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TIFFFormat: correct calibration data
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Was mistakenly populating private fields in the Metadata instead of
putting calibration values on the actual CalibratedAxes.

Removed the superfluous fields and accessors. The TIFFFormat$Metadata
axes should now have their x/y/z calibration values populated correctly.
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@hinerm
hinerm committed Dec 26, 2013
1 parent 8681733 commit 232261b
Showing 1 changed file with 14 additions and 57 deletions.
71 changes: 14 additions & 57 deletions scifio/src/main/java/io/scif/formats/TIFFFormat.java
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Expand Up @@ -117,13 +117,10 @@ public static class Metadata extends MinimalTIFFFormat.Metadata {
private String experimenterLastName;
private String experimenterEmail;
private String imageDescription;
private double physicalSizeX;
private double physicalSizeY;

private String companionFile;
private String description;
private String calibrationUnit;
private Double physicalSizeZ;
private Double timeIncrement;
private Integer xOrigin, yOrigin;

Expand Down Expand Up @@ -153,14 +150,6 @@ public void setCalibrationUnit(final String calibrationUnit) {
this.calibrationUnit = calibrationUnit;
}

public Double getPhysicalSizeZ() {
return physicalSizeZ == null ? 1.0 : physicalSizeZ;
}

public void setPhysicalSizeZ(final Double physicalSizeZ) {
this.physicalSizeZ = physicalSizeZ;
}

public Double getTimeIncrement() {
return timeIncrement == null ? 1.0 : timeIncrement;
}
Expand Down Expand Up @@ -225,22 +214,6 @@ public void setImageDescription(final String imageDescription) {
this.imageDescription = imageDescription;
}

public double getPhysicalSizeX() {
return physicalSizeX;
}

public void setPhysicalSizeX(final double physicalSizeX) {
this.physicalSizeX = physicalSizeX;
}

public double getPhysicalSizeY() {
return physicalSizeY;
}

public void setPhysicalSizeY(final double physicalSizeY) {
this.physicalSizeY = physicalSizeY;
}

// -- Metadata API Methods --

@Override
Expand All @@ -265,7 +238,6 @@ public void close(final boolean fileOnly) throws IOException {
companionFile = null;
description = null;
calibrationUnit = null;
physicalSizeZ = null;
timeIncrement = null;
xOrigin = null;
yOrigin = null;
Expand Down Expand Up @@ -407,7 +379,6 @@ protected void initMetadataStore(final Metadata meta)
// if (meta.getDescription() != null) {
// store.setImageDescription(description, 0);
// }
populateMetadataStoreImageJ(meta);
}

// -- Helper methods --
Expand Down Expand Up @@ -469,8 +440,16 @@ else if (token.startsWith("finterval=")) {
put("Frame Interval", meta.getTimeIncrement());
}
else if (token.startsWith("spacing=")) {
meta.setPhysicalSizeZ(parseDouble(value));
put("Spacing", meta.getPhysicalSizeZ());
final double physicalSizeZ = parseDouble(value);
if (physicalSizeZ >= 0) {
if (meta.get(0).getAxis(Axes.Z) == null) {
meta.get(0).addAxis(Axes.Z, 1);
}

FormatTools
.calibrate(meta.get(0).getAxis(Axes.Z), physicalSizeZ, 0);
}
put("Spacing", physicalSizeZ);
}
else if (token.startsWith("xorigin=")) {
meta.setxOrigin(parseInt(value));
Expand Down Expand Up @@ -583,28 +562,6 @@ else if (z * t == ifds.size()) {
m.setAxes(validAxes.toArray(new CalibratedAxis[validAxes.size()]));
}

/**
* Checks the original metadata table for ImageJ-specific information to
* propagate into the metadata store.
*/
private void populateMetadataStoreImageJ(final Metadata meta) {
// TODO: Perhaps we should only populate the physical Z size if the unit
// is
// a known, physical quantity such as "micron" rather than "pixel".
// e.g.: if (calibrationUnit.equals("micron"))
if (meta.getPhysicalSizeZ() != null) {
double zDepth = meta.getPhysicalSizeZ();
if (zDepth < 0) zDepth = -zDepth;
if (zDepth > 0) {
meta.setPhysicalSizeZ(zDepth);
}
else {
log()
.warn("Expected positive value for PhysicalSizeZ; got " + zDepth);
}
}
}

private void
parseCommentMetamorph(final Metadata meta, final String comment)
{
Expand Down Expand Up @@ -1050,13 +1007,13 @@ protected void initMetadataStore(final Metadata meta)
final double pixY = firstIFD.getYResolution();

if (pixX > 0 && pixX < Double.POSITIVE_INFINITY) {
meta.setPhysicalSizeX(pixX);
FormatTools.calibrate(meta.get(0).getAxis(Axes.X), pixX, 0);
}
else {
log().warn("Expected positive value for PhysicalSizeX; got " + pixX);
}
if (pixY > 0 && pixX < Double.POSITIVE_INFINITY) {
meta.setPhysicalSizeY(pixY);
FormatTools.calibrate(meta.get(0).getAxis(Axes.Y), pixY, 0);
}
else {
log().warn("Expected positive value for PhysicalSizeY; got " + pixY);
Expand Down Expand Up @@ -1437,13 +1394,13 @@ private long prepareToWriteImage(final int imageIndex, final long planeIndex,
ifd.put(new Integer(IFD.IMAGE_WIDTH), new Long(width));
ifd.put(new Integer(IFD.IMAGE_LENGTH), new Long(height));

Double physicalSizeX = meta.getPhysicalSizeX();
Double physicalSizeX = meta.get(0).getAxis(Axes.X).averageScale(0, 1);
if (physicalSizeX == null || physicalSizeX.doubleValue() == 0) {
physicalSizeX = 0d;
}
else physicalSizeX = 1d / physicalSizeX;

Double physicalSizeY = meta.getPhysicalSizeY();
Double physicalSizeY = meta.get(0).getAxis(Axes.Y).averageScale(0, 1);
if (physicalSizeY == null || physicalSizeY.doubleValue() == 0) {
physicalSizeY = 0d;
}
Expand Down

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