All Classes and Interfaces
Class
Description
AAM-API LICENSE - file: license.txt
This software is freely available for non-commercial use such as research and education.
This is the Java modified version of C++ active appearance model API
(AAM_API).
A base class for all non-algorithmic (not JDialog*) script actions.
A script action which changes the image's endianess
A script action which changes the image's modality
A script action which changes the name of an image.
A script action which changes the image's orientations
A script action which changes the image's origin
A script action which changes the image's resolutions.
A script action which changes the image's talairach information
A script action which changes the image's resolutions
A script action which changes the image's resolutions
A script action which clones an input image and puts it into a new image frame.
An action which closes the frame containing an image.
Forces the JVM to perform a garbage collection of un-referenced memory.
A script action which creates a new blank image with a set of characteristics.
Classes which implement this interface are able to report metainformation about themselves, return their input and
output parameters, run their action using a set of input parameters, retrieve the real name of images they output,
and return whether they have completed successfully.
A script action which causes MIPAV to exit completely.
An action which extracts the imageB from a frame and puts it into a new image frame.
A base class for script actions which perform their action using an input image.
A script action which generates a paint mask based on a mask image.
A script action which generates a VOI from a mask image.
A script action which opens all VOIs from the directory where VOIs are saved by default when a SaveAllVOIs action is executed.
An action for the mipav system data provenance that records the opening of an image
A script action which opens a VOI from disk and adds it to an image.
A script action which converts all paint within an image to some type of mask image (short, binary, ubyte).
A script action which generates a VOI based on the paint mask of an image.
A script action which saves all the VOIs in an image to disk.
A script action which writes out an image to disk.
A script action which writes out an image to disk.
A script action which writes out an image to disk.
A script action which records saves the text contained in one of the output frame's tabs.
A script action which saves all the VOI intensities in an image to disk.
An action for the mipav system data provenance that records the starting of MIPAV
An action for the mipav system data provenance that records the closing of MIPAV
A script action which converts all VOIs within an image to some type of mask image (short, binary, ubyte).
agast5 - AGAST, an adaptive and generic corner detector based on the
accelerated segment test for a 8 pixel mask
Copyright (c) 2010, Elmar Mair
All rights reserved.
Copyright (C) 2007-11, Andrea Vedaldi and Brian Fulkerson
Copyright (C) 2012-13, The VLFeat Team
All rights reserved.
This algorithm is created from the description provided in the article:
"Adaptive Kuwahara Filter" by Krzysztof Bartyzel, Published online
July 6, 2015.
Algorithm to add or remove margins around the image.
Snake-like algorithm deriviative.
algorithm to apply an adaptive histogram to an image, placing it in a new ModelImage, or returning the changed
picture to the same image.
algorithm to apply an adaptive histogram to an image, placing it in a new ModelImage, or returning the changed
picture to the same image.
This algorithm anisotropically diffuses an image.
This is a port of the files anitgradient2.m and antigradient2.c created by Gunnar Farneback in the
Spatial domain toolbox at http://www.imt.liu.se/mi/Tools.
This algorithm calculates the arc-length of a Bspline fit to user defined control points.
Reference: Digital Image Processing, Second Edition by Rafael C.
let deli(x,y) = (i(x,y) - invalid input: '<'i(x,y)>)/invalid input: '<'i(x,y)> where the angle brackets are used to denote a spatial average.
This is a port of the file AutoSeedWatershed.cpp which calls openCV written by Ravimal Bandara.
Corrects barrel and/or pin cushion distortion for 2D images.
Base abstract class for algorithms.
Bilateral filtering smooths an image or VOI region of the image while preserving edges with 2 Gaussian functions.
Attenuate around the boundary of an object defined by a VOI in an image volume.
A class for segmenting the brain from a 3D MRI.
This class provides an implementation of a second method for segmentation of the brain from a 3D MRI, as opposed to
the BET algorithm implemented in AlgorithmBrainExtractor.
BRISK - Binary Robust Invariant Scalable Keypoints
Reference implementation of
[1] Stefan Leutenegger,Margarita Chli and Roland Siegwart, BRISK:
Binary Robust Invariant Scalable Keypoints, in Proceedings of
the IEEE International Conference on Computer Vision (ICCV2011).
Smoothing of VOI using 1 iteration of bSplines.
Snake-like algorithm derivative using BSplines.
Modified code from Aaron Carass's Java implementation of
Philippe Thevenaz's Cubic B-spline Interpolation.
Active Contour class optimized for Cell Tacking, based on the following paper:
This algorithm calculates the center of mass for 2D and 3D black and white images.
* This algorithm calculates the red, green, and blue center of mass for 2D and 3D color images.
This is a convenience function to convert from one image type to another and remap the data into a new range.
This module draws uniformly randomly positioned circles with a specified radius.
References: 1.)
This software uses 2D conformal mapping in converting a circular sector defined by 4 user points at the sector corners
to a rectangle of user specified size.
Algorithm to apply Coherence Enhancing Anisotropic Diffusion
An optional registration may be performed before colocalization.
This algorithm creates a 2D histogram from 2 colors of a single image or from 2 black and white images and uses an
orthogonal line fit of the histogram data to generate a correlation line thru the histogram.
This algorithm uses a hypercomplex filter to find the edges between a region of two
user specified colors.
This algorithm changes the saturation of a color image while keeping the hue and intensity constant.
Simple algorithm that generates a complex image from real data and imaginary data.
Simple algorithm that converts an RGB image to a single greyscale image.
Assumes the pixel resolutions are equal.
Runs ELSUNC for a 3D image.
Runs Powell's method for a 3D image.
Powell's Method
This is an automatic registration method based on FLIRT.
This is an automatic registration method based on FLIRT.
Converts a 3D dataset that is really a 4D dataset into a 4D dataset.
The image is converted from a 4D to a 3D image.
Convolves kernel with a 2D or 3D image - only pixels where the kernel is completely contained in the image are
convolved, otherwise they are set to zero.
Algorithm to adjust image volume for cases when the slice spacing is not equal to the slice thickness.
CostFunction - class for specifying optimization function.
CostFunction - class for specifying optimization function.
Crops 2D and 3D images using a supplied VOI.
Algorithm to crop a tilted rectangle
This is a polynomial p of degree 3 which interpolates a given function f at the points x(-1), x(0), x(1), and x(2),
and is given by p(x) = sum from i = -1 to i = 2 of li(x)*f(xi), where li, i = -1,0,1,2, which are called the
fundamental polynomials, are given by li(x) = product from k = -1 to k = 2 for k !
Convolves kernel with a 2D or 3D image - only pixels where the kernel is completely contained in the image are
convolved, otherwise they are set to zero.
Algorithm for non-linear registration with the DEMONS algorithm
3 model parameters are fit for each voxel in 3D:
1) K_trans in [0, 0.99]
2) User choice of k_ep in [0, 0.99] or ve
3) f_vp in [0, 0.99]
K_trans and k_ep default to rates per second, but the user changed select rates per minute.
Put 3D dataset into dicom order.
Recursively traverses a directory and its subfolders, converting all 3D DICOM files to AVI with MP42 Compression.
Algorithm requires input of a Diffusion Tensor Image to calculate an Apparent Diffusion Coefficient Image,
Functional Anisotropy Image, Color Image, Eigen Value Image, Eigen Vector Image, Relative Anisotropy Image,
Trace Image, and Volume Ratio Image
This algorithm works in conjunction with AlgorithmDTITract to create the
MIPAV DTI Fiber Tracking/ Statistics Dialog
See: Introduction to Diffusion Tensor Imaging, by Susumu Mori
Algorithm requires input of previous calculated FA, EigenVector and EigenValue images from
AlgorithmDTI2EGFA to calculate fiber bundle tracts
This algorithm works in conjunction with AlgorithmDTI2EGFA to create the
MIPAV DTI Fiber Tracking/ Statistics Dialog
See:Introduction to Diffusion Tensor Imaging, by Susumu Mori
Algorithm calculates a Diffusion Tensor Image from a series of Diffusion Weighted Images.
Calculates the EdgeLap of an image at a scale defined by the user.
Calculates the EdgeLap of an image at a scale defined by the user.
Calculates the non-maximum suppression of an image at a scale defined by the user.
These are Maximum Homogeneity Neighbor Filters.
This module draws uniformly randomly positioned ellipses with a specified semi-major axis, semi-minor axis,
and angle phi between the x-axis and the major axis of the ellipse.
This program performs the conformal mapping of an ellipse to a circle.
This program performs the conformal mapping of an ellipse to a rectangle.
This code fits data points to a 3D ellipsoid.
This module contains a port from FORTRAN to Java of the FORTRAN program for designing elliptic-function
filters and a port from MATLAB to Java of the MATLAB program ellipap1 for designing an elliptic
analog lowpass filter prototype found in "Elliptic Functions for Filter Design" by H.
Smoothing VOI with Elliptic Fourier Descriptors.
Runs ELSUNC, LEVENBERG_MARQUARDT, or NL2SOL for a 2D image.
Runs ELSUNC, LEVENBERG_MARQUARDT, or NL2SOL for a 3D image.
The java code is ported from C++ code downloaded from http://coewww.rutgers.edu/riul/research/code.html.
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Compares segmentation results of a test image to segmentation results of an ideal gold standard true image.
Compares segmentation results of a test image to segmentation results of an ideal gold standard true image.
Algorithm that extracts the slices indicated in the list from the srcImage and puts them into the destImage.
Title: AlgorithmExtractIndividualSlices
Extracts a surface using Tetrahedron Extraction.
Extracts a surface using Marching Cube Extraction.
FaceAnonymizer algorithm computes the "face" from a ModelImage based on input parameters that specify the min/max
voxel values for the face voxels, and the maximum skin thinkness.
Anonymize an image of a patient's head by removing the face.
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Processing images by filtering in the frequency domain is a 3 step process: 1.)
Processing images by filtering in the frequency domain is a 3 step process: 1.)
References:
1.)
Flips 2D, 3D or 4D grays scale or color dataset about X, Y, or Z axis (when applicable) when AlgorithmFlip.IMAGE is
passed to the constructor.
Stack based flood-fill for 2D and 3D images.
Fluorescence Recovery after PhotoBleaching Only 1 color will be used from a
color image.
AlgorithmFrequencyFilter.java.
AlgorithmFrequencyFilterColor.java.
Fluorescence Resonance Energy Transfer FRET refers to the nonradiative transfer of energy from an excited state donor
fluorescent molecule to a nearby acceptor fluorescent molecule.
Fluorescence Resonance Energy Transfer FRET refers to the nonradiative transfer of energy from an excited state donor
fluorescent molecule to a nearby acceptor fluorescent molecule.
Fluorescence Resonance Energy Transfer FRET refers to the nonradiative transfer of energy from an excited state donor
fluorescent molecule to a nearby acceptor fluorescent molecule.
This algorithm performs minimization of fuzziness, a reduction of the amount of fuzziness.
Fuzzy C-Means Segmentation algorithm
This algorithm performs minimization of fuzziness, a reduction of the amount of fuzziness.
The application of this algorithm blurs an image or VOI region of the image with a Gaussian function at a user
defined scale (sigma - standard deviation).
Calculates the gaussian blur of an image at a scale defined by the user (using separable convolutions).
Copyright (c) 1995 The Board of Trustees of Purdue University.
Calculates the gradient magnitude of an image at a scale defined by the user.
Calculates the gradient magnitude of an image at a scale defined by the user (using separable convolutions).
2.5D mathematical morphology class applied to Gray scale images. (2D morphology on 3D volumes).
Two-Dimensional mathematical morphology class applied to Gray scale images.
Three-Dimensional mathematical morphology class applied to Gray scale images.
The MIT License (MIT)
Copyright (c) 2014 Atilim Cetin
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.
Snake-like algorithm derivative using BSplines.
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The class generates a triangle or quad mesh of a 2D dataset (image) to be displayed in the surface viewer.
This is a polynomial p of degree 7 which interpolates a given function f at the points x(-3), x(-2), x(-1), x(0),
x(1), x(2), x(3), and x(4) and is given by p(x) = sum from i = -3 to i = 4 of li(x)*f(xi), where li, i =
-3,-2,-1,0,1,2,3,4 which are called the fundamental polynomials, are given by li(x) = product from k = -3 to k = 4
for k !
Provides functions to convolve an image with the second derivitive of the Gaussian function to obtain the Hessian
matrix for a particular point on the image.
Calculates the histogram for an image.
This algorithm creates a two dimensional histogram of the data in 2 black and white images or 1 color image. if
doLinearRescale is true, the range of data in the second image is rescaled to be the same as the range of data in the
first image.
Algorithm that matches the transforms a match or source image so as to make its histogram equal to the histogram of a
base image.
Algorithm that matches or transforms a match or source slice so as to make its histogram equal to the histogram of a
base slice.
This is a port of the MATLAB files HMRF_EM.m and MRF_MAP.m written by Quan Wang to Java
This Hough transform uses (xi, yi) points in the original image space to generate theta0, a0 points in the Hough
transform.
This Hough transform uses (xi, yi) points in the original image space to generate x0, y0, rad points in the Hough
transform.
This Hough transform uses (xi, yi) points in the original image space to generate p, q, r1, r2, and theta points in the Hough
transform.
This work is made possible by the following mathematical theorem proved by Professor Alan Horwitz
of Penn State University:
Finding the Center of a Hyperbola, H, given three nonparallel tangent lines to H and
the corresponding points of tangency.
This Hough transform uses (xi, yi) points in the original image space to generate rho, theta points in the Hough
transform.
[(y - vy)*cos(phi) - (x - vx)*sin(phi)]**2 =
4*p*[(y - vy)*sin(phi) + (x - vx)*cos(phi)]
where vx, vy are the coordinates of the parabola vertex
p is the distance between the vertex and focus of the parabola
This Hough transform uses (xi, yi) points in the original image space to generate vx, vy, phi, p points in the Hough
transform.
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N3 Inhomogeneity correction This is based on code by John G.
Algorithm that adds, subtracts, multiplies, or divides an image by by another image.
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Algorithm that adds, subtracts, multiplies, or divides an image by some user specified value.
This algorithm operates on 2D and 3D black and white and color images.
Algorithm to insert a slice.
The interface used by all classes which want to respond to the conclusion of an algorithm.
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This is a port of MATLAB routines contained in kernelRegressionBasedImageProcessingToolBox_ver1-2beta written by
Hiroyuki Takeda, Sina Farsiu, and Peyman Milanfar.
This program can be run on data of any dimensionality.
Calculates the Laplacian of the gaussian of an image at a scale defined by the user.
Calculates the Laplacian of the gaussian of an image at a scale defined by the user.
This algorithm iteratively expands or contracts one or more contours to a boundary.
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Local Normalisation equalises colour levels among pixels by removing variations due to lighting; this brings out
contrasts in detail.
Allow the user to fill a VOI or fill everything outside the VOI with a specific fill value.
Will take Two 2D images (one Reference, one Adjusted) and use the Reference image's Resolutions to transform the
adjusted Image into a new size and resolution that the Reference Image can then be matched to, while preserving all
Field of Views (there is no loss of FOV).
Matches two ModelImages.
Computes the maximum or the minimum intensity along each projection of a 3D image.
An implementation of Maximum Likelihood Iterated Blind Deconvolution based on the following papers:
Algorithm to apply a mean filter to an image, placing it in a new ModelImage if New image is selected or returning
the changed picture to the same image if Replace image is selected.
The java code is ported from C++ code downloaded from http://coewww.rutgers.edu/riul/research/code.html.
The java code is ported from C++ code downloaded from http://coewww.rutgers.edu/riul/research/code.html.
Algorithm to apply a median filter to an image, placing it in a new ModelImage, or returning the changed picture to
the same image.
Finds the midsagittal line of a brain MRI by:
Flipping the image horizontally.
Registering the flipped image against the original.
Getting the angle that the registration rotated the image.
Transforming the original image by half the registration rotation.
Smoothing VOI with minimum perimeter polygon.
AlgorithmMode applies one of the user specified kernels to a 2D or 3D BYTE, SHORT, INTEGER, UBYTE, USHORT, UINTEGER.
Performs morphological filtering on black and white images.
2.5D mathmatical morphology class (2D morphology on 3D volumes).
Two-Dimensional mathmatical morphology class.
Three-Dimensional mathmatical morphology class.
Algorithm requires input of 2D or 3D mosaics.
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Fuzzy C-Means Segmentation algorithm
This program performs the conformal mapping of a nearly circular region to a circle.
Copyright (c) 2011, The University of Nottingham
All rights reserved.
This is a port of the SUSAN Nonlinear Noise reduction program.
Calculates the non-maximum suppression of an image at a scale defined by the user Edges are defined as the union of
points for which the gradient magnitude assumes a maximum in the gradient direction.
Algorithm used to add Gaussian, Poisson, Uniform, Rayleigh, or Rician noise to an image.
This is a port of the 09/03/2006 NLmeansfilter.m and UNLmeansfilter2.m on 02/15/2008 by Jose Vicente
Manjon Herrera invalid input: '&' Antoni Buades.
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A class for segmenting objects.
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This class standardizes the parameter names given to many common parameters used in algorithms.
Compute probability of boundary using brightness gradient and texture gradient
Original MATLAB code written by David R.
Ported from Peter Kovesi's MATLAB code for Phase Congruency
Available from: http://www.csse.uwa.edu.au/~pk/research/matlabfns/PhaseCongruency/phasecong3.m
and: http://www.csse.uwa.edu.au/~pk/research/matlabfns/FrequencyFilt/lowpassfilter.m
in reference to the method lowpassFilter();
% References:
%
% Peter Kovesi, "Image Features From Phase Congruency".
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Runs Powell's method for a 2D image.
Runs Powell's method for a 3D image.
Powell's Method
This is a port of C code written by Camille Couprie in 2009.
This algorithm operates on 3D black and white images and on 2D and 3D color images.
This algorithm traces the prostate boundary from the target image, non prostate binary mask image and
prostate boundary binary mask image.
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This class save the Coherence Enhanced Diffusion (CED) 2D slice based features, which are Hurst index
and Haralick features.
Approximate a set of points by a quadric surface.
Quantify image data based on a mask image.
Algorithm that does basic calculations on Mask images (boolean/ubyte/short)
calculates Center of Mass, area (in resolutions), and number of pixels per mask
This is a polynomial p of degree 5 which interpolates a given function f at the points x(-2), x(-1), x(0), x(1),
x(2), and x(3) and is given by p(x) = sum from i = -2 to i = 3 of li(x)*f(xi), where li, i = -2,-1,0,1,2,3 which are
called the fundamental polynomials, are given by li(x) = product from k = -2 to k = 3 for k !
Algorithm that randomizes the order of 3D dataset.
This is a common base class which provides common methods and data members for all BSpline based registration.
Data structure which contains the parameters or options used to perform a BSpline based registration of two
images.
BSpline based registration of 2.5D images.
BSpline based registration of 2D images.
BSpline registration of 3D images.
AlgorithmRegChamfer First slice is template (base image) to which match image is registered.
This is an automatic registration method based on FLIRT.
This is an automatic registration method based on FLIRT.
This is an automatic registration method based on FLIRT.
This is an automatic registration method based on FLIRT.
Fills a region based on average intensity +or- standard deviation.
"Least-Squares Fitting of 2 3-D Point Sets", K.
This is an automatic registration method based on FLIRT.
This is an automatic registration method based on FLIRT.
This is an automatic registration method based on FLIRT.
This is an automatic registration method based on FLIRT.
Use origin and image orientations to align images based on patient position.
Algorithm to apply Regularized Isotropic Nonlinear Diffusion as described by:
Uses a selected
RegistrationMeasure and the user-specified points to
output the relevant measure back to the user.AlgorithmRegVOILandmark First slice is template (base image) to which subsequent slices are registered.
Algorithm verifies the z-th slice should be in included in the destination image, as defined in the list, remove.
Algorithm to run the remove T slices.
This algorithm is used to insert averaged slices where slices have been removed -If slices were removed at the
beginning of the original movie, these slices will not be replaced. - Slices are only inserted between the first and
last kept slices
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Title: AlgorithmReplaceValue
Reslices 3D image into (isotropic)cubic voxels.
Simple algorithm that generates an RGB image from three gray images.
Simple algorithm that converts an RGB image to a single greyscale image.
Simple algorithm that converts an RGB image to a red, green, and blue greyscale images.
Simple algorithm that converts an RGB image to a hue, saturation and brightness greyscale images.
This "rice-wlet-tools", version 2.4
Released - invalid input: '<'Dec 1 2002>
CONDITIONS FOR USE:
Copyright (c) 2000 RICE UNIVERSITY.
An Algorithm to rotate 3D or 4D dataset 90 or 180 degrees about X, Y, or Z axis. 2D Images can also be rotated.
This algorithm uses an equation with 3 membership functions, udark, ugray, and ubright, to transform a gray level g
to a new gray level g' for histogram enhancement.
Original source code in C and MATLAB is Copyright 1998-2004 by Timor Kadir Version 1.5
Kadir/Brady Feature detector (Scale Saliency) Code
For non-commercial use only
Ported by to Java by William Gandler
References:
1.)
Convolves an image with a separable (symmetric) kernel and returns the result.
This program uses a mandatory signal 1 VOI, an optional signal 2 VOI, a mandatory noise background VOI, and the
number of NMR receivers to calculate the signal to noise ratio for the signal VOI(s).
Algorithm Implementation
1.
This algorithm averages together slices of a 3D image.
Based on the document provided by Daniel Reich: Notes on DCE with SM2 (standard model, aka Tofts model,
2-compartment) 3 model parameters are fit for each voxel in 3D: 1) K_trans in [1.0E-5, 5.0] in /min On input ktrans
is converted from /min to /sec and on output ktrans is converted from /sec to /min. 2) ve in [1.0E-5, 0.99] 3) f_vp
in [0, 0.99]
srcImage is a dynamic "4D volume" of MRI signal (3D over time).
Snake-like algorithm deriviative.
This module draws uniformly randomly positioned spheres with a specified radius.
The Standard Deviation Threshold works by first having an active VOI in which the standard deviation and other
statistics are calculated.
Takes in an image and subsamples it to a new set of dimensions.
Algorithm to create a 3D subset image from a 4D image.
Algorithm that subtracts the mean or median value of a VOI from the image.
Swaps third and fourth dimensions in 4D dataset.
Swaps dimensions in 4D dataset.
Title: AlgorithmSwapSlicesVolume
This class recalculates mo and dceFullTre to provide better estimates using the inverse Ernst equation
Performs original to ACPC, original to Talairach, ACPC to original, ACPC to Talairach, Talairach to original, or
Talairach to ACPC transformation.
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Overview
This code contains the texture analysis functions for the paper `Texture
Analysis and Segmentation Using Modulation Features, Generative Models, and
Weighted Curve Evolution', by I.
This software implements the factorization-based segmentation algorithm.
This algorithm has two modes of operation:
Runs threshold (lower and upper) on color images and replaces values either outside (inverse) or inside (normal) with
the fill values specified.
This abstract class defines terms common to both T1 and T2 processing, such as thresholding and
multithreading management methods.
Thin plate spline Warning: If the supplied (x,y) data set in setupTPSpline2D is nearly collinear, singular matrices
will result and a matrix inversion will fail.
Title:
Transforms Volume by resampling using transformation matrix and the choice of nearest-neighbor, trilinear
interpolation, 3rd order Bspline, 4th order Bspline, cubic Lagrangian, quintic Lagrangian, heptic Lagrangian, or
windowed sinc.
TransformBSpline algorithm This algorithm takes a source image and uses information read in from a .nlt file to
perform a nonlinear B-Spline transformation on the image.
This interface contains convenience enumerations for going between the dialog and algorithm of the TRE framework.
Specifies the magnetic field strength of the scanner used.
Specifies the inversion method used for the scan.
Designates the brand of scanner used for processing.
A three way boolean operator to designate the thresholding option used.
This class is adapted from the ImageJ version originally written by Sean Deoni while working at the
National Institutes of Health.
This class is adapted from the ImageJ version originally written by Sean Deoni while working at the National
Institutes of Health.
This is a port of openCVtrilateralFilter.h and openCVtrilateralFilter.cpp
written by Tobi Vaudrey.
This module implements the National Electrical Manufacturers Association (NEMA) standard for SNR estimation in
diagnostic MRI.
Calculates the Unsharp Mask of an image at a scale defined by the user ( unsharp image = original image - weight *
blurred image); weight invalid input: '<' 1;
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Algorithm class for finding Hausdorff distance on 2 VOIs
Algorithm class for performing logical operations on VOIs
This class calculates a properties of an image defined by a VOI.
Perform Simplex Optimization on a VOI that has been propagated to a slice to find a transformation which will make an
affine "fit" a structure which the VOI fit on the previous slice (used in RFASegTool when propagating liver
segmentation VOIs).
This program applies the watershed algorithm to the image.
MIT License
Copyright (c) 2021 Hans Brouwer, Riyo Wanagiri
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.
In hard thresholding a wavelet coefficient whose magnitude is below the product of threshold and the maximum wavelet
magnitude is zeroed, and a wavelet coefficient whose magnitude is greater than or equal to the product is left
unchanged.
Sinc function windowed with Hanning window function used for interpolation This function will create images with
greater maximums and lower minimums than the original image, so if the input image type is BYTE or UBYTE, the output
image type should be a SHORT.
Title: AlternatingTableCellRenderer
Copyright (c) 2007-2014 The LIBLINEAR Project.
A class containing Array-related helper methods.
MIT License
Copyright (c) 2016 Jason Wu
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.
BarMeter presents a vertical, block-style meter to present numerical information as a fraction of a number of
divisions (eg, progress or resource consumption).
BasicGrid
Basic Class abstracting a gridded structure in a 3d space;
Usueful for having coherent float to integer conversion in a unique place:
Some Notes:
- bbox is the real occupation of the box in the space;
- siz is the number of cells for each side
OBJTYPE: Type of the indexed objects.
Big Endian Input Array Stream, works as a replacement for BERandomAccessFile
at the input of Jpeg2K decoder.
Big Endian Output Array Stream, works as a replacement for FileFormatWriter
at the output of Jpeg2K encoder.
This module computes Bessel functions of complex arguments and a nonnegative order.
This module computes Bessel functions of complex arguments and a nonnegative order.
Copyright (c) 2012, Brian Moore
Copyright (c) 2004, Ben Barrowes
All rights reserved.
This class is an example class for tying existing plugins into the JIST interface.
This class was created for use in the JDialogMultiPaint class.
This class manages a 2D lattice of control points given a discretized B-Spline basis for each axis.
This class manages a 3D lattice of control points given a discretized B-Spline basis for each axis.
This class is used to register a 2D source image to a 2D target image.
This class is used to register a 3D source image to a 3D target image.
This is a common base class for all BSpline-based registrations.
This is an abstract buffer class that indicates the required methods of the sub-classes.
This class extends the abstract BufferBase class.
This class extends the abstract BufferBase class.
This class extends the abstract BufferBase class.
This class extends the abstract BufferBase class.
This class extends the abstract BufferBase class.
This class extends the abstract BufferBase class.
This class extends the abstract BufferBase class.
This class extends the abstract BufferBase class.
This class extends the abstract BufferBase class.
This class extends the abstract BufferBase class.
This interface binds a PlugIn to a PlugInBundle.
Class that holds the information about each surface; the BranchGroup which holds the surface subtree, the name of the
surface in the dialog, the color of the surface, the shininess of the surface, the level of detail (for clod meshes),
the number of triangles (changes with level of detail), the polygon mode (fill, line, or point), and a flag
indicating if this is a clod mesh.
Title: BurnBase
The default probe burning type view.
The default probe burning type view.
The default probe burning type view.
The default probe burning type view.
Base class for both the compress and decompress classes.
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API (AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API (AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API (AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
Copyright (c) 2000-2014 Chih-Chung Chang and Chih-Jen Lin
All rights reserved.
An input stream that decompresses from the BZip2 format (without the file
header chars) to be read as any other stream.
An output stream that compresses into the BZip2 format (without the file
header chars) into another stream.
Legalities
==========
We place our efforts in writing this package in the public domain.
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
This is the Java modified version of C++ active appearance model API
(AAM_API).
Correct values for ndtri are taken from scipy-main/scipy/special/tests/test_ndtr.py under the BSD-3 license:
Copyright (c) 2001-2002 Enthought, Inc. 2003-2022, SciPy Developers.
This is a port of the C++ files in ceres-solver-1.14.0 under the BSD license:
Ceres Solver - A fast non-linear least squares minimizer Copyright 2015
Google Inc.
This is a port of the C++ files in ceres-solver-1.14.0 under the BSD license:
Ceres Solver - A fast non-linear least squares minimizer Copyright 2015
Google Inc.
Ported from C++ to Java by William Gandler
BSD 3-Clause License
Copyright (c) 2007, Jan de Vaan and Victor Derks
All rights reserved.
Creates the circle widget for the multi-histogram interface.
Public utility class for generating approximations to circles and spheres.
This is the base class for the Multi-histogram widgets.
This class sets up and communicates with the GLSL shader program used to render the
interior of the widget in the multi-histogram panel.
This class stores the information needed for calculating how the multi-histogram is applied to the volume
to create the rendered image.
This is an icon which is a block of color with bounds specified in the constructor.
A MIPAV command line parser reads the arguments provided to MIPAV at the command line.
This code calculates the confluent hypergeometric function of the first and second kinds For the confluent
hypergeometric function of the first kind a typical usage for the routine requiring real parameters and a real
argument would be:
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.
MIT License
Copyright (c) 2018 Komahan Boopathy
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.
MIT License
Copyright (c) 2018 Komahan Boopathy
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 Contours class provides methods to compute contour lines and contour bands
from a 2D regular grid of scalar values.
The AdaptableView interface defines the
ContourPlot.AdaptableView.setView(Rectangle2D)
method.Class providing convenience methods for converting Images to BufferedImages.
The CharacterAtlas class is a texture atlas for looking up character textures.
The ColorMap interface defines discrete mapping from a fixed integer
interval [0..N-1] to colors through the
ContourPlot.ColorMap.getColor(int) method.The ColorOperations class contains methods for manipulating
32bit ARGB color values.
The CoordinateViewListener is a listener that listens on changes to a
ContourPlot.CoordSysRenderer's coordinate view
(i.e.Enum containing predefined
ContourPlot.ColorSchemes,
which can be accessed through ContourPlot.DefaultColorScheme.get().Implementation of the extended Wilkinson algorithm for tick label positioning.
The Glyph interface has to be implemented by a class that realizes
a graphical representation of a 2D point (e.g. a cross or a circle).
Class providing convenience methods for saving Images to file.
RuntimeException class for Exceptions that occur during image saving.
Base interface for imagingkit's Img classes.
Class holding all of the
Iterator and Spliterator classes
used in the ContourPlot.ImgBase interface.Special Spliterator which guarantees that each split will cover at least
an entire column of the image.
The standard iterator class for iterating over an area of an image.
Spliterator class for images bound to a specific area
The standard
Iterator class for images.The standard
Spliterator class for images.Special Spliterator for images which guarantees that each split will cover at least
an entire row of the image.
This interface defines the methods required by an implementation of a
canvas
or
Component for use with JPlotter ContourPlot.Renderers such as
invalid reference
BlankCanvasContourPlot.BlankCanvasFallback.The Legend class is
ContourPlot.Renderable and its own ContourPlot.Renderer at once.Pair class.
The PDFRenderer interface defines the method
ContourPlot.PDFRenderer.renderPDF(PDDocument, PDPage, int, int, int, int)
which 'renders' the PDFRenderers's content as pdf objects
in content streams, i.e. fills content streams with elements and appends them to the specified page.Basic interface for Pixel classes of
ContourPlot.ImgBase implementations.The PixelConvertingSpliterator enables iterating an
ContourPlot.Img with a
different datatype than ContourPlot.Pixel (ContourPlot.ImgBase.spliterator()).The PixelManipulator interface defines an action to be performed on a pixel.
Class for storing all the details of a single point to be rendered.
Interface for an object that can be rendered by a
ContourPlot.Renderer e.g. the ContourPlot.GenericRenderer.The Renderer interface defines methods to
initialize the renderer,
execute a rendering pass,
close the renderer.
The SignedDistanceCharacters class comprises signed distance fields
of a set of characters.
The TickMarkGenerator interface provides the
ContourPlot.TickMarkGenerator.genTicksAndLabels(double, double, int, boolean) method.Class containing utility methods
The CoolTip probe has its own geometry and type of burning.
This interface identifies a class which wants to know about changes to the current coordinates of another frame (such
as ViewJFrameTriImage).
Cortical analysis applet and viewer.
Copyright (C) 2013-14 Andrea Vedaldi.
A simple class the hold and calculate the CRC for sanity checking
of the data.
Title: CubeBounds
This is a port of code written by Gerolamo Cardano under the Code Project Open Licence.
CustomHashtable extends the Hashtable class and adds some methods for generating keys for new elements to the
Hashtable.
Class that holds the parameters for creating/catching common buttons and menu items
* AAM-API LICENSE - file: license.txt
This software is freely available for non-commercial use such as
research and education.
* AAM-API LICENSE - file: license.txt
This software is freely available for non-commercial use such as
research and education.
CVisRect
* AAM-API LICENSE - file: license.txt
This software is freely available for non-commercial use such as
research and education.
* AAM-API LICENSE - file: license.txt
This software is freely available for non-commercial use such as
research and education.
INTERNAL EXTERNAL VISSHAPE
Objects derived from which also contain a number of
bands.
This code calculates the Ksquared statistic of an input array x[].
This class standardizes the parameter names given to many common parameters used in algorithms.
% Copyright (c) 2013 Peter Kovesi
% www.peterkovesi.com/matlabfns/
%
% 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, 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.
This class is the main class of JJ2000's decoder.
This class is the main class of JJ2000's decoder.
Title: DefaultPorbe
Edgeset of Delaunay triangulation ( L2-norm).
This class is a random access file that has an internal delimiter for fast
processing of text files.
This algorithm handles registration algorithms
of images with the Demons algorithm
and a simple multiscale technique
(Demons variant from Tom Vercauteren's 2009 paper,
"Diffeomorphic demons: Efficient non-parametric image registration by
Tom Vercauteren, Xavier Pennec, Aymeric Perchant, and Nicholas Ayache,
NeuroImage, 45, 2009, S61-S72.)
Simple interface for loading and saving default settings for dialogs.
DICOM Association Abort PDU Type.
Implements a DICOM Association Acceptance PDU Type.
DICOM Association Rejection.
DICOM Association Request PDU Type class.
DICOM Association Release Request.
DICOM Association Release Response.
DICOM AsyncOpWindowSubItem PDU Item Type - Not supported but we read it in.
This class is used as a base class for all DICOM file and network I/O.
It is a bit odd since it both extends DICOM_Comms and has a DICOM_Comms object.
Useful DICOM constants.
DIMSE-C service implementations.
This is the base class for DIMSE-C response messages.
Used to for DICOM communication error handling.
DICOM communication package reads the data from the socket and saves the data to a file stream.
Simple class that implements a Maximum SubLength PDU type.
This is the DICOM move class that defines functions to compose and send move requests to the server found in the
.preferences file.
The DICOM data object for storing DICOM tags (i.e. groups, elements).
Vector of DICOM_Objects.
Used to exchange application information (i.e.
This class implements a 2 byte item length (DICOM_PDUType implements 4 byte item length.
The Protocol Data Units (PDU) - PDU_Service class is a wrapper of all the lower level DICOM messaging classes.
This an abstract class implements a 4 byte item length (DICOM_PDUItemType implements 2 byte item length.
DICOMPDUTypeBase abstract base class that is extended by DICOMPDUType and DICOMPDUItemType.
DICOM Presentation Context PDU Item Type.
DICOM Presentation Context Acceptance PDU Item Type.
This is the DICOM query class that defines functions to compose and send a patient root, patient level DICOM query
request to the image file server located in NIH's Clinical Center.
This is the DICOM server class that hangs a listener on a given port for incoming image store requests from a remote
DICOM client.
RTC - Run Time Class (although it is actually statically defined here) This allows access to information in the DICOM
data dictionary.
This class generates the DICOM_RTC class file from the master DICOM tag list file (whose entries are obtained through
calls to DicomDictionary).
DICOM SCP/SCU Role Selection PDU Item Type.
Simple class to setup and the socket and streams.
This is a base class for all SOP Class implementations.
DICOM Retrieve SOP Class.
A DICOM Storage SOP Class.
This is the DICOM store class that defines functions to compose and send a store request to a DICOM image file
archive such as the image file server located in NIH's Clinical Center.
Simple utilities to convert transfer syntaxes to a different form.
DICOM_UID.
DICOM User Information PDU Item Type (part 8 section 9.3).
Static DICOM and general utilities to support DICOM interfacing.
This is the DICOM verification class that defines functions to perform Verification to a DICOM image file archive
such as the Kodak PACS image file server located in NIH's Clinical Center.
DICOM Value Representation.
This class reads a text file that lists all the tags that the DICOM file reader will need to know about.
This class is simply a table that goes in the query GUI and displays progress and error messages.
Dialogs which implement this interface are eligible to use the JDialogDicomTagSelector for selecting DICOM tags within a given image file.
Contains information for a point used in the the Dijkstra minimum cost path algorithm.
Implementation of the Dijkstra minimum cost path algorithm through a binary volume.
This routines except the SLOW routines are ported from FORTRAN to Java from:
ALGORITHM 749, COLLECTED ALGORITHMS FROM ACM.
Copyright (c) 2007-2014 The LIBLINEAR Project.
Immutable, extended-precision floating-point numbers
which maintain 106 bits (approximately 30 decimal digits) of precision.
The DTI gradient table correction after transformation algorithm corrects gradients after their corresponding
DWI volumes have been registered using OAR35D to a B0 image.
Object to store parameters in the ModelImage acquired from DWI image file or ImageInfo DTI tab
Eigenvalues and eigenvectors of a real matrix.
DOCUMENT ME!
This class is the main class of JJ2000's encoder.
This class is the main class of JJ2000's encoder.
Ported to Java from C code from
http://www8.cs.umu.se/kurser/TDBAfl/VT06/algorithms/WEBSITE/IMPLEMEN/TURN/IMPLEMEN.HTM
May only be used for non-commercial purposes.
Ported to Java from C code from
http://www8.cs.umu.se/kurser/TDBAfl/VT06/algorithms/WEBSITE/IMPLEMEN/TURN/IMPLEMEN.HTM
May only be used for non-commercial purposes.
These enumerations are used by the GuiBuilder to indicate the pre-processing results of user
entry fields for the user interface.
Copyright (c) 2007-2014 The LIBLINEAR Project.
This FFT should only be used when it is necessary to perform a N-dimensional FFT on non-power of two data without
adding padding.
This extended precision FFT should only be used when it is necessary to perform a N-dimensional FFT on non-power of
two data without adding padding.
Afni file format.
The class reads and writes Analyze Version 7.5.x files.
AVI file writer and reader.
FileBase is an abstract class that has many methods that support the reading/writing of files.
Reads BioRaD pic file format.
Reads a BRUKER file by first reading in the d3proc header file or if the d3proc header file is not\
present the visu_pars file, second the reco header file, third the acqp file in the
same directory or up one or two two parent directories, then the method file,l and finally the 2dseq binary file.
The class reads Cheshire file images.
Addresses and lengths are always contained in 4 bytes.
FreeSurfer COR files are used to store 3 dimensional unsigned byte data.
File written using Zeiss Release Version 1.1 for ZEN 2012
Class to safely delete a file using a looped thread.
This class reads and writes DICOM files.
FileDICOMBase is an class that supports the reading/writing of DICOM files.
Class that reads a lossless compressed JPEG file.
FileDicomKey goes along with FileDicomTag - it is the key into the hashtable that corresponds to a tag.
This is a class for reading in a DICOM sequence tag.
A table containing dicom tags.
This class holds all the important information about each DICOM tag.
Information about a DICOM tag, stored in the DicomDictionary table once for each DICOM tag.
A table containing dicom tags.
Some of this code is derived from DM3_Reader.java in ImageJ.
A simple file filter to select only files with the specified extensions for display in a JFileChooser instance.
Some of this code is derived from FITS.java in ImageJ.
Fixed format header
Image data is not compressed
Image data fixed offset 14336 bytes
Data General host
The image files are of fixed layout, described here as a series of 256 by 16
bit word blocks (512 bytes), blocks numbered from 0.
Reads both GE Neducak Systems MR 5X and LX.
HistoLUT reader/writer.
Reference: 1.
File class for reading/writing Image.XML file headers and their associated images.
This structures contains the information that describes how an Afni image is stored on disk.
This structures contains the information that describes how an analyze image is stored on disk.
This structures contains the information that describes how an Avi image is stored on disk.
This structure contains the basic information that describes how the image is stored on disk.
Each unit has a unit type with a given base.
This structures contains the information that describes how a Biorad image is stored on disk.
File info storage container.
File information related to the Bruker/Biospin scanner format.
This structures contains the information that describes how an analyze image is stored on disk.
File info storage container.
File info storage container.
This class contains DICOM header information.
This structures contains the information that describes how a DM3 image is stored on disk.
This structures contains the information that describes how a Fits image is stored on disk.
This structures contains the information that describes how a GE Signa 5X image is stored on disk.
This structures contains the information that describes how a GE Signa 5X image is stored on disk.
This structures contains the information that describes how an ICS image is stored on disk.
This structure contains the information that describes how an XML image is stored on disk.
Title: Investigator
This structures contains the information that describes how an Interfile image is stored on disk.
This structures contains the information that describes how a JP2 compressed image of 3D medical image is stored on disk.
This structures contains the information that describes how a Fits image is stored on disk.
This structure contains the information that describes how a Lattice image is stored on disk.
File info storage container.
This structures contains the information that describes how a LSM image is stored on disk.
This structures contains the information that describes how a Siemens MagnetomVision image is stored on disk.
File info storage container.
This structure contains the information that describes how an MedVision image is stored on disk, as well as header
information.
This structures contains the information that describes how a MetaImage image is stored on disk.
This structures contains the information that describes how.
This class holds all the file information for a MINC file.
This structures contains the information that describes how a MRC image is stored on disk.
This structures contains the information that describes how a NIFTI image is stored on disk.
Title:
Created by IntelliJ IDEA.
This structure contains the information that describes how a RAW image is stored on disk.
This structures contains the information that describes how an SPM image is stored on disk.
This structures contains the information that describes how a STK image is stored on disk.
This structure contains the information that describes how an XML surface (see surface.xsd and FileSurfaceXML.java)
is stored on disk.
This structure contains the information that describes how an XML surface (see surface.xsd and FileSurfaceXML.java)
is stored on disk.
This structure contains the information that describes how an XML surface (see surface.xsd and FileSurfaceXML.java)
is stored on disk.
This structure contains the information that describes how an XML surface (see surface.xsd and FileSurfaceXML.java)
is stored on disk.
This structure contains the information that describes how an XML surface (see surface.xsd and FileSurfaceXML.java)
is stored on disk.
This structure contains the information that describes how an XML surface (see surface.xsd and FileSurfaceXML.java)
is stored on disk.
This structures contains the information that describes how a SVS image is stored on disk.
This structures contains the information that describes how a Tiff image is stored on disk.
This structures contains the information that describes how a TMG image is stored on disk.
File Info Vista
Abstract base clase contains the information that contains the shared information for XML images and XML surfaces.
File info storage container.
This class controls the file input/output of most formats that MIPAV supports, including tiff, raw, analyze, DICOM,
and Medvision.
Jpeg2K reader/ writer for 3D images.
Reads Zeiss LSM 510 image files - an extension of the TIFF format.
Class that reads Siemens Magnetom Vision files.
Special for Benes.
The class reads MedVision files that have been saved as MAC bin files.
The class reads MGH files.
The MINC file format is built on top of NetCDF.
This class represents a MINC atrribute element.
This class represents a MINC dimension element.
HDF5 based reader/writer for MINC 2.0
Currently, for the image max and image min nodes: in the case of 3d images in which 1 image min and 1 image max is to
be written out per slice, the dimorder is hardcoded to zspace.
This class represents a MINC variable element.
Comments from David Mastronarde:
I am not familiar with the latest standards for MRC files, but typically the extra header information has been used to save information about each section in the file.
I am not familiar with the latest standards for MRC files, but typically the extra header information has been used to save information about each section in the file.
DOCUMENT ME!
The class reads and writes NIFTI files.
DOCUMENT ME!
The class reads and writes packed bit files for tiff formatted images (including STK).
The class reads and writes PAR/REC files.
FilePolyline.
The class reads and writes raw files of all data types: boolean, byte, short, int, long, float, and double.
The class reads and writes raw files of all data types: boolean, byte, short, int, long, float, and double.
The FileSelector interface defines the interface for file selector
which is used to select files.
The implementation of the FileSelector interface for the local file
system, for the remote file system you should have different implementation,
basically this class is a wrapper of the JFileChooser.
Reads a spar/sdat file.
The class reads and writes SPM files.
The MetaMorph Stack (STK) file format is derived from the TIFF format.
FileSurface.
FileSurface.
Inherits from FileXML, reads SurfaceRef.XML files based on the "surfaceref.xsd" file.
Inherits from FileXML, reads gifti xml files based on the "gifti.xsd" file.
Inherits from FileXML, reads SurfaceRef.XML files based on the "surfaceref.xsd" file.
Inherits from FileXML, reads SurfaceRef.XML files based on the "surfaceref.xsd" file.
Inherits from FileXML, reads SurfaceRef.XML files based on the "surfaceref.xsd" file.
This class facilitates reading and writing vtk xml
This class facilitates reading and writing vtk xml
This class facilitates reading and writing vtk xml
Inherits from FileXML, reads Surface.XML files based on the "surface.xsd" file.
Inherits from FileXML, reads Surface.XML files based on the "surface.xsd" file.
Tagged Image File Format (TIFF 6.0) reader/ writer.
Tiff Types.
Tagged Image File Format (TIFF 6.0) reader/ writer.
Tiff Types.
DOCUMENT ME!
Reads a .trk track file as a MIPAV mask image.
This class stores information about a file type, including the type description (i.e., 'NRRD') and allowed extensions
(i.e., '.nrrd,.nhdr').
Constants and static methods which relate to file input, output or processing.
VOI reader/writer.
This structure contains information to direct file writing.
Abstract base class for reading/writing .XML file headers.
Documentation used was the ZVI Format Specification V 2.0.5 - August, 2010.
FitExponential -fits an array of points to an exponential of the type y = a0 + a1*exp(a2*x).
FitGaussian -fits an array of points to a normal curve, general from f = a*exp(-(x-b)^2/2sigma^2)
Will also perform thresholding techniques to determine useful data points for fitting
FitLaplace -fits an array of points to a normal curve, general from f = a*exp(Math.abs(x-mu)/beta)
Will also perform thresholding techniques to determine useful data points for fitting
y = mx + b;.
FitLorentz -fits an array of points to a lorentz distribution, thresholding techniques come from ViewJFrameGraph,
no need to implement here
FitMultiExponential -fits an array of points to an multiexponential of the type
y = a0 + a1*exp(a2*x) + a3*exp(a4*x) + ...
For -infinity invalid input: '<' a invalid input: '<' +infinity and b > 0
y = scale factor * (2/b)*(x - a)*exp(-((x-a)**2)/b)*u(x - a)
where u(x-a) = 0 for x invalid input: '<' a and = 1 for x >= a.
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This behavior is supposed to emulate a pilot directing an aircraft.
This behavior is supposed to emulate a pilot directing an aircraft.
Container which stores annotations which include the following: - point position and normal - branch and location
along branch when point annotated - geometry and appearance - description.
Container which stores annotations which include the following: - point position and normal - camera location, view up and view direction, branch and location
along branch when point annotated - geometry and appearance - description.
Behavior which allows for flying down a specified path and looking around.
Behavior which allows for flying down a specified path and looking around.
Instances which want to be notified of updates to this behavior should implement this interface by providing the
viewChanged method implementation.
Instances which want to be notified of updates to this behavior should implement this interface by providing the
viewChanged method implementation.
Basic graph structure which identifies relationship between nodes by their indexes.
This class is an implementation of a bidirectional graph of nodes where each node is a curve segment used to define
branched paths.
Extension of the FlyPathGraph class which allows for the storage of the samples used to generate the individual
curves where curves are the nodes of the graph.
Interface between the graphics-independent Fly-through user-interface and the
graphics-dependent Fly-through renderers.
Virtual colonoscopy viewer.
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Copyright (c) 2007-2014 The LIBLINEAR Project.
This code calculates the gamma function of an input argument x.
dirichletRnd ported from mixGaussRnd.m by Mo Chen
Copyright (c) 2016, Mo Chen
All rights reserved.
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This file contains 1 user callable eigenvalue function and 2 user callable generalized eigenvalue functions.
This class maintains an instance of a SoftwareLight and a (Java3D) Light where these instances are of the same type:
Calculates an n-dimensional gaussian volume at a given scale, kernel size, and normalized derivative (through the
fourth order) in any of the dimensions.
Calculates an n-dimensional gaussian volume at a given scale, kernel size, and normalized derivative (through the
fourth order) in any of the dimensions.
Introduction: The goal of this task is to add the ability for the user to draw a region of interest on a triangle
mesh surface, by allowing the user to select points on the mesh surface and calculating the connecting polyline on
the surface between the points.
This is a static helper class for finding the path to a number of important files to the MIPAV application.
Provides methods for quickly building panel components.
The MIT License (MIT)
Copyright (c) 2015 Eugeniy Sokol
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.
Smithsonian Astrophysical Observatory
Submillimeter Receiver Laboratory
am
transform.c S.
Copyright (C) 2007-11, Andrea Vedaldi and Brian Fulkerson
Copyright (C) 2012-13, The VLFeat Team
All rights reserved.
Common interface for swing containers which hold a HistoLUT component so that the image frames and thresholding text
areas can be updated correctly.
This class is used specifically for the watershed algorithm.
The function
2F1(a,b,c,x) is the hypergeometric function or Gauss's hypergeometric function.Tracks registered images, and notifies anybody who is interested in finding out about them.
Stores image names, which are referenced by placeholder variable strings (e.g., '$image1').
This class implements the ImgData interface for reading 16 bit unsigned data
from a binary RAW file.
This class implements the ImgData interface for reading slices of 16 bit unsigned data
from a 3D RAW image file.
This class extends the ImgWriter abstract class for writing JP2 3D files.
The VOI instance holds the file name and directory name for each type of the VOIs (Axial, Sagittal, Coronal)
Additionally, myContourVector is the chunk vector to hold the 3D coordinate points of VOIs for each type.
The VOI instance holds the file name and directory name for each type of the VOIs (Axial, Sagittal, Coronal)
Additionally, myContourVector is the chunk vector to hold the 3D coordinate points of VOIs for each type.
Copyright (c) 2007-2014 The LIBLINEAR Project.
This is a port of FORTRAN numerical integration routines in QUADPACK found at http://www.netlib.org/quadpack
Reference: R.
This is a port of FORTRAN numerical integration routines in QUADPACK found at http://www.netlib.org/quadpack
Reference: R.
Integer Vector is very similar to the Vector class except that it is designed specifically to store integers.
Copyright (c) 2007-2014 The LIBLINEAR Project.
This is a port of the MATLAB INVLAP.M, a numerical inverse Laplace transform using the de Hoog algorithm, copyright
by Karl Hollenbeck on November 22, 1996, Department of Hydrodynamics and Water Resources, Technical University of
Denmark, DK-2800 Lyngby email:karl@isv16.isva.dtu.dk Downloaded from MATLAB central in ECP1 Software.zip.
This is a port of the numerical inverse Laplace transform found as the FORTRAN implementation of Algorithm 619 from
the collected algorithms from the ACM found at http://www.netlib.org/toms/619.
This is a port of niltqd.m, a fast numerical inverse Laplace transform based on FFT and quotient-difference algorithm
by Lubomir Brancik, 2001, Brno University of Technology.
Calculate Jacobian Elliptic functions.
Wrapper around Jama package, @see src/Jama/
Provides access to features unique to Jama lib,
otherwise use WildMagic Matrix3f, Matrix4f and GMatrix classes.
Dialog to get user input, then call the algorithm.
The class is the driver for the AAM classification.
The class is the driver for the AAM classification.
This class is the combined Atlas based AAM and SVM model to automatically
segment the MRI prostate.
Dialog to enter points for creating an ACPC image.
Dialog to get user input, then call the algorithm.
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Creates the dialog to add margins around the image.
Dialog used by the MipavGraphPanel to add a node to the graph, or to modify the Notes
attribute of a node.
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Dialog to get user input, then call the snake-like algorithm.
Adaptive Histogram Equlization.
Dialog to get user input, then call the algorithm.
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Confirmation Dialog giving user the choice to write an analyze file , interfile file, or a nifti file.
Dialog to get scale factor and interpolation method to create initial image forwarded to ViewJFrameAnimate.
Dialog to get user input, then call the algorithm.
Dialog for creating new/editing existing on-screen annotations.
Visual Interface to anonymize DICOM images by the directory-full.
REALLY like JDialogRemoveSlices except it does not have an "algorithm"
Dialog to get user input, then call the algorithm.
Dialog to get user input any two images SNR Algorithms are executed in their own thread.
Dialog to call AlgorithmAutoCorrelation.
Dialog to call AlgorithmAutoCovariance.
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Confirmation Dialog giving user the choice to choose what type of compression to use when saving to AVI format.
Dialog for correcting barrel and/or pincushion distortion
This class is the base for all the other dialogs.
Dialog to get user input, then call the algorithm for BG distance map.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get image type for blank image.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog for an algorithm which reduces the intensity of an image near the boundary of the VOIs within an image volume.
Dialog to call AlgorithmBoxCount.
This dialog collects parameters for the BSE algorithm and then starts it up.
This class creates a simple dialog in which the user can specify a brightness integer and a contrast float using
sliders.
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Dialog to get user input, then call the algorithm for smoothing VOIs.
Dialog to get user input, then call the algorithm.
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Dialog for creating and saving a screen capture to a TIFF file.
Dialog (invisible) for capturing slices of a 3d/4d image into a new image.
Dialog to get user input, then call the algorithm.
Title: JDialogCenterOfMassRGB
Creates the dialog to input inital centroid values and threshold value for each class for
AlgorithmMSpectralFuzzyCMeans.
This is a dialog that allows the user to change the mask number on the buttons
Dialog to get the row and column numbers of checkerboard squares
Dialog to create an image with randomly spaced, aggregated, regular or uniform, or constrained circles of the same size
Dialog to get user input of circle center and point on circle curve and output xDim and yDim of rectangle created
from transformed circle.
Dialog to get user input of 4 bounding sector points and output xDim and yDim of rectangle created from transformed
sector.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call a specified diffusion algorithm.
Dialog to get user input Identify colocalized pixels Algorithms are executed in their own thread.
Dialog to get user input Calculate Pearson's correlation coefficient Calculate P value for this correlation
coefficient Identify colocalized pixels Algorithms are executed in their own thread.
GUI for entering parameters for the Color Edge algorithm and making it scriptable.
Dialog for adjusting color saturation
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call algorithm RegistrationOAR3D.
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Dialog to call the AlgorithmConvert3Dto4D to convert a 3D data set into a 4D data set.
Dialog to call the AlgorithmConvert4Dto3D to convert the current image from a 4D one to a 3D one.
Simple dialog to convert the type of an image.
This dialog converts the VOI lines or VOI contour lines into .ply file format as the point cloud based file.
Dialog to get user input, then call the algorithm for smoothing VOIs.
This class convert the 3D images to 2D slices based atlas.
Algorithm to adjust image volume for cases when the slice spacing is not equal to the slice thickness.
This code is used to create VOI from Alexnet generated energy maps.
This class convert the 3D images to 2D slices based atlas.
This class convert the 3D images to 2D slices based atlas.
Dialog to get user input, then call the crop algorithm.
Creates the dialog to crop pixels around the image.
Creates the dialog to crop pixels around the selected point.
Creates the dialog to crop pixels around the 8 selected tilted cuboid points.
Creates the dialog to crop pixels around the 4 selected tilted rectangle points.
Simple dialog for CT window presets.
Simple dialog for CT window presets.
Simple dialog for CT window presets.
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Creates the dialog to cyclically permute pixels around the image.
Simple dialog used to show the image or system data provenance (by passing in a provenanceholder
Displays data in table format, and the currently selected item will show up in the JTextArea (not editable, but selectable)
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog box for Demons
Dialog to get user input for 3 parameter dynamic (contrast) enhanced MRI model or DEMRI model
Dialog to select DICOM files to convert to MIPAV XML or Minc 2.0 HDF format.
dialog for deleting DICOM tag information currently allows a limited number of special tags (procssing of which must
be performed by the DICOM tag itself), but allows editing seperate multiplicity values.
Simple dialog used to show the contents of a selected DICOMDIR file.
dialog for adding new DICOM tag information currently allows a limited number of special tags (procssing of which must
be performed by the DICOM tag itself), but allows editing seperate multiplicity values.
dialog for editing DICOM tag information currently allows a limited number of special tags (procssing of which must
be performed by the DICOM tag itself), but allows editing seperate multiplicity values.
This class allows for DICOM tags to be selected.
Title: JDialogDICOMtoAVI
Dialog to get user input, then call the algorithm.
Dialog to ask user to resample the images or not.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get Schwarz-Christoffel mapping of region between 2 polygons to an annulus
Dialog for specifying Diffusion Tensor Images.
Dialog to get user search for best boundary between 2 contours
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Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Simple editor using JPanelEdits.
This class is the dialog that allows the user to edit the user defined file extensions filter
Dialog to get user input, then call the algorithm.
Dialog to create an image with randomly spaced, aggregated, regular or uniform, or constrained ellipses of the same size
Dialog to get user input of ellipse which will be conformally mapped to a circle.
Dialog to get user input of ellipse which will be conformally mapped to a rectangle.
Confirmation Dialog giving user the choice to write an enhanced dicom MR, CT, XA, or Other file.
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Dialog to get user input, then call the algorithm.
Dialog to get user input, then call AlgorithmEvaluateMaskSegmentation.
Dialog to get user input, then call AlgorithmEvaluateSegmentation.
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Dialog to call the extractSlices.
Creates the dialog to remove separate slices in an image.
Extracts a surface using Cube Extraction.
Dialog used to input parameters and start the BET-based face anonymizer.
Dialog to get user input, then call the algorithm.
The class is the driver for the AAM classification.
The class is the driver for the AAM classification.
The class is the driver for the AAM classification.
Dialog to get user input, then call the algorithm.
This class shows the dialog which conatains the file-info header information as used in the FileInfoBase class.
This class shows the dialog which contains the DICOM header information as contained in the FileInfoDicom class.
Text dialog filled with the a minc image's file info.
This class shows the dialog which conatains the file-info header information as used in the FileInfoBase class.
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Simple dialog to choose the filter for the view image directory.
Dialog to get user input, then call the algorithm.
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Dialog to call the image flip.
Dialog to get user input, then call the algorithm.
Dialog to get user input Fluorescence recovery after photobleaching Algorithms are executed in their own thread.
Dialog to get user input, then call the algorithm.
Dialog to get user input Fluorescence resonance energy transfer Algorithms are executed in their own thread.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
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Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
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Dialog to get user input, then call the algorithm.
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Sets options for overlaying a grid on the image.
Title:
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
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Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input Create 2D histogram of images with equal dimensions or 2D histograms with 2 colors inside a
RGB image.
Deprecated.
Dialog to get user input Selected image is match image, the image that gets transformed until it is histogram matched
to the base image.
Dialog to get user input reference slice.
Dialog to choose images, then call the RGBConcat algorithm.
Dialog to get user input, then call the algorithm.
Dialog to create Hough transform with x0, y0, rad output for cardioid detection in
binary image, where sqrt((x - x0)**2 + (y - y0)**2) = a*(1 - cos(theta + theta0))
sqrt((x - x0)**2 + (y - y0)**2) = a*(1 + cos(theta)) for cusp on left
sqrt((x - x0)**2 + (y - y0)**2) = a*(1 - cos(theta)) for cusp on right
sqrt((x - x0)**2 + (y - y0)**2) = a*(1 + sin(theta)) for cusp on top
sqrt((x - x0)**2 + (y - y0)**2) = a*(1 - sin(theta)) for cusp on bottom
Confirmation Dialog giving user the choice to choose which cardioids to draw.
Dialog to create Hough transform with x0, y0, rad output for circle detection in
binary image, where (x - x0)**2 + (y - y0)**2 = rad**2
Confirmation Dialog giving user the choice to choose which circles to draw.
Dialog to create Hough transform with p, q, r1, r2, and theta output for ellipse detection in
binary image, where p is the x coordinate of the ellipse center, q is the y coordinate of the
ellipse center, r1 is the semimajor axis (or major radius), r2 is the semiminor axis (or
minor radius), and theta is the angle of the major axis with the x axis.
Confirmation Dialog giving user the choice to choose which ellipses to draw.
Dialog to create Hough transform with p, q, r1, r2, and theta output for hyperbola detection in
binary image, where p is the x coordinate of the hyperbola center, q is the y coordinate of the
hyperbola center, r1 is the 1/2 the transverse axis, r2 is 1/2 the conjugate axis, and theta is
the angle of the transverse axis with the x axis.
Confirmation Dialog giving user the choice to choose which hyperbolas to draw.
Dialog to create Hough transform with rho, theta output for line detection of binary image
Confirmation Dialog giving user the choice to choose which lines to fill gaps on and
the maximum distance of the gap to be filled for each line..
Dialog to create Hough transform with xv, yv, phi, p output for parabola detection in
binary image, where [(y - yv)*cos(phi) - (x - xv)*sin(phi)]**2 =
4*p*[(y - vy)*sin(phi) + (x - vx)*cos(phi)]
where vx, vy are the coordinates of the parabola vertex
p is the distance between the vertex and focus of the parabola
Confirmation Dialog giving user the choice to choose which parabolas to draw.
Dialog to get user input, then call the algorithm.
Frame and user interface for displaying a HyperGraph in MIPAV.
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Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
The image attribute input dialog, which consists of six tabbled panes allowing the user to edit image name,
resolutions, orientations, dataset origin, history, and transformation matrix.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Creates the dialog to input inital centroid values for each class for AlgorithmFuzzyCMeans.
Creates the dialog to insert missing slices into an image.
Creates the dialog to insert slice into an image.
Simple dialog to install a plugin.
Title:
Simple dialog to change desired intensity level for painting.
Title:
Simple dialog to invert an image - substitute light intensities for dark intensities and dark intensities for light
intensities.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
For knees project, reconstruct the 3D surface from VOIs.
This class converts the original knees MRI images into isotropic images.
1) Convert the VOIs into binary image masks.
2) Convert the original images into isotropic images
3) Convert the isotropic images from sagittal to axial; sagittal to coronal.
4) Along each orietation, generate the CED image in addition to MRI.
5) Save all the images (isotropic axial, sagittal, coronal images with corresponding binary masks).
This class convert the 3D images to 2D slices based png files for single MRI GRE image alone.
Test case: generate the femur VOI contours from Alexnet generated deep learning energy maps.
--------------------------------------------------------
No longer need it.
This class generates the knees VOI contours from the deep learning HED MRI and CED energy maps.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Generate the 2D 32x32 patches for both training and testing cased.
1) AAM generates the initial contours.
2) Alone each normal line of the contour point, extract 32x32 patches for both training and testing cases
--------------------------------------------------------
No longer need it.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
This class builds the control dialog used in ViewJFrameLightbox class.
Dialog to get user input, then call the algorithm...
A basic dialog to read and parse the two options files, display the options in the files, and allow file action
between the two.
Simple dialog to choose which cost function to use for the live wire.
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JDialogLoadImage allows the MIPAV user to import an image (namely, ImageA) from another image frame.
JDialogLoadImage allows the MIPAV user to import an image (namely, ImageA) from another image frame.
Creates the dialog to remove separate slices in an image.
This is the dialog to permit user to perform Local Normalization.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
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Simple dialog to change Magnification Box Settings.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm...
Dialog to call Maximum Intensity Projection.
Dialog that launches the Maximum likelihood iterated blind deconvolution
algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to alter memory allocation of the runtime environment.
Confirmation Dialog giving user the choice to choose what type of MetaImage file to write.
Dialog to get user input, then call the midsagittal alignment algorithm.
This dialog contains access to MIPAV preferences.
Dialog to get user input, then call AlgorithmMode.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
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Dialog to get user input, then call the algorithm.
.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input any two images optical flow estimation based on multi scale Horn-Schunk are executed in their own thread.
Dialog to get user input, then call the algorithm.
Simple dialog to change the number of colors in the histogram LUT.
Dialog to get user input of a nearly circular region which will be conformally mapped to a circle.
Confirmation Dialog giving user the choice to choose what type of NIFTI file to write.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
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Dialog to get user input, then call the algorithm.
Simple dialog to change Opacity Settings (1 = opaque, 0 = transparent).
Dialog to get user input, then call the algorithm.
Confirmation dialog used in AFNI to decide whether to reorder the image to dicom order.
Dialog used to determine how the transformation matrix should be adjusted to account for different coordinate
systems.
Title: JDialogOverlay
Creates the dialog to pad blank images to an active image.
Dialog to get the upper and lower bounds for the region grow used by the paint functions.
Simple dialog to change Opacity Settings (1 = opaque, 0 = transparent).
Dialog to facilitate the painting of a region of an image (such as the vascualture in a liver mip).
Dialog to get user input, then call the algorithm.
Patella segmentation for Netherland data.
The class is the driver for the AAM classification.
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Dialog that will call AlgorithmPointArea in order to calculate the average intensity through a volume around an area
with a given size (x by y) at a given point.
Dialog to get user input of 3 or more counterclockwise ordered polygon points
for polygon to circle conformal mapping.
Dialog to get user input of counterclockwise ordered polygon points,
followed by selecting 4 of these vertices in counterclockwise order to be
the corners of the rectangle.
Dialog box for the paint power tools: morphology operations, object delete, etc.
DOCUMENT ME!
Dialog to create a filtered image using only selected principal components in the reconstruction and also to create
an averaged image slice by simple averaging of the reconstructed image.
For Miccai promise 12 prostate data, we apply wp segmentation using HED deep learning model.
This class convert the 3D images to 2D slices based atlas.
This is the first try to 3D convolution deep learning models. 3D-Unet.
This class simply convert the prostate images into isotropic (same x, y resolution ) images.
Atfer N4 correction, take those images with binary masks, transform again
to 0.5mm x 0.5mm x 1.5 mm images.
Atfer N4 correction, take those images with binary masks, transform again
to 0.5mm x 0.5mm x 1.5 mm images.
After 0.5mm x 0.5mm x 1.5 mm transform, apply the intensity normalization [0, 1000], save image and masks.
After 0.5mm x 0.5mm x 1.5 mm transform, apply the intensity normalization [0, 1000], save image and masks.
This is the first try to 3D convolution deep learning models. 3D-Unet.
This is the first try to 3D convolution deep learning models. 3D-Unet.
This is the first try to 3D convolution deep learning models. 3D-Unet.
This class convert the 3D images to 2D slices based atlas.
This class convert the 3D images to 2D slices based atlas.
This class generates the VOIs from HED prediction maps.
This class generates the VOIs from HED prediction maps.
This class generates the VOIs from HED prediction maps.
This class generates the VOIs from HED prediction maps.
This class convert the 3D images to 2D slices based atlas.
This class copy ground truth stl file to destination directory.
This class convert the 3D images to 2D slices based atlas.
This class convert the 3D images to 2D slices based atlas.
For ISBI 2017 paper:
Data given: Dr.
This class attempts to generate the VOI from the HED predicted edge map (boundary map).
For ISBI 2017 paper:
ISBI, we only use MR images slices, no CED involved.
For ISBI 2017 paper:
This class converts the HED generated energy maps into VOI contours.
This class convert the 3D images to 2D slices based atlas.
This class convert the 3D images to 2D slices based atlas.
This class is the trial-and-error approach for HED deep learning experiment.
This class convert the 3D images to 2D slices based atlas.
This class is the trial-and-error approach for HED deep learning experiment.
This class is the trial-and-error approach for HED deep learning experiment.
This class is the trial-and-error approach for HED deep learning experiment.
This class is the trial-and-error approach for HED deep learning experiment.
This is the trial-and-error test, which applying the NIH data for training, Prostate promise 12 data for testing.
This is the first attempt to apply prostate segmentation on Promise 12 data.
This is the third attempt to apply prostate segmentation on Promise 12 data.
This is the third attempt to apply prostate segmentation on Promise 12 data.
This is the third attempt to apply prostate segmentation on Promise 12 data.
This is the third attempt to apply prostate segmentation on Promise 12 data.
This is the third attempt to apply prostate segmentation on Promise 12 data.
This is the second attempt to apply prostate segmentation on Promise 12 data.
This class is for SPIE paper: HED prostate MRI segmentation.
For JMI 2017 paper: this class uses image processing methods that are different to the SPIE paper.
1) Read the MRI image with VOIs
2) Generate the binary masks
2) Crop the image with the 25% deduction
3) Scale image intensity to range 0 to 1000.
4) Generate the CED image.
5) Extract MRI image and CED image slices with corresponding binary image masks for HED to train the
deep learning model.
This is for the SPIE paper: HED prostate segmentation.
For JMI 2017 paper: this class uses image processing methods that are different to the SPIE paper.
1) Read the MRI image with VOIs
2) Generate the binary masks
2) Crop the image with the 25% deduction
3) Scale image intensity to range 0 to 1000.
4) Generate the CED image.
5) Extract MRI image and CED image slices with corresponding binary image masks for HED to train the
deep learning model.
For rest of the papers: this class generates the training list from the training fold.
5 fold cross-validation, each training fold contains the png slices from all other folds.
The class converts the 2D-volumetric approach axial, sagittal and coronal MRI and CED png slices
into a file list.
This class simply converts the MRI and CED slices png files into a list file.
The class generates the png file list for test cases.
The class converts the MRI and CED png slices into a file list.
The class reconstructs the 3D surface from the axial, coronal, sagittal VOI contours.
For the Miccai promise 12 data, this class simply read the png files and generates
the png file list for HED to train the deep learning model.
The class reconstruct the 3D prostate surface from the Deep learning generated VOIs.
This class convert the 3D images to 2D slices based atlas.
The class reads the nii binary masks and generates the comparison list for shell script.
This class generates the EvaluateSegmentation shell script to evaluate the binary masks between
AAM vs.
After the 3D images convert to 2D slices ( 512x512 ), this class picks the 2D
slices, extracts the Coherence Enhanced diffusion based features, and saves
those features with linear SVM readable file formats.
This class exhaustively trains the 2D slices based Active Appearance Model
(AAM).
This class converts 3D prostate surface into VOIs; saving them for comparison.
This class converts 3D prostate surface into nii binary mask images.
This class read nii binary mask files, convert them into a shell script list.
For testing phase: This class reads the original MRI images and HED deep learning model predicted
MRI and CED energy map results, generates the final VOI contours.
For the JMI paper, this class converts VOI contours back to binary image masks.
This class convert the 3D images to 2D slices based atlas.
This class convert the 3D images to 2D slices based atlas.
Semi-automatic MR Prostate segmentation - Registration and Fuzzy-C guided
segmentation model.
Semi-automatic MR Prostate segmentation - Registration guided segmentation
model.
This class is for ProstateX 2017 MICCAI challenge.
This class generates the VOI contours from HED predicted energy maps.
For MICCAI ProstateX 2017 challenge testing cases,
this file generates the VOI contours from HED predicted MRI+CED energy maps.
The MICCAI ProstateX challenge is the first try on MRI image alone.
After the MICCAI ProstateX challenge, I try to apply the prostate boundary based training on HED model.
The MICCAI ProstateX challenge is rolling over to prostate segmentation, which includes the
whole prostate(wp) and central gland(cg).
The MICCAI ProstateX challenge is rolling over to prostate segmentation, which includes the
whole prostate(wp) and central gland(cg).
The MICCAI ProstateX challenge is rolling over to prostate segmentation, which includes the
whole prostate(wp) and central gland(cg).
The MICCAI ProstateX challenge is rolling over to prostate segmentation, which includes the
whole prostate(wp) and central gland(cg).
For NIH prostate data, we apply wp and cg segmentation using HED deep learning model.
This class simply read the MR, CED images with corresponding binary image masks, converting them
into image pairs ( MR slice with binary mask, CED slice with binary mask ).
Dialog to get user input, then call the algorithm.
Simple dialog to change the number of colors in the histogram LUT.
Dialog to call the randomize the order of 3D dataset.
Simple dialog to indicate type, dimensionality, of a raw image or image with a fixed length header in front of the
image data.
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This class is used to display the options to the user for performing 2D, 3D, and 2.5D B-Spline registration.
Private class which holds dialog controls associated with the values in the AlgorithmRegBSpline.Options class for
a "pass" of registration.
Dialog to get user input, then call algorithmChamfer.
Dialog to get user input, then call algorithmRegLeastSquares.
Dialog to get user input, then call AlgorithmRegOAR25D.
Dialog to get user input, then call AlgorithmRegOAR2D.
Dialog to get user input, then call AlgorithmRegOAR35D.
Dialog to get user input, then call algorithm RegistrationOAR3D.
Dialog to get user input, then call algorithmRegLeastSquares.
Dialog to get user input Selected image is match image, the image that gets transformed until it is registered to the
base image.
Dialog to get user input, then call algorithmRegValidation.
Dialog to get user input, then call algorithmRegPatientPos.
Dialog to get user input, then call a specified diffusion algorithm.
Dialog to register Kidney images, same spacial location, over time.
Simple dialog to remove a plugin.
Creates the dialog to remove separate slices in an image.
Creates the dialog to remove separate time slices in an image.
Dialog that gets input needed for saving the 3D rendering motions to an AVI file.
Dialog box for basic image processing tools
Dialog to replace the blank slices in 3D images with averages.
Title:
Dialog which replaces all occurances of one value in an image with another value.
Dialog to get interpolation choice, then call reslice algorithm.
Dialog to choose images, then call the RGBConcat algorithm.
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Dialog to call a algorithm to convert an RGB to a grayscale images.
Dialog to separate RGB channels into grayscale Hue, Saturation, and Brightness channels.
Dialog to call the image rotate.
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Simple dialog to tell the program important information necessary for saving the DICOM file.
Simple dialog to save the 3 VOIs ( Sagittal, Coronal, Axial ) for each view, and merge them into one cloud points.
Simple dialog to tell the program important information about the MINC file.
Confirmation Dialog giving user the choice to write an analyze file , interfile file, or a nifti file.
Simple dialog to indicate which slices should be saved.
Dialog to get user input, then call the algorithm.
All scriptable dialogs should inherit from this abstract class.
Dialog to get user input, then call algorithmTransform.
This is the "record script" dialog.
The purpose of this dialog is to allow the user to rearrange the channel order of an image before it is loaded.
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Dialog to get user input, then call the algorithm.
Simple dialog to set certain values for the new or edited server or destination.
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Dialog to get user input, then call the algorithm.
Calculate costs for various voxel similarity cost functions that are used in registration and output them to the data
window.
This class simply shuffle the H5 list randomly.
Dialog to get user input, then call the algorithm.
Simple dialog that requests a name for the view.
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Dialog to get user input signal 1 VOI, optional signal 2 VOI, background VOI or signal to use fuzzy c means to
separate all pixels into signal and background and number of NMR receivers needed for
MRI image SNR calculation.
Dialog to get user input any two images optical flow estimation based on single scale Horn-Schunk are executed in their own thread.
This class generates the knees VOI contours from the deep learning (HNN) MRI
and CED energy maps.
This class generates the knees VOI contours from the deep learning HED MRI maps.
Dialog to get user input, then call the algorithm.
The class prepare the evalution masks for segmentation result and ground truth label.
This class converts the original knees MRI images into isotropic images.
1) Convert the VOIs into binary image masks.
2) Transform the binary mask images to original image resolution.
3) Then, save the binary mask into .nii file format for comparison.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input for 3 parameter dynamic (contrast) enhanced MRI model or SM2 model
User-interface for smoothing the ModelTriangleMesh surfaces.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input any two images optical flow estimation based on Brox et al. method (spatial version) are executed in their own thread.
Dialog to create an image with randomly spaced, aggregated, regular or uniform, or constrained spheres of the same size
Dialog to get user input, then call the algorithm.
This is an abstract class which should be subclassed by Generic plug-in dialogs which want to support being run with
the -p command line switch without the rest of MIPAV (using the -hide option).
This is an abstract class which should be subclassed by Generic plug-in dialogs which want to support being run with
the -p command line switch without the rest of MIPAV (using the -hide option).
The Standard Deviation Threshold works by first having an active VOI in which the standard deviation and other
statistics are calculated.
Dialog for subsampling a 2D or 3D or 4D image by 2, 4, or 8.
Creates the dialog to create a 3D subset image from a 4D image.
Dialog to get user input, then call the algorithm.
Dialog that gets input needed for saving the 3D rendering motions to an AVI file.
Dialog to call the AlgorithmSwap34 to delete the current image and create a new image with the third and fourth
dimensions swapped.
Dialog to call the AlgorithmSwap34 to delete the current image and create a new image with the third and fourth
dimensions swapped.
Creates the dialog for swapping slices/volumes.
This class displays a basic dialog for a MIPAV plug-in.
Dialog to enter points for creating an Talaraich image.
Interface for the TalairachTransform plugin.
Dialog to get user input, then call the algorithm.
Dialog to get user input any two images optical flow estimation based on Brox et al. method (temporal version) are executed in their own thread.
This is simple text dialog that displays in the center of the screen.
This is simple text dialog that displays in the center of the screen.
This is simple text dialog that displays in the center of the screen.
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Dialog to get user input, then call the algorithm.
Dialog is used by the ViewJFrameHistoLUT frame.
Title: JDialogThresholdRGB
Dialog to get user input, then call the algorithm.
Dialog to enter points for creating an Talaraich image.
Dialog to get user input, then call the algorithm.
The class converts the 2D-volumetric approach axial, sagittal and coronal MRI and CED png slices (or MRI png slices alone)
into a file list.
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The dialog for the calculation of Tre methods.
Dialog to get user input, then call the algorithm.
Dialog to transform an image in the tri planar view based on a bounding box.
Simple dialog to change trim parameters.
Dialog to get user input any two images optical flow estimation based on total variation and the L1 norm are executed in their own thread.
Dialog to get user input two MRI image SNR Algorithms are executed in their own thread.
Dialog to get user input, then call the algorithm.
Simple dialog to uninstall a plugin.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Simple dialog to indicate type of image when the program doesn't recognize the name.
Dialog to get user input, then call the algorithm.
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Dialog to use difference, intersection, exclusive or, or intersection on 2 VOIs
Dialog to call the VOI extraction.
Title:
Dialog for calculating statistics of a (set of) Volumes of Interest.
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Dialog to ask user to resample the images to power of 2 before volume rendering.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
Dialog to get user input, then call the algorithm.
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Dialog creates 2 sliders which adjust the level and window of an image.
This is a custom swing dialog that sets variables for zooming in and out.
Lookup table interface for either grayscale or color (RGB) images.
JFrameRegistrationMosaic is a window/gui that enables the user to manually align two images with the mouse and then
call the AlgorithmRegOAR2D registration algorithm to create a mosaic image with the two aligned images.
Window for setting the surface material properties.
Window for setting the surface material properties.
This panel encapsulates radio buttons which allow the user to indicate whether a new image should be generated by the
algorithm dialog parent of the panel and whether the whole image or a VOI region should be processed.
Custom panel for anonymizing DICOM images.
The panel class used in anonymize image/directory that displays the private
tags in a tree format along with check boxes so that the organization between
groups is apparent.
The panel class used in anonymize image/directory that displays the public
tags in a tree format along with check boxes so that the organization between
groups is apparent.
Title: JDialogAVIChoice
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JPanelCamera creates the camera control panel for the 3D visulization frame.
Creates a JPanel to hold a scrolling list of checkboxes.
Title: JPanelClip
A panel containing checkboxes which allow the user to indicate which channels of a color image should be processed.
The display panel control the red bounding box frame ( on/off ), texture aligned rendering mode, cubic controk,
perspective and parrallel viewing mode, and back ground color.
The display panel control the red bounding box frame ( on/off ), texture aligned rendering mode, cubic controk,
perspective and parallel viewing mode, and back ground color.
The copyright below only pertains to methods within JDialogImageInfo that relate to the Gradient Table Creator for
Philips PAR/REC files V3/V4 that is displayed in the DTI tab.
An abstract class for editing a single, specfic value.
An EditPanel which allows the user to select among the Analyze possibilities for image orientation.
An EditPanel which allows the user to select a boolean value ('true' or 'false').
Very simple EditPanel which merely edit a letter at a time.
panel contains 3 fields: 2 comboboxes (day, month), 1 text field (year), panel handles proper day/month and leap-year
input.
Very simple EditPanel which merely contains some text.
An EditPanel which allows the user to select among the Analyze possibilities for image orientation.
An EditPanel which allows the user to select from a list of modalities (from FileInfoBase.modalityStr).
An EditPanel which allows the user to select among the Analyze possibilities for image orientation.
An EditPanel which allows the user to select from a list of races.
Very simple EditPanel which merely contains some text.
adds panel with combobox to change field containing the patient's sex.
panel contains 4 fields:
3 comboboxes (hour, minute, second),
1 text field (decimal fraction of a second),
An EditPanel which allows the user to select from a list of parameter value types.
provides a nice plug-in swing panel to simplify the file-selection process.
Title: JPanelFlythruMove
Title: JPanelGeodesic
Title: JPanelGeodesic
Deprecated.
Deprecated.
Dialog to turn slices bounding box of surface renderer on and off, and to change the color of the frame.
Dialog to turn slices bounding box of surface renderer on and off, and to change the color of the frame.
panel to hold and transfer items between two lists. extend to modify the application of the 'left', 'right', and
'delete' or 'up', 'down' and 'delete'.
Mouse recorded dialog.
Mouse recorded dialog.
This panel contains the display panel for the 2D Histogram user-interface.
The navigation (for virtual bronchoscopy) fly-thru control panel.
A dialog to permits choosing a range (positive or negative, and floating-point) of values with the intention of the
selection indicating a range of values.
Dialog to turn slices bounding box of surface renderer on and off, and to change the color of the frame.
Title: JPanelProgressBar
This class is the base for all the other dialogs.
This class is the base for all the other dialogs.
Dialog to turn bounding box of surface renderer on and off, and to change the color of the frame.
Dialog to turn bounding box of surface renderer on and off, and to change the color of the frame.
Title: JPanelSculptor
Title: JPanelSculptor
A panel containing fields which allow the user to input sigmas in three dimensions (of, for example, a gaussian
kernel).
Dialog to turn slices bounding box of surface renderer on and off, and to
change the color of the frame.
Dialog to turn slices bounding box of surface renderer on and off, and to
change the color of the frame.
Custom panel for placing statistics in a selectable checklist panel.
A Java3D-based dialog for surfaces represented as triangle meshes.
Dialog to turn bounding box of surface renderer on and off, and to change the color of the frame.
JPanelSurfaceTexture.
JPanelSurfaceTexture.
panel to hold and transfer items between two trees. extend to modify the application of the 'left', 'right', and
'delete' or 'up', 'down' and 'delete'.
Dialog to control the view of the 3D surface viewer and renderer.
Control panel to set up the virtual endoscopy volume view.
Control panel to set up the virtual endoscopy volume view.
Deprecated.
Deprecated.
Deprecated.
Simple panel containing the volume renderer opacity controls.
This program takes a list of JPEG image files and convert them into a QuickTime movie.
Class JStereoWindow:
Copyright 2022-2024 Leo Izen (Traneptora)
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.
This must be separate because TransformType's static initializers won't fire in time
Copyright (c) 2009, Ehud Schreiber
All rights reserved.
Original code Copyright (C) 2007-2011 John Tsiombikas invalid input: '<'nuclear@member.fsf.org>
Ported to Java by William Gandler
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1.
This class converts the original knees MRI images into isotropic images.
1) Convert the VOIs into binary image masks.
2) Convert the original images into isotropic images
3) Convert the isotropic images from sagittal to axial; sagittal to coronal.
4) Along each orietation, generate the CED image in addition to MRI.
5) Save all the images (isotropic axial, sagittal, coronal images with corresponding binary masks).
This is a port of the FORTRAN 77 L-BFGS-B code to Java
L-BFGS-B is released under the “New BSD License” (aka “Modified BSD License”
or “3-clause license”)
=========== L-BFGS-B (version 3.0.
Copyright (c) 2007-2014 The LIBLINEAR Project.
Copyright (c) 2007-2014 The LIBLINEAR Project.
Supports the worm-straightening algorithms that use a 3D lattice as the basis of the straightening process.
Created by IntelliJ IDEA.
The Class LEFileWriter.
Ported to Java from C code from
http://www8.cs.umu.se/kurser/TDBAfl/VT06/algorithms/WEBSITE/IMPLEMEN/TURN/IMPLEMEN.HTM
May only be used for non-commercial purposes.
libdt - OpenCV library for Dynamic Textures - version 1.0
Copyright (c) 2011-2014 Antoni B.
regularization method.
type of covariance matrix.
Normalization mode for each patch.
Options for modeling the observation mean, Ymean.
Ported from C to Java by William Gandler
LEGAL ISSUES
============
In plain English:
1.
Ported from C to Java by William Gandler
LEGAL ISSUES
============
In plain English:
1.
Copyright (c) 2000-2023 Chih-Chung Chang and Chih-Jen Lin
All rights reserved.
JPEG XL image format reference implementation ported from C++ to Java by William Gandler
Copyright (c) the JPEG XL Project Authors.
Settings for the interpretation of UINT input and output buffers.
Frame blend modes.
Defines which color profile to get: the profile from the codestream
metadata header, which represents the color profile of the original image,
or the color profile from the pixel data produced by the decoder.
Color space of the image data.
Data type for the sample values per channel per pixel.
Error conditions:
API usage errors have the 0x80 bit set to 1
Other errors have the 0x80 bit set to 0
Id of encoder options for a frame.
Data type for querying @ref JxlEncoderStats object
Ordering of multi-byte data.
Given type of an extra channel.
Image orientation metadata.
Built-in primaries for color encoding.
Types of progressive detail.
Rendering intent for color encoding, as specified in ISO 15076-1:2010
The result of @ref JxlSignatureCheck.
Built-in transfer functions for color encoding.
Built-in white points for color encoding.
The class creates a RGB image of a 3d image in a Lightbox type format.
Copyright (c) 2007-2014 The LIBLINEAR Project.
used as complex return type
LineMeter is a history-graph panel which updates its display once a second, drawing a curve of the history of inputs
to setAmplitude().
To run self tests in another module put:
if (testMode) {
new FitAll();
setCompleted(false);
return;
}
class FitAll extends Lmmin {
public FitAll() {
super();
}
public void fitToFunction(double x[], double fvec[], int info[]) {
return;
}
}
Title:
Port of LSCM, Least squares conformal mapping
This package includes the prototype code for implementing least squares conformal maps.
This class implements the curvature flow filter for 2D images
using a finite-difference-based solver for the partial differential
equation:
du/dt = |grad(u)|*divergence(grad(u)/|grad(u)|)
where u(x,y,t) is the evolved image at time t, du/dt is the time derivative of u, and grad(u) is the gradient of u with respect to the spatial variables.
du/dt = |grad(u)|*divergence(grad(u)/|grad(u)|)
where u(x,y,t) is the evolved image at time t, du/dt is the time derivative of u, and grad(u) is the gradient of u with respect to the spatial variables.
This class implements the curvature flow filter for 3D images
using a finite-difference-based solver for the partial differential
equation:
du/dt = |grad(u)|*divergence(grad(u)/|grad(u)|)
where u(x,y,z,t) is the evolved image at time t, du/dt is the time derivative of u, and grad(u) is the gradient of u with respect to the spatial variables.
du/dt = |grad(u)|*divergence(grad(u)/|grad(u)|)
where u(x,y,z,t) is the evolved image at time t, du/dt is the time derivative of u, and grad(u) is the gradient of u with respect to the spatial variables.
The abstract base class for level-set evolution of 2D images.
The abstract base class for level-set evolution of 3D images.
The abstract base class for fast-marching methods of images.
The fast-marching method for 2D images.
The fast-marching method for 3D images.
This class implements the Gaussian blur filter for 2D images
using a finite-difference-based solver for the partial differential
equation:
du/dt = Laplacian(u)
where u(x,y,t) is the evolved image at time t, du/dt is the time derivative of u, and Laplacian(u) = u_xx + u_yy, a sum of second-order derivatives of u.
du/dt = Laplacian(u)
where u(x,y,t) is the evolved image at time t, du/dt is the time derivative of u, and Laplacian(u) = u_xx + u_yy, a sum of second-order derivatives of u.
This class implements the Gaussian blur filter for 3D images
using a finite-difference-based solver for the partial differential
equation:
du/dt = Laplacian(u)
where u(x,y,z,t) is the evolved image at time t, du/dt is the time derivative of u, and Laplacian(u) = u_xx + u_yy + u_zz, a sum of second-order derivatives of u.
du/dt = Laplacian(u)
where u(x,y,z,t) is the evolved image at time t, du/dt is the time derivative of u, and Laplacian(u) = u_xx + u_yy + u_zz, a sum of second-order derivatives of u.
A level-set evolver for 2D images.
A level-set evolver for 3D images.
This class implements the gradient anistropic curvature flow
filter for 2D images using a finite-difference-based solver for the
partial differential equation:
du/dt = divergence(exp(-0.5*|grad(u)|^2/(k^2*average(|grad(u)|^2))*grad(u))
where u(x,y,t) is the evolved image at time t, du/dt is the time derivative of u, and grad(u) is the gradient of u with respect to the spatial variables.
du/dt = divergence(exp(-0.5*|grad(u)|^2/(k^2*average(|grad(u)|^2))*grad(u))
where u(x,y,t) is the evolved image at time t, du/dt is the time derivative of u, and grad(u) is the gradient of u with respect to the spatial variables.
This class implements the gradient anistropic curvature flow
filter for 3D images using a finite-difference-based solver for the
partial differential equation:
du/dt = divergence(exp(-0.5*|grad(u)|^2/(k^2*average(|grad(u)|^2))*grad(u))
where u(x,y,z,t) is the evolved image at time t, du/dt is the time derivative of u, and grad(u) is the gradient of u with respect to the spatial variables.
du/dt = divergence(exp(-0.5*|grad(u)|^2/(k^2*average(|grad(u)|^2))*grad(u))
where u(x,y,z,t) is the evolved image at time t, du/dt is the time derivative of u, and grad(u) is the gradient of u with respect to the spatial variables.
A class that encapsules a min-heap data structure.
This class is a simple wrapper for the parameters that occur in the
level-set evolution, which is controlled by the partial differential
equation:
du/dt = -a*A(x).grad(u) - b*P(x)*|grad(u)| + c*Z(x)*K(u)*|grad(u)| + d*Laplacian(u)
where u(x,t) is the evolved image at time t, du/dt is the time derivative of u, grad(u) is the gradient of u with respect to the x-variable, A(x) is the advection term with advection weight a, P(x) is the propagation term with propagation weight b, Z(x) is the curvature term with curvature weight c, K(u) is the mean curvature of level curves (in 2D) or surfaces (in 3D), and Laplacian(u) is the sum of second-order unmixed derivatives with Laplacian weight d.
du/dt = -a*A(x).grad(u) - b*P(x)*|grad(u)| + c*Z(x)*K(u)*|grad(u)| + d*Laplacian(u)
where u(x,t) is the evolved image at time t, du/dt is the time derivative of u, grad(u) is the gradient of u with respect to the x-variable, A(x) is the advection term with advection weight a, P(x) is the propagation term with propagation weight b, Z(x) is the curvature term with curvature weight c, K(u) is the mean curvature of level curves (in 2D) or surfaces (in 3D), and Laplacian(u) is the sum of second-order unmixed derivatives with Laplacian weight d.
The abstract base class for finite-difference-based solvers for partial
differential equations.
The abstract base class for finite-difference-based solvers for partial
differential equations in 2D.
The abstract base class for finite-difference-based solvers for partial
differential equations in 3D.
A segmenter for 2D images based on the PDE described in
LseGeodesicActiveContour2.
A segmenter for 3D images based on the PDE described in
LseGeodesicActiveContour3.
The abstract base class for segmentation via level-set evolution.
A segmenter for 2D images based on the PDE described in LseShapeDetection2.
A segmenter for 3D images based on the PDE described in LseShapeDetection3.
A segmenter for 2D images based on the PDE described in LseThreshold2.
A segmenter for 3D images based on the PDE described in LseThreshold3.
A level-set evolver for 2D images.
A level-set evolver for 3D images.
A level-set evolver for 2D images.
A level-set evolver for 3D images.
LsqFit.jl is licensed under the MIT License:
Returns the argmin over x of `sum(f(x).^2)` using the Levenberg-Marquardt
algorithm, and an estimate of the Jacobian of `f` at x
LUSOL maintains LU factors of a square or rectangular sparse matrix.
LUSOL maintains LU factors of a square or rectangular sparse matrix.
Stores the default manifest file as a static reference, or optionally can be used for creating custom manifest files.
Title: MaskBurnAtribute
Class that stores matrices (owned by ModelImage) with accessor functions to the matrix map/adding and changing
matrices.
Helper class to make it easy to store the necessary information about a minimum.
A limited-functionality binary property list (BPLIST) utility.
A data structure to hold the BPLIST trailer data.
A checked replacement for
IndexOutOfBoundsException.Enumeration of supported file types.
A series of utility methods for working with the file system.
Defines an object that extracts metadata from in JPEG segments.
Performs read functions of JPEG files, returning specific file segments.
An enumeration of the known segment types found in JPEG files.
Defines an object capable of processing a particular type of metadata from a
MetadataExtractor.RandomAccessReader.Contains helper methods that perform photographic conversions.
Used to suppress specific code analysis warnings produced by the Findbugs tool.
Interface of an class capable of handling events raised during the reading of a TIFF file
via
MetadataExtractor.TiffReader.MipavCoordinateSystems class.
Displays the Mipav HyperGraph.
Parses the MIPAX Graph XML file.
Writes the mipav graph to .xml format.
MipavLightingEffect uses the lights defined in the Volume/Surface/Tri-Planar view in the light shader.
Math functions not found in Java's Math class or they are slow.
Overrides how the Nodes are displayed in the HyperGraph.
SAX Reader for the HyperGraph display.
Title: MIPAVTableCellRenderer
A collection of static methods and frequently used and useful constants are in this utility class.
Static abstract class similar to mouseAdapter to allow the catching of actionevents from components without
having to implement ActionListener.
Cortical analysis applet and viewer.
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Limited implementation of a floating-point polynomial of 1 variable.
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Ray is R(t) = P+t*D for t >= 0.
Segment is S(t) = P+t*D for 0 invalid input: '<'= t invalid input: '<'= 1.
Sparse matrix implemented with a hash map.
Used to reference a single element in the matrix.
Add methods which make the Vector2f more robust and flexible to use.
Add methods which make the Vector3f more robust and flexible to use.
Copyright (c) 2007-2014 The LIBLINEAR Project.
A triangle mesh that represents a level surface.
A simple triangle mesh that represents a level surface.
Histogram model extends ModelStorageBase and stores and processes information about histograms.
This class extends the generic buffer class ModelStorageArray and is used to store n-dimensional images and buffer
class that supports boolean, byte, short, int, long, float, double, etc. data types.
Used to store the information and layout which describes a volume of data.
Stores the indexes into a linear array for the samples to use in computing finite difference based gradients as
follows:
Model of a Lookup Table (LUT).
A helper class to map image values to RGB colors.
A simple quadrilateral mesh that represents a level surface.
Model of a RGB Table. 256 length red, green, and blue tables are constructed from the red, green, and blue transfer
functions.
This class clones (copies) by serializing the object (providing it can be serialized).
Used in ModelSurfaceDecimator and ModelSurfaceTopology.
This is very simple class to store a float type image of up to four dimensions.
A triangle decimator that is used for continuous level of detail of a triangle mesh.
A level surface extractor that is based on decomposing voxels into tetrahedra, assuming a linear interpolation on the
tetrahedra, and extracting triangular level sets for those tetrahedra.
A level surface extractor that is based on decomposing voxels into cubes, assuming a linear interpolation on the
cubes, and extracting triangular level sets for those cubes.
This is an implementation of a vertex-edge-triangle table.
For debugging and testing.
A simple triangle mesh that represents a level surface.
Storage representation for a triangle mesh.
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Copyright (c) 2015, Sheung Hun Cheng and Nicholas J.
MIT License
Copyright (c) 2021 Jitendra Singh Bisht
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.
Abstract class which implements much of the event tracking and state updating shared between Fly and Pointer
behavior.
Title: MouseBehavior
Also added this line: public final static int SELECTION=4; And this method: public void transformClicked Also added
this line: public final static int PROPERTIES=5; Added this method: public void transformDoubleClicked.
Abstract class which implements much of the event tracking and state updating shared between Fly and Pointer
behavior.
This class holds the necessary information for each "mouse event" that shows up in the list.
This class holds the necessary information for each "mouse event" that shows up in the list.
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Converting a copy of MouseSelection to be used to with DoubleClicking (PickProperties).
MouseRotate is a Java3D behavior object that lets users control the rotation of an object via a mouse.
MouseRotateExt extends the MouseRotate class by providing public access to certain states of the MouseBehavior that
are stored as protected values with no other public accesss.
Converting a copy of MouseRotation to be used to with picking (PickSelection).
MouseTranslate is a Java3D behavior object that lets users control the translation (X, Y) of an object via a mouse
drag motion with the third mouse button (alt-click on PC).
MouseTranslate is a Java3D behavior object that lets users control the translation (X, Y) of an object via a mouse
drag motion with the third mouse button (alt-click on PC).
MouseZoom is a Java3D behavior object that lets users control the Z axis translation of an object via a mouse drag
motion with the second mouse button.
MouseZoom is a Java3D behavior object that lets users control the Z axis translation of an object via a mouse drag
motion with the second mouse button.
This class creates AVIs (.avi) out of a list of JPEG files or out of an array of java.awt.Image objects.
The java.awt.Image-based source stream to go along with ImageDataSource.
A DataSource to read from a list of JPEG image files or java.awt.Images, and turn that into a stream of JMF
buffers.
The jpeg-based source stream to go along with ImageDataSource.
This class is an example class for tying existing plugins into the JIST interface.
This is a port of multi_guided_est.py by Yiqian Wang.
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This is a port of multi_bilateral.py by Yiqian Wang.
Handle events generated while parsing the XML file.
Handle events generated while parsing the XML file.
Static methods for extracting and loading native libraries that were previously loaded directly in the MIPAV JRE.
Behavior which allows for flying down a specified path and looking around.
Instances which want to be notified of updates to this behavior should
implement this interface by providing the viewChanged method
implementation.
Navigation fly-thru mode picker, which pick the fly-thru direction.
Nelder-Mead original code copyright 2017 by Matteo Maggioni under the MIT Licence.
This is a port of nesolve.m and supporting files coded in MATLAB by Richard T.
This is a port of the source code nl2sol.f90 and the nl2sol_prb2.f90 extensive set of tests from FORTRAN into Java.
Display results of displaying exponential fitting parameters.
Display results of displaying exponential fitting parameters.
Example
public class Objfunc implements Objfun
{
public double evalObjfun(double x[]){
return (100*(x[1]-x[0]*x[0])*(x[1]-x[0]*x[0])+(1.0-x[0])*(1.0-x[0]));
}
}
public class Constraint implements Constraints
{
double round2(double num, int precision)
{
double rnum;
int tnum;
rnum = num*Math.pow(10,precision);
tnum = (int)(rnum invalid input: '<' 0 ?
Used to generate a scene node item that that represents the rendering of the volume using texture maps.
Used to generate a scene node item that that represents the rendering of the volume using texture maps.
oast9 - OAST, an optimal corner detector based on the
accelerated segment test for a 16 pixel mask
Copyright (c) 2010, Elmar Mair
All rights reserved.
An interface for the Observable
An interface for the Observer pattern.
Abstract base class for implementing Algorithms in OpenCL.
OpenCL Algorithm convolves a kernel with a 2D, 3D or 4D image.
OpenCL Algorithm computes Deconvolution for a 3D or 4D image.
OpenCL Algorithm computes the GaussianBlur of a 2D, 3D or 4D image.
OpenCL Algorithm computes the Gradient Magnitude of a 2D, 3D or 4D image.
OpenCL Algorithm computes the Laplacian of a 2D, 3D or 4D image.
OpenCL Algorithm implementation calculate the volume normals of a 3D image.
Displays OpenCL information in a table.
This class sets up the final pass in rendering multiple semi-transparent surfaces.
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Interface to allow different types of ViewJComponents* to work with region grow dialogs.
Manages the adding of components to a panel, automatically tranlating between logical element placement and the
panel's layout.
This is an abstract base class for all script action parameters.
Copyright (c) 2007-2014 The LIBLINEAR Project.
A boolean parameter used in either the recording or execution of a script action.
A double parameter used in either the recording or execution of a script action.
Exception indicating an error encounted while retrieving a script parameter (i.e., it doesn't exist or is of an unexpected type).
A image placeholder variable parameter used in either the recording or execution of a script action.
Factory methods for the creation of various types of Parameters.
A file parameter used in either the recording or execution of a script action.
A floating point parameter used in either the recording or execution of a script action.
A image placeholder variable parameter used in either the recording or execution of a script action.
A integer parameter used in either the recording or execution of a script action.
This is a special kind of script parameter, which contains other parameters.
A long parameter used in either the recording or execution of a script action.
A singed short parameter used in either the recording or execution of a script action.
A string parameter used in either the recording or execution of a script action.
A lookup table containing Parameters keyed by a label/name.
A unsigned short parameter used in either the recording or execution of a script action.
This object holds data parsed from a single line in a script, including the action to be taken and the parameters to pass to that action.
This is the main class used to parse and run scripts.
Performs the heavy-lifting of parsing out individual lines from a script.
Provides information about an error encountered while parsing a script.
PatientSlice provides oriented or non-oriented interface to the ModelImage data for rendering, with LUT changes.
Simple class located in the icons directory (package).
Class PlaneRender: renders a single dimension of the ModelImage data as a
texture-mapped polygon.
Class PlaneRenderWM: renders a single dimension of the ModelImage data as a
texture-mapped polygon.
Class PlaneRenderWM: renders a single dimension of the ModelImage data as a texture-mapped polygon.
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This is the MIPAV plugin interface for Algorithms.
An abstract class for a plugin which reports other available plugins bundled inside of it.
An interface for a plugin which reads/writes images.
An interface for a plugin which transfers files between two file systems.
An interface for generic MIPAV Plug-Ins which don't require an open image and can be run from the ViewUserInterface
menu.
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Ported to Java from C code from
http://www8.cs.umu.se/kurser/TDBAfl/VT06/algorithms/WEBSITE/IMPLEMEN/TURN/IMPLEMEN.HTM
May only be used for non-commercial purposes.
Simple integer 3D point.
This behavior is supposed to "fly by pointer" - that is, zoom in, translate, and rotate to where the mouse is
currently pointing.
PointStack is a structure used specifically in ViewComponentEditImage for use in the active level set generation and
was built for speed.
Ported to Java from C code from
http://www8.cs.umu.se/kurser/TDBAfl/VT06/algorithms/WEBSITE/IMPLEMEN/TURN/IMPLEMEN.HTM
May only be used for non-commercial purposes.
Solution of cubic, quartic, and quintic equations
Ported from code written by (c) Khashin S.I. http://math.ivanovo.ac.ru/dalgebra/Khashin/index.html
// khash2 (at) gmail.com
// Thanks to Alexandr Rakhmanin invalid input: '<'rakhmanin (at) gmail.com>
// public domain
Ported to Java from C code from
http://www8.cs.umu.se/kurser/TDBAfl/VT06/algorithms/WEBSITE/IMPLEMEN/TURN/IMPLEMEN.HTM
May only be used for non-commercial purposes.
MIT License
Copyright (c) 2018 Komahan Boopathy
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.
Copyright (c) 2007-2014 The LIBLINEAR Project.
This class reads the MIPAV preference file.
Defines options for displaying pixel values of complex images.
Defines options for defining color and brightness display based on pixel values.
Defines options for interpolating displayed image slices.
Defines operating system on which MIPAV is running.
Defines system architecture on which MIPAV is running.
Title: PreviewImageContainer
Note does not use hashtable since two Private keys can have same hashcode.
Associates a FileDicomKey with a particular publisher to denote the source of the FileDicomKey.
Title: Probe
Copyright (c) 2007-2014 The LIBLINEAR Project.
Title: ProgressBarInterface
ProgressChangeEvent is used to notify interested parties that progress
state has changed in the event source
Defines an object which listens for the ProgressChangeEvent.
Provenance Change event for listeners to update (jtable provenance viewing)
Used by JDialogDataProvenance to display changes in the provenanceholder (when entries are added)
Class that stores matrices (owned by ModelImage) with accessor functions to the matrix map/adding and changing
matrices.
Singleton class modelled after ScriptRecorder that is turned on when Mipav starts if
DATA_PROVENANCE boolean is set to true in preferences (set through Mipav-Options)
Records data provenance line by line (after running algorithms or doing other important actions (Change name) etc
images are placed in registers (similar to the script recorder) but there are also Vectors of input and output images
so that the data provenance is placed into the correct place(s)
This code calculates the psi function of an input argument x.
Ported to Java from C code from
http://www8.cs.umu.se/kurser/TDBAfl/VT06/algorithms/WEBSITE/IMPLEMEN/TURN/IMPLEMEN.HTM
May only be used for non-commercial purposes.
Copyright (c) 2006-2012 Filip Wasilewski invalid input: '<'http://en.ig.ma/>
Copyright (c) 2012-2017 The PyWavelets Developers invalid input: '<'https://github.com/PyWavelets/pywt>
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.
Copyright Yair Chuchem 2011.
Copyright Yair Chuchem 2011.
Copyright (c) 2000-2009, Jay St.
This is the local implementation of quicksort for delaunay triangulation.
Algorithm that produces a random number (Gaussian or uniform) in a specific user/programmer defined range.
Class designed to hold pre-loaded information for opening RAW images.
3D JP2 image header reader/writer.
A ray tracer for 3D color images.
Ray traced rendering of the volume using composition of colors and alpha values at each voxel.
A ray tracer for 3D images.
Ray traced rendering of the level surface within the voxel for the fixed level value of 0.0.
Maximum intensity projection volume rendering for color-based volumes.
Ray traced rendering of the level surface within the voxel for the fixed level value of 0.0.
A ray tracer for 3D intensity images.
A ray tracer for 3D images.
A sample ray tracer that extends RayTrace.
A sample ray tracer that extends RayTrace.
A ray tracer for 3D images.
Interface for dialogs which gather region grow information and then update a list of listeners who want to know about
the region grow.
This is an abstract class used to compute the measure of registration between the specified target image and a
registered source image.
Concrete implementation of the RegistrationMeasure class based on the correlation ratio computed as follows:
Concrete implementation of the RegistrationMeasure class based on sum of the squared differences between the target
image and the registered source image.
Concrete implementation of the RegistrationMeasure class based on the normalized mutual information computed as
follows:
Title: RegualorProbe
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A ray tracer for 3D images.
Storage of values for a 3D volume used by the volume renderers.
An interface to be used to color-based Renderer implementations.
An interface to be used to intensity-based Renderer implementations.
A helper class to map RGB color image values to an intensity value.
A helper class to map image values to RBB colors.
This is an abstract class.
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An abstract base class for rubberbands.
A Rubberband that does ellipses.
A Rubberband that does lines.
A Livewire rubberband.
A Rubberband that does polylines and polygons.
A Rubberband that does protractors.
A Rubberband that does rectangles.
A Rubberband that does rectangles.
Collectiing the current virtualization toolbox values for both volume and slices render dialogs.
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ScreenCoordinateListener
This interface defines functions that convert mouse coordinates to image file coordinates.
An interface for classes which want to allow themselves to be scripted.
Given the name of a script action, this class searches a number of locations for a class to load with that name and
returns a new instance of that class.
A singleton class used to add lines to the script currently being recorded (if one is being recorded at all).
An interface for classes which want to be notified of changes to the script currently being recorded by MIPAV.
Executes a script with a set of images.
Class used as a DefaultMutableTreeNode, except it stores a default name that can be recalled at any time if the
users deletes the image/voi.
Corrects a strange behaviour with JScrollPane when lines are appended from another thread.
Volume Sculpturing allows the user to draw a region on the screen in the volume render view, and to remove the parts
of the volume covered by that region.
Volume Sculpturing allows the user to draw a region on the screen in the volume render view, and to remove the parts
of the volume covered by that region.
Ported to Java from C code from
http://www8.cs.umu.se/kurser/TDBAfl/VT06/algorithms/WEBSITE/IMPLEMEN/TURN/IMPLEMEN.HTM
May only be used for non-commercial purposes.
The base class renderer to support shear-warp rendering of color images.
A renderer for composition of voxel RGB color values with alpha blending and no lighting.
A renderer for color volume data.
A renderer for RGBA+lighting volume data.
A renderer for color volume data.
The base class renderer to support shear-warp rendering of intensity images (gray scale).
A renderer for intensity volume data.
A renderer for intensity volume data.
The base class renderer to support shear-warp rendering.
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Copyright (C) 2007-11, Andrea Vedaldi and Brian Fulkerson
Copyright (C) 2012-13, The VLFeat Team
All rights reserved.
Singular Value Decomposition.
Implementation of the 3D skeletonization of a binary volume based on the paper "Penalized-distance volumetric
skeleton algorithm"; I.
One dimensional forward and inverse slant transforms are ported from FORATRAN programs in Appendix A
of AD-767 758 Technical Report Slant Transform Image Coding by Wen-Hsiung Cheng of the University of
Southern California, prepared for the Advanced Research Projects Agency, Air Force Eastern Test Range, May 1973.
The base class for lights in a general lighting system to calculate colors at a point in space.
The class for ambient lights in a general lighting system to calculate ambient colors at a point in space.
The class for directional lights in a general lighting system to calculate diffuse and specular colors at a point in
space.
The class for point lights in a general lighting system to calculate diffuse and specular colors at a point in space.
This class maintains a set of SoftwareLight instances where each light can be of type ambient, directional, point, or
spot.
The class for spot lights in a general lighting system to calculate diffuse and specular colors at a point in space.
This class maintains the following material properties:
This class maintains the following properties for a vertex.
Copyright (c) 2007-2014 The LIBLINEAR Project.
Copyright (c) 2007-2014 The LIBLINEAR Project.
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Quick and merge sort implementations that create no garbage, unlike
Arrays.sort(int[]).Allows for controlling a SpaceNavigator, could also be generalized for any joystick-type device.
Allows events to originate from GPURenderBase
Interface for receiving space navigator events.
Polls the space navigator.
These sparse symmetric eigenvalue and eigenvector routines are ported from the FORTRAN ARPACK package.
This class implements a 2D Square-shaped ClassficiationWidget.
The source code is distributed under BSD license, see the file License.txt
at the top-level directory.
The matrix types are defined as follows
Class that holds the information about each surface displayed in the
SurfaceRenderer.
Surface clipping.
A level surface extractor that is based on decomposing voxels into tetrahedra, assuming a linear interpolation on the
tetrahedra, and extracting triangular level sets for those tetrahedra.
A level surface extractor that is based on decomposing voxels into cubes, assuming a linear interpolation on the
cubes, and extracting triangular level sets for those cubes.
Surface lighting uses the lights defined in the Volume/Surface/Tri-Planar view in the vertex and pixel shaders.
Class used to load a surface stored in an file using the SUR format.
SurfaceMask.
Display component in the dialog that displays the material parameters for the surface.
Frame that holds the surface plotter.
Frame that holds the surface renderer.
Frame that holds the surface renderer.
Copyright (c) 2000-2014 Chih-Chung Chang and Chih-Jen Lin
All rights reserved.
Copyright (c) 2000-2014 Chih-Chung Chang and Chih-Jen Lin
All rights reserved.
Copyright (c) 2000-2014 Chih-Chung Chang and Chih-Jen Lin
All rights reserved.
Copyright (c) 2000-2014 Chih-Chung Chang and Chih-Jen Lin
All rights reserved.
Copyright (c) 2000-2014 Chih-Chung Chang and Chih-Jen Lin
All rights reserved.
Copyright (c) 2000-2014 Chih-Chung Chang and Chih-Jen Lin
All rights reserved.
Copyright (c) 2000-2014 Chih-Chung Chang and Chih-Jen Lin
All rights reserved.
Copyright (c) 2000-2014 Chih-Chung Chang and Chih-Jen Lin
All rights reserved.
Copyright (c) 2000-2014 Chih-Chung Chang and Chih-Jen Lin
All rights reserved.
TableSorter is a decorator for TableModels; adding sorting functionality to a supplied TableModel.
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This is the structure to store information needed to compute ACPC and Talairach normalization.
Ported to Java from C code from
http://www8.cs.umu.se/kurser/TDBAfl/VT06/algorithms/WEBSITE/IMPLEMEN/TURN/IMPLEMEN.HTM
May only be used for non-commercial purposes.
Volume Sculpting for the VolumeTexture Rendering.
Title: ThermalProbe
A class for performing LZW decoding.
Thread which sleeps for a pre-determined amount of time, then calls a method (if the thread hasn't had its shutdown
method called).
Exception to indicate that a problem was encountered parsing a string.
Copyright (c) 2007-2014 The LIBLINEAR Project.
Title: TransferFunction
Transformation matrix class is an affine homogeneous class that can be used
to rotate objects like images and VOIs.
Transformation matrix class is an affine homogeneous class that can be used
to rotate objects like images and VOIs.
Information about a set of burns attempting to treat one of the target surfaces from the target list.
This class implements a 2D Triangle-shaped ClassficiationWidget.
Copyright (c) 2007-2014 The LIBLINEAR Project.
Ported to Java from C code from
http://www8.cs.umu.se/kurser/TDBAfl/VT06/algorithms/WEBSITE/IMPLEMEN/TURN/IMPLEMEN.HTM
May only be used for non-commercial purposes.
Ported to Java from C code from
http://www8.cs.umu.se/kurser/TDBAfl/VT06/algorithms/WEBSITE/IMPLEMEN/TURN/IMPLEMEN.HTM
May only be used for non-commercial purposes.
Ported to Java from C code from
http://www8.cs.umu.se/kurser/TDBAfl/VT06/algorithms/WEBSITE/IMPLEMEN/TURN/IMPLEMEN.HTM
May only be used for non-commercial purposes.
Title: UneditableTableModel
Utility for making deep copies (vs. clone()'s shallow copies) of
objects.
presents an event to regard a changed VOI.
UpdateVOISelectionListener permits objects to listen for updates to a VOI.A table used to store variables and their values.
N dimension vector class with the cost value.
This class builds the control panel used in ViewJFrameImage frames.
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THIS CLASS IS MOST LIKELY TO BE DESTROYED!!!!!!!!!!
Encapsulates a JFileChooser with MIPAV related components.
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This class is used to represent a file system in a tree.
Tree of images beneath the given directory.
A simple file filter to display only files with the appropriate extension in the file dialog.
Interface to update display of an image.
This is a color chooser designed so that the preview panel is not shown.
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Abstract class used for displaying images in the program MIPAV.
The red bounding box of the surface renderer.
Four lines that are the border of a slice in the surface renderer.
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ViewJComponent DTI Image
Basic displayable image object in MIPAV.
This is a custom made Swing component.
This is a custom made Swing component.
This class extends the ViewJComponentHLUTBase class and used to coordinate how a histogram and LUT for an image are
to be displayed to the screen.
This class extends the ViewJComponentHLUTBase class and used to coordinate how a histogram and LUT for an image are
to be displayed to the screen.
Abstract class used for generating custom components, especially within images.
Holds parent BranchGroup and an array of 8 spheres that represent the lights on the surface.
Component LUT - the vertical or horizontal bar that gives a visual representation of the lookup table.
Component LUT - the vertical or horizontal bar that gives a visual representation of the lookup table.
Preview image displayed when the user clicks on an image file in the directory tree.
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Abstract class used for displaying images in the program MIPAV.
Need to add.
Need to add.
Extended version of ViewJComponentEditImage, used ONLY within the ViewJFrameRegistrationTool This class is tailored
to support Reference and Adjusted markers for use with Least Squares and Thin Plate Splines registration operations.
Component surface created from a 2D image.
Texture mapped image volume displayed in the surface renderer. .
One of the component images that make up the triplanar view (AXIAL, SAGITTAL, and CORONAL views).
Image plane displayed in the surface renderer.
This class is used to coordinate how a histogram and LUT for an image are to be displayed to the screen.
Abstract class used for generating custom components, especially within images.
Created so the JPanelVolOpacity can be used in more generic container classes.
This class extends the ViewJComponentVolOpacityBase class and used to coordinate how a histogram and LUT for an image
are to be displayed to the screen.
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This class produces a frame surrounding an image whose slices are animated.
This class produces a frame surrounding an image whose slices are animated.
This is an abstract class used to display images in a 2D planar format.
This class produces a frame surrounding a 2D histogram with ellipses surrounding the most prominent clusters.
This class produces a frame surrounding a 2D histogram with a orthogonal least squares regression line and a
threshold point that slides along the line.
Frame that allows the creation of custom paint brushes.
DICOM parser - shows pertinent DICOM tags, allows user to sort on specific values in the tags and open the proper
images.
GUI for DICOM Query and retreival from DICOM compliant servers.
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This is a frame which holds a graph in one panel and a set of user buttons in the other.
Deprecated.
Deprecated.
Makes a frame and put a single image component into it.
This class builds a "light box" view of a 3D or 4D dataset.
Contains a seperatly running thread which checks the currently used and available memory.
This class produces a message frame where user data, logging and debug information can be displayed.
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This class produces a message frame where user data and program can be displayed.
Generates a MIP image from a 3D volume.
Title: ViewJFramePlotterView
Contains a seperatly running thread which checks the list of registered images.
ViewJFrameRegistration is called in ViewJFrameImage.
ViewJFrameRegistrationTool is called in ViewJFrameImage.
This class builds a "light box" view of a 3D or 4D dataset.
This program works with 3D and 4D images.
The volume view frame of the visualization.
Panel containing the histogram component (the graph) and the lut component (the gradient vertical bar).
Deprecated.
Pop-up menu for uninstalling a plugin.
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Progress bar used everywhere for displaying to the user how long the current process is going to take.
Extension of ViewJProgressBar, ViewJProgressBarMulti is used to keep track of multiple
algorithms or threads at a single time.
Wraps the ViewJProgressBar instance which allows an arbitrary minimum and maximum value to be specified for the ends
of the progress bar.
This class extends Java's JSlider to give basic solutions to common slider needs in
image processing tasks.
Build the menus for an image loaded into MIPAV.
This class provides a number of helper methods for building and manipulating menus.
Opens an image file by calling FileIO.readImage and puts it into an image frame.
Simple interface to allow JDialogs to open up a new frame of the same type as was used to create the dialog
This allows stand-alone plugins that extend ViewJFrameImage to instantiate a new frame of the same type.
The purpose of this class is to present the user with a window enabling him/her to open a sequence of TIFF files
based on timepoint-channel-slice ordering.
User interface to open a VOI.
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Shows the MIPAV splash screen until the user clicks the image or a few seconds (4 currently).
This is a simple class that creates a DefaultTableModel with uneditable cells.
Builds the GUI toolbars for the user interface.
This class is the _glue_ keeps a record of the present structure of the application.
A simple class that extends Vector mostly to clean-up syntax access to VOI info. in ViewComponentEditImage
((VOI)(VOIs.elementAt(i))).isActive() would be a good example can be re-written as as:
VOIs.VOIAt(i).isActive()This the Volume Of Interest (VOI) structure.
Base which holds the functions common to both Contour, Line and Point type VOI.
This class is fundamental to the VOI class in which points are stored that
describe a curve of an VOI.
This class is used to represent a contour node in a tree.
An event from a VOI.
This class is used to represent a frame, such as a slice number.
This class is used to represent a VOI in a tree.
wrapper class for JTree.
VOIHandlerInterface.
Class for line, a simple extension of VOIBase.
VOIListener permits objects to listen for updates to a VOI.VOIManager class performs all direct user-manipulation of VOIs.
VOIManagerInterface manages all the VOI user-interaction for classes that display the ModelImage.
VOIManagerInterfaceListener interface.
This class is used to represent the orientation of a set of VOI curves.
Class for a point VOI, a simple extension of CurveBase.
PolyLineSlice is implemented as a list of
Each VOIPoint in the list may be on a different slice of the image.
This class is fundamental to the VOI class in which points are stored that describe a Protractor VOI.
$Logfile: /mipav/src/gov/nih/mipav/model/structures/VOIStatisticalProperties.java $ $Revision: 4 $ $Date: 7/27/04
1:42p $
interface to carry statistic list information. all users of VOI statistics ought to implement this interface.
A table which manages paths to VOIs which should be used for specific images used within a script.
Title: VOI Text
Class extends ViewVOIVector to finish cleaning up access syntax to the volumes of interest vector.
An event from a VOIVector.
VOISelectionListener permits objects to listen for updates to a VOI.Displays the BoundingBox frame around the volume data in the VolumeViewer.
ShaderEffect class for calculating the volume normals on the GPU.
Extension of Canvas3D to allow for customization as needed.
Displays the Clipping frames in the VolumeViewer.
Clipping effect for Volume Objects.
Displays the Diffusion Tensor tracts in the VolumeViewer.
The VolumePlaneEffect ShaderEffect creates shaders for mapping the volume
data onto the planes for the 3-orthogonal planes displayed in the
VolumeViewer and for the PlaneRender objects.
The VolumeImage class provides an interface between the MIPAV ModelImage and the 2D and 3D Textures used to render
the ModelImage on the GPU.
This class implements the 2D Histogram display and user-interaction widget in the JPanelMultiDimensionalTransfer class.
VolumeObect: abstract base class for all rendered objects in the Volume
Tri-Planar view.
Displays the Orientation Cube in the VolumeViewer.
The VolumePlaneEffect ShaderEffect creates shaders for mapping the volume
data onto the planes for the 3-orthogonal planes displayed in the
VolumeViewer and for the PlaneRender objects.
VolumePositionFrame, used by the ViewJFrameTriImage class to display the volume position data.
Common interface for all volume renderers.
Frame that holds the surface renderer.
Frame that holds the surface renderer.
Implementation of Volume Sculpting for the RayCast and ShearWarp Volume Renderers.
VolumeShaderEffect is the workhorse of the GPU-based rendering in MIPAV.
Displays the three orthogonal planes with the volume data.
Defines 3D texture node for a volume of data.
Displays the VOIBase in the GPU-based VolumeRenderer.
Voro++ Copyright (c) 2008, The Regents of the University of California, through
Lawrence Berkeley National Laboratory (subject to receipt of any required
approvals from the U.S.
A type associated with a c_loop_subset class, determining what type of
geometrical region to loop over.
Copyright (c) 2016, suresh
All rights reserved.
This class is a collection of GUI widget generation methods.
ScrollPane with an accessible JTextArea
The WindowLevel class provides mouse-driven window-level controls for the
ModelLUT or ModelRGB lookup tables.
Ported from original FORTRAN code Algorithm AS 53: Wishart Variate Generator
Authors: W.
Error handler to report errors and warnings from the XML parser.
Error handler to report errors and warnings from the XML parser.
Error handler to report errors and warnings from the XML parser.
Title: Parameter
Title: PSet