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add excludeSameMfovNeighbors option to TilePairDerivationParameters, …
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…rename multisem.Utilities as MultiSemUtilities and move from render-ws-java-client module to render-app module
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@trautmane
trautmane committed Dec 6, 2024
1 parent 92675be commit 1674081
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Showing 17 changed files with 191 additions and 123 deletions.
6 changes: 6 additions & 0 deletions ...pp/src/main/java/org/janelia/alignment/match/parameters/TilePairDerivationParameters.java
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,12 @@ public class TilePairDerivationParameters implements Serializable {
arity = 1)
public boolean excludeSameSectionNeighbors = false;

@Parameter(
names = "--excludeSameMfovNeighbors",
description = "Exclude neighbor tiles in the same layer (z) and MFOV as the source tile",
arity = 1)
public boolean excludeSameMfovNeighbors = false;

@Parameter(
names = "--excludePairsInMatchCollection",
description = "Name of match collection whose existing pairs should be excluded from the generated list (default is to include all pairs)"
Expand Down
39 changes: 11 additions & 28 deletions ...lia/render/client/multisem/Utilities.java → ...alignment/multisem/MultiSemUtilities.java
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
package org.janelia.render.client.multisem;
package org.janelia.alignment.multisem;

import java.io.IOException;
import java.nio.file.Files;
Expand All @@ -9,16 +9,6 @@
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;

import org.janelia.alignment.match.CanvasId;
import org.janelia.alignment.match.CanvasMatchResult;
import org.janelia.alignment.match.CanvasMatches;
import org.janelia.alignment.match.OrderedCanvasIdPair;
import org.janelia.alignment.spec.TileSpec;
import org.janelia.render.client.RenderDataClient;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import mpicbg.models.AbstractAffineModel2D;
import mpicbg.models.CoordinateTransform;
Expand All @@ -28,12 +18,20 @@
import mpicbg.models.Point;
import mpicbg.models.PointMatch;

import org.janelia.alignment.match.CanvasId;
import org.janelia.alignment.match.CanvasMatchResult;
import org.janelia.alignment.match.CanvasMatches;
import org.janelia.alignment.match.OrderedCanvasIdPair;
import org.janelia.alignment.spec.TileSpec;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
* Utility methods for working with Multi-SEM data sets.
*
* @author Eric Trautman
*/
public class Utilities {
public class MultiSemUtilities {

/**
* @return 0399_m0013 for w60_magc0399_scan005_m0013_s001
Expand Down Expand Up @@ -229,20 +227,5 @@ public static List<Point> getMatchingTransformedCornersForTile(final TileSpec ti
return tileSpec.getMatchingTransformedPoints(rawLocations);
}

/**
* @return list of distinct sorted MFOV names for the specified stack z-layer.
*/
public static List<String> getMFOVNames(final RenderDataClient renderDataClient,
final String stack,
final Double z)
throws IOException {
return renderDataClient.getTileBounds(stack, z)
.stream()
.map(tileBounds -> getMFOVForTileId(tileBounds.getTileId()))
.distinct()
.sorted()
.collect(Collectors.toList());
}

private static final Logger LOG = LoggerFactory.getLogger(Utilities.class);
private static final Logger LOG = LoggerFactory.getLogger(MultiSemUtilities.class);
}
16 changes: 13 additions & 3 deletions render-app/src/main/java/org/janelia/alignment/spec/TileBoundsRTree.java
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Expand Up @@ -17,6 +17,7 @@

import org.janelia.alignment.match.CanvasId;
import org.janelia.alignment.match.OrderedCanvasIdPair;
import org.janelia.alignment.multisem.MultiSemUtilities;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

Expand Down Expand Up @@ -193,7 +194,8 @@ public Set<OrderedCanvasIdPair> getCircleNeighbors(final List<TileBounds> source
final Double explicitRadius,
final boolean excludeCornerNeighbors,
final boolean excludeSameLayerNeighbors,
final boolean excludeSameSectionNeighbors) {
final boolean excludeSameSectionNeighbors,
final boolean excludeSameMfovNeighbors) {

String firstTileId = null;
if (! sourceTileBoundsList.isEmpty()) {
Expand Down Expand Up @@ -232,14 +234,16 @@ public Set<OrderedCanvasIdPair> getCircleNeighbors(final List<TileBounds> source

neighborTileIdPairs.addAll(
getDistinctPairs(tileBounds, searchResults,
excludeCornerNeighbors, excludeSameSectionNeighbors, true));
excludeCornerNeighbors, excludeSameSectionNeighbors, excludeSameMfovNeighbors,
true));
}

for (final TileBoundsRTree neighborTree : neighborTrees) {
searchResults = neighborTree.findTilesInCircle(circle);
neighborTileIdPairs.addAll(
getDistinctPairs(tileBounds, searchResults,
excludeCornerNeighbors, excludeSameSectionNeighbors, false));
excludeCornerNeighbors, excludeSameSectionNeighbors, excludeSameMfovNeighbors,
false));
}
}

Expand Down Expand Up @@ -281,9 +285,11 @@ public static Set<OrderedCanvasIdPair> getDistinctPairs(final TileBounds fromTil
final List<TileBounds> toTiles,
final boolean excludeCornerNeighbors,
final boolean excludeSameSectionNeighbors,
final boolean excludeSameMfovNeighbors,
final boolean includeRelativePosition) {
final Set<OrderedCanvasIdPair> pairs = new HashSet<>(toTiles.size() * 2);
final String pTileId = fromTile.getTileId();
final String pMfov = excludeSameMfovNeighbors ? MultiSemUtilities.getMFOVForTileId(pTileId) : null;

final double fromMinX = fromTile.getMinX();
final double fromMaxX = fromTile.getMaxX();
Expand All @@ -302,6 +308,10 @@ public static Set<OrderedCanvasIdPair> getDistinctPairs(final TileBounds fromTil
isNeighborCenterInRange(fromMinX, fromMaxX, toTile.getMinX(), toTile.getMaxX()) ||
isNeighborCenterInRange(fromMinY, fromMaxY, toTile.getMinY(), toTile.getMaxY())) {

if (excludeSameMfovNeighbors && (pMfov.equals(MultiSemUtilities.getMFOVForTileId(qTileId)))) {
continue;
}

final OrderedCanvasIdPair pair;
if (includeRelativePosition) {
pair = OrderedCanvasIdPair.withRelativeMontagePositions(fromTile, toTile);
Expand Down
24 changes: 24 additions & 0 deletions render-app/src/test/java/org/janelia/alignment/multisem/MultiSemUtilitiesTest.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,24 @@
package org.janelia.alignment.multisem;

import org.junit.Assert;
import org.junit.Test;

/**
* Tests the {@link MultiSemUtilities} class.
*
* @author Eric Trautman
*/
public class MultiSemUtilitiesTest {

@Test
public void testTileIdParsers() {
final String tileId = "w60_magc0399_scan005_m0013_s001";
Assert.assertEquals("invalid MFOVForTileId",
"0399_m0013", MultiSemUtilities.getMFOVForTileId(tileId));
Assert.assertEquals("invalid SFOVForTileId",
"0399_m0013_s001", MultiSemUtilities.getSFOVForTileId(tileId));
Assert.assertEquals("invalid SFOVIndexForTileId",
"001", MultiSemUtilities.getSFOVIndexForTileId(tileId));
}

}
45 changes: 43 additions & 2 deletions render-app/src/test/java/org/janelia/alignment/spec/TileBoundsRTreeTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -74,6 +74,7 @@ public void testGetCircleNeighbors() {
null,
false,
false,
false,
false);

final Set<OrderedCanvasIdPair> expectedPairs = new TreeSet<>();
Expand All @@ -94,6 +95,7 @@ public void testGetCircleNeighbors() {
explicitRadius,
false,
false,
false,
false);

expectedPairs.clear();
Expand Down Expand Up @@ -123,6 +125,7 @@ public void testGetCircleNeighborsWithFullyOverlappingTiles() {
null,
false,
false,
false,
false);

final Set<OrderedCanvasIdPair> expectedPairs = new TreeSet<>();
Expand All @@ -147,17 +150,55 @@ public void testGetCanvasIdPairs() {
final TileBounds centerTile = tileBoundsList.get(4);

Set<OrderedCanvasIdPair> pairs =
TileBoundsRTree.getDistinctPairs(centerTile, tileBoundsList, false, false, false);
TileBoundsRTree.getDistinctPairs(centerTile,
tileBoundsList,
false,
false,
false,
false);
int expectedNumberOfCombinations = tileBoundsList.size() - 1; // all tiles except the center
Assert.assertEquals("incorrect number of combinations (with corner neighbors) in " + pairs,
expectedNumberOfCombinations, pairs.size());

expectedNumberOfCombinations = expectedNumberOfCombinations - 4; // remove the 4 corner tiles
pairs = TileBoundsRTree.getDistinctPairs(centerTile, tileBoundsList, true, false, true);
pairs = TileBoundsRTree.getDistinctPairs(centerTile,
tileBoundsList,
true,
false,
false,
true);
Assert.assertEquals("incorrect number of combinations (without corner neighbors) in " + pairs,
expectedNumberOfCombinations, pairs.size());
}

@Test
public void testGetDifferentMFovCanvasIdPairs() {

final Double z = 1.0;
final String sectionId = String.valueOf(z);
// s082 s083 s084
// s071 s070
final List<TileBounds> tileBoundsList = Arrays.asList(
new TileBounds("w60_magc0399_scan012_m0013_s082", sectionId, z, 5.0, 0.0, 17.0, 12.0),
new TileBounds("w60_magc0399_scan012_m0013_s083", sectionId, z, 15.0, 0.0, 27.0, 12.0),
new TileBounds("w60_magc0399_scan012_m0013_s084", sectionId, z, 25.0, 0.0, 37.0, 12.0),
new TileBounds("w60_magc0399_scan012_m0014_s071", sectionId, z, 10.0, 10.0, 22.0, 22.0),
new TileBounds("w60_magc0399_scan012_m0014_s070", sectionId, z, 20.0, 10.0, 32.0, 22.0)
);

final TileBounds testTile = tileBoundsList.get(1); // s083

final Set<OrderedCanvasIdPair> pairs =
TileBoundsRTree.getDistinctPairs(testTile,
tileBoundsList,
false,
false,
true,
false);
Assert.assertEquals("incorrect number of combinations in " + pairs,
2, pairs.size());
}

@Test
public void testFindCompletelyObscuredTiles() {

Expand Down
22 changes: 13 additions & 9 deletions ...ws-java-client/src/main/java/org/janelia/render/client/DebugTransformedCornersClient.java
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Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,7 @@ public Parameters() {
}

public boolean hasTileIds() {
return (tileIds != null) && (tileIds.size() > 0);
return (tileIds != null) && (! tileIds.isEmpty());
}
}

Expand Down Expand Up @@ -154,7 +154,7 @@ public void runClient(final String[] args)
parameters.layerRange.minZ,
parameters.layerRange.maxZ,
explicitZValues);
if (this.zValues.size() == 0) {
if (this.zValues.isEmpty()) {
throw new IllegalArgumentException(
"stack " + firstStackName + " does not contain any layers with the specified z values, " +
"confirm --minZ and --maxZ are correct");
Expand Down Expand Up @@ -262,6 +262,7 @@ private List<String> debugPairsForStack(final String stackName)
null,
false,
false,
false,
false);

neighborPairs.addAll(currentNeighborPairs);
Expand All @@ -271,7 +272,7 @@ private List<String> debugPairsForStack(final String stackName)
final List<Point> pTransformedCornersAll = new ArrayList<>();
final List<Point> qTransformedCornersAll = new ArrayList<>();

if (neighborPairs.size() > 0) {
if (! neighborPairs.isEmpty()) {
final Map<Double, ResolvedTileSpecCollection> zToTilesMap = new HashMap<>(zValues.size());
for (final Double zVal : zValues) {
zToTilesMap.put(zVal, renderDataClient.getResolvedTiles(stackName, zVal));
Expand Down Expand Up @@ -329,8 +330,9 @@ private List<String> debugPairsForStack(final String stackName)
}
//System.out.println( model + ", " + model.getClass().getSimpleName());
//System.exit( 0 );
} catch (NotEnoughDataPointsException | IllDefinedDataPointsException e) {
e.printStackTrace();
} catch (final NotEnoughDataPointsException | IllDefinedDataPointsException e) {
//noinspection CallToPrintStackTrace
e.printStackTrace();
}
}

Expand Down Expand Up @@ -366,14 +368,15 @@ private List<String> debugPairsForStack(final String stackName)
}

// e.g. "[1.0, 0.0, 957.4067568339881], [0.0, 1.0, -1640.2727272727273]"
public static AffineModel2D stringToModel( String modelString )
@SuppressWarnings("unused")
public static AffineModel2D stringToModel(String modelString )
{
modelString = modelString.replace("[", "" );
modelString = modelString.replace("]", "" );
modelString = modelString.replace(" ", "" );
modelString = modelString.trim();

String[] s = modelString.split( "," );
final String[] s = modelString.split( "," );

final AffineModel2D model = new AffineModel2D();
model.set(Double.parseDouble(s[0]), Double.parseDouble(s[1]), Double.parseDouble(s[3]), Double.parseDouble(s[4]), Double.parseDouble(s[2]), Double.parseDouble(s[5]));
Expand Down Expand Up @@ -417,9 +420,10 @@ public static void computeError( final List<PointMatch> matches, final Model<?>
model.setCost( error );
System.out.println( "maxE=" + maxError + " " + model + ", " + model.getClass().getSimpleName());

} catch (NotEnoughDataPointsException | IllDefinedDataPointsException e) {
} catch (final NotEnoughDataPointsException | IllDefinedDataPointsException e) {
// TODO Auto-generated catch block
e.printStackTrace();
//noinspection CallToPrintStackTrace
e.printStackTrace();
}

}
Expand Down
9 changes: 5 additions & 4 deletions ...-java-client/src/main/java/org/janelia/render/client/ExampleMatchVisualizationClient.java
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Original file line number Diff line number Diff line change
Expand Up @@ -170,7 +170,6 @@ public void runClient(final String[] args) throws Exception {
* ('::' for existing connections and '??' for missing connections) to standard out.
* This is sufficient for the single row FIB-SEM stacks with the same number of tiles in each layer.
* It won't work for many other cases.
*
* Since the primary goal of the client is to demonstrate how to pull tile and match data from render,
* it has been left in its current less-than-ideal state.
*
Expand All @@ -185,7 +184,7 @@ void printConnections()

final List<Double> zValues = zToSectionIdMap.keySet().stream().sorted().collect(Collectors.toList());

if (zValues.size() == 0) {
if (zValues.isEmpty()) {
throw new IllegalArgumentException(
"stack " + parameters.stack + " does not contain any layers with the specified z values");
}
Expand All @@ -209,7 +208,8 @@ void printConnections()
null,
true,
false,
false)
false,
false)
.stream()
.map(pair -> {
// Minor Hack: Remove same layer relative position data inserted by
Expand Down Expand Up @@ -245,7 +245,8 @@ void printConnections()
null,
true,
true,
false)
false,
false)
.stream().sorted().collect(Collectors.toList());

for (final OrderedCanvasIdPair pair : crossLayerNeighborPairs) {
Expand Down
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