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)); } }