Example usage for org.opencv.core Mat get

Introduction

In this page you can find the example usage for org.opencv.core Mat get.

Prototype

public double[] get(int row, int col) 

Source Link

Usage

From source file:uk.ac.horizon.artcodes.detect.marker.MarkerDetector.java

License:Open Source License

@Override
public void process(ImageBuffers buffers) {
    final ArrayList<MatOfPoint> contours = new ArrayList<>();
    final Mat hierarchy = new Mat();
    // Make sure the image is rotated before the contours are generated, if necessary
    //if (Feature.get(this.context, R.bool.feature_combined_markers).isEnabled() || outlineDisplay != OutlineDisplay.none || codeDisplay == CodeDisplay.visible)
    //{/*from  www  . j av a  2s  .  c  o m*/
    // if statement commented out as there was a bug where the overlay was not getting cleared
    // after cycling through the threshold views.
    buffers.getOverlay();
    //}
    try {
        final List<Marker> foundMarkers = new ArrayList<>();
        Imgproc.findContours(buffers.getImageInGrey(), contours, hierarchy, Imgproc.RETR_TREE,
                Imgproc.CHAIN_APPROX_NONE);
        for (int i = 0; i < contours.size(); i++) {
            final Marker marker = createMarkerForNode(i, contours, hierarchy);
            if (marker != null) {
                final String markerCode = getCodeKey(marker);
                if (validCodes.isEmpty() || validCodes.contains(markerCode)) {
                    // If this marker has a minimum size set and is smaller: continue in loop.
                    Action action = experience.getActionForCode(markerCode);
                    if (action != null && action.getMinimumSize() != null) {
                        double minimumSize = action.getMinimumSize();
                        Rect boundingRect = Imgproc.boundingRect(contours.get(i));
                        if (!(boundingRect.width / (float) buffers.getImageInAnyFormat().cols() > minimumSize
                                || boundingRect.height
                                        / (float) buffers.getImageInAnyFormat().rows() > minimumSize)) {
                            continue;
                        }
                    }

                    foundMarkers.add(marker);

                    if (outlineDisplay != OutlineDisplay.none) {
                        Mat overlay = buffers.getOverlay();
                        if (outlineDisplay == OutlineDisplay.regions) {
                            double[] nodes = hierarchy.get(0, i);
                            int currentRegionIndex = (int) nodes[FIRST_NODE];

                            while (currentRegionIndex >= 0) {
                                Imgproc.drawContours(overlay, contours, currentRegionIndex, outlineColour, 4);
                                Imgproc.drawContours(overlay, contours, currentRegionIndex, regionColour, 2);

                                nodes = hierarchy.get(0, currentRegionIndex);
                                currentRegionIndex = (int) nodes[NEXT_NODE];
                            }
                        }

                        Imgproc.drawContours(overlay, contours, i, outlineColour, 7);
                        Imgproc.drawContours(overlay, contours, i, detectedColour, 5);
                    }

                    if (codeDisplay == CodeDisplay.visible) {
                        Mat overlay = buffers.getOverlay();
                        Rect bounds = Imgproc.boundingRect(contours.get(i));
                        Imgproc.putText(overlay, markerCode, bounds.tl(), Core.FONT_HERSHEY_SIMPLEX, 1,
                                outlineColour, 5);
                        Imgproc.putText(overlay, markerCode, bounds.tl(), Core.FONT_HERSHEY_SIMPLEX, 1,
                                detectedColour, 3);
                    }
                }
            }
        }

        buffers.setDetected(!foundMarkers.isEmpty());
        handler.onMarkersDetected(foundMarkers, contours, hierarchy, buffers.getImageInGrey().size());
    } finally {
        contours.clear();
        hierarchy.release();
    }
}

---

From source file:uk.ac.horizon.artcodes.detect.marker.MarkerDetector.java

License:Open Source License

protected boolean isValidDot(int nodeIndex, Mat hierarchy) {
    double[] nodes = hierarchy.get(0, nodeIndex);
    return nodes[FIRST_NODE] < 0;
}

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From source file:uk.ac.horizon.artcodes.detect.marker.MarkerDetector.java

License:Open Source License

protected Marker createMarkerForNode(int nodeIndex, List<MatOfPoint> contours, Mat hierarchy) {
    List<MarkerRegion> regions = null;
    for (int currentNodeIndex = (int) hierarchy.get(0,
            nodeIndex)[FIRST_NODE]; currentNodeIndex >= 0; currentNodeIndex = (int) hierarchy.get(0,
                    currentNodeIndex)[NEXT_NODE]) {
        final MarkerRegion region = createRegionForNode(currentNodeIndex, contours, hierarchy);
        if (region != null) {
            if (this.ignoreEmptyRegions && region.value == 0) {
                continue;
            } else if (regions == null) {
                regions = new ArrayList<>();
            } else if (regions.size() >= maxRegions) {
                return null;
            }//from  w w  w.j a  v a 2  s.c  o  m

            regions.add(region);
        } else {
            return null;
        }
    }

    if (regions != null) {
        Marker marker = new Marker(nodeIndex, regions);
        sortCode(marker);
        if (isValidRegionList(marker)) {
            return marker;
        }
    }

    return null;
}

---

From source file:uk.ac.horizon.artcodes.detect.marker.MarkerDetector.java

License:Open Source License

protected MarkerRegion createRegionForNode(int regionIndex, List<MatOfPoint> contours, Mat hierarchy) {
    // Find the first dot index:
    double[] nodes = hierarchy.get(0, regionIndex);
    int currentNodeIndex = (int) nodes[FIRST_NODE];
    if (currentNodeIndex < 0 && !(this.ignoreEmptyRegions || this.maxEmptyRegions > 0)) {
        return null; // There are no dots in this region, and empty regions are not allowed.
    }//from  w  w  w.  ja va 2s. c  o  m

    // Count all the dots and check if they are leaf nodes in the hierarchy:
    int dotCount = 0;
    while (currentNodeIndex >= 0) {
        if (isValidDot(currentNodeIndex, hierarchy)) {
            dotCount++;
            // Get next dot node:
            nodes = hierarchy.get(0, currentNodeIndex);
            currentNodeIndex = (int) nodes[NEXT_NODE];

            if (dotCount > maxRegionValue) {
                // Too many dots
                return null;
            }
        } else {
            // Not a dot
            return null;
        }
    }

    return new MarkerRegion(regionIndex, dotCount);
}

---

From source file:uk.ac.horizon.artcodes.detect.marker.MarkerEmbeddedChecksumAreaOrderDetector.java

License:Open Source License

protected Marker createMarkerForNode(int nodeIndex, List<MatOfPoint> contours, Mat hierarchy) {
    List<MarkerRegion> regions = null;
    MarkerRegion checksumRegion = null;//w w  w .  j  a  v a  2 s.  c  o m
    for (int currentNodeIndex = (int) hierarchy.get(0,
            nodeIndex)[FIRST_NODE]; currentNodeIndex >= 0; currentNodeIndex = (int) hierarchy.get(0,
                    currentNodeIndex)[NEXT_NODE]) {
        final MarkerRegion region = createRegionForNode(currentNodeIndex, contours, hierarchy);
        if (region != null) {
            if (this.ignoreEmptyRegions && region.value == 0) {
                continue;
            } else if (regions == null) {
                regions = new ArrayList<>();
            } else if (regions.size() >= maxRegions) {
                return null;
            }

            regions.add(region);
        } else if (checksumRegion == null) {
            checksumRegion = getChecksumRegionAtNode(currentNodeIndex, hierarchy);
            if (checksumRegion == null) {
                return null;
            }
        } else {
            return null;
        }
    }

    if (regions != null && checksumRegion != null) {
        Marker marker = new MarkerWithEmbeddedChecksum(nodeIndex, regions, checksumRegion);
        sortByValue(marker);
        if (isValidRegionList(marker)) {
            addAreaToRegions(marker, contours);
            sortByArea(marker);
            return marker;
        }
    }

    return null;
}

---

From source file:uk.ac.horizon.artcodes.detect.marker.MarkerEmbeddedChecksumDetector.java

License:Open Source License

protected Marker createMarkerForNode(int nodeIndex, List<MatOfPoint> contours, Mat hierarchy) {
    List<MarkerRegion> regions = null;
    MarkerRegion checksumRegion = null;/*ww  w  .  j a va  2  s  .c o m*/
    for (int currentNodeIndex = (int) hierarchy.get(0,
            nodeIndex)[FIRST_NODE]; currentNodeIndex >= 0; currentNodeIndex = (int) hierarchy.get(0,
                    currentNodeIndex)[NEXT_NODE]) {
        final MarkerRegion region = createRegionForNode(currentNodeIndex, contours, hierarchy);
        if (region != null) {
            if (this.ignoreEmptyRegions && region.value == 0) {
                continue;
            } else if (regions == null) {
                regions = new ArrayList<>();
            } else if (regions.size() >= maxRegions) {
                return null;
            }

            regions.add(region);
        } else if (checksumRegion == null) {
            checksumRegion = getChecksumRegionAtNode(currentNodeIndex, hierarchy);
            if (checksumRegion == null) {
                return null;
            }
        } else {
            return null;
        }
    }

    if (regions != null) {
        Marker marker = new MarkerWithEmbeddedChecksum(nodeIndex, regions, checksumRegion);
        sortCode(marker);
        if (isValidRegionList(marker)) {
            return marker;
        }
    }

    return null;
}

---

From source file:uk.ac.horizon.artcodes.detect.marker.MarkerEmbeddedChecksumDetector.java

License:Open Source License

protected MarkerRegion getChecksumRegionAtNode(int regionIndex, Mat hierarchy) {
    // Find the first dot index:
    double[] nodes = hierarchy.get(0, regionIndex);
    int currentDotIndex = (int) nodes[FIRST_NODE];
    if (currentDotIndex < 0) {
        return null; // There are no dots in this region.
    }//from ww  w  .ja  va 2  s.c o  m

    // Count all the dots and check if they are leaf nodes in the hierarchy:
    int dotCount = 0;
    while (currentDotIndex >= 0) {
        if (isValidHollowDot(currentDotIndex, hierarchy)) {
            dotCount++;
        } else if (!(this.relaxedEmbeddedChecksumIgnoreNonHollowDots
                && this.isValidDot(currentDotIndex, hierarchy))) {
            return null; // Dot is not a leaf in the hierarchy.
        }

        // Get next dot node:
        nodes = hierarchy.get(0, currentDotIndex);
        currentDotIndex = (int) nodes[NEXT_NODE];
    }

    return new MarkerRegion(regionIndex, dotCount);
}

---

From source file:uk.ac.horizon.artcodes.detect.marker.MarkerEmbeddedChecksumDetector.java

License:Open Source License

private boolean isValidHollowDot(int nodeIndex, Mat hierarchy) {
    double[] nodes = hierarchy.get(0, nodeIndex);
    return nodes[FIRST_NODE] >= 0 && // has a child node, and
            (hierarchy.get(0, (int) nodes[FIRST_NODE])[NEXT_NODE] < 0
                    || this.relaxedEmbeddedChecksumIgnoreMultipleHollowSegments)
            && //the child has no siblings, and
            isValidDot((int) nodes[FIRST_NODE], hierarchy);// the child is a leaf
}

---

From source file:uom.research.thalassemia.logic.BloodCellData.java

private void process(final Mat currentSelection) {
    sgf = 0;//from   w  w w  .  j  a  va 2 s . c o  m
    getMinMaxDiameter(currentSelection);
    if (minDiameter != 0) {
        //calculate shape geometric factor
        sgf = maxDiameter / minDiameter;
    }
    double[] circles;

    for (int a = 0; a < currentSelection.cols(); a++) {

        Map<Point, Double> points = getPallorBloodCellsPointList();
        areaPreparation = 0;
        circles = currentSelection.get(0, a);
        x = circles[0];
        y = circles[1];
        r = Math.round(circles[2]);

        //get area value
        area = calculateArea(r);
        //get perimeter value
        perimeter = calculatePerimeter(r);
        //get diameter value
        diameter = calculateDiameter(area, perimeter);
        // calculate deviational value
        deviationValue = sgf / area;

        Point point = new Point(x, y);
        if (points.containsKey(point)) {
            areaPreparation = calculateArea(points.get(point)) / area;
        }
        getAbnormalCellTypes();
    }
}

---

From source file:uom.research.thalassemia.logic.BloodCellData.java

/**
 * get min and max diameters./*from  w  w  w  .ja v a  2s  .c  o m*/
 *
 * @param currentSelection currentSelection of Mat
 */
private void getMinMaxDiameter(final Mat currentSelection) {
    double[] circles;
    List<Double> diameters = new ArrayList<>();
    double r, diameter;
    for (int a = 0; a < currentSelection.cols(); a++) {
        circles = currentSelection.get(0, a);
        r = Math.round(circles[2]);
        diameter = calculateDiameter(r);
        diameters.add(diameter);
    }
    if (diameters.size() > 1) {
        diameters.sort(null);
    }
    minDiameter = diameters.get(0);
    maxDiameter = diameters.get(diameters.size() - 1);
}

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