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Remove usage of bioformats order argument #6

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Merged
jburel merged 2 commits into from
Jul 18, 2025
Merged

Remove usage of bioformats order argument #6

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6945b90
Clarify order
dominikl Jul 15, 2025
bd1bac4
Remove usage of BF --order argument
dominikl Jul 15, 2025
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9 changes: 8 additions & 1 deletion src/test/java/com/glencoesoftware/omero/zarr/TestZarr.java
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ public class TestZarr {
private int sizeZ = 5;
private int sizeT = 10;
private int sizeC = 3;
private String order = "TCZYX";
private String order = "TCZYX"; // Note: Reverse for ome.model.enums.DimensionOrder
private Path path = Path.of("./test.zarr");
private DataType dataType = DataType.u1;
private boolean overwrite = false;
Expand Down Expand Up @@ -356,6 +356,13 @@ public String getOrder() {
return order;
}

/**
* Set the order of the dimensions.
* Note: Reverse of ome.model.enums.DimensionOrder,
* e.g. DimensionOrder.XYZCT -> use "TCZYX"
* @param order
* @return
*/
public TestZarr setOrder(String order) {
this.order = order;
return this;
Expand Down
144 changes: 82 additions & 62 deletions src/test/java/com/glencoesoftware/omero/zarr/ZarrPixelBufferTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,6 @@
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.OptionalInt;
import java.util.stream.IntStream;

import org.junit.Assert;
Expand Down Expand Up @@ -192,8 +191,7 @@ public Path writeTestZarr(
int sizeY,
int sizeX,
String pixelType,
int resolutions,
String order) throws IOException {
int resolutions) throws IOException {

Path input = fake(
"sizeT", Integer.toString(sizeT),
Expand All @@ -204,21 +202,14 @@ public Path writeTestZarr(
"pixelType", pixelType,
"resolutions", Integer.toString(resolutions));
Path output = tmpDir.getRoot().toPath().resolve("output.zarr");
if (order != null) {
assertBioFormats2Raw(input, output, "--dimension-order", order);
} else {
assertBioFormats2Raw(input, output);
}
assertBioFormats2Raw(input, output);

List<Object> msArray = new ArrayList<>();
Map<String, Object> msData = new HashMap<>();
Map<String, Object> msMetadata = new HashMap<>();
msMetadata.put("method", "loci.common.image.SimpleImageScaler");
msMetadata.put("version", "Bio-Formats 6.5.1");
msData.put("metadata", msMetadata);
if (order != null) {
msData.put("axes", getAxes(new StringBuffer(order).reverse().toString()));
}
msData.put("datasets", getDatasets(resolutions));
msData.put("version", "0.1");
msArray.add(msData);
Expand All @@ -229,17 +220,6 @@ public Path writeTestZarr(
return output;

}
public Path writeTestZarr(
int sizeT,
int sizeC,
int sizeZ,
int sizeY,
int sizeX,
String pixelType,
int resolutions) throws IOException {
return writeTestZarr(sizeT, sizeC, sizeZ, sizeY, sizeX, pixelType,
resolutions, null);
}

List<Map<String, String>> getDatasets(int resolutions) {
List<Map<String, String>> datasets = new ArrayList<>();
Expand Down Expand Up @@ -852,14 +832,26 @@ public void testReadDataNonDefaultAxes()
int sizeZ = 4;
int sizeY = 1024;
int sizeX = 2048;
int resolutions = 1;
String order = DimensionOrder.VALUE_XYCTZ;
String order = DimensionOrder.VALUE_XYCTZ; // Default XYZCT
String rev_order = new StringBuilder(order).reverse().toString();
Pixels pixels = new Pixels(
null, new PixelsType(PixelsType.VALUE_INT32),
sizeX, sizeY, sizeZ, sizeC, sizeT, "", new DimensionOrder(order));
Path output = writeTestZarr(
sizeT, sizeC, sizeZ, sizeY, sizeX, "int32", resolutions, order);
String reverse_order = new StringBuilder(order).reverse().toString();
null, null, sizeX, sizeY, sizeZ, sizeC, sizeT, "", new DimensionOrder(order));

Path output = tmpDir.getRoot().toPath().resolve("test.zarr");
new TestZarr()
.setPath(output)
.setOverwrite(true)
.setSizeX(sizeX)
.setSizeY(sizeY)
.setSizeZ(sizeZ)
.setSizeT(sizeT)
.setSizeC(sizeC)
.setOrder(rev_order)
.setDataType(com.bc.zarr.DataType.i4) // getStack expects int32
.init()
.createImage()
.createMetadata();

try (ZarrPixelBuffer zpbuf =
createPixelBuffer(pixels, output.resolve("0"), sizeX, sizeY)) {
for (int t = 0; t < sizeT; t++) {
Expand All @@ -869,14 +861,14 @@ null, new PixelsType(PixelsType.VALUE_INT32),
// Assert stack
byte[] stack = zpbuf.getStack(c, t).getData().array();
byte[] stackFromTimepoint =
getStack(timepoint, c, sizeC, sizeZ, sizeX, sizeY, reverse_order);
getStack(timepoint, c, sizeC, sizeZ, sizeX, sizeY, rev_order);
Assert.assertArrayEquals(stack, stackFromTimepoint);
for (int z = 0; z < sizeZ; z++) {
// Assert plane
byte[] plane =
zpbuf.getPlane(z, c, t).getData().array();
byte[] planeFromStack =
getPlane(stack, z, sizeZ, sizeX, sizeY);
getPlane(stack, z, sizeZ, sizeX, sizeY, rev_order);
Assert.assertArrayEquals(plane, planeFromStack);
// Assert row
int y = sizeY / 2;
Expand All @@ -898,37 +890,7 @@ null, new PixelsType(PixelsType.VALUE_INT32),
}

@Test
public void testNonDefaultAxes()
throws IOException, InvalidRangeException {
int sizeT = 1;
int sizeC = 2;
int sizeZ = 16;
int sizeY = 256;
int sizeX = 512;
int resolutions = 1;
String order = DimensionOrder.VALUE_XYCTZ; // Default: TCZYX -> XYZCT
Pixels pixels = new Pixels(
null, null, sizeX, sizeY, sizeZ, sizeC, sizeT, "", new DimensionOrder(order));
Path output = writeTestZarr(
sizeT, sizeC, sizeZ, sizeY, sizeX, "uint8", resolutions, order);
try (ZarrPixelBuffer zpbuf =
createPixelBuffer(pixels, output.resolve("0"), sizeX, sizeY)) {
Map<Axis, Integer> axes = zpbuf.getAxesOrder();
Assert.assertEquals(0, axes.get(Axis.Z).intValue());
Assert.assertEquals(1, axes.get(Axis.T).intValue());
Assert.assertEquals(2, axes.get(Axis.C).intValue());
Assert.assertEquals(3, axes.get(Axis.Y).intValue());
Assert.assertEquals(4, axes.get(Axis.X).intValue());
Assert.assertEquals(sizeT, zpbuf.getSizeT());
Assert.assertEquals(sizeC, zpbuf.getSizeC());
Assert.assertEquals(sizeZ, zpbuf.getSizeZ());
Assert.assertEquals(sizeY, zpbuf.getSizeY());
Assert.assertEquals(sizeX, zpbuf.getSizeX());
}
}

@Test
public void testDefaultAxes()
public void test_default_order()
throws IOException, InvalidRangeException {
// Check that if access are not in the file it defaults to TCZYX order when no axes found

Expand Down Expand Up @@ -1000,6 +962,64 @@ public void test_XY() throws IOException, InvalidRangeException {
testDimensions(512, 1024, 0, 0, 0);
}

@Test
public void test_Order_XYCTZ() throws IOException, InvalidRangeException {
testOrder(DimensionOrder.VALUE_XYCTZ);
}

@Test
public void test_Order_XYCZT() throws IOException, InvalidRangeException {
testOrder(DimensionOrder.VALUE_XYCZT);
}

@Test
public void test_Order_XYTCZ() throws IOException, InvalidRangeException {
testOrder(DimensionOrder.VALUE_XYTCZ);
}

@Test
public void test_Order_XYTZC() throws IOException, InvalidRangeException {
testOrder(DimensionOrder.VALUE_XYTZC);
}

@Test
public void test_Order_XYZCT() throws IOException, InvalidRangeException {
testOrder(DimensionOrder.VALUE_XYZCT);
}

@Test
public void test_Order_XYZTC() throws IOException, InvalidRangeException {
testOrder(DimensionOrder.VALUE_XYZTC);
}

private void testOrder(String order) throws IOException, InvalidRangeException {
Path testZarrPath = tmpDir.getRoot().toPath().resolve("test.zarr");
TestZarr testZarr = new TestZarr()
.setPath(testZarrPath)
.setOrder(new StringBuilder(order).reverse().toString())
.init()
.createImage()
.createMetadata();

Pixels pixels = new Pixels(
null, null, testZarr.getSizeX(), testZarr.getSizeY(), testZarr.getSizeZ(), testZarr.getSizeC(), testZarr.getSizeT(), "", new DimensionOrder(order));

try (ZarrPixelBuffer zpbuf =
createPixelBuffer(pixels, testZarrPath.resolve("0"), testZarr.getSizeX(), testZarr.getSizeY())) {
Map<Axis, Integer> axes = zpbuf.getAxesOrder();
Assert.assertEquals(4 - order.indexOf("Z"), axes.get(Axis.Z).intValue());
Assert.assertEquals(4 - order.indexOf("T"), axes.get(Axis.T).intValue());
Assert.assertEquals(4 - order.indexOf("C"), axes.get(Axis.C).intValue());
Assert.assertEquals(4 - order.indexOf("Y"), axes.get(Axis.Y).intValue());
Assert.assertEquals(4 - order.indexOf("X"), axes.get(Axis.X).intValue());
Assert.assertEquals(testZarr.getSizeT(), zpbuf.getSizeT());
Assert.assertEquals(testZarr.getSizeC(), zpbuf.getSizeC());
Assert.assertEquals(testZarr.getSizeZ(), zpbuf.getSizeZ());
Assert.assertEquals(testZarr.getSizeY(), zpbuf.getSizeY());
Assert.assertEquals(testZarr.getSizeX(), zpbuf.getSizeX());
}
}

private void testDimensions(int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT) throws IOException, InvalidRangeException {
int textX = 10;
int textY = 10;
Expand Down