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Merge pull request #504 from cmhulbert/feat/smoothAction
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Feat/smooth action
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@cmhulbert
cmhulbert authored Sep 1, 2023
2 parents b6eac3d + 606731c commit 84e364b
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Showing 19 changed files with 314 additions and 395 deletions.
4 changes: 1 addition & 3 deletions src/main/java/org/janelia/saalfeldlab/paintera/PainteraCommandLineArgs.java
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Expand Up @@ -76,8 +76,6 @@
import java.util.stream.Collectors;
import java.util.stream.Stream;

import static org.janelia.saalfeldlab.util.n5.N5Helpers.getReaderOrGetWriterIfExistsAndWritable;

@Command(name = "Paintera", showDefaultValues = true, resourceBundle = "org.janelia.saalfeldlab.paintera.PainteraCommandLineArgs", usageHelpWidth = 120,
parameterListHeading = "%n@|bold,underline Parameters|@:%n",
optionListHeading = "%n@|bold,underline Options|@:%n")
Expand Down Expand Up @@ -649,7 +647,7 @@ private void addToViewer(final PainteraBaseView viewer, final Supplier<String> p
for (final String container : containers) {
LOG.debug("Adding datasets for container {}", container);

N5Reader n5Container = getReaderOrGetWriterIfExistsAndWritable(container);
N5Reader n5Container = Paintera.getN5Factory().openWriterElseOpenReader(container);

final Predicate<String> datasetFilter = options.useDataset();
final ExecutorService es = getDiscoveryExecutorService();
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15 changes: 5 additions & 10 deletions src/main/java/org/janelia/saalfeldlab/paintera/data/n5/CommitCanvasN5.java
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Expand Up @@ -37,12 +37,7 @@
import org.janelia.saalfeldlab.labels.blocks.LabelBlockLookupKey;
import org.janelia.saalfeldlab.labels.blocks.n5.IsRelativeToContainer;
import org.janelia.saalfeldlab.labels.downsample.WinnerTakesAll;
import org.janelia.saalfeldlab.n5.ByteArrayDataBlock;
import org.janelia.saalfeldlab.n5.DataBlock;
import org.janelia.saalfeldlab.n5.DatasetAttributes;
import org.janelia.saalfeldlab.n5.LongArrayDataBlock;
import org.janelia.saalfeldlab.n5.N5Reader;
import org.janelia.saalfeldlab.n5.N5Writer;
import org.janelia.saalfeldlab.n5.*;
import org.janelia.saalfeldlab.n5.imglib2.N5LabelMultisets;
import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
import org.janelia.saalfeldlab.paintera.data.mask.persist.PersistCanvas;
Expand All @@ -57,7 +52,6 @@

import java.io.IOException;
import java.lang.invoke.MethodHandles;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
Expand Down Expand Up @@ -136,7 +130,8 @@ public void updateLabelBlockLookup(final List<TLongObjectMap<BlockDiff>> blockDi

LOG.debug("Found scale datasets {}", (Object)scaleUniqueLabels);
for (int level = 0; level < scaleUniqueLabels.length; ++level) {
final DatasetSpec datasetUniqueLabels = DatasetSpec.of(n5Writer, Paths.get(uniqueLabelsPath, scaleUniqueLabels[level]).toString());
final String uniqueLabelScalePath = N5URI.normalizeGroupPath(uniqueLabelsPath + n5Writer.getGroupSeparator() + scaleUniqueLabels[level]);
final DatasetSpec datasetUniqueLabels = DatasetSpec.of(n5Writer, uniqueLabelScalePath);
final TLongObjectMap<TLongHashSet> removedById = new TLongObjectHashMap<>();
final TLongObjectMap<TLongHashSet> addedById = new TLongObjectHashMap<>();
final TLongObjectMap<BlockDiff> blockDiffs = blockDiffsByLevel.get(level);
Expand Down Expand Up @@ -262,8 +257,8 @@ public List<TLongObjectMap<BlockDiff>> persistCanvas(final CachedCellImg<Unsigne

final TLongObjectHashMap<BlockDiff> blockDiffsAt = new TLongObjectHashMap<>();
blockDiffs.add(blockDiffsAt);
final DatasetSpec targetDataset = DatasetSpec.of(n5Writer, Paths.get(dataset, scaleDatasets[level]).toString());
final DatasetSpec previousDataset = DatasetSpec.of(n5Writer, Paths.get(dataset, scaleDatasets[level - 1]).toString());
final DatasetSpec targetDataset = DatasetSpec.of(n5Writer, N5URI.normalizeGroupPath(dataset + n5Writer.getGroupSeparator() + scaleDatasets[level]));
final DatasetSpec previousDataset = DatasetSpec.of(n5Writer, N5URI.normalizeGroupPath(dataset + n5Writer.getGroupSeparator() + scaleDatasets[level - 1]));

final double[] targetDownsamplingFactors = N5Helpers.getDownsamplingFactors(n5Writer, targetDataset.dataset);
final double[] previousDownsamplingFactors = N5Helpers.getDownsamplingFactors(n5Writer, previousDataset.dataset);
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7 changes: 4 additions & 3 deletions ...rg/janelia/saalfeldlab/paintera/ui/dialogs/opendialog/menu/n5/GenericBackendDialogN5.java
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Expand Up @@ -406,10 +406,11 @@ public BooleanProperty discoveryIsActive() {

public FragmentSegmentAssignmentState assignments() throws IOException {

if (getContainer().isReadOnly())
throw new N5ReadOnlyException();

final var writer = getContainer().getWriter();

if (writer == null) {
throw new N5ReadOnlyException();
}
return N5Helpers.assignments(writer, getDatasetPath());
}

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100 changes: 6 additions & 94 deletions .../java/org/janelia/saalfeldlab/paintera/ui/dialogs/opendialog/menu/n5/N5FactoryOpener.java
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Expand Up @@ -12,9 +12,7 @@
import javafx.beans.value.ObservableValue;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.scene.control.Alert;
import javafx.scene.control.MenuButton;
import javafx.scene.control.TextArea;
import javafx.scene.control.TextField;
import javafx.scene.control.Tooltip;
import javafx.scene.input.KeyCode;
Expand All @@ -25,12 +23,10 @@
import org.janelia.saalfeldlab.fx.Tasks;
import org.janelia.saalfeldlab.fx.ui.ObjectField;
import org.janelia.saalfeldlab.n5.N5Reader;
import org.janelia.saalfeldlab.n5.N5Writer;
import org.janelia.saalfeldlab.n5.hdf5.N5HDF5Reader;
import org.janelia.saalfeldlab.paintera.Paintera;
import org.janelia.saalfeldlab.paintera.PainteraConfigYaml;
import org.janelia.saalfeldlab.paintera.state.metadata.N5ContainerState;
import org.janelia.saalfeldlab.paintera.ui.PainteraAlerts;
import org.janelia.saalfeldlab.util.PainteraCache;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
Expand Down Expand Up @@ -162,37 +158,6 @@ private Optional<N5Reader> openN5Reader(final String url) {
return Optional.empty();
}

/**
* Open {@code url} as an N5Writer if possible, else empty.
*
* @param url location of the container we wish to open as an N5Writer.
* @return N5Writer of {@code url} if valid N5 container which we can write to; else empty
*/
private Optional<N5Writer> openN5Writer(final String url) {

try {
final var writer = Paintera.getN5Factory().openWriter(url);
LOG.debug("{} was opened as an N5Writer.", url);
return Optional.of(writer);
} catch (Exception e) {
LOG.debug("{} cannot be opened as an N5Writer.", url);
}
return Optional.empty();
}

private static boolean isN5Container(final String pathToDirectory) {

try {
final var reader = Paintera.getN5Factory().openReader(pathToDirectory);
boolean openableAsN5 = reader != null;
if (reader instanceof N5HDF5Reader)
reader.close();
return openableAsN5;
} catch (Exception e) {
return false;
}
}

private void updateFromFileChooser(final File initialDirectory, final Window owner) {

final FileChooser fileChooser = new FileChooser();
Expand All @@ -214,8 +179,7 @@ private void updateFromDirectoryChooser(final File initialDirectory, final Windo
.ifPresent(directoryChooser::setInitialDirectory);
Optional.ofNullable(directoryChooser.showDialog(ownerWindow)).ifPresent(updatedRoot -> {
LOG.debug("Updating root to {} (was {})", updatedRoot, selectionProperty.get());

if (fileOpenableAsN5(updatedRoot)) {
if (Paintera.getN5Factory().openReaderOrNull(updatedRoot.getAbsolutePath()) != null) {
// set null first to make sure that selectionProperty will be invalidated even if directory is the same
String updatedAbsPath = updatedRoot.getAbsolutePath();
if (updatedAbsPath.equals(selectionProperty.get())) {
Expand All @@ -224,26 +188,6 @@ private void updateFromDirectoryChooser(final File initialDirectory, final Windo
selectionProperty.set(updatedAbsPath);
}
});

}

private boolean fileOpenableAsN5(File updatedRoot) {

if (updatedRoot == null) {
/* They probably just canceled out of browse; just silently return false; */
return false;
} else if (!isN5Container(updatedRoot.getAbsolutePath())) {
final Alert alert = PainteraAlerts.alert(Alert.AlertType.INFORMATION);
alert.setHeaderText("Selected path cannot be opened as an N5 container.");
final TextArea ta = new TextArea("The selected path is not a valid N5 container\n\n" + updatedRoot.getAbsolutePath() + "\n\n" +
"A valid N5 container is a directory that contains a file attributes.json with a key \"n5\"."); //FIXME meta need a more accurate message
ta.setEditable(false);
ta.setWrapText(true);
alert.getDialogPane().setContent(ta);
alert.show();
return false;
}
return true;
}

private void selectionChanged(ObservableValue<? extends String> obs, String oldSelection, String newSelection) {
Expand All @@ -258,44 +202,12 @@ private void selectionChanged(ObservableValue<? extends String> obs, String oldS
invoke(() -> this.isOpeningContainer.set(true));
final var newContainerState = Optional.ofNullable(n5ContainerStateCache.get(newSelection)).orElseGet(() -> {

/* This particular shortcut is if the N5Reader/Writer is cached, but from
* deserialization, not from open source */
N5Reader initialReader = Paintera.getN5Factory().getFromCache(newSelection);
if (initialReader != null) return new N5ContainerState(initialReader);

/* Ok we don't want to do the writer first, even though it means we need to create a separate writer in the case that it can have both.
* This is because if the path provided doesn't currently contain a writer, but it has permissions to create a writer, it will do so.
* This means that if there is no N5 container, it will create one.
*
* In this case, we only want to create a writer if there is already an N5 container. To check, we create a reader first, and see if it
* exists. */
final var optReader = openN5Reader(newSelection);
if (optReader.isEmpty()) {
return null;
} else {
initialReader = optReader.get();
var container = Paintera.getN5Factory().openReaderOrNull(newSelection);
if (container == null) return null;
if (container instanceof N5HDF5Reader) {
container.close();
container = Paintera.getN5Factory().openWriterElseOpenReader(newSelection);
}

/* Another wrinkle though; For HDF5, you can't open a reader and a writer at the same time, even with permission. So
* Now that we know the container actually exists, we need to check if it's HDF5. If it is, we need to close the reader,
* Then try to open a writer. If that isn't possible, we need to re-open a reader. */

final N5Reader container;
if (initialReader instanceof N5HDF5Reader) { /* Check if we are an HDF5 container*/
initialReader.close();
final var optWriter = openN5Writer(newSelection);
if (optWriter.isEmpty()) { /* if we don't have a writer, re-open the reader */
container = openN5Reader(newSelection).orElseThrow(() ->
new RuntimeException("HDF5 container at " + newSelection
+ " was initially opened as a reader, but failed after attempt to open as a writer")
);
} else { /* if we have the writer, use it as a reader also */
container = optWriter.get();
}
} else {
container = openN5Writer(newSelection).map(N5Reader.class::cast).orElse(initialReader);
}

return new N5ContainerState(container);
});
if (newContainerState == null)
Expand Down
10 changes: 5 additions & 5 deletions src/main/java/org/janelia/saalfeldlab/util/n5/N5Data.java
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Expand Up @@ -380,7 +380,7 @@ ImagesWithTransform<T, V>[] openRawMultiscale(

final double[] initialDonwsamplingFactors = N5Helpers.getDownsamplingFactors(
reader,
Paths.get(dataset, scaleDatasets[0]).toString()
N5URI.normalizeGroupPath(dataset + reader.getGroupSeparator() + scaleDatasets[0])
);
LOG.debug("Initial transform={}", transform);
final ExecutorService es = Executors.newFixedThreadPool(
Expand All @@ -393,7 +393,7 @@ ImagesWithTransform<T, V>[] openRawMultiscale(
final int fScale = scale;
futures.add(es.submit(ThrowingSupplier.unchecked(() -> {
LOG.debug("Populating scale level {}", fScale);
final String scaleDataset = Paths.get(dataset, scaleDatasets[fScale]).toString();
final String scaleDataset = N5URI.normalizeGroupPath(dataset + reader.getGroupSeparator() + scaleDatasets[fScale]);
imagesWithInvalidate[fScale] = openRaw(reader, scaleDataset, transform.copy(), queue, priority);
final double[] downsamplingFactors = N5Helpers.getDownsamplingFactors(reader, scaleDataset);
LOG.debug("Read downsampling factors: {}", Arrays.toString(downsamplingFactors));
Expand Down Expand Up @@ -685,7 +685,7 @@ public static ImagesWithTransform<LabelMultisetType, VolatileLabelMultisetType>[

final double[] initialDonwsamplingFactors = N5Helpers.getDownsamplingFactors(
reader,
Paths.get(dataset, scaleDatasets[0]).toString());
N5URI.normalizeGroupPath(dataset + reader.getGroupSeparator() + scaleDatasets[0]));
final ExecutorService es = Executors.newFixedThreadPool(
scaleDatasets.length,
new NamedThreadFactory("populate-mipmap-scales-%d", true));
Expand All @@ -695,7 +695,7 @@ public static ImagesWithTransform<LabelMultisetType, VolatileLabelMultisetType>[
final int fScale = scale;
futures.add(es.submit(ThrowingSupplier.unchecked(() -> {
LOG.debug("Populating scale level {}", fScale);
final String scaleDataset = Paths.get(dataset, scaleDatasets[fScale]).toString();
final String scaleDataset = N5URI.normalizeGroupPath(dataset + reader.getGroupSeparator() + scaleDatasets[fScale]);
imagesWithInvalidate[fScale] = openLabelMultiset(reader, scaleDataset, transform.copy(), queue, priority);
final double[] downsamplingFactors = N5Helpers.getDownsamplingFactors(reader, scaleDataset);
LOG.debug("Read downsampling factors: {}", Arrays.toString(downsamplingFactors));
Expand Down Expand Up @@ -795,7 +795,7 @@ public static void createEmptyLabelDataset(

final Map<String, String> pd = new HashMap<>();
pd.put("type", "label");
final N5Writer n5 = Paintera.getN5Factory().openWriter(container);
final N5Writer n5 = Paintera.getN5Factory().createWriter(container);
final String uniqueLabelsGroup = String.format("%s/unique-labels", group);

if (!ignoreExisiting && n5.datasetExists(group))
Expand Down
116 changes: 0 additions & 116 deletions src/main/java/org/janelia/saalfeldlab/util/n5/universe/N5FactoryWithCache.java
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