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VSI: surface CALIBRATION lookup table as named slope/origin/final keys #4427

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Merged
melissalinkert merged 2 commits into from
Jul 21, 2026
+32 −0
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VSI: surface CALIBRATION lookup table as named slope/origin/final keys #4427

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VSI: surface CALIBRATION lookup table as named slope/origin/final keys
PEEKPerformer Apr 28, 2026
1676a74
CellSensReader: use Constants.EPSILON instead of != for float comparison
PEEKPerformer Jul 18, 2026
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32 changes: 32 additions & 0 deletions components/formats-gpl/src/loci/formats/in/CellSensReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@
import java.util.Hashtable;

import loci.common.ByteArrayHandle;
import loci.common.Constants;
import loci.common.DataTools;
import loci.common.DateTools;
import loci.common.Location;
Expand Down Expand Up @@ -1862,6 +1863,37 @@ else if (tag == RWC_FRAME_ORIGIN) {
pyramid.originY = doubleValues[1];
}
}
else if (tag == VALUE
&& "Calibration Function ".equals(tagPrefix)
&& realType == DOUBLE_2
&& nDoubleValues >= 4
&& (nDoubleValues % 2) == 0)
{
// Tag 20051 (CALIBRATION) sub-volumes carry a piecewise-
// linear lookup table mapping a raw axis (e.g. uint16
// pixel value) to a calibrated axis (e.g. Z position in
// micrometres for DSX EFI height maps, or intensity in
// counts for deconvolved fluorescence images). The LUT
// is stored as (raw, calibrated) DOUBLE_2 pairs and is
// linear, so a single (slope, origin) suffices to
// reconstruct the mapping. Surface those summary values
// as named metadata so downstream tools can convert
// pixel values to calibrated units without reparsing
// the full table from a long string.
int nPairs = nDoubleValues / 2;
double rawFirst = doubleValues[0];
double calFirst = doubleValues[1];
double rawLast = doubleValues[2 * (nPairs - 1)];
double calLast = doubleValues[2 * (nPairs - 1) + 1];
double dRaw = rawLast - rawFirst;
if (Math.abs(dRaw) > Constants.EPSILON) {
double slope = (calLast - calFirst) / dRaw;
addGlobalMeta("Calibration Function Slope", slope);
addGlobalMeta("Calibration Function Origin", calFirst);
addGlobalMeta("Calibration Function Final", calLast);
addGlobalMeta("Calibration Function NPoints", nPairs);
}
}
break;
case RGB:
int red = vsi.read();
Expand Down
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