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Merge pull request #22 from alanocallaghan/tiler
Add tiler
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| /** | ||
| * Copyright 2023 University of Edinburgh | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
| package qupath.ext.wsinfer; | ||
|
|
||
| import org.locationtech.jts.geom.Coordinate; | ||
| import org.locationtech.jts.geom.Geometry; | ||
| import qupath.lib.objects.PathAnnotationObject; | ||
| import qupath.lib.objects.PathObject; | ||
| import qupath.lib.objects.PathObjects; | ||
| import qupath.lib.objects.PathTileObject; | ||
| import qupath.lib.regions.ImagePlane; | ||
| import qupath.lib.roi.GeometryTools; | ||
| import qupath.lib.roi.interfaces.ROI; | ||
|
|
||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import java.util.function.Function; | ||
| import java.util.stream.Collectors; | ||
|
|
||
| /** | ||
| * A class used to split {@link ROI} or {@link Geometry} objects into | ||
| * rectangular tiles. Useful for parallel processing. | ||
| */ | ||
| public class Tiler { | ||
| private int tileWidth; | ||
| private int tileHeight; | ||
| private boolean trimToParent = true; | ||
| private boolean symmetric = true; | ||
| private boolean filterByCentroid = true; | ||
|
|
||
| /** | ||
| * Create a Tiler object. | ||
| * @param tileWidth the width in pixels. | ||
| * @param tileHeight the height in pixels. | ||
| */ | ||
| public Tiler(int tileWidth, int tileHeight) { | ||
| this.tileWidth = tileWidth; | ||
| this.tileHeight = tileHeight; | ||
| } | ||
|
|
||
| /** | ||
| * | ||
| * @param tileWidth tile width in pixels. | ||
| * @param tileHeight tile height in pixels. | ||
| * @param trimToParent controls whether tiles should be trimmed to fit | ||
| * within the parent object. | ||
| * @param symmetric controls whether the Tiler should aim to split the | ||
| * parent object symmetrically. If false, it will | ||
| * begin at the top left of the parent. | ||
| * @param filterByCentroid controls whether tiles whose centroid is outwith | ||
| * the parent object will be removed from the | ||
| * output. | ||
| */ | ||
| public Tiler(int tileWidth, int tileHeight, | ||
| boolean trimToParent, boolean symmetric, | ||
| boolean filterByCentroid) { | ||
| this(tileWidth, tileHeight); | ||
| this.trimToParent = trimToParent; | ||
| this.symmetric = symmetric; | ||
| this.filterByCentroid = filterByCentroid; | ||
| } | ||
|
|
||
| /** | ||
| * Get the width of output tiles | ||
| * @return the width in pixels | ||
| */ | ||
| public int getTileWidth() { | ||
| return tileWidth; | ||
| } | ||
|
|
||
| /** | ||
| * Change the width of output tiles | ||
| * @param tileWidth the new width in pixels | ||
| */ | ||
| public void setTileWidth(int tileWidth) { | ||
| this.tileWidth = tileWidth; | ||
| } | ||
|
|
||
| /** | ||
| * Change the height of output tiles | ||
| * @return the height in pixels | ||
| */ | ||
| public int getTileHeight() { | ||
| return tileHeight; | ||
| } | ||
|
|
||
| /** | ||
| * Change the height of output tiles | ||
| * @param tileHeight the new height in pixels | ||
| */ | ||
| public void setTileHeight(int tileHeight) { | ||
| this.tileHeight = tileHeight; | ||
| } | ||
|
|
||
| /** | ||
| * Check if the tiler is set to trim output to the input parent. | ||
| * @return whether the tiler is set to trim output to the parent object | ||
| */ | ||
| public boolean isTrimToParent() { | ||
| return trimToParent; | ||
| } | ||
|
|
||
| /** | ||
| * Set whether the tiler is set to trim output to the input parent. | ||
| * @param trimToParent the new setting | ||
| */ | ||
| public void setTrimToParent(boolean trimToParent) { | ||
| this.trimToParent = trimToParent; | ||
| } | ||
|
|
||
| /** | ||
| * Check if the tiler will try to tile symmetrically, or will start | ||
| * directly from the top-left of the parent. | ||
| * @return The current setting | ||
| */ | ||
| public boolean isSymmetric() { | ||
| return symmetric; | ||
| } | ||
|
|
||
| /** | ||
| * Set if the tiler will try to tile symmetrically, or will start | ||
| * directly from the top-left of the parent. | ||
| * @param symmetric The new setting | ||
| */ | ||
| public void setSymmetric(boolean symmetric) { | ||
| this.symmetric = symmetric; | ||
| } | ||
|
|
||
| /** | ||
| * Check if the tiler will filter the output based on whether the centroid | ||
| * of tiles lies within the parent | ||
| * @return The current setting | ||
| */ | ||
| public boolean isFilterByCentroid() { | ||
| return filterByCentroid; | ||
| } | ||
|
|
||
| /** | ||
| * Set if the tiler will filter the output based on whether the centroid | ||
| * of tiles lies within the parent | ||
| * @param filterByCentroid the new setting | ||
| */ | ||
| public void setFilterByCentroid(boolean filterByCentroid) { | ||
| this.filterByCentroid = filterByCentroid; | ||
| } | ||
|
|
||
| /** | ||
| * Create a list of {@link Geometry} tiles from the input. These may | ||
| * not all be rectangular based on the settings used. | ||
| * @param parent the object that will be split into tiles. | ||
| * @return a list of tiles | ||
| */ | ||
| public List<Geometry> createGeometries(Geometry parent) { | ||
| if (parent == null) { | ||
| return new ArrayList<>(); | ||
| } | ||
| Geometry boundingBox = parent.isRectangle() ? parent : parent.getEnvelope(); | ||
| Coordinate[] coordinates = boundingBox.getCoordinates(); // (minx miny, minx maxy, maxx maxy, maxx miny, minx miny). | ||
| double xStart = coordinates[0].x; | ||
| double yStart = coordinates[0].y; | ||
| double xEnd = coordinates[2].x; | ||
| double yEnd = coordinates[2].y; | ||
|
|
||
| double bBoxWidth = xEnd - xStart; | ||
| double bBoxHeight = yEnd - yStart; | ||
|
|
||
| if (symmetric) { | ||
| xStart += calculateOffset(tileWidth, bBoxWidth); | ||
| yStart += calculateOffset(tileHeight, bBoxHeight); | ||
| } | ||
| List<Geometry> tiles = new ArrayList<>(); | ||
| for (int x = (int) xStart; x < xEnd; x += tileWidth) { | ||
| for (int y = (int) yStart; y < yEnd; y += tileHeight) { | ||
| Geometry tile = GeometryTools.createRectangle(x, y, tileWidth, tileHeight); | ||
| // straightforward case 1: | ||
| // if there's no intersection, we're in the bounding box but not | ||
| // the parent | ||
| if (!parent.intersects(tile)) { | ||
| continue; | ||
| } | ||
| // straightforward case 2: | ||
| // tile is cleanly within roi | ||
| if (parent.contains(tile)) { | ||
| tiles.add(tile); | ||
| continue; | ||
| } | ||
|
|
||
| // trimming: | ||
| if (trimToParent) { | ||
| // trim the tile to fit the parent | ||
| tile = tile.intersection(parent); | ||
| tiles.add(tile); | ||
| } else if (!filterByCentroid | parent.contains(tile.getCentroid())) { | ||
| // If we aren't trimming based on centroids, | ||
| // or it'd be included anyway | ||
| tiles.add(tile); | ||
| } | ||
| } | ||
| } | ||
| return tiles; | ||
| } | ||
|
|
||
| /** | ||
| * Create a list of {@link ROI} tiles from the input. These may | ||
| * not all be rectangular based on the settings used. | ||
| * @param parent the object that will be split into tiles. | ||
| * @return a list of tiles | ||
| */ | ||
| public List<ROI> createROIs(ROI parent) { | ||
| return createGeometries(parent.getGeometry()).stream() | ||
| .map(g -> GeometryTools.geometryToROI(g, parent.getImagePlane())) | ||
| .collect(Collectors.toList()); | ||
| } | ||
|
|
||
| /** | ||
| * Create a list of {@link PathObject} tiles from the input. These may | ||
| * not all be rectangular based on the settings used. | ||
| * @param parent the object that will be split into tiles. | ||
| * @param creator a function used to create the desired type | ||
| * of {@link PathObject} | ||
| * @return a list of tiles | ||
| */ | ||
| public List<PathObject> createObjects(ROI parent, Function<ROI, PathObject> creator) { | ||
| return createROIs(parent).stream().map(creator).collect(Collectors.toList()); | ||
| } | ||
|
|
||
| /** | ||
| * Create a list of {@link PathTileObject} tiles from the input. These may | ||
| * not all be rectangular based on the settings used. | ||
| * @param parent the object that will be split into tiles. | ||
| * @return a list of tiles | ||
| */ | ||
| public List<PathObject> createTiles(ROI parent) { | ||
| return createObjects(parent, PathObjects::createTileObject); | ||
| } | ||
|
|
||
| /** | ||
| * Create a list of {@link PathAnnotationObject} tiles from the input. These may | ||
| * not all be rectangular based on the settings used. | ||
| * @param parent the object that will be split into tiles. | ||
| * @return a list of tiles | ||
| */ | ||
| public List<PathObject> createAnnotations(ROI parent) { | ||
| return createObjects(parent, PathObjects::createAnnotationObject); | ||
| } | ||
|
|
||
| private static double calculateOffset(final int tileDim, final double parentDim) { | ||
| double mod = parentDim % tileDim; | ||
| if (mod == 0) { | ||
| return 0; | ||
| } | ||
| return mod / 2; | ||
| } | ||
| } |
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