Example 6 with Worker
use of ini.trakem2.utils.Worker in project TrakEM2 by trakem2.
the class Loader method insertGrid.
/**
* Insert grid in layer (with optional stitching)
*
* @param layer The Layer to inser the grid into
* @param dir The base dir of the images to open
* @param first_image_name name of the first image in the list
* @param cols The list of columns, containing each an array of String file names in each column.
* @param bx The top-left X coordinate of the grid to insert
* @param by The top-left Y coordinate of the grid to insert
* @param bt_overlap bottom-top overlap of the images
* @param lr_overlap left-right overlap of the images
* @param link_images Link images to their neighbors
* @param stitch_tiles montage option
* @param cc_percent_overlap tiles overlap
* @param cc_scale tiles scaling previous to stitching (1 = no scaling)
* @param min_R regression threshold (minimum acceptable R)
* @param homogenize_contrast contrast homogenization option
* @param stitching_rule stitching rule (upper left corner or free)
*/
private void insertGrid(final Layer layer, final String dir_, final String first_image_name, final int n_images, final ArrayList<String[]> cols, final double bx, final double by, final double bt_overlap, final double lr_overlap, final boolean link_images, final boolean stitch_tiles, final boolean homogenize_contrast, final StitchingTEM.PhaseCorrelationParam pc_param, final Worker worker) {
// create a Worker, then give it to the Bureaucrat
try {
String dir = dir_;
final ArrayList<Patch> al = new ArrayList<Patch>();
Utils.showProgress(0.0D);
// less repaints on IJ status bar
opener.setSilentMode(true);
int x = 0;
int y = 0;
int largest_y = 0;
ImagePlus img = null;
// open the selected image, to use as reference for width and height
// w1nd0wz safe
dir = dir.replace('\\', '/');
if (!dir.endsWith("/"))
dir += "/";
String path = dir + first_image_name;
// TODO arbitrary x3 factor
releaseToFit(new File(path).length() * 3);
IJ.redirectErrorMessages();
ImagePlus first_img = openImagePlus(path);
if (null == first_img) {
Utils.log("Selected image to open first is null.");
return;
}
if (null == first_img)
return;
final int first_image_width = first_img.getWidth();
final int first_image_height = first_img.getHeight();
final int first_image_type = first_img.getType();
// start
final Patch[][] pall = new Patch[cols.size()][((String[]) cols.get(0)).length];
int width, height;
// counter
int k = 0;
boolean auto_fix_all = false;
boolean ignore_all = false;
boolean resize = false;
if (!ControlWindow.isGUIEnabled()) {
// headless mode: autofix all
auto_fix_all = true;
resize = true;
}
// Accumulate mipmap generation tasks
final ArrayList<Future<?>> fus = new ArrayList<Future<?>>();
startLargeUpdate();
for (int i = 0; i < cols.size(); i++) {
final String[] rows = (String[]) cols.get(i);
if (i > 0) {
x -= lr_overlap;
}
for (int j = 0; j < rows.length; j++) {
if (Thread.currentThread().isInterrupted()) {
Display.repaint(layer);
rollback();
return;
}
if (j > 0) {
y -= bt_overlap;
}
// get file name
final String file_name = (String) rows[j];
path = dir + file_name;
if (null != first_img && file_name.equals(first_image_name)) {
img = first_img;
// release pointer
first_img = null;
} else {
// open image
releaseToFit(first_image_width, first_image_height, first_image_type, 1.5f);
try {
IJ.redirectErrorMessages();
img = openImagePlus(path);
} catch (final OutOfMemoryError oome) {
printMemState();
throw oome;
}
}
if (null == img) {
Utils.log("null image! skipping.");
pall[i][j] = null;
continue;
}
width = img.getWidth();
height = img.getHeight();
int rw = width;
int rh = height;
if (width != first_image_width || height != first_image_height) {
int new_width = first_image_width;
int new_height = first_image_height;
if (!auto_fix_all && !ignore_all) {
final GenericDialog gdr = new GenericDialog("Size mismatch!");
gdr.addMessage("The size of " + file_name + " is " + width + " x " + height);
gdr.addMessage("but the selected image was " + first_image_width + " x " + first_image_height);
gdr.addMessage("Adjust to selected image dimensions?");
gdr.addNumericField("width: ", (double) first_image_width, 0);
// should not be editable ... or at least, explain in some way that the dimensions can be edited just for this image --> done below
gdr.addNumericField("height: ", (double) first_image_height, 0);
gdr.addMessage("[If dimensions are changed they will apply only to this image]");
gdr.addMessage("");
final String[] au = new String[] { "fix all", "ignore all" };
gdr.addChoice("Automate:", au, au[1]);
gdr.addMessage("Cancel == NO OK = YES");
gdr.showDialog();
if (gdr.wasCanceled()) {
resize = false;
// do nothing: don't fix/resize
}
resize = true;
// catch values
new_width = (int) gdr.getNextNumber();
new_height = (int) gdr.getNextNumber();
final int iau = gdr.getNextChoiceIndex();
if (new_width != first_image_width || new_height != first_image_height) {
auto_fix_all = false;
} else {
auto_fix_all = (0 == iau);
}
ignore_all = (1 == iau);
if (ignore_all)
resize = false;
}
if (resize) {
// resize Patch dimensions
rw = first_image_width;
rh = first_image_height;
}
}
// add new Patch at base bx,by plus the x,y of the grid
// will call back and cache the image
final Patch patch = new Patch(layer.getProject(), img.getTitle(), bx + x, by + y, img);
if (width != rw || height != rh)
patch.setDimensions(rw, rh, false);
addedPatchFrom(path, patch);
if (// prevent it
homogenize_contrast)
// prevent it
setMipMapsRegeneration(false);
else
fus.add(regenerateMipMaps(patch));
//
// after the above two lines! Otherwise it will paint fine, but throw exceptions on the way
layer.add(patch, true);
// otherwise when reopening it has to fetch all ImagePlus and scale and zip them all! This method though creates the awt and the snap, thus filling up memory and slowing down, but it's worth it.
patch.updateInDatabase("tiff_snapshot");
pall[i][j] = patch;
al.add(patch);
if (ControlWindow.isGUIEnabled()) {
// northwest to prevent screwing up Patch coordinates.
layer.getParent().enlargeToFit(patch, LayerSet.NORTHWEST);
}
y += img.getHeight();
Utils.showProgress((double) k / n_images);
k++;
}
x += img.getWidth();
if (largest_y < y) {
largest_y = y;
}
// resetting!
y = 0;
}
// build list
final Patch[] pa = new Patch[al.size()];
int f = 0;
// list in row-first order
for (int j = 0; j < pall[0].length; j++) {
// 'j' is row
for (int i = 0; i < pall.length; i++) {
// 'i' is column
pa[f++] = pall[i][j];
}
}
// optimize repaints: all to background image
Display.clearSelection(layer);
// make the first one be top, and the rest under it in left-right and top-bottom order
for (int j = 0; j < pa.length; j++) {
layer.moveBottom(pa[j]);
}
// make picture
// getFlatImage(layer, layer.getMinimalBoundingBox(Patch.class), 0.25, 1, ImagePlus.GRAY8, Patch.class, null, false).show();
// optimize repaints: all to background image
Display.clearSelection(layer);
if (homogenize_contrast) {
if (null != worker)
worker.setTaskName("Enhancing contrast");
// 0 - check that all images are of the same type
int tmp_type = pa[0].getType();
for (int e = 1; e < pa.length; e++) {
if (pa[e].getType() != tmp_type) {
// can't continue
tmp_type = Integer.MAX_VALUE;
Utils.log("Can't homogenize histograms: images are not all of the same type.\nFirst offending image is: " + al.get(e));
break;
}
}
if (Integer.MAX_VALUE != tmp_type) {
// checking on error flag
// Set min and max for all images
// 1 - fetch statistics for each image
final ArrayList<ImageStatistics> al_st = new ArrayList<ImageStatistics>();
// list of Patch ordered by stdDev ASC
final ArrayList<Patch> al_p = new ArrayList<Patch>();
int type = -1;
for (int i = 0; i < pa.length; i++) {
if (Thread.currentThread().isInterrupted()) {
Display.repaint(layer);
rollback();
return;
}
ImagePlus imp = fetchImagePlus(pa[i]);
// speed-up trick: extract data from smaller image
if (imp.getWidth() > 1024) {
releaseToFit(1024, (int) ((imp.getHeight() * 1024) / imp.getWidth()), imp.getType(), 1.1f);
// cheap and fast nearest-point resizing
imp = new ImagePlus(imp.getTitle(), imp.getProcessor().resize(1024));
}
if (-1 == type)
type = imp.getType();
final ImageStatistics i_st = imp.getStatistics();
// order by stdDev, from small to big
int q = 0;
for (final ImageStatistics st : al_st) {
q++;
if (st.stdDev > i_st.stdDev)
break;
}
if (q == al.size()) {
// append at the end. WARNING if importing thousands of images, this is a potential source of out of memory errors. I could just recompute it when I needed it again below
al_st.add(i_st);
al_p.add(pa[i]);
} else {
al_st.add(q, i_st);
al_p.add(q, pa[i]);
}
}
// shallow copy of the ordered list
final ArrayList<Patch> al_p2 = new ArrayList<Patch>(al_p);
// 2 - discard the first and last 25% (TODO: a proper histogram clustering analysis and histogram examination should apply here)
if (pa.length > 3) {
// under 4 images, use them all
int i = 0;
while (i <= pa.length * 0.25) {
al_p.remove(i);
i++;
}
final int count = i;
i = pa.length - 1 - count;
while (i > (pa.length * 0.75) - count) {
al_p.remove(i);
i--;
}
}
// 3 - compute common histogram for the middle 50% images
final Patch[] p50 = new Patch[al_p.size()];
al_p.toArray(p50);
final StackStatistics stats = new StackStatistics(new PatchStack(p50, 1));
// 4 - compute autoAdjust min and max values
// extracting code from ij.plugin.frame.ContrastAdjuster, method autoAdjust
int autoThreshold = 0;
double min = 0;
double max = 0;
// once for 8-bit and color, twice for 16 and 32-bit (thus the 2501 autoThreshold value)
final int limit = stats.pixelCount / 10;
final int[] histogram = stats.histogram;
// else autoThreshold /= 2;
if (ImagePlus.GRAY16 == type || ImagePlus.GRAY32 == type)
autoThreshold = 2500;
else
autoThreshold = 5000;
final int threshold = stats.pixelCount / autoThreshold;
int i = -1;
boolean found = false;
int count;
do {
i++;
count = histogram[i];
if (count > limit)
count = 0;
found = count > threshold;
} while (!found && i < 255);
final int hmin = i;
i = 256;
do {
i--;
count = histogram[i];
if (count > limit)
count = 0;
found = count > threshold;
} while (!found && i > 0);
final int hmax = i;
if (hmax >= hmin) {
min = stats.histMin + hmin * stats.binSize;
max = stats.histMin + hmax * stats.binSize;
if (min == max) {
min = stats.min;
max = stats.max;
}
}
// 5 - compute common mean within min,max range
final double target_mean = getMeanOfRange(stats, min, max);
Utils.log2("Loader min,max: " + min + ", " + max + ", target mean: " + target_mean);
// 6 - apply to all
for (i = al_p2.size() - 1; i > -1; i--) {
// the order is different, thus getting it from the proper list
final Patch p = (Patch) al_p2.get(i);
final double dm = target_mean - getMeanOfRange((ImageStatistics) al_st.get(i), min, max);
// displacing in the opposite direction, makes sense, so that the range is drifted upwards and thus the target 256 range for an awt.Image will be closer to the ideal target_mean
p.setMinAndMax(min - dm, max - dm);
// OBSOLETE and wrong //p.putMinAndMax(fetchImagePlus(p));
}
setMipMapsRegeneration(true);
if (isMipMapsRegenerationEnabled()) {
// recreate files
for (final Patch p : al) fus.add(regenerateMipMaps(p));
}
Display.repaint(layer, new Rectangle(0, 0, (int) layer.getParent().getLayerWidth(), (int) layer.getParent().getLayerHeight()), 0);
// make picture
// getFlatImage(layer, layer.getMinimalBoundingBox(Patch.class), 0.25, 1, ImagePlus.GRAY8, Patch.class, null, false).show();
}
}
if (stitch_tiles) {
// Wait until all mipmaps for the new images have been generated before attempting to register
Utils.wait(fus);
// create undo
layer.getParent().addTransformStep(new HashSet<Displayable>(layer.getDisplayables(Patch.class)));
// wait until repainting operations have finished (otherwise, calling crop on an ImageProcessor fails with out of bounds exception sometimes)
if (null != Display.getFront())
Display.getFront().getCanvas().waitForRepaint();
if (null != worker)
worker.setTaskName("Stitching");
StitchingTEM.stitch(pa, cols.size(), bt_overlap, lr_overlap, true, pc_param).run();
}
// link with images on top, bottom, left and right.
if (link_images) {
if (null != worker)
worker.setTaskName("Linking");
for (int i = 0; i < pall.length; i++) {
// 'i' is column
for (int j = 0; j < pall[0].length; j++) {
// 'j' is row
final Patch p = pall[i][j];
// can happen if a slot is empty
if (null == p)
continue;
if (i > 0 && null != pall[i - 1][j])
p.link(pall[i - 1][j]);
if (i < pall.length - 1 && null != pall[i + 1][j])
p.link(pall[i + 1][j]);
if (j > 0 && null != pall[i][j - 1])
p.link(pall[i][j - 1]);
if (j < pall[0].length - 1 && null != pall[i][j + 1])
p.link(pall[i][j + 1]);
}
}
}
commitLargeUpdate();
// resize LayerSet
// int new_width = x;
// int new_height = largest_y;
// Math.abs(bx) + new_width, Math.abs(by) + new_height);
layer.getParent().setMinimumDimensions();
// update indexes
// so its done once only
layer.updateInDatabase("stack_index");
// create panels in all Displays showing this layer
/* // not needed anymore
Iterator it = al.iterator();
while (it.hasNext()) {
Display.add(layer, (Displayable)it.next(), false); // don't set it active, don't want to reload the ImagePlus!
}
*/
// update Displays
Display.update(layer);
layer.recreateBuckets();
// debug:
} catch (final Throwable t) {
IJError.print(t);
rollback();
setMipMapsRegeneration(true);
}
}
Also used :
ArrayList(java.util.ArrayList)
Rectangle(java.awt.Rectangle)
GenericDialog(ij.gui.GenericDialog)
ZDisplayable(ini.trakem2.display.ZDisplayable)
Displayable(ini.trakem2.display.Displayable)
StackStatistics(ij.process.StackStatistics)
ImagePlus(ij.ImagePlus)
PatchStack(ini.trakem2.imaging.PatchStack)
ImageStatistics(ij.process.ImageStatistics)
Future(java.util.concurrent.Future)
Patch(ini.trakem2.display.Patch)
File(java.io.File)
Example 7 with Worker
use of ini.trakem2.utils.Worker in project TrakEM2 by trakem2.
the class Loader method setMinAndMax.
public Bureaucrat setMinAndMax(final Collection<? extends Displayable> patches, final double min, final double max) {
final Worker worker = new Worker("Set min and max") {
@Override
public void run() {
try {
startedWorking();
if (Double.isNaN(min) || Double.isNaN(max)) {
Utils.log("WARNING:\nUnacceptable min and max values: " + min + ", " + max);
finishedWorking();
return;
}
final ArrayList<Future<?>> fus = new ArrayList<Future<?>>();
for (final Displayable d : patches) {
if (d.getClass() != Patch.class)
continue;
final Patch p = (Patch) d;
p.setMinAndMax(min, max);
// Will also flush the cache for Patch p:
fus.add(regenerateMipMaps(p));
}
Utils.wait(fus);
} catch (final Exception e) {
IJError.print(e);
} finally {
finishedWorking();
}
}
};
return Bureaucrat.createAndStart(worker, Project.findProject(this));
}
Also used :
ZDisplayable(ini.trakem2.display.ZDisplayable)
Displayable(ini.trakem2.display.Displayable)
ArrayList(java.util.ArrayList)
Worker(ini.trakem2.utils.Worker)
Future(java.util.concurrent.Future)
Patch(ini.trakem2.display.Patch)
IOException(java.io.IOException)
FormatException(loci.formats.FormatException)
Example 8 with Worker
use of ini.trakem2.utils.Worker in project TrakEM2 by trakem2.
the class Loader method importStack.
/**
* Imports an image stack from a multitiff file and places each slice in the proper layer, creating new layers as it goes. If the given stack is null, popup a file dialog to choose one
*/
public Bureaucrat importStack(final Layer first_layer, final double x, final double y, final ImagePlus imp_stack_, final boolean ask_for_data, final String filepath_, final boolean one_patch_per_layer_) {
Utils.log2("Loader.importStack filepath: " + filepath_);
if (null == first_layer)
return null;
final Worker worker = new Worker("import stack") {
@Override
public void run() {
startedWorking();
try {
String filepath = filepath_;
boolean one_patch_per_layer = one_patch_per_layer_;
/* On drag and drop the stack is not null! */
// Utils.log2("imp_stack_ is " + imp_stack_);
ImagePlus[] stks = null;
boolean choose = false;
if (null == imp_stack_) {
stks = Utils.findOpenStacks();
choose = null == stks || stks.length > 0;
} else {
stks = new ImagePlus[] { imp_stack_ };
}
ImagePlus imp_stack = null;
// ask to open a stack if it's null
if (null == stks) {
// choose one
imp_stack = openStack();
} else if (choose) {
// choose one from the list
final GenericDialog gd = new GenericDialog("Choose one");
gd.addMessage("Choose a stack from the list or 'open...' to bring up a file chooser dialog:");
final String[] list = new String[stks.length + 1];
for (int i = 0; i < list.length - 1; i++) {
list[i] = stks[i].getTitle();
}
list[list.length - 1] = "[ Open stack... ]";
gd.addChoice("choose stack: ", list, list[0]);
gd.showDialog();
if (gd.wasCanceled()) {
finishedWorking();
return;
}
final int i_choice = gd.getNextChoiceIndex();
if (list.length - 1 == i_choice) {
// the open... command
imp_stack = first_layer.getProject().getLoader().openStack();
} else {
imp_stack = stks[i_choice];
}
} else {
imp_stack = imp_stack_;
}
// check:
if (null == imp_stack) {
finishedWorking();
return;
}
final String props = (String) imp_stack.getProperty("Info");
// check if it's amira labels stack to prevent missimports
if (null != props && -1 != props.indexOf("Materials {")) {
final YesNoDialog yn = new YesNoDialog(IJ.getInstance(), "Warning", "You are importing a stack of Amira labels as a regular image stack. Continue anyway?");
if (!yn.yesPressed()) {
finishedWorking();
return;
}
}
// String dir = imp_stack.getFileInfo().directory;
final double layer_width = first_layer.getLayerWidth();
final double layer_height = first_layer.getLayerHeight();
final double current_thickness = first_layer.getThickness();
double thickness = current_thickness;
boolean expand_layer_set = false;
boolean lock_stack = false;
// int anchor = LayerSet.NORTHWEST; //default
if (ask_for_data) {
// ask for slice separation in pixels
final GenericDialog gd = new GenericDialog("Slice separation?");
gd.addMessage("Please enter the slice thickness, in pixels");
// assuming pixelWidth == pixelHeight
gd.addNumericField("slice_thickness: ", Math.abs(imp_stack.getCalibration().pixelDepth / imp_stack.getCalibration().pixelHeight), 3);
if (layer_width != imp_stack.getWidth() || layer_height != imp_stack.getHeight()) {
gd.addCheckbox("Resize canvas to fit stack", true);
// gd.addChoice("Anchor: ", LayerSet.ANCHORS, LayerSet.ANCHORS[0]);
}
gd.addCheckbox("Lock stack", false);
final String[] importStackTypes = { "One slice per layer (Patches)", "Image volume (Stack)" };
if (imp_stack.getStack().isVirtual()) {
one_patch_per_layer = true;
}
gd.addChoice("Import stack as:", importStackTypes, importStackTypes[0]);
((Component) gd.getChoices().get(0)).setEnabled(!imp_stack.getStack().isVirtual());
gd.showDialog();
if (gd.wasCanceled()) {
if (null == stks) {
// flush only if it was not open before
flush(imp_stack);
}
finishedWorking();
return;
}
if (layer_width != imp_stack.getWidth() || layer_height != imp_stack.getHeight()) {
expand_layer_set = gd.getNextBoolean();
// anchor = gd.getNextChoiceIndex();
}
lock_stack = gd.getNextBoolean();
thickness = gd.getNextNumber();
// check provided thickness with that of the first layer:
if (thickness != current_thickness) {
if (1 == first_layer.getParent().size() && first_layer.isEmpty()) {
final YesNoCancelDialog yn = new YesNoCancelDialog(IJ.getInstance(), "Mismatch!", "The current layer's thickness is " + current_thickness + "\nwhich is " + (thickness < current_thickness ? "larger" : "smaller") + " than\nthe desired " + thickness + " for each stack slice.\nAdjust current layer's thickness to " + thickness + " ?");
if (yn.cancelPressed()) {
// was opened new
if (null != imp_stack_)
flush(imp_stack);
finishedWorking();
return;
} else if (yn.yesPressed()) {
first_layer.setThickness(thickness);
// The rest of layers, created new, will inherit the same thickness
}
} else {
final YesNoDialog yn = new YesNoDialog(IJ.getInstance(), "WARNING", "There's more than one layer or the current layer is not empty\nso the thickness cannot be adjusted. Proceed anyway?");
if (!yn.yesPressed()) {
finishedWorking();
return;
}
}
}
one_patch_per_layer = imp_stack.getStack().isVirtual() || 0 == gd.getNextChoiceIndex();
}
if (null == imp_stack.getStack()) {
Utils.showMessage("Not a stack.");
finishedWorking();
return;
}
// WARNING: there are fundamental issues with calibration, because the Layer thickness is disconnected from the Calibration pixelDepth
// set LayerSet calibration if there is no calibration
boolean calibrate = true;
if (ask_for_data && first_layer.getParent().isCalibrated()) {
if (!ControlWindow.isGUIEnabled()) {
Utils.log2("Loader.importStack: overriding LayerSet calibration with that of the imported stack.");
} else {
final YesNoDialog yn = new YesNoDialog("Calibration", "The layer set is already calibrated. Override with the stack calibration values?");
if (!yn.yesPressed()) {
calibrate = false;
}
}
}
if (calibrate) {
first_layer.getParent().setCalibration(imp_stack.getCalibration());
}
if (layer_width < imp_stack.getWidth() || layer_height < imp_stack.getHeight()) {
expand_layer_set = true;
}
if (imp_stack.getStack().isVirtual()) {
// do nothing
} else if (null == filepath) {
// try to get it from the original FileInfo
final FileInfo fi = imp_stack.getOriginalFileInfo();
if (null != fi && null != fi.directory && null != fi.fileName) {
filepath = fi.directory.replace('\\', '/');
if (!filepath.endsWith("/"))
filepath += '/';
filepath += fi.fileName;
}
Utils.log2("Getting filepath from FileInfo: " + filepath);
// check that file exists, otherwise save a copy in the storage folder
if (null == filepath || (!filepath.startsWith("http://") && !new File(filepath).exists())) {
filepath = handlePathlessImage(imp_stack);
}
} else {
filepath = filepath.replace('\\', '/');
}
// Import as Stack ZDisplayable object:
if (!one_patch_per_layer) {
final Stack st = new Stack(first_layer.getProject(), new File(filepath).getName(), x, y, first_layer, filepath);
first_layer.getParent().add(st);
finishedWorking();
return;
}
// Place the first slice in the current layer, and then query the parent LayerSet for subsequent layers, and create them if not present.
final Patch last_patch = Loader.this.importStackAsPatches(first_layer.getProject(), first_layer, x, y, imp_stack, null != imp_stack_ && null != imp_stack_.getCanvas(), filepath);
if (null != last_patch) {
last_patch.setLocked(lock_stack);
Display.updateCheckboxes(last_patch.getLinkedGroup(null), DisplayablePanel.LOCK_STATE, true);
}
if (expand_layer_set) {
last_patch.getLayer().getParent().setMinimumDimensions();
}
Utils.log2("props: " + props);
// check if it's an amira stack, then ask to import labels
if (null != props && -1 == props.indexOf("Materials {") && -1 != props.indexOf("CoordType")) {
final YesNoDialog yn = new YesNoDialog(IJ.getInstance(), "Amira Importer", "Import labels as well?");
if (yn.yesPressed()) {
// select labels
final Collection<AreaList> alis = AmiraImporter.importAmiraLabels(first_layer, last_patch.getX(), last_patch.getY(), imp_stack.getOriginalFileInfo().directory);
if (null != alis) {
// import all created AreaList as nodes in the ProjectTree under a new imported_segmentations node
first_layer.getProject().getProjectTree().insertSegmentations(alis);
// link them to the images
for (final AreaList ali : alis) {
ali.linkPatches();
}
}
}
}
// it is safe not to flush the imp_stack, because all its resources are being used anyway (all the ImageProcessor), and it has no awt.Image. Unless it's being shown in ImageJ, and then it will be flushed on its own when the user closes its window.
} catch (final Exception e) {
IJError.print(e);
}
finishedWorking();
}
};
return Bureaucrat.createAndStart(worker, first_layer.getProject());
}
Also used :
AreaList(ini.trakem2.display.AreaList)
ImagePlus(ij.ImagePlus)
IOException(java.io.IOException)
FormatException(loci.formats.FormatException)
LazyVirtualStack(ini.trakem2.imaging.LazyVirtualStack)
PatchStack(ini.trakem2.imaging.PatchStack)
ImageStack(ij.ImageStack)
VirtualStack(ij.VirtualStack)
Stack(ini.trakem2.display.Stack)
FileInfo(ij.io.FileInfo)
GenericDialog(ij.gui.GenericDialog)
YesNoDialog(ini.trakem2.display.YesNoDialog)
Worker(ini.trakem2.utils.Worker)
YesNoCancelDialog(ij.gui.YesNoCancelDialog)
Component(java.awt.Component)
File(java.io.File)
Patch(ini.trakem2.display.Patch)
Example 9 with Worker
use of ini.trakem2.utils.Worker in project TrakEM2 by trakem2.
the class Loader method makePrescaledTiles.
/**
* Generate 256x256 tiles, as many as necessary, to cover the given srcRect, starting at max_scale. Designed to be slow but memory-capable.
*
* filename = z + "/" + row + "_" + column + "_" + s + ".jpg";
*
* row and column run from 0 to n stepsize 1
* that is, row = y / ( 256 * 2^s ) and column = x / ( 256 * 2^s )
*
* z : z-level (slice)
* x,y: the row and column
* s: scale, which is 1 / (2^s), in integers: 0, 1, 2 ...
*
* var MAX_S = Math.floor( Math.log( MAX_Y + 1 ) / Math.LN2 ) - Math.floor( Math.log( Y_TILE_SIZE ) / Math.LN2 ) - 1;
*
* The module should not be more than 5
* At al levels, there should be an even number of rows and columns, except for the coarsest level.
* The coarsest level should be at least 5x5 tiles.
*
* Best results obtained when the srcRect approaches or is a square. Black space will pad the right and bottom edges when the srcRect is not exactly a square.
* Only the area within the srcRect is ever included, even if actual data exists beyond.
*
* @return The watcher thread, for joining purposes, or null if the dialog is canceled or preconditions are not passed.
* @throws IllegalArgumentException if the type is not ImagePlus.GRAY8 or Imageplus.COLOR_RGB.
*/
public Bureaucrat makePrescaledTiles(final Layer[] layers, final Class<?> clazz, final Rectangle srcRect, double max_scale_, final int c_alphas, final int type, String target_dir, final boolean from_original_images, final Saver saver, final int tileSide) {
if (null == layers || 0 == layers.length)
return null;
switch(type) {
case ImagePlus.GRAY8:
case ImagePlus.COLOR_RGB:
break;
default:
throw new IllegalArgumentException("Can only export for web with 8-bit or RGB");
}
// choose target directory
if (null == target_dir) {
final DirectoryChooser dc = new DirectoryChooser("Choose target directory");
target_dir = dc.getDirectory();
if (null == target_dir)
return null;
}
if (IJ.isWindows())
target_dir = target_dir.replace('\\', '/');
if (!target_dir.endsWith("/"))
target_dir += "/";
if (max_scale_ > 1) {
Utils.log("Prescaled Tiles: using max scale of 1.0");
// no point
max_scale_ = 1;
}
final String dir = target_dir;
final double max_scale = max_scale_;
final Worker worker = new Worker("Creating prescaled tiles") {
private void cleanUp() {
finishedWorking();
}
@Override
public void run() {
startedWorking();
try {
// project name
// String pname = layer[0].getProject().getTitle();
// create 'z' directories if they don't exist: check and ask!
// start with the highest scale level
final int[] best = determineClosestPowerOfTwo(srcRect.width > srcRect.height ? srcRect.width : srcRect.height);
final int edge_length = best[0];
final int n_edge_tiles = edge_length / tileSide;
Utils.log2("srcRect: " + srcRect);
Utils.log2("edge_length, n_edge_tiles, best[1] " + best[0] + ", " + n_edge_tiles + ", " + best[1]);
// thumbnail dimensions
// LayerSet ls = layer[0].getParent();
final double ratio = srcRect.width / (double) srcRect.height;
double thumb_scale = 1.0;
if (ratio >= 1) {
// width is larger or equal than height
thumb_scale = 192.0 / srcRect.width;
} else {
thumb_scale = 192.0 / srcRect.height;
}
// Figure out layer indices, given that layers are not necessarily evenly spaced
final TreeMap<Integer, Layer> indices = new TreeMap<Integer, Layer>();
final ArrayList<Integer> missingIndices = new ArrayList<Integer>();
final double resolution_z_px;
final int smallestIndex, largestIndex;
if (1 == layers.length) {
indices.put(0, layers[0]);
resolution_z_px = layers[0].getZ();
smallestIndex = 0;
largestIndex = 0;
} else {
// Ensure layers are sorted by Z index and are unique pointers and unique in Z coordinate:
final TreeMap<Double, Layer> t = new TreeMap<Double, Layer>();
for (final Layer l1 : new HashSet<Layer>(Arrays.asList(layers))) {
final Layer l2 = t.get(l1.getZ());
if (null == l2) {
t.put(l1.getZ(), l1);
} else {
// Ignore the layer with less objects
if (l1.getDisplayables().size() > l2.getDisplayables().size()) {
t.put(l1.getZ(), l1);
Utils.log("Ignoring duplicate layer: " + l2);
}
}
}
// What is the mode thickness, measured by Z(i-1) - Z(i)?
// (Distance between the Z of two consecutive layers)
final HashMap<Double, Integer> counts = new HashMap<Double, Integer>();
final Layer prev = t.get(t.firstKey());
double modeThickness = 0;
int modeThicknessCount = 0;
for (final Layer la : t.tailMap(prev.getZ(), false).values()) {
// Thickness with 3-decimal precision only
final double d = ((int) ((la.getZ() - prev.getZ()) * 1000 + 0.5)) / 1000.0;
Integer c = counts.get(d);
//
if (null == c)
c = 0;
++c;
counts.put(d, c);
//
if (c > modeThicknessCount) {
modeThicknessCount = c;
modeThickness = d;
}
}
// Not pixelDepth
resolution_z_px = modeThickness * prev.getParent().getCalibration().pixelWidth;
// Assign an index to each layer, approximating each layer at modeThickness intervals
for (final Layer la : t.values()) {
indices.put((int) (la.getZ() / modeThickness + 0.5), la);
}
// First and last
smallestIndex = indices.firstKey();
largestIndex = indices.lastKey();
Utils.logAll("indices: " + smallestIndex + ", " + largestIndex);
// Which indices are missing?
for (int i = smallestIndex + 1; i < largestIndex; ++i) {
if (!indices.containsKey(i)) {
missingIndices.add(i);
}
}
}
// JSON metadata for CATMAID
{
final StringBuilder sb = new StringBuilder("{");
final LayerSet ls = layers[0].getParent();
final Calibration cal = ls.getCalibration();
sb.append("\"volume_width_px\": ").append(srcRect.width).append(',').append('\n').append("\"volume_height_px\": ").append(srcRect.height).append(',').append('\n').append("\"volume_sections\": ").append(largestIndex - smallestIndex + 1).append(',').append('\n').append("\"extension\": \"").append(saver.getExtension()).append('\"').append(',').append('\n').append("\"resolution_x\": ").append(cal.pixelWidth).append(',').append('\n').append("\"resolution_y\": ").append(cal.pixelHeight).append(',').append('\n').append("\"resolution_z\": ").append(resolution_z_px).append(',').append('\n').append("\"units\": \"").append(cal.getUnit()).append('"').append(',').append('\n').append("\"offset_x_px\": 0,\n").append("\"offset_y_px\": 0,\n").append("\"offset_z_px\": ").append(indices.get(indices.firstKey()).getZ() * cal.pixelWidth / cal.pixelDepth).append(',').append('\n').append("\"missing_layers\": [");
for (final Integer i : missingIndices) sb.append(i - smallestIndex).append(',');
// remove last comma
sb.setLength(sb.length() - 1);
sb.append("]}");
if (!Utils.saveToFile(new File(dir + "metadata.json"), sb.toString())) {
Utils.logAll("WARNING: could not save " + dir + "metadata.json\nThe contents was:\n" + sb.toString());
}
}
for (final Map.Entry<Integer, Layer> entry : indices.entrySet()) {
if (this.quit) {
cleanUp();
return;
}
final int index = entry.getKey() - smallestIndex;
final Layer layer = entry.getValue();
// 1 - create a directory 'z' named as the layer's index
String tile_dir = dir + index;
File fdir = new File(tile_dir);
final int tag = 1;
// Ensure there is a usable directory:
while (fdir.exists() && !fdir.isDirectory()) {
fdir = new File(tile_dir + "_" + tag);
}
if (!fdir.exists()) {
fdir.mkdir();
Utils.log("Created directory " + fdir);
}
// if the directory exists already just reuse it, overwritting its files if so.
final String tmp = fdir.getAbsolutePath().replace('\\', '/');
if (!tile_dir.equals(tmp))
Utils.log("\tWARNING: directory will not be in the standard location.");
// debug:
Utils.log2("tile_dir: " + tile_dir + "\ntmp: " + tmp);
tile_dir = tmp;
if (!tile_dir.endsWith("/"))
tile_dir += "/";
// 2 - create layer thumbnail, max 192x192
ImagePlus thumb = getFlatImage(layer, srcRect, thumb_scale, c_alphas, type, clazz, true);
saver.save(thumb, tile_dir + "small");
// ImageSaver.saveAsJpeg(thumb.getProcessor(), tile_dir + "small.jpg", jpeg_quality, ImagePlus.COLOR_RGB != type);
flush(thumb);
thumb = null;
// 3 - fill directory with tiles
if (edge_length < tileSide) {
// edge_length is the largest length of the tileSide x tileSide tile map that covers an area equal or larger than the desired srcRect (because all tiles have to be tileSide x tileSide in size)
// create single tile per layer
makeTile(layer, srcRect, max_scale, c_alphas, type, clazz, tile_dir + "0_0_0", saver);
} else {
// create pyramid of tiles
if (from_original_images) {
Utils.log("Exporting from web using original images");
// Create a giant 8-bit image of the whole layer from original images
double scale = 1;
Utils.log("Export srcRect: " + srcRect);
// WARNING: the snapshot will most likely be smaller than the virtual square image being chopped into tiles
ImageProcessor snapshot = null;
if (ImagePlus.COLOR_RGB == type) {
Utils.log("WARNING: ignoring alpha masks for 'use original images' and 'RGB color' options");
snapshot = Patch.makeFlatImage(type, layer, srcRect, scale, (ArrayList<Patch>) (List) layer.getDisplayables(Patch.class, true), Color.black, true);
} else if (ImagePlus.GRAY8 == type) {
// Respect alpha masks and display range:
Utils.log("WARNING: ignoring scale for 'use original images' and '8-bit' options");
snapshot = ExportUnsignedShort.makeFlatImage((ArrayList<Patch>) (List) layer.getDisplayables(Patch.class, true), srcRect, 0).convertToByte(true);
} else {
Utils.log("ERROR: don't know how to generate mipmaps for type '" + type + "'");
cleanUp();
return;
}
int scale_pow = 0;
int n_et = n_edge_tiles;
final ExecutorService exe = Utils.newFixedThreadPool("export-for-web");
final ArrayList<Future<?>> fus = new ArrayList<Future<?>>();
try {
while (n_et >= best[1]) {
final int snapWidth = snapshot.getWidth();
final int snapHeight = snapshot.getHeight();
final ImageProcessor source = snapshot;
for (int row = 0; row < n_et; row++) {
for (int col = 0; col < n_et; col++) {
final String path = new StringBuilder(tile_dir).append(row).append('_').append(col).append('_').append(scale_pow).toString();
final int tileXStart = col * tileSide;
final int tileYStart = row * tileSide;
final int pixelOffset = tileYStart * snapWidth + tileXStart;
fus.add(exe.submit(new Callable<Boolean>() {
@Override
public Boolean call() {
if (ImagePlus.GRAY8 == type) {
final byte[] pixels = (byte[]) source.getPixels();
final byte[] p = new byte[tileSide * tileSide];
for (int y = 0, sourceIndex = pixelOffset; y < tileSide && tileYStart + y < snapHeight; sourceIndex = pixelOffset + y * snapWidth, y++) {
final int offsetL = y * tileSide;
for (int x = 0; x < tileSide && tileXStart + x < snapWidth; sourceIndex++, x++) {
p[offsetL + x] = pixels[sourceIndex];
}
}
return saver.save(new ImagePlus(path, new ByteProcessor(tileSide, tileSide, p, GRAY_LUT)), path);
} else {
final int[] pixels = (int[]) source.getPixels();
final int[] p = new int[tileSide * tileSide];
for (int y = 0, sourceIndex = pixelOffset; y < tileSide && tileYStart + y < snapHeight; sourceIndex = pixelOffset + y * snapWidth, y++) {
final int offsetL = y * tileSide;
for (int x = 0; x < tileSide && tileXStart + x < snapWidth; sourceIndex++, x++) {
p[offsetL + x] = pixels[sourceIndex];
}
}
return saver.save(new ImagePlus(path, new ColorProcessor(tileSide, tileSide, p)), path);
}
}
}));
}
}
//
scale_pow++;
// works as magnification
scale = 1 / Math.pow(2, scale_pow);
n_et /= 2;
//
Utils.wait(fus);
fus.clear();
// Scale snapshot in half with area averaging
final ImageProcessor nextSnapshot;
if (ImagePlus.GRAY8 == type) {
nextSnapshot = new ByteProcessor((int) (srcRect.width * scale), (int) (srcRect.height * scale));
final byte[] p1 = (byte[]) snapshot.getPixels();
final byte[] p2 = (byte[]) nextSnapshot.getPixels();
final int width1 = snapshot.getWidth();
final int width2 = nextSnapshot.getWidth();
final int height2 = nextSnapshot.getHeight();
int i = 0;
for (int y1 = 0, y2 = 0; y2 < height2; y1 += 2, y2++) {
final int offset1a = y1 * width1;
final int offset1b = (y1 + 1) * width1;
for (int x1 = 0, x2 = 0; x2 < width2; x1 += 2, x2++) {
p2[i++] = (byte) (((p1[offset1a + x1] & 0xff) + (p1[offset1a + x1 + 1] & 0xff) + (p1[offset1b + x1] & 0xff) + (p1[offset1b + x1 + 1] & 0xff)) / 4);
}
}
} else {
nextSnapshot = new ColorProcessor((int) (srcRect.width * scale), (int) (srcRect.height * scale));
final int[] p1 = (int[]) snapshot.getPixels();
final int[] p2 = (int[]) nextSnapshot.getPixels();
final int width1 = snapshot.getWidth();
final int width2 = nextSnapshot.getWidth();
final int height2 = nextSnapshot.getHeight();
int i = 0;
for (int y1 = 0, y2 = 0; y2 < height2; y1 += 2, y2++) {
final int offset1a = y1 * width1;
final int offset1b = (y1 + 1) * width1;
for (int x1 = 0, x2 = 0; x2 < width2; x1 += 2, x2++) {
final int ka = p1[offset1a + x1], kb = p1[offset1a + x1 + 1], kc = p1[offset1b + x1], kd = p1[offset1b + x1 + 1];
// Average each channel independently
p2[i++] = (((// red
((ka >> 16) & 0xff) + ((kb >> 16) & 0xff) + ((kc >> 16) & 0xff) + ((kd >> 16) & 0xff)) / 4) << 16) + (((// green
((ka >> 8) & 0xff) + ((kb >> 8) & 0xff) + ((kc >> 8) & 0xff) + ((kd >> 8) & 0xff)) / 4) << 8) + (// blue
(ka & 0xff) + (kb & 0xff) + (kc & 0xff) + (kd & 0xff)) / 4;
}
}
}
// Assign for next iteration
snapshot = nextSnapshot;
// Scale snapshot with a TransformMesh
/*
AffineModel2D aff = new AffineModel2D();
aff.set(0.5f, 0, 0, 0.5f, 0, 0);
ImageProcessor scaledSnapshot = new ByteProcessor((int)(snapshot.getWidth() * scale), (int)(snapshot.getHeight() * scale));
final CoordinateTransformMesh mesh = new CoordinateTransformMesh( aff, 32, snapshot.getWidth(), snapshot.getHeight() );
final mpicbg.ij.TransformMeshMapping<CoordinateTransformMesh> mapping = new mpicbg.ij.TransformMeshMapping<CoordinateTransformMesh>( mesh );
mapping.mapInterpolated(snapshot, scaledSnapshot, Runtime.getRuntime().availableProcessors());
// Assign for next iteration
snapshot = scaledSnapshot;
snapshotPixels = (byte[]) scaledSnapshot.getPixels();
*/
}
} catch (final Throwable t) {
IJError.print(t);
} finally {
exe.shutdown();
}
} else {
// max_scale; // WARNING if scale is different than 1, it will FAIL to set the next scale properly.
double scale = 1;
int scale_pow = 0;
// cached for local modifications in the loop, works as loop controler
int n_et = n_edge_tiles;
while (n_et >= best[1]) {
// best[1] is the minimal root found, i.e. 1,2,3,4,5 from which then powers of two were taken to make up for the edge_length
// 0 < scale <= 1, so no precision lost
final int tile_side = (int) (256 / scale);
for (int row = 0; row < n_et; row++) {
for (int col = 0; col < n_et; col++) {
final int i_tile = row * n_et + col;
Utils.showProgress(i_tile / (double) (n_et * n_et));
if (0 == i_tile % 100) {
// RGB int[] images
releaseToFit(tile_side * tile_side * 4 * 2);
}
if (this.quit) {
cleanUp();
return;
}
final Rectangle tile_src = new // TODO row and col are inverted
Rectangle(// TODO row and col are inverted
srcRect.x + tile_side * row, srcRect.y + tile_side * col, tile_side, // in absolute coords, magnification later.
tile_side);
// crop bounds
if (tile_src.x + tile_src.width > srcRect.x + srcRect.width)
tile_src.width = srcRect.x + srcRect.width - tile_src.x;
if (tile_src.y + tile_src.height > srcRect.y + srcRect.height)
tile_src.height = srcRect.y + srcRect.height - tile_src.y;
// negative tile sizes will be made into black tiles
// (negative dimensions occur for tiles beyond the edges of srcRect, since the grid of tiles has to be of equal number of rows and cols)
// should be row_col_scale, but results in transposed tiles in googlebrains, so I reversed the order.
makeTile(layer, tile_src, scale, c_alphas, type, clazz, new StringBuilder(tile_dir).append(col).append('_').append(row).append('_').append(scale_pow).toString(), saver);
}
}
scale_pow++;
// works as magnification
scale = 1 / Math.pow(2, scale_pow);
n_et /= 2;
}
}
}
}
} catch (final Exception e) {
IJError.print(e);
} finally {
Utils.showProgress(1);
}
cleanUp();
finishedWorking();
}
};
// watcher thread
return Bureaucrat.createAndStart(worker, layers[0].getProject());
}
Also used :
ByteProcessor(ij.process.ByteProcessor)
HashMap(java.util.HashMap)
ArrayList(java.util.ArrayList)
Rectangle(java.awt.Rectangle)
Callable(java.util.concurrent.Callable)
ImageProcessor(ij.process.ImageProcessor)
ColorProcessor(ij.process.ColorProcessor)
Worker(ini.trakem2.utils.Worker)
HashSet(java.util.HashSet)
LayerSet(ini.trakem2.display.LayerSet)
Calibration(ij.measure.Calibration)
TreeMap(java.util.TreeMap)
Layer(ini.trakem2.display.Layer)
ImagePlus(ij.ImagePlus)
IOException(java.io.IOException)
FormatException(loci.formats.FormatException)
AtomicInteger(java.util.concurrent.atomic.AtomicInteger)
ExecutorService(java.util.concurrent.ExecutorService)
Future(java.util.concurrent.Future)
File(java.io.File)
Map(java.util.Map)
TreeMap(java.util.TreeMap)
HashMap(java.util.HashMap)
DirectoryChooser(ij.io.DirectoryChooser)
Example 10 with Worker
use of ini.trakem2.utils.Worker in project TrakEM2 by trakem2.
the class Loader method importLabelsAsAreaLists.
/**
* 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());
}
Also used :
AreaList(ini.trakem2.display.AreaList)
Layer(ini.trakem2.display.Layer)
ImagePlus(ij.ImagePlus)
IOException(java.io.IOException)
FormatException(loci.formats.FormatException)
OpenDialog(ij.io.OpenDialog)
AmiraMeshDecoder(amira.AmiraMeshDecoder)
GenericDialog(ij.gui.GenericDialog)
Worker(ini.trakem2.utils.Worker)
File(java.io.File)
Aggregations
Worker (ini.trakem2.utils.Worker)20
ArrayList (java.util.ArrayList)10
ImagePlus (ij.ImagePlus)9
Patch (ini.trakem2.display.Patch)8
File (java.io.File)8
GenericDialog (ij.gui.GenericDialog)7
Displayable (ini.trakem2.display.Displayable)7
Rectangle (java.awt.Rectangle)7
HashSet (java.util.HashSet)7
IOException (java.io.IOException)6
Future (java.util.concurrent.Future)6
FormatException (loci.formats.FormatException)6
DirectoryChooser (ij.io.DirectoryChooser)5
Project (ini.trakem2.Project)5
Layer (ini.trakem2.display.Layer)5
VectorString3D (ini.trakem2.vector.VectorString3D)5
HashMap (java.util.HashMap)5
AtomicInteger (java.util.concurrent.atomic.AtomicInteger)5
Calibration (ij.measure.Calibration)4
ZDisplayable (ini.trakem2.display.ZDisplayable)4
