Java Code Examples for ij.gui.GenericDialog#addSlider()
The following examples show how to use
ij.gui.GenericDialog#addSlider() .
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Example 1
| Source File: ShenCastan.java From Scripts with GNU General Public License v3.0 | 6 votes |
|
/** Displays the dialog prompt. */
@Override
public int showDialog(final ImagePlus imp, final String command, final PlugInFilterRunner pfr) {
this.pfr = pfr;
final String msg = "<html><div WIDTH=350>"
+ "<a href='https://github.com/tferr/Scripts/blob/master/Segmentation/README.md#shen-castan-edge-detector'>"
+ "Shen-Castan</a> filtering is an edge detection technique. It is an alternative "
+ "to other popular approaches such as "
+ "<a href='http://en.wikipedia.org/wiki/Canny_edge_detector'>Canny</a>-"
+ "<a href='http://en.wikipedia.org/wiki/Deriche_edge_detector'>Deriche</a> filtering.</p>"
+ "<p>The Shen-Castan coefficient corresponds to a smooting factor <i>alpha</i>. "
+ "<i>Alpha</i> can vary between 0 (high smoothing, suitable for noisy images) "
+ "and 1 (no smoothing, suitable for non-noisy images).</p></div></html>";
final GenericDialog gd = new GenericDialog(command);
gd.addSlider("Coefficient:", 0.0001d, 1.0001d, f);
gd.addPreviewCheckbox(pfr);
gd.addDialogListener(this);
gd.addHelp(msg);
gd.showDialog();
if (gd.wasCanceled() || !dialogItemChanged(gd, null)) // read parameters
return DONE;
return IJ.setupDialog(imp, flags);
}
Example 2
| Source File: SkewImagesPopup.java From BigStitcher with GNU General Public License v2.0 | 5 votes |
|
@Override
public void actionPerformed(ActionEvent e)
{
final SpimData spimData = (SpimData)panel.getSpimData();
final List< ViewId > views = ((GroupedRowWindow) panel).selectedRowsViewIdGroups().stream().reduce(new ArrayList<>(), (a,b) -> {a.addAll( b ); return a;} );
final Map<ViewId, Dimensions> dims = new HashMap<>();
views.forEach( v -> dims.put( v, spimData.getSequenceDescription().getViewDescriptions() .get( v ).getViewSetup().getSize()) );
GenericDialog gd = new GenericDialog( "(De)Skew Parameters" );
gd.addChoice( "Skew Direction", axesChoice, axesChoice[0] );
gd.addChoice( "Skew Along Which Axis", axesChoice, axesChoice[2] );
gd.addSlider( "Angle", -90, 90, 45 );
gd.showDialog();
if (gd.wasCanceled())
return;
final int direction = gd.getNextChoiceIndex();
final int skewAxis = gd.getNextChoiceIndex();
final double angle = gd.getNextNumber() / 180 * Math.PI;
SkewImages.applySkewToData( spimData.getViewRegistrations(), dims, views, direction, skewAxis, angle );
panel.updateContent();
panel.bdvPopup().updateBDV();
}
Example 3
| Source File: StitchingTEM.java From TrakEM2 with GNU General Public License v3.0 | 5 votes |
|
/**
* Returns false when canceled.
* @param ref is an optional Patch from which to estimate an appropriate image scale
* at which to perform the phase correlation, for performance reasons.
* */
public boolean setup(final Patch ref)
{
final GenericDialog gd = new GenericDialog("Montage with phase correlation");
if (overlap < 0) overlap = 0.1f;
else if (overlap > 1) overlap = 1;
gd.addSlider("tile_overlap (%): ", 1, 100, overlap * 100);
int sc = (int)cc_scale * 100;
if (null != ref) {
// Estimate scale from ref Patch dimensions
final int w = ref.getOWidth();
final int h = ref.getOHeight();
sc = (int)((512.0 / (w > h ? w : h)) * 100); // guess a scale so that image is 512x512 aprox
}
if (sc <= 0) sc = 25;
else if (sc > 100) sc = 100;
gd.addSlider("scale (%):", 1, 100, sc);
gd.addNumericField( "max/avg displacement threshold: ", mean_factor, 2 );
gd.addNumericField("regression threshold (R):", min_R, 2);
gd.addCheckbox("hide disconnected", false);
gd.addCheckbox("remove disconnected", false);
gd.showDialog();
if (gd.wasCanceled()) return false;
overlap = (float)gd.getNextNumber() / 100f;
cc_scale = gd.getNextNumber() / 100.0;
mean_factor = gd.getNextNumber();
min_R = gd.getNextNumber();
hide_disconnected = gd.getNextBoolean();
remove_disconnected = gd.getNextBoolean();
return true;
}
Example 4
| Source File: Display3D.java From TrakEM2 with GNU General Public License v3.0 | 5 votes |
|
synchronized private final int adjustResampling() {
if (resample > 0) return resample;
final GenericDialog gd = new GenericDialog("Resample");
final int default_resample = estimateResamplingFactor();
gd.addSlider("Resample: ", 1, Math.max(default_resample, 100), -1 != resample ? resample : default_resample);
gd.showDialog();
if (gd.wasCanceled()) {
resample = -1 != resample ? resample : default_resample; // current or default value
return resample;
}
resample = ((java.awt.Scrollbar)gd.getSliders().get(0)).getValue();
return resample;
}
Example 5
| Source File: AreaWrapper.java From TrakEM2 with GNU General Public License v3.0 | 5 votes |
|
public boolean setup() {
GenericDialog gd = new GenericDialog("Paint parameters");
gd.addSlider("Default_alpha", 0, 100, default_alpha * 100);
final String[] modes = {"Allow overlap", "Exclude others", "Erode others"};
gd.addChoice("Paint mode", modes, modes[paint_mode]);
gd.showDialog();
if (gd.wasCanceled()) return false;
this.default_alpha = (float) gd.getNextNumber();
if (this.default_alpha > 1) this.default_alpha = 1f;
else if (this.default_alpha < 0) this.default_alpha = 0.4f; // back to default's default value
this.paint_mode = gd.getNextChoiceIndex();
// trigger update of GUI radio buttons on all displays:
Display.toolChanged(ProjectToolbar.BRUSH);
return true;
}
Example 6
| Source File: BoundingBoxGUI.java From SPIM_Registration with GNU General Public License v2.0 | 5 votes |
|
protected GenericDialog getSimpleDialog( final boolean compress, final boolean allowModifyDimensions )
{
final int[] rangeMin = new int[ 3 ];
final int[] rangeMax = new int[ 3 ];
setUpDefaultValues( rangeMin, rangeMax );
final GenericDialog gd = new GenericDialog( "Manually define Bounding Box" );
gd.addMessage( "Note: Coordinates are in global coordinates as shown " +
"in Fiji status bar of a fused datasets", GUIHelper.smallStatusFont );
if ( !compress )
gd.addMessage( "", GUIHelper.smallStatusFont );
gd.addSlider( "Minimal_X", rangeMin[ 0 ], rangeMax[ 0 ], this.min[ 0 ] );
gd.addSlider( "Minimal_Y", rangeMin[ 1 ], rangeMax[ 1 ], this.min[ 1 ] );
gd.addSlider( "Minimal_Z", rangeMin[ 2 ], rangeMax[ 2 ], this.min[ 2 ] );
if ( !compress )
gd.addMessage( "" );
gd.addSlider( "Maximal_X", rangeMin[ 0 ], rangeMax[ 0 ], this.max[ 0 ] );
gd.addSlider( "Maximal_Y", rangeMin[ 1 ], rangeMax[ 1 ], this.max[ 1 ] );
gd.addSlider( "Maximal_Z", rangeMin[ 2 ], rangeMax[ 2 ], this.max[ 2 ] );
if ( !allowModifyDimensions )
{
for ( int i = gd.getSliders().size() - 6; i < gd.getSliders().size(); ++i )
((Scrollbar)gd.getSliders().get( i )).setEnabled( false );
for ( int i = gd.getNumericFields().size() - 6; i < gd.getNumericFields().size(); ++i )
((TextField)gd.getNumericFields().get( i )).setEnabled( false );
}
return gd;
}
Example 7
| Source File: RGLDM.java From SPIM_Registration with GNU General Public License v2.0 | 5 votes |
|
@Override
public void addQuery( final GenericDialog gd, final RegistrationType registrationType )
{
gd.addChoice( "Transformation model", TransformationModel.modelChoice, TransformationModel.modelChoice[ defaultModel ] );
gd.addCheckbox( "Regularize_model", defaultRegularize );
gd.addSlider( "Number_of_neighbors for the descriptors", 3, 10, RGLDMParameters.numNeighbors );
gd.addSlider( "Redundancy for descriptor matching", 0, 10, RGLDMParameters.redundancy );
gd.addSlider( "Significance required for a descriptor match", 1.0, 10.0, RGLDMParameters.ratioOfDistance );
gd.addSlider( "Allowed_error_for_RANSAC (px)", 0.5, 20.0, RANSACParameters.max_epsilon );
}
Example 8
| Source File: IterativeClosestPoint.java From SPIM_Registration with GNU General Public License v2.0 | 5 votes |
|
@Override
public void addQuery( final GenericDialog gd, final RegistrationType registrationType )
{
gd.addChoice( "Transformation model", TransformationModel.modelChoice, TransformationModel.modelChoice[ defaultModel ] );
gd.addCheckbox( "Regularize_model", defaultRegularize );
gd.addSlider( "Maximal_distance for correspondence (px)", 0.25, 40.0, IterativeClosestPointParameters.maxDistance );
gd.addNumericField( "Maximal_number of iterations", IterativeClosestPointParameters.maxIterations, 0 );
}
Example 9
| Source File: GeometricHashing.java From SPIM_Registration with GNU General Public License v2.0 | 5 votes |
|
@Override
public void addQuery( final GenericDialog gd, final RegistrationType registrationType )
{
gd.addChoice( "Transformation model", TransformationModel.modelChoice, TransformationModel.modelChoice[ defaultModel ] );
gd.addCheckbox( "Regularize_model", defaultRegularize );
gd.addSlider( "Allowed_error_for_RANSAC (px)", 0.5, 20.0, RANSACParameters.max_epsilon );
gd.addSlider( "Significance required for a descriptor match", 1.0, 20.0, GeometricHashingParameters.ratioOfDistance );
}
Example 10
| Source File: ExtendedMinAndMaxPlugin.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 5 votes |
|
public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
// Normal setup
this.imagePlus = imp;
this.baseImage = imp.getProcessor().duplicate();
// Create the configuration dialog
GenericDialog gd = new GenericDialog("Extended Min & Max");
gd.addChoice("Operation", Operation.getAllLabels(), Operation.EXTENDED_MINIMA.label);
boolean isGray8 = (this.baseImage instanceof ByteProcessor);
double minValue = isGray8 ? 1 : this.baseImage.getMin();
double maxValue = isGray8 ? 255 : this.baseImage.getMax();
gd.addSlider("Dynamic", minValue, maxValue, 10);
gd.addChoice("Connectivity", connectivityLabels, connectivityLabels[0]);
gd.addPreviewCheckbox(pfr);
gd.addDialogListener(this);
previewing = true;
gd.addHelp("https://imagej.net/MorphoLibJ");
gd.showDialog();
previewing = false;
if (gd.wasCanceled()) {
return DONE;
}
parseDialogParameters(gd);
// clean up an return
gd.dispose();
return flags;
}
Example 11
| Source File: SkewImagesCommand.java From BigStitcher with GNU General Public License v2.0 | 5 votes |
|
@Override
public void run()
{
// load SpimData
final LoadParseQueryXML result = new LoadParseQueryXML();
if ( !result.queryXML( "to load a TileConfiguration for", false, false, false, false, false ) )
return;
final SpimData2 data = result.getData();
// get views to process
final ArrayList< ViewId > views = SpimData2.getAllViewIdsSorted( result.getData(),
result.getViewSetupsToProcess(), result.getTimePointsToProcess() );
// get dimensions for selected views
final Map< ViewId, Dimensions > dims = new HashMap<>();
views.forEach( v -> dims.put( v,
data.getSequenceDescription().getViewDescriptions().get( v ).getViewSetup().getSize() ) );
// query parameters in dialog
GenericDialog gd = new GenericDialog( "(De)Skew Parameters" );
gd.addChoice( "Skew_Direction", axesChoice, axesChoice[0] );
gd.addChoice( "Skew_Along_Which_Axis", axesChoice, axesChoice[2] );
gd.addSlider( "Angle", -90, 90, 45 );
gd.showDialog();
if (gd.wasCanceled())
return;
// get parameters from dialog
final int direction = gd.getNextChoiceIndex();
final int skewAxis = gd.getNextChoiceIndex();
final double angle = gd.getNextNumber() / 180 * Math.PI;
SkewImages.applySkewToData( data.getViewRegistrations(), dims, views, direction, skewAxis, angle );
// save result
SpimData2.saveXML( data, result.getXMLFileName(), result.getClusterExtension() );
}
Example 12
| Source File: AutomaticBoundingBox.java From SPIM_Registration with GNU General Public License v2.0 | 4 votes |
|
@Override
public boolean queryParameters( final Fusion fusion, final ImgExport imgExport )
{
// first get an idea of the maximal bounding box
final double[] minBB = new double[ 3 ];
final double[] maxBB = new double[ 3 ];
BoundingBoxGUI.computeMaxBoundingBoxDimensions( spimData, viewIdsToProcess, minBB, maxBB );
// compute dimensions and update size for this instance
final long[] dim = new long[ maxBB.length ];
// first time called on this object
if ( this.min == null || this.max == null )
{
this.min = new int[ minBB.length ];
this.max = new int[ minBB.length ];
}
for ( int d = 0; d < dim.length; ++d )
{
this.min[ d ] = (int)Math.round( minBB[ d ] );
this.max[ d ] = (int)Math.round( maxBB[ d ] );
dim[ d ] = this.max[ d ] - this.min[ d ] + 1;
}
final GenericDialog gd = new GenericDialog( "Automatically define Bounding Box" );
final List< TimePoint > timepointsToProcess = SpimData2.getAllTimePointsSorted( spimData, viewIdsToProcess );
final List< Channel > channelsToProcess = SpimData2.getAllChannelsSorted( spimData, viewIdsToProcess );
final String[] timepoints = assembleTimepoints( timepointsToProcess );
final String[] channels = assembleChannels( channelsToProcess );
if ( defaultTimepointIndex >= timepoints.length )
defaultTimepointIndex = 0;
if ( defaultChannelIndex >= channels.length )
defaultChannelIndex = 0;
gd.addMessage( "Parameters for automatic segmentation", GUIHelper.largestatusfont );
gd.addChoice( "Timepoint", timepoints, timepoints[ defaultTimepointIndex ] );
gd.addChoice( "Channel", channels, channels[ defaultChannelIndex ] );
gd.addSlider( "Background intensity [%]", 1.0, 99.0, defaultBackgroundIntensity );
gd.addSlider( "Size_of_objects to be discarded", 1, 100, defaultDiscardedObjectSize );
gd.addMessage( "" );
gd.addSlider( "Downsampling", 1.0, 10.0, defaultDownsamplingAutomatic );
gd.addCheckbox( "Load_input_images sequentially", defaultLoadSequentially );
gd.addCheckbox( "Display_image_used for segmentation", defaultDisplaySegmentationImage );
gd.addMessage( "Image size: ???x???x??? pixels", GUIHelper.mediumstatusfont, GUIHelper.good );
Label l = (Label)gd.getMessage();
// add listeners and update values
addListeners( gd, gd.getNumericFields(), l, dim );
gd.showDialog();
if ( gd.wasCanceled() )
return false;
final TimePoint timepoint = timepointsToProcess.get( defaultTimepointIndex = gd.getNextChoiceIndex() );
final Channel channel = channelsToProcess.get( defaultChannelIndex = gd.getNextChoiceIndex() );
final double background = defaultBackgroundIntensity = gd.getNextNumber();
final int discardedObjectSize = defaultDiscardedObjectSize = (int)Math.round( gd.getNextNumber() );
this.downsampling = defaultDownsamplingAutomatic = (int)Math.round( gd.getNextNumber() );
final boolean loadSequentially = defaultLoadSequentially = gd.getNextBoolean();
final boolean displaySegmentationImage = defaultDisplaySegmentationImage = gd.getNextBoolean();
// compute approx bounding box
final MinFilterThreshold automatic = new MinFilterThreshold(
spimData,
viewIdsToProcess,
channel,
timepoint,
this,
background,
discardedObjectSize,
loadSequentially,
displaySegmentationImage );
if ( !automatic.run() )
{
return false;
}
else
{
this.min = automatic.getMin().clone();
this.max = automatic.getMax().clone();
BoundingBoxGUI.defaultMin = automatic.getMin().clone();
BoundingBoxGUI.defaultMax = automatic.getMax().clone();
}
return super.queryParameters( fusion, imgExport );
}
Example 13
| Source File: BoundingBoxGUI.java From SPIM_Registration with GNU General Public License v2.0 | 4 votes |
|
/**
* Query the necessary parameters for the bounding box
*
* @param fusion - the fusion for which the bounding box is computed, can be null
* @param imgExport - the export module used, can be null
* @return
*/
public boolean queryParameters( final Fusion fusion, final ImgExport imgExport, final boolean allowModifyDimensions )
{
final boolean compress = fusion == null ? false : fusion.compressBoundingBoxDialog();
final boolean supportsDownsampling = fusion == null ? false : fusion.supportsDownsampling();
final boolean supports16BitUnsigned = fusion == null ? false : fusion.supports16BitUnsigned();
final GenericDialog gd = getSimpleDialog( compress, allowModifyDimensions );
if ( !compress )
gd.addMessage( "" );
if ( supportsDownsampling )
gd.addSlider( "Downsample fused dataset", 1.0, 10.0, BoundingBoxGUI.staticDownsampling );
if ( supports16BitUnsigned )
gd.addChoice( "Pixel_type", pixelTypes, pixelTypes[ defaultPixelType ] );
if ( fusion != null && imgExport != null )
gd.addChoice( "ImgLib2_container", imgTypes, imgTypes[ defaultImgType ] );
if ( fusion != null )
fusion.queryAdditionalParameters( gd );
if ( imgExport != null )
imgExport.queryAdditionalParameters( gd, spimData );
gd.addMessage( "Estimated size: ", GUIHelper.largestatusfont, GUIHelper.good );
Label l1 = (Label)gd.getMessage();
gd.addMessage( "???x???x??? pixels", GUIHelper.smallStatusFont, GUIHelper.good );
Label l2 = (Label)gd.getMessage();
final ManageListeners m = new ManageListeners( gd, gd.getNumericFields(), gd.getChoices(), l1, l2, fusion, imgExport, supportsDownsampling, supports16BitUnsigned );
if ( fusion != null )
fusion.registerAdditionalListeners( m );
m.update();
gd.showDialog();
if ( gd.wasCanceled() )
return false;
if ( allowModifyDimensions )
{
this.min[ 0 ] = (int)Math.round( gd.getNextNumber() );
this.min[ 1 ] = (int)Math.round( gd.getNextNumber() );
this.min[ 2 ] = (int)Math.round( gd.getNextNumber() );
this.max[ 0 ] = (int)Math.round( gd.getNextNumber() );
this.max[ 1 ] = (int)Math.round( gd.getNextNumber() );
this.max[ 2 ] = (int)Math.round( gd.getNextNumber() );
}
else
{
setNFIndex( gd, 6 );
}
if ( supportsDownsampling )
this.downsampling = BoundingBoxGUI.staticDownsampling = (int)Math.round( gd.getNextNumber() );
else
this.downsampling = 1;
if ( supports16BitUnsigned )
this.pixelType = BoundingBoxGUI.defaultPixelType = gd.getNextChoiceIndex();
else
this.pixelType = BoundingBoxGUI.defaultPixelType = 0; //32-bit
if ( fusion != null && imgExport != null )
this.imgtype = BoundingBoxGUI.defaultImgType = gd.getNextChoiceIndex();
if ( min[ 0 ] > max[ 0 ] || min[ 1 ] > max[ 1 ] || min[ 2 ] > max[ 2 ] )
{
IOFunctions.println( "Invalid coordinates, min cannot be larger than max" );
return false;
}
if ( fusion != null )
if ( !fusion.parseAdditionalParameters( gd ) )
return false;
if ( imgExport != null )
if ( !imgExport.parseAdditionalParameters( gd, spimData ) )
return false;
BoundingBoxGUI.defaultMin[ 0 ] = min[ 0 ];
BoundingBoxGUI.defaultMin[ 1 ] = min[ 1 ];
BoundingBoxGUI.defaultMin[ 2 ] = min[ 2 ];
BoundingBoxGUI.defaultMax[ 0 ] = max[ 0 ];
BoundingBoxGUI.defaultMax[ 1 ] = max[ 1 ];
BoundingBoxGUI.defaultMax[ 2 ] = max[ 2 ];
return true;
}
Example 14
| Source File: EfficientBayesianBased.java From SPIM_Registration with GNU General Public License v2.0 | 4 votes |
|
protected boolean getBlending()
{
if ( adjustBlending )
{
final GenericDialog gd = new GenericDialog( "Adjust blending parameters" );
if ( defaultBlendingBorder == null || defaultBlendingBorder.length < 3 )
defaultBlendingBorder = new int[]{ defaultBlendingBorderNumber, defaultBlendingBorderNumber, Math.round( defaultBlendingBorderNumber/2.5f ) };
if ( defaultBlendingRange == null || defaultBlendingRange.length < 3 )
defaultBlendingRange = new int[]{ defaultBlendingRangeNumber, defaultBlendingRangeNumber, defaultBlendingRangeNumber };
gd.addSlider( "Boundary_pixels_X", -50, 50, defaultBlendingBorder[ 0 ] );
gd.addSlider( "Boundary_pixels_Y", -50, 50, defaultBlendingBorder[ 1 ] );
gd.addSlider( "Boundary_pixels_Z", -50, 50, defaultBlendingBorder[ 2 ] );
gd.addSlider( "Blending_range_X", 0, 100, defaultBlendingRange[ 0 ] );
gd.addSlider( "Blending_range_Y", 0, 100, defaultBlendingRange[ 1 ] );
gd.addSlider( "Blending_range_Z", 0, 100, defaultBlendingRange[ 2 ] );
gd.addMessage( "" );
gd.addMessage( "Note: both sizes are in local coordinates of the input views. Increase one or both of those values if stripy artifacts\n" +
"are visible in the deconvolution result.\n" +
"The boundary pixels describe a range of pixels at the edge of each input view that are discarded because of the PSF size,\n" +
"it should typically correspond to half the size of the extracted PSF.\n" +
"The blending range defines in which outer part of each view the cosine blending is performed. You can manually inspect\n" +
"the results of these operations by choosing 'Illustrate overlap of views per pixel (do not deconvolve)' in the previous\n" +
"dialog. Choose just one input view to get an idea of what is cut off for individual stacks.", GUIHelper.mediumstatusfont );
gd.showDialog();
if ( gd.wasCanceled() )
return false;
blendingBorderX = defaultBlendingBorder[ 0 ] = (int)Math.round( gd.getNextNumber() );
blendingBorderY = defaultBlendingBorder[ 1 ] = (int)Math.round( gd.getNextNumber() );
blendingBorderZ = defaultBlendingBorder[ 2 ] = (int)Math.round( gd.getNextNumber() );
blendingRangeX = defaultBlendingRange[ 0 ] = (int)Math.round( gd.getNextNumber() );
blendingRangeY = defaultBlendingRange[ 1 ] = (int)Math.round( gd.getNextNumber() );
blendingRangeZ = defaultBlendingRange[ 2 ] = (int)Math.round( gd.getNextNumber() );
}
else
{
if ( defaultBlendingBorder != null && defaultBlendingBorder.length >= 3 )
{
blendingBorderX = defaultBlendingBorder[ 0 ];
blendingBorderY = defaultBlendingBorder[ 1 ];
blendingBorderZ = defaultBlendingBorder[ 2 ];
}
else
{
blendingBorderX = defaultBlendingBorderNumber;
blendingBorderY = defaultBlendingBorderNumber;
blendingBorderZ = Math.round( defaultBlendingBorderNumber/2.5f );
}
if ( defaultBlendingRange != null && defaultBlendingRange.length >= 3 )
{
blendingRangeX = defaultBlendingRange[ 0 ];
blendingRangeY = defaultBlendingRange[ 1 ];
blendingRangeZ = defaultBlendingRange[ 2 ];
}
else
{
blendingRangeX = defaultBlendingRangeNumber;
blendingRangeY = defaultBlendingRangeNumber;
blendingRangeZ = defaultBlendingRangeNumber;
}
}
return true;
}
Example 15
| Source File: Loader.java From TrakEM2 with GNU General Public License v3.0 | 4 votes |
|
/** If base_x or base_y are Double.MAX_VALUE, then those values are asked for in a GenericDialog. */
public Bureaucrat importLabelsAsAreaLists(final Layer first_layer, final String path_, final double base_x_, final double base_y_, final float alpha_, final boolean add_background_) {
final Worker worker = new Worker("Import labels as arealists") {
@Override
public void run() {
startedWorking();
try {
String path = path_;
if (null == path) {
final OpenDialog od = new OpenDialog("Select stack", "");
final String name = od.getFileName();
if (null == name || 0 == name.length()) {
return;
}
String dir = od.getDirectory().replace('\\', '/');
if (!dir.endsWith("/")) dir += "/";
path = dir + name;
}
if (path.toLowerCase().endsWith(".xml")) {
Utils.log("Avoided opening a TrakEM2 project.");
return;
}
double base_x = base_x_;
double base_y = base_y_;
float alpha = alpha_;
boolean add_background = add_background_;
Layer layer = first_layer;
if (Double.MAX_VALUE == base_x || Double.MAX_VALUE == base_y || alpha < 0 || alpha > 1) {
final GenericDialog gd = new GenericDialog("Base x, y");
Utils.addLayerChoice("First layer:", first_layer, gd);
gd.addNumericField("Base_X:", 0, 0);
gd.addNumericField("Base_Y:", 0, 0);
gd.addSlider("Alpha:", 0, 100, 40);
gd.addCheckbox("Add background (zero)", false);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
layer = first_layer.getParent().getLayer(gd.getNextChoiceIndex());
base_x = gd.getNextNumber();
base_y = gd.getNextNumber();
if (Double.isNaN(base_x) || Double.isNaN(base_y)) {
Utils.log("Base x or y is NaN!");
return;
}
alpha = (float)(gd.getNextNumber() / 100);
add_background = gd.getNextBoolean();
}
releaseToFit(new File(path).length() * 3);
final ImagePlus imp;
if (path.toLowerCase().endsWith(".am")) {
final AmiraMeshDecoder decoder = new AmiraMeshDecoder();
if (decoder.open(path)) imp = new ImagePlus(path, decoder.getStack());
else imp = null;
} else {
imp = openImagePlus(path);
}
if (null == imp) {
Utils.log("Could not open image at " + path);
return;
}
final Map<Float,AreaList> alis = AmiraImporter.extractAreaLists(imp, layer, base_x, base_y, alpha, add_background);
if (!hasQuitted() && alis.size() > 0) {
layer.getProject().getProjectTree().insertSegmentations(alis.values());
}
} catch (final Exception e) {
IJError.print(e);
} finally {
finishedWorking();
}
}
};
return Bureaucrat.createAndStart(worker, first_layer.getProject());
}
Example 16
| Source File: InteractivePlotter.java From Scripts with GNU General Public License v3.0 | 4 votes |
|
private void setPlotOptions() {
if (plot == null)
return;
final int DEF_LINE_WIDTH = 1;
final int DEF_MAX_INTERVALS = 12;
final int DEF_TICK_LENGTH = 7;
final int DEF_MINOR_TICK_LENGTH = 3;
final int[] NUM_DEFAULTS = { DEF_LINE_WIDTH, DEF_MAX_INTERVALS, DEF_TICK_LENGTH, DEF_MINOR_TICK_LENGTH };
final String DEF_BACKGROUND_COLOR = "white";
final String title = plot.getTitle();
final GenericDialog ogd = new GenericDialog("Options for " + title);
ogd.setInsets(0, 10, 10);
ogd.addMessage("This prompt allows you access customizations that\n"
+ "are not accessible through the plot's \"More \u00bb\" menu");
if (!pwClosed)
ogd.addStringField("Plot title:", title, 27);
ogd.addSlider("Line width:", 1, 20, 1);
ogd.addSlider("Max. n. of intervals:", 1, 40, 12);
ogd.addSlider("Major ticks length:", 1, 14, 7);
ogd.addSlider("Minor ticks length:", 1, 14, 3);
ogd.addChoice("Backgrond color:", Colors.colors, DEF_BACKGROUND_COLOR);
final Panel buttonPanel = new Panel();
final Button fontButton = new Button(" Text & Font... ");
fontButton.addActionListener(ogd);
buttonPanel.add(fontButton);
final Button templateButton = new Button("Apply Template...");
templateButton.addActionListener(ogd);
buttonPanel.add(templateButton);
ogd.addPanel(buttonPanel, GridBagConstraints.EAST, new Insets(0, 0, 0, 0));
ogd.hideCancelButton();
ogd.addHelp("");
ogd.setHelpLabel("Apply Defaults");
ogd.addDialogListener(new DialogListener() {
@Override
public boolean dialogItemChanged(final GenericDialog gd, final AWTEvent e) {
if (e != null && e.toString().contains("Apply Defaults")) {
@SuppressWarnings("unchecked")
final Vector<TextField> nFields = gd.getNumericFields();
for (final TextField field : nFields)
field.setText(Integer.toString(NUM_DEFAULTS[nFields.indexOf(field)]));
@SuppressWarnings("unchecked")
final Vector<Choice> nChoices = gd.getChoices();
nChoices.firstElement().select(DEF_BACKGROUND_COLOR);
} else if (e != null && e.toString().contains("Font")) {
setPlotFont();
return true;
} else if (e != null && e.toString().contains("Template")) {
setTemplate();
return true;
}
plot.setLineWidth((int) ogd.getNextNumber());
plot.setMaxIntervals((int) ogd.getNextNumber());
plot.setTickLength((int) ogd.getNextNumber());
plot.setBackgroundColor(Colors.colors[ogd.getNextChoiceIndex()]);
plot.updateImage();
return true;
}
});
showAsSubDialog(ogd);
if (!ogd.wasOKed())
return;
if (!pwClosed)
plot.getImagePlus().setTitle(WindowManager.makeUniqueName(ogd.getNextString()));
}
Example 17
| Source File: InteractivePlotter.java From Scripts with GNU General Public License v3.0 | 4 votes |
|
private void setPlotFont() {
if (plot == null)
return;
final String[] FONTS = new String[] { Font.SANS_SERIF, Font.MONOSPACED, Font.SERIF };
final String[] STYLES = { "Plain", "Bold", "Italic", "Bold+Italic" };
final String[] JUSTIFICATIONS = { "Left", "Center", "Right" };
final String[] SCOPES = { "Plot", "Both Axes Titles", "X-axis Title", "Y-axis Title" };
final String[] CHOICE_DEFAULTS = { FONTS[0], STYLES[0], JUSTIFICATIONS[0], SCOPES[0] };
final int[] INT_STYLES = { Font.PLAIN, Font.BOLD, Font.ITALIC, Font.BOLD + Font.ITALIC };
final int[] INT_JUSTIFICATIONS = { Plot.LEFT, Plot.CENTER, Plot.RIGHT };
final int DEF_SIZE = 12;
final boolean DEF_ANTIALISED = true;
final GenericDialog fgd = new GenericDialog("Font Options");
fgd.addChoice("Type:", FONTS, CHOICE_DEFAULTS[0]);
fgd.addChoice("Style:", STYLES, CHOICE_DEFAULTS[1]);
fgd.addChoice("Justification:", JUSTIFICATIONS, CHOICE_DEFAULTS[2]);
fgd.addSlider("Size:", 9, 24, DEF_SIZE);
fgd.setInsets(0, 20, 15);
fgd.addCheckbox("Antialiased text", DEF_ANTIALISED);
fgd.addChoice("Apply to:", SCOPES, CHOICE_DEFAULTS[3]);
fgd.hideCancelButton();
fgd.addHelp("");
fgd.setHelpLabel("Apply Defaults");
fgd.addDialogListener(new DialogListener() {
@Override
public boolean dialogItemChanged(final GenericDialog gd, final AWTEvent e) {
if (e != null && e.toString().contains("Apply Defaults")) {
@SuppressWarnings("unchecked")
final Vector<Choice> nChoices = gd.getChoices();
for (final Choice choice : nChoices)
choice.select(CHOICE_DEFAULTS[nChoices.indexOf(choice)]);
((TextField) gd.getNumericFields().get(0)).setText(Integer.toString(DEF_SIZE));
((Checkbox) gd.getCheckboxes().get(0)).setState(DEF_ANTIALISED);
}
final String type = FONTS[fgd.getNextChoiceIndex()];
final int style = INT_STYLES[fgd.getNextChoiceIndex()];
final int justification = INT_JUSTIFICATIONS[fgd.getNextChoiceIndex()];
final int size = (int) fgd.getNextNumber();
final int scopeIdx = fgd.getNextChoiceIndex();
plot.setJustification(justification);
plot.setAntialiasedText(fgd.getNextBoolean());
final Font font = new Font(type, style, size);
switch (scopeIdx) {
case 1: // SCOPES[1]
plot.setXLabelFont(font);
plot.setYLabelFont(font);
break;
case 2: // SCOPES[2]
plot.setXLabelFont(font);
break;
case 3: // SCOPES[3]
plot.setYLabelFont(font);
break;
default:
plot.setFont(font);
plot.setXLabelFont(font);
plot.setYLabelFont(font);
break;
}
plot.updateImage();
return true;
}
});
showAsSubDialog(fgd);
if (!fgd.wasOKed())
return;
}
Example 18
| Source File: Displayable.java From TrakEM2 with GNU General Public License v3.0 | 4 votes |
|
protected GenericDialog makeAdjustPropertiesDialog() {
Rectangle box = getBoundingBox(null);
GenericDialog gd = new GD("Properties of #" + id, this);
gd.addStringField("title: ", title);
gd.addNumericField("x: ", box.x, 2);
gd.addNumericField("y: ", box.y, 2);
gd.addNumericField("scale_x: ", 1, 2);
gd.addNumericField("scale_y: ", 1, 2);
gd.addNumericField("rot (degrees): ", 0, 2);
gd.addSlider("alpha: ", 0, 100, (int)(alpha*100));
gd.addCheckbox("visible", visible);
gd.addSlider("Red: ", 0, 255, color.getRed());
gd.addSlider("Green: ", 0, 255, color.getGreen());
gd.addSlider("Blue: ", 0, 255, color.getBlue());
gd.addCheckbox("locked", locked);
// add slider listener
final Scrollbar alp = (Scrollbar)gd.getSliders().get(0);
final Scrollbar red = (Scrollbar)gd.getSliders().get(1);
final Scrollbar green = (Scrollbar)gd.getSliders().get(2);
final Scrollbar blue = (Scrollbar)gd.getSliders().get(3);
final TextField talp = (TextField)gd.getNumericFields().get(5);
final TextField tred = (TextField)gd.getNumericFields().get(6);
final TextField tgreen = (TextField)gd.getNumericFields().get(7);
final TextField tblue = (TextField)gd.getNumericFields().get(8);
SliderListener sla = new SliderListener() {
public void update() {
setAlpha((float)alp.getValue()/100);
}
};
SliderListener slc = new SliderListener() {
public void update() {
setColor(new Color(red.getValue(), green.getValue(), blue.getValue()));
}
};
alp.addAdjustmentListener(sla);
red.addAdjustmentListener(slc);
green.addAdjustmentListener(slc);
blue.addAdjustmentListener(slc);
talp.addTextListener(sla);
tred.addTextListener(slc);
tgreen.addTextListener(slc);
tblue.addTextListener(slc);
gd.addChoice( "composite mode: ", compositeModes, compositeModes[ compositeMode ] );
return gd;
}
Example 19
| Source File: ExtendedMinAndMax3DPlugin.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 4 votes |
|
@Override
public void run(String arg) {
if ( IJ.getVersion().compareTo("1.48a") < 0 )
{
IJ.error( "Regional Minima and Maxima", "ERROR: detected ImageJ version " + IJ.getVersion()
+ ".\nThis plugin requires version 1.48a or superior, please update ImageJ!" );
return;
}
ImagePlus imagePlus = IJ.getImage();
if (imagePlus.getStackSize() == 1) {
IJ.error("Requires a Stack");
return;
}
ImageStack stack = imagePlus.getStack();
int sizeX = stack.getWidth();
int sizeY = stack.getHeight();
int sizeZ = stack.getSize();
boolean isGray8 = stack.getBitDepth() == 8;
double minValue, maxValue;
if (isGray8) {
minValue = 1;
maxValue = 255;
} else {
minValue = Double.MAX_VALUE;
maxValue = Double.MIN_VALUE;
for (int z = 0; z < sizeZ; z++) {
for (int y = 0; y < sizeY; y++) {
for (int x = 0; x < sizeX; x++) {
double val = stack.getVoxel(x, y, z);
minValue = Math.min(minValue, val);
maxValue = Math.max(maxValue, val);
}
}
}
}
// Create the configuration dialog
GenericDialog gd = new GenericDialog("Extended Min & Max 3D");
gd.addChoice("Operation", Operation.getAllLabels(),
Operation.EXTENDED_MINIMA.label);
gd.addSlider("Dynamic", minValue, maxValue, 10);
gd.addChoice("Connectivity", connectivityLabels, connectivityLabels[0]);
// gd.addHelp("http://imagejdocu.tudor.lu/doku.php?id=plugin:morphology:fast_morphological_filters:start");
gd.showDialog();
if (gd.wasCanceled())
return;
long t0 = System.currentTimeMillis();
// extract chosen parameters
Operation op = Operation.fromLabel(gd.getNextChoice());
int dynamic = (int) gd.getNextNumber();
int conn = connectivityValues[gd.getNextChoiceIndex()];
ImageStack result = op.apply(stack, dynamic, conn);
String newName = createResultImageName(imagePlus, op);
ImagePlus resultPlus = new ImagePlus(newName, result);
resultPlus.copyScale(imagePlus);
resultPlus.show();
resultPlus.setSlice(imagePlus.getCurrentSlice());
long t1 = System.currentTimeMillis();
IJUtils.showElapsedTime(op.toString(), t1 - t0, imagePlus);
}
Example 20
| Source File: Utils.java From TrakEM2 with GNU General Public License v3.0 | 4 votes |
|
static public final void addRGBColorSliders(final GenericDialog gd, final Color color) {
gd.addSlider("Red: ", 0, 255, color.getRed());
gd.addSlider("Green: ", 0, 255, color.getGreen());
gd.addSlider("Blue: ", 0, 255, color.getBlue());
}
