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

Example 46 with ROI

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

the class VFrap_ROIAssistPanel method createROISourceData.

private void createROISourceData(boolean bNew) throws Exception {
    final ROI oldROI = frapData.getRoi(VFrap_ROISourceData.VFRAP_ROI_ENUM.ROI_CELL.name());
    // new short[oldROI.getISize().getXYZ()];
    short[] roiSourceData = null;
    if (roiSourceComboBox.getSelectedIndex() == 0) {
        // timeAverage
        if (roiTimeAverageDataShort == null) {
            createScaledTimeAverageData();
        }
        roiSourceData = roiTimeAverageDataShort.clone();
    } else {
        final int timeIndex = roiSourceComboBox.getSelectedIndex() - 1;
        roiSourceData = collectAllZAtOneTimepointIntoOneArray(frapData.getImageDataset(), timeIndex);
    }
    scaleDataInPlace(roiSourceData);
    if (spatialEnhanceComboBox.getSelectedIndex() > 0) {
        short[] enhacedBytes = new short[roiSourceData.length];
        int radius = (spatialEnhanceComboBox.getSelectedItem().equals(ENHANCE_AVG_3X3) ? 1 : 0) + (spatialEnhanceComboBox.getSelectedItem().equals(ENHANCE_AVG_5x5) ? 2 : 0) + (spatialEnhanceComboBox.getSelectedItem().equals(ENHANCE_AVG_7x7) ? 3 : 0) + (spatialEnhanceComboBox.getSelectedItem().equals(ENHANCE_MEDIAN_3X3) ? 1 : 0) + (spatialEnhanceComboBox.getSelectedItem().equals(ENHANCE_MEDIAN_5x5) ? 2 : 0);
        int pixelIndex = 0;
        int accum = 0;
        int convSize = (radius * 2 + 1) * (radius * 2 + 1);
        int[] convPixels = new int[convSize];
        for (int z = 0; z < oldROI.getISize().getZ(); z++) {
            int zOffset = z * oldROI.getISize().getX() * oldROI.getISize().getY();
            for (int y = 0; y < oldROI.getISize().getY(); y++) {
                int yoffset = y * oldROI.getISize().getX();
                for (int x = 0; x < oldROI.getISize().getX(); x++) {
                    accum = 0;
                    for (int xbox = -radius; xbox <= radius; xbox++) {
                        for (int ybox = -radius; ybox <= radius; ybox++) {
                            if (x + xbox >= 0 && x + xbox < oldROI.getISize().getX() && y + ybox >= 0 && y + ybox < oldROI.getISize().getY()) {
                                convPixels[accum] = 0x0000FFFF & roiSourceData[zOffset + yoffset + x + xbox + (ybox * oldROI.getISize().getX())];
                            } else {
                                convPixels[accum] = 0x0000FFFF & roiSourceData[zOffset + yoffset + x];
                            }
                            accum++;
                        }
                    }
                    if (spatialEnhanceComboBox.getSelectedItem().equals(ENHANCE_AVG_3X3) || spatialEnhanceComboBox.getSelectedItem().equals(ENHANCE_AVG_5x5) || spatialEnhanceComboBox.getSelectedItem().equals(ENHANCE_AVG_7x7)) {
                        accum = 0;
                        for (int i = 0; i < convPixels.length; i++) {
                            accum += convPixels[i];
                        }
                    } else {
                        Arrays.sort(convPixels);
                        accum = convPixels[convSize / 2] * convSize;
                    }
                    enhacedBytes[pixelIndex] |= ((accum / (convSize)) & 0x0000FFFF);
                    pixelIndex++;
                }
            }
        }
        roiSourceData = enhacedBytes;
    }
    final short[] finalROISourceData = new short[oldROI.getISize().getX() * oldROI.getISize().getY()];
    System.arraycopy(roiSourceData, finalROISourceData.length * overlayEditorPanelJAI.getZ(), finalROISourceData, 0, finalROISourceData.length);
    SwingUtilities.invokeAndWait(new Runnable() {

        public void run() {
            // }});
            try {
                overlayEditorPanelJAI.displaySpecialData(finalROISourceData, oldROI.getISize().getX(), oldROI.getISize().getY());
            } catch (Exception e) {
                throw new RuntimeException("Error displaying TimeAverage data.  " + e.getMessage());
            }
        }
    });
    Integer oldThreshold = (bNew ? null : thresholdSliderIntensityLookup[thresholdSlider.getValue()]);
    lastROISourceDataShort = roiSourceData;
    TreeMap<Integer, Integer> condensedBins = getCondensedBins(lastROISourceDataShort, originalROI.getROIName());
    Integer[] intensityIntegers = condensedBins.keySet().toArray(new Integer[0]);
    thresholdSliderIntensityLookup = new int[intensityIntegers.length];
    for (int i = 0; i < intensityIntegers.length; i++) {
        thresholdSliderIntensityLookup[i] = intensityIntegers[i];
    }
    thresholdSlider.removeChangeListener(processTimepointChangeListener);
    SwingUtilities.invokeAndWait(new Runnable() {

        public void run() {
            // }});
            thresholdSlider.setMaximum(thresholdSliderIntensityLookup.length - 1);
        }
    });
    int newThresholdIndex = thresholdSliderIntensityLookup.length / 2;
    if (bNew) {
        newThresholdIndex = getHistogramIntensityAtHalfPixelCount(condensedBins);
        newThresholdIndex = (originalROI.getROIName().equals(VFrap_ROISourceData.VFRAP_ROI_ENUM.ROI_CELL.name()) ? thresholdSliderIntensityLookup.length - newThresholdIndex - 1 : newThresholdIndex);
    } else {
        for (int i = 0; i < thresholdSliderIntensityLookup.length; i++) {
            if (thresholdSliderIntensityLookup[i] >= oldThreshold) {
                newThresholdIndex = i;
                break;
            }
        }
    }
    final int finalNewThresholdIndex = newThresholdIndex;
    SwingUtilities.invokeAndWait(new Runnable() {

        public void run() {
            // }});
            thresholdSlider.setValue(finalNewThresholdIndex);
            processTimepointChangeListener.stateChanged(null);
        }
    });
    thresholdSlider.addChangeListener(processTimepointChangeListener);
}

Example 47 with ROI

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

the class VFrap_ROIAssistPanel method pickKeepRegionInfoFromCurrentROI.

private RegionInfo pickKeepRegionInfoFromCurrentROI() throws Exception {
    if (lastRegionInfos == null) {
        throw new Exception("No regionInfo to resolve");
    }
    final Vector<RegionInfo> roiRegionInfoV2 = new Vector<RegionInfo>();
    for (int i = 0; i < lastRegionInfos.length; i++) {
        if (lastRegionInfos[i].getPixelValue() == 1) {
            roiRegionInfoV2.add(lastRegionInfos[i]);
        }
    }
    if (roiRegionInfoV2.size() <= 1) {
        throw new Exception("No regionInfo to resolve");
    }
    final RegionInfo[] regionInfoArr = roiRegionInfoV2.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";
    }
    ROI beforeROI = new ROI(frapData.getCurrentlyDisplayedROI());
    int[] resultArr = null;
    // SwingUtilities.invokeAndWait(new Runnable(){public void run(){//}});
    try {
        resultArr = /*DialogUtils.*/
        showComponentOKCancelTableList(this, "Select ROI to Keep", new String[] { "ROI Size (pixel count)" }, rowData, ListSelectionModel.SINGLE_SELECTION, regionInfoArr, beforeROI.getPixelsXYZ());
    } catch (UserCancelException e) {
        resultArr = null;
    }
    // }});
    if (resultArr != null && resultArr.length > 0) {
        return (resultArr == null ? null : regionInfoArr[resultArr[0]]);
    } else {
        // SwingUtilities.invokeAndWait(new Runnable(){public void run(){//}});
        frapData.addReplaceRoi(beforeROI);
        applyROIButton.setEnabled(false);
        resolveROIButton.setEnabled(true);
        fillVoidsButton.setEnabled(false);
    // }});
    }
    return null;
}

Example 48 with ROI

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

the class VFrap_ROIAssistPanel method resolveCurrentROI.

private void resolveCurrentROI(RegionInfo keepRegion) throws Exception {
    short[] removePixels = frapData.getCurrentlyDisplayedROI().getPixelsXYZ();
    for (int i = 0; i < removePixels.length; i++) {
        if (!keepRegion.isIndexInRegion(i)) {
            removePixels[i] = 0;
        }
    }
    final boolean hasInternalVoids = fillVoids(removePixels, true);
    UShortImage ushortImage = new UShortImage(removePixels, frapData.getCurrentlyDisplayedROI().getRoiImages()[0].getOrigin(), frapData.getCurrentlyDisplayedROI().getRoiImages()[0].getExtent(), frapData.getCurrentlyDisplayedROI().getISize().getX(), frapData.getCurrentlyDisplayedROI().getISize().getY(), frapData.getCurrentlyDisplayedROI().getISize().getZ());
    final ROI newCellROI = new ROI(ushortImage, frapData.getCurrentlyDisplayedROI().getROIName());
    SwingUtilities.invokeAndWait(new Runnable() {

        public void run() {
            // }});
            frapData.addReplaceRoi(newCellROI);
            applyROIButton.setEnabled(!hasInternalVoids);
            resolveROIButton.setEnabled(false);
            fillVoidsButton.setEnabled(hasInternalVoids);
        }
    });
}

Example 49 with ROI

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

the class AnnotatedImageDataset method setCurrentlyDisplayedROI.

public void setCurrentlyDisplayedROI(ROI argCurrentlyDisplayedROI, boolean bSave) {
    ROI oldDisplayedROI = this.currentlyDisplayedROI;
    this.currentlyDisplayedROI = argCurrentlyDisplayedROI;
    if (bSave) {
        propertyChangeSupport.firePropertyChange(PROPERTY_CHANGE_CURRENTLY_DISPLAYED_ROI_WITH_SAVE, oldDisplayedROI, currentlyDisplayedROI);
    } else {
        propertyChangeSupport.firePropertyChange(PROPERTY_CHANGE_CURRENTLY_DISPLAYED_ROI_WITHOUT_SAVE, oldDisplayedROI, currentlyDisplayedROI);
    }
}

Example 50 with ROI

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

the class MicroscopyXmlReader method getROI.

/**
 * This method returns a Biomodel object from a XML Element.
 * Creation date: (3/13/2001 12:35:00 PM)
 * @param param org.jdom.Element
 * @return cbit.vcell.biomodel.BioModel
 * @throws XmlParseException
 */
private ROI getROI(Element param) throws XmlParseException {
    String roiName = param.getAttributeValue(MicroscopyXMLTags.ROITypeAttrTag);
    List<Element> ushortImageElementList = param.getChildren(MicroscopyXMLTags.UShortImageTag);
    Iterator<Element> imageElementIter = ushortImageElementList.iterator();
    UShortImage[] images = new UShortImage[ushortImageElementList.size()];
    int imageIndex = 0;
    while (imageElementIter.hasNext()) {
        images[imageIndex++] = getUShortImage(imageElementIter.next());
    }
    ROI roi = new ROI(images, roiName);
    return roi;
}