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SVS: check for label/macro instead of assuming they exist #3733

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merged 3 commits into from
Nov 24, 2021
Merged

SVS: check for label/macro instead of assuming they exist #3733

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758a5f9
SVS: check for label/macro instead of assuming they exist
melissalinkert Aug 10, 2021
d8fbb9a
Fix label/macro comment detection
melissalinkert Nov 23, 2021
cc1112f
Fix remaining places where SVS label/macro images are assumed to exist
melissalinkert Nov 23, 2021
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78 changes: 48 additions & 30 deletions components/formats-gpl/src/loci/formats/in/SVSReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -90,6 +90,9 @@ public class SVSReader extends BaseTiffReader {
private ArrayList<String> dyeNames = new ArrayList<String>();

private transient Color displayColor = null;
private int labelIndex = -1;
private int macroIndex = -1;
private int extraImages = 0;

// -- Constructor --

Expand Down Expand Up @@ -181,11 +184,11 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
/* @see loci.formats.IFormatReader#openThumbBytes(int) */
@Override
public byte[] openThumbBytes(int no) throws FormatException, IOException {
if (core.size() == 1 || getSeries() >= getSeriesCount() - 2) {
return super.openThumbBytes(no);
if (core.size() == 1 || getSeries() >= getSeriesCount() - extraImages) {
return FormatTools.openThumbBytes(this, no);
}

int smallestSeries = getSeriesCount() - 3;
int smallestSeries = getSeriesCount() - extraImages - 1;
if (smallestSeries >= 0) {
int thisSeries = getSeries();
int resolution = getResolution();
Expand Down Expand Up @@ -218,6 +221,9 @@ public void close(boolean fileOnly) throws IOException {
time = null;
dyeNames.clear();
displayColor = null;
extraImages = 0;
labelIndex = -1;
macroIndex = -1;
}
}

Expand Down Expand Up @@ -279,6 +285,7 @@ protected void initStandardMetadata() throws FormatException, IOException {
if (comment == null) {
continue;
}
comments[i] = comment;
String[] lines = comment.split("\n");
String[] tokens;
String key, value;
Expand All @@ -295,6 +302,12 @@ else if (key.equals("OffsetZ")) {
zPosition[index] = DataTools.parseDouble(value);
}
}
else if (t.toLowerCase().indexOf("label") >= 0) {
labelIndex = i;
}
else if (t.toLowerCase().indexOf("macro") >= 0) {
macroIndex = i;
}
}
}
if (zPosition[index] != null) {
Expand All @@ -303,11 +316,23 @@ else if (key.equals("OffsetZ")) {
}
setSeries(0);

// based on whether label and/or macro are present,
// determine how many resolutions in pyramid

int resolutions = getSeriesCount();
if (labelIndex >= 0) {
resolutions--;
}
if (macroIndex >= 0) {
resolutions--;
}
extraImages = getSeriesCount() - resolutions;

// repopulate core metadata

// remove any invalid pyramid resolutions
IFD firstIFD = ifds.get(getIFDIndex(0, 0));
for (int s=1; s<getSeriesCount() - 2; s++) {
for (int s=1; s<resolutions; s++) {
int index = getIFDIndex(s, 0);
IFD ifd = ifds.get(index);
tiffParser.fillInIFD(ifd);
Expand All @@ -328,16 +353,17 @@ else if (key.equals("OffsetZ")) {
}
zPosition = uniqueZ.toArray(new Double[uniqueZ.size()]);
Arrays.sort(zPosition);
seriesCount = ((ifds.size() - 2) / uniqueZ.size()) + 2;
seriesCount = ((ifds.size() - extraImages) / uniqueZ.size()) + extraImages;

core.clear();
if (seriesCount > 2) {
if (seriesCount > extraImages) {
core.add();
for (int r=0; r < seriesCount - 2; r++) {
for (int r=0; r < seriesCount - extraImages; r++) {
core.add(0, new SVSCoreMetadata());
}
core.add(new SVSCoreMetadata());
core.add(new SVSCoreMetadata());
for (int extra=0; extra<extraImages; extra++) {
core.add(new SVSCoreMetadata());
}
}
else {
// Should never happen unless the SVS is corrupt?
Expand All @@ -352,8 +378,8 @@ else if (key.equals("OffsetZ")) {

SVSCoreMetadata ms = (SVSCoreMetadata) core.get(pos[0], pos[1]);

if (s == 0 && seriesCount > 2) {
ms.resolutionCount = seriesCount - 2;
if (s == 0 && seriesCount > extraImages) {
ms.resolutionCount = seriesCount - extraImages;
}

IFD ifd = ifds.get(getIFDIndex(s, 0));
Expand All @@ -364,7 +390,7 @@ else if (key.equals("OffsetZ")) {

ms.sizeX = (int) ifd.getImageWidth();
ms.sizeY = (int) ifd.getImageLength();
if (s < seriesCount - 2) {
if (s < seriesCount - extraImages) {
ms.sizeZ = uniqueZ.size();
}
else {
Expand Down Expand Up @@ -472,26 +498,18 @@ protected void initMetadataStore() throws FormatException {
store.setImageInstrumentRef(instrument, i);
store.setObjectiveSettingsID(objective, i);

if (hasFlattenedResolutions() || i > 2) {
if (hasFlattenedResolutions() || i > extraImages) {
store.setImageName("Series " + (i + 1), i);
}
else {
switch (i) {
case 0:
store.setImageName("", i);
break;
case 1:
// if there are only two images, assume that there is no label
if (lastImage == 1) {
store.setImageName("macro image", i);
}
else {
store.setImageName("label image", i);
}
break;
case 2:
store.setImageName("macro image", i);
break;
if (i == 0) {
store.setImageName("", i);
}
else if (i == labelIndex) {
store.setImageName("label image", i);
}
else if (i == macroIndex) {
store.setImageName("macro image", i);
}
}
String comment = ((SVSCoreMetadata) getCurrentCore()).comment;
Expand Down Expand Up @@ -538,7 +556,7 @@ protected void initMetadataStore() throws FormatException {

private int getIFDIndex(int coreIndex, int no) {
int index = coreIndex;
int coreCount = core.flattenedSize() - 2;
int coreCount = core.flattenedSize() - extraImages;
if (coreIndex > 0 && coreIndex < coreCount) {
if (core.get(0, 0).imageCount > 1) {
index++;
Expand Down