Examples with UShortImage cbit.vcell.VirtualMicroscopy.UShortImage used on opensource projects

Example 46 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage in project vcell by virtualcell.

the class ROIMultiPaintManager method applyPixelClasses.

private void applyPixelClasses(VCPixelClass[] vcPixelClasses, Component parentComponent) {
    if (vcPixelClasses != null) {
        int backgroundIndex = -1;
        int[] pixelValMapPixelClassIndex = new int[256];
        Arrays.fill(pixelValMapPixelClassIndex, -1);
        String[][] rowData = new String[vcPixelClasses.length][1];
        for (int i = 0; i < vcPixelClasses.length; i++) {
            pixelValMapPixelClassIndex[vcPixelClasses[i].getPixel()] = i;
            rowData[i][0] = vcPixelClasses[i].getPixelClassName();
            if (vcPixelClasses[i].getPixel() == 0 && vcPixelClasses[i].getPixelClassName().equals(RESERVED_NAME_BACKGROUND)) {
                // choose background automatically
                backgroundIndex = i;
            }
        }
        // Create ROIs from VCPixelclasses
        // start 1 after background index color
        int roiCount = 1;
        int[] pixelClassIndexMaproiIndex = new int[vcPixelClasses.length];
        for (int i = 0; i < vcPixelClasses.length; i++) {
            if (i == backgroundIndex) {
                // background
                pixelClassIndexMaproiIndex[i] = 0;
                continue;
            }
            overlayEditorPanelJAI.addROIName(vcPixelClasses[i].getPixelClassName(), true, vcPixelClasses[0].getPixelClassName(), true, /*true,true,*/
            roiCount);
            pixelClassIndexMaproiIndex[i] = roiCount;
            roiCount++;
        }
        // fill in rois using pixel value and VCPixelClass mappings
        for (int zindex = 0; zindex < roiComposite.length; zindex++) {
            byte[] zdata = ((DataBufferByte) roiComposite[zindex].getRaster().getDataBuffer()).getData();
            UShortImage uShortImage = initImageDataSetChannels[0].getImage(zindex, 0, 0);
            for (int xyindex = 0; xyindex < zdata.length; xyindex++) {
                // unsigned short
                int pixelval = uShortImage.getPixels()[xyindex] & 0x000000FF;
                zdata[xyindex] = (byte) pixelClassIndexMaproiIndex[pixelValMapPixelClassIndex[pixelval]];
            }
        }
    }
}

Example 47 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage in project vcell by virtualcell.

the class ROIAssistPanel method pickKeepRegionInfoFromCurrentROI.

private RegionInfo[] pickKeepRegionInfoFromCurrentROI() throws Exception {
    RegionInfo[] thresholdRegionInfos = calculateRegionInfos(dataToThreshold.getCurrentlyDisplayedROI().getPixelsXYZ());
    Vector<RegionInfo> roiRegionInfoV = new Vector<RegionInfo>();
    for (int i = 0; i < thresholdRegionInfos.length; i++) {
        if (thresholdRegionInfos[i].getPixelValue() == 1) {
            roiRegionInfoV.add(thresholdRegionInfos[i]);
        }
    }
    if (roiRegionInfoV.size() == 0) {
        DialogUtils.showInfoDialog(this, "There are no Regions Of Interest to resolve.");
        return null;
    }
    // Present list to pick from
    final RegionInfo[] regionInfoArr = roiRegionInfoV.toArray(new RegionInfo[0]);
    Arrays.sort(regionInfoArr, new Comparator<RegionInfo>() {

        public int compare(RegionInfo o1, RegionInfo o2) {
            return o2.getNumPixels() - o1.getNumPixels();
        }
    });
    final Object[][] rowData = new Object[regionInfoArr.length][1];
    for (int i = 0; i < regionInfoArr.length; i++) {
        rowData[i][0] = regionInfoArr[i].getNumPixels() + " pixels";
    }
    final ROI beforeROI = new ROI(dataToThreshold.getCurrentlyDisplayedROI());
    int[] resultArr = null;
    ListSelectionListener listSelectionListener = new ListSelectionListener() {

        public void valueChanged(ListSelectionEvent e) {
            if (!e.getValueIsAdjusting()) {
                try {
                    DefaultListSelectionModel defaultListSelectionModel = (DefaultListSelectionModel) e.getSource();
                    Vector<Integer> pickedIndexes = new Vector<Integer>();
                    if (!defaultListSelectionModel.isSelectionEmpty()) {
                        for (int i = defaultListSelectionModel.getMinSelectionIndex(); i <= defaultListSelectionModel.getMaxSelectionIndex(); i++) {
                            if (defaultListSelectionModel.isSelectedIndex(i)) {
                                pickedIndexes.add(i);
                            }
                        }
                    }
                    // beforeROI.getPixelsXYZ();
                    short[] pickedPixels = new short[beforeROI.getISize().getXYZ()];
                    for (int i = 0; i < pickedPixels.length; i++) {
                        for (int j = 0; j < pickedIndexes.size(); j++) {
                            if (regionInfoArr[pickedIndexes.elementAt(j)].isIndexInRegion(i)) {
                                pickedPixels[i] = 1;
                            }
                        }
                    }
                    ROI newCellROI = null;
                    if (pickedIndexes.size() == 0) {
                        newCellROI = beforeROI;
                    } else {
                        UShortImage ushortImage = new UShortImage(pickedPixels, originalROI.getRoiImages()[0].getOrigin(), originalROI.getRoiImages()[0].getExtent(), originalROI.getISize().getX(), originalROI.getISize().getY(), originalROI.getISize().getZ());
                        newCellROI = new ROI(ushortImage, originalROI.getROIName());
                    }
                    dataToThreshold.addReplaceRoi(newCellROI);
                } catch (Exception e2) {
                    e2.printStackTrace();
                    throw new RuntimeException("Error selecting resolved ROI", e2);
                }
            }
        }
    };
    try {
        resultArr = DialogUtils.showComponentOptionsTableList(this, "Select 1 or more pixel regions to keep in ROI", new String[] { "ROI Size (pixel count)" }, rowData, ListSelectionModel.MULTIPLE_INTERVAL_SELECTION, listSelectionListener, null, null, null).selectedTableRows;
    } catch (UserCancelException e) {
        resultArr = null;
    }
    if (resultArr != null && resultArr.length > 0) {
        RegionInfo[] pickedRegions = new RegionInfo[resultArr.length];
        for (int i = 0; i < resultArr.length; i++) {
            pickedRegions[i] = regionInfoArr[resultArr[i]];
        }
        // (resultArr == null?null:regionInfoArr[resultArr]);
        return pickedRegions;
    } else {
        dataToThreshold.addReplaceRoi(beforeROI);
    }
    return null;
}

Example 48 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage in project vcell by virtualcell.

the class ROIAssistPanel method fillVoidsAction.

private void fillVoidsAction() {
    final String CELL_ROI = "CELL_ROI";
    AsynchClientTask voidTask = new AsynchClientTask("Finding voids", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            short[] filledVoidsPixels = dataToThreshold.getCurrentlyDisplayedROI().getPixelsXYZ();
            boolean bVoidsExisted = fillVoids(filledVoidsPixels, false);
            if (!bVoidsExisted) {
                DialogUtils.showInfoDialog(ROIAssistPanel.this, "No internal voids were found, no changes were made.");
                throw UserCancelException.CANCEL_GENERIC;
            }
            UShortImage ushortImage = new UShortImage(filledVoidsPixels, originalROI.getRoiImages()[0].getOrigin(), originalROI.getRoiImages()[0].getExtent(), originalROI.getISize().getX(), originalROI.getISize().getY(), originalROI.getISize().getZ());
            ROI newCellROI = new ROI(ushortImage, originalROI.getROIName());
            hashTable.put(CELL_ROI, newCellROI);
        }
    };
    AsynchClientTask updateDisplayTask = new AsynchClientTask("Updating display", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            dataToThreshold.addReplaceRoi((ROI) hashTable.get(CELL_ROI));
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { voidTask, updateDisplayTask }, false, false, null, true);
}

Example 49 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage in project vcell by virtualcell.

the class ROIAssistPanel method processTimepoint.

private void processTimepoint() {
    final String NEW_ROI = "NEW_ROI";
    AsynchClientTask calcROI = new AsynchClientTask("Calculating ROI", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            short[] shortPixels = new short[enhancedDataToThresholdShort.length];
            for (int i = 0; i < enhancedDataToThresholdShort.length; i++) {
                shortPixels[i] = (short) (isSet(/*originalROI.getROIName(),*/
                enhancedDataToThresholdShort[i], thresholdSlider.getValue(), thresholdSliderIntensityLookup, (maskBitSet != null ? maskBitSet.get(i) : true)) ? 0xFFFF : 0);
            }
            UShortImage ushortImage = new UShortImage(shortPixels, originalROI.getRoiImages()[0].getOrigin(), originalROI.getRoiImages()[0].getExtent(), originalROI.getISize().getX(), originalROI.getISize().getY(), originalROI.getISize().getZ());
            final ROI newCellROI = new ROI(ushortImage, originalROI.getROIName());
            hashTable.put(NEW_ROI, newCellROI);
        }
    };
    AsynchClientTask displayROI = new AsynchClientTask("displayROI", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            dataToThreshold.addReplaceRoi((ROI) hashTable.get(NEW_ROI));
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { calcROI, displayROI }, false, false, null, true);
}

Example 50 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage in project vcell by virtualcell.

the class ROIMultiPaintManager method askApplyHighlightToROI.

private boolean askApplyHighlightToROI() {
    UShortImage[] roiZ = overlayEditorPanelJAI.getHighliteInfo().getRoiImages();
    boolean bOverWrite = true;
    // Check for existing ROI
    final String OVERWRITE_ALL = "Overwrite any existing Domain Regionss";
    final String KEEP_EXISTING = "Keep existing Domain Regions when overlapping";
    final String CANCEL_ROI_UPDATE = "Cancel";
    // boolean bHadAny = false;
    for (int i = 0; i < roiZ.length; i++) {
        boolean bDone = false;
        short[] pixels = roiZ[i].getPixels();
        byte[] compositePixels = ((DataBufferByte) roiComposite[i].getRaster().getDataBuffer()).getData();
        for (int j = 0; j < compositePixels.length; j++) {
            // bHadAny|= pixels[j] != 0;
            if (compositePixels[j] != 0 && pixels[j] != 0) /* && compositePixels[j] != (byte)roiColorIndex*/
            {
                bDone = true;
                String result = DialogUtils.showWarningDialog(overlayEditorPanelJAI, "Some areas of the new Domain Regions overlap with existing Domain Regions.", new String[] { OVERWRITE_ALL, KEEP_EXISTING, CANCEL_ROI_UPDATE }, OVERWRITE_ALL);
                if (result.equals(KEEP_EXISTING)) {
                    bOverWrite = false;
                } else if (result.equals(CANCEL_ROI_UPDATE)) {
                    throw UserCancelException.CANCEL_GENERIC;
                }
                break;
            }
        }
        if (bDone) {
            break;
        }
    }
    return bOverWrite;
}