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Correct stupid width and height calculation bug when deriving width a…
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…nd height for tile render parameters. Refactor core logic into separate method to simplify testing. Add test to catch bug. This fixes #24.
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@trautmane
trautmane committed Mar 22, 2017
1 parent a0870ea commit a9e9a8f
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Showing 2 changed files with 123 additions and 69 deletions.
143 changes: 74 additions & 69 deletions render-ws/src/main/java/org/janelia/render/service/TileDataService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -142,80 +142,13 @@ public RenderParameters getRenderParameters(@PathParam("owner") final String own

RenderParameters parameters = null;
try {
final TileSpec tileSpec = getTileSpec(owner, project, stack, tileId, true);
tileSpec.flattenTransforms();

double tileRenderX = tileSpec.getMinX();
double tileRenderY = tileSpec.getMinY();

int tileRenderWidth;
if (width == null) {
tileRenderWidth = (int) (tileSpec.getMaxX() - tileSpec.getMinX());
} else {
tileRenderWidth = width;
}

int tileRenderHeight;
if (height == null) {
tileRenderHeight = (int) (tileSpec.getMaxY() - tileSpec.getMinY());
} else {
tileRenderHeight = height;
}

final StackId stackId = new StackId(owner, project, stack);
final StackMetaData stackMetaData = getStackMetaData(stackId);

if ((normalizeForMatching != null) && normalizeForMatching) {

// When deriving point matches for a tile pair in which each tile has different lens correction
// transformations, the bounding box for each rendered tile needs to be normalized.
//
// Normalization is achieved by:
// (1) Removing the last transform spec (assumed to be an affine that positions the tile in the world).
// (2) Setting the render start coordinate to (0,0).
// (3) Padding the raw tile width and height by multiplying a normalization factor (1.05).
// Assuming that all tiles in a stack have the same raw width and height, this ensures
// that normalized tiles also have the same width and height with a little extra room
// for edges that are rotated/skewed by lens correction.
// (4) Ensuring that the normalized width and height are even by adding a pixel as needed.
//
// Consistent and even tile sizes are currently a requirement for generating DMesh point matches.

final double normalizationFactor = 1.05;
if (width == null) {
tileRenderWidth = (int) (tileSpec.getWidth() * normalizationFactor);
}
if (height == null) {
tileRenderHeight = (int) (tileSpec.getHeight() * normalizationFactor);
}

tileSpec.removeLastTransformSpec();
final TileSpec tileSpec = getTileSpec(owner, project, stack, tileId, true);

// If the tile still has more than 3 transforms, remove all but the last 3.
// This assumes that the last 3 transforms are for lens correction.
// Hopefully at some point we'll label transforms so that it is possible to
// explicitly include only lens correction transforms.
while (tileSpec.getTransforms().size() > 3) {
tileSpec.removeLastTransformSpec();
}

tileRenderX = 0;
tileRenderY = 0;

if ((tileRenderWidth % 2) == 1) {
tileRenderWidth++;
}
if ((tileRenderHeight % 2) == 1) {
tileRenderHeight++;
}
}
parameters = getCoreTileRenderParameters(width, height, scale, normalizeForMatching, tileSpec);

parameters = new RenderParameters(null,
tileRenderX,
tileRenderY,
tileRenderWidth,
tileRenderHeight,
scale);
parameters.setDoFilter(filter);
parameters.setBinaryMask(binaryMask);
parameters.setExcludeMask(excludeMask);
Expand Down Expand Up @@ -340,6 +273,78 @@ public RenderParameters getTileWithNeighborsRenderParameters(@PathParam("owner")
return parameters;
}

protected static RenderParameters getCoreTileRenderParameters(final Integer width,
final Integer height,
final Double scale,
final Boolean normalizeForMatching,
final TileSpec tileSpec) {
tileSpec.flattenTransforms();

double tileRenderX = tileSpec.getMinX();
double tileRenderY = tileSpec.getMinY();

int tileRenderWidth;
if (width == null) {
tileRenderWidth = (int) (tileSpec.getMaxX() - tileSpec.getMinX() + 1);
} else {
tileRenderWidth = width;
}

int tileRenderHeight;
if (height == null) {
tileRenderHeight = (int) (tileSpec.getMaxY() - tileSpec.getMinY() + 1);
} else {
tileRenderHeight = height;
}

if ((normalizeForMatching != null) && normalizeForMatching) {

// When deriving point matches for a tile pair in which each tile has different lens correction
// transformations, the bounding box for each rendered tile needs to be normalized.
//
// Normalization is achieved by:
// (1) Removing the last transform spec (assumed to be an affine that positions the tile in the world).
// (2) Setting the render start coordinate to (0,0).
// (3) Padding the raw tile width and height by multiplying a normalization factor (1.05).
// Assuming that all tiles in a stack have the same raw width and height, this ensures
// that normalized tiles also have the same width and height with a little extra room
// for edges that are rotated/skewed by lens correction.
// (4) Ensuring that the normalized width and height are even by adding a pixel as needed.
//
// Consistent and even tile sizes are currently a requirement for generating DMesh point matches.

final double normalizationFactor = 1.05;
if (width == null) {
tileRenderWidth = (int) (tileSpec.getWidth() * normalizationFactor);
}
if (height == null) {
tileRenderHeight = (int) (tileSpec.getHeight() * normalizationFactor);
}

tileSpec.removeLastTransformSpec();

// If the tile still has more than 3 transforms, remove all but the last 3.
// This assumes that the last 3 transforms are for lens correction.
// Hopefully at some point we'll label transforms so that it is possible to
// explicitly include only lens correction transforms.
while (tileSpec.getTransforms().size() > 3) {
tileSpec.removeLastTransformSpec();
}

tileRenderX = 0;
tileRenderY = 0;

if ((tileRenderWidth % 2) == 1) {
tileRenderWidth++;
}
if ((tileRenderHeight % 2) == 1) {
tileRenderHeight++;
}
}

return new RenderParameters(null, tileRenderX, tileRenderY, tileRenderWidth, tileRenderHeight, scale);
}

private StackMetaData getStackMetaData(final StackId stackId)
throws ObjectNotFoundException {

Expand Down
49 changes: 49 additions & 0 deletions render-ws/src/test/java/org/janelia/render/service/TileDataServiceTest.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,49 @@
package org.janelia.render.service;

import org.janelia.alignment.RenderParameters;
import org.janelia.alignment.spec.TileSpec;
import org.junit.Assert;
import org.junit.Test;

/**
* Tests the {@link TileDataService} class.
*
* @author Eric Trautman
*/
public class TileDataServiceTest {

@Test
public void testGetCoreTileRenderParameters() throws Exception {

final String json =
"{\n" +
" \"tileId\" : \"1,3484_aligned_0_1_flip\",\n" +
" \"z\" : 3484.0, \"minX\" : 1896.0, \"minY\" : 876.0, \"maxX\" : 2919.0, \"maxY\" : 1899.0,\n" +
" \"width\" : 1024.0, \"height\" : 1024.0,\n" +
" \"mipmapLevels\" : {\n" +
" \"0\" : {\n" +
" \"imageUrl\" : \"file:///data/nc-em/russelt/20170227_Princeton_Pinky40/4_aligned_tiled/1,3484_aligned_0_1_flip.png\"\n" +
" }\n" +
" },\n" +
" \"transforms\" : {\n" +
" \"type\" : \"list\",\n" +
" \"specList\" : [ {\n" +
" \"className\" : \"mpicbg.trakem2.transform.AffineModel2D\",\n" +
" \"dataString\" : \"1.0000000000 0.0000000000 0.0000000000 1.0000000000 1896.0000000000 -876.0000000000\"\n" +
" }, {\n" +
" \"className\" : \"mpicbg.trakem2.transform.AffineModel2D\",\n" +
" \"dataString\" : \"1.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 1752.0000000000\"\n" +
" } ]\n" +
" }\n" +
"}";

final TileSpec tileSpec = TileSpec.fromJson(json);

final RenderParameters renderParameters =
TileDataService.getCoreTileRenderParameters(null, null, null, null, tileSpec);

Assert.assertEquals("invalid width for tile", 1024, renderParameters.getWidth());
Assert.assertEquals("invalid height for tile", 1024, renderParameters.getHeight());
}

}

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