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Imaris HDF: allow paths to be in a subdirectory #4421

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Imaris HDF: allow paths to be in a subdirectory #4421

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ce304f9
Imaris HDF: allow paths to be in a subdirectory
melissalinkert Mar 23, 2026
b417b7b
Use `ImarisDataSet` attribute to determine path to image data
melissalinkert Mar 25, 2026
c0e8d88
Simplify plane path retrieval
melissalinkert Mar 26, 2026
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57 changes: 40 additions & 17 deletions components/formats-gpl/src/loci/formats/in/ImarisHDFReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,7 @@ public class ImarisHDFReader extends SubResolutionFormatReader {

// -- Fields --

private String pathPrefix = "";
private double pixelSizeX, pixelSizeY, pixelSizeZ;
private double minX, minY, minZ, maxX, maxY, maxZ;
private int seriesCount;
Expand Down Expand Up @@ -229,6 +230,7 @@ else if (image instanceof double[][]) {
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
pathPrefix = "";
seriesCount = 0;
pixelSizeX = pixelSizeY = pixelSizeZ = 0;
minX = minY = minZ = maxX = maxY = maxZ = 0;
Expand Down Expand Up @@ -287,8 +289,7 @@ protected void initFile(String id) throws FormatException, IOException {
if (seriesCount > 1) {
for (int i=1; i<seriesCount; i++) {
CoreMetadata ms = new CoreMetadata();
String groupPath =
"DataSet/ResolutionLevel_" + i + "/TimePoint_0/Channel_0";
String groupPath = getPlanePath(i, 0, 0);
ms.sizeX =
Integer.parseInt(netcdf.getAttributeValue(groupPath + "/ImageSizeX"));
ms.sizeY =
Expand Down Expand Up @@ -317,13 +318,13 @@ protected void initFile(String id) throws FormatException, IOException {
// read block sizes for caching
blockSizeZPerResolution = new int[seriesCount];
for (int res = 0; res < seriesCount; res++) {
String datasetPath = "DataSet/ResolutionLevel_" + res + "/TimePoint_0/Channel_0/Data";
String datasetPath = getPlaneDataPath(res, 0, 0);
Hashtable<String, Object> table = netcdf.getVariableAttributes(datasetPath);
String chunkSizesString = (String) table.get("_ChunkSizes");
String[] sizes = chunkSizesString.split(" ");
blockSizeZPerResolution[res] = Integer.parseInt(sizes[0]);
}

// determine pixel type - this isn't stored in the metadata, so we need
// to check the pixels themselves

Expand Down Expand Up @@ -492,7 +493,8 @@ private Object getImageData(int no, int x, int y, int width, int height)

// cache dataset blocks to avoid multiple reads.
// use caching for 3D datasets and only if the size of the required buffer is < maxBufferSize
if (getSizeZ() > 1 && getSizeX() * getSizeY() * blockSizeZPerResolution[resolutionIndex] * getSizeC() * FormatTools.getBytesPerPixel(getPixelType()) < maxBufferSize) {
long blockSize = (long) getSizeX() * getSizeY() * blockSizeZPerResolution[resolutionIndex] * getSizeC() * FormatTools.getBytesPerPixel(getPixelType());
if (getSizeZ() > 1 && blockSize < maxBufferSize) {
// update buffer if needed
if (zct[0] < lastMinZ || zct[0] > lastMaxZ || zct[2] != lastT || resolutionIndex != lastRes || buffer == null) {
buffer = new Object[getSizeC()];
Expand All @@ -510,7 +512,7 @@ private Object getImageData(int no, int x, int y, int width, int height)
try {
String path;
for (int ch = 0; ch < getSizeC(); ch++) {
path = "/DataSet/ResolutionLevel_" + resolutionIndex + "/TimePoint_" + zct[2] + "/Channel_" + ch + "/Data";
path = getPlaneDataPath(resolutionIndex, zct[2], ch);
buffer[ch] = netcdf.getArray(path, idcs, dims);
}
}
Expand Down Expand Up @@ -568,14 +570,14 @@ else if (buffer[zct[1]] instanceof float[][][]) {
int[] dimensions = new int[] {1, height, width};
int[] indices = new int[] {zct[0], y, x};
try {
String path = "/DataSet/ResolutionLevel_" + resolutionIndex + "/TimePoint_" + zct[2] + "/Channel_" + zct[1] + "/Data";
String path = getPlaneDataPath(resolutionIndex, zct[2], zct[1]);
image = netcdf.getArray(path, indices, dimensions);
}
catch (ServiceException e) {
throw new FormatException(e);
}
}

return image;
}

Expand All @@ -587,7 +589,7 @@ private Object getSampleData()
int[] dimensions = new int[] {1, 2, 2};
int[] indices = new int[] {0, 0, 0};
try {
String path = "/DataSet/ResolutionLevel_" + resolutionIndex + "/TimePoint_0/Channel_0/Data";
String path = getPlaneDataPath(resolutionIndex, 0, 0);
image = netcdf.getArray(path, indices, dimensions);
}
catch (ServiceException e) {
Expand All @@ -607,23 +609,27 @@ private void parseAttributes() {
if (value == null) continue;
value = value.trim();

if (name.equals("X") || (attr.startsWith("DataSet/ResolutionLevel_0") && name.equals("ImageSizeX"))) {
if (name.equals("ImarisDataSet")) {
pathPrefix = attr.substring(0, attr.lastIndexOf("/"));
LOGGER.debug("Set path prefix to {}", pathPrefix);
}
else if (name.equals("X") || (attr.startsWith(getPath("DataSet/ResolutionLevel_0")) && name.equals("ImageSizeX"))) {
try {
ms0.sizeX = Integer.parseInt(value);
}
catch (NumberFormatException e) {
LOGGER.trace("Failed to parse '" + name + "'", e);
}
}
else if (name.equals("Y") || (attr.startsWith("DataSet/ResolutionLevel_0") && name.equals("ImageSizeY"))) {
else if (name.equals("Y") || (attr.startsWith(getPath("DataSet/ResolutionLevel_0")) && name.equals("ImageSizeY"))) {
try {
ms0.sizeY = Integer.parseInt(value);
}
catch (NumberFormatException e) {
LOGGER.trace("Failed to parse '" + name + "'", e);
}
}
else if (name.equals("Z") || (attr.startsWith("DataSet/ResolutionLevel_0") && name.equals("ImageSizeZ"))) {
else if (name.equals("Z") || (attr.startsWith(getPath("DataSet/ResolutionLevel_0")) && name.equals("ImageSizeZ"))) {
try {
ms0.sizeZ = Integer.parseInt(value);
}
Expand Down Expand Up @@ -653,14 +659,16 @@ else if (name.equals("RecordingEntryPlaneSpacing")) {
else if (name.equals("ExtMin1")) minY = Double.parseDouble(value);
else if (name.equals("ExtMin2")) minZ = Double.parseDouble(value);

if (attr.startsWith("DataSet/ResolutionLevel_")) {
int slash = attr.indexOf("/", 24);
int n = Integer.parseInt(attr.substring(24, slash == -1 ?
attr.length() : slash));
String resolutionCheck = getPath("DataSet/ResolutionLevel_");
if (attr.startsWith(resolutionCheck)) {
int slash = attr.indexOf("/", resolutionCheck.length());
String resIndex = attr.substring(resolutionCheck.length(),
slash == -1 ? attr.length() : slash);
int n = Integer.parseInt(resIndex);
if (n >= seriesCount) seriesCount = n + 1;
}

if (attr.startsWith("DataSetInfo/Channel_")) {
if (attr.startsWith(getPath("DataSetInfo/Channel_"))) {
String originalValue = value;
for (String d : DELIMITERS) {
if (value.indexOf(d) != -1) {
Expand Down Expand Up @@ -724,4 +732,19 @@ private void addValue(List l, Object value, int index) {
}
}

private String getPlanePath(int res, int t, int c) {
return getPath("DataSet/ResolutionLevel_" + res + "/TimePoint_" + t + "/Channel_" + c);
}

private String getPlaneDataPath(int res, int t, int c) {
return getPlanePath(res, t, c) + "/Data";
}

private String getPath(String path) {
if (pathPrefix.isEmpty()) {
return path;
}
return pathPrefix + "/" + path;
}

}
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