Package com.openinventor.ldm.nodes

Class SoDataSet

  • All Implemented Interfaces:
    SafeDisposable
    Direct Known Subclasses:
    SoVolumeData
    public class SoDataSet
extends SoNode
    Data set node. This class specifies a data set and its properties, and also provides utilities for extracting a subset of the data set and for resampling the data set. The data can be read directly from a file or can be accessed via a user-defined volume reader. This class is the parent class of the VolumeViz data nodes: SoVolumeData, SoHeightFieldGeometry, SoHeightFieldProperty, etc. Those nodes provide the data for VolumeViz rendering nodes: SoVolumeRender, SoOrthoSlice, SoObliqueSlice, etc. See SoVolumeData for more details about loading and managing volume data.

    The data set can be specified by:

    • Setting the fileName field
      This implies that the data set is stored on disk, in one of the file formats for which LDM has a built-in reader. LDM will automatically select a reader based on the file extension, for example ".am" for the AmiraMesh file format.
    • Calling the setReader() method
      This is the most general method because an application can specify one of the standard LDM readers or implement a customized subclass of SoVolumeReader. LDM will get the data set properties (dimensions, size, data type, etc) and access the data through the specified reader object. This allows the application to completely control how, and from where, the data is loaded.

    SoDataSetId, SoDataCompositor, SoVolumeData, SoMeshGeometry, SoMeshProperty

    • Field Detail

      • dataSetId

        public final SoSFInt32 dataSetId
        When using multiple SoDataSet nodes, the dataSetId field uniquely identifies each data set used in the compositing. It also specifies the OpenGL texture unit in which the textures for this data set will be stored when doing render compositing. It is 1 by default (texture unit 0 is reserved for the color lookup table by default). The number of available texture units depends on your hardware. You can query this number using getMaxNumDataSets.

        Note: The SoDataSetId node can also be used to define dataSetId. If an SoDataSetId node is traversed before the SoDataSet node, the id from the SoDataSetId node is used and this field is ignored.

        Since:
        Open Inventor 6.0

      • useCompressedTexture

        public final SoSFBool useCompressedTexture
        Controls use of OpenGL lossy texture compression for RGBA data (if available). Default is true.

        A significant advantage of compressed textures is that they conserve texture memory space. At the moment, the extension works on RGBA textures only, not on paletted textures. The compression factor is about 5.

        A potential drawback of compressed textures is that lossy compression can result in values on the GPU that are slightly different from the actual value in the volume. For example "gray scale" colors could have a slight color in some cases. You should always set this option to false when using "RGBA" data to store 32-bit "id" values.

      • texturePrecision

        public final SoSFUShort texturePrecision
        For scalar (non-RGBA) data, specifies the size of voxel values on the GPU in bits. The valid values are: 0 (default), 8 and 16.
        When set to 0, LDM chooses the best precision based on the size of the data type (or if specified, the number of significant bits) - meaning that LDM will store 8-bit values on the GPU for 8-bit data and store 16-bit values for all other data types.

        There are several trade-offs influenced by this value, including:

        • 8 bit values use less memory on the GPU than 16-bit values, allowing more data to be stored on the GPU. 8-bit values are adequate for many visualization tasks. But...
        • If the specified (or chosen) precision is smaller than the data type, then LDM must scale down the data values before sending them to the GPU.
          • Limitation: This is currently unavoidable for 32-bit data.
          • Down scaling adds some time whenever a tile of data must be sent to the GPU.
          • In particular, all tiles currently stored on the GPU must be rescaled if the application changes the data range (SoDataRange node).
            Note: As a result, changing the data range may be slow for large volumes.
          • Down scaling also means "aliasing" data values, i.e. multiple data values may scale to the same value on the GPU.

        Since:
        Open Inventor 6.0

    • extent

      public final SoSFBox3f extent
      The real size (extent) of the volume in modeling coordinates. Default is -1,-1,-1 to 1,1,1.

      Note this can be used to define a volume with non-uniform voxel spacing. For example, if the volume dimensions (voxels) are 64x64x64, but the voxel spacing in Z is twice the X and Y spacing, then you might specify the volume size as -1 to 1 for X and Y but -2 to 2 for Z.

    • dataTransform

      public final SoSFLDMDataTransform dataTransform
      If set to an appropriate SoLDMDataTransform object, the object's transformFunction method is called after each tile is loaded, but before it is stored in main memory. This allows you to modify the original data (for example, scaling or filtering) before it is displayed. Default is no transform.

      Note: Before Open Inventor 8.0, the data transformFunction was set using the setLDMDataModifier method. That method is now deprecated.

      Since:
      Open Inventor 8.0

    • allocateResourceOnRender

      public final SoSFBool allocateResourceOnRender
      Indicates if resource allocation is done only on first render traversal or as soon as the node is created. Default is true. It must be set to false if the dataset is not inserted in a scene graph but will be used for data access for example. Otherwise, memory resources will still remain on default value.

    • undefinedValue

      public final SoSFDouble undefinedValue
      Data with this value won't be rendered.
      Default is NaN (Not a Number) which means that this value is not taken into account. Otherwise, value must be in agreement with data type. Limitations: There are several limitations in order for the undefined value to work :
      • The texturePrecision must be at least equal to the number of significant bits of the data type.
      • The data type must be BYTE, SHORT (either SIGNED or UNSIGNED) or FLOAT
      • The field is ignored in the following classes : SoHeightFieldProperty, SoHeightFieldPropertyMask and SoVolumeMask. Setting this field has no effect in these cases.
      • In the case of multiple SoVolumeData,the undefinedValue must be the same in all SoVolumeData. If different values are provided, only the latest one on the state will be considered for the rendering.

      Since:
      Open Inventor 10.11

  • Method Detail

    • setLDMDataModifier

      @Deprecated(since="9.9")
public void setLDMDataModifier​(SoDataSet.LDMDataModifier transformer)
      Deprecated.
      As of Open Inventor 9.9, should use dataTransform field instead.
      This method allows you to modify the original data (for example, attribute calculation) before it's displayed. The modifyData method of the given LDMDataModifier is called after each tile is loaded.
      Since:
      6.0

    • setReader

      public void setReader​(SoVolumeReader reader)
      Calls setReader(reader, false).

    • isDataInMemory

      public boolean isDataInMemory​(SoLDMTileID tileID)
      Indicates whether the data attached to a tile is in main memory. Called when the node front manager evaluates the texture front.

      This allows to manage data that implements SoBufferAsyncInterface. If the specified tile does not implement SoBufferAsyncInterface then this method always returns true. So effectively it always returns true for non-LDM volumes.

    • dataSize

      public static int dataSize​(SoDataSet.DataTypes dataType)
      Returns the number of bytes per voxel of the specified data type.

    • isInMemory

      public boolean isInMemory​(SoLDMTileID tileID)
      Indicates whether a tile is in main memory. Called when the node front manager evaluates the texture front.

    • isDataSigned

      public static boolean isDataSigned​(SoDataSet.DataTypes dataType)
      Returns true if the given data type is a signed integer data type.

    • voxelToXYZ

      public SbVec3f voxelToXYZ​(SbVec3f dataPosition)
      Converts the specified point in voxel coordinates (I,J,K) to geometric coordinates (X,Y,Z). The geometric coordinates are expressed in "extent" space, where voxel coordinates are mapped to the box defined by the volume extent.

      The left bottom coordinate of the voxel is returned. Correctly converts coordinates that are outside the volume dimensions, but the resulting geometric coordinate is outside the volume extent.

      See Also:
      voxelToXYZ(const SbBox3f) const, XYZToVoxel(const SbVec3f) const, XYZToVoxel(const SbBox3f) const

    • getLDMReader

      public SoLDMReader getLDMReader()
      Returns a pointer to the current data set reader object.
      The actual type will be a subclass of SoVolumeReader, either one of the predefined subclasses or an application-defined subclass. Returns NULL if no reader is currently being used (for example if setVolumeData() was called).

    • getLDMTopoOctree

      public SoLDMTopoOctree getLDMTopoOctree()
      Returns the LDMTopoOctree used by this SoDataSet. The LDMTopoOctree is initialized at the initialization of the reader.

    • getOverlapping

      @Deprecated(since="9.0.0.0")
public int getOverlapping()
      Deprecated.
      As of Open Inventor 9.0.0.0. No longer used.
      Returns the tile border (overlap) in voxels. Since OIV 9.0 always returns 0.

      Warning Deprecated since Open Inventor 9000. No longer used.

    • resetReader

      public void resetReader()
      Resets previously set custom reader setup by setReader call.

    • XYZToVoxel

      public SbVec3f XYZToVoxel​(SbVec3f dataPosition)
      Converts the specified point in geometric coordinates (X,Y,Z) to voxel coordinates (I,J,K). The geometric coordinates are expressed in "extent" space, where voxel coordinates are mapped to the box defined by the volume extent.

      Correctly converts coordinates that are outside the volume extent, but the resulting voxel coordinate is outside the volume dimensions.

      See Also:
      voxelToXYZ(const SbVec3f) const, voxelToXYZ(const SbBox3f) const, XYZToVoxel(const SbBox3f) const

    • getDatumSize

      public int getDatumSize()
      Returns the number of bytes per voxel.

    • getDimension

      public SbVec3i32 getDimension()
      Returns the data set dimension.

    • getTileDimension

      public SbVec3i32 getTileDimension()
      Returns the tile dimension.

    • getMaxNumDataSets

      public static int getMaxNumDataSets()
      Returns the maximum number of data sets that can be render composited on the current hardware (essentially the number of texture units - 1).

    • isDataFloat

      public static boolean isDataFloat​(SoDataSet.DataTypes dataType)
      Returns true if the given data type is a float data type.

    • readTile

      public void readTile​(SoLDMTileID tileID,
                     SoBufferObject buffer,
                     boolean transform)
      Copies the specified tile into the provided buffer.
      Applies the data transformation (set in dataTransform field) if transform is true.

    • getDataSize

      public int getDataSize()
      Returns the number of bytes per voxel in VolumeViz.

    • getReader

      public SoVolumeReader getReader()
      Returns the current data set reader object.
      The actual type will be a subclass of SoVolumeReader, either one of the predefined subclasses or an application-defined subclass. Returns null if no reader is currently set. Applications should always verify the class type before using the returned object as a specific sub-class of SoVolumeReader.

    • setLDMReader

      public void setLDMReader​(SoLDMReader reader)
      Sets the LDM volume reader object to use.
      This method allows the data to be read directly from the disk using the specified subclass of SoVolumeReader.

    • getDoubleMinMax

      public double[] getDoubleMinMax()
      Returns min and max values of the data set.
      Returns nullif the requested data is not available (for example, if no data set exists).

      NOTE: This method might force LDM to load the entire data set if the volume reader does not respond to the getMinMax query. Normally for an LDM format data set, the min and max values are stored in the LDM header. For a non-LDM data set, if a filename and/or reader have been specified and the data set has not yet been loaded, LDM will load the entire data set to compute the min and max values. For a large data set this may take a long time.

    • numSigBits

      public int numSigBits()
      Returns the number of significant bits.

    • getMinMax

      public long[] getMinMax()
      Returns min and max values of the data set data.
      Returns nullif the requested data is not available (for example, if no data set exists).

      NOTE: This method might force LDM to load the entire data set if the volume reader does not respond to the getMinMax query. Normally for an LDM format data set, the min and max values are stored in the LDM header. For a non-LDM data set, if a filename and/or reader have been specified and the data set has not yet been loaded, LDM will load the entire data set to compute the min and max values. For a large data set this may take a long time.

    • setReader

      public void setReader​(SoVolumeReader reader,
                      boolean takeOwnership)
      This method allows the data to be read directly from the disk using the specified subclass of SoVolumeReader. If the takeOwnership parameter is false (default), LDM will not delete the specified instance. Otherwise, LDM will automatically delete the specified instance, for example, when the SoDataSet node is deleted. If filename is not set before setting the reader, LDM will display an error message just to warn that the reader has not opened any file yet. LDM continues to work as expected.

      Note: When using a custom reader, any reader method that changes the volume properties (dimension, size, data type, etc) should notify the SoVolumeData node by calling the reader's touch() method. If this notification is not done, SoDataSet fields, for example SoDataSet.extent, won't be updated correctly.

    • editSubVolume

      public int editSubVolume​(SbBox3i32 subVolume,
                         SoBufferObject userData)
      Replaces the contents of a subvolume with the given data.
      The buffer size (in bytes) must match the subvolume size (in bytes) exactly. The subvolume is specified in voxel/cell coordinates. Call startEditing() before calling this method. Returns 0 if successful.

      Warning The modification may be postponed until the tiles are really needed. Therefore the contents of the userData buffer must not be modified until after saveEditing() is called.

    • editTile

      public int editTile​(SoLDMTileID tileId,
                    double value)
      Replaces the contents of a tile with the specified value.
      Call startEditing() before calling this method. Returns 0 if successful.

    • editSubVolume

      public int editSubVolume​(SbBox3i32 subVolume,
                         double value)
      Replaces the contents of a subvolume with the specified value.
      The subvolume is specified in voxel/cell coordinates. Call startEditing() before calling this method. Returns 0 if successful.

    • editTile

      public int editTile​(SoLDMTileID tileId,
                    SoBufferObject userData)
      Replaces the contents of a tile with the given data.
      The buffer size (in bytes) must match the tile size (in bytes) exactly. Call startEditing() before calling this method. Returns 0 if successful.

      Warning The modification may be postponed until the tile is really needed. Therefore the contents of the userData buffer must not be modified until after saveEditing() is called.

    • getLdmDataAccess

      public SoLDMDataAccess getLdmDataAccess()
      Returns a reference to the SoLDMDataAccess object.
      This object can be used to query data from the volume.

    • startEditing

      public int startEditing()
      Initiate an editing transaction.
      Returns true if successful and also returns a unique transaction id. This value is required for finishing the edit transaction (see finishEditing()) and for undo/redo (see undoEditing() and redoEditing()). Multiple transactions may be active at the same time.

    • finishEditing

      public boolean finishEditing​(int transactionId)
      Terminates an editing transaction.
      Returns true if successful. May only be called with a valid transaction id returned by the startEditing() method. On error does nothing. The finish method will schedule a redraw so the correct data is displayed. To commit the edits, in other words to save the edited data back to the data source, call saveEditing().

    • redoEditing

      public boolean redoEditing​(int transactionId)
      Redo all modifications associated with the specified transaction id. Returns true if successful. On error does nothing. May only be called after the specified transaction has been terminated (see finishEditing() method) and undone (see undoEditing() method). Schedules a redraw so the correct data is displayed.

      Note: Redo is no longer available after transactions are saved. After calling saveEditing(), the transaction ids are no longer valid and the modified data is the new reference.

    • hasEditedTile

      public boolean hasEditedTile()
      Returns true if DataSet has edited tiles.

    • undoEditing

      public boolean undoEditing​(int transactionId)
      Undo all modifications associated with the specified transaction id. Returns true if successful. On error does nothing. May only be called after the specified transaction has been terminated (see finishEditing() method). Schedules a redraw so the correct data is displayed.

      Note: Undo is no longer available after transactions are saved. After calling saveEditing(), the transaction ids are no longer valid and the modified data is the new reference.

    • editSurfaceShape

      public int editSurfaceShape​(SoNode surfaceShape,
                            float thickness,
                            double value)
      Replaces all voxels intersecting the polygons or lines defined by the surfaceShape and given thickness with the specified value. surfaceShape is defined in the same 3D space as the dataSet. thickness is defined in voxels. The surfaceShape can be deleted after calling this function.

      Call startEditing() before calling this method. Returns 0 if successful.

      Warning The modification may be postponed until the tiles are really needed. Therefore the surfaceShape node (and children if any) must not be modified until after saveEditing() is called.

    • editSolidShape

      public int editSolidShape​(SoNode solidShape,
                          double value)
      Replaces all voxels intersecting the given shape with the specified value. The geometry defined under solidShape must represent a list of closed surfaces otherwise the result is unpredictable. solidShape must not contain any lines or open polyhedrons (polyhedron with shapes). The result is based on the odd-winding rule, so the result is not necessarily the union or the intersection of the closed surfaces. If you want to voxelize lines or single polygons, see also the editSurfaceShape method.

      If the goal is to define a shape which is the result of the intersection/union of multiple closed surfaces, see the SoCSGShape node.

      solidShape is defined in the same 3D space as the dataSet. The solidShape can be deleted after calling this function.

      Call startEditing() before calling this method. Returns 0 if successful.

      Warning The modification may be postponed until the tiles are really needed. Therefore the surfaceShape node (and children if any) must not be modified until after saveEditing() is called.

    • editBoxes

      public int editBoxes​(java.util.Collection<SbVec3i32> boxCenters,
                     int boxSize,
                     double newValue)
      Replace all voxels in the region defined by a list of boxes with the specified value. boxCenter and boxSize are defined in ijk (voxel) space.

      Call startEditing() before calling this method. Returns 0 if successful.