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Merge pull request #6 from dominikl/remove_bf_dim_order
Remove usage of bioformats order argument
2 parents a0b3c47 + bd1bac4 commit 57bffda

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2 files changed

+90
-63
lines changed

2 files changed

+90
-63
lines changed

‎src/test/java/com/glencoesoftware/omero/zarr/TestZarr.java‎

Lines changed: 8 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -56,7 +56,7 @@ public class TestZarr {
5656
private int sizeZ = 5;
5757
private int sizeT = 10;
5858
private int sizeC = 3;
59-
private String order = "TCZYX";
59+
private String order = "TCZYX"; // Note: Reverse for ome.model.enums.DimensionOrder
6060
private Path path = Path.of("./test.zarr");
6161
private DataType dataType = DataType.u1;
6262
private boolean overwrite = false;
@@ -356,6 +356,13 @@ public String getOrder() {
356356
return order;
357357
}
358358

359+
/**
360+
* Set the order of the dimensions.
361+
* Note: Reverse of ome.model.enums.DimensionOrder,
362+
* e.g. DimensionOrder.XYZCT -> use "TCZYX"
363+
* @param order
364+
* @return
365+
*/
359366
public TestZarr setOrder(String order) {
360367
this.order = order;
361368
return this;

‎src/test/java/com/glencoesoftware/omero/zarr/ZarrPixelBufferTest.java‎

Lines changed: 82 additions & 62 deletions
Original file line numberDiff line numberDiff line change
@@ -32,7 +32,6 @@
3232
import java.util.HashMap;
3333
import java.util.List;
3434
import java.util.Map;
35-
import java.util.OptionalInt;
3635
import java.util.stream.IntStream;
3736

3837
import org.junit.Assert;
@@ -192,8 +191,7 @@ public Path writeTestZarr(
192191
int sizeY,
193192
int sizeX,
194193
String pixelType,
195-
int resolutions,
196-
String order) throws IOException {
194+
int resolutions) throws IOException {
197195

198196
Path input = fake(
199197
"sizeT", Integer.toString(sizeT),
@@ -204,21 +202,14 @@ public Path writeTestZarr(
204202
"pixelType", pixelType,
205203
"resolutions", Integer.toString(resolutions));
206204
Path output = tmpDir.getRoot().toPath().resolve("output.zarr");
207-
if (order != null) {
208-
assertBioFormats2Raw(input, output, "--dimension-order", order);
209-
} else {
210-
assertBioFormats2Raw(input, output);
211-
}
205+
assertBioFormats2Raw(input, output);
212206

213207
List<Object> msArray = new ArrayList<>();
214208
Map<String, Object> msData = new HashMap<>();
215209
Map<String, Object> msMetadata = new HashMap<>();
216210
msMetadata.put("method", "loci.common.image.SimpleImageScaler");
217211
msMetadata.put("version", "Bio-Formats 6.5.1");
218212
msData.put("metadata", msMetadata);
219-
if (order != null) {
220-
msData.put("axes", getAxes(new StringBuffer(order).reverse().toString()));
221-
}
222213
msData.put("datasets", getDatasets(resolutions));
223214
msData.put("version", "0.1");
224215
msArray.add(msData);
@@ -229,17 +220,6 @@ public Path writeTestZarr(
229220
return output;
230221

231222
}
232-
public Path writeTestZarr(
233-
int sizeT,
234-
int sizeC,
235-
int sizeZ,
236-
int sizeY,
237-
int sizeX,
238-
String pixelType,
239-
int resolutions) throws IOException {
240-
return writeTestZarr(sizeT, sizeC, sizeZ, sizeY, sizeX, pixelType,
241-
resolutions, null);
242-
}
243223

244224
List<Map<String, String>> getDatasets(int resolutions) {
245225
List<Map<String, String>> datasets = new ArrayList<>();
@@ -852,14 +832,26 @@ public void testReadDataNonDefaultAxes()
852832
int sizeZ = 4;
853833
int sizeY = 1024;
854834
int sizeX = 2048;
855-
int resolutions = 1;
856-
String order = DimensionOrder.VALUE_XYCTZ;
835+
String order = DimensionOrder.VALUE_XYCTZ; // Default XYZCT
836+
String rev_order = new StringBuilder(order).reverse().toString();
857837
Pixels pixels = new Pixels(
858-
null, new PixelsType(PixelsType.VALUE_INT32),
859-
sizeX, sizeY, sizeZ, sizeC, sizeT, "", new DimensionOrder(order));
860-
Path output = writeTestZarr(
861-
sizeT, sizeC, sizeZ, sizeY, sizeX, "int32", resolutions, order);
862-
String reverse_order = new StringBuilder(order).reverse().toString();
838+
null, null, sizeX, sizeY, sizeZ, sizeC, sizeT, "", new DimensionOrder(order));
839+
840+
Path output = tmpDir.getRoot().toPath().resolve("test.zarr");
841+
new TestZarr()
842+
.setPath(output)
843+
.setOverwrite(true)
844+
.setSizeX(sizeX)
845+
.setSizeY(sizeY)
846+
.setSizeZ(sizeZ)
847+
.setSizeT(sizeT)
848+
.setSizeC(sizeC)
849+
.setOrder(rev_order)
850+
.setDataType(com.bc.zarr.DataType.i4) // getStack expects int32
851+
.init()
852+
.createImage()
853+
.createMetadata();
854+
863855
try (ZarrPixelBuffer zpbuf =
864856
createPixelBuffer(pixels, output.resolve("0"), sizeX, sizeY)) {
865857
for (int t = 0; t < sizeT; t++) {
@@ -869,14 +861,14 @@ null, new PixelsType(PixelsType.VALUE_INT32),
869861
// Assert stack
870862
byte[] stack = zpbuf.getStack(c, t).getData().array();
871863
byte[] stackFromTimepoint =
872-
getStack(timepoint, c, sizeC, sizeZ, sizeX, sizeY, reverse_order);
864+
getStack(timepoint, c, sizeC, sizeZ, sizeX, sizeY, rev_order);
873865
Assert.assertArrayEquals(stack, stackFromTimepoint);
874866
for (int z = 0; z < sizeZ; z++) {
875867
// Assert plane
876868
byte[] plane =
877869
zpbuf.getPlane(z, c, t).getData().array();
878870
byte[] planeFromStack =
879-
getPlane(stack, z, sizeZ, sizeX, sizeY);
871+
getPlane(stack, z, sizeZ, sizeX, sizeY, rev_order);
880872
Assert.assertArrayEquals(plane, planeFromStack);
881873
// Assert row
882874
int y = sizeY / 2;
@@ -898,37 +890,7 @@ null, new PixelsType(PixelsType.VALUE_INT32),
898890
}
899891

900892
@Test
901-
public void testNonDefaultAxes()
902-
throws IOException, InvalidRangeException {
903-
int sizeT = 1;
904-
int sizeC = 2;
905-
int sizeZ = 16;
906-
int sizeY = 256;
907-
int sizeX = 512;
908-
int resolutions = 1;
909-
String order = DimensionOrder.VALUE_XYCTZ; // Default: TCZYX -> XYZCT
910-
Pixels pixels = new Pixels(
911-
null, null, sizeX, sizeY, sizeZ, sizeC, sizeT, "", new DimensionOrder(order));
912-
Path output = writeTestZarr(
913-
sizeT, sizeC, sizeZ, sizeY, sizeX, "uint8", resolutions, order);
914-
try (ZarrPixelBuffer zpbuf =
915-
createPixelBuffer(pixels, output.resolve("0"), sizeX, sizeY)) {
916-
Map<Axis, Integer> axes = zpbuf.getAxesOrder();
917-
Assert.assertEquals(0, axes.get(Axis.Z).intValue());
918-
Assert.assertEquals(1, axes.get(Axis.T).intValue());
919-
Assert.assertEquals(2, axes.get(Axis.C).intValue());
920-
Assert.assertEquals(3, axes.get(Axis.Y).intValue());
921-
Assert.assertEquals(4, axes.get(Axis.X).intValue());
922-
Assert.assertEquals(sizeT, zpbuf.getSizeT());
923-
Assert.assertEquals(sizeC, zpbuf.getSizeC());
924-
Assert.assertEquals(sizeZ, zpbuf.getSizeZ());
925-
Assert.assertEquals(sizeY, zpbuf.getSizeY());
926-
Assert.assertEquals(sizeX, zpbuf.getSizeX());
927-
}
928-
}
929-
930-
@Test
931-
public void testDefaultAxes()
893+
public void test_default_order()
932894
throws IOException, InvalidRangeException {
933895
// Check that if access are not in the file it defaults to TCZYX order when no axes found
934896

@@ -1000,6 +962,64 @@ public void test_XY() throws IOException, InvalidRangeException {
1000962
testDimensions(512, 1024, 0, 0, 0);
1001963
}
1002964

965+
@Test
966+
public void test_Order_XYCTZ() throws IOException, InvalidRangeException {
967+
testOrder(DimensionOrder.VALUE_XYCTZ);
968+
}
969+
970+
@Test
971+
public void test_Order_XYCZT() throws IOException, InvalidRangeException {
972+
testOrder(DimensionOrder.VALUE_XYCZT);
973+
}
974+
975+
@Test
976+
public void test_Order_XYTCZ() throws IOException, InvalidRangeException {
977+
testOrder(DimensionOrder.VALUE_XYTCZ);
978+
}
979+
980+
@Test
981+
public void test_Order_XYTZC() throws IOException, InvalidRangeException {
982+
testOrder(DimensionOrder.VALUE_XYTZC);
983+
}
984+
985+
@Test
986+
public void test_Order_XYZCT() throws IOException, InvalidRangeException {
987+
testOrder(DimensionOrder.VALUE_XYZCT);
988+
}
989+
990+
@Test
991+
public void test_Order_XYZTC() throws IOException, InvalidRangeException {
992+
testOrder(DimensionOrder.VALUE_XYZTC);
993+
}
994+
995+
private void testOrder(String order) throws IOException, InvalidRangeException {
996+
Path testZarrPath = tmpDir.getRoot().toPath().resolve("test.zarr");
997+
TestZarr testZarr = new TestZarr()
998+
.setPath(testZarrPath)
999+
.setOrder(new StringBuilder(order).reverse().toString())
1000+
.init()
1001+
.createImage()
1002+
.createMetadata();
1003+
1004+
Pixels pixels = new Pixels(
1005+
null, null, testZarr.getSizeX(), testZarr.getSizeY(), testZarr.getSizeZ(), testZarr.getSizeC(), testZarr.getSizeT(), "", new DimensionOrder(order));
1006+
1007+
try (ZarrPixelBuffer zpbuf =
1008+
createPixelBuffer(pixels, testZarrPath.resolve("0"), testZarr.getSizeX(), testZarr.getSizeY())) {
1009+
Map<Axis, Integer> axes = zpbuf.getAxesOrder();
1010+
Assert.assertEquals(4 - order.indexOf("Z"), axes.get(Axis.Z).intValue());
1011+
Assert.assertEquals(4 - order.indexOf("T"), axes.get(Axis.T).intValue());
1012+
Assert.assertEquals(4 - order.indexOf("C"), axes.get(Axis.C).intValue());
1013+
Assert.assertEquals(4 - order.indexOf("Y"), axes.get(Axis.Y).intValue());
1014+
Assert.assertEquals(4 - order.indexOf("X"), axes.get(Axis.X).intValue());
1015+
Assert.assertEquals(testZarr.getSizeT(), zpbuf.getSizeT());
1016+
Assert.assertEquals(testZarr.getSizeC(), zpbuf.getSizeC());
1017+
Assert.assertEquals(testZarr.getSizeZ(), zpbuf.getSizeZ());
1018+
Assert.assertEquals(testZarr.getSizeY(), zpbuf.getSizeY());
1019+
Assert.assertEquals(testZarr.getSizeX(), zpbuf.getSizeX());
1020+
}
1021+
}
1022+
10031023
private void testDimensions(int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT) throws IOException, InvalidRangeException {
10041024
int textX = 10;
10051025
int textY = 10;

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