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Add planeInfo=true support to FakeReader (rebased onto develop) #806

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merged 3 commits into from
Nov 25, 2013
Merged

Add planeInfo=true support to FakeReader (rebased onto develop) #806

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db2f716
Add planeInfo=true support to FakeReader
joshmoore Nov 19, 2013
0de8987
Replace planeInfo by exposureTime
joshmoore Nov 21, 2013
c69295b
Remove invalid 'planeInfo' line from rebase
joshmoore Nov 25, 2013
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23 changes: 21 additions & 2 deletions components/scifio/src/loci/formats/in/FakeReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -108,6 +108,9 @@ public class FakeReader extends FormatReader {

// -- Fields --

/** exposure time per plane info */
private Float exposureTime = null;

/** Scale factor for gradient, if any. */
private double scaleFactor = 1;

Expand Down Expand Up @@ -463,6 +466,8 @@ else if (key.equals("pixelType")) {
else if (key.equals("series")) seriesCount = intValue;
else if (key.equals("lutLength")) lutLength = intValue;
else if (key.equals("scaleFactor")) scaleFactor = doubleValue;
else if (key.equals("exposureTime")) exposureTime = (float) doubleValue;
else if (key.equals("planeInfo")) planeInfo = boolValue;
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This line needs to be removed, as it causes a compile error.

else if (key.equals("plates")) plates = intValue;
else if (key.equals("plateRows")) plateRows = intValue;
else if (key.equals("plateCols")) plateCols = intValue;
Expand Down Expand Up @@ -550,7 +555,9 @@ else if (key.equals("color")) {
}

// populate OME metadata
MetadataTools.populatePixels(store, this);
boolean planeInfo = (exposureTime != null);
MetadataTools.populatePixels(store, this, planeInfo);
fillExposureTime(store);
for (int s=0; s<seriesCount; s++) {
String imageName = s > 0 ? name + " " + (s + 1) : name;
store.setImageName(imageName, s);
Expand Down Expand Up @@ -596,7 +603,19 @@ else if (pixelType == FormatTools.UINT16) {
}
}

// -- Helper methods --
private void fillExposureTime(MetadataStore store) {
if (exposureTime == null) return;
int oldSeries = getSeries();
for (int s=0; s<getSeriesCount(); s++) {
setSeries(s);
for (int i=0; i<getImageCount(); i++) {
store.setPlaneExposureTime(exposureTime.doubleValue(), s, i);
}
setSeries(oldSeries);
}
}

// -- Helper methods --

private String[] extractTokensFromFakeSeries(String path) {
List<String> tokens = new ArrayList<String>();
Expand Down