Package gov.nih.mipav.view.renderer.WildMagic.AAM

Class CAAMPropsReader

  • public class CAAMPropsReader
extends CAAMObject
    This is the Java modified version of C++ active appearance model API (AAM_API). It is modified with a subset of required functions for automatic MRI prostate segmentation. AAM-API LICENSE - file: license.txt This software is freely available for non-commercial use such as research and education. Please see the full disclaimer below. All publications describing work using this software should cite the reference given below. Copyright (c) 2000-2003 Mikkel B. Stegmann, mbs@imm.dtu.dk IMM, Informatics & Mathematical Modelling DTU, Technical University of Denmark Richard Petersens Plads, Building 321 DK-2800 Lyngby, Denmark http://www.imm.dtu.dk/~aam/ REFERENCES Please use the reference below, when writing articles, reports etc. where the AAM-API has been used. A draft version the article is available from the homepage. I will be happy to receive pre- or reprints of such articles. /Mikkel ------------- M. B. Stegmann, B. K. Ersboll, R. Larsen, "FAME -- A Flexible Appearance Modelling Environment", IEEE Transactions on Medical Imaging, IEEE, 2003 (to appear) ------------- 3RD PART SOFTWARE The software is partly based on the following libraries: - The Microsoft(tm) Vision Software Developers Kit, VisSDK - LAPACK DISCLAIMER This software is provided 'as-is', without any express or implied warranty. In no event will the author be held liable for any damages arising from the use of this software. Permission is granted to anyone to use this software for any non-commercial purpose, and to alter it, subject to the following restrictions: 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. -- No guarantees of performance accompany this software, nor is any responsibility assumed on the part of the author or IMM. This software is provided by Mikkel B. Stegmann and IMM ``as is'' and any express or implied warranties, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose are disclaimed. In no event shall IMM or Mikkel B. Stegmann be liable for any direct, indirect, incidental, special, exemplary, or consequential damages (including, but not limited to, procurement of substitute goods or services; loss of use, data, or profits; or business interruption) however caused and on any theory of liability, whether in contract, strict liability, or tort (including negligence or otherwise) arising in any way out of the use of this software, even if advised of the possibility of such damage. $Revision: 1.4 $ $Date: 2003/04/23 14:49:15 $ Simple lo-fi property reader. Used as naive parser/scanner for the .asf, acf files.
    Author:
    Ruida Cheng

    • Field Summary

      Fields 
      Modifier and Type Field Description
      char COMMENT_CHAR  
      char CR  
      java.util.Scanner in
      Java Scanner API.
      char LF  
      private java.lang.String previousLine  
      java.io.FileReader reader
      File reader

    • Constructor Summary

      Constructors 
      Constructor Description
      CAAMPropsReader​(java.lang.String filename)
      Constructor.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void CalcShapeDistances​(CAAMShape optimized, CAAMShape groundTruth, double[] ptpt, double[] ptcrv, CDVector pvDists)
      Calculates optimization results.
      void dispose()
      dispose memory
      void ExpandImg2DyadicSize​(ModelSimpleImage img, ModelSimpleImage out)
      Expands an image to have dynamic size.
      java.lang.String FindVacantFilename​(java.lang.String filename_suggestion)
      Finds a file name that is not 'occupied'.
      boolean IsValid()
      Returns true if the file is valid.
      void MirrorEdge​(ModelSimpleImage img, ModelSimpleImage mask, int edgeWidth)
      Mirrors the edge of an arbitrary shape mask in an image using poor-mans mirroring.
      void MirrorEdge​(CDMatrix m, ModelSimpleImage mask, int edgeWidth)
      Mirrors the edge of an arbitrary shape mask in a matrix using poor-mans mirroring.
      void processCoordinatePoints​(int[] path_id, int[] type, float[] x_rel, float[] y_rel, int[] point_nb, int[] from, int[] to)
      Process point info from the in stream line
      void processImageName​(java.lang.String[] fileName)
      Process image file.
      void RegistrationMovie​(java.lang.String filename, java.lang.String asfPath, boolean useConvexHull, boolean writeRefShape)
      Writes a movie file containing all shapes from a directory warped to their mean shape.
      void SampleTextures​(CAAMShapeCollection unalignedShapes, java.util.Vector<CDVector> vTextures, CAAMReferenceFrame outputRF, int imageReduction, boolean removeMean, boolean useTSP, boolean useConvexHull)
      Samples a set of texture vectors given a set of shape in absolute (i.e. image) coordinates.
      java.lang.String Secs2Mins​(double secs)
      Converts seconds to a MM:SS string.
      boolean ShapeInsideImage​(CAAMShape s, ModelSimpleImage img)
      Tests if a shape is fully inside an image.
      double ShapeOverlap​(CAAMShape model, CAAMShape gt)
      Calculates the overlap between two shapes as specified in "Active Shape Model Segmentation With Optimal Features" Bram van Ginneken et al., IEEE TMI 21(8) Aug. 2002.
      void SkipLines()
      Skip comment line or empty line
      int Sync()
      Sync to read number.

      • Methods inherited from class java.lang.Object

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

    • Field Detail

      • reader

        public java.io.FileReader reader
        File reader

      • in

        public java.util.Scanner in
        Java Scanner API.

      • CR

        public final char CR

      • LF

        public final char LF

      • COMMENT_CHAR

        public final char COMMENT_CHAR

      • previousLine

        private java.lang.String previousLine

    • Constructor Detail

      • CAAMPropsReader

        public CAAMPropsReader​(java.lang.String filename)
        Constructor. Opens the file.
        Parameters:
        filename - The file to open.

    • Method Detail

      • processCoordinatePoints

        public void processCoordinatePoints​(int[] path_id,
                                    int[] type,
                                    float[] x_rel,
                                    float[] y_rel,
                                    int[] point_nb,
                                    int[] from,
                                    int[] to)
        Process point info from the in stream line
        Parameters:
        path_id - path id
        type - point type
        x_rel - x coordinate
        y_rel - y coordinate
        point_nb - point number
        from - from index
        to - to index

      • processImageName

        public void processImageName​(java.lang.String[] fileName)
        Process image file.
        Parameters:
        fileName - image file name

      • Sync

        public int Sync()
        Sync to read number.
        Returns:
        -1 fail, otherwise, return int number.

      • SkipLines

        public void SkipLines()
        Skip comment line or empty line

      • IsValid

        public boolean IsValid()
        Returns true if the file is valid.
        Returns:
        if in stream is valid

      • dispose

        public void dispose()
        dispose memory

      • ExpandImg2DyadicSize

        public void ExpandImg2DyadicSize​(ModelSimpleImage img,
                                 ModelSimpleImage out)
        Expands an image to have dynamic size.
        Parameters:
        img - Input image.
        out - Output dyadic image.

      • MirrorEdge

        public void MirrorEdge​(CDMatrix m,
                       ModelSimpleImage mask,
                       int edgeWidth)
        Mirrors the edge of an arbitrary shape mask in a matrix using poor-mans mirroring.
        Parameters:
        img - Input matrix. Overwritten by mirrored version.
        mask - Image mask defining the shape.
        edgeWidth - The width of the edge.

      • MirrorEdge

        public void MirrorEdge​(ModelSimpleImage img,
                       ModelSimpleImage mask,
                       int edgeWidth)
        Mirrors the edge of an arbitrary shape mask in an image using poor-mans mirroring.
        Parameters:
        img - Input image. Overwritten by mirrored version.
        mask - Image mask defining the shape.
        edgeWidth - The width of the edge.

      • ShapeInsideImage

        public boolean ShapeInsideImage​(CAAMShape s,
                                ModelSimpleImage img)
        Tests if a shape is fully inside an image.
        Parameters:
        s - Input shape.
        img - Input image.
        Returns:
        True if the shape is fully inside the image.

      • CalcShapeDistances

        public void CalcShapeDistances​(CAAMShape optimized,
                               CAAMShape groundTruth,
                               double[] ptpt,
                               double[] ptcrv,
                               CDVector pvDists)
        Calculates optimization results.
        Parameters:
        optimized - Model shape.
        groundTruth - Ground truth shape.
        ptpt - Average point to point landmark error.
        ptcrv - Average point to curve landmark error. NOTICE: This is not a symmetric measure!

      • Secs2Mins

        public java.lang.String Secs2Mins​(double secs)
        Converts seconds to a MM:SS string.
        Parameters:
        secs - Time in seconds.
        Returns:
        The time in MM:SS.

      • FindVacantFilename

        public java.lang.String FindVacantFilename​(java.lang.String filename_suggestion)
        Finds a file name that is not 'occupied'. This method finds a file name that is not 'occupied' by adding at number to the base part of the suggested file name.
        Parameters:
        filename_suggestion - Suggestion including extension.
        Returns:
        An unused filename resembling the suggstion.

      • SampleTextures

        public void SampleTextures​(CAAMShapeCollection unalignedShapes,
                           java.util.Vector<CDVector> vTextures,
                           CAAMReferenceFrame outputRF,
                           int imageReduction,
                           boolean removeMean,
                           boolean useTSP,
                           boolean useConvexHull)
        Samples a set of texture vectors given a set of shape in absolute (i.e. image) coordinates.
        Parameters:
        unalignedShapes - Shapes in absolute coordinates.
        vTextures - The set of textures.
        outputRF - The output reference frame generated for sampling the textures.
        removeMean - If true the mean from each texture vector (i.e. the DC) is removed.
        useTSP - Use tangent space projection to align the shapes.
        useConvexHull - If true the convex hull is used to determine the extent of a shape.

      • RegistrationMovie

        public void RegistrationMovie​(java.lang.String filename,
                              java.lang.String asfPath,
                              boolean useConvexHull,
                              boolean writeRefShape)
        Writes a movie file containing all shapes from a directory warped to their mean shape.
        Parameters:
        filename - Output movie filename.
        asfPath - Path to annotation files.
        useConvexHull - If true the convex hull is used to determine the extent of a shape.
        writeRefShape - If true the reference shape corresponding to the movie file is written as "regshape.asf".

      • ShapeOverlap

        public double ShapeOverlap​(CAAMShape model,
                           CAAMShape gt)
        Calculates the overlap between two shapes as specified in "Active Shape Model Segmentation With Optimal Features" Bram van Ginneken et al., IEEE TMI 21(8) Aug. 2002. Notice that this only makes sense for one-path closed shapes.
        Parameters:
        model - Model shape
        gt - Ground truth shape
        Returns:
        The shape overlap (1 = perfect match, 0 = no overlap).