use of ij.process.ByteProcessor in project TrakEM2 by trakem2.
the class ImageArrayConverter method ImageToDoubleArray1DZeroPadding.
public static double[] ImageToDoubleArray1DZeroPadding(ImageProcessor ip, int width, int height) {
double[] image;
Object pixelArray = ip.getPixels();
int count = 0;
int offsetX = (width - ip.getWidth()) / 2;
int offsetY = (height - ip.getHeight()) / 2;
if (offsetX < 0) {
System.err.println("mpi.fruitfly.general.ImageArrayConverter.ImageToDoubleArray1DZeroPadding(): Zero-Padding size in X smaller than image! " + width + " < " + ip.getWidth());
return null;
}
if (offsetY < 0) {
System.err.println("mpi.fruitfly.general.ImageArrayConverter.ImageToDoubleArray1DZeroPadding(): Zero-Padding size in Y smaller than image! " + height + " < " + ip.getHeight());
return null;
}
if (ip instanceof ByteProcessor) {
image = new double[width * height];
byte[] pixels = (byte[]) pixelArray;
for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image[(y + offsetY) * width + x + offsetX] = pixels[count++] & 0xff;
} else if (ip instanceof ShortProcessor) {
image = new double[width * height];
short[] pixels = (short[]) pixelArray;
for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image[(y + offsetY) * width + x + offsetX] = pixels[count++] & 0xffff;
} else if (ip instanceof FloatProcessor) {
image = new double[width * height];
float[] pixels = (float[]) pixelArray;
for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image[(y + offsetY) * width + x + offsetX] = pixels[count++];
} else // RGB
{
image = new double[width * height];
int[] pixels = (int[]) pixelArray;
// still unknown how to do...
/*
for (int y = 0; y < ip.getHeight(); y++)
for (int x = 0; x < ip.getWidth(); x++)
image[x][y] = pixels[count++];// & 0xffffff;
*/
}
return image;
}
use of ij.process.ByteProcessor in project TrakEM2 by trakem2.
the class ImageArrayConverter method ImageToIntArray.
public static int[][] ImageToIntArray(ImageProcessor ip) {
int[][] image;
Object pixelArray = ip.getPixels();
int count = 0;
if (ip instanceof ByteProcessor) {
image = new int[ip.getWidth()][ip.getHeight()];
byte[] pixels = (byte[]) pixelArray;
for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image[x][y] = pixels[count++] & 0xff;
} else if (ip instanceof ShortProcessor) {
image = new int[ip.getWidth()][ip.getHeight()];
short[] pixels = (short[]) pixelArray;
for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image[x][y] = pixels[count++] & 0xffff;
} else if (ip instanceof FloatProcessor) {
image = new int[ip.getWidth()][ip.getHeight()];
float[] pixels = (float[]) pixelArray;
for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image[x][y] = (int) pixels[count++];
} else // RGB
{
image = new int[ip.getWidth()][ip.getHeight()];
int[] pixels = (int[]) pixelArray;
// still unknown how to do...
/*
for (int y = 0; y < ip.getHeight(); y++)
for (int x = 0; x < ip.getWidth(); x++)
image[x][y] = pixels[count++];// & 0xffffff;
*/
}
return image;
}
use of ij.process.ByteProcessor in project TrakEM2 by trakem2.
the class ImageArrayConverter method ImageToFloatArray2DZeroPadding.
public static FloatArray2D ImageToFloatArray2DZeroPadding(ImageProcessor ip, int width, int height) {
FloatArray2D image = new FloatArray2D(width, height);
Object pixelArray = ip.getPixels();
int count = 0;
int offsetX = (width - ip.getWidth()) / 2;
int offsetY = (height - ip.getHeight()) / 2;
if (offsetX < 0) {
System.err.println("mpi.fruitfly.general.ImageArrayConverter.ImageToFloatArray2DZeroPadding(): Zero-Padding size in X smaller than image! " + width + " < " + ip.getWidth());
return null;
}
if (offsetY < 0) {
System.err.println("mpi.fruitfly.general.ImageArrayConverter.ImageToFloatArray2DZeroPadding(): Zero-Padding size in Y smaller than image! " + height + " < " + ip.getHeight());
return null;
}
if (ip instanceof ByteProcessor) {
byte[] pixels = (byte[]) pixelArray;
for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image.set(pixels[count++] & 0xff, x + offsetX, y + offsetY);
} else if (ip instanceof ShortProcessor) {
short[] pixels = (short[]) pixelArray;
for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image.set(pixels[count++] & 0xffff, x + offsetX, y + offsetY);
} else if (ip instanceof FloatProcessor) {
float[] pixels = (float[]) pixelArray;
for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image.set(pixels[count++], x + offsetX, y + offsetY);
} else // RGB
{
int[] pixels = (int[]) pixelArray;
// still unknown how to do...
/*
for (int y = 0; y < ip.getHeight(); y++)
for (int x = 0; x < ip.getWidth(); x++)
image[x][y] = pixels[count++];// & 0xffffff;
*/
}
return image;
}
use of ij.process.ByteProcessor in project TrakEM2 by trakem2.
the class ImageArrayConverter method ImageToDoubleArray1D.
public static double[] ImageToDoubleArray1D(ImageProcessor ip) {
double[] image;
Object pixelArray = ip.getPixels();
int count = 0;
if (ip instanceof ByteProcessor) {
image = new double[ip.getWidth() * ip.getHeight()];
byte[] pixels = (byte[]) pixelArray;
for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image[count] = pixels[count++] & 0xff;
} else if (ip instanceof ShortProcessor) {
image = new double[ip.getWidth() * ip.getHeight()];
short[] pixels = (short[]) pixelArray;
for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image[count] = pixels[count++] & 0xffff;
} else if (ip instanceof FloatProcessor) {
image = new double[ip.getWidth() * ip.getHeight()];
float[] pixels = (float[]) pixelArray;
for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image[count] = pixels[count++];
} else // RGB
{
image = new double[ip.getWidth() * ip.getHeight()];
int[] pixels = (int[]) pixelArray;
// still unknown how to do...
/*
for (int y = 0; y < ip.getHeight(); y++)
for (int x = 0; x < ip.getWidth(); x++)
image[x][y] = pixels[count++];// & 0xffffff;
*/
}
return image;
}
use of ij.process.ByteProcessor in project TrakEM2 by trakem2.
the class Compare method variabilityAnalysis.
/**
* @param reference_project If null, then the first one found in the Project.getProjects() lists is used.
* @param regex A String (can be null) to filter objects by, to limit what gets processed.
* If regex is not null, then only ProjectThing nodes with the matching regex are analyzed (shallow: none of their children are questioned, but pipes will be built from them all).
* @param generate_plots Whether to generate the variability plots at all.
* @param show_plots If generate_plots, whether to show the plots in a stack image window or to save them.
* @param show_3D Whether to show any 3D data.
* @param show_condensed_3D If show_3D, whether to show the condensed vector strings, i.e. the "average" pipes.
* @param show_sources_3D If show_3D, whether to show the source pipes from which the condensed vector string was generated.
* @param sources_color_table Which colors to give to the pipes of which Project.
* @param show_envelope_3D If show_3D, whether to generate the variability envelope.
* @param envelope_alpha If show_envelope_3D, the envelope takes an alpha value between 0 (total transparency) and 1 (total opacity)
* @param delta_envelope The delta to resample the envelope to. When smaller than or equal to 1, no envelope resampling occurs.
* @param show_axes_3D If show_3D, whether to display the reference axes as well.
* @param heat_map If show_3D, whether to color the variability with a Fire LUT.
* If not show_condensed_3D, then the variability is shown in color-coded 3D spheres placed at the entry point to the neuropile.
* @param map_condensed If not null, all VectorString3D are put into this map.
* @param projects The projects to use.
*/
public static Bureaucrat variabilityAnalysis(final Project reference_project, final String regex, final String[] ignore, final boolean show_cata_dialog, final boolean generate_plots, final boolean show_plots, final String plot_dir_, final boolean show_3D, final boolean show_condensed_3D, final boolean show_sources_3D, final Map<Project, Color> sources_color_table, final boolean show_envelope_3D, final float envelope_alpha, final double delta_envelope, final int envelope_type, final boolean show_axes_3D, final boolean heat_map, final Map<String, VectorString3D> map_condensed, final Project[] projects) {
// gather all open projects
final Project[] p = null == projects ? Project.getProjects().toArray(new Project[0]) : projects;
// make the reference_project be the first in the array
if (null != reference_project && reference_project != p[0]) {
for (int i = 0; i < p.length; i++) {
if (reference_project == p[i]) {
p[i] = p[0];
p[0] = reference_project;
break;
}
}
}
final Worker worker = new Worker("Comparing all to all") {
@Override
public void run() {
startedWorking();
try {
Utils.log2("Asking for CATAParameters...");
final CATAParameters cp = new CATAParameters();
cp.regex = regex;
cp.delta_envelope = delta_envelope;
cp.envelope_type = envelope_type;
if (show_cata_dialog && !cp.setup(false, regex, true, true)) {
finishedWorking();
return;
}
// so source points are stored in VectorString3D for each resampled and interpolated point
cp.with_source = true;
// Store a series of results, depending on options
final HashMap<String, Display3D> results = new HashMap<String, Display3D>();
String plot_dir = plot_dir_;
if (generate_plots && !show_plots) {
// Save plots
if (null == plot_dir) {
final DirectoryChooser dc = new DirectoryChooser("Choose plots directory");
plot_dir = dc.getDirectory();
if (null == plot_dir) {
finishedWorking();
return;
}
}
if (IJ.isWindows())
plot_dir = plot_dir.replace('\\', '/');
if (!plot_dir.endsWith("/"))
plot_dir += "/";
}
Utils.log2("Gathering chains...");
// Gather chains that do not match the ignore regexes
// will transform them as well to the reference found in the first project in the p array
Object[] ob = gatherChains(p, cp, ignore);
ArrayList<Chain> chains = (ArrayList<Chain>) ob[0];
// to keep track of each project's chains
final ArrayList[] p_chains = (ArrayList[]) ob[1];
ob = null;
if (null == chains) {
finishedWorking();
return;
}
Utils.log2("Collecting bundles...");
final HashMap<Project, HashMap<String, VectorString3D>> axes = new HashMap<Project, HashMap<String, VectorString3D>>();
// Sort out into groups by unique names of lineage bundles
final HashMap<String, ArrayList<Chain>> bundles = new HashMap<String, ArrayList<Chain>>();
for (final Chain chain : chains) {
String title = chain.getCellTitle();
final String t = title.toLowerCase();
// unnamed
if (0 == t.indexOf('[') || 0 == t.indexOf('#'))
continue;
Utils.log("Accepting " + title);
title = title.substring(0, title.indexOf(' '));
// lineage bundle instance chains
ArrayList<Chain> bc = bundles.get(title);
if (null == bc) {
bc = new ArrayList<Chain>();
bundles.put(title, bc);
}
bc.add(chain);
}
Utils.log2("Found " + bundles.size() + " bundles.");
chains = null;
if (null != cp.regex && show_axes_3D && axes.size() < 3) {
// Must find the Mushroom Body lobes separately
final String cp_regex = cp.regex;
cp.regex = "mb";
final Object[] o = gatherChains(p, cp, ignore);
final ArrayList<Chain> lobes = (ArrayList<Chain>) o[0];
Utils.logAll("Found " + lobes.size() + " chains for lobes");
for (final Chain chain : lobes) {
final String t = chain.getCellTitle().toLowerCase();
if (-1 != t.indexOf("peduncle") || -1 != t.indexOf("medial lobe") || -1 != t.indexOf("dorsal lobe")) {
Utils.logAll("adding " + t);
final Project pr = chain.pipes.get(0).getProject();
HashMap<String, VectorString3D> m = axes.get(pr);
if (null == m) {
m = new HashMap<String, VectorString3D>();
axes.put(pr, m);
}
m.put(t, chain.vs);
continue;
}
}
cp.regex = cp_regex;
} else {
Utils.logAll("Not: cp.regex = " + cp.regex + " show_axes_3D = " + show_axes_3D + " axes.size() = " + axes.size());
}
final HashMap<String, VectorString3D> condensed = new HashMap<String, VectorString3D>();
Utils.log2("Condensing each bundle...");
// Condense each into a single VectorString3D
for (final Map.Entry<String, ArrayList<Chain>> entry : bundles.entrySet()) {
final ArrayList<Chain> bc = entry.getValue();
if (bc.size() < 2) {
Utils.log2("Skipping single: " + entry.getKey());
continue;
}
final VectorString3D[] vs = new VectorString3D[bc.size()];
for (int i = 0; i < vs.length; i++) vs[i] = bc.get(i).vs;
final VectorString3D c = condense(cp, vs, this);
c.setCalibration(p[0].getRootLayerSet().getCalibrationCopy());
condensed.put(entry.getKey(), c);
if (this.hasQuitted())
return;
}
// Store:
if (null != map_condensed) {
map_condensed.putAll(condensed);
}
if (generate_plots) {
Utils.log2("Plotting stdDev for each condensed bundle...");
// Y axis: the stdDev at each point, computed from the group of points that contribute to each
for (final Map.Entry<String, VectorString3D> e : condensed.entrySet()) {
final String name = e.getKey();
final VectorString3D c = e.getValue();
final Plot plot = makePlot(cp, name, c);
// FAILS//plot.addLabel(10, cp.plot_height-5, name); // must be added after setting size
if (show_plots)
plot.show();
else if (null != plot_dir)
new FileSaver(plot.getImagePlus()).saveAsPng(plot_dir + name.replace('/', '-') + ".png");
}
}
if (show_3D) {
final HashMap<String, Color> heat_table = new HashMap<String, Color>();
if (heat_map || show_envelope_3D) {
// Create a Fire LUT
final ImagePlus lutimp = new ImagePlus("lut", new ByteProcessor(4, 4));
IJ.run(lutimp, "Fire", "");
final IndexColorModel icm = (IndexColorModel) lutimp.getProcessor().getColorModel();
final byte[] reds = new byte[256];
final byte[] greens = new byte[256];
final byte[] blues = new byte[256];
icm.getReds(reds);
icm.getGreens(greens);
icm.getBlues(blues);
final List<String> names = new ArrayList<String>(bundles.keySet());
Collections.sort(names);
// find max stdDev
double max = 0;
final HashMap<String, Double> heats = new HashMap<String, Double>();
for (final String name : names) {
final VectorString3D vs_merged = condensed.get(name);
if (null == vs_merged) {
Utils.logAll("WARNING could not find a condensed pipe for " + name);
continue;
}
final double[] stdDev = vs_merged.getStdDevAtEachPoint();
// double avg = 0;
// for (int i=0; i<stdDev.length; i++) avg += stdDev[i];
// avg = avg/stdDev.length;
Arrays.sort(stdDev);
// median is more representative than average
final double median = stdDev[stdDev.length / 2];
if (max < median)
max = median;
heats.put(name, median);
}
for (final Map.Entry<String, Double> e : heats.entrySet()) {
final String name = e.getKey();
final double median = e.getValue();
// scale between 0 and max to get a Fire LUT color:
int index = (int) ((median / max) * 255);
if (index > 255)
index = 255;
final Color color = new Color(0xff & reds[index], 0xff & greens[index], 0xff & blues[index]);
Utils.log2(new StringBuilder(name).append('\t').append(median).append('\t').append(reds[index]).append('\t').append(greens[index]).append('\t').append(blues[index]).toString());
heat_table.put(name, color);
}
}
final LayerSet common_ls = new LayerSet(p[0], -1, "Common", 10, 10, 0, 0, 0, 512, 512, false, 2, new AffineTransform());
final Display3D d3d = Display3D.get(common_ls);
float env_alpha = envelope_alpha;
if (env_alpha < 0) {
Utils.log2("WARNING envelope_alpha is invalid: " + envelope_alpha + "\n Using 0.4f instead");
env_alpha = 0.4f;
} else if (env_alpha > 1)
env_alpha = 1.0f;
for (final String name : bundles.keySet()) {
final ArrayList<Chain> bc = bundles.get(name);
final VectorString3D vs_merged = condensed.get(name);
if (null == vs_merged) {
Utils.logAll("WARNING: could not find a condensed vs for " + name);
continue;
}
if (show_sources_3D) {
if (null != sources_color_table) {
final HashSet<String> titles = new HashSet<String>();
for (final Chain chain : bc) {
final Color c = sources_color_table.get(chain.getRoot().getProject());
final String title = chain.getCellTitle();
String t = title;
int i = 2;
while (titles.contains(t)) {
t = title + "-" + i;
i += 1;
}
titles.add(t);
Display3D.addMesh(common_ls, chain.vs, t, null != c ? c : Color.gray);
}
} else {
for (final Chain chain : bc) Display3D.addMesh(common_ls, chain.vs, chain.getCellTitle(), Color.gray);
}
}
if (show_condensed_3D) {
Display3D.addMesh(common_ls, vs_merged, name + "-condensed", heat_map ? heat_table.get(name) : Color.red);
}
if (show_envelope_3D) {
double[] widths = makeEnvelope(cp, vs_merged);
if (cp.delta_envelope > 1) {
vs_merged.addDependent(widths);
vs_merged.resample(cp.delta_envelope);
widths = vs_merged.getDependent(0);
}
Display3D.addMesh(common_ls, vs_merged, name + "-envelope", heat_map ? heat_table.get(name) : Color.red, widths, env_alpha);
} else if (heat_map) {
// Show spheres in place of envelopes, at the starting tip (neuropile entry point)
final double x = vs_merged.getPoints(0)[0];
final double y = vs_merged.getPoints(1)[0];
final double z = vs_merged.getPoints(2)[0];
final double r = 10;
final Color color = heat_table.get(name);
if (null == color) {
Utils.logAll("WARNING: heat table does not have a color for " + name);
continue;
}
final Content sphere = d3d.getUniverse().addMesh(ij3d.Mesh_Maker.createSphere(x, y, z, r), new Color3f(heat_table.get(name)), name + "-sphere", 1);
}
}
if (show_axes_3D) {
for (int i = 0; i < p.length; i++) {
final Map<String, VectorString3D> m = axes.get(p[i]);
if (null == m) {
Utils.log2("No axes found for project " + p[i]);
continue;
}
for (final Map.Entry<String, VectorString3D> e : m.entrySet()) {
Display3D.addMesh(common_ls, e.getValue(), e.getKey() + "-" + i, Color.gray);
}
}
}
results.put("d3d", Display3D.get(common_ls));
}
this.result = results;
Utils.log2("Done.");
} catch (final Exception e) {
IJError.print(e);
} finally {
finishedWorking();
}
}
};
return Bureaucrat.createAndStart(worker, p[0]);
}
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