Examples with BioFormatsBdvOpener ch.epfl.biop.bdv.bioformats.bioformatssource.BioFormatsBdvOpener used on opensource projects

Example 1 with BioFormatsBdvOpener

use of ch.epfl.biop.bdv.bioformats.bioformatssource.BioFormatsBdvOpener in project bigdataviewer-biop-tools by BIOP.

the class QuPathImageLoader method getSetupImgLoader.

@Override
public BioFormatsSetupLoader<?, ?> getSetupImgLoader(int setupId) {
    if (imgLoaders.containsKey(setupId)) {
        // Already created - return it
        return imgLoaders.get(setupId);
    } else {
        QuPathEntryAndChannel qec = viewSetupToQuPathEntryAndChannel.get(setupId);
        BioFormatsBdvOpener opener = this.openerMap.get(qec.entry.uri);
        int iS = qec.entry.bioformatsIndex;
        int iC = qec.iChannel;
        logger.debug("loading qupath entry number = " + qec.entry + "setupId = " + setupId + " series" + iS + " channel " + iC);
        BioFormatsSetupLoader<?, ?> imgL = new BioFormatsSetupLoader(opener, iS, iC, tTypeGetter.get(setupId), vTypeGetter.get(setupId));
        imgLoaders.put(setupId, imgL);
        return imgL;
    }
}

Example 2 with BioFormatsBdvOpener

use of ch.epfl.biop.bdv.bioformats.bioformatssource.BioFormatsBdvOpener in project bigdataviewer-biop-tools by BIOP.

the class QuPathToSpimData method getSpimDataInstance.

public AbstractSpimData getSpimDataInstance(URI quPathProject, final BioFormatsBdvOpener openerModel) {
    viewSetupCounter = 0;
    nTileCounter = 0;
    maxTimepoints = -1;
    channelCounter = 0;
    // No Illumination
    Illumination dummy_ill = new Illumination(0);
    // No Angle
    Angle dummy_ang = new Angle(0);
    // Many View Setups
    List<ViewSetup> viewSetups = new ArrayList<>();
    try {
        JsonObject projectJson = ProjectIO.loadRawProject(new File(quPathProject));
        Gson gson = new Gson();
        MinimalQuPathProject project = gson.fromJson(projectJson, MinimalQuPathProject.class);
        logger.debug("Opening QuPath project " + project.uri);
        Set<QuPathImageLoader.QuPathBioFormatsSourceIdentifier> quPathSourceIdentifiers = new HashSet<>();
        // Performance
        Map<BioFormatsBdvOpener, IFormatReader> cachedReaders = new HashMap<>();
        project.images.forEach(image -> {
            logger.debug("Opening qupath image " + image);
            QuPathImageLoader.QuPathBioFormatsSourceIdentifier identifier = new QuPathImageLoader.QuPathBioFormatsSourceIdentifier();
            if (image.serverBuilder.builderType.equals("rotated")) {
                // "ROTATE_ANGLE" for instance "ROTATE_0", "ROTATE_270", etc
                String angleDegreesStr = image.serverBuilder.rotation.substring(7);
                logger.debug("Rotated image server (" + angleDegreesStr + ")");
                if (angleDegreesStr.equals("NONE")) {
                    identifier.angleRotationZAxis = 0;
                } else {
                    identifier.angleRotationZAxis = (Double.valueOf(angleDegreesStr) / 180.0) * Math.PI;
                }
                // To keep the metadata (pixel size for instance)
                MinimalQuPathProject.ServerBuilderMetadata metadata = image.serverBuilder.metadata;
                // Skips the rotation
                image.serverBuilder = image.serverBuilder.builder;
                image.serverBuilder.metadata = metadata;
            }
            if (image.serverBuilder.builderType.equals("uri")) {
                logger.debug("URI image server");
                if (image.serverBuilder.providerClassName.equals("qupath.lib.images.servers.bioformats.BioFormatsServerBuilder")) {
                    try {
                        URI uri = new URI(image.serverBuilder.uri.getScheme(), image.serverBuilder.uri.getHost(), image.serverBuilder.uri.getPath(), null);
                        // This appears to work more reliably than converting to a File
                        String filePath = Paths.get(uri).toString();
                        if (!openerMap.keySet().contains(image.serverBuilder.uri)) {
                            BioFormatsBdvOpener opener = new BioFormatsBdvOpener(openerModel).location(Paths.get(uri).toString());
                            opener = opener.ignoreMetadata();
                            openerMap.put(image.serverBuilder.uri, opener);
                            cachedReaders.put(opener, opener.getNewReader());
                            uriToFileIndexMap.put(image.serverBuilder.uri, fileIndexCounter);
                            fileIndexCounter++;
                        }
                        identifier.uri = image.serverBuilder.uri;
                        identifier.sourceFile = filePath;
                        identifier.indexInQuPathProject = project.images.indexOf(image);
                        identifier.entryID = project.images.get(identifier.indexInQuPathProject).entryID;
                        int iSerie = image.serverBuilder.args.indexOf("--series");
                        Tile tile = new Tile(nTileCounter);
                        nTileCounter++;
                        if (iSerie == -1) {
                            logger.error("Series not found in qupath project server builder!");
                            identifier.bioformatsIndex = -1;
                        } else {
                            identifier.bioformatsIndex = Integer.valueOf(image.serverBuilder.args.get(iSerie + 1));
                        }
                        logger.debug(identifier.toString());
                        quPathSourceIdentifiers.add(identifier);
                        BioFormatsBdvOpener opener = openerMap.get(image.serverBuilder.uri);
                        IFormatReader memo = cachedReaders.get(opener);
                        memo.setSeries(identifier.bioformatsIndex);
                        logger.debug("Number of Series : " + memo.getSeriesCount());
                        IMetadata omeMeta = (IMetadata) memo.getMetadataStore();
                        memo.setMetadataStore(omeMeta);
                        logger.debug("\t Serie " + identifier.bioformatsIndex + " Number of timesteps = " + omeMeta.getPixelsSizeT(identifier.bioformatsIndex).getNumberValue().intValue());
                        // ---------- Serie > Channels
                        logger.debug("\t Serie " + identifier.bioformatsIndex + " Number of channels = " + omeMeta.getChannelCount(identifier.bioformatsIndex));
                        IntStream channels = IntStream.range(0, omeMeta.getChannelCount(identifier.bioformatsIndex));
                        if (omeMeta.getPixelsSizeT(identifier.bioformatsIndex).getNumberValue().intValue() > maxTimepoints) {
                            maxTimepoints = omeMeta.getPixelsSizeT(identifier.bioformatsIndex).getNumberValue().intValue();
                        }
                        // number of pixels .. no calibration
                        Dimensions dims = BioFormatsMetaDataHelper.getSeriesDimensions(omeMeta, identifier.bioformatsIndex);
                        logger.debug("X:" + dims.dimension(0) + " Y:" + dims.dimension(1) + " Z:" + dims.dimension(2));
                        VoxelDimensions voxDims = BioFormatsMetaDataHelper.getSeriesVoxelDimensions(omeMeta, identifier.bioformatsIndex, opener.u, opener.voxSizeReferenceFrameLength);
                        QuPathEntryEntity qpentry = new QuPathEntryEntity(identifier.entryID);
                        qpentry.setName(QuPathEntryEntity.getNameFromURIAndSerie(identifier.uri, identifier.bioformatsIndex));
                        qpentry.setQuPathProjectionLocation(Paths.get(quPathProject).toString());
                        channels.forEach(iCh -> {
                            QuPathImageLoader.QuPathEntryAndChannel usc = new QuPathImageLoader.QuPathEntryAndChannel(identifier, iCh);
                            viewSetupToQuPathEntryAndChannel.put(viewSetupCounter, usc);
                            int ch_id = getChannelId(omeMeta, identifier.bioformatsIndex, iCh, memo.isRGB());
                            String setupName = image.imageName + "_" + getChannelName(omeMeta, identifier.bioformatsIndex, iCh);
                            logger.debug(setupName);
                            ViewSetup vs = new ViewSetup(viewSetupCounter, setupName, dims, voxDims, // Tile is index of Serie
                            tile, channelIdToChannel.get(ch_id), dummy_ang, dummy_ill);
                            viewSetupToImageEntry.put(viewSetupCounter, image);
                            FileIndex fi = new FileIndex(uriToFileIndexMap.get(identifier.uri), identifier.sourceFile);
                            vs.setAttribute(fi);
                            SeriesNumber sn = new SeriesNumber(identifier.bioformatsIndex);
                            vs.setAttribute(sn);
                            vs.setAttribute(qpentry);
                            // Attempt to set color
                            Displaysettings ds = new Displaysettings(viewSetupCounter);
                            ds.min = 0;
                            ds.max = 255;
                            ds.isSet = false;
                            // ----------- Color
                            ARGBType color = BioFormatsMetaDataHelper.getColorFromMetadata(omeMeta, identifier.bioformatsIndex, iCh);
                            if (color != null) {
                                ds.isSet = true;
                                ds.color = new int[] { ARGBType.red(color.get()), ARGBType.green(color.get()), ARGBType.blue(color.get()), ARGBType.alpha(color.get()) };
                            }
                            vs.setAttribute(ds);
                            viewSetups.add(vs);
                            logger.debug("View Setup " + viewSetupCounter + " series " + iSerie + " channel " + iCh);
                            viewSetupCounter++;
                        });
                    } catch (URISyntaxException e) {
                        logger.error("URI Syntax error " + e.getMessage());
                        e.printStackTrace();
                    }
                } else {
                    logger.error("Unsupported " + image.serverBuilder.providerClassName + " class name provider");
                    IJ.log("Unsupported " + image.serverBuilder.providerClassName + " class name provider");
                }
            } else {
                logger.error("Unsupported " + image.serverBuilder.builderType + " server builder");
                IJ.log("Unsupported " + image.serverBuilder.builderType + " server builder");
            }
        });
        // ------------------- BUILDING SPIM DATA
        List<TimePoint> timePoints = new ArrayList<>();
        IntStream.range(0, maxTimepoints).forEach(tp -> timePoints.add(new TimePoint(tp)));
        final ArrayList<ViewRegistration> registrations = new ArrayList<>();
        List<ViewId> missingViews = new ArrayList<>();
        for (int iViewSetup = 0; iViewSetup < viewSetupCounter; iViewSetup++) {
            QuPathImageLoader.QuPathEntryAndChannel usc = viewSetupToQuPathEntryAndChannel.get(iViewSetup);
            BioFormatsBdvOpener opener = openerMap.get(usc.entry.uri);
            IFormatReader memo = cachedReaders.get(openerMap.get(usc.entry.uri));
            final IMetadata omeMeta = (IMetadata) memo.getMetadataStore();
            final int bfIndex = usc.entry.bioformatsIndex;
            final int nTimepoints = omeMeta.getPixelsSizeT(bfIndex).getNumberValue().intValue();
            final int vs = iViewSetup;
            AffineTransform3D affine = BioFormatsMetaDataHelper.getSeriesRootTransform(omeMeta, bfIndex, opener.u, // AffineTransform3D positionPreTransform,
            opener.positionPreTransformMatrixArray, // AffineTransform3D positionPostTransform,
            opener.positionPostTransformMatrixArray, opener.positionReferenceFrameLength, // boolean positionIsImageCenter,
            opener.positionIsImageCenter, // voxSizePreTransform,
            opener.voxSizePreTransformMatrixArray, // AffineTransform3D voxSizePostTransform,
            opener.voxSizePostTransformMatrixArray, // null, //Length voxSizeReferenceFrameLength,
            opener.voxSizeReferenceFrameLength, // axesOfImageFlip
            opener.axesOfImageFlip);
            MinimalQuPathProject.PixelCalibrations pixelCalibrations = null;
            if (viewSetupToImageEntry.get(vs) != null) {
                if (viewSetupToImageEntry.get(vs).serverBuilder != null)
                    if (viewSetupToImageEntry.get(vs).serverBuilder.metadata != null)
                        pixelCalibrations = viewSetupToImageEntry.get(vs).serverBuilder.metadata.pixelCalibration;
            }
            boolean performQuPathRescaling = false;
            AffineTransform3D quPathRescaling = new AffineTransform3D();
            if (pixelCalibrations != null) {
                double scaleX = 1.0;
                double scaleY = 1.0;
                double scaleZ = 1.0;
                Length[] voxSizes = BioFormatsMetaDataHelper.getSeriesVoxelSizeAsLengths(omeMeta, bfIndex);
                if (pixelCalibrations.pixelWidth != null) {
                    MinimalQuPathProject.PixelCalibration pc = pixelCalibrations.pixelWidth;
                    // if (pc.unit.equals("um")) {
                    if ((voxSizes[0] != null) && (voxSizes[0].value(UNITS.MICROMETER) != null)) {
                        logger.debug("xVox size = " + pc.value + " micrometer");
                        scaleX = pc.value / voxSizes[0].value(UNITS.MICROMETER).doubleValue();
                    } else {
                        Length defaultxPix = new Length(1, opener.u);
                        scaleX = pc.value / defaultxPix.value(UNITS.MICROMETER).doubleValue();
                        logger.debug("rescaling x");
                    }
                /*} else {
                            logger.warn("Unrecognized unit in QuPath project: "+pc.unit);
                        }*/
                }
                if (pixelCalibrations.pixelHeight != null) {
                    MinimalQuPathProject.PixelCalibration pc = pixelCalibrations.pixelHeight;
                    // if (pc.unit.equals("um")) {
                    if ((voxSizes[1] != null) && (voxSizes[1].value(UNITS.MICROMETER) != null)) {
                        scaleY = pc.value / voxSizes[1].value(UNITS.MICROMETER).doubleValue();
                    } else {
                        Length defaultxPix = new Length(1, opener.u);
                        scaleY = pc.value / defaultxPix.value(UNITS.MICROMETER).doubleValue();
                        logger.debug("rescaling y");
                    }
                /*} else {
                            logger.warn("Unrecognized unit in QuPath project: "+pc.unit);
                        }*/
                }
                if (pixelCalibrations.zSpacing != null) {
                    MinimalQuPathProject.PixelCalibration pc = pixelCalibrations.zSpacing;
                    // if (pc.unit.equals("um")) { problem with micrometer character
                    if ((voxSizes[2] != null) && (voxSizes[2].value(UNITS.MICROMETER) != null)) {
                        scaleZ = pc.value / voxSizes[2].value(UNITS.MICROMETER).doubleValue();
                    } else {
                        if ((voxSizes[2] != null)) {
                        } else {
                            logger.warn("Null Z voxel size");
                        }
                    // logger.warn("Null Z voxel size");
                    }
                /*} else {
                            logger.warn("Unrecognized unit in QuPath project: "+pc.unit);
                        }*/
                }
                logger.debug("ScaleX: " + scaleX + " scaleY:" + scaleY + " scaleZ:" + scaleZ);
                if ((Math.abs(scaleX - 1.0) > 0.0001) || (Math.abs(scaleY - 1.0) > 0.0001) || (Math.abs(scaleZ - 1.0) > 0.0001)) {
                    logger.debug("Perform QuPath rescaling");
                    quPathRescaling.scale(scaleX, scaleY, scaleZ);
                    double oX = affine.get(0, 3);
                    double oY = affine.get(1, 3);
                    double oZ = affine.get(2, 3);
                    affine.preConcatenate(quPathRescaling);
                    affine.set(oX, 0, 3);
                    affine.set(oY, 1, 3);
                    affine.set(oZ, 2, 3);
                }
            }
            logger.debug("ViewSetup : " + vs + " append view registrations ");
            timePoints.forEach(iTp -> {
                if (iTp.getId() < nTimepoints) {
                    registrations.add(new ViewRegistration(iTp.getId(), vs, affine));
                } else {
                    missingViews.add(new ViewId(iTp.getId(), vs));
                }
            });
        }
        // Cleaning opened readers
        cachedReaders.values().forEach(reader -> {
            try {
                reader.close();
            } catch (IOException e) {
                e.printStackTrace();
            }
        });
        SequenceDescription sd = new SequenceDescription(new TimePoints(timePoints), viewSetups, null, new MissingViews(missingViews));
        sd.setImgLoader(new QuPathImageLoader(quPathProject, openerModel, sd, openerModel.nFetcherThread, openerModel.numPriorities));
        final SpimData spimData = new SpimData(null, sd, new ViewRegistrations(registrations));
        return spimData;
    } catch (Exception e) {
        e.printStackTrace();
    }
    return null;
}

Example 3 with BioFormatsBdvOpener

use of ch.epfl.biop.bdv.bioformats.bioformatssource.BioFormatsBdvOpener in project bigdataviewer-biop-tools by BIOP.

the class ReorderDatasetCommand method run.

@Override
public void run() {
    if (xmlout.exists()) {
        IJ.error("The output file already exist! Skipping execution");
    } else {
        try {
            BioFormatsBdvOpener opener = BioFormatsConvertFilesToSpimData.getDefaultOpener(file.getAbsolutePath()).micrometer();
            IFormatReader reader = opener.getNewReader();
            // .getSeriesRootTransform()
            Length[] voxSizes = BioFormatsMetaDataHelper.getSeriesVoxelSizeAsLengths((IMetadata) reader.getMetadataStore(), 0);
            double pixSizeXYMicrometer = voxSizes[0].value(UNITS.MICROMETER).doubleValue();
            double scalingForBigStitcher = 1 / pixSizeXYMicrometer;
            reader.close();
            AbstractSpimData<?> asd = BioFormatsConvertFilesToSpimData.getSpimData(opener.voxSizeReferenceFrameLength(new Length(1, UNITS.MICROMETER)).positionReferenceFrameLength(new Length(1, UNITS.MICROMETER)));
            String intermediateXml = FilenameUtils.removeExtension(xmlout.getAbsolutePath()) + "_nonreordered.xml";
            System.out.println(intermediateXml);
            // Remove display settings attributes because this causes issues with BigStitcher
            SpimDataHelper.removeEntities(asd, Displaysettings.class, FileIndex.class);
            // Save non reordered dataset
            asd.setBasePath((new File(intermediateXml)).getParentFile());
            if (asd instanceof SpimData) {
                (new XmlIoSpimData()).save((SpimData) asd, intermediateXml);
            } else if (asd instanceof SpimDataMinimal) {
                (new XmlIoSpimDataMinimal()).save((SpimDataMinimal) asd, FilenameUtils.getName(intermediateXml));
            }
            // Creates reordered dataset
            LifReOrdered kd = new LifReOrdered(intermediateXml, nTiles, nChannels);
            kd.initialize();
            AbstractSpimData reshuffled = kd.constructSpimData();
            // TODO TOFIX
            reshuffled.setBasePath(new File(xmlout.getAbsolutePath()).getParentFile());
            new XmlIoSpimData().save((SpimData) reshuffled, xmlout.getAbsolutePath());
            SpimDataHelper.scale(reshuffled, "BigStitcher Scaling", scalingForBigStitcher);
            String bigstitcherXml = FilenameUtils.removeExtension(xmlout.getAbsolutePath()) + "_bigstitcher.xml";
            new XmlIoSpimData().save((SpimData) reshuffled, bigstitcherXml);
            IJ.log("- Dataset created - " + intermediateXml);
            IJ.log("- Reordered Dataset created - " + xmlout.getAbsolutePath());
            IJ.log("- Reordered Dataset created, rescaled for BigStitched - " + bigstitcherXml);
            IJ.log("Done!");
        } catch (Exception e) {
            e.printStackTrace();
        }
    }
}

Example 4 with BioFormatsBdvOpener

use of ch.epfl.biop.bdv.bioformats.bioformatssource.BioFormatsBdvOpener in project bigdataviewer-biop-tools by BIOP.

the class XmlIoQuPathImgLoader method fromXml.

@Override
public QuPathImageLoader fromXml(Element elem, File basePath, AbstractSequenceDescription<?, ?, ?> sequenceDescription) {
    try {
        final int numFetcherThreads = XmlHelpers.getInt(elem, CACHE_NUM_FETCHER);
        final int numPriorities = XmlHelpers.getInt(elem, CACHE_NUM_PRIORITIES);
        String openerClassName = XmlHelpers.getText(elem, OPENER_CLASS_TAG);
        if (!openerClassName.equals(BioFormatsBdvOpener.class.getName())) {
            throw new UnsupportedOperationException("Error class " + openerClassName + " not recognized.");
        }
        Gson gson = new Gson();
        String jsonInString = XmlHelpers.getText(elem, OPENER_MODEL_TAG);
        BioFormatsBdvOpener modelOpener = gson.fromJson(jsonInString, BioFormatsBdvOpener.class);
        // , Paths.get(imgLoader.getProjectURI()).toString());
        String qupathProjectUri = XmlHelpers.getText(elem, QUPATH_PROJECT_TAG);
        URI qpProjURI = (new Gson()).fromJson(qupathProjectUri, URI.class);
        return new QuPathImageLoader(qpProjURI, modelOpener, sequenceDescription, numFetcherThreads, numPriorities);
    } catch (final Exception e) {
        e.printStackTrace();
        throw new RuntimeException(e);
    }
}

Example 5 with BioFormatsBdvOpener

use of ch.epfl.biop.bdv.bioformats.bioformatssource.BioFormatsBdvOpener in project bigdataviewer-biop-tools by BIOP.

the class FileToBigStitcherDatasetCommand method run.

@Override
public void run() {
    if (xmlout.exists()) {
        IJ.error("The output file already exist! Skipping execution");
        return;
    }
    try {
        BioFormatsBdvOpener opener = BioFormatsConvertFilesToSpimData.getDefaultOpener(file.getAbsolutePath()).micrometer();
        IFormatReader reader = opener.getNewReader();
        // .getSeriesRootTransform()
        Length[] voxSizes = BioFormatsMetaDataHelper.getSeriesVoxelSizeAsLengths((IMetadata) reader.getMetadataStore(), 0);
        double pixSizeXYMicrometer = voxSizes[0].value(UNITS.MICROMETER).doubleValue();
        double scalingForBigStitcher = 1 / pixSizeXYMicrometer;
        reader.close();
        AbstractSpimData<?> asd = BioFormatsConvertFilesToSpimData.getSpimData(opener.voxSizeReferenceFrameLength(new Length(1, UNITS.MICROMETER)).positionReferenceFrameLength(new Length(1, UNITS.MICROMETER)));
        // Remove display settings attributes because this causes issues with BigStitcher
        SpimDataHelper.removeEntities(asd, Displaysettings.class, FileIndex.class);
        // Scaling such as size of one pixel = 1
        SpimDataHelper.scale(asd, "BigStitcher Scaling", scalingForBigStitcher);
        // TODO TOFIX
        asd.setBasePath(new File(xmlout.getAbsolutePath()).getParentFile());
        new XmlIoSpimData().save((SpimData) asd, xmlout.getAbsolutePath());
        IJ.log("- Done! Dataset created - " + xmlout.getAbsolutePath());
    } catch (Exception e) {
        e.printStackTrace();
    }
}