Examples with N5CosemMetadataParser org.janelia.saalfeldlab.n5.metadata.N5CosemMetadataParser used on opensource projects

Example 1 with N5CosemMetadataParser

use of org.janelia.saalfeldlab.n5.metadata.N5CosemMetadataParser in project bigwarp by saalfeldlab.

the class BigWarpInit method loadN5Source.

public static Source<?> loadN5Source(final String n5Root, final String n5Dataset) {
    final N5Reader n5;
    try {
        n5 = new N5Factory().openReader(n5Root);
    } catch (IOException e) {
        e.printStackTrace();
        return null;
    }
    final N5MetadataParser<?>[] PARSERS = new N5MetadataParser[] { new ImagePlusLegacyMetadataParser(), new N5CosemMetadataParser(), new N5SingleScaleMetadataParser(), new CanonicalMetadataParser(), new N5GenericSingleScaleMetadataParser() };
    final N5MetadataParser<?>[] GROUP_PARSERS = new N5MetadataParser[] { new N5CosemMultiScaleMetadata.CosemMultiScaleParser(), new N5ViewerMultiscaleMetadataParser(), new CanonicalMetadataParser() };
    N5Metadata meta = null;
    try {
        final N5DatasetDiscoverer discoverer = new N5DatasetDiscoverer(n5, N5DatasetDiscoverer.fromParsers(PARSERS), N5DatasetDiscoverer.fromParsers(GROUP_PARSERS));
        final N5TreeNode node = discoverer.discoverAndParseRecursive(n5Dataset);
        meta = node.getMetadata();
    } catch (IOException e) {
    }
    if (meta instanceof MultiscaleMetadata) {
        return openAsSourceMulti(n5, (MultiscaleMetadata<?>) meta, true);
    } else {
        return openAsSource(n5, meta, true);
    }
}

Example 2 with N5CosemMetadataParser

use of org.janelia.saalfeldlab.n5.metadata.N5CosemMetadataParser in project mars-fx by duderstadt-lab.

the class BdvViewTable method buildBdvTableIndex.

protected BorderPane buildBdvTableIndex() {
    TableView<MarsBdvSource> bdvTable = new TableView<MarsBdvSource>();
    addBdvSourceNameField = new CustomTextField();
    TableColumn<MarsBdvSource, String> typeColumn = new TableColumn<>();
    typeColumn.setCellFactory(TextFieldTableCell.forTableColumn());
    typeColumn.setCellValueFactory(bdvSource -> new ReadOnlyObjectWrapper<>((bdvSource.getValue().isN5()) ? "N5" : "HD5"));
    typeColumn.setSortable(false);
    typeColumn.setEditable(false);
    typeColumn.setPrefWidth(40);
    typeColumn.setMinWidth(40);
    typeColumn.setStyle("-fx-alignment: CENTER-LEFT;");
    bdvTable.getColumns().add(typeColumn);
    TableColumn<MarsBdvSource, MarsBdvSource> deleteColumn = new TableColumn<>();
    deleteColumn.setPrefWidth(30);
    deleteColumn.setMinWidth(30);
    deleteColumn.setCellValueFactory(param -> new ReadOnlyObjectWrapper<>(param.getValue()));
    deleteColumn.setCellFactory(param -> new TableCell<MarsBdvSource, MarsBdvSource>() {

        private final Button removeButton = new Button();

        @Override
        protected void updateItem(MarsBdvSource pRow, boolean empty) {
            super.updateItem(pRow, empty);
            if (pRow == null) {
                setGraphic(null);
                return;
            }
            removeButton.setGraphic(FontAwesomeIconFactory.get().createIcon(de.jensd.fx.glyphs.fontawesome.FontAwesomeIcon.MINUS, "1.0em"));
            removeButton.setCenterShape(true);
            removeButton.setStyle("-fx-background-radius: 5em; " + "-fx-min-width: 18px; " + "-fx-min-height: 18px; " + "-fx-max-width: 18px; " + "-fx-max-height: 18px;");
            setGraphic(removeButton);
            removeButton.setOnAction(e -> {
                marsImageMetadata.removeBdvSource(pRow.getName());
                loadBdvSources();
            });
        }
    });
    deleteColumn.setStyle("-fx-alignment: CENTER;");
    deleteColumn.setSortable(false);
    bdvTable.getColumns().add(deleteColumn);
    TableColumn<MarsBdvSource, String> nameColumn = new TableColumn<>("Name");
    nameColumn.setCellFactory(column -> EditCell.createStringEditCell());
    nameColumn.setOnEditCommit(event -> {
        String newBdvName = event.getNewValue();
        if (!marsImageMetadata.hasBdvSource(newBdvName)) {
            MarsBdvSource bdvSource = event.getRowValue();
            String oldName = bdvSource.getName();
            bdvSource.setName(newBdvName);
            // We need to rebuild the map to maintain the order in the table
            List<MarsBdvSource> bdvSourceList = new ArrayList<MarsBdvSource>();
            for (String key : marsImageMetadata.getBdvSourceNames()) {
                if (key.equals(oldName))
                    bdvSourceList.add(bdvSource);
                else
                    bdvSourceList.add(marsImageMetadata.getBdvSource(key));
            }
            marsImageMetadata.removeAllBdvSources();
            for (MarsBdvSource item : bdvSourceList) marsImageMetadata.putBdvSource(item);
        } else {
            ((MarsBdvSource) event.getTableView().getItems().get(event.getTablePosition().getRow())).setName(event.getOldValue());
            bdvTable.refresh();
        }
    });
    nameColumn.setCellValueFactory(bdvSource -> new ReadOnlyObjectWrapper<>(bdvSource.getValue().getName()));
    nameColumn.setSortable(false);
    nameColumn.setPrefWidth(100);
    nameColumn.setMinWidth(100);
    nameColumn.setStyle("-fx-alignment: CENTER-LEFT;");
    bdvTable.getColumns().add(nameColumn);
    bdvTable.setItems(bdvRowList);
    bdvTable.setEditable(true);
    bdvIndexTableListener = new ChangeListener<MarsBdvSource>() {

        public void changed(ObservableValue<? extends MarsBdvSource> observable, MarsBdvSource oldMarsBdvSource, MarsBdvSource newMarsBdvSource) {
            if (newMarsBdvSource != null)
                bdvSourceOptionsPane.setMarsBdvSource(newMarsBdvSource);
            else
                bdvSourceOptionsPane.setMarsBdvSource(null);
        }
    };
    bdvTable.getSelectionModel().selectedItemProperty().addListener(bdvIndexTableListener);
    Button addButton = new Button();
    addButton.setGraphic(FontAwesomeIconFactory.get().createIcon(de.jensd.fx.glyphs.fontawesome.FontAwesomeIcon.PLUS, "1.0em"));
    addButton.setCenterShape(true);
    addButton.setCursor(Cursor.DEFAULT);
    addButton.setStyle("-fx-background-radius: 5em; " + "-fx-min-width: 18px; " + "-fx-min-height: 18px; " + "-fx-max-width: 18px; " + "-fx-max-height: 18px;");
    addButton.setOnAction(e -> {
        if (!addBdvSourceNameField.getText().equals("") && !marsImageMetadata.hasBdvSource(addBdvSourceNameField.getText())) {
            MarsBdvSource bdvSource = new MarsBdvSource(addBdvSourceNameField.getText());
            switch(this.buttonType) {
                case 0:
                    bdvSource.setN5(true);
                    break;
                case 1:
                    bdvSource.setN5(false);
                    break;
            }
            if (bdvSource.isN5()) {
                SwingUtilities.invokeLater(new Runnable() {

                    @Override
                    public void run() {
                        DatasetSelectorDialog selectionDialog = new DatasetSelectorDialog(new N5ViewerReaderFun(), new N5BasePathFun(), System.getProperty(// no
                        "user.home"), // no
                        new N5MetadataParser[] {}, // parsers
                        new N5MetadataParser[] { new ImagePlusLegacyMetadataParser(), new N5CosemMetadataParser(), new N5SingleScaleMetadataParser(), new CanonicalMetadataParser(), new N5GenericSingleScaleMetadataParser() });
                        selectionDialog.setVirtualOption(false);
                        selectionDialog.setCropOption(false);
                        selectionDialog.setTreeRenderer(new N5DatasetTreeCellRenderer(true));
                        // Prevents NullPointerException
                        selectionDialog.setContainerPathUpdateCallback(x -> {
                        });
                        final Consumer<DataSelection> callback = (DataSelection dataSelection) -> {
                            Platform.runLater(new Runnable() {

                                @Override
                                public void run() {
                                    bdvSource.setPath(selectionDialog.getN5RootPath());
                                    bdvSource.setN5Dataset(dataSelection.metadata.get(0).getPath());
                                    bdvSource.setProperty("info", getDatasetInfo(((N5DatasetMetadata) dataSelection.metadata.get(0)).getAttributes()));
                                    marsImageMetadata.putBdvSource(bdvSource);
                                    loadBdvSources();
                                }
                            });
                        };
                        selectionDialog.run(callback);
                    }
                });
            } else {
                FileChooser fileChooser = new FileChooser();
                fileChooser.setTitle("Select xml");
                fileChooser.setInitialDirectory(new File(System.getProperty("user.home")));
                fileChooser.getExtensionFilters().add(new ExtensionFilter("xml file", "*.xml"));
                File path = fileChooser.showOpenDialog(getNode().getScene().getWindow());
                if (path != null) {
                    bdvSource.setPath(path.getAbsolutePath());
                    marsImageMetadata.putBdvSource(bdvSource);
                    loadBdvSources();
                }
            }
        }
    });
    addBdvSourceNameField.textProperty().addListener((observable, oldValue, newValue) -> {
        if (addBdvSourceNameField.getText().isEmpty()) {
            addBdvSourceNameField.setRight(new Label(""));
        } else {
            addBdvSourceNameField.setRight(addButton);
        }
    });
    addBdvSourceNameField.setStyle("-fx-background-radius: 2em; ");
    typeButton = new Button();
    typeButton.setText("N5");
    typeButton.setCenterShape(true);
    typeButton.setStyle("-fx-background-radius: 2em; " + "-fx-min-width: 60px; " + "-fx-min-height: 30px; " + "-fx-max-width: 60px; " + "-fx-max-height: 30px;");
    typeButton.setOnAction(e -> {
        buttonType++;
        if (buttonType > 1)
            buttonType = 0;
        switch(buttonType) {
            case 0:
                typeButton.setText("N5");
                typeButton.setGraphic(null);
                break;
            case 1:
                typeButton.setText("HD5");
                typeButton.setGraphic(null);
                break;
        }
    });
    BorderPane bomttomPane = new BorderPane();
    bomttomPane.setCenter(addBdvSourceNameField);
    bomttomPane.setLeft(typeButton);
    BorderPane bdvTableIndex = new BorderPane();
    bdvTableIndex.setCenter(bdvTable);
    bdvTableIndex.setBottom(bomttomPane);
    BorderPane.setMargin(addBdvSourceNameField, new Insets(5));
    BorderPane.setMargin(typeButton, new Insets(5));
    return bdvTableIndex;
}

Example 3 with N5CosemMetadataParser

use of org.janelia.saalfeldlab.n5.metadata.N5CosemMetadataParser in project bigwarp by saalfeldlab.

the class ApplyBigwarpPlugin method runN5Export.

public static <S, T extends NativeType<T> & NumericType<T>> void runN5Export(final BigWarpData<S> data, final List<SourceAndConverter<S>> sources, final String fieldOfViewOption, final Interval outputInterval, final Interpolation interp, final double[] offset, final double[] resolution, final String unit, final ProgressWriter progressWriter, final WriteDestinationOptions writeOpts, final ExecutorService exec) {
    final int nd = BigWarp.detectNumDims(data.sources);
    // setup n5 parameters
    final String dataset = writeOpts.n5Dataset;
    final int[] blockSize = writeOpts.blockSize;
    final Compression compression = writeOpts.compression;
    if (dataset == null || dataset.isEmpty()) {
        return;
    }
    N5Writer n5;
    try {
        n5 = new N5Factory().openWriter(writeOpts.pathOrN5Root);
    } catch (IOException e1) {
        e1.printStackTrace();
        return;
    }
    // build metadata
    final String[] axes = nd == 2 ? new String[] { "y", "x" } : new String[] { "z", "y", "x" };
    final String[] units = nd == 2 ? new String[] { unit, unit } : new String[] { unit, unit, unit };
    final N5CosemMetadata metadata = new N5CosemMetadata("", new N5CosemMetadata.CosemTransform(axes, resolution, offset, units), null);
    N5CosemMetadataParser parser = new N5CosemMetadataParser();
    // setup physical to pixel transform
    final AffineTransform3D resolutionTransform = new AffineTransform3D();
    resolutionTransform.set(resolution[0], 0, 0);
    resolutionTransform.set(resolution[1], 1, 1);
    if (resolution.length > 2)
        resolutionTransform.set(resolution[2], 2, 2);
    final AffineTransform3D offsetTransform = new AffineTransform3D();
    offsetTransform.set(offset[0], 0, 3);
    offsetTransform.set(offset[1], 1, 3);
    if (resolution.length > 2)
        offsetTransform.set(offset[2], 2, 3);
    final AffineTransform3D pixelRenderToPhysical = new AffineTransform3D();
    pixelRenderToPhysical.concatenate(resolutionTransform);
    pixelRenderToPhysical.concatenate(offsetTransform);
    // render and write
    final int N = data.movingSourceIndices.length;
    for (int i = 0; i < N; i++) {
        final int movingSourceIndex = data.movingSourceIndices[i];
        @SuppressWarnings("unchecked") final RealRandomAccessible<T> raiRaw = (RealRandomAccessible<T>) sources.get(movingSourceIndex).getSpimSource().getInterpolatedSource(0, 0, interp);
        // to pixel space
        final AffineRandomAccessible<T, AffineGet> rai = RealViews.affine(raiRaw, pixelRenderToPhysical.inverse());
        final IntervalView<T> img = Views.interval(Views.raster(rai), Intervals.zeroMin(outputInterval));
        final String srcName = data.sources.get(data.movingSourceIndices[i]).getSpimSource().getName();
        String destDataset = dataset;
        if (N > 1)
            destDataset = dataset + String.format("/%s", srcName.replace(" ", "_"));
        RandomAccessibleInterval<T> imgToWrite;
        if (nd == 2)
            imgToWrite = Views.hyperSlice(img, 2, 0);
        else
            imgToWrite = img;
        try {
            N5Utils.save(imgToWrite, n5, destDataset, blockSize, compression, exec);
            if (parser != null && metadata != null)
                parser.writeMetadata(metadata, n5, destDataset);
        } catch (Exception e) {
            e.printStackTrace();
        }
        progressWriter.setProgress((i + 1) / ((double) N));
    }
    progressWriter.setProgress(1.0);
}