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Remove unused functions from ZarrAxes #120

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merged 6 commits into from
Sep 14, 2022
Merged

Remove unused functions from ZarrAxes #120

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21b7673
Remove unused functions from ZarrAxes
constantinpape Sep 13, 2022
60fc3d4
Simplify getXYZScale, remove isSpatial3D
constantinpape Sep 13, 2022
02638c4
Fix typo
constantinpape Sep 13, 2022
bfe7b68
Remove zarr.Axes.is2D
constantinpape Sep 13, 2022
2ba8c25
Update ZarrArrayCreator.getCellDims, remove more unused ZarrAxes func…
constantinpape Sep 14, 2022
f094a81
Remove zarrAxes.is5D
constantinpape Sep 14, 2022
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51 changes: 11 additions & 40 deletions src/main/java/org/embl/mobie/io/ome/zarr/loaders/N5OMEZarrImageLoader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -370,34 +370,11 @@ private double[] getXYZScale(OmeZarrMultiscales.CoordinateTransformations coordi
double[] scale = coordinateTransformations.scale;
double[] xyzScale = null;
if (scale != null && zarrAxesList != null) {
int scalesFirstIndexBackward = scale.length - 1;
if (zarrAxes.hasChannels()) {
if (zarrAxes.is2D()) {
xyzScale = new double[]{
scale[scalesFirstIndexBackward],
scale[scalesFirstIndexBackward - 1],
1.0
};
} else {
xyzScale = new double[]{
scale[scalesFirstIndexBackward],
scale[scalesFirstIndexBackward - 1],
scale[scalesFirstIndexBackward - 2]};
}
} else {
if (zarrAxes.isSpatial3D()) {
xyzScale = new double[]{
scale[scalesFirstIndexBackward],
scale[scalesFirstIndexBackward - 1],
scale[scalesFirstIndexBackward - 2]};
} else {
xyzScale = new double[]{
scale[scalesFirstIndexBackward],
scale[scalesFirstIndexBackward - 1],
1.0
};
}
}
xyzScale = new double[]{
scale[zarrAxes.axisIndex("x", false)],
scale[zarrAxes.axisIndex("y", false)],
zarrAxes.hasZAxis() ? scale[zarrAxes.axisIndex("z", false)] : 1.0
};
}
return xyzScale;
}
Expand Down Expand Up @@ -429,10 +406,10 @@ private VoxelDimensions getVoxelDimensions3D(int setupId, int datasetId) {
String unit = zarrAxesList.get(zarrAxesList.size() - 1).getUnit();

if (scale != null && unit != null) {
if (zarrAxes.is2D()) {
return new FinalVoxelDimensions(unit, new double[]{scale[0], scale[1], 1.0});
} else {
if (zarrAxes.hasZAxis()) {
return new FinalVoxelDimensions(unit, scale);
} else {
return new FinalVoxelDimensions(unit, new double[]{scale[0], scale[1], 1.0});
}
}
}
Expand Down Expand Up @@ -591,16 +568,10 @@ private double[][] readMipmapResolutions() throws IOException {
for (int level = 1; level < mipmapResolutions.length; level++) {
long[] dimensions = getDatasetAttributes(getPathName(setupId, level)).getDimensions();
mipmapResolutions[level] = new double[3];
if (multiscale.axes.is2D()) {
for (int d = 0; d < 2; d++) {
mipmapResolutions[level][d] = Math.round(1.0 * dimensionsOfLevel0[d] / dimensions[d]);
}
mipmapResolutions[level][2] = 1.0;
} else {
for (int d = 0; d < 3; d++) {
mipmapResolutions[level][d] = 1.0 * dimensionsOfLevel0[d] / dimensions[d];
}
for (int d = 0; d < 2; d++) {
mipmapResolutions[level][d] = Math.round(1.0 * dimensionsOfLevel0[d] / dimensions[d]);
}
mipmapResolutions[level][2] = multiscale.axes.hasZAxis() ? Math.round(1.0 * dimensionsOfLevel0[2] / dimensions[2]) : 1.0;
}

return mipmapResolutions;
Expand Down
26 changes: 6 additions & 20 deletions src/main/java/org/embl/mobie/io/ome/zarr/util/ZarrArrayCreator.java
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Expand Up @@ -29,28 +29,14 @@ public A createArray(DataBlock<?> dataBlock, long[] gridPosition) {

@Override
public long[] getCellDims(long[] gridPosition) {
long[] cellMin = new long[3];
int[] cellDims = new int[3];

// TODO: do something like in: private long[] toZarrChunkIndices( long[] gridPosition )
if (zarrAxes.is4DWithChannels() || zarrAxes.is4DWithTimepoints()) {
cellMin = new long[4];
cellDims = new int[4];
cellDims[3] = 1; // channel
}
long[] cellMin = new long[Math.max(zarrAxes.getNumDimension(), 3)];
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int[] cellDims = new int[Math.max(zarrAxes.getNumDimension(), 3)];

if (zarrAxes.is4DWithTimepointsAndChannels()) {
cellMin = new long[4];
cellDims = new int[4];
cellDims[2] = 1; // channel
cellDims[3] = 1; // timepoint
if(zarrAxes.hasChannels()) {
cellDims[zarrAxes.channelIndex()] = 1;
}

if (zarrAxes.is5D()) {
cellMin = new long[5];
cellDims = new int[5];
cellDims[3] = 1; // channel
cellDims[4] = 1; // timepoint
if(zarrAxes.hasTimepoints()) {
cellDims[zarrAxes.timeIndex()] = 1;
}

cellGrid.getCellDimensions(gridPosition, cellMin, cellDims);
Expand Down
50 changes: 13 additions & 37 deletions src/main/java/org/embl/mobie/io/ome/zarr/util/ZarrAxes.java
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Expand Up @@ -83,39 +83,6 @@ public List<ZarrAxis> toAxesList(String spaceUnit, String timeUnit) {
return zarrAxesList;
}

public boolean is2D() {
return this.axes.equals(YX.axes) || this.axes.equals(CYX.axes); // XYT XYC
}

public boolean is5D() {
return this.axes.equals(TCZYX.axes);
}

public boolean isSpatial3D() {
return this.axes.equals(CZYX.axes) || this.axes.equals(TZYX.axes) || this.axes.equals(ZYX.axes);
}

public boolean is4D() {
return this.axes.equals(CZYX.axes) || this.axes.equals(TZYX.axes) || this.axes.equals(TCYX.axes);
}

public boolean is3DWithTimepoints() {
return this.axes.equals(TYX.axes);
}

public boolean is4DWithTimepoints() {
return this.axes.equals(TZYX.axes);
}

public boolean is4DWithChannels() {
return this.axes.equals(CZYX.axes);
}

// not used anymore
public boolean is4DWithTimepointsAndChannels() {
return this.axes.equals(TCYX.axes);
}

public boolean hasTimepoints() {
return this.axes.equals(TCYX.axes) || this.axes.equals(TZYX.axes) || this.axes.equals(TYX.axes) ||
this.axes.equals(TCZYX.axes);
Expand All @@ -126,14 +93,23 @@ public boolean hasChannels() {
this.axes.equals(TCZYX.axes);
}

// the flag reverseAxes determines whether the index will be given w.r.t.
// reversedAxes=true corresponds to the java/bdv axis convention
// reversedAxes=false corresponds to the zarr axis convention
public int axisIndex(String axisName, boolean reverseAxes) {
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if(reverseAxes) {
List<String> reverseAxesList = Lists.reverse(getAxesList());
return reverseAxesList.indexOf(axisName);
}
return getAxesList().indexOf(axisName);
}

public int timeIndex() {
List<String> reverseAxesList = Lists.reverse(getAxesList());
return reverseAxesList.indexOf("t");
return axisIndex("t", true);
}

public int channelIndex() {
List<String> reverseAxesList = Lists.reverse(getAxesList());
return reverseAxesList.indexOf("c");
return axisIndex("c", true);
}

// spatial: 0,1,2 (x,y,z)
Expand Down
6 changes: 6 additions & 0 deletions src/test/java/projects/remote/BaseTest.java
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Expand Up @@ -17,6 +17,9 @@ public abstract class BaseTest extends BaseSpimDataChecker {
protected int expectedChannelsNumber = 1;
protected Dimensions expectedShape;
protected String expectedDType;
// TODO refactor the base test into a zarr base test so that we can also check for zarr specific attributes
// like the expected scale
//protected int [] expectedScale = null;

protected BaseTest(String path, ImageDataFormat format) throws SpimDataException {
super(new SpimDataOpener().openSpimData(path, format));
Expand All @@ -32,6 +35,9 @@ public void baseTest() {
Assertions.assertEquals(expectedChannelsNumber, getAllChannelsSize());
Assertions.assertEquals(expectedShape, getShape());
Assertions.assertEquals(expectedDType, getDType());
// if(expectedScale != null) {
// Assertions.assertEquals(expectedScale, getScale());
//}
}

public int getExpectedTimePoints() {
Expand Down