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Added reader for TIFFs produced by Nikon Elements. Closes #529.
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@melissalinkert
melissalinkert committed Aug 19, 2010
1 parent d7b5a3a commit d171869
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Showing 5 changed files with 314 additions and 39 deletions.
74 changes: 73 additions & 1 deletion components/bio-formats/src/loci/formats/in/ND2Handler.java
View file
Expand Up @@ -27,9 +27,15 @@
import java.util.ArrayList;
import java.util.Hashtable;

import loci.common.DateTools;
import loci.formats.CoreMetadata;
import loci.formats.FormatException;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.meta.MetadataStore;

import ome.xml.model.primitives.NonNegativeInteger;
import ome.xml.model.primitives.PositiveInteger;

import org.xml.sax.Attributes;
import org.xml.sax.helpers.DefaultHandler;
Expand All @@ -43,6 +49,10 @@
*/
public class ND2Handler extends DefaultHandler {

// -- Constants --

private static final String DATE_FORMAT = "dd/MM/yyyy HH:mm:ss";

// -- Fields --

private String prefix = null;
Expand Down Expand Up @@ -80,6 +90,7 @@ public class ND2Handler extends DefaultHandler {

private String cameraModel;
private int fieldIndex = 0;
private String date;

// -- Constructor --

Expand All @@ -90,6 +101,56 @@ public ND2Handler(CoreMetadata[] core) {

// -- ND2Handler API methods --

public void populateROIs(MetadataStore store) {
for (int r=0; r<rois.size(); r++) {
Hashtable<String, String> roi = rois.get(r);
String type = roi.get("ROIType");

if (type.equals("Text")) {
store.setROIID(MetadataTools.createLSID("ROI", r), r);
store.setTextID(MetadataTools.createLSID("Shape", r, 0), r, 0);
store.setTextFontSize(
NonNegativeInteger.valueOf(roi.get("fHeight")), r, 0);
store.setTextValue(roi.get("eval-text"), r, 0);
store.setTextStrokeWidth(new Double(roi.get("line-width")), r, 0);

String rectangle = roi.get("rectangle");
String[] p = rectangle.split(",");
double[] points = new double[p.length];
for (int i=0; i<p.length; i++) {
points[i] = Double.parseDouble(p[i]);
}

store.setRectangleID(MetadataTools.createLSID("Shape", r, 1), r, 1);
store.setRectangleX(points[0], r, 1);
store.setRectangleY(points[1], r, 1);
store.setRectangleWidth(points[2] - points[0], r, 1);
store.setRectangleHeight(points[3] - points[1], r, 1);
}
else if (type.equals("HorizontalLine") || type.equals("VerticalLine")) {
store.setROIID(MetadataTools.createLSID("ROI", r), r);

String segments = roi.get("segments");
segments = segments.replaceAll("\\[\\]", "");
String[] points = segments.split("\\)");

StringBuffer sb = new StringBuffer();
for (int i=0; i<points.length; i++) {
points[i] = points[i].substring(points[i].indexOf(":") + 1);
sb.append(points[i]);
if (i < points.length - 1) sb.append(" ");
}

store.setPolylineID(MetadataTools.createLSID("Shape", r, 0), r, 0);
store.setPolylinePoints(sb.toString(), r, 0);
}
}
}

public String getDate() {
return date;
}

public Hashtable<String, Object> getMetadata() {
return metadata;
}
Expand Down Expand Up @@ -339,7 +400,9 @@ else if (key.endsWith("dObjectiveNA")) {
else if (key.endsWith("dRefractIndex1")) {
refractiveIndex = new Double(sanitizeDouble(value));
}
else if (key.equals("sObjective") || key.equals("wsObjectiveName")) {
else if (key.equals("sObjective") || key.equals("wsObjectiveName") ||
key.equals("sOptics"))
{
String[] tokens = value.split(" ");
int magIndex = -1;
for (int i=0; i<tokens.length; i++) {
Expand Down Expand Up @@ -536,6 +599,15 @@ else if (v.length > 1) {
}
}
}
else if (key.equals("CameraUniqueName")) {
cameraModel = value;
}
else if (key.equals("ExposureTime")) {
exposureTime.add(new Double(value) / 1000d);
}
else if (key.equals("sDate")) {
date = DateTools.formatDate(value, DATE_FORMAT);
}
}

private String sanitizeDouble(String value) {
Expand Down
38 changes: 1 addition & 37 deletions components/bio-formats/src/loci/formats/in/NativeND2Reader.java
View file
Expand Up @@ -969,43 +969,7 @@ private void populateMetadataStore(ND2Handler handler) throws FormatException
if (getMetadataOptions().getMetadataLevel() == MetadataLevel.NO_OVERLAYS) {
return;
}
for (int r=0; r<rois.size(); r++) {
Hashtable<String, String> roi = rois.get(r);
String type = roi.get("ROIType");

if (type.equals("Text")) {
store.setTextFontSize(
NonNegativeInteger.valueOf(roi.get("fHeight")), r, 0);
store.setTextValue(roi.get("eval-text"), r, 0);
store.setTextStrokeWidth(new Double(roi.get("line-width")), r, 0);

String rectangle = roi.get("rectangle");
String[] p = rectangle.split(",");
double[] points = new double[p.length];
for (int i=0; i<p.length; i++) {
points[i] = Double.parseDouble(p[i]);
}

store.setRectangleX(points[0], r, 1);
store.setRectangleY(points[1], r, 1);
store.setRectangleWidth(points[2] - points[0], r, 1);
store.setRectangleHeight(points[3] - points[1], r, 1);
}
else if (type.equals("HorizontalLine") || type.equals("VerticalLine")) {
String segments = roi.get("segments");
segments = segments.replaceAll("\\[", "");
segments = segments.replaceAll("\\]", "");
String[] points = segments.split("\\)");

StringBuffer sb = new StringBuffer();
for (int i=0; i<points.length; i++) {
points[i] = points[i].substring(points[i].indexOf(":") + 1);
sb.append(points[i]);
if (i < points.length - 1) sb.append(" ");
}
store.setPolylinePoints(sb.toString(), r, 0);
}
}
handler.populateROIs(store);
}

private Codec createCodec(boolean isJPEG) {
Expand Down

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