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Fix --fill-value to use setFillColor(...) API #257

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Fix --fill-value to use setFillColor(...) API #257

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74d643e
Fix `--fill-value` to use setFillColor(...) API
melissalinkert Sep 23, 2024
e3dd7ca
Fix getFillColor() implementation
melissalinkert Sep 30, 2024
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2 changes: 1 addition & 1 deletion src/main/java/com/glencoesoftware/bioformats2raw/BioTekReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -176,7 +176,7 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
{
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);

Arrays.fill(buf, (byte) 0);
Arrays.fill(buf, getFillColor());

BioTekWell well = wells.get(getWellIndex(getSeries()));
String file = well.getFile(getFieldIndex(getSeries()), getZCTCoords(no));
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12 changes: 3 additions & 9 deletions src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
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Expand Up @@ -708,8 +708,7 @@ public void setOverwrite(boolean canOverwrite) {
*/
@Option(
names = "--fill-value",
description = "Default value to fill in for missing tiles (0-255)" +
" (currently .mrxs only)",
description = "Default value to fill in for missing tiles (0-255)",
defaultValue = Option.NULL_VALUE
)
public void setFillValue(Short tileFill) {
Expand Down Expand Up @@ -1251,11 +1250,6 @@ public void convert()
// First find which reader class we need
Class<?> readerClass = getBaseReaderClass();

if (!readerClass.equals(MiraxReader.class) && fillValue != null) {
throw new IllegalArgumentException(
"--fill-value not yet supported for " + readerClass);
}

// Now with our found type instantiate our queue of readers for use
// during conversion
boolean savedMemoFile = false;
Expand All @@ -1264,8 +1258,8 @@ public void convert()
Memoizer memoizer;
try {
reader = (IFormatReader) readerClass.getConstructor().newInstance();
if (fillValue != null && reader instanceof MiraxReader) {
((MiraxReader) reader).setFillValue(fillValue.byteValue());
if (fillValue != null) {
reader.setFillColor(fillValue.byteValue());
}
memoizer = createMemoizer(reader);
}
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4 changes: 2 additions & 2 deletions src/main/java/com/glencoesoftware/bioformats2raw/MetaxpressReader.java
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Expand Up @@ -114,12 +114,12 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
planeReader.openBytes(0, buf, x, y, w, h);
}
catch (IOException e) {
Arrays.fill(buf, (byte) 0);
Arrays.fill(buf, getFillColor());
}
s.stop("openBytes(0) on " + file);
}
else {
Arrays.fill(buf, (byte) 0);
Arrays.fill(buf, getFillColor());
}

return buf;
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17 changes: 12 additions & 5 deletions src/main/java/com/glencoesoftware/bioformats2raw/MiraxReader.java
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Expand Up @@ -131,7 +131,6 @@ public class MiraxReader extends FormatReader {
JPEG2000CodecOptions.getDefaultOptions();

private boolean fluorescence = false;
private Byte fillValue = null;

private transient JPEGXRCodec jpegxrCodec = new JPEGXRCodec();

Expand Down Expand Up @@ -217,7 +216,7 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)

// set background color to black instead of the stored fill color
// this is to match the default behavior of Pannoramic Viewer
Arrays.fill(buf, getFillValue());
Arrays.fill(buf, getFillColor());

if (tileCache == null) {
tileCache = CacheBuilder.newBuilder()
Expand Down Expand Up @@ -1057,9 +1056,10 @@ else if (name.equals("VIMSLIDE_POSITION_BUFFER")) {
* Set the fill value for missing tiles.
*
* @param fill the fill value, or null to use the reader's default value
* @deprecated used setFillColor(Byte)
*/
public void setFillValue(Byte fill) {
fillValue = fill;
setFillColor(fill);
}

/**
Expand All @@ -1069,10 +1069,17 @@ public void setFillValue(Byte fill) {
* for brightfield.
*
* @return fill value for missing tiles
* @deprecated use getFillColor()
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As this is planned for 0.10.0, is there a value in going through a deprecation rather than dropping these in favor of the new API defined upstream?

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I wasn't totally sure what the best approach would be here, so went with deprecating to be on the safer side. If we're all OK with just removing getFillValue() and setFillValue(), I'm fine with that - it would only impact anyone using MiraxReader directly, either by extending the reader or by calling those methods directly.

*/
public byte getFillValue() {
if (fillValue != null) {
return fillValue;
return getFillColor();
}

@Override
public Byte getFillColor() {
Byte color = super.getFillColor();
if (color != null) {
return color;
}
return fluorescence ? (byte) 0 : (byte) 255;
}
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2 changes: 1 addition & 1 deletion src/main/java/com/glencoesoftware/bioformats2raw/ND2PlateReader.java
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Expand Up @@ -90,7 +90,7 @@ public String[] getSeriesUsedFiles(boolean noPixels) {
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException
{
Arrays.fill(buf, (byte) 0);
Arrays.fill(buf, getFillColor());

int fileIndex = getFileIndex(getSeries());
if (fileIndex >= 0 && fileIndex < files.length) {
Expand Down