Package gov.nih.mipav.view.dialogs
package gov.nih.mipav.view.dialogs
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ClassDescriptionClasses 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.This class standardizes the parameter names given to many common parameters used in algorithms.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 an example class for tying existing plugins into the JIST interface.This class standardizes the parameter names given to many common parameters used in algorithms.Dialogs which implement this interface are eligible to use the JDialogDicomTagSelector for selecting DICOM tags within a given image file.These enumerations are used by the GuiBuilder to indicate the pre-processing results of user entry fields for the user interface.Provides methods for quickly building panel components.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.Dialog to get user input, then call the algorithm.Dialog to enter points for creating an ACPC image.Dialog to get user input, then call the algorithm.DOCUMENT ME!Creates the dialog to add margins around the image.DOCUMENT ME!Dialog to get user input, then call the snake-like algorithm.Adaptive Histogram Equlization.Dialog to get user input, then call the algorithm.DOCUMENT ME!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.DOCUMENT ME!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 distortionThis 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.DOCUMENT ME!Dialog to get user input, then call the algorithm for smoothing VOIs.Dialog to get user input, then call the algorithm.DOCUMENT ME!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: JDialogCenterOfMassRGBCreates 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 buttonsDialog to get the row and column numbers of checkerboard squaresDialog to create an image with randomly spaced, aggregated, regular or uniform, or constrained circles of the same sizeDialog 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 saturationDialog to get user input, then call the algorithm.Dialog to get user input, then call algorithm RegistrationOAR3D.DOCUMENT ME!DOCUMENT ME!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.Dialog to get user input, then call the algorithm for smoothing VOIs.Algorithm to adjust image volume for cases when the slice spacing is not equal to the slice thickness.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.DOCUMENT ME!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 DemonsDialog to get user input for 3 parameter dynamic (contrast) enhanced MRI model or DEMRI modelDialog 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: JDialogDICOMtoAVIDialog 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 annulusDialog to get user search for best boundary between 2 contoursDOCUMENT ME!DOCUMENT ME!DOCUMENT ME!DOCUMENT ME!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 filterDialog 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 sizeDialog 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.DOCUMENT ME!DOCUMENT ME!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.DOCUMENT ME!DOCUMENT ME!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.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.DOCUMENT ME!Simple dialog to choose the filter for the view image directory.Dialog to get user input, then call the algorithm.DOCUMENT ME!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.DOCUMENT ME!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.DOCUMENT ME!Dialog to get user input, then call the algorithm.DOCUMENT ME!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.DOCUMENT ME!DOCUMENT ME!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 bottomConfirmation 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**2Confirmation 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 imageConfirmation 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 parabolaConfirmation Dialog giving user the choice to choose which parabolas to draw.Dialog to get user input, then call the algorithm.DOCUMENT ME!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.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.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.DOCUMENT ME!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.DOCUMENT ME!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.DOCUMENT ME!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.DOCUMENT ME!DOCUMENT ME!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: JDialogOverlayCreates 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.DOCUMENT ME!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.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.DOCUMENT ME!DOCUMENT ME!DOCUMENT ME!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 box for basic image processing toolsDialog 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.DOCUMENT ME!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.DOCUMENT ME!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.DOCUMENT ME!Dialog to get user input, then call the algorithm.Simple dialog to set certain values for the new or edited server or destination.DOCUMENT ME!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.Dialog to get user input, then call the algorithm.DOCUMENT ME!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.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 for 3 parameter dynamic (contrast) enhanced MRI model or SM2 modelUser-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 sizeDialog to get user input, then call the algorithm.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 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.DOCUMENT ME!DOCUMENT ME!Dialog to get user input, then call the algorithm.Dialog is used by the ViewJFrameHistoLUT frame.Title: JDialogThresholdRGBDialog 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.DOCUMENT ME!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.DOCUMENT ME!Dialog to use difference, intersection, exclusive or, or intersection on 2 VOIsDialog to call the VOI extraction.Title:Dialog for calculating statistics of a (set of) Volumes of Interest.DOCUMENT ME!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.DOCUMENT ME!DOCUMENT ME!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.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.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.This class is an example class for tying existing plugins into the JIST interface.DOCUMENT ME!Handle events generated while parsing the XML file.DOCUMENT ME!Interface for dialogs which gather region grow information and then update a list of listeners who want to know about the region grow.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.Error handler to report errors and warnings from the XML parser.