First draft of preview client that handles import of h5 tile data fol…

…lowed by n5 export of the data in one spark run. Import logic adapted from EM_recon_pipeline python code. Export logic specific to previews pulled from N5Client. N5Client.renderStack method is used to do the primary export work.

render-app/src/main/java/org/janelia/alignment/util/H5Util.java

@@ -0,0 +1,169 @@
+package org.janelia.alignment.util;
+
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.janelia.alignment.ImageAndMask;
+import org.janelia.alignment.loader.DynamicMaskLoader;
+import org.janelia.alignment.loader.ImageLoader.LoaderType;
+import org.janelia.alignment.spec.ChannelSpec;
+import org.janelia.alignment.spec.LayoutData;
+import org.janelia.alignment.spec.LeafTransformSpec;
+import org.janelia.alignment.spec.ListTransformSpec;
+import org.janelia.alignment.spec.ReferenceTransformSpec;
+import org.janelia.alignment.spec.TileSpec;
+import org.janelia.saalfeldlab.n5.DatasetAttributes;
+import org.janelia.saalfeldlab.n5.hdf5.N5HDF5Reader;
+
+/**
+ * Utilities for working with HDF5 files.
+ *
+ * @author Eric Trautman
+ */
+public class H5Util {
+
+    /**
+     * @param  h5Reader              reader for HDF5 data set.
+     * @param  h5Path                path of HDF5 file containing tile data.
+     * @param  row                   tile row.
+     * @param  column                tile column.
+     * @param  z                     z coordinate of tile.
+     * @param  maskWidth             width of masked area at left edge of tile (or null to leave left edge unmasked).
+     * @param  maskHeight            height of masked area at top of tile (or null to leave top unmasked).
+     * @param  referenceTransformId  id of scan correction transform used for all tiles (or null to skip correction).
+     *
+     * @return a {@link TileSpec} without setting the bounding box.
+     *
+     * @throws IllegalArgumentException
+     *   if the h5 tile data cannot be read or is missing any required attributes.
+     */
+    public static TileSpec buildTileSpecWithoutBoundingBox(final N5HDF5Reader h5Reader,
+                                                           final String h5Path,
+                                                           final int row,
+                                                           final int column,
+                                                           final double z,
+                                                           final Integer maskWidth,
+                                                           final Integer maskHeight,
+                                                           final String referenceTransformId)
+            throws IllegalArgumentException {
+
+        final String tileGroup = String.format("/0-%d-%d", row, column);
+
+        final String tileIdPrefix;
+        final String datFileNameKey = "dat_file_name";
+
+        final String datFileName;
+        try {
+            datFileName = h5Reader.getAttribute(tileGroup, datFileNameKey, String.class);
+        } catch (final NoSuchMethodError e) {
+            throw new IllegalArgumentException(
+                    "Failed to read " + datFileNameKey + " attribute from dataSet '" + tileGroup + "' of " + h5Path +
+                    ".  If you are running within a Spark job, this error could occur because the default GSON " +
+                    "library is very old (GSON 2.2.4) for many versions of Spark.  To fix this, add something like " +
+                    "--conf spark.executor.extraClassPath=.../gson-2.10.1.jar to your launch command.", e);
+        }
+
+        final Matcher matcher = DAT_FILE_NAME_PATTERN.matcher(datFileName);
+        if (matcher.matches() && matcher.groupCount() == 1) {
+            tileIdPrefix = matcher.group(1);
+        } else {
+            throw new IllegalArgumentException("invalid dat_file_name '" + datFileName +
+                                               "' for group '" + tileGroup + "' of " + h5Path);
+        }
+        final String tileId = tileIdPrefix + "." + z;
+
+        final TileSpec tileSpec = new TileSpec();
+        tileSpec.setTileId(tileId);
+
+        final Integer stageX = h5Reader.getAttribute(tileGroup, "FirstX", Integer.class);
+        if (stageX == null) {
+            throw new IllegalArgumentException("no FirstX defined for group '" + tileGroup + "' of " + h5Path);
+        }
+
+        final Integer stageY = h5Reader.getAttribute(tileGroup, "FirstY", Integer.class);
+        if (stageY == null) {
+            throw new IllegalArgumentException("no FirstY defined for group '" + tileGroup + "' of " + h5Path);
+        }
+
+        final Integer imageWidth = h5Reader.getAttribute(tileGroup, "XResolution", Integer.class);
+        if (imageWidth == null) {
+            throw new IllegalArgumentException("no XResolution defined for group '" + tileGroup + "' of " + h5Path);
+        }
+
+        final Integer imageHeight = h5Reader.getAttribute(tileGroup, "YResolution", Integer.class);
+        if (imageHeight == null) {
+            throw new IllegalArgumentException("no YResolution defined for group '" + tileGroup + "' of " + h5Path);
+        }
+
+        // make sure the mipmap.0 group and datasetAttributes exist, though we don't use them directly here
+        final String mipmapZeroGroup = tileGroup + "/mipmap.0";
+        final DatasetAttributes datasetAttributes = h5Reader.getDatasetAttributes(mipmapZeroGroup);
+        if (datasetAttributes == null) {
+            throw new IllegalArgumentException("no datasetAttributes defined for group '" + mipmapZeroGroup +
+                                               "' of " + h5Path);
+        }
+
+        // TODO: figure out how to include/derive distanceZ if that ever becomes relevant
+        //       - python code calculates distanceZ from working distances (WD) of current and prior layer tiles:
+        //         distance_z = (working_distance - prior_working_distance) * 1000000
+
+        final LayoutData layoutData = new LayoutData(String.valueOf(z),
+                                                     null,
+                                                     null,
+                                                     row,
+                                                     column,
+                                                     stageX.doubleValue(),
+                                                     stageY.doubleValue(),
+                                                     null);
+        tileSpec.setLayout(layoutData);
+        tileSpec.setZ(z);
+        tileSpec.setWidth(imageWidth.doubleValue());
+        tileSpec.setHeight(imageHeight.doubleValue());
+
+        // all HDF5 source data is assumed to be 8-bit unsigned data
+        tileSpec.setMinAndMaxIntensity(0.0, 255.0, null);
+
+        final ChannelSpec channelSpec = new ChannelSpec();
+
+        // file:///nrs/cellmap/data/jrc_mus-pancreas-5/align/Merlin-6262/2023/10/06/19/Merlin-6262_23-10-06_195119.uint8.h5
+        //   ?dataSet=/0-0-0/mipmap.0&z=0
+        final String imageUrl = "file://" + h5Path + "?dataSet=" + mipmapZeroGroup + "&z=0";
+
+        String maskUrl = null;
+        LoaderType maskLoaderType = null;
+        if ((maskWidth != null) || (maskHeight != null)) {
+            final int minX = maskWidth == null ? 0 : maskWidth;
+            final int minY = maskHeight == null ? 0 : maskHeight;
+            final DynamicMaskLoader.DynamicMaskDescription maskDescription =
+                    new DynamicMaskLoader.DynamicMaskDescription(minX, minY,
+                                                                 imageWidth, imageHeight,
+                                                                 imageWidth, imageHeight);
+
+            // mask://outside-box?minX=100&minY=30&maxX=8625&maxY=8250&width=8625&height=8250
+            maskUrl = maskDescription.toString();
+            maskLoaderType = LoaderType.DYNAMIC_MASK;
+        }
+
+        final ImageAndMask imageAndMask = new ImageAndMask(imageUrl, LoaderType.H5_SLICE, null,
+                                                           maskUrl, maskLoaderType, null);
+        channelSpec.putMipmap(0, imageAndMask);
+        tileSpec.addChannel(channelSpec);
+
+        final ListTransformSpec transformList = new ListTransformSpec();
+        if (referenceTransformId != null) {
+            transformList.addSpec(new ReferenceTransformSpec(referenceTransformId));
+        }
+        transformList.addSpec(new LeafTransformSpec("mpicbg.trakem2.transform.AffineModel2D",
+                                                    "1 0 0 1 " + stageX + " " + stageY));
+        tileSpec.setTransforms(transformList);
+
+        // simplify the channel spec by converting it to legacy form
+        tileSpec.convertSingleChannelSpecToLegacyForm();
+
+        return tileSpec;
+    }
+
+    // Merlin-6262_23-10-06_195119_0-0-0.dat
+    private static final Pattern DAT_FILE_NAME_PATTERN =
+            Pattern.compile("^.*_(\\d{2}-\\d{2}-\\d{2}_\\d{6}_\\d-\\d-\\d)\\.dat$");
+}