |
| Modifier and Type | Method and Description |
|---|---|
Rectangle3D |
DoseReader.convDose2CTscannerCoords(java.util.Properties[] CTprops,
Point3D imgTLFmm,
Rectangle3D roi,
float[] CTdepthCoords,
float[] CTwidthCoords,
float[] CTheightCoords)
returns the shifts needed to align the dose field to the image set, and
// sets doseDepths, widths, heights [mm] and other parameters read from dicom header
// WO 10/12/2012 modified to use dose data as 3D dicom image.
|
Rectangle3D |
DoseVsIntensity.getDefDoseBoundingRect() |
| Modifier and Type | Method and Description |
|---|---|
Rectangle3D |
DoseReader.convDose2CTscannerCoords(java.util.Properties[] CTprops,
Point3D imgTLFmm,
Rectangle3D roi,
float[] CTdepthCoords,
float[] CTwidthCoords,
float[] CTheightCoords)
returns the shifts needed to align the dose field to the image set, and
// sets doseDepths, widths, heights [mm] and other parameters read from dicom header
// WO 10/12/2012 modified to use dose data as 3D dicom image.
|
protected void |
VesselSegm.cropToRect(Rectangle3D curRect) |
protected void |
RatImageAdjuster.cropToRect(Rectangle3D curRect) |
protected void |
PulmonaryTrunkSegm.cropToRect(Rectangle3D curRect) |
protected void |
noduleDetectionModule.cropToRect(Rectangle3D curRect) |
protected void |
ColonSegm.cropToRect(Rectangle3D curRect) |
void |
ImgRegistration.doreg(ij.ImagePlus firstset,
short[][][] firstimg,
Rectangle3D firstCroppedRect,
ij.ImagePlus secondset,
short[][][] secimg,
Rectangle3D secondCroppedRect) |
| Constructor and Description |
|---|
HistoMR_registration(short[][][] refImg,
java.util.Properties[] Props1,
Rectangle3D refRoi,
short[][][] defImg,
java.util.Properties[] Props2,
Rectangle3D defRoi,
ArrayColorDisplay3D sumAd) |
ImageRegistration(short[][][] refImg,
java.util.Properties[] Props1,
Rectangle3D refRoi,
ij.io.FileInfo reffileinfo,
short[][][] defImg,
java.util.Properties[] Props2,
Rectangle3D defRoi,
ij.io.FileInfo deffileinfo) |
ImageRegistration(short[][][] refImg,
java.util.Properties[] Props1,
Rectangle3D refRoi,
short[][][] defImg,
java.util.Properties[] Props2,
Rectangle3D defRoi) |
| Modifier and Type | Field and Description |
|---|---|
Rectangle3D |
VesselBranch.Roi |
protected Rectangle3D |
SeriesImagesClass.roiRect |
Rectangle3D |
Image3Dinfo.roiRect |
| Modifier and Type | Method and Description |
|---|---|
Rectangle3D |
Rectangle3D.combinedRoi(Rectangle3D roi2) |
static Rectangle3D |
ImgProc.getBoundingBox(boolean[][][] A) |
static Rectangle3D |
ImgProc.getBoundingBox(boolean[][][] A,
int buffer) |
static Rectangle3D |
ImgProc.getBoundingBox(boolean[][][] A,
int buffer,
float zscale) |
static Rectangle3D |
ImgProc.getBoundingBox(byte[][][] A) |
static Rectangle3D |
ImgProc.getBoundingBox(byte[][][] A,
int buffer) |
static Rectangle3D |
ImgProc.getBoundingBox(byte[][][] A,
int buffer,
float zscale) |
static Rectangle3D |
ImgProc.getBoundingBox(byte[][][] A,
int buffer,
float zscale,
int thresh) |
static Rectangle3D |
ImgProc.getBoundingBox(short[][][] A) |
static Rectangle3D |
ImgProc.getBoundingBox(short[][][] A,
int buffer) |
static Rectangle3D |
ImgProc.getBoundingBox(short[][][] A,
int buffer,
float zscale) |
static Rectangle3D |
ImgProc.getBoundingBox(short[][][] A,
int buffer,
float zscale,
int thresh) |
static Rectangle3D |
ImgProc.getObjectBoundingBox(byte[][][] image,
int seedx,
int seedy,
int seedz)
WO 12/22/10 get bounding box for the object connected to pointinside within the thresholded (binary) image
|
static Rectangle3D |
ImgProc.getObjectBoundingBox(byte[][][] image,
int seedx,
int seedy,
int seedz,
int pixelbuffer) |
Rectangle3D |
VesselBranch.getSmoothPtsBoundingBox(float currad) |
| Modifier and Type | Method and Description |
|---|---|
static boolean[][][] |
ImgProc.closeOp(boolean[][][] A,
float searchRad,
float zscale,
Rectangle3D roi) |
static boolean[][][] |
ImgProc.closeOp(boolean[][][] A,
float searchRad,
Rectangle3D roi) |
static boolean[][][] |
ImgProc.closeOp(boolean[][][] A,
int searchRad,
float zscale,
Rectangle3D roi) |
static boolean[][][] |
ImgProc.closeOp(boolean[][][] A,
int searchRad,
Rectangle3D roi) |
static byte[][][] |
ImgProc.closeOp(byte[][][] A,
float searchRad,
float zscale,
Rectangle3D roi) |
static byte[][][] |
ImgProc.closeOp(byte[][][] A,
float searchRad,
Rectangle3D roi) |
static byte[][][] |
ImgProc.closeOp(byte[][][] A,
int searchRad,
float zscale,
Rectangle3D roi) |
static byte[][][] |
ImgProc.closeOp(byte[][][] A,
int searchRad,
Rectangle3D roi) |
Rectangle3D |
Rectangle3D.combinedRoi(Rectangle3D roi2) |
void |
Rectangle3D.Copy(Rectangle3D origrec) |
static boolean[][][] |
ArraysI.copyOutsideRoi(boolean[][][] A,
Rectangle3D roi) |
static byte[][][] |
ArraysI.copyOutsideRoi(byte[][][] A,
Rectangle3D roi) |
byte[][][] |
VesselBranch.createElemSimImage(byte[][][] simImg,
int elemAt,
float radiusAt,
float taperAt,
Rectangle3D curRoi,
VesselBranch parentBr,
boolean withContrast) |
byte[][][] |
VesselBranch.createElemSimImage(byte[][][] simImg,
int elemAt,
float radiusAt,
Rectangle3D curRoi,
VesselBranch parentBr) |
byte[][][] |
VesselBranch.createElemSimImage(byte[][][] simImg,
int elemAt,
Rectangle3D curRoi,
VesselBranch parentBr)
WO 3/18/2013 intent is to create an image from the current vessel info for use later as a template
to match for the vessel tree.
|
byte[][][] |
VesselBranch.createElemSimImage(byte[][][] simImg,
int elemAt,
Rectangle3D curRoi,
VesselBranch parentBr,
boolean withContrast) |
byte[][][] |
VesselBranch.createSimImage(byte[][][] simImg,
boolean doAsSubImg,
int smPtStart,
int smPtEnd,
float radiusAt,
float taperAt,
Rectangle3D roi,
VesselBranch parentBr,
boolean withContrast,
boolean fitEnds)
intent is to use the branch smoothed centerline (in pixel units) and passed in radius (in mm) to create a
simulated image, based on the known voxel dimensions.
|
byte[][][] |
VesselBranch.createSimImage(byte[][][] simImg,
float radiusAt,
float taperAt,
Rectangle3D roi,
VesselBranch parentBr) |
byte[][][] |
VesselBranch.createSimImage(byte[][][] simImg,
float radiusAt,
float taperAt,
Rectangle3D roi,
VesselBranch parentBr,
boolean withContrast) |
byte[][][] |
VesselBranch.createSimImage(byte[][][] simImg,
float radiusAt,
Rectangle3D roi,
VesselBranch parentBr,
boolean withContrast) |
byte[][][] |
VesselBranch.createSimImage(byte[][][] simImg,
float radiusAt,
Rectangle3D roi,
VesselBranch parentBr,
boolean withContrast,
boolean fitEnds) |
byte[][][] |
VesselBranch.createSimImage(byte[][][] simImg,
int smPtStart,
int smPtEnd,
float radiusAt,
float taperAt,
Rectangle3D roi,
VesselBranch parentBr,
boolean withContrast) |
byte[][][] |
VesselBranch.createSimImage(byte[][][] simImg,
Rectangle3D roi,
VesselBranch parentBr) |
byte[][][] |
VesselBranch.createSimImage(byte[][][] simImg,
Rectangle3D roi,
VesselBranch parentBr,
boolean withContrast) |
byte[][][] |
VesselBranch.createSimImage(float radiusAt,
float taperAt,
Rectangle3D roi,
VesselBranch parentBr) |
byte[][][] |
VesselBranch.createSimImage(float radiusAt,
float taperAt,
Rectangle3D roi,
VesselBranch parentBr,
boolean withContrast) |
void |
VesselTree.createSimImage(int depth,
int width,
int ht,
float radiusExpansion,
Rectangle3D roi) |
void |
VesselTree.createSimImage(int depth,
int width,
int ht,
float radiusExpansion,
Rectangle3D roi,
boolean createEndCaps) |
void |
VesselTree.createSimImage(int depth,
int width,
int ht,
Rectangle3D roi) |
byte[][][] |
VesselBranch.createSimImage(Rectangle3D roi,
VesselBranch parentBr) |
byte[][][] |
VesselBranch.createSimImage(Rectangle3D roi,
VesselBranch parentBr,
boolean withContrast) |
static boolean[][][] |
ImgProc.dilate(boolean[][][] A,
float searchRad,
float zscale,
Rectangle3D roi)
WO 10/3/2012 parallel version.
|
static boolean[][][] |
ImgProc.dilate(boolean[][][] A,
float searchRad,
Rectangle3D roi) |
static boolean[][][] |
ImgProc.dilate(boolean[][][] A,
int searchRad,
float zscale,
Rectangle3D roi) |
static boolean[][][] |
ImgProc.dilate(boolean[][][] A,
int searchRad,
Rectangle3D roi) |
static byte[][][] |
ImgProc.dilate(byte[][][] A,
float searchRad,
float zscale,
Rectangle3D roi) |
static byte[][][] |
ImgProc.dilate(byte[][][] A,
float searchRad,
Rectangle3D roi) |
static byte[][][] |
ImgProc.dilate(byte[][][] A,
int searchRad,
float zscale,
Rectangle3D roi) |
static byte[][][] |
ImgProc.dilate(byte[][][] A,
int searchRad,
Rectangle3D roi) |
static boolean[][][] |
ImgProc.doDilate(boolean[][][] A,
float searchRad,
float zscale,
Rectangle3D roi)
10/4/2012 intent is to invoke this through the parallel version.
|
static boolean[][][] |
ImgProc.doErode(boolean[][][] A,
float searchRad,
float zscale,
Rectangle3D roi)
10/4/2012 intent is to run this through the parallel version
|
static int |
ImgProc.doOutsideRoiFill(boolean[][][] A,
Rectangle3D roi) |
static int |
ImgProc.doOutsideRoiFill(byte[][][] A,
Rectangle3D roi,
byte fillval) |
static int |
ImgProc.doOutsideRoiFill(short[][][] A,
Rectangle3D roi,
short fillval) |
static int |
ImgProc.edgeFill3D(boolean[][][] A,
Rectangle3D roi,
int conn) |
static int |
ImgProc.edgeFill3D(byte[][][] A,
Rectangle3D roi,
byte fillval,
int conn) |
static int |
ImgProc.edgeFill3D(short[][][] A,
Rectangle3D roi,
short fillval,
int conn) |
static boolean[][][] |
ImgProc.erode(boolean[][][] A,
float searchRad,
float zscale,
Rectangle3D roi)
WO 10/3/2012 parallel version.
|
static boolean[][][] |
ImgProc.erode(boolean[][][] A,
float searchRad,
Rectangle3D roi) |
static boolean[][][] |
ImgProc.erode(boolean[][][] A,
int searchRad,
float zscale,
Rectangle3D roi)
10/19/11 WO in 2004 had problem of wrap-around in slice(Z) direction.
|
static boolean[][][] |
ImgProc.erode(boolean[][][] A,
int searchRad,
Rectangle3D roi) |
static byte[][][] |
ImgProc.erode(byte[][][] A,
float searchRad,
float zscale,
Rectangle3D roi) |
static byte[][][] |
ImgProc.erode(byte[][][] A,
float searchRad,
Rectangle3D roi) |
static byte[][][] |
ImgProc.erode(byte[][][] A,
int searchRad,
float zscale,
Rectangle3D roi)
10/19/11 WO in 2004 had problem of wrap-around in slice(Z) direction.
|
static byte[][][] |
ImgProc.erode(byte[][][] A,
int searchRad,
Rectangle3D roi) |
static int |
ImgProc.floodFill(boolean[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi) |
static int |
ImgProc.floodFill(boolean[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi,
boolean displayWarnings) |
static int |
ImgProc.floodFill(boolean[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi,
int connectivity) |
static int |
ImgProc.floodFill(boolean[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi,
int connectivity,
boolean displayWarnings)
WO 4/15/08 passing fillval of 0 interpreted as flag to do labeled version
|
static int |
ImgProc.floodFill(byte[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi) |
static int |
ImgProc.floodFill(byte[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi,
byte fillval) |
static int |
ImgProc.floodFill(byte[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi,
byte fillval,
float zscale) |
static int |
ImgProc.floodFill(byte[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi,
byte fillval,
int connectivity)
WO 4/15/08 passing fillval of 0 interpreted as flag to do labeled version
|
static int |
ImgProc.floodFill(byte[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi,
byte fillval,
int connectivity,
float zscale)
WO 4/15/08 passing fillval of 0 interpreted as flag to do labeled version
|
static int |
ImgProc.floodFill(byte[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi,
float zscale) |
static int |
ImgProc.floodFill(byte[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi,
int conn) |
static int |
ImgProc.floodFill(byte[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi,
int conn,
float zscale) |
static int |
ImgProc.floodFill(short[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi) |
static int |
ImgProc.floodFill(short[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi,
float zscale) |
static int |
ImgProc.floodFill(short[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi,
int conn) |
static int |
ImgProc.floodFill(short[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi,
int conn,
float zscale) |
static int |
ImgProc.floodFill(short[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi,
short fillval) |
static int |
ImgProc.floodFill(short[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi,
short fillval,
float zscale) |
static int |
ImgProc.floodFill(short[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi,
short fillval,
int connectivity)
WO 4/15/08 passing fillval of 0 interpreted as flag to do labeled version
|
static int |
ImgProc.floodFill(short[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi,
short fillval,
int connectivity,
float zscale)
This is equivalent to seeded region growing but where the fill occurs only to zero-valued pixels.
|
static int |
ImgProc.floodFillNlabel(byte[][][] A,
int seedx,
int seedy,
int seedz,
Rectangle3D roi,
int connectivity) |
byte[][][] |
VesselTree.getBranchNodeSimImage(int brAt,
int nodeAt,
Rectangle3D nodROI)
Intent is to create the similated vessel image only over the node of interest, over which
to compute the correlation (NCCC) to the original image, for optimizing the nodal parameters.
|
byte[][][] |
VesselBranch.getNodeSimImage(int nodeAt,
float radiusAt,
float taperAt,
Rectangle3D curRoi,
VesselBranch parentBr,
boolean withContrast) |
byte[][][] |
VesselBranch.getNodeSimImage(int nodeAt,
float radiusAt,
Rectangle3D curRoi,
VesselBranch parentBr) |
byte[][][] |
VesselBranch.getNodeSimImage(int nodeAt,
Rectangle3D curRoi,
VesselBranch parentBr) |
byte[][][] |
VesselBranch.getNodeSimImage(int nodeAt,
Rectangle3D curRoi,
VesselBranch parentBr,
boolean withContrast) |
static Polygon3D |
ImgProc.getOuterContour(byte[][][] image,
Rectangle3D roi)
WO 2/14/11 true 3D version
|
static float[] |
ImgProc.getPixel3Dcoords(int pxdepth,
int pxwidth,
int pxheight,
Rectangle3D rect,
java.util.Properties[] DicomHeaders)
get 3D mm coords for pixel.
|
static Point3D[][][] |
ImgProc.getROI3Dcoords(short[][][] img,
Rectangle3D rect,
java.util.Properties[] DicomHeaders)
get 3D mm coords and pixel value of each pixel within the ROI rectangle.
|
byte[][][] |
VesselTree.getSimImage(int depth,
int width,
int ht,
Rectangle3D roi) |
static Point3D[][][] |
ImgProc.getTransformedImageCoords_mm(short[][][] img,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
float xshift,
float yshift,
float zshift,
float drot,
float wrot,
float hrot,
float dscale,
float wscale,
float hscale,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi) |
static Point3D[][][] |
ImgProc.getTransformedImageCoords_mm(short[][][] img,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
ImageRegistration imgreg,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi)
get 3D mm transformed coords and pixel value of each pixel within the ROI rectangle, using the same code as above.
|
static float[] |
ImgProc.getTransformedPtCoords_mm(float ptdepth,
float ptwidth,
float ptheight,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
float xshift,
float yshift,
float zshift,
float drot,
float wrot,
float hrot,
float dscale,
float wscale,
float hscale,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi) |
static float[] |
ImgProc.getTransformedPtCoords_mm(float ptdepth,
float ptwidth,
float ptheight,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
ImageRegistration imgreg,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi) |
static float[] |
ImgProc.getTransformedPtCoords_mm(int ptdepth,
int ptwidth,
int ptheight,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
float xshift,
float yshift,
float zshift,
float drot,
float wrot,
float hrot,
float dscale,
float wscale,
float hscale,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi) |
static float[] |
ImgProc.getTransformedPtCoords_mm(int ptdepth,
int ptwidth,
int ptheight,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
ImageRegistration imgreg,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi)
Intent is to pass in the image pixel coords d,w,h and transform them according to the existing registration
parameters to get the tranformed 3D point coords in mm in scanner coords of the target set.
|
static float[] |
ImgProc.getTransformedPtCoords_px(float ptdepth,
float ptwidth,
float ptheight,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
float xshift,
float yshift,
float zshift,
float drot,
float wrot,
float hrot,
float dscale,
float wscale,
float hscale,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi) |
static float[] |
ImgProc.getTransformedPtCoords_px(float ptdepth,
float ptwidth,
float ptheight,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
ImageRegistration imgreg,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi) |
static float[] |
ImgProc.getTransformedPtCoords_px(int ptdepth,
int ptwidth,
int ptheight,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
float xshift,
float yshift,
float zshift,
float drot,
float wrot,
float hrot,
float dscale,
float wscale,
float hscale,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi) |
static float[] |
ImgProc.getTransformedPtCoords_px(int ptdepth,
int ptwidth,
int ptheight,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
ImageRegistration imgreg,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi)
Intent is to pass in the image pixel coords d,w,h and transform them according to the existing registration
parameters to get the tranformed 3D pixel coords in (dwh) with sub-pixel precision in the scanner coords of the
target set.
|
static short[][][] |
ArraysI.gradient(byte[][][] A,
Rectangle3D roi) |
static short[][][] |
ArraysI.gradient(short[][][] A,
Rectangle3D roi) |
static short[][][] |
ArraysI.gradient2D(byte[][][] A,
Rectangle3D roi) |
static short[][][] |
ArraysI.gradient2D(short[][][] A,
Rectangle3D roi) |
static boolean[][][] |
ArraysI.gradientMag(boolean[][][] A,
Rectangle3D roi) |
static byte[][][] |
ArraysI.gradientMag(byte[][][] A,
Rectangle3D roi) |
static boolean[][][] |
ArraysI.gradientMag2D(boolean[][][] A,
Rectangle3D roi) |
static byte[][][] |
ArraysI.gradientMag2D(byte[][][] A,
Rectangle3D roi) |
void |
ArrayColorDisplay.ImageOverlay(short[][][] img2,
float dshift,
float wshift,
float hshift,
float drot,
float wrot,
float hrot,
Rectangle3D roi) |
void |
ArrayColorDisplay.ImageOverlay(short[][][] img2,
float dshift,
float wshift,
float hshift,
float drot,
float wrot,
float hrot,
Rectangle3D roi,
java.lang.String colorStr) |
void |
ArrayColorDisplay3D.ImageOverlay(short[][][] img2,
java.util.Properties[] props2,
Rectangle3D roi2,
float dshift,
float wshift,
float hshift,
float drot,
float wrot,
float hrot) |
void |
ArrayColorDisplay3D.ImageOverlay(short[][][] img2,
java.util.Properties[] props2,
Rectangle3D roi2,
float dshift,
float wshift,
float hshift,
float drot,
float wrot,
float hrot,
java.lang.String colorStr) |
static float |
ImgProc.imageStatsCorrelation(byte[][][] A,
byte[][][] B,
boolean[][][] roiMask,
Rectangle3D roi) |
static float |
ImgProc.imageStatsCorrelation(byte[][][] A,
byte[][][] B,
Rectangle3D roi) |
static float |
ImgProc.imageStatsCorrelation(short[][][] A,
byte[][][] B,
boolean[][][] roiMask,
Rectangle3D roi) |
static float |
ImgProc.imageStatsCorrelation(short[][][] A,
byte[][][] B,
Rectangle3D roi) |
static float |
ImgProc.imageStatsCorrelation(short[][][] A,
short[][][] B,
boolean[][][] roiMask,
Rectangle3D roi) |
static float |
ImgProc.imageStatsCorrelation(short[][][] A,
short[][][] B,
Rectangle3D roi) |
static float[] |
ImgProc.invTransformPt_px(float ptdepth,
float ptwidth,
float ptheight,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
float xshift,
float yshift,
float zshift,
float drot,
float wrot,
float hrot,
float dscale,
float wscale,
float hscale,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi) |
static float[] |
ImgProc.invTransformPt_px(float ptdepth,
float ptwidth,
float ptheight,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
ImageRegistration imgreg,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi) |
static float[] |
ImgProc.invTransformPt_px(int ptdepth,
int ptwidth,
int ptheight,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
float xshift,
float yshift,
float zshift,
float drot,
float wrot,
float hrot,
float dscale,
float wscale,
float hscale,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi) |
static float[] |
ImgProc.invTransformPt_px(int ptdepth,
int ptwidth,
int ptheight,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
ImageRegistration imgreg,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi)
Intent is to inverse-transform the voxel in the target image back to it's beginning voxel in the reference
image using the existing affine image registration values, and using a cheap iterative approach.
WO 4/25/20913 This seems to be working correctly. |
static boolean[][][] |
ImgProc.openOp(boolean[][][] A,
float searchRad,
float zscale,
Rectangle3D roi) |
static boolean[][][] |
ImgProc.openOp(boolean[][][] A,
float searchRad,
Rectangle3D roi) |
static boolean[][][] |
ImgProc.openOp(boolean[][][] A,
int searchRad,
float zscale,
Rectangle3D roi) |
static boolean[][][] |
ImgProc.openOp(boolean[][][] A,
int searchRad,
Rectangle3D roi) |
static byte[][][] |
ImgProc.openOp(byte[][][] A,
float searchRad,
float zscale,
Rectangle3D roi) |
static byte[][][] |
ImgProc.openOp(byte[][][] A,
float searchRad,
Rectangle3D roi) |
static byte[][][] |
ImgProc.openOp(byte[][][] A,
int searchRad,
float zscale,
Rectangle3D roi) |
static byte[][][] |
ImgProc.openOp(byte[][][] A,
int searchRad,
Rectangle3D roi) |
static byte[][][] |
ArraysI.restoreArray(byte[][][] A,
Rectangle3D croppedroi,
Rectangle3D origroi) |
void |
ArrayDisplay.setRoi(Rectangle3D rect) |
static boolean[][][] |
ArraysI.subArray(boolean[][][] A,
Rectangle3D roi) |
static byte[][][] |
ArraysI.subArray(byte[][][] A,
Rectangle3D roi) |
static float[][][] |
ArraysI.subArray(float[][][] A,
Rectangle3D roi) |
static int[][][] |
ArraysI.subArray(int[][][] A,
Rectangle3D roi) |
static short[][][] |
ArraysI.subArray(short[][][] A,
Rectangle3D roi) |
void |
Rectangle3D.subRect(Rectangle3D subroi) |
static short[][][] |
ImgProc.transform(short[][][] img,
float dshift,
float wshift,
float hshift,
float drot,
float wrot,
float hrot,
Rectangle3D roi)
this is used by ArrayDisplay.overlapImage()
|
static short[][][] |
ImgProc.transformImage_mm(short[][][] img,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
float xshift,
float yshift,
float zshift,
float drot,
float wrot,
float hrot,
float dscale,
float wscale,
float hscale,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi)
version that creates and returns the transformed Image.
WO 4/25/20913 This seems to be working correctly. |
static void |
ImgProc.transformImage_mm(short[][][] img,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
float xshift,
float yshift,
float zshift,
float drot,
float wrot,
float hrot,
float dscale,
float wscale,
float hscale,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi,
short[][][] transformedImage,
boolean useTriLinearInt)
version with resulting transformed Image as parameter for case when need to save memory upon multiple calls.
WO 4/25/20913 This seems to be working correctly. |
static short[][][] |
ImgProc.transformImage_mm(short[][][] img,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
float xshift,
float yshift,
float zshift,
float drot,
float wrot,
float hrot,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi) |
static void |
ImgProc.transformImage_mm(short[][][] img,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
float xshift,
float yshift,
float zshift,
float drot,
float wrot,
float hrot,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi,
short[][][] transformedImage) |
static short[][][] |
ImgProc.transformImage_mm(short[][][] img,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
ImageRegistration imgreg,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi)
version that creates and returns the transformed Image.
WO 4/25/20913 This seems to be working correctly. |
static void |
ImgProc.transformImage_mm(short[][][] img,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
ImageRegistration imgreg,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi,
short[][][] transformedImage) |
static void |
ImgProc.transformImage_mm(short[][][] img,
java.util.Properties[] selfHeaders,
Rectangle3D selfroi,
ImageRegistration imgreg,
java.util.Properties[] targetHeaders,
Rectangle3D targetroi,
short[][][] transformedImage,
boolean useTriLinearInt) |
| Constructor and Description |
|---|
ArrayColorDisplay3D(byte[][][] vals,
java.lang.String label,
java.util.Properties[] props,
Rectangle3D curroi) |
ArrayColorDisplay3D(byte[][][] vals,
java.lang.String label,
java.util.Properties[] props,
Rectangle3D curroi,
int stretchdw,
int stretchdh) |
ArrayColorDisplay3D(short[][][] vals,
java.lang.String label,
java.util.Properties[] props,
Rectangle3D curroi) |
ArrayColorDisplay3D(short[][][] vals,
java.lang.String label,
java.util.Properties[] props,
Rectangle3D curroi,
int stretchdw,
int stretchdh) |
DilateThread(boolean[][][] A,
float searchRad,
float zscale,
Rectangle3D roi) |
ErodeThread(boolean[][][] A,
float searchRad,
float zscale,
Rectangle3D roi) |
Image3Dinfo(java.lang.String label,
int nslices,
Rectangle3D roi,
float[][] TLFcrds,
float[] xdir,
float[] ydir,
float[] zdir,
float mmxy,
float mmz,
int[] ntimes,
float[][] acqtimes,
java.lang.String[][] timeFNs) |
Rectangle3D(Rectangle3D origrec) |
SeriesImagesClass(java.lang.String label,
short[][][] origImg,
boolean[][][] mask,
Rectangle3D roi) |