Examples with AstroImageJ ij.astro.AstroImageJ used on opensource projects

Example 6 with AstroImageJ

use of ij.astro.AstroImageJ in project astroimagej by keastrid.

the class PlotObject method drawAxesTicksGridNumbers.

/**
 * Draws ticks, grid and axis label for each tick/grid line.
 *	The grid or major tick spacing in each direction is given by steps
 */
@AstroImageJ(reason = "Set font size to 12 for axis labels", modified = true)
void drawAxesTicksGridNumbers(double[] steps) {
    if (ip == null)
        return;
    // create categories for the axes (if any)
    String[] xCats = labelsInBraces('x');
    String[] yCats = labelsInBraces('y');
    // for scientific notation
    String multiplySymbol = getMultiplySymbol();
    Font scFont = scFont(pp.frame.getFont());
    // for axis numbers if full size does not fit
    Font scFontMedium = scFont.deriveFont(scFont.getSize2D() * 10f / 12f);
    // for subscripts
    Font scFontSmall = scFont.deriveFont(scFont.getSize2D() * 9f / 12f);
    ip.setFont(scFont);
    ip.setFontSize(12);
    FontMetrics fm = ip.getFontMetrics();
    int fontAscent = fm.getAscent();
    ip.setJustification(LEFT);
    // ---	A l o n g	X	A x i s
    int yOfXAxisNumbers = topMargin + frameHeight + fm.getHeight() * 5 / 4 + sc(2);
    if (hasFlag(X_NUMBERS | (logXAxis ? (X_TICKS | X_MINOR_TICKS) : X_LOG_TICKS) + X_GRID)) {
        Font baseFont = scFont;
        boolean majorTicks = logXAxis ? hasFlag(X_LOG_TICKS) : hasFlag(X_TICKS);
        boolean minorTicks = hasFlag(X_MINOR_TICKS);
        minorTicks = minorTicks && (xCats == null);
        double step = steps[0];
        int i1 = (int) Math.ceil(Math.min(xMin, xMax) / step - 1.e-10);
        int i2 = (int) Math.floor(Math.max(xMin, xMax) / step + 1.e-10);
        // is not given, NaN cast to 0
        int suggestedDigits = (int) Tools.getNumberFromList(pp.frame.options, "xdecimals=");
        int digits = getDigits(xMin, xMax, step, 7, suggestedDigits);
        int y1 = topMargin;
        int y2 = topMargin + frameHeight;
        if (xMin == xMax) {
            if (hasFlag(X_NUMBERS)) {
                String s = IJ.d2s(xMin, getDigits(xMin, 0.001 * xMin, 5, suggestedDigits));
                int y = yBasePxl;
                ip.drawString(s, xBasePxl - ip.getStringWidth(s) / 2, yOfXAxisNumbers);
            }
        } else {
            if (hasFlag(X_NUMBERS)) {
                int w1 = ip.getStringWidth(IJ.d2s(currentMinMax[0], logXAxis ? -1 : digits));
                int w2 = ip.getStringWidth(IJ.d2s(currentMinMax[1], logXAxis ? -1 : digits));
                int wMax = Math.max(w1, w2);
                if (wMax > Math.abs(step * xScale) - sc(8)) {
                    // small font if there is not enough space for the numbers
                    baseFont = scFontMedium;
                    ip.setFont(baseFont);
                }
            }
            for (int i = 0; i <= (i2 - i1); i++) {
                double v = (i + i1) * step;
                int x = (int) Math.round((v - xMin) * xScale) + leftMargin;
                if (xCats != null) {
                    int index = (int) v;
                    double remainder = Math.abs(v - Math.round(v));
                    if (index >= 0 && index < xCats.length && remainder < 1e-9) {
                        String s = xCats[index];
                        String[] parts = s.split("\n");
                        int w = 0;
                        for (int jj = 0; jj < parts.length; jj++) w = Math.max(w, ip.getStringWidth(parts[jj]));
                        ip.drawString(s, x - w / 2, yOfXAxisNumbers);
                    // ip.drawString(s, x-ip.getStringWidth(s)/2, yOfXAxisNumbers);
                    }
                    continue;
                }
                if (hasFlag(X_GRID)) {
                    ip.setColor(gridColor);
                    ip.drawLine(x, y1, x, y2);
                    ip.setColor(Color.black);
                }
                if (majorTicks) {
                    ip.drawLine(x, y1, x, y1 + sc(tickLength));
                    ip.drawLine(x, y2, x, y2 - sc(tickLength));
                }
                if (hasFlag(X_NUMBERS)) {
                    if (logXAxis || digits < 0) {
                        drawExpString(logXAxis ? Math.pow(10, v) : v, logXAxis ? -1 : -digits, x, yOfXAxisNumbers - fontAscent / 2, CENTER, fontAscent, baseFont, scFontSmall, multiplySymbol);
                    } else {
                        String s = IJ.d2s(v, digits);
                        ip.drawString(s, x - ip.getStringWidth(s) / 2, yOfXAxisNumbers);
                    }
                }
            }
            // nunbers on log minor ticks only if < 2 decades
            boolean haveMinorLogNumbers = i2 - i1 < 2;
            if (minorTicks && (!logXAxis || step > 1.1)) {
                // 'standard' log minor ticks only for full decades
                // non-log: 4 or 5 minor ticks per major tick
                double mstep = niceNumber(step * 0.19);
                double minorPerMajor = step / mstep;
                if (// major steps are not an integer multiple of minor steps? (e.g. user step 90 deg)
                Math.abs(minorPerMajor - Math.round(minorPerMajor)) > 1e-10)
                    mstep = step / 4;
                if (logXAxis && mstep < 1)
                    mstep = 1;
                i1 = (int) Math.ceil(Math.min(xMin, xMax) / mstep - 1.e-10);
                i2 = (int) Math.floor(Math.max(xMin, xMax) / mstep + 1.e-10);
                for (int i = i1; i <= i2; i++) {
                    double v = i * mstep;
                    int x = (int) Math.round((v - xMin) * xScale) + leftMargin;
                    ip.drawLine(x, y1, x, y1 + sc(minorTickLength));
                    ip.drawLine(x, y2, x, y2 - sc(minorTickLength));
                }
            } else if (logXAxis && majorTicks && Math.abs(xScale) > sc(MIN_X_GRIDSPACING)) {
                // minor ticks for log
                // more numbers on minor ticks when zoomed in
                int minorNumberLimit = haveMinorLogNumbers ? (int) (0.12 * Math.abs(xScale) / (fm.charWidth('0') + sc(2))) : 0;
                i1 = (int) Math.floor(Math.min(xMin, xMax) - 1.e-10);
                i2 = (int) Math.ceil(Math.max(xMin, xMax) + 1.e-10);
                for (int i = i1; i <= i2; i++) {
                    for (int m = 2; m < 10; m++) {
                        double v = i + Math.log10(m);
                        if (v > Math.min(xMin, xMax) && v < Math.max(xMin, xMax)) {
                            int x = (int) Math.round((v - xMin) * xScale) + leftMargin;
                            ip.drawLine(x, y1, x, y1 + sc(minorTickLength));
                            ip.drawLine(x, y2, x, y2 - sc(minorTickLength));
                            if (m <= minorNumberLimit)
                                drawExpString(Math.pow(10, v), 0, x, yOfXAxisNumbers - fontAscent / 2, CENTER, fontAscent, baseFont, scFontSmall, multiplySymbol);
                        }
                    }
                }
            }
        }
    }
    // ---	A l o n g	Y	A x i s
    ip.setFont(scFont);
    ip.setFontSize(12);
    int maxNumWidth = 0;
    int xNumberRight = leftMargin - sc(2) - ip.getStringWidth("0") / 2;
    Rectangle rect = ip.getStringBounds("0169");
    int yNumberOffset = -rect.y - rect.height / 2;
    if (hasFlag(Y_NUMBERS | (logYAxis ? (Y_TICKS | Y_MINOR_TICKS) : Y_LOG_TICKS) + Y_GRID)) {
        ip.setJustification(RIGHT);
        Font baseFont = scFont;
        boolean majorTicks = logYAxis ? hasFlag(Y_LOG_TICKS) : hasFlag(Y_TICKS);
        boolean minorTicks = logYAxis ? hasFlag(Y_LOG_TICKS) : hasFlag(Y_MINOR_TICKS);
        minorTicks = minorTicks && (yCats == null);
        double step = steps[1];
        int i1 = (int) Math.ceil(Math.min(yMin, yMax) / step - 1.e-10);
        int i2 = (int) Math.floor(Math.max(yMin, yMax) / step + 1.e-10);
        // is not given, NaN cast to 0
        int suggestedDigits = (int) Tools.getNumberFromList(pp.frame.options, "ydecimals=");
        int digits = getDigits(yMin, yMax, step, 5, suggestedDigits);
        int x1 = leftMargin;
        int x2 = leftMargin + frameWidth;
        if (yMin == yMax) {
            if (hasFlag(Y_NUMBERS)) {
                String s = IJ.d2s(yMin, getDigits(yMin, 0.001 * yMin, 5, suggestedDigits));
                maxNumWidth = ip.getStringWidth(s);
                int y = yBasePxl;
                ip.drawString(s, xNumberRight, y + fontAscent / 2 + sc(1));
            }
        } else {
            int digitsForWidth = logYAxis ? -1 : digits;
            if (digitsForWidth < 0) {
                // "1.0*10^5" etc. needs more space than 1.0*5, simulate by adding one decimal
                digitsForWidth--;
                xNumberRight += sc(1) + ip.getStringWidth("0") / 4;
            }
            String str1 = IJ.d2s(currentMinMax[2], digitsForWidth);
            String str2 = IJ.d2s(currentMinMax[3], digitsForWidth);
            if (digitsForWidth < 0) {
                str1 = str1.replaceFirst("E", multiplySymbol);
                str2 = str2.replaceFirst("E", multiplySymbol);
            }
            int w1 = ip.getStringWidth(str1);
            int w2 = ip.getStringWidth(str2);
            int wMax = Math.max(w1, w2);
            if (hasFlag(Y_NUMBERS)) {
                if (wMax > xNumberRight - sc(4) - (pp.yLabel.label.length() > 0 ? fm.getHeight() : 0)) {
                    // small font if there is not enough space for the numbers
                    baseFont = scFontMedium;
                    ip.setFont(baseFont);
                }
            }
            // IJ.log(IJ.d2s(currentMinMax[2],digits)+": w="+w1+"; "+IJ.d2s(currentMinMax[3],digits)+": w="+w2+baseFont+" Space="+(leftMargin-sc(4+5)-fm.getHeight()));
            for (int i = i1; i <= i2; i++) {
                double v = step == 0 ? yMin : i * step;
                int y = topMargin + frameHeight - (int) Math.round((v - yMin) * yScale);
                if (yCats != null) {
                    int index = (int) v;
                    double remainder = Math.abs(v - Math.round(v));
                    if (index >= 0 && index < yCats.length && remainder < 1e-9) {
                        String s = yCats[index];
                        // multi-line cat labels
                        int multiLineOffset = 0;
                        for (int jj = 0; jj < s.length(); jj++) if (s.charAt(jj) == '\n')
                            multiLineOffset -= rect.height / 2;
                        ip.drawString(s, xNumberRight, y + yNumberOffset + multiLineOffset);
                    }
                    continue;
                }
                if (hasFlag(Y_GRID)) {
                    ip.setColor(gridColor);
                    ip.drawLine(x1, y, x2, y);
                    ip.setColor(Color.black);
                }
                if (majorTicks) {
                    ip.drawLine(x1, y, x1 + sc(tickLength), y);
                    ip.drawLine(x2, y, x2 - sc(tickLength), y);
                }
                if (hasFlag(Y_NUMBERS)) {
                    int w = 0;
                    if (logYAxis || digits < 0) {
                        w = drawExpString(logYAxis ? Math.pow(10, v) : v, logYAxis ? -1 : -digits, xNumberRight, y, RIGHT, fontAscent, baseFont, scFontSmall, multiplySymbol);
                    } else {
                        String s = IJ.d2s(v, digits);
                        w = ip.getStringWidth(s);
                        ip.drawString(s, xNumberRight, y + yNumberOffset);
                    }
                    if (w > maxNumWidth)
                        maxNumWidth = w;
                }
            }
            // numbers on log minor ticks only if < 2 decades
            boolean haveMinorLogNumbers = i2 - i1 < 2;
            if (minorTicks && (!logYAxis || step > 1.1)) {
                // 'standard' log minor ticks only for full decades
                // non-log: 4 or 5 minor ticks per major tick
                double mstep = niceNumber(step * 0.19);
                double minorPerMajor = step / mstep;
                if (// major steps are not an integer multiple of minor steps? (e.g. user step 90 deg)
                Math.abs(minorPerMajor - Math.round(minorPerMajor)) > 1e-10)
                    mstep = step / 4;
                if (logYAxis && step < 1)
                    mstep = 1;
                i1 = (int) Math.ceil(Math.min(yMin, yMax) / mstep - 1.e-10);
                i2 = (int) Math.floor(Math.max(yMin, yMax) / mstep + 1.e-10);
                for (int i = i1; i <= i2; i++) {
                    double v = i * mstep;
                    int y = topMargin + frameHeight - (int) Math.round((v - yMin) * yScale);
                    ip.drawLine(x1, y, x1 + sc(minorTickLength), y);
                    ip.drawLine(x2, y, x2 - sc(minorTickLength), y);
                }
            }
            if (logYAxis && majorTicks && Math.abs(yScale) > sc(MIN_X_GRIDSPACING)) {
                // minor ticks for log within the decade
                // more numbers on minor ticks when zoomed in
                int minorNumberLimit = haveMinorLogNumbers ? (int) (0.4 * Math.abs(yScale) / fm.getHeight()) : 0;
                i1 = (int) Math.floor(Math.min(yMin, yMax) - 1.e-10);
                i2 = (int) Math.ceil(Math.max(yMin, yMax) + 1.e-10);
                for (int i = i1; i <= i2; i++) {
                    for (int m = 2; m < 10; m++) {
                        double v = i + Math.log10(m);
                        if (v > Math.min(yMin, yMax) && v < Math.max(yMin, yMax)) {
                            int y = topMargin + frameHeight - (int) Math.round((v - yMin) * yScale);
                            ip.drawLine(x1, y, x1 + sc(minorTickLength), y);
                            ip.drawLine(x2, y, x2 - sc(minorTickLength), y);
                            if (m <= minorNumberLimit) {
                                int w = drawExpString(Math.pow(10, v), 0, xNumberRight, y, RIGHT, fontAscent, baseFont, scFontSmall, multiplySymbol);
                                if (w > maxNumWidth)
                                    maxNumWidth = w;
                            }
                        }
                    }
                }
            }
        }
    }
    // --- Write min&max of range if simple style without any axis format flags
    ip.setFont(scFont);
    ip.setJustification(LEFT);
    String xLabelToDraw = pp.xLabel.label;
    String yLabelToDraw = pp.yLabel.label;
    if (simpleYAxis()) {
        // y-axis min&max
        int digits = getDigits(yMin, yMax, 0.001 * (yMax - yMin), 6, 0);
        String s = IJ.d2s(yMax, digits);
        int sw = ip.getStringWidth(s);
        if ((sw + sc(4)) > leftMargin)
            ip.drawString(s, sc(4), topMargin - sc(4));
        else
            ip.drawString(s, leftMargin - ip.getStringWidth(s) - sc(4), topMargin + 10);
        s = IJ.d2s(yMin, digits);
        sw = ip.getStringWidth(s);
        if ((sw + 4) > leftMargin)
            ip.drawString(s, sc(4), topMargin + frame.height);
        else
            ip.drawString(s, leftMargin - ip.getStringWidth(s) - sc(4), topMargin + frame.height);
        if (logYAxis)
            yLabelToDraw += " (LOG)";
    }
    int y = yOfXAxisNumbers;
    if (simpleXAxis()) {
        // x-axis min&max
        int digits = getDigits(xMin, xMax, 0.001 * (xMax - xMin), 7, 0);
        ip.drawString(IJ.d2s(xMin, digits), leftMargin, y);
        String s = IJ.d2s(xMax, digits);
        ip.drawString(s, leftMargin + frame.width - ip.getStringWidth(s) + 6, y);
        y -= fm.getHeight();
        if (logXAxis)
            xLabelToDraw += " (LOG)";
    } else
        y += sc(1);
    // --- Write x and y axis text labels
    if (xCats == null) {
        ip.setFont(pp.xLabel.getFont() == null ? scFont : scFont(pp.xLabel.getFont()));
        ip.setFontSize(12);
        ImageProcessor xLabel = stringToPixels(xLabelToDraw);
        if (xLabel != null) {
            int xpos = leftMargin + (frame.width - xLabel.getWidth()) / 2;
            // topMargin + frame.height + bottomMargin-xLabel.getHeight();
            int ypos = y + scFont.getSize() / 3;
            ip.insert(xLabel, xpos, ypos);
        }
    }
    if (yCats == null) {
        ip.setFont(pp.yLabel.getFont() == null ? scFont : scFont(pp.yLabel.getFont()));
        ImageProcessor yLabel = stringToPixels(yLabelToDraw);
        ip.setFontSize(12);
        if (yLabel != null) {
            yLabel = yLabel.rotateLeft();
            int xRightOfYLabel = xNumberRight - maxNumWidth - sc(2);
            int xpos = xRightOfYLabel - yLabel.getWidth() - sc(2);
            int ypos = topMargin + (frame.height - yLabel.getHeight()) / 2;
            ip.insert(yLabel, xpos, ypos);
        }
    }
}

Example 7 with AstroImageJ

use of ij.astro.AstroImageJ in project astroimagej by keastrid.

the class ImagePlus method setSlice.

/**
 * Displays the specified stack image, where 1<=n<=stackSize.
 * Does nothing if this image is not a stack.
 * @see #setPosition
 * @see #setC
 * @see #setZ
 * @see #setT
 */
@AstroImageJ(reason = "Add reset if color type is RGB", modified = true)
public synchronized void setSlice(int n) {
    if (getType() == ImagePlus.COLOR_RGB)
        ip.reset();
    if (stack == null || (n == currentSlice && ip != null)) {
        if (!noUpdateMode)
            updateAndRepaintWindow();
        return;
    }
    if (n >= 1 && n <= stack.size()) {
        Roi roi = getRoi();
        if (roi != null)
            roi.endPaste();
        if (isProcessor()) {
            if (currentSlice == 0)
                currentSlice = 1;
            stack.setPixels(ip.getPixels(), currentSlice);
        }
        setCurrentSlice(n);
        Object pixels = null;
        Overlay overlay2 = null;
        if (stack.isVirtual() && !((stack instanceof FileInfoVirtualStack) || (stack instanceof AVI_Reader))) {
            ImageProcessor ip2 = stack.getProcessor(currentSlice);
            overlay2 = ip2 != null ? ip2.getOverlay() : null;
            if (overlay2 != null)
                setOverlay(overlay2);
            if (stack instanceof VirtualStack) {
                Properties props = ((VirtualStack) stack).getProperties();
                if (props != null)
                    setProperty("FHT", props.get("FHT"));
            }
            if (ip2 != null)
                pixels = ip2.getPixels();
        } else
            pixels = stack.getPixels(currentSlice);
        if (ip != null && pixels != null) {
            try {
                ip.setPixels(pixels);
                ip.setSnapshotPixels(null);
            } catch (Exception e) {
            }
        } else {
            ImageProcessor ip2 = stack.getProcessor(n);
            if (ip2 != null)
                ip = ip2;
        }
        if (compositeImage && getCompositeMode() == IJ.COMPOSITE && ip != null) {
            int channel = getC();
            if (channel > 0 && channel <= getNChannels())
                ip.setLut(((CompositeImage) this).getChannelLut(channel));
        }
        if (win != null && win instanceof StackWindow)
            ((StackWindow) win).updateSliceSelector();
        if (Prefs.autoContrast && nChannels == 1 && imageType != COLOR_RGB) {
            (new ContrastEnhancer()).stretchHistogram(ip, 0.35, ip.getStats());
            ContrastAdjuster.update();
        // IJ.showStatus(n+": min="+ip.getMin()+", max="+ip.getMax());
        }
        if (imageType == COLOR_RGB)
            ContrastAdjuster.update();
        if (!noUpdateMode)
            updateAndRepaintWindow();
        else
            img = null;
    }
}

Example 8 with AstroImageJ

use of ij.astro.AstroImageJ in project astroimagej by keastrid.

the class PlotWindow method draw.

/**
 * Displays the plot.
 */
@AstroImageJ(reason = "Disable 'More' plot option by setting it invisiblel List -> PDF; add copy button", modified = true)
public void draw() {
    Panel bottomPanel = new Panel();
    int hgap = IJ.isMacOSX() ? 1 : 5;
    list = new Button(" PDF ");
    list.addActionListener(this);
    if (getTitle().startsWith("Seeing Profile")) {
        copy.addActionListener(this);
        bottomPanel.add(copy);
    }
    bottomPanel.add(list);
    bottomPanel.setLayout(new FlowLayout(FlowLayout.RIGHT, hgap, 0));
    data = new Button(dataButtonLabel);
    data.addActionListener(this);
    bottomPanel.add(data);
    more = new Button(moreButtonLabel);
    more.setVisible(false);
    more.addActionListener(this);
    bottomPanel.add(more);
    if (plot != null && plot.getPlotMaker() != null) {
        live = new Button("Live");
        live.addActionListener(this);
        bottomPanel.add(live);
    }
    statusLabel = new Label();
    statusLabel.setFont(new Font("Monospaced", Font.PLAIN, 12));
    statusLabel.setBackground(new Color(220, 220, 220));
    bottomPanel.add(statusLabel);
    add(bottomPanel);
    data.add(getDataPopupMenu());
    more.add(getMorePopupMenu());
    plot.draw();
    LayoutManager lm = getLayout();
    if (lm instanceof ImageLayout)
        // don't expand size to make the panel fit
        ((ImageLayout) lm).ignoreNonImageWidths(true);
    GUI.scale(bottomPanel);
    maximizeCoordinatesLabelWidth();
    pack();
    ImageProcessor ip = plot.getProcessor();
    boolean ipIsColor = ip instanceof ColorProcessor;
    boolean impIsColor = imp.getProcessor() instanceof ColorProcessor;
    if (ipIsColor != impIsColor)
        imp.setProcessor(null, ip);
    else
        imp.updateAndDraw();
    if (listValues)
        showList(/*useLabels=*/
        false);
    else
        // have focus on the canvas, not the button, so that pressing the space bar allows panning
        ic.requestFocus();
}

Example 9 with AstroImageJ

use of ij.astro.AstroImageJ in project astroimagej by keastrid.

the class GenericDialog method setIcon.

@AstroImageJ(reason = "Use astronomy icon instead of default image")
void setIcon() {
    URL url = this.getClass().getClassLoader().getResource("astronomy_icon.png");
    if (url == null)
        return;
    Image img = null;
    try {
        img = createImage((ImageProducer) url.getContent());
    } catch (IOException ignored) {
    }
    if (img != null)
        setIconImage(img);
}

Example 10 with AstroImageJ

use of ij.astro.AstroImageJ in project astroimagej by keastrid.

the class ImageWindow method setImageJMenuBar.

@AstroImageJ(modified = true, reason = "Don't run for AstroStackWindow")
public static void setImageJMenuBar(ImageWindow win) {
    if (win.getClass().getName().contains("AstroStackWindow"))
        return;
    ImageJ ij = IJ.getInstance();
    boolean setMenuBar = true;
    ImagePlus imp = win.getImagePlus();
    if (imp != null)
        setMenuBar = imp.setIJMenuBar();
    MenuBar mb = Menus.getMenuBar();
    if (mb != null && mb == win.getMenuBar())
        setMenuBar = false;
    setMenuBarTime = 0L;
    if (setMenuBar && ij != null && !ij.quitting() && !Interpreter.nonBatchMacroRunning()) {
        // may be needed for Java 1.4 on OS X
        IJ.wait(10);
        long t0 = System.currentTimeMillis();
        win.setMenuBar(mb);
        long time = System.currentTimeMillis() - t0;
        setMenuBarTime = time;
        Menus.setMenuBarCount++;
        if (IJ.debugMode)
            IJ.log("setMenuBar: " + time + "ms (" + Menus.setMenuBarCount + ")");
        if (time > 2000L)
            Prefs.setIJMenuBar = false;
    }
    if (imp != null)
        imp.setIJMenuBar(true);
}