Package gov.nih.mipav.model.algorithms

Class Confmap

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.Confmap

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener

public class Confmap
extends AlgorithmBase

MIT License Copyright (c) 2022 Ruslan Guseinov Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Implementation of conformal mapping methods CETM and BFF. Based on papers [Conformal Equivalence of Triangle Meshes](https://dl.acm.org/doi/10.1145/1360612.1360676), B. Springborn, P. Schröder, U. Pinkall, *ACM Transactions on Graphics* (2008) and [Boundary First Flattening](https://dl.acm.org/doi/10.1145/3132705), R. Sawhney, K. Crane, *ACM Transactions on Graphics* (2018). ## Usage example Read an OBJ file from data folder, generate a minimum distortion conformal map using BFF method, and output the original mesh with the UV conformal map as a new OBJ file. vertices, faces = read_obj('../data/bumpcap.obj') cm = BFF(vertices, faces) image = cm.layout() write_obj('bumpcap_with_uv.obj', cm.vertices, cm.faces, image.vertices, image.faces)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	Confmap.BFF
(package private) class	Confmap.CETM
(package private) class	Confmap.confMap
private class	Confmap.indexValComparator
private class	Confmap.indexValItem
private class	Confmap.indexValueComparator
private class	Confmap.indexValueItem
(package private) class	Confmap.NewtonSolver
(package private) class	Confmap.Pair<T,U>
(package private) class	Confmap.ParametricCircle
(package private) class	Confmap.ParametricCurve
(package private) class	Confmap.TriangleMesh

Nested classes/interfaces inherited from class java.lang.Thread

java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
(package private) double[]	_clausen1
(package private) double[]	_clausen2
(package private) double[][]	_MX

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor	Description
Confmap()	Confmap - default constructor.

Method Summary

Modifier and Type	Method	Description
(package private) double[]	chebyshev(double[] x, double[] coeff)
(package private) double[]	clausen(double[] x)
(package private) double[]	compute_exterior_angles_2d(double[][] points, boolean ccw)
int[][]	compute_mesh_edges(int[][] face_edges, java.util.Vector<int[]> boundary_loops, int[][] faces, boolean only_manifold)
(package private) void	conformal_equivalence(double[] u, double[] u_err, double[][] points, int[][] faces, double[][][] image_points)
int[][]	cut_faces(int[][] original_faces, java.util.Vector<java.lang.Integer> start_vertices, java.util.HashMap<java.lang.Integer,java.util.HashSet<java.lang.Integer>> cut_tree)
void	demo_tools(java.lang.String file_name, java.lang.String method, java.lang.String output)
void	face_face_adjacency(int[][] face_face, int[][] face_face_ind, int[][] faces)
void	finalize()	finalize -
int[]	get_vertex_faces(int[][] ff, int[][] ffi, int[] vf, int[] vfi, int vertex_id)
(package private) double[][]	inverse3by3(double[][] A)
(package private) boolean	isclose(double a, double b, double rtol, double atol, boolean equal_nan)
(package private) double[]	lobachevsky(double[] x)
void	main_demo()
Confmap.BFF	make_BFF_confmap(java.lang.String file_name, java.lang.String mode)
Confmap.CETM	make_CETM_confmap(java.lang.String file_name, java.lang.String mode)
(package private) double	median(double[] nums)
(package private) double[][]	mobius_normalize_layout(double[][] uvoriginal, double eps, int max_iter)
(package private) double[]	quantize_value(double[] value, double quant)
(package private) double	quantize_value(double value, double quant)
double[]	quasi_conformal_error_map(double[][][] source_points, double[][][] image_points)
void	read_obj(java.util.Vector<double[]> vertices, java.util.Vector<int[]> faces, java.lang.String file_path)
(package private) double[]	remainder(double[] x, double val)
(package private) double	remainder(double x, double val)
void	runAlgorithm()	Starts the program.
void	simple_demo()
void	test_boundary_loops()
void	test_clausen()
void	test_face_face_adjacency()
void	test_quantize_value()
void	test_read_write_obj()
void	test_tri_angles()
double[][]	tri_angles(double[][] lengths, boolean ineq_violation)
void	write_obj(java.lang.String file_path, double[][] vertices, int[][] faces, double[][] uvs, int[][] uv_faces)
void	write_obj(java.util.Vector<double[]> vertices, java.util.Vector<int[]> faces, java.lang.String file_path)

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread

activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

Methods inherited from class java.lang.Object

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

Field Detail

_clausen1

double[] _clausen1

_clausen2

double[] _clausen2

_MX

double[][] _MX

Constructor Detail

Confmap

public Confmap()

Confmap - default constructor.

Method Detail

finalize

public void finalize()

finalize -

Overrides:

finalize in class AlgorithmBase

runAlgorithm

public void runAlgorithm()

Starts the program.

Specified by:

runAlgorithm in class AlgorithmBase

test_quantize_value

public void test_quantize_value()

test_clausen

public void test_clausen()

test_tri_angles

public void test_tri_angles()

test_read_write_obj

public void test_read_write_obj()

test_boundary_loops

public void test_boundary_loops()

test_face_face_adjacency

public void test_face_face_adjacency()

quantize_value

double[] quantize_value(double[] value,
                        double quant)

quantize_value

double quantize_value(double value,
                      double quant)

isclose

boolean isclose(double a,
                double b,
                double rtol,
                double atol,
                boolean equal_nan)

chebyshev

double[] chebyshev(double[] x,
                   double[] coeff)

remainder

double[] remainder(double[] x,
                   double val)

remainder

double remainder(double x,
                 double val)

clausen

double[] clausen(double[] x)

lobachevsky

double[] lobachevsky(double[] x)

tri_angles

public double[][] tri_angles(double[][] lengths,
                             boolean ineq_violation)

compute_exterior_angles_2d

double[] compute_exterior_angles_2d(double[][] points,
                                    boolean ccw)

mobius_normalize_layout

double[][] mobius_normalize_layout(double[][] uvoriginal,
                                   double eps,
                                   int max_iter)

inverse3by3

double[][] inverse3by3(double[][] A)

median

double median(double[] nums)

quasi_conformal_error_map

public double[] quasi_conformal_error_map(double[][][] source_points,
                                          double[][][] image_points)

conformal_equivalence

void conformal_equivalence(double[] u,
                           double[] u_err,
                           double[][] points,
                           int[][] faces,
                           double[][][] image_points)

read_obj

public void read_obj(java.util.Vector<double[]> vertices,
                     java.util.Vector<int[]> faces,
                     java.lang.String file_path)

write_obj

public void write_obj(java.util.Vector<double[]> vertices,
                      java.util.Vector<int[]> faces,
                      java.lang.String file_path)

write_obj

public void write_obj(java.lang.String file_path,
                      double[][] vertices,
                      int[][] faces,
                      double[][] uvs,
                      int[][] uv_faces)

compute_mesh_edges

public int[][] compute_mesh_edges(int[][] face_edges,
                                  java.util.Vector<int[]> boundary_loops,
                                  int[][] faces,
                                  boolean only_manifold)

face_face_adjacency

public void face_face_adjacency(int[][] face_face,
                                int[][] face_face_ind,
                                int[][] faces)

get_vertex_faces

public int[] get_vertex_faces(int[][] ff,
                              int[][] ffi,
                              int[] vf,
                              int[] vfi,
                              int vertex_id)

cut_faces

public int[][] cut_faces(int[][] original_faces,
                         java.util.Vector<java.lang.Integer> start_vertices,
                         java.util.HashMap<java.lang.Integer,java.util.HashSet<java.lang.Integer>> cut_tree)

simple_demo

public void simple_demo()

main_demo

public void main_demo()

demo_tools

public void demo_tools(java.lang.String file_name,
                       java.lang.String method,
                       java.lang.String output)

make_BFF_confmap

public Confmap.BFF make_BFF_confmap(java.lang.String file_name,
                                    java.lang.String mode)

make_CETM_confmap

public Confmap.CETM make_CETM_confmap(java.lang.String file_name,
                                      java.lang.String mode)