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ZarrReader: Update to support 0.4.0 datasets #8

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merged 10 commits into from
Mar 14, 2022
Merged

ZarrReader: Update to support 0.4.0 datasets #8

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f214a66
ZarrReader: Update to support 0.3.0 datasets
dgault Sep 29, 2021
c5aad70
Merge 'origin/main' into pr-8
joshmoore Nov 8, 2021
e0bb79b
Merge branch 'main' into 0.3.0-support
joshmoore Nov 29, 2021
dd2cecd
ZarrReader: Filter out directories from usedFiles
dgault Jan 26, 2022
fed421b
Add support for 0.4 axes and coordinateTransformations
dgault Feb 10, 2022
a196f39
Set requiredDirectories to 1 to preserve the .zarr folder
joshmoore Feb 22, 2022
f962c21
ZarrReader: Plate and Well fixes
dgault Mar 4, 2022
401d8b2
ZarrReader: Only use relative path for resolution data
dgault Mar 4, 2022
13c9bbc
ZarrReader: Multiscale fixes when no flat
dgault Mar 9, 2022
be19208
ZarrReader: No need for x offset when unpacking bytes
dgault Mar 10, 2022
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203 changes: 149 additions & 54 deletions src/loci/formats/in/ZarrReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.TransformerException;

import org.apache.commons.lang.StringUtils;
import org.apache.commons.io.FileUtils;
import org.w3c.dom.Document;
import org.xml.sax.SAXException;
Expand Down Expand Up @@ -73,6 +74,7 @@ public class ZarrReader extends FormatReader {
private HashMap<Integer, ArrayList<String>> resSeries = new HashMap<Integer, ArrayList<String>>();
private HashMap<String, Integer> resCounts = new HashMap<String, Integer>();
private HashMap<String, Integer> resIndexes = new HashMap<String, Integer>();
private String dimensionOrder = "XYCZT";

private boolean hasSPW = false;

Expand All @@ -82,6 +84,14 @@ public ZarrReader() {
domains = new String[] {FormatTools.UNKNOWN_DOMAIN};
}

/* @see loci.formats.IFormatReader#getRequiredDirectories(String[]) */
@Override
public int getRequiredDirectories(String[] files)
throws FormatException, IOException
{
return 1;
}

/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
Expand Down Expand Up @@ -180,7 +190,6 @@ protected void initFile(String id) throws FormatException, IOException {
for (int i=0; i<numDatasets; i++) {
CoreMetadata ms = new CoreMetadata();
core.add(ms);

setSeries(i);

Integer w = omexmlMeta.getPixelsSizeX(i).getValue();
Expand Down Expand Up @@ -275,19 +284,18 @@ protected void initFile(String id) throws FormatException, IOException {

arrayPaths = new ArrayList<String>();
arrayPaths.addAll(zarrService.getArrayKeys(zarrRootPath));

orderArrayPaths(zarrRootPath);

core.clear();
int resolutionTotal = 0;
for (int i=0; i<arrayPaths.size(); i++) {
int resolutionCount = 1;
if (resCounts.get(zarrRootPath+File.separator+arrayPaths.get(i)) != null) {
resolutionCount = resCounts.get(zarrRootPath+File.separator+arrayPaths.get(i));
if (resCounts.get(arrayPaths.get(i)) != null) {
resolutionCount = resCounts.get(arrayPaths.get(i));
}
int resolutionIndex= 0;
if (resIndexes.get(zarrRootPath+File.separator+arrayPaths.get(i)) != null) {
resolutionIndex = resIndexes.get(zarrRootPath+File.separator+arrayPaths.get(i));
if (resIndexes.get(arrayPaths.get(i)) != null) {
resolutionIndex = resIndexes.get(arrayPaths.get(i));
}

CoreMetadata ms = new CoreMetadata();
Expand All @@ -306,13 +314,16 @@ protected void initFile(String id) throws FormatException, IOException {

ms.pixelType = zarrService.getPixelType();
int[] shape = zarrService.getShape();
if (shape.length < 5) {
shape = get5DShape(shape);
}

ms.sizeX = shape[4];
ms.sizeY = shape[3];
ms.sizeT = shape[0];
ms.sizeZ = shape[2];
ms.sizeC = shape[1];
ms.dimensionOrder = "XYCZT";
ms.dimensionOrder = dimensionOrder;
ms.imageCount = getSizeZ() * getSizeC() * getSizeT();
ms.littleEndian = zarrService.isLittleEndian();
ms.rgb = false;
Expand All @@ -327,8 +338,39 @@ protected void initFile(String id) throws FormatException, IOException {
}
parsePlate(zarrRootPath, "", store);
setSeries(0);
//hasSPW = store.getPlateCount() > 0;
}

/**
* In the event that .zarray does not contain a 5d shape
* The dimensions of the original shape will be assumed based on tczyx
* @param originalShape as found in .zarray
* @return a 5D shape to be used within the reader
*/
private int[] get5DShape(int [] originalShape) {
int [] shape = new int[] {1,1,1,1,1};
int shapeIndex = 4;
for (int s = originalShape.length - 1; s >= 0; s--) {
shape[shapeIndex] = originalShape[s];
shapeIndex --;
}
return shape;
}

/**
* In the event that .zarray does not contain a 5d shape
* The 5D shape will be reduced to match the original representation
* @param shape5D - the 5D representation used within this reader
* @param size of the shape required by jzarr
* @return a 5D shape to be used within the reader
*/
private int[] getOriginalShape(int [] shape5D, int size) {
int [] shape = new int[size];
int shape5DIndex = 4;
for (int s = shape.length - 1; s >= 0; s--) {
shape[s] = shape5D[shape5DIndex];
shape5DIndex --;
}
return shape;
}

/* @see loci.formats.FormatReader#reopenFile() */
Expand All @@ -343,14 +385,6 @@ public void reopenFile() throws IOException {
}

protected void initializeZarrService(String rootPath) throws IOException, FormatException {
// TODO: ZarrService needs to be added to ServiceFactory but will require a release of ome-common
// try {
// ServiceFactory factory = new ServiceFactory();
// zarrService = factory.getInstance(ZarrService.class);
// zarrService.open(id);
// } catch (DependencyException e) {
// throw new MissingLibraryException(ZarrServiceImpl.NO_ZARR_MSG, e);
// }
zarrService = new JZarrServiceImpl(rootPath);
openZarr();
}
Expand All @@ -360,7 +394,14 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws F
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
int[] coordinates = getZCTCoords(no);
int [] shape = {1, 1, 1, h, w};
int zarrArrayShapeSize = zarrService.getShape().length;
if (zarrArrayShapeSize < 5) {
shape = getOriginalShape(shape, zarrArrayShapeSize);
}
int [] offsets = {coordinates[2], coordinates[1], coordinates[0], y, x};
if (zarrArrayShapeSize < 5) {
offsets = getOriginalShape(offsets, zarrArrayShapeSize);
}
Object image = zarrService.readBytes(shape, offsets);

boolean little = zarrService.isLittleEndian();
Expand All @@ -373,7 +414,7 @@ else if (image instanceof short[]) {
for (int row = 0; row < h; row++) {
int base = row * w * bpp;
for (int i = 0; i < w; i++) {
DataTools.unpackBytes(data[(row * w) + i + x], buf, base + 2 * i, 2, little);
DataTools.unpackBytes(data[(row * w) + i], buf, base + 2 * i, 2, little);
}
}
}
Expand All @@ -382,7 +423,7 @@ else if (image instanceof int[]) {
for (int row = 0; row < h; row++) {
int base = row * w * bpp;
for (int i = 0; i < w; i++) {
DataTools.unpackBytes(data[(row * w) + i + x], buf, base + 4 * i, 4, little);
DataTools.unpackBytes(data[(row * w) + i], buf, base + 4 * i, 4, little);
}
}
}
Expand All @@ -391,7 +432,7 @@ else if (image instanceof float[]) {
for (int row = 0; row < h; row++) {
int base = row * w * bpp;
for (int i = 0; i < w; i++) {
int value = Float.floatToIntBits(data[(row * w) + i + x]);
int value = Float.floatToIntBits(data[(row * w) + i]);
DataTools.unpackBytes(value, buf, base + 4 * i, 4, little);
}
}
Expand All @@ -401,7 +442,7 @@ else if (image instanceof double[]) {
for (int row = 0; row < h; row++) {
int base = row * w * bpp;
for (int i = 0; i < w; i++) {
long value = Double.doubleToLongBits(data[(row * w) + i + x]);
long value = Double.doubleToLongBits(data[(row * w) + i]);
DataTools.unpackBytes(value, buf, base + 8 * i, 8, little);
}
}
Expand All @@ -414,14 +455,24 @@ public void setSeries(int no) {
super.setSeries(no);
openZarr();
}

@Override
public void setResolution(int no) {
super.setResolution(no);
openZarr();
}

private void openZarr() {
try {
if (currentId != null && zarrService != null) {
String zarrRootPath = currentId.substring(0, currentId.indexOf(".zarr")+5);
String newZarrPath = zarrRootPath;
if (arrayPaths != null && !arrayPaths.isEmpty()) {
newZarrPath += File.separator + arrayPaths.get(series);
int seriesIndex = seriesToCoreIndex(series);
if (!hasFlattenedResolutions()) {
seriesIndex += resolution;
}
newZarrPath += File.separator + arrayPaths.get(seriesIndex);
zarrService.open(newZarrPath);
}
}
Expand All @@ -446,24 +497,52 @@ private void parseResolutionCount(String root, String key) throws IOException, F
Map<String, Object> attr = zarrService.getGroupAttr(path);
ArrayList<Object> multiscales = (ArrayList<Object>) attr.get("multiscales");
if (multiscales != null) {
Map<String, Object> datasets = (Map<String, Object>) multiscales.get(0);
ArrayList<Object> multiscalePaths = (ArrayList<Object>)datasets.get("datasets");
resSeries.put(resCounts.size(), new ArrayList<String>());
for (int i = 0; i < multiscalePaths.size(); i++) {
Map<String, Object> multiScale = (Map<String, Object>) multiscalePaths.get(i);
String scalePath = (String) multiScale.get("path");
int numRes = multiscalePaths.size();
if (i == 0) {
resCounts.put(path+File.separator+scalePath, numRes);
for (int x = 0; x < multiscales.size(); x++) {
Map<String, Object> datasets = (Map<String, Object>) multiscales.get(x);
ArrayList<Object> multiscalePaths = (ArrayList<Object>)datasets.get("datasets");
resSeries.put(resCounts.size(), new ArrayList<String>());
for (int i = 0; i < multiscalePaths.size(); i++) {
Map<String, Object> multiScale = (Map<String, Object>) multiscalePaths.get(i);
String scalePath = (String) multiScale.get("path");
int numRes = multiscalePaths.size();
if (i == 0) {
resCounts.put(scalePath, numRes);
}
resIndexes.put(scalePath, i);
ArrayList<String> list = resSeries.get(resCounts.size() - 1);
list.add(key.isEmpty() ? scalePath : key + File.separator + scalePath);
resSeries.put(resCounts.size() - 1, list);
}
List<Object> multiscaleAxes = (List<Object>)datasets.get("axes");
if (multiscaleAxes != null) {
for (int i = 0; i < multiscaleAxes.size(); i++) {
if (multiscaleAxes.get(i) instanceof String) {
String axis = (String) multiscaleAxes.get(i);
addGlobalMeta(MetadataTools.createLSID("Axis", x, i), axis);
}
else if (multiscaleAxes.get(i) instanceof HashMap) {
HashMap<String, String> axis = (HashMap<String, String>) multiscaleAxes.get(i);
String type = axis.get("type");
addGlobalMeta(MetadataTools.createLSID("Axis type", x, i), type);
String name = axis.get("name");
addGlobalMeta(MetadataTools.createLSID("Axis name", x, i), name);
String units = axis.get("units");
addGlobalMeta(MetadataTools.createLSID("Axis units", x, i), units);
}
}
}
List<Object> coordinateTransformations = (List<Object>)datasets.get("coordinateTransformations");
if (coordinateTransformations != null) {
for (int i = 0; i < coordinateTransformations.size(); i++) {
HashMap<String, Object> transformation = (HashMap<String, Object>) coordinateTransformations.get(i);
String type = (String)transformation.get("type");
addGlobalMeta(MetadataTools.createLSID("Coordinate Transformation type", x, i), type);
ArrayList<Object> scale = (ArrayList<Object>)transformation.get("scale");
if (scale != null)addGlobalMeta(MetadataTools.createLSID("Coordinate Transformation scale", x, i), scale);
ArrayList<Object> translation = (ArrayList<Object>)transformation.get("translation");
if (translation != null)addGlobalMeta(MetadataTools.createLSID("Coordinate Transformation translation", x, i), translation);
}
}
resIndexes.put(path+File.separator+scalePath, i);
ArrayList<String> list = resSeries.get(resCounts.size() - 1);
list.add(key.isEmpty() ? scalePath : key + File.separator + scalePath);
resSeries.put(resCounts.size() - 1, list);
}
List<String> multiscaleAxes = (List<String>)datasets.get("axes");
for (int i = 0; i < multiscaleAxes.size(); i++) {
String axis = (String) multiscaleAxes.get(i);
}
}
}
Expand All @@ -487,11 +566,24 @@ private void parsePlate(String root, String key, MetadataStore store) throws IOE
store.setPlateID(plate_id, p);
store.setPlateName(plateName, p);
int wellSamplesCount = 0;
HashMap<Integer, Integer> acqIdsIndexMap = new HashMap<Integer, Integer>();
for (int a = 0; a < acquistions.size(); a++) {
Map<String, Object> acquistion = (Map<String, Object>) acquistions.get(a);
String acqId = (String) acquistion.get("id");
Integer acqId = (Integer) acquistion.get("id");
String acqName = (String) acquistion.get("name");
String acqStartTime = (String) acquistion.get("starttime");
Integer maximumfieldcount = (Integer) acquistion.get("maximumfieldcount");
acqIdsIndexMap.put(acqId, a);
store.setPlateAcquisitionID(
MetadataTools.createLSID("PlateAcquisition", p, Integer.parseInt(acqId)), p, Integer.parseInt(acqId));
MetadataTools.createLSID("PlateAcquisition", p, acqId), p, a);
}
for (int c = 0; c < columns.size(); c++) {
Map<String, Object> column = (Map<String, Object>) columns.get(c);
String colName = (String) column.get("name");
}
for (int r = 0; r < rows.size(); r++) {
Map<String, Object> row = (Map<String, Object>) rows.get(r);
String rowName = (String) row.get("name");
}
for (int w = 0; w < wells.size(); w++) {
Map<String, Object> well = (Map<String, Object>) wells.get(w);
Expand All @@ -501,10 +593,10 @@ private void parsePlate(String root, String key, MetadataStore store) throws IOE
String well_id = MetadataTools.createLSID("Well", w);
store.setWellID(well_id, p, w);
String[] parts = wellPath.split("/");
if (wellRow.isEmpty()) {
if (StringUtils.isEmpty(wellRow)) {
wellRow = parts[parts.length - 2];
}
if (wellCol.isEmpty()) {
if (StringUtils.isEmpty(wellCol)) {
wellCol = parts[parts.length - 1];
}
int rowIndex = "ABCDEFGHIJKLMNOPQRSTUVWXYZ".indexOf(wellRow.toUpperCase());
Expand All @@ -518,13 +610,14 @@ private void parsePlate(String root, String key, MetadataStore store) throws IOE
store.setWellRow(new NonNegativeInteger(rowIndex), p, w);
store.setWellColumn(new NonNegativeInteger(colIndex), p, w);
store.setWellExternalIdentifier(wellPath, p, w);
wellSamplesCount = parseWells(root, wellPath, store, p, w, wellSamplesCount);
wellSamplesCount = parseWells(root, wellPath, store, p, w, wellSamplesCount, acqIdsIndexMap);
}
}
}
}

private int parseWells(String root, String key, MetadataStore store, int plateIndex, int wellIndex, int wellSamplesCount) throws IOException, FormatException {
private int parseWells(String root, String key, MetadataStore store, int plateIndex, int wellIndex, int wellSamplesCount,
HashMap<Integer, Integer> acqIdsIndexMap) throws IOException, FormatException {
String path = key.isEmpty() ? root : root + File.separator + key;
Map<String, Object> attr = zarrService.getGroupAttr(path);
Map<Object, Object> wells = (Map<Object, Object>) attr.get("well");
Expand All @@ -535,8 +628,10 @@ private int parseWells(String root, String key, MetadataStore store, int plateIn
for (int i = 0; i < images.size(); i++) {
Map<String, Object> image = (Map<String, Object>) images.get(i);
String imagePath = (String) image.get("path");
double acquisition = (double) image.get("acquisition");

Integer acquisition = (Integer) image.get("acquisition");
if (acqIdsIndexMap.containsKey(acquisition)) {
acquisition = acqIdsIndexMap.get(acquisition);
}
String site_id = MetadataTools.createLSID("WellSample", wellSamplesCount);
store.setWellSampleID(site_id, plateIndex, wellIndex, i);
store.setWellSampleIndex(new NonNegativeInteger(i), plateIndex, wellIndex, i);
Expand Down Expand Up @@ -587,7 +682,7 @@ private void parseImageLabels(String root, String key) throws IOException, Forma
}
}
}
ArrayList<Object> sources = (ArrayList<Object>) attr.get("sources");
ArrayList<Object> sources = (ArrayList<Object>) attr.get("source");
if (sources != null) {
for (int s = 0; s < sources.size(); s++) {
Map<String, Object> source = (Map<String, Object>) sources.get(s);
Expand Down Expand Up @@ -618,10 +713,10 @@ private void parseOmeroMetadata(String root, String key) throws IOException, For
String channelLabel = (String) channel.get("label");
Map<String, Object> window = (Map<String, Object>)channel.get("window");
if (window != null) {
Double windowStart = getDouble(window, "start");
Double windowEnd = getDouble(window, "end");
Double windowMin = getDouble(window, "min");
Double windowMax = getDouble(window, "max");
Double windowStart = getDouble(window, "start");
Double windowEnd = getDouble(window, "end");
Double windowMin = getDouble(window, "min");
Double windowMax = getDouble(window, "max");
}
}
Map<String, Object> rdefs = (Map<String, Object>)omeroMetadata.get("rdefs");
Expand All @@ -644,16 +739,16 @@ private Double getDouble(Map<String, Object> src, String key) {
/* @see loci.formats.IFormatReader#getUsedFiles(boolean) */
@Override
public String[] getUsedFiles(boolean noPixels) {

FormatTools.assertId(currentId, true, 1);
String zarrRootPath = currentId.substring(0, currentId.indexOf(".zarr") + 5);
ArrayList<String> usedFiles = new ArrayList<String>();
if (!zarrRootPath.toLowerCase().contains("s3:")) {
usedFiles.add(zarrRootPath);
File folder = new File(zarrRootPath);
Collection<File> libs = FileUtils.listFiles(folder, null, true);
for (File file : libs) {
usedFiles.add(file.getAbsolutePath());
if (!file.isDirectory()) {
usedFiles.add(file.getAbsolutePath());
}
}
}
else {
Expand Down