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Adds multiscale registration command for Warpy and QuPath
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292 changes: 292 additions & 0 deletions
292
...ain/java/ch/epfl/biop/scijava/command/source/register/WarpyMultiscaleRegisterCommand.java
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| package ch.epfl.biop.scijava.command.source.register; | ||
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| import bdv.util.QuPathBdvHelper; | ||
| import bdv.viewer.SourceAndConverter; | ||
| import ij.IJ; | ||
| import net.imglib2.realtransform.AffineTransform3D; | ||
| import net.imglib2.realtransform.InvertibleRealTransform; | ||
| import net.imglib2.realtransform.InvertibleRealTransformSequence; | ||
| import net.imglib2.realtransform.RealTransform; | ||
| import net.imglib2.realtransform.RealTransformSequence; | ||
| import org.apache.commons.io.FileUtils; | ||
| import org.scijava.Context; | ||
| import org.scijava.ItemVisibility; | ||
| import org.scijava.command.Command; | ||
| import org.scijava.command.CommandModule; | ||
| import org.scijava.command.CommandService; | ||
| import org.scijava.plugin.Parameter; | ||
| import org.scijava.plugin.Plugin; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
| import sc.fiji.bdvpg.scijava.ScijavaBdvDefaults; | ||
| import sc.fiji.bdvpg.scijava.command.BdvPlaygroundActionCommand; | ||
| import sc.fiji.bdvpg.services.SourceAndConverterServices; | ||
| import sc.fiji.persist.ScijavaGsonHelper; | ||
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| import java.io.File; | ||
| import java.nio.charset.Charset; | ||
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| @Plugin(type = BdvPlaygroundActionCommand.class, menuPath = ScijavaBdvDefaults.RootMenu+"Sources>Register>QuPath - Create Warpy Multiscale Registration") | ||
| public class WarpyMultiscaleRegisterCommand implements Command { | ||
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| private static Logger logger = LoggerFactory.getLogger(WarpyMultiscaleRegisterCommand.class); | ||
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| @Parameter(visibility = ItemVisibility.MESSAGE, persist = false, style = "message") | ||
| String message = "<html><h1>QuPath Warpy multiscale registration</h1>Please select a list of moving and a list of fixed source<br></html>"; | ||
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| @Parameter(label = "Number of registration scales (# registration x2 per scale)", style = "slider", min = "2", max="8", callback = "updateInfo") | ||
| int n_scales = 4; | ||
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| @Parameter(visibility = ItemVisibility.MESSAGE, required = false) | ||
| String infoRegistration = ""; | ||
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| @Parameter(label = "Fixed source", callback = "updateMessage", style = "sorted") | ||
| SourceAndConverter<?>[] fixed_sources; | ||
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| @Parameter(label = "Moving source", callback = "updateMessage", style = "sorted") | ||
| SourceAndConverter<?>[] moving_sources; | ||
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| @Parameter(label = "Remove images z-offsets") | ||
| boolean remove_z_offset = true; | ||
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| @Parameter(label = "Center moving image with fixed image") | ||
| boolean center_moving_image = true; | ||
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| @Parameter(label = "Number of pixel for each block of image used for the registration (default 128)") | ||
| int pixels_per_block = 128; | ||
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| @Parameter(label = "Number of iterations for each registration (default 100)") | ||
| int max_iteration_number_per_scale = 100; | ||
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| @Parameter | ||
| CommandService cs; | ||
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| @Parameter | ||
| Context scijavaCtx; | ||
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| @Override | ||
| public void run() { | ||
| try { | ||
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| // Several checks before we even start the registration | ||
| // - Is there an associated qupath project ? | ||
| if (!QuPathBdvHelper.isSourceLinkedToQuPath(fixed_sources[0])) { | ||
| logger.error("Error : the fixed source is not associated to a QuPath project"); | ||
| IJ.error("Error : the fixed source is not associated to a QuPath project"); | ||
| return; | ||
| } | ||
| if (!QuPathBdvHelper.isSourceLinkedToQuPath(moving_sources[0])) { | ||
| logger.error("Error : the moving source is not associated to a QuPath project"); | ||
| IJ.error("Error : the moving source is not associated to a QuPath project"); | ||
| return; | ||
| } | ||
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| // - Is it the same project ? | ||
| String qupathProjectMoving = QuPathBdvHelper.getProjectFile(moving_sources[0]).getAbsolutePath(); | ||
| String qupathProjectFixed = QuPathBdvHelper.getProjectFile(fixed_sources[0]).getAbsolutePath(); | ||
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| if (!qupathProjectMoving.equals(qupathProjectFixed)) { | ||
| logger.error("Error : the moving source and the fixed source are not from the same qupath project"); | ||
| IJ.error("Error : the moving source and the fixed source are not from the same qupath project"); | ||
| return; | ||
| } | ||
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| // - Are they different entries ? | ||
| File moving_entry_folder = QuPathBdvHelper.getDataEntryFolder(moving_sources[0]); | ||
| File fixed_entry_folder = QuPathBdvHelper.getDataEntryFolder(fixed_sources[0]); | ||
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| if (moving_entry_folder.getAbsolutePath().equals(fixed_entry_folder.getAbsolutePath())) { | ||
| logger.error("Error : the moving source and the fixed source should belong to different qupath entries (you can't move two channels of the same image, unless you duplicate the images in QuPath)"); | ||
| IJ.error("Error : the moving source and the fixed source should belong to different qupath entries (you can't move two channels of the same image, unless you duplicate the images in QuPath)"); | ||
| return; | ||
| } | ||
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| CommandModule module = cs.run(MultiscaleRegisterCommand.class, true, | ||
| "fixed", fixed_sources, | ||
| "moving", moving_sources, | ||
| "sources_to_transform", moving_sources, | ||
| "n_scales", n_scales, | ||
| "remove_z_offset", remove_z_offset, | ||
| "center_moving_image", center_moving_image, | ||
| "pixels_per_block", pixels_per_block, | ||
| "max_iteration_number_per_scale", max_iteration_number_per_scale, | ||
| "show_details", false, | ||
| "debug", false | ||
| ).get(); | ||
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| // Get transform | ||
| RealTransform rt = (RealTransform) module.getOutput("transformation"); | ||
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| // We don't want to keep the transformed sources in memory | ||
| SourceAndConverterServices | ||
| .getSourceAndConverterService() | ||
| .remove((SourceAndConverter[]) module.getOutput("transformedSources")); | ||
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| RealTransform transformSequence; | ||
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| // Because QuPath works in pixel coordinates and bdv playground in real space coordinates | ||
| // We need to account for this | ||
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| AffineTransform3D movingToPixel = new AffineTransform3D(); | ||
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| moving_sources[0].getSpimSource().getSourceTransform(0,0,movingToPixel); | ||
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| AffineTransform3D fixedToPixel = new AffineTransform3D(); | ||
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| fixed_sources[0].getSpimSource().getSourceTransform(0,0,fixedToPixel); | ||
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| if (rt instanceof InvertibleRealTransform) { | ||
| InvertibleRealTransformSequence irts = new InvertibleRealTransformSequence(); | ||
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| irts.add(fixedToPixel); | ||
| irts.add((InvertibleRealTransform) rt); | ||
| irts.add(movingToPixel.inverse()); | ||
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| transformSequence = irts; | ||
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| } else { | ||
| RealTransformSequence rts = new RealTransformSequence(); | ||
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| rts.add(fixedToPixel); | ||
| rts.add(rt); | ||
| rts.add(movingToPixel.inverse()); | ||
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| transformSequence = rts; | ||
| } | ||
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| String jsonMovingToFixed = ScijavaGsonHelper.getGson(scijavaCtx).toJson(transformSequence, RealTransform.class); | ||
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| //QuPathEntryEntity movingEntity = QuPathBdvHelper.getQuPathEntityFromSource(moving_source); | ||
| //QuPathEntryEntity fixedEntity = QuPathBdvHelper.getQuPathEntityFromSource(fixed_source); | ||
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| //int moving_series_index = movingEntity.getId(); | ||
| //int fixed_series_index = fixedEntity.getId(); | ||
| int moving_series_entry_id = QuPathBdvHelper.getEntryId(moving_sources[0]); | ||
| int fixed_series_entry_id = QuPathBdvHelper.getEntryId(fixed_sources[0]); | ||
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| String movingToFixedLandmarkName = "transform_"+moving_series_entry_id+"_"+fixed_series_entry_id+".json"; | ||
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| File result = new File(moving_entry_folder.getAbsolutePath(), movingToFixedLandmarkName); | ||
| FileUtils.writeStringToFile(result, jsonMovingToFixed, Charset.defaultCharset()); | ||
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| IJ.log("Fixed: "+fixed_sources[0].getSpimSource().getName()+" | Moving: "+moving_sources[0].getSpimSource().getName()); | ||
| IJ.log("Transformation file successfully written to QuPath project: "+result); | ||
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| } catch (Exception e) { | ||
| e.printStackTrace(); | ||
| } | ||
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| } | ||
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| public void updateMessage() { | ||
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| String message = "<html><h1>QuPath Warpy multiscale registration</h1>"; | ||
| if (fixed_sources == null) { | ||
| message += "Please select one (or several) moving sources<br></html>"; | ||
| this.message = message; | ||
| return; | ||
| } | ||
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| if (moving_sources == null) { | ||
| message += "Please select one (or several) fixed sources<br></html>"; | ||
| this.message = message; | ||
| return; | ||
| } | ||
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| if (fixed_sources.length>1) { | ||
| message+="Only the first fixed source will be used. <br>"; | ||
| } | ||
| if (moving_sources.length>1) { | ||
| message+="Only the first moving source will be used. <br>"; | ||
| } | ||
| SourceAndConverter fixed_source = fixed_sources[0]; | ||
| SourceAndConverter moving_source = moving_sources[0]; | ||
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| if (fixed_source==null) { | ||
| message+="Please select a fixed source <br>"; | ||
| } else { | ||
| if (!QuPathBdvHelper.isSourceLinkedToQuPath(fixed_source)) { | ||
| message+="The fixed source is not originating from a QuPath project! <br>"; | ||
| } else { | ||
| if (moving_source == null) { | ||
| message += "Please select a moving source <br>"; | ||
| } else { | ||
| if (!QuPathBdvHelper.isSourceLinkedToQuPath(moving_source)) { | ||
| message += "The moving source is not originating from a QuPath project! <br>"; | ||
| } else { | ||
| try { | ||
| String qupathProjectMoving = QuPathBdvHelper.getProjectFile(moving_source).getAbsolutePath(); | ||
| String qupathProjectFixed = QuPathBdvHelper.getProjectFile(fixed_source).getAbsolutePath(); | ||
| if (!qupathProjectMoving.equals(qupathProjectFixed)) { | ||
| message+="Error : the moving source and the fixed source are not from the same qupath project"; | ||
| } else { | ||
| // - Are they different entries ? | ||
| File moving_entry_folder = QuPathBdvHelper.getDataEntryFolder(moving_source); | ||
| File fixed_entry_folder = QuPathBdvHelper.getDataEntryFolder(fixed_source); | ||
| if (moving_entry_folder.getAbsolutePath().equals(fixed_entry_folder.getAbsolutePath())) { | ||
| message+="Error : moving and fixed source should belong to different qupath entries. <br>"; | ||
| message+="You can't move two channels of the same image, <br>"; | ||
| message+="unless you duplicate the images in QuPath. <br>"; | ||
| message+="<ul>"; | ||
| message += "<li>Fixed: "+fixed_source.getSpimSource().getName()+"</li>"; | ||
| message += "<li>Moving: "+moving_source.getSpimSource().getName()+"</li>"; | ||
| message+="<ul>"; | ||
| } else { | ||
| message += "Registration task properly set: <br>"; | ||
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| message+="<ul>"; | ||
| message += "<li>Fixed: "+fixed_source.getSpimSource().getName()+"</li>"; | ||
| message += "<li>Moving: "+moving_source.getSpimSource().getName()+"</li>"; | ||
| message+="</ul>"; | ||
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| //QuPathEntryEntity movingEntity = QuPathBdvHelper.getQuPathEntityFromSource(moving_source); | ||
| //QuPathEntryEntity fixedEntity = QuPathBdvHelper.getQuPathEntityFromSource(fixed_source); | ||
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| int moving_series_index = QuPathBdvHelper.getEntryId(moving_source);//movingEntity.getId(); | ||
| int fixed_series_index = QuPathBdvHelper.getEntryId(fixed_source);//fixedEntity.getId(); | ||
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| String movingToFixedLandmarkName = "transform_"+moving_series_index+"_"+fixed_series_index+".json"; | ||
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| File result = new File(moving_entry_folder.getAbsolutePath(), movingToFixedLandmarkName); | ||
| if (result.exists()) { | ||
| message+="WARNING! A REGISTRATION FILE ALREADY EXISTS! You can:<br>"; | ||
| message+="<ul><li> Click <b>OK</b> to re-run the wizard and override it</li>"; | ||
| message+="<li> Run the command <b>Edit QuPath Registration</b> to edit this existing registration</li></ul>"; | ||
| } | ||
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| movingToFixedLandmarkName = "transform_"+fixed_series_index+"_"+moving_series_index+".json"; | ||
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| result = new File(fixed_entry_folder.getAbsolutePath(), movingToFixedLandmarkName); | ||
| if (result.exists()) { | ||
| message+="WARNING! AN <b>INVERSE</b> REGISTRATION FILE ALREADY EXISTS! You can:<br>"; | ||
| message+="<ul><li> Switch your fixed and moving selected source</li>"; | ||
| message+="<li> Erase the transformation file and run the wizard.</li></ul>"; | ||
| message+="Keeping both the forward and inverse transformation <br>"; | ||
| message+="will cause some ambiguity in QuPath. <br>"; | ||
| message+="Inverse transformation file:<br>"; | ||
| message+= result.getAbsolutePath().replace("\\","\\\\")+"<br>"; | ||
| } | ||
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| } | ||
| } | ||
| } catch (Exception e) { | ||
| message+= "Could not fetch the QuPath project error: "+e.getMessage()+"<br>"; | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| message+="</html>"; | ||
| this.message = message; | ||
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| } | ||
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| void updateInfo() { | ||
| int nReg = 4*((int) (Math.pow(2, n_scales-1)-1)); | ||
| infoRegistration = nReg+" registrations will be computed, resulting in "+(int) Math.pow(2, n_scales)+" control points"; | ||
| } | ||
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| } |
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