boolean init_functions() {
GenericDialog gd = new GenericDialog("Fitting Options");
gd.addStringField("Extra Definitions", exdef, 50);
gd.addCheckbox("Weight Using Plot Errors", false);
gd.addStringField("Weighting Equation (y is for data)", weightfunction, 50);
gd.addStringField("Fit_Equation", function, 50);
gd.showDialog();
if (gd.wasCanceled()) {
return false;
}
exdef = gd.getNextString();
boolean errweights = gd.getNextBoolean();
weightfunction = gd.getNextString();
function = gd.getNextString();
// first initialize the weights
weights = new float[tempdata.length];
if (errweights
|| weightfunction.equals("")
|| weightfunction == null
|| weightfunction == "1.0") {
if (errweights) {
for (int i = 0; i < tempdata.length; i++) weights[i] = 1.0f / (errs[i] * errs[i]);
} else {
for (int i = 0; i < tempdata.length; i++) weights[i] = 1.0f;
}
} else {
for (int i = 0; i < tempdata.length; i++) {
String script =
"y =" + tempdata[i] + "; " + "x =" + tempx[i] + "; " + "retval=" + weightfunction + ";";
Double temp = new Double(0.0);
try {
temp = (Double) engine.eval(script);
} catch (Exception e) {
IJ.log(e.getMessage());
}
if (!(temp.isInfinite() || temp.isNaN())) {
weights[i] = temp.floatValue();
}
}
}
// now compile the function script
try {
String script1 = exdef + "; retval=" + function + ";";
cs = ce.compile(script1);
} catch (Exception e) {
IJ.log(e.toString());
return false;
}
return true;
}
// Input/Output options
void io() {
GenericDialog gd = new GenericDialog("I/O Options");
gd.addNumericField("JPEG quality (0-100):", FileSaver.getJpegQuality(), 0, 3, "");
gd.addNumericField("GIF and PNG transparent index:", Prefs.getTransparentIndex(), 0, 3, "");
gd.addStringField(
"File extension for tables (.txt, .xls or .csv):", Prefs.get("options.ext", ".csv"), 4);
gd.addCheckbox("Use JFileChooser to open/save", Prefs.useJFileChooser);
if (!IJ.isMacOSX())
gd.addCheckbox("Use_file chooser to import sequences", Prefs.useFileChooser);
gd.addCheckbox("Save TIFF and raw in Intel byte order", Prefs.intelByteOrder);
gd.addCheckbox("Skip dialog when opening .raw files", Prefs.skipRawDialog);
gd.setInsets(15, 20, 0);
gd.addMessage("Results Table Options");
gd.setInsets(3, 40, 0);
gd.addCheckbox("Copy_column headers", Prefs.copyColumnHeaders);
gd.setInsets(0, 40, 0);
gd.addCheckbox("Copy_row numbers", !Prefs.noRowNumbers);
gd.setInsets(0, 40, 0);
gd.addCheckbox("Save_column headers", !Prefs.dontSaveHeaders);
gd.setInsets(0, 40, 0);
gd.addCheckbox("Save_row numbers", !Prefs.dontSaveRowNumbers);
gd.showDialog();
if (gd.wasCanceled()) return;
int quality = (int) gd.getNextNumber();
if (quality < 0) quality = 0;
if (quality > 100) quality = 100;
FileSaver.setJpegQuality(quality);
int transparentIndex = (int) gd.getNextNumber();
Prefs.setTransparentIndex(transparentIndex);
String extension = gd.getNextString();
if (!extension.startsWith(".")) extension = "." + extension;
Prefs.set("options.ext", extension);
Prefs.useJFileChooser = gd.getNextBoolean();
if (!IJ.isMacOSX()) Prefs.useFileChooser = gd.getNextBoolean();
Prefs.intelByteOrder = gd.getNextBoolean();
Prefs.skipRawDialog = gd.getNextBoolean();
Prefs.copyColumnHeaders = gd.getNextBoolean();
Prefs.noRowNumbers = !gd.getNextBoolean();
Prefs.dontSaveHeaders = !gd.getNextBoolean();
Prefs.dontSaveRowNumbers = !gd.getNextBoolean();
return;
}
// Miscellaneous Options
void miscOptions() {
String key = IJ.isMacintosh() ? "command" : "control";
GenericDialog gd = new GenericDialog("Miscellaneous Options", IJ.getInstance());
gd.addStringField("Divide by zero value:", "" + FloatBlitter.divideByZeroValue, 10);
gd.addCheckbox("Use pointer cursor", Prefs.usePointerCursor);
gd.addCheckbox("Hide \"Process Stack?\" dialog", IJ.hideProcessStackDialog);
gd.addCheckbox("Require " + key + " key for shortcuts", Prefs.requireControlKey);
gd.addCheckbox("Move isolated plugins to Misc. menu", Prefs.moveToMisc);
if (!IJ.isMacOSX()) gd.addCheckbox("Run single instance listener", Prefs.runSocketListener);
gd.addCheckbox("Enhanced line tool", Prefs.enhancedLineTool);
gd.addCheckbox("Reverse CZT order of \">\" and \"<\"", Prefs.reverseNextPreviousOrder);
gd.addCheckbox("Debug mode", IJ.debugMode);
gd.addHelp(IJ.URL + "/docs/menus/edit.html#misc");
gd.showDialog();
if (gd.wasCanceled()) return;
String divValue = gd.getNextString();
if (divValue.equalsIgnoreCase("infinity") || divValue.equalsIgnoreCase("infinite"))
FloatBlitter.divideByZeroValue = Float.POSITIVE_INFINITY;
else if (divValue.equalsIgnoreCase("NaN")) FloatBlitter.divideByZeroValue = Float.NaN;
else if (divValue.equalsIgnoreCase("max")) FloatBlitter.divideByZeroValue = Float.MAX_VALUE;
else {
Float f;
try {
f = new Float(divValue);
} catch (NumberFormatException e) {
f = null;
}
if (f != null) FloatBlitter.divideByZeroValue = f.floatValue();
}
IJ.register(FloatBlitter.class);
Prefs.usePointerCursor = gd.getNextBoolean();
IJ.hideProcessStackDialog = gd.getNextBoolean();
Prefs.requireControlKey = gd.getNextBoolean();
Prefs.moveToMisc = gd.getNextBoolean();
if (!IJ.isMacOSX()) Prefs.runSocketListener = gd.getNextBoolean();
Prefs.enhancedLineTool = gd.getNextBoolean();
Prefs.reverseNextPreviousOrder = gd.getNextBoolean();
IJ.setDebugMode(gd.getNextBoolean());
}
/** Displays a modal options dialog. */
public boolean showDialog() {
Calibration cal = imp != null ? imp.getCalibration() : (new Calibration());
double unitSquared = cal.pixelWidth * cal.pixelHeight;
if (pixelUnits) unitSquared = 1.0;
if (Macro.getOptions() != null) {
boolean oldMacro = updateMacroOptions();
if (oldMacro) unitSquared = 1.0;
staticMinSize = 0.0;
staticMaxSize = DEFAULT_MAX_SIZE;
staticMinCircularity = 0.0;
staticMaxCircularity = 1.0;
staticShowChoice = NOTHING;
}
GenericDialog gd = new GenericDialog("Analyze Particles");
minSize = staticMinSize;
maxSize = staticMaxSize;
minCircularity = staticMinCircularity;
maxCircularity = staticMaxCircularity;
showChoice = staticShowChoice;
if (maxSize == 999999) maxSize = DEFAULT_MAX_SIZE;
options = staticOptions;
String unit = cal.getUnit();
boolean scaled = cal.scaled();
if (unit.equals("inch")) {
unit = "pixel";
unitSquared = 1.0;
scaled = false;
pixelUnits = true;
}
String units = unit + "^2";
int places = 0;
double cmin = minSize * unitSquared;
if ((int) cmin != cmin) places = 2;
double cmax = maxSize * unitSquared;
if ((int) cmax != cmax && cmax != DEFAULT_MAX_SIZE) places = 2;
String minStr = ResultsTable.d2s(cmin, places);
if (minStr.indexOf("-") != -1) {
for (int i = places; i <= 6; i++) {
minStr = ResultsTable.d2s(cmin, i);
if (minStr.indexOf("-") == -1) break;
}
}
String maxStr = ResultsTable.d2s(cmax, places);
if (maxStr.indexOf("-") != -1) {
for (int i = places; i <= 6; i++) {
maxStr = ResultsTable.d2s(cmax, i);
if (maxStr.indexOf("-") == -1) break;
}
}
if (scaled) gd.setInsets(5, 0, 0);
gd.addStringField("Size (" + units + "):", minStr + "-" + maxStr, 12);
if (scaled) {
gd.setInsets(0, 40, 5);
gd.addCheckbox("Pixel units", pixelUnits);
}
gd.addStringField("Circularity:", IJ.d2s(minCircularity) + "-" + IJ.d2s(maxCircularity), 12);
gd.addChoice("Show:", showStrings, showStrings[showChoice]);
String[] labels = new String[8];
boolean[] states = new boolean[8];
labels[0] = "Display results";
states[0] = (options & SHOW_RESULTS) != 0;
labels[1] = "Exclude on edges";
states[1] = (options & EXCLUDE_EDGE_PARTICLES) != 0;
labels[2] = "Clear results";
states[2] = (options & CLEAR_WORKSHEET) != 0;
labels[3] = "Include holes";
states[3] = (options & INCLUDE_HOLES) != 0;
labels[4] = "Summarize";
states[4] = (options & DISPLAY_SUMMARY) != 0;
labels[5] = "Record starts";
states[5] = (options & RECORD_STARTS) != 0;
labels[6] = "Add to Manager";
states[6] = (options & ADD_TO_MANAGER) != 0;
labels[7] = "In_situ Show";
states[7] = (options & IN_SITU_SHOW) != 0;
gd.addCheckboxGroup(4, 2, labels, states);
gd.addHelp(IJ.URL + "/docs/menus/analyze.html#ap");
gd.showDialog();
if (gd.wasCanceled()) return false;
String size = gd.getNextString(); // min-max size
if (scaled) pixelUnits = gd.getNextBoolean();
if (pixelUnits) unitSquared = 1.0;
else unitSquared = cal.pixelWidth * cal.pixelHeight;
String[] minAndMax = Tools.split(size, " -");
double mins = gd.parseDouble(minAndMax[0]);
double maxs = minAndMax.length == 2 ? gd.parseDouble(minAndMax[1]) : Double.NaN;
minSize = Double.isNaN(mins) ? DEFAULT_MIN_SIZE : mins / unitSquared;
maxSize = Double.isNaN(maxs) ? DEFAULT_MAX_SIZE : maxs / unitSquared;
if (minSize < DEFAULT_MIN_SIZE) minSize = DEFAULT_MIN_SIZE;
if (maxSize < minSize) maxSize = DEFAULT_MAX_SIZE;
staticMinSize = minSize;
staticMaxSize = maxSize;
minAndMax = Tools.split(gd.getNextString(), " -"); // min-max circularity
double minc = gd.parseDouble(minAndMax[0]);
double maxc = minAndMax.length == 2 ? gd.parseDouble(minAndMax[1]) : Double.NaN;
minCircularity = Double.isNaN(minc) ? 0.0 : minc;
maxCircularity = Double.isNaN(maxc) ? 1.0 : maxc;
if (minCircularity < 0.0 || minCircularity > 1.0) minCircularity = 0.0;
if (maxCircularity < minCircularity || maxCircularity > 1.0) maxCircularity = 1.0;
if (minCircularity == 1.0 && maxCircularity == 1.0) minCircularity = 0.0;
staticMinCircularity = minCircularity;
staticMaxCircularity = maxCircularity;
if (gd.invalidNumber()) {
IJ.error("Bins invalid.");
canceled = true;
return false;
}
showChoice = gd.getNextChoiceIndex();
staticShowChoice = showChoice;
if (gd.getNextBoolean()) options |= SHOW_RESULTS;
else options &= ~SHOW_RESULTS;
if (gd.getNextBoolean()) options |= EXCLUDE_EDGE_PARTICLES;
else options &= ~EXCLUDE_EDGE_PARTICLES;
if (gd.getNextBoolean()) options |= CLEAR_WORKSHEET;
else options &= ~CLEAR_WORKSHEET;
if (gd.getNextBoolean()) options |= INCLUDE_HOLES;
else options &= ~INCLUDE_HOLES;
if (gd.getNextBoolean()) options |= DISPLAY_SUMMARY;
else options &= ~DISPLAY_SUMMARY;
if (gd.getNextBoolean()) options |= RECORD_STARTS;
else options &= ~RECORD_STARTS;
if (gd.getNextBoolean()) options |= ADD_TO_MANAGER;
else options &= ~ADD_TO_MANAGER;
if (gd.getNextBoolean()) options |= IN_SITU_SHOW;
else options &= ~IN_SITU_SHOW;
staticOptions = options;
options |= SHOW_PROGRESS;
if ((options & DISPLAY_SUMMARY) != 0)
Analyzer.setMeasurements(Analyzer.getMeasurements() | AREA);
return true;
}
public boolean analyseParticles(MyFunctions f) {
GenericDialog gd = new GenericDialog("Analyse PALM/STORM Particles");
gd.addNumericField("Minimum SNR", prefs.get("QuickPALM.snr", 5), 2);
gd.addNumericField("Maximum FWHM (in px)", prefs.get("QuickPALM.fwhm", 4), 0);
gd.addNumericField("Image plane pixel size (nm)", prefs.get("QuickPALM.pixelsize", 106), 2);
gd.addCheckbox("Smart SNR", prefs.get("QuickPALM.smartsnr", true));
gd.addCheckbox(
"3D PALM (astigmatism) - will require calibration file",
prefs.get("QuickPALM.is3d", false));
gd.addCheckbox("Online rendering", prefs.get("QuickPALM.view", true));
gd.addCheckbox("Attach to running acquisition", prefs.get("QuickPALM.attach", false));
gd.addCheckbox("Stream particle info directly into file", prefs.get("QuickPALM.stream", true));
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Online rendering settings (used only if selected) --");
gd.addMessage("\n");
gd.addNumericField("Pixel size of rendered image (nm)", 30, 2);
gd.addNumericField("Accumulate last (0 to accumulate all frames)", 0, 0);
gd.addNumericField("Update every (frames)", 10, 0);
// gd.addNumericField("Allow color saturation (%)", 50, 0);
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Attach to running acquisition settings (used only if selected) --");
gd.addMessage("\n");
gd.addStringField(
"_Image name pattern (NN...NN represents the numerical change)",
prefs.get("QuickPALM.pattern", "imgNNNNNNNNN.tif"),
20);
gd.addNumericField("Start NN...NN with", 0, 0);
gd.addNumericField("In acquisition max. wait time for new image (ms)", 50, 0);
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Advanced settings (don't normally need to be changed) --");
gd.addMessage("\n");
gd.addNumericField("_Minimum symmetry (%)", prefs.get("QuickPALM.symmetry", 50), 0);
gd.addNumericField(
"Local threshold (% maximum intensity)", prefs.get("QuickPALM.lthreshold", 20), 0);
gd.addNumericField("_Maximum iterations per frame", prefs.get("QuickPALM.maxiter", 1000), 0);
gd.addNumericField(
"Threads (each takes ~3*[frame size] in memory)", prefs.get("QuickPALM.nthreads", 50), 0);
gd.addMessage("\n\nDon't forget to save the table in the end...");
gd.showDialog();
if (gd.wasCanceled()) return false;
snr = (int) gd.getNextNumber();
prefs.set("QuickPALM.snr", snr);
fwhm = gd.getNextNumber();
prefs.set("QuickPALM.fwhm", fwhm);
pixelsize = gd.getNextNumber();
prefs.set("QuickPALM.pixelsize", pixelsize);
smartsnr = gd.getNextBoolean();
prefs.set("QuickPALM.smartsnr", smartsnr);
is3d = gd.getNextBoolean();
prefs.set("QuickPALM.is3d", is3d);
view = gd.getNextBoolean();
prefs.set("QuickPALM.view", view);
attach = gd.getNextBoolean();
prefs.set("QuickPALM.attach", attach);
if (gd.getNextBoolean()) {
f.psave = new ParticleSaver();
f.psave.setup();
prefs.set("QuickPALM.stream", true);
} else prefs.set("QuickPALM.stream", false);
// --
magn = pixelsize / gd.getNextNumber();
viewer_accumulate = (int) gd.getNextNumber();
viewer_update = (int) gd.getNextNumber();
// --
pattern = gd.getNextString().trim();
prefs.set("QuickPALM.pattern", pattern);
prefix = pattern.substring(0, pattern.indexOf("N"));
sufix = pattern.substring(pattern.lastIndexOf("N") + 1, pattern.length());
nimchars = pattern.split("N").length - 1;
nimstart = (int) gd.getNextNumber();
waittime = (int) gd.getNextNumber();
// --
symmetry = gd.getNextNumber() / 100;
prefs.set("QuickPALM.symmetry", symmetry);
pthrsh = gd.getNextNumber() / 100;
prefs.set("QuickPALM.lthreshold", pthrsh * 100);
maxpart = (int) gd.getNextNumber();
prefs.set("QuickPALM.maxiter", maxpart);
threads = (int) gd.getNextNumber();
prefs.set("QuickPALM.nthreads", threads);
return true;
}
boolean showDialog(ImageProcessor ip) {
int bitDepth = imp.getBitDepth();
boolean isStack = imp.getStackSize() > 1;
r = ip.getRoi();
int width = newWidth;
if (width == 0) width = r.width;
int height = (int) ((double) width * r.height / r.width);
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
if (xscale != 0.0 && yscale != 0.0) {
width = (int) (r.width * xscale);
height = (int) (r.height * yscale);
} else {
xstr = "-";
ystr = "-";
}
GenericDialog gd = new GenericDialog("Scale");
gd.addStringField("X Scale (0.05-25):", xstr);
gd.addStringField("Y Scale (0.05-25):", ystr);
gd.setInsets(5, 0, 5);
gd.addStringField("Width (pixels):", "" + width);
gd.addStringField("Height (pixels):", "" + height);
fields = gd.getStringFields();
for (int i = 0; i < 3; i++) {
((TextField) fields.elementAt(i)).addTextListener(this);
((TextField) fields.elementAt(i)).addFocusListener(this);
}
xField = (TextField) fields.elementAt(0);
yField = (TextField) fields.elementAt(1);
widthField = (TextField) fields.elementAt(2);
heightField = (TextField) fields.elementAt(3);
fieldWithFocus = xField;
gd.addCheckbox("Interpolate", interpolate);
if (bitDepth == 8 || bitDepth == 24)
gd.addCheckbox("Fill with Background Color", fillWithBackground);
if (isStack) gd.addCheckbox("Process Entire Stack", processStack);
gd.addCheckbox("Create New Window", newWindow);
title = WindowManager.getUniqueName(imp.getTitle());
gd.setInsets(10, 0, 0);
gd.addStringField("Title:", title, 12);
gd.showDialog();
if (gd.wasCanceled()) return false;
xstr = gd.getNextString();
ystr = gd.getNextString();
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
String wstr = gd.getNextString();
newWidth = (int) Tools.parseDouble(wstr, 0);
newHeight = (int) Tools.parseDouble(gd.getNextString(), 0);
if (newHeight != 0 && (wstr.equals("-") || wstr.equals("0")))
newWidth = (int) (newHeight * (double) r.width / r.height);
if (newWidth == 0 || newHeight == 0) {
IJ.error("Invalid width or height entered");
return false;
}
if (xscale > 25.0) xscale = 25.0;
if (yscale > 25.0) yscale = 25.0;
if (xscale > 0.0 && yscale > 0.0) {
newWidth = (int) (r.width * xscale);
newHeight = (int) (r.height * yscale);
}
interpolate = gd.getNextBoolean();
if (bitDepth == 8 || bitDepth == 24) fillWithBackground = gd.getNextBoolean();
if (isStack) processStack = gd.getNextBoolean();
newWindow = gd.getNextBoolean();
if (!newWindow && xscale == 0.0) {
xscale = (double) newWidth / r.width;
yscale = (double) newHeight / r.height;
}
title = gd.getNextString();
if (fillWithBackground) {
Color bgc = Toolbar.getBackgroundColor();
if (bitDepth == 8) bgValue = ip.getBestIndex(bgc);
else if (bitDepth == 24) bgValue = bgc.getRGB();
} else {
if (bitDepth == 8) bgValue = ip.isInvertedLut() ? 0.0 : 255.0; // white
else if (bitDepth == 24) bgValue = 0xffffffff; // white
}
return true;
}
boolean showDialog(ImageProcessor ip) {
String macroOptions = Macro.getOptions();
if (macroOptions != null) {
if (macroOptions.indexOf(" interpolate") != -1)
macroOptions.replaceAll(" interpolate", " interpolation=Bilinear");
else if (macroOptions.indexOf(" interpolation=") == -1)
macroOptions = macroOptions + " interpolation=None";
Macro.setOptions(macroOptions);
}
int bitDepth = imp.getBitDepth();
int stackSize = imp.getStackSize();
boolean isStack = stackSize > 1;
oldDepth = stackSize;
if (isStack) {
xstr = "1.0";
ystr = "1.0";
zstr = "1.0";
}
r = ip.getRoi();
int width = newWidth;
if (width == 0) width = r.width;
int height = (int) ((double) width * r.height / r.width);
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
zscale = 1.0;
if (xscale != 0.0 && yscale != 0.0) {
width = (int) (r.width * xscale);
height = (int) (r.height * yscale);
} else {
xstr = "-";
ystr = "-";
}
GenericDialog gd = new GenericDialog("Scale");
gd.addStringField("X Scale:", xstr);
gd.addStringField("Y Scale:", ystr);
if (isStack) gd.addStringField("Z Scale:", zstr);
gd.setInsets(5, 0, 5);
gd.addStringField("Width (pixels):", "" + width);
gd.addStringField("Height (pixels):", "" + height);
if (isStack) {
String label = "Depth (images):";
if (imp.isHyperStack()) {
int slices = imp.getNSlices();
int frames = imp.getNFrames();
if (slices == 1 && frames > 1) {
label = "Depth (frames):";
oldDepth = frames;
} else {
label = "Depth (slices):";
oldDepth = slices;
}
}
gd.addStringField(label, "" + oldDepth);
}
fields = gd.getStringFields();
for (int i = 0; i < fields.size(); i++) {
((TextField) fields.elementAt(i)).addTextListener(this);
((TextField) fields.elementAt(i)).addFocusListener(this);
}
xField = (TextField) fields.elementAt(0);
yField = (TextField) fields.elementAt(1);
if (isStack) {
zField = (TextField) fields.elementAt(2);
widthField = (TextField) fields.elementAt(3);
heightField = (TextField) fields.elementAt(4);
depthField = (TextField) fields.elementAt(5);
} else {
widthField = (TextField) fields.elementAt(2);
heightField = (TextField) fields.elementAt(3);
}
fieldWithFocus = xField;
gd.addChoice("Interpolation:", methods, methods[interpolationMethod]);
if (bitDepth == 8 || bitDepth == 24)
gd.addCheckbox("Fill with background color", fillWithBackground);
gd.addCheckbox("Average when downsizing", averageWhenDownsizing);
boolean hyperstack = imp.isHyperStack() || imp.isComposite();
if (isStack && !hyperstack) gd.addCheckbox("Process entire stack", processStack);
gd.addCheckbox("Create new window", newWindow);
title = WindowManager.getUniqueName(imp.getTitle());
gd.setInsets(10, 0, 0);
gd.addStringField("Title:", title, 12);
gd.showDialog();
if (gd.wasCanceled()) return false;
xstr = gd.getNextString();
ystr = gd.getNextString();
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
if (isStack) {
zstr = gd.getNextString();
zscale = Tools.parseDouble(ystr, 0.0);
}
String wstr = gd.getNextString();
newWidth = (int) Tools.parseDouble(wstr, 0);
newHeight = (int) Tools.parseDouble(gd.getNextString(), 0);
if (newHeight != 0 && (wstr.equals("-") || wstr.equals("0")))
newWidth = (int) (newHeight * (double) r.width / r.height);
if (newWidth == 0 || newHeight == 0) {
IJ.error("Scaler", "Width or height is 0");
return false;
}
if (xscale > 0.0 && yscale > 0.0) {
newWidth = (int) (r.width * xscale);
newHeight = (int) (r.height * yscale);
}
if (isStack) newDepth = (int) Tools.parseDouble(gd.getNextString(), 0);
interpolationMethod = gd.getNextChoiceIndex();
if (bitDepth == 8 || bitDepth == 24) fillWithBackground = gd.getNextBoolean();
averageWhenDownsizing = gd.getNextBoolean();
if (isStack && !hyperstack) processStack = gd.getNextBoolean();
if (hyperstack) processStack = true;
newWindow = gd.getNextBoolean();
if (xscale == 0.0) {
xscale = (double) newWidth / r.width;
yscale = (double) newHeight / r.height;
}
title = gd.getNextString();
if (fillWithBackground) {
Color bgc = Toolbar.getBackgroundColor();
if (bitDepth == 8) bgValue = ip.getBestIndex(bgc);
else if (bitDepth == 24) bgValue = bgc.getRGB();
} else bgValue = 0.0;
return true;
}
/* Setup GUI */
protected final boolean setup() {
if (IJ.versionLessThan("1.40c")) {
return false;
} else {
int[] ids = WindowManager.getIDList();
if (ids != null && ids.length >= 2) {
ArrayList titlesList = new ArrayList();
ArrayList idsList = new ArrayList();
String currentTitle = null;
for (int titles = 0; titles < ids.length; ++titles) {
ImagePlus var1 = WindowManager.getImage(ids[titles]);
titlesList.add(var1.getTitle());
idsList.add(Integer.valueOf(ids[titles]));
if (var1 == WindowManager.getCurrentImage()) {
currentTitle = var1.getTitle();
}
}
if (titlesList.size() < 2) {
IJ.showMessage("You should have at least two stacks - stimulus and response.");
return false;
} else {
String[] var8 = new String[titlesList.size()];
titlesList.toArray(var8);
if (currentTitle == null) {
currentTitle = var8[0];
}
SubstackMaker sm = new SubstackMaker();
GenericDialog gd = new GenericDialog("AAP - 1.1.0");
// gd.setInsets(10, 45, 0);
gd.addChoice("Stimulus stack", var8, currentTitle);
gd.addChoice("Response stack", var8, currentTitle.equals(var8[0]) ? var8[1] : var8[0]);
String defautltSlices =
"1-" + WindowManager.getImage(((Integer) idsList.get(0)).intValue()).getStackSize();
gd.addMessage("Enter a range (e.g. 2-14)...", null, Color.darkGray);
gd.addStringField("Slices of Response:", defautltSlices, 40);
gd.addCheckbox("Remove first slice", true);
gd.addCheckbox("Use Artifact from response", true);
gd.showDialog();
if (gd.wasCanceled()) {
return false;
} else {
this.imp_s =
WindowManager.getImage(((Integer) idsList.get(gd.getNextChoiceIndex())).intValue());
this.imp_r =
WindowManager.getImage(((Integer) idsList.get(gd.getNextChoiceIndex())).intValue());
String userInput = gd.getNextString();
this.dt_r = Activity_Analysis.findSignalDt(this.imp_r.getTitle());
if (userInput == null) {
return false;
}
IJ.showStatus(" Making substack copy of selection...");
this.imp_r = sm.makeSubstack(this.imp_r, userInput);
this.imp_s_index = getFirstNLast(this.imp_r, userInput);
if (this.imp_s_index[0] != 1 | !gd.getNextBoolean()) this.removeFirst = false;
if (gd.getNextBoolean()) this.useArtifact = true;
// this.imp_s = makeStimSubstack(this.imp_s , userInput);
return true;
}
}
} else {
IJ.showMessage("You should have at least two stacks open.");
return false;
}
}
}