public void run(ImageProcessor ip) {
dimz = stack.getSize();
dimy = stack.getWidth();
dimx = stack.getHeight();
SaveDialog sd = new SaveDialog("Save Measurements as Text...", "res", ".dat");
String name = sd.getFileName();
if (name == null) return;
String directory = sd.getDirectory();
nb = calculnb(stack); // -1;
IJ.showStatus("Measure parameters for the " + nb + " objects ...");
if (nb < 1) {
IJ.showMessage("volume must be labeled");
} else {
double[] volume_m = new double[nb];
int[] volume_p = new int[nb];
double[] surface = new double[nb];
double[] surfacenb = new double[nb];
double[][][] I = new double[3][3][nb];
double[][] J = new double[3][nb];
double[][][] dir = new double[3][3][nb];
double[] xg = new double[nb];
double[] yg = new double[nb];
double[] zg = new double[nb];
byte[] bord = new byte[nb];
// double[] a = new double[nb];
// double[] b = new double[nb];
// double[] c = new double[nb];
// double[] Fab = new double[nb];
// double[] Fac = new double[nb];
// double[] Fbc = new double[nb];
// double[] sp = new double[nb];
double[][] lmin = new double[nb][3];
double[][] lmax = new double[nb][3];
IJ.showStatus("Measure surfaces ...");
calculmarchsurfstack(stack, nb, surface, volume_m);
calculmarchsurfstacknb(stack, nb, surfacenb);
// calculvolumestack(stack,nb,volume_p);
IJ.showStatus("Measure volumes and inertia ...");
calculcgstack(stack, nb, volume_p, xg, yg, zg);
calculinertiestack(stack, nb, xg, yg, zg, I);
inertie(nb, I, J, dir);
IJ.showStatus("Measure bounding boxes ...");
boitestack(stack, nb, xg, yg, zg, dir, lmin, lmax);
borderstack(stack, nb, bord);
IJ.showStatus("Save results ...");
sauvegarde(
volume_p, volume_m, surface, surfacenb, xg, yg, zg, J, dir, nb, bord, lmin, lmax,
directory, name);
volume_m = null;
volume_p = null;
surface = null;
xg = null;
yg = null;
zg = null;
}
}
String showDialog() {
if (defaultDir == null) defaultDir = Menus.getMacrosPath();
OpenDialog od = new OpenDialog("Install Macros", defaultDir, fileName);
String name = od.getFileName();
if (name == null) return null;
String dir = od.getDirectory();
if (!(name.endsWith(".txt") || name.endsWith(".ijm"))) {
IJ.showMessage("Macro Installer", "File name must end with \".txt\" or \".ijm\" .");
return null;
}
fileName = name;
defaultDir = dir;
return dir + name;
}
private void showioerror() {
IJ.showMessage("Error in file io");
}
private void geterrors() {
GenericDialog gd = new GenericDialog("Options");
float conf = 0.67f;
gd.addNumericField("Confidence Limit", (int) (conf * 100.0f), 5, 10, null);
gd.addChoice("Error Parameter", paramsnames, paramsnames[0]);
double spacing = 0.01;
gd.addNumericField("Chi^2 plot spacing (% of value)?", spacing * 100.0, 2, 10, null);
boolean globalerror = false;
gd.addCheckbox("Global Fit Error?", globalerror);
int dataset = 0;
gd.addNumericField("Data Set (for Global Error)", dataset, 0);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
conf = 0.01f * (float) gd.getNextNumber();
int paramindex = (int) gd.getNextChoiceIndex();
spacing = 0.01 * gd.getNextNumber();
globalerror = gd.getNextBoolean();
dataset = (int) gd.getNextNumber();
if (globalerror) {
support_plane_errors erclass = new support_plane_errors(this, 0.0001, 50, true, 0.1);
int[] erindeces = {paramindex, dataset};
// need to set up all the matrices
int nsel = 0;
int nparams = 11;
for (int i = 0; i < ncurves; i++) {
if (include[i]) {
nsel++;
}
}
double[][] params = new double[nsel][nparams];
String[][] tempformulas = new String[nsel][nparams];
double[][][] constraints = new double[2][nsel][nparams];
int[][] vflmatrix = new int[nsel][nparams];
float[][] tempdata = new float[nsel][xpts * ypts];
float[][] tempweights = new float[nsel][xpts * ypts];
int nfit = 0;
int counter = 0;
for (int i = 0; i < ncurves; i++) {
if (include[i]) {
for (int j = 0; j < nparams; j++) {
params[counter][j] = globalparams[i][j];
tempformulas[counter][j] = globalformulas[i][j];
constraints[0][counter][j] = globalconstraints[0][i][j];
constraints[1][counter][j] = globalconstraints[1][i][j];
vflmatrix[counter][j] = globalvflmatrix[i][j];
if (vflmatrix[counter][j] == 0 || (j == 0 && vflmatrix[counter][j] == 2)) {
nfit++;
}
}
for (int j = 0; j < xpts; j++) {
for (int k = 0; k < ypts; k++) {
tempdata[counter][j + k * xpts] = (float) ((double) pch[i][j][k] / (double) nmeas[i]);
tempweights[counter][j + k * xpts] = weights[i][j][k];
}
}
counter++;
}
}
int dofnum = xpts * ypts * nsel - (nfit - 1) - 1;
int dofden = xpts * ypts * nsel - nfit - 1;
// double flim=FLimit(dofnum,dofden,(double)conf);
double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf);
IJ.log("FLimit = " + (float) flim);
if (flim == Double.NaN && flim < 1.0) {
IJ.showMessage("Invalid Limiting F Value");
return;
}
double truespacing = Math.abs(params[erindeces[1]][erindeces[0]] * spacing);
double[][] c2plot =
erclass.geterrorsglobal(
params,
vflmatrix,
tempformulas,
paramsnames,
constraints,
tempdata,
tempweights,
flim,
truespacing,
erindeces);
IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]);
int templength = c2plot[0].length;
float[][] c2plotf = new float[2][templength - 1];
for (int i = 0; i < (templength - 1); i++) {
c2plotf[0][i] = (float) c2plot[0][i + 1];
c2plotf[1][i] = (float) c2plot[1][i + 1];
}
new PlotWindow4(
"c2 plot",
paramsnames[paramindex] + "[" + dataset + "]",
"Chi^2",
c2plotf[0],
c2plotf[1])
.draw();
} else {
support_plane_errors erclass = new support_plane_errors(this, 0.0001, 50, false, 0.1);
int errindex = paramindex;
float[] tempdata = new float[xpts * ypts];
float[] tempweights = new float[xpts * ypts];
for (int i = 0; i < xpts; i++) {
for (int j = 0; j < ypts; j++) {
tempdata[i + j * xpts] = (float) ((double) avg[i][j] / (double) nmeas[ncurves]);
tempweights[i + j * xpts] = avgweights[i][j];
}
}
int nfit = 0;
for (int i = 0; i < 7; i++) {
if (avgfixes[i] == 0) {
nfit++;
}
}
int dofnum = xpts * ypts - (nfit - 1) - 1;
int dofden = xpts * ypts - nfit - 1;
double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf);
IJ.log("FLimit = " + (float) flim);
if (flim == Double.NaN && flim < 1.0) {
IJ.showMessage("Invalid Limiting F Value");
return;
}
double truespacing = Math.abs(avgparams[errindex] * spacing);
double[][] c2plot =
erclass.geterrors(
avgparams,
avgfixes,
avgconstraints,
tempdata,
tempweights,
flim,
truespacing,
errindex);
IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]);
int templength = c2plot[0].length;
float[][] c2plotf = new float[2][templength - 1];
for (int i = 0; i < (templength - 1); i++) {
c2plotf[0][i] = (float) c2plot[0][i + 1];
c2plotf[1][i] = (float) c2plot[1][i + 1];
}
new PlotWindow4("c2 plot", paramsnames[errindex], "Chi^2", c2plotf[0], c2plotf[1]).draw();
}
}
public void run(String arg) {
Frame[] niframes = WindowManager.getNonImageWindows();
String[] titles = new String[niframes.length + 1];
for (int i = 0; i < niframes.length; i++) {
titles[i] = niframes[i].getTitle();
}
titles[niframes.length] = "Clipboard";
GenericDialog gd = new GenericDialog("Windows");
boolean importfile = false;
gd.addCheckbox("Import from file?", importfile);
gd.addChoice("Windows", titles, titles[0]);
boolean hasxvals = false;
gd.addCheckbox("X Vals Column?", hasxvals);
boolean multix = false;
gd.addCheckbox("Multi_X_Columns?", multix);
boolean skipendzeros = false;
gd.addCheckbox("Skip_end_zeros?", skipendzeros);
String[] delimiters = {"Tab", "Comma", "Space"};
gd.addChoice("Delimiter", delimiters, delimiters[0]);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
importfile = gd.getNextBoolean();
int index = gd.getNextChoiceIndex();
hasxvals = gd.getNextBoolean();
multix = gd.getNextBoolean();
skipendzeros = gd.getNextBoolean();
int delimindex = gd.getNextChoiceIndex();
if (multix) hasxvals = true;
String textdata = "";
if (importfile) {
OpenDialog od = new OpenDialog("Open File", "", ".txt");
String directory = od.getDirectory();
String name = od.getFileName();
if (name == null) {
return;
}
try {
File infile = new File(directory + name);
BufferedReader b = new BufferedReader(new FileReader(infile));
textdata = (new jdataio()).readstringfile(b);
b.close();
} catch (IOException e) {
return;
}
} else {
if (index == niframes.length) {
// here we get the data from the clipboard
Transferable t = Toolkit.getDefaultToolkit().getSystemClipboard().getContents(null);
try {
if (t != null && t.isDataFlavorSupported(DataFlavor.stringFlavor)) {
textdata = (String) t.getTransferData(DataFlavor.stringFlavor);
}
} catch (UnsupportedFlavorException e) {
} catch (IOException e) {
}
if (textdata.equals("")) {
IJ.error("Error copying from clipboard.");
return;
}
} else {
if (niframes[index] instanceof Editor) {
Editor tw = (Editor) niframes[index];
textdata = tw.getText();
} else {
if (niframes[index] instanceof TextWindow) {
TextWindow tw = (TextWindow) niframes[index];
textdata = tw.getTextPanel().getText();
} else {
IJ.showMessage("Not a valid text window");
return;
}
}
}
}
if (textdata == null) {
IJ.showMessage("Error in Obtaining String");
return;
}
if (textdata.indexOf("\r") >= 0) {
textdata = textdata.replace('\r', '\n');
}
char[] delims = {'\t', ',', ' '};
delimit_string ds = new delimit_string(delims[delimindex]);
String[] rows = ds.getrows(textdata);
int lines = rows.length;
int columns = ds.getnumcolumns(rows[0]);
int ycolumns = columns;
if (hasxvals) {
if (multix) {
ycolumns /= 2;
} else {
ycolumns--;
}
}
if (multix) {
float[][] ydata = new float[ycolumns][lines];
float[][] xdata = new float[ycolumns][lines];
for (int i = 0; i < lines; i++) {
float[] temp = ds.delim2float(rows[i], columns);
for (int j = 0; j < ycolumns; j++) {
ydata[j][i] = temp[2 * j + 1];
xdata[j][i] = temp[2 * j];
}
}
int[] npts = new int[ycolumns];
for (int i = 0; i < ycolumns; i++) {
npts[i] = lines;
}
if (skipendzeros) {
for (int i = 0; i < ycolumns; i++) {
int counter = lines - 1;
while ((xdata[i][counter] == 0.0f || Float.isNaN(xdata[i][counter])) && counter > 0) {
xdata[i][counter] = 0.0f;
ydata[i][counter] = 0.0f;
npts[i]--;
counter--;
}
}
}
(new PlotWindow4("Text Plot", "x", "y", xdata, ydata, npts)).draw();
} else {
float[][] tempydata = new float[ycolumns][lines];
float[] tempxdata = new float[lines];
float[][] xdata = null;
float[][] ydata = null;
int startcolumn = 0;
if (hasxvals) startcolumn = 1;
for (int i = 0; i < lines; i++) {
float[] temp = ds.delim2float(rows[i], columns);
if (hasxvals) {
tempxdata[i] = temp[0];
} else {
tempxdata[i] = (float) (i + 1);
}
for (int j = 0; j < ycolumns; j++) {
tempydata[j][i] = temp[j + startcolumn];
}
}
int[] npts = new int[ycolumns];
npts[0] = lines;
if (skipendzeros) {
int maxpts = 0;
for (int i = 0; i < ycolumns; i++) {
int counter = lines - 1;
npts[i] = lines;
while ((tempydata[i][counter] == 0.0f || Float.isNaN(tempydata[i][counter]))
&& counter > 0) {
npts[i]--;
counter--;
}
if (npts[i] > maxpts) maxpts = npts[i];
IJ.log("" + npts[i]);
}
ydata = new float[ycolumns][maxpts];
xdata = new float[ycolumns][maxpts];
for (int i = 0; i < ycolumns; i++) {
// npts[i]=npts[0];
System.arraycopy(tempxdata, 0, xdata[i], 0, npts[i]);
System.arraycopy(tempydata[i], 0, ydata[i], 0, npts[i]);
}
} else {
ydata = tempydata;
xdata = new float[ycolumns][];
for (int i = 0; i < ycolumns; i++) {
npts[i] = npts[0];
xdata[i] = tempxdata.clone();
}
}
(new PlotWindow4("Text Plot", "x", "y", xdata, ydata, npts)).draw();
}
}
void install() {
subMenus.clear();
if (text != null) {
Tokenizer tok = new Tokenizer();
pgm = tok.tokenize(text);
}
if (macrosMenu != null) IJ.showStatus("");
int[] code = pgm.getCode();
Symbol[] symbolTable = pgm.getSymbolTable();
int count = 0, token, nextToken, address;
String name;
Symbol symbol;
shortcutsInUse = null;
inUseCount = 0;
nShortcuts = 0;
toolCount = 0;
macroStarts = new int[MAX_MACROS];
macroNames = new String[MAX_MACROS];
boolean isPluginsMacrosMenu = false;
if (macrosMenu != null) {
int itemCount = macrosMenu.getItemCount();
isPluginsMacrosMenu = macrosMenu == Menus.getMacrosMenu();
int baseCount = isPluginsMacrosMenu ? MACROS_MENU_COMMANDS : Editor.MACROS_MENU_ITEMS;
if (itemCount > baseCount) {
for (int i = itemCount - 1; i >= baseCount; i--) macrosMenu.remove(i);
}
}
if (pgm.hasVars() && pgm.macroCount() > 0 && pgm.getGlobals() == null)
new Interpreter().saveGlobals(pgm);
ArrayList tools = new ArrayList();
for (int i = 0; i < code.length; i++) {
token = code[i] & TOK_MASK;
if (token == MACRO) {
nextToken = code[i + 1] & TOK_MASK;
if (nextToken == STRING_CONSTANT) {
if (count == MAX_MACROS) {
if (isPluginsMacrosMenu)
IJ.error("Macro Installer", "Macro sets are limited to " + MAX_MACROS + " macros.");
break;
}
address = code[i + 1] >> TOK_SHIFT;
symbol = symbolTable[address];
name = symbol.str;
macroStarts[count] = i + 2;
macroNames[count] = name;
if (name.indexOf('-') != -1
&& (name.indexOf("Tool") != -1 || name.indexOf("tool") != -1)) {
tools.add(name);
toolCount++;
} else if (name.startsWith("AutoRun")) {
if (autoRunCount == 0 && !openingStartupMacrosInEditor) {
new MacroRunner(pgm, macroStarts[count], name, (String) null);
if (name.equals("AutoRunAndHide")) autoRunAndHideCount++;
}
autoRunCount++;
count--;
} else if (name.equals("Popup Menu")) installPopupMenu(name, pgm);
else if (!name.endsWith("Tool Selected")) {
if (macrosMenu != null) {
addShortcut(name);
int pos = name.indexOf(">");
boolean inSubMenu = name.startsWith("<") && (pos > 1);
if (inSubMenu) {
Menu parent = macrosMenu;
Menu subMenu = null;
String parentStr = name.substring(1, pos).trim();
String childStr = name.substring(pos + 1).trim();
MenuItem mnuItem = new MenuItem();
mnuItem.setActionCommand(name);
mnuItem.setLabel(childStr);
for (int jj = 0; jj < subMenus.size(); jj++) {
String aName = subMenus.get(jj).getName();
if (aName.equals(parentStr)) subMenu = subMenus.get(jj);
}
if (subMenu == null) {
subMenu = new Menu(parentStr);
subMenu.setName(parentStr);
subMenu.addActionListener(this);
subMenus.add(subMenu);
parent.add(subMenu);
}
subMenu.add(mnuItem);
} else macrosMenu.add(new MenuItem(name));
}
}
// IJ.log(count+" "+name+" "+macroStarts[count]);
count++;
}
} else if (token == EOF) break;
}
nMacros = count;
if (toolCount > 0 && (isPluginsMacrosMenu || macrosMenu == null) && installTools) {
Toolbar tb = Toolbar.getInstance();
if (toolCount == 1) tb.addMacroTool((String) tools.get(0), this);
else {
for (int i = 0; i < tools.size(); i++) {
String toolName = (String) tools.get(i);
if (toolName.startsWith("Abort Macro or Plugin") && toolCount > 6)
toolName = "Unused " + toolName;
tb.addMacroTool(toolName, this, i);
}
}
if (toolCount > 1 && Toolbar.getToolId() >= Toolbar.CUSTOM1) tb.setTool(Toolbar.RECTANGLE);
tb.repaint();
}
if (macrosMenu != null) this.instance = this;
if (shortcutsInUse != null && text != null)
IJ.showMessage(
"Install Macros",
(inUseCount == 1 ? "This keyboard shortcut is" : "These keyboard shortcuts are")
+ " already in use:"
+ shortcutsInUse);
if (nMacros == 0 && fileName != null) {
if (text == null || text.length() == 0) return;
int dotIndex = fileName.lastIndexOf('.');
if (dotIndex > 0) anonymousName = fileName.substring(0, dotIndex);
else anonymousName = fileName;
if (macrosMenu != null) macrosMenu.add(new MenuItem(anonymousName));
macroNames[0] = anonymousName;
nMacros = 1;
}
String word = nMacros == 1 ? " macro" : " macros";
if (isPluginsMacrosMenu) IJ.showStatus(nMacros + word + " installed");
}