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Replace Doubles with Integers #7

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merged 2 commits into from
Sep 22, 2021
Merged

Replace Doubles with Integers #7

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443231c
Replace Doubles with Integers
joshmoore Sep 19, 2021
8d7904b
Use Number.doubleValue to handle JSON parsing
joshmoore Sep 20, 2021
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98 changes: 53 additions & 45 deletions src/loci/formats/in/ZarrReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -11,12 +11,12 @@
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 2 of the
* License, or (at your option) any later version.
*
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
*
* You should have received a copy of the GNU General Public
* License along with this program. If not, see
* <http://www.gnu.org/licenses/gpl-2.0.html>.
Expand Down Expand Up @@ -72,15 +72,15 @@ 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 boolean hasSPW = false;

public ZarrReader() {
super("Zarr", "zarr");
suffixSufficient = false;
domains = new String[] {FormatTools.UNKNOWN_DOMAIN};
}

/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
Expand All @@ -90,7 +90,7 @@ public boolean isThisType(String name, boolean open) {
}
return super.isThisType(name, open);
}

/* @see loci.formats.IFormatReader#close() */
@Override
public void close() throws IOException {
Expand All @@ -110,14 +110,14 @@ public int getOptimalTileHeight() {
FormatTools.assertId(currentId, true, 1);
return zarrService.getChunkSize()[1];
}

/* @see loci.formats.IFormatReader#getOptimalTileHeight() */
@Override
public int getOptimalTileWidth() {
FormatTools.assertId(currentId, true, 1);
return zarrService.getChunkSize()[0];
}

/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
Expand All @@ -128,9 +128,9 @@ protected void initFile(String id) throws FormatException, IOException {
String zarrRootPath = zarrPath.substring(0, zarrPath.indexOf(".zarr") + 5);
String name = zarrRootPath.substring(zarrRootPath.lastIndexOf(File.separator)+1, zarrRootPath.length() - 5);
Location omeMetaFile = new Location( zarrRootPath, name+".ome.xml" );

initializeZarrService(zarrRootPath);

/*
* Open OME metadata file
* TODO: Old code to either be reworked with writer or removed entirely
Expand All @@ -150,7 +150,7 @@ protected void initFile(String id) throws FormatException, IOException {
}
}
omeDocument.getDocumentElement().normalize();

OMEXMLService service = null;
String xml = null;
try
Expand All @@ -171,17 +171,17 @@ protected void initFile(String id) throws FormatException, IOException {
{
LOGGER.debug( "", e1 );
}

int numDatasets = omexmlMeta.getImageCount();

int oldSeries = getSeries();
core.clear();
for (int i=0; i<numDatasets; i++) {
CoreMetadata ms = new CoreMetadata();
core.add(ms);

setSeries(i);

Integer w = omexmlMeta.getPixelsSizeX(i).getValue();
Integer h = omexmlMeta.getPixelsSizeY(i).getValue();
Integer t = omexmlMeta.getPixelsSizeT(i).getValue();
Expand All @@ -190,7 +190,7 @@ protected void initFile(String id) throws FormatException, IOException {
if (w == null || h == null || t == null || z == null | c == null) {
throw new FormatException("Image dimensions not found");
}

Boolean endian = null;
String pixType = omexmlMeta.getPixelsType(i).toString();
ms.dimensionOrder = omexmlMeta.getPixelsDimensionOrder(i).toString();
Expand Down Expand Up @@ -225,14 +225,14 @@ protected void initFile(String id) throws FormatException, IOException {
try {
jsonAttr = ZarrUtils.toJson(attr, true);
store.setXMLAnnotationValue(jsonAttr, attrIndex);
String xml_id = MetadataTools.createLSID("AttributesAnnotation:", attrIndex);
String xml_id = MetadataTools.createLSID("AttributesAnnotation:", attrIndex);
store.setXMLAnnotationID(xml_id, attrIndex);
} catch (JZarrException e) {
LOGGER.warn("Failed to convert attributes to JSON");
e.printStackTrace();
}
}

// Parse group attributes
for (String key: zarrService.getGroupKeys(zarrRootPath)) {
Map<String, Object> attributes = zarrService.getGroupAttr(zarrRootPath+File.separator+key);
Expand All @@ -245,15 +245,15 @@ protected void initFile(String id) throws FormatException, IOException {
try {
jsonAttr = ZarrUtils.toJson(attributes, true);
store.setXMLAnnotationValue(jsonAttr, attrIndex);
String xml_id = MetadataTools.createLSID("AttributesAnnotation:"+key, attrIndex);
String xml_id = MetadataTools.createLSID("AttributesAnnotation:"+key, attrIndex);
store.setXMLAnnotationID(xml_id, attrIndex);
} catch (JZarrException e) {
LOGGER.warn("Failed to convert attributes to JSON");
e.printStackTrace();
}
}
}

// Parse array attributes
for (String key: zarrService.getArrayKeys(zarrRootPath)) {
Map<String, Object> attributes = zarrService.getArrayAttr(zarrRootPath+File.separator+key);
Expand All @@ -263,7 +263,7 @@ protected void initFile(String id) throws FormatException, IOException {
try {
jsonAttr = ZarrUtils.toJson(attributes, true);
store.setXMLAnnotationValue(jsonAttr, attrIndex);
String xml_id = MetadataTools.createLSID("AttributesAnnotation:"+key, attrIndex);
String xml_id = MetadataTools.createLSID("AttributesAnnotation:"+key, attrIndex);
store.setXMLAnnotationID(xml_id, attrIndex);
} catch (JZarrException e) {
LOGGER.warn("Failed to convert attributes to JSON");
Expand All @@ -274,9 +274,9 @@ 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++) {
Expand All @@ -288,10 +288,10 @@ protected void initFile(String id) throws FormatException, IOException {
if (resIndexes.get(zarrRootPath+File.separator+arrayPaths.get(i)) != null) {
resolutionIndex = resIndexes.get(zarrRootPath+File.separator+arrayPaths.get(i));
}

CoreMetadata ms = new CoreMetadata();
core.add(ms);

if (hasFlattenedResolutions()) {
setSeries(i);
}
Expand All @@ -305,7 +305,7 @@ protected void initFile(String id) throws FormatException, IOException {

ms.pixelType = zarrService.getPixelType();
int[] shape = zarrService.getShape();

ms.sizeX = shape[4];
ms.sizeY = shape[3];
ms.sizeT = shape[0];
Expand Down Expand Up @@ -353,7 +353,7 @@ protected void initializeZarrService(String rootPath) throws IOException, Format
zarrService = new JZarrServiceImpl(rootPath);
openZarr();
}

@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
Expand Down Expand Up @@ -407,13 +407,13 @@ else if (image instanceof double[]) {
}
return buf;
}

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

private void openZarr() {
try {
if (currentId != null && zarrService != null) {
Expand All @@ -428,7 +428,7 @@ private void openZarr() {
e.printStackTrace();
}
}

private void orderArrayPaths(String root) {
for (int i = 0; i < resSeries.size(); i++) {
for (String arrayPath: resSeries.get(i)) {
Expand All @@ -439,7 +439,7 @@ private void orderArrayPaths(String root) {
}
}
}

private void parseResolutionCount(String root, String key) throws IOException, FormatException {
String path = key.isEmpty() ? root : root + File.separator + key;
Map<String, Object> attr = zarrService.getGroupAttr(path);
Expand All @@ -462,7 +462,7 @@ private void parseResolutionCount(String root, String key) throws IOException, F
}
}
}

private void parsePlate(String root, String key, MetadataStore store) throws IOException, FormatException {
String path = key.isEmpty() ? root : root + File.separator + key;
Map<String, Object> attr = zarrService.getGroupAttr(path);
Expand All @@ -477,7 +477,7 @@ private void parsePlate(String root, String key, MetadataStore store) throws IOE
ArrayList<Object> acquistions = (ArrayList<Object> )plates.get("acquisitions");
String plateName = (String) plates.get("name");
String fieldCount = (String) plates.get("filed_count");

String plate_id = MetadataTools.createLSID("Plate", p);
store.setPlateID(plate_id, p);
store.setPlateName(plateName, p);
Expand Down Expand Up @@ -518,7 +518,7 @@ private void parsePlate(String root, String key, MetadataStore store) throws IOE
}
}
}

private int parseWells(String root, String key, MetadataStore store, int plateIndex, int wellIndex, int wellSamplesCount) throws IOException, FormatException {
String path = key.isEmpty() ? root : root + File.separator + key;
Map<String, Object> attr = zarrService.getGroupAttr(path);
Expand All @@ -530,8 +530,8 @@ 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");
double acquisition = (double) image.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 All @@ -543,7 +543,7 @@ private int parseWells(String root, String key, MetadataStore store, int plateIn
}
return wellSamplesCount;
}

private void parseLabels(String root, String key) throws IOException, FormatException {
String path = key.isEmpty() ? root : root + File.separator + key;
Map<String, Object> attr = zarrService.getGroupAttr(path);
Expand All @@ -554,7 +554,7 @@ private void parseLabels(String root, String key) throws IOException, FormatExce
}
}
}

private void parseImageLabels(String root, String key) throws IOException, FormatException {
String path = key.isEmpty() ? root : root + File.separator + key;
Map<String, Object> attr = zarrService.getGroupAttr(path);
Expand Down Expand Up @@ -593,7 +593,7 @@ private void parseImageLabels(String root, String key) throws IOException, Forma
}
}
}

private void parseOmeroMetadata(String root, String key) throws IOException, FormatException {
String path = key.isEmpty() ? root : root + File.separator + key;
Map<String, Object> attr = zarrService.getGroupAttr(path);
Expand All @@ -613,10 +613,10 @@ 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 = (Double) window.get("start");
Double windowEnd = (Double) window.get("end");
Double windowMin = (Double) window.get("min");
Double windowMax = (Double) window.get("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 @@ -627,11 +627,19 @@ private void parseOmeroMetadata(String root, String key) throws IOException, For
}
}
}


private Double getDouble(Map<String, Object> src, String key) {
Number val = (Number) src.get(key);
if (val == null) {
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return null;
}
return val.doubleValue();
}

/* @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>();
Expand All @@ -654,7 +662,7 @@ public String[] getUsedFiles(boolean noPixels) {
fileArr = usedFiles.toArray(fileArr);
return fileArr;
}

/* @see loci.formats.SubResolutionFormatReader#getDomains() */
@Override
public String[] getDomains() {
Expand Down