public void getUserPreferences() {
if (maincont == null) {
return;
}
Preferences p =
NbPreferences.forModule(
com.iontorrent.torrentscout.explorer.options.TorrentExplorerPanel.class);
int span = p.getInt("span", 8);
int size = p.getInt("masksize", 100);
automatic_nn = p.getBoolean("automatic_nn", true);
maincont.setRasterSize(size);
maincont.setSpan(span);
maincont.setMedianFunction("median");
}
@Override
public void flowChanged(ArrayList<Integer> flows) {
int f = flows.get(0);
if (maincont == null) {
return;
}
if (f == maincont.getFlow()) {
return;
}
p("flow changed");
maincont.setFlow(f);
// this.rasterViewCreate(true, null);
// recomputeChart();
}
protected boolean getExpContext() {
// Exception e = new Exception("showing stack trace");
// p(ErrorHandler.getString(e));
if (expContext == null) {
expContext = GlobalContext.getContext().getExperimentContext();
}
if (expContext == null) {
GuiUtils.showNonModalMsg("Got no experiment context from global contexet");
return false;
}
maincont = ExplorerContext.getCurContext(expContext);
info.setText(expContext.getRawDir());
this.btnreload.setToolTipText(
"Reload data from dir " + expContext.getRawDir() + " at " + maincont.getAbsDataAreaCoord());
return true;
}
public ProcessTopComponent() {
initComponents();
setName(NbBundle.getMessage(ProcessTopComponent.class, "CTL_ProcessTopComponent"));
setToolTipText(NbBundle.getMessage(ProcessTopComponent.class, "HINT_ProcessTopComponent"));
flowPanel = new FlowNrPanel(this);
if (maincont == null) {
flowPanel.setFlow(0);
} else {
flowPanel.setFlow(maincont.getFlow());
typePanel.setType(maincont.getFiletype());
}
typePanel = new FiletypePanel(this);
this.toolbar.add(this.flowPanel, null, 0);
toolbar.add(this.typePanel, null, 0);
}
@Override
public void taskDone(Task t) {
p("Task " + t + " is done");
setCursor(null);
// if (t.isSuccess()) {
this.data = ((ComputeNN) t).getData();
p("Got nndata " + data);
if (data == null) {
JOptionPane.showMessageDialog(this, "There was a problem in nn compute, I got no result");
} else {
maincont.setData(data);
rasterViewCreate(
false,
"After masked neighbor subtraction, span="
+ maincont.getSpan()
+ ", BG mask="
+ maincont.getBgMask());
}
}
public boolean doSelectCoord() throws HeadlessException {
SingleCoordSelectionPanel pan = new SingleCoordSelectionPanel();
// pan.setMaxX(this.expContext.getNrcols());
// pan.setMaxY(this.expContext.getNrrows());
if (maincont.getAbsDataAreaCoord() != null) {
pan.setCoord1(maincont.getAbsDataAreaCoord());
}
int ans =
JOptionPane.showConfirmDialog(
this, pan, "Enter a selection:", JOptionPane.OK_CANCEL_OPTION);
if (ans == JOptionPane.CANCEL_OPTION) {
return true;
}
// RELATIVE to current sub experiment
WellCoordinate c1 =
new WellCoordinate(
pan.getCoord1().getCol() - maincont.getExp().getColOffset(),
pan.getCoord1().getRow() - maincont.getExp().getRowOffset());
WellCoordinate c2 = c1.add(100, 100);
WellSelection sel = new WellSelection(c1, c2);
WellCoordinate abs = pan.getCoord1();
if (maincont.getAbsDataAreaCoord() != null && abs.equals(maincont.getAbsDataAreaCoord())) {
GuiUtils.showNonModalMsg("Same coordinates, I won't to anything", "Process");
return true;
}
maincont.setAbsDataAreaCoord(abs);
LookupUtils.publish(wellSelectionContent, sel);
return false;
}
@Override
public void fileTypeChanged(RawType filetype) {
if (maincont == null) {
return;
}
if (maincont != null) {
maincont.setFiletype(filetype);
}
p("filetypechanged");
// this.rasterViewCreate(true, null);
}
private void update(ExperimentContext result) {
if (result == null) {
result = GlobalContext.getContext().getExperimentContext();
}
if (result == null) {
// GuiUtils.showNonModalMsg("Got no experiment context");
return;
}
if (result != null) {
this.expContext = result;
maincont = ExplorerContext.getCurContext(result);
getUserPreferences();
addGui();
}
}
private void subtractActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_subtractActionPerformed
RasterData data = maincont.getData();
if (data == null) {
JOptionPane.showMessageDialog(this, "I have no data yet to subtract anything from :-)");
return;
}
if (subtract_type == null) {
subtract_type = maincont.getFiletype();
}
FlowSelection pan =
new FlowSelection(
"Select the flow and file type you wish to subtract from the currently selected data");
pan.setFlow(subtract_flow);
pan.setFiletype(subtract_type);
int ans =
JOptionPane.showConfirmDialog(
this,
pan,
"Data Subtraction",
JOptionPane.OK_CANCEL_OPTION,
JOptionPane.QUESTION_MESSAGE);
if (ans != JOptionPane.OK_OPTION) {
return;
}
subtract_flow = pan.getFlow();
subtract_type = pan.getFiletype();
// otherwise load the data and then subtract
RasterData sub = null;
DataAccessManager manager = DataAccessManager.getManager(maincont.getExp().getWellContext());
try {
p("Loading subregion, RELATIVE coord " + maincont.getRelativeDataAreaCoord());
sub =
manager.getRasterDataForArea(
null,
maincont.getRasterSize(),
maincont.getRelativeDataAreaCoord(),
pan.getFlow(),
pan.getFiletype(),
null,
0,
-1);
// now subtract first frame
} catch (Exception ex) {
p("Error when loading: " + ErrorHandler.getString(ex));
}
if (sub == null) {
JOptionPane.showMessageDialog(
this,
"I could not load flow "
+ pan.getFlow()
+ ", "
+ pan.getFiletype()
+ ", @ "
+ maincont.getAbsDataAreaCoord());
return;
}
String what = "raw";
if (this.automatic_nn) {
GuiUtils.showNonModalMsg("Computing NN before subtraction");
sub = computeNN(null, sub);
what = "NN subtracted";
}
data.subtract(sub);
JOptionPane.showMessageDialog(
this,
"I subtracted the "
+ what
+ " data from "
+ pan.getFlow()
+ ", "
+ pan.getFiletype()
+ ", @ "
+ maincont.getAbsDataAreaCoord());
this.rasterViewUpdate();
} // GEN-LAST:event_subtractActionPerformed
private void btnNNActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_btnNNActionPerformed
p(" about to compute nn. Maincont is: " + maincont + ", data is: " + maincont.getData());
ComputeNN task = new ComputeNN(this);
task.execute();
} // GEN-LAST:event_btnNNActionPerformed
public void rasterViewCreate(boolean load, String title) {
p("=========rasterViewCreate called: load=" + load);
// if (load) {
// Exception e = new Exception("Tracing call");
// p(ErrorHandler.getString(e));
// }
if (!getExpContext()) {
return;
}
if (load) {
if (selection != null)
GuiUtils.showNonModalMsg(
"Loading "
+ selection
+ " for "
+ maincont.getFiletype()
+ ", flow "
+ maincont.getFlow(),
"Process");
}
String base = "?";
if (maincont.getFiletype() == RawType.ACQ) {
base = "" + maincont.getExp().getWellContext().getBase(maincont.getFlow());
}
this.flowPanel.setToolTipText(
"<html>Base for flow "
+ maincont.getFlow()
+ ":"
+ base
+ "<br>Flow order: "
+ maincont.getExp().getFlowOrder()
+ "</html>");
raster = new RasterView(maincont, load);
this.panImage.removeAll();
panImage.add(raster);
// repaint();
// p("adding raster view");
if (load) {
this.getUserPreferences();
}
raster.update(load, maincont);
// paintImmediately(0,0,1000,1000);
panImage.repaint();
raster.repaint();
if (load) {
title = "Raw data";
}
title += " flow " + maincont.getFlow() + "=" + base;
chartViewCreate(title);
invalidate();
revalidate();
// this.paintAll(getGraphics());
repaint();
if (load) {
if (this.automatic_nn) {
p("also doing nn - disable nn");
this.btnNN.setEnabled(false);
btnNN.setText("");
btnNN.setToolTipText(
"Automatically computing NN - check Explorer Options if you wish to change it!");
RasterData data = computeNN(null);
maincont.setData(data);
rasterViewCreate(
false,
"After masked neighbor subtraction, span="
+ maincont.getSpan()
+ ", BG mask="
+ maincont.getBgMask());
} else {
this.btnNN.setEnabled(true);
btnNN.setText("Compute NN");
btnNN.setToolTipText(
"Click to compute NN bg subtraction - check Explorer Options if you wish <b>automate</b> this!");
}
}
}
private RasterData computeNN(ProgressListener prog, RasterData rawdata) {
// p("computeNN. Maincont is: " + maincont);
if (rawdata == null) {
GuiUtils.showNonModalDialog(
"<html>I see no data yet - did you already pick a region?<br>"
+ "(Even if you see something somewhere, if you didn't actually select a region, it might just show some sample data)</html>",
"No data - region selected?");
return null;
}
RasterData nndata = null;
try {
if (maincont == null) {
maincont = ExplorerContext.getCurContext(expContext);
}
int span = Math.max(1, this.maincont.getSpan());
NearestNeighbor nn = new NearestNeighbor(span, maincont.getMedianFunction());
BitMask ignore = maincont.getIgnoreMask();
BitMask take = maincont.getBgMask();
if (take != null && take == ignore) {
JOptionPane.showMessageDialog(
this,
"You select the same mask for ignore and bg :-). \nYou should select another mask for the bg (or you get a null result. I will just return the old data.");
return rawdata;
}
if (take != null && take.computePercentage() < 1) {
int ans =
JOptionPane.showConfirmDialog(
this,
"<html>The bg mask only has "
+ take.computePercentage()
+ "% wells, do you want to still use it?"
+ "<br><b>Did you already select a region?</b>"
+ "<br>You might want to use the MaskEditor (and <b>refresh</b> the masks possibly) to check them</html>",
"Few wells",
JOptionPane.OK_CANCEL_OPTION);
if (ans == JOptionPane.CANCEL_OPTION) {
return rawdata;
}
}
maincont.setBgMask(take);
maincont.setIgnoreMask(ignore);
if (prog != null)
prog.setMessage(
"Masked neighbor subtraction: ignore mask " + ignore + " and empty mask " + take);
// RasterData nndata = nn.compute(rawdata, mask, prog, span);
// p("calling computebetter");
// if (boxslow.isSelected()) nndata =nn.computeSlow(rawdata, ignore, take, prog, span);
nndata = nn.computeBetter(rawdata, ignore, take, prog, span);
} catch (Exception e) {
p("Error with nn: " + ErrorHandler.getString(e));
JOptionPane.showMessageDialog(
this,
"I was not able to do the masked neighbor subtraction:\n" + ErrorHandler.getString(e));
return null;
}
if (nndata == null) {
JOptionPane.showMessageDialog(
this,
"I was not able to do the masked neighbor subtraction - I got no error but also no result :-) ");
}
return nndata;
}
private RasterData computeNN(ProgressListener prog) {
return computeNN(prog, maincont.getData());
}
// private class WellSelectionListener implements LookupListener {
//
// @Override
// public void resultChanged(LookupEvent ev) {
// //ask
// int ans = JOptionPane.showConfirmDialog(ProcessTopComponent.this, "Would you like to
// reload the data with the updated coordinate?");
// if (ans == JOptionPane.OK_OPTION) getLatestSelection();
// }
// }
// private void getLatestSelection() {
// final Collection<? extends WellSelection> selections =
// selectionSelection.allInstances();
// if (!selections.isEmpty()) {
// // p("Getting last selection");
// selection = null;
// Iterator<WellSelection> it = (Iterator<WellSelection>) selections.iterator();
// while (it.hasNext()) {
// selection = it.next();
// }
// p("Got a selection: " + selection);
// maincont.setDataAreaCoord(selection.getCoord1());
// maincont.getExp().getWellContext().setSelection(selection);
//
// // p("SubscriberListener Got WellSelection:" + cur_context);
// GuiUtils.showNonModalMsg("Process: Got a well selection: " + selection);
// // rasterViewUpdate(true);
// }
//
// }
private void addGui() {
if (expContext == null) {
expContext = GlobalContext.getContext().getExperimentContext();
}
if (expContext == null) {
// GuiUtils.showNonModalMsg("Got no experiment context");
return;
}
maincont = ExplorerContext.getCurContext(expContext);
getUserPreferences();
rasterViewCreate(true, null);
maincont.addListener(
new ContextChangeAdapter() {
@Override
public void fileTypeChanged(RawType t) {
p("RawType chnaged: " + t);
typePanel.setType(t);
// rasterViewCreate(true, null);
}
@Override
public void flowChanged(int flow) {
p("flow changed: " + flow);
rasterViewCreate(true, "Raw data");
}
@Override
public void dataChanged(
RasterData data,
int startrow,
int startcol,
int startflow,
int endrow,
int endcol,
int endflow) {
p(
"RasterData chnged: "
+ startrow
+ "/"
+ startcol
+ "/"
+ startflow
+ ", NOT reloading automatically");
// rasterViewUpdate();
}
@Override
public void coordChanged(WellCoordinate coord) {
// p("coord chnged: " + coord);
chartViewUpdate();
}
@Override
public void dataAreaCoordChanged(WellCoordinate coord) {
p("data area coord changed: " + coord);
btnreload.setToolTipText("Reload data from at " + maincont.getAbsDataAreaCoord());
// rebuildMaskComboBoxes();
rasterViewCreate(true, "Raw data");
}
@Override
public void widgetChanged(Widget w) {
p("widget chnged: " + w);
chartViewUpdate();
}
});
if (expContext.getWellContext().getCoordinate() == null) {
expContext.getWellContext().setCoordinate(new WellCoordinate(100, 100));
}
}
