com.openinventor.medical.helpers

Class MedicalHelper

java.lang.Object

com.openinventor.medical.helpers.MedicalHelper

public class MedicalHelper
extends java.lang.Object

Utility class for medical applications using Open Inventor. Open Inventor includes a general purpose 3D graphics core library plus optimized extensions for specific data types and markets, including medical visualization. We recommend using these utility functions (and the Medical utility nodes) to get the best performance and productivity from the Open Inventor Medical Edition.

Summary:

• dicomAdjustVolume()
  Call this method to adjust VolumeViz parameters for optimal performance with medical data and to position a DICOM volume correctly in 3D space.
• dicomAdjustDataRange()
  Call this method to set the VolumeViz data range based on the Window Center and Window Width tags in a DICOM file. If those tags are not present, automatically sets the data range to the actual range of values in the data.
• dicomSetWindowCenterWidth() and dicomGetWindowCenterWidth()
  In Open Inventor the range of voxel values that map onto the color map are specified as the 'min' and 'max' values of the range (see SoDataRange). These methods provide a convenient way to set and query the data range using the medical convention of 'window center' and 'window width'.
• dicomFindFilesbySeries()
  Call this method to build a list of DICOM image files in a directory that belong to the same series as the specified file. This list can be passed to the DICOM volume reader using the setFileList() method.
• orientView()
  This method is useful for orienting the camera to view a single image (a slice in VolumeViz jargon) along one of the standard axes (Axial, Coronal or Sagittal). But remember that the volume is always a 3D object to Open Inventor and you must also set the 'axis' field on the SoOrthoSlice node. See the dicomImageViewer example.

See Also:

DicomInfo, Gnomon, Magnifier, OrthoSliceBorder, Ruler, SliceOrientationMarkers, SliceScaleBar, TextBox

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MedicalHelper.Axis Medical axis names.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	EXAMPLE_LOGO
static short	WINDOW_HEIGHT
static short	WINDOW_WIDTH

Constructor Summary

Constructors

Constructor and Description
MedicalHelper()

Method Summary

Modifier and Type	Method and Description
static SoSeparator	buildSliceAnnotation(SoCamera camera, SoOrthoSlice sliceNode, java.lang.String filename) Slice viewer annotations.
static SoSeparator	buildSliceOrientationMarkers(SoOrthoSlice orthoSlice) Build a scene graph to display slice orientation markers.
static SoSeparator	buildSliceScaleBars(SoCamera camera) Build a scene graph to display dynamic scale bars for slice viewing.
static SoSeparator	createBoundingBox(SbBox3f bbox, SbColor color) Convenience function to draw a specified bounding box as a wireframe
static SoSeparator	createCube(SbBox3f bbox) Convenience function to retrieve the cube corresponding to the specified bounding box.
static boolean	dicomAdjustDataRange(SoDataRange rangeNode, SoVolumeData volume) Adjust data range based on values in the DICOM file, i.e.
static boolean	dicomAdjustVolume(SoVolumeData volume, boolean useImagePosition) Optimize volume data node for DICOM volumes.
static boolean	dicomAdjustVolume(SoVolumeData volume, SoMatrixTransform imgToPatient) Similar to dicomAdjustVolume( SoVolumeData, boolean ) above but returns an SoMatrixTransform that can be used to properly locate VolumeData in patient space in case of non axis aligned acquisition:
static SbVec3f	dicomGetImagePosition(SoVolumeData volume) Get the "Image Position (Patient)" attribute (0020,0032) from a DICOM volume.
static boolean	dicomGetWindowCenterWidth(SoVolumeData volume, SbVec2f winCW) Get the window center (level) and width values from a DICOM volume.
static void	dollyZoom(float value, SoCameraInteractor cameraInteractor) Make the scene appear larger or smaller.
static SoNode	exampleDicomAnnotation(java.lang.String filename) Returns a collection of DicomInfo annotation nodes for Open Inventor medical examples.
static <NodeClass extends SoNode> NodeClass	find(SoNode root, java.lang.Class<NodeClass> nodeClass) Convenience function to find first specified node in the scene graph.
static <NodeClass extends SoNode> NodeClass	find(SoNode root, java.lang.Class<NodeClass> nodeClass, java.lang.String nodeName) Convenience function to find first specified node in the scene graph.
static SbBox3f	getBoundingBox(SoNode node) Convenience function to retrieve the bounding box of the specified node.
static SoNode	getExampleLogoNode() Returns the example logo node
static boolean	orientView(MedicalHelper.Axis axis, SoCamera camera, SoVolumeData volume) Equivalent to orientView(axis, camera, volume, 1.01f)
static boolean	orientView(MedicalHelper.Axis axis, SoCamera camera, SoVolumeData volume, float slack) Adjusts the camera to view a slice or volume along the specified axis.
static SoSeparator	readFile(java.lang.String filename) Convenience function to read a .iv file and return pointer to the root of the created scene graph.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

EXAMPLE_LOGO

public static final java.lang.String EXAMPLE_LOGO

See Also:

Constant Field Values

WINDOW_HEIGHT

public static final short WINDOW_HEIGHT

See Also:

Constant Field Values

WINDOW_WIDTH

public static final short WINDOW_WIDTH

See Also:

Constant Field Values

Constructor Detail

MedicalHelper

public MedicalHelper()

Method Detail

exampleDicomAnnotation

public static SoNode exampleDicomAnnotation(java.lang.String filename)

Returns a collection of DicomInfo annotation nodes for Open Inventor medical examples. This method is not important for customer applications, but the technique can be useful for adding annotation text to an application window.

Parameters:

filename - Path to a DICOM file from which info will be extracted

Returns:

Root of the annotation scene graph.

dollyZoom

public static void dollyZoom(float value,
                             SoCameraInteractor cameraInteractor)

Make the scene appear larger or smaller.

Provided as a convenience to simplify application code. Values greater than 1 make the scene appear larger. Values less than 1 make the scene appear smaller. For example a of 2 will make the scene approximately 2 times larger in the rendering window. The specific effect on the camera is a 'dolly' or a 'zoom' depending on the type of camera.

This is often useful after calling viewAll(). That method sets the camera parameters based on a bounding sphere around the scene which often leaves the scene not "filling" the viewport.

Details:

• SoPerspectiveCamera:
  changes the camera 'position' field. For example, values greater than 1 move the camera closer to the focal point (divide the camera's distance from the focal point by the given value), which makes the scene appear larger. This is a 'dolly'.
• SoOrthographicCamera:
  changes the camera 'height' field. For example, values greater than 1 decrease the view volume height (scale the height by the inverse of the given value), which makes the scene appear larger. This is a 'zoom' operation.
• No effect if value is <= 0 or camera is null.

Note that the value expected by SoCameraInteractor.dolly is the inverse, which is less intuitive.

Parameters:

value - The dolly value (ignored if zero).

cameraInteractor - The interactor used to modify the camera (ignored if null).

getExampleLogoNode

public static SoNode getExampleLogoNode()
                                 throws java.io.FileNotFoundException

Returns the example logo node

Returns:

Example logo node

Throws:

java.io.FileNotFoundException - If the example logo resource is not found

dicomAdjustDataRange

public static boolean dicomAdjustDataRange(SoDataRange rangeNode,
                                           SoVolumeData volume)

Adjust data range based on values in the DICOM file, i.e. the window center (0028,1050) and window width (0028,1051) values. If there are multiple slices, values are taken from the first slice. Volume is needed to get DICOM attributes, but is not modified.

Returns:

true if successful. Assigns default values if necessary.

dicomGetWindowCenterWidth

public static boolean dicomGetWindowCenterWidth(SoVolumeData volume,
                                                SbVec2f winCW)

Get the window center (level) and width values from a DICOM volume. If the query fails, returns false and sets 'winCW' to 0,0.

Uses the Window Center (0028,1050) and Window Width (0028,1051) tags from the first image in the stack. If these tags do not exist in the volume, then window center and width are computed from the actual data min and max values. (Note that querying the actual min and max values may take some time because every voxel must be loaded.) This method may be called with a non-DICOM volume. In that case the actual min and max data values are used.

Returns:

false if the query fails

buildSliceOrientationMarkers

public static SoSeparator buildSliceOrientationMarkers(SoOrthoSlice orthoSlice)

Build a scene graph to display slice orientation markers. This is just a convenience method and helps keep the demo/example programs consistent. Applications can use SliceOrientationMarkers directly.

buildSliceScaleBars

public static SoSeparator buildSliceScaleBars(SoCamera camera)

Build a scene graph to display dynamic scale bars for slice viewing.

This is just a convenience method and helps keep the demo/example programs consistent. Applications can use SliceScaleBar directly.

Note that a typical length, 10 cm, is assumed.

buildSliceAnnotation

public static SoSeparator buildSliceAnnotation(SoCamera camera,
                                               SoOrthoSlice sliceNode,
                                               java.lang.String filename)

Slice viewer annotations. This is just a convenience method and helps keep the demo/example programs consistent. Applications can use SliceScaleBar (etc) directly.

dicomAdjustVolume

public static boolean dicomAdjustVolume(SoVolumeData volume,
                                        boolean useImagePosition)

Optimize volume data node for DICOM volumes.

The volume properties are modified (but not the data values). Do not call this method before setting the volume data node's fileName field or calling setReader.

• First, adjusts the LDM tile size to optimize data loading. Note this adjustment is valid for any data format that is not already tiled, i.e. most formats except .lda and .ldm.
• Second, adjusts the volume extent in 3D to be the actual physical extent of the data set measured from outside edge to outside edge of the voxels. This is a DICOM specific adjustment.
• Third, if 'useImagePosition' is true, adjusts the volume extent so the center of the first voxel is positioned at the coordinates specified in the data set's "Image position" (0020,0032) attribute. By default the DICOM volume reader sets the volume extent so the center of the volume is positioned at 0,0,0 in 3D space. This is a DICOM specific adjustment.

Returns:

true if successful

dicomAdjustVolume

public static boolean dicomAdjustVolume(SoVolumeData volume,
                                        SoMatrixTransform imgToPatient)

Similar to dicomAdjustVolume( SoVolumeData, boolean ) above but returns an SoMatrixTransform that can be used to properly locate VolumeData in patient space in case of non axis aligned acquisition:

 ...
 SoMatrixTransform matrixTransform = new SoMatrixTransfrom();
 dicomAdjustVolume(volumeData, matrixTransfrom)
 root.addChild(matrixTransform);
 root.addChild(volumeData);
 ...
 

The computed matrix embeds the image position and image orientation as described here: https://dicom.innolitics.com/ciods/ct-image/image-plane/00200037 Scaling part is embedded in VolumeData extent.

If SoVolumeData is not a DICOM volume, imgToPatient will be set to identity.

Returns:

true if successful

dicomGetImagePosition

public static SbVec3f dicomGetImagePosition(SoVolumeData volume)

Get the "Image Position (Patient)" attribute (0020,0032) from a DICOM volume.

DICOM calls this the upper left hand corner of the image, but more precisely it's the center of the first voxel, in millimeters (mm). For VolumeViz the upper left hand corner of the image is literally the corner of the voxel, one-half voxel different from Image Position.

Note the SoVRDicomData getPosition() method does not return the value of the Image Position attribute. It returns a value computed from Image Position. If there are multiple slices, value is taken from the first slice.

Returns:

0,0,0 if not successful.

createBoundingBox

public static SoSeparator createBoundingBox(SbBox3f bbox,
                                            SbColor color)

Convenience function to draw a specified bounding box as a wireframe

getBoundingBox

public static SbBox3f getBoundingBox(SoNode node)

Convenience function to retrieve the bounding box of the specified node. If node contains SoVolumeData, use SoVolumeData extent.

createCube

public static SoSeparator createCube(SbBox3f bbox)

Convenience function to retrieve the cube corresponding to the specified bounding box.

orientView

public static boolean orientView(MedicalHelper.Axis axis,
                                 SoCamera camera,
                                 SoVolumeData volume)

Equivalent to orientView(axis, camera, volume, 1.01f)

orientView

public static boolean orientView(MedicalHelper.Axis axis,
                                 SoCamera camera,
                                 SoVolumeData volume,
                                 float slack)

Adjusts the camera to view a slice or volume along the specified axis.

The camera is rotated to give the conventional orientation for the specified axis. If the volume data is specified, then viewAll() is called to center the volume in the view volume.

If the camera is an SoOrthographicCamera (the usual case for viewing a slice) and the volume data node is specified, then the camera (specifically the view volume height) is adjusted to make the slice image fill the viewport. This is convenient because the viewAll() method gives a very loose fit around the slice image.

If the camera is an SoPerspectiveCamera (commonly used for viewing a 3D volume) or the volume data node is specified, then viewAll() is called, but no additional adjustment is done to the camera. 'slack' is ignored in this case.

Axial -> "Feet" view. Coronal -> "Anterior" view. Sagittal -> "Left" view.

Parameters:

axis - Axial, Coronal or Sagittal

camera - The camera node that will be modified (fails if null).

volume - The data volume that is being viewed (used to compute view volume, not modified)

slack - Values greater than 1 will leave additional space between image and window edge.

Returns:

true if the operation succeeded.

find

public static <NodeClass extends SoNode> NodeClass find(SoNode root,
                                                        java.lang.Class<NodeClass> nodeClass,
                                                        java.lang.String nodeName)

Convenience function to find first specified node in the scene graph.

Parameters:

root - root of scene graph you want to search

nodeClass - class of the node you want to find

nodeName - Name of the node you want to find

Returns:

The found node or null if nothing found

find

public static <NodeClass extends SoNode> NodeClass find(SoNode root,
                                                        java.lang.Class<NodeClass> nodeClass)

Convenience function to find first specified node in the scene graph.

Parameters:

root - root of scene graph you want to search

nodeClass - class of the node you want to find

Returns:

The found node or null if nothing found

readFile

public static SoSeparator readFile(java.lang.String filename)

Convenience function to read a .iv file and return pointer to the root of the created scene graph.

Parameters:

filename - of file containing a scene graph.

Returns:

Root of the read scene graph or null if the file cannot be read.