diff --git a/core/pom.xml b/core/pom.xml
index 6cdb1ef..83a1ef8 100644
--- a/core/pom.xml
+++ b/core/pom.xml
@@ -6,7 +6,6 @@
io.scif
pom-scifio-tutorials
1.0.0-SNAPSHOT
-
io.scif
diff --git a/core/src/main/java/io/scif/tutorials/core/FakeTutorialImages.java b/core/src/main/java/io/scif/tutorials/core/FakeTutorialImages.java
new file mode 100644
index 0000000..3184322
--- /dev/null
+++ b/core/src/main/java/io/scif/tutorials/core/FakeTutorialImages.java
@@ -0,0 +1,47 @@
+package io.scif.tutorials.core;
+
+import org.scijava.io.location.Location;
+import org.scijava.io.location.LocationService;
+
+import io.scif.io.location.TestImgLocation;
+import io.scif.io.location.TestImgLocation.Builder;
+
+// A collection of functions creating fake image {@link Location}s for the SCIFIO
+// tutorials using {@link TestImgLocation.Builder}
+public class FakeTutorialImages {
+
+ public static Location hugeImage() {
+ TestImgLocation.Builder b = new Builder();
+ b.axes("X","Y");
+ b.lengths(70000, 80000);
+ Location location = b.build();
+ return location;
+ }
+
+ // Note:
+ // This is equivalent to using the LocationService to resolve the String input image from
+ // T1aIntroToSCIFIO
+ // final String sampleImage =
+ // "8bit-unsigned&pixelType=uint8&lengths=50,50,3,5,7&axes=X,Y,Z,Channel,Time.fake";
+ // Location location = scifio.location().resolve(sampleImage);
+ public static Location sampleImage() {
+ TestImgLocation.Builder b = new Builder();
+ b.pixelType("uint8"); // set the pixel type
+ b.axes("X", "Y", "Z", "Channel", "Time"); // set new axis names
+ b.lengths(50, 50, 3, 5, 7); // set new axis lengths
+ Location location = b.build(); // build the final location
+ return location;
+ }
+
+ public static Location sampleIndexedImage() {
+ TestImgLocation.Builder b = new Builder();
+ b.pixelType("uint8"); // set the pixel type
+ b.indexed(true);
+ b.planarDims(3);
+ b.axes("X", "Y", "Channel"); // set new axis names
+ b.lengths(50, 50, 3); // set new axis lengths
+ Location location = b.build(); // build the final location
+ return location;
+ }
+
+}
diff --git a/core/src/main/java/io/scif/tutorials/core/T1aIntroToSCIFIO.java b/core/src/main/java/io/scif/tutorials/core/T1aIntroToSCIFIO.java
index bbd1ae1..684c342 100644
--- a/core/src/main/java/io/scif/tutorials/core/T1aIntroToSCIFIO.java
+++ b/core/src/main/java/io/scif/tutorials/core/T1aIntroToSCIFIO.java
@@ -23,6 +23,10 @@
import io.scif.SCIFIO;
import java.io.IOException;
+import java.net.URISyntaxException;
+
+import org.scijava.io.location.Location;
+import org.scijava.io.location.LocationService;
/**
* An introduction to the SCIFIO API. Demonstrates basic plane reading.
@@ -32,7 +36,7 @@
public class T1aIntroToSCIFIO {
public static void main(final String... agrs) throws FormatException,
- IOException
+ IOException, URISyntaxException
{
// The most convenient way to program against the SCIFIO API is by using
// an io.scif.SCIFIO instance. This is basically a "SCIFIO lens" on an
@@ -48,12 +52,17 @@ public static void main(final String... agrs) throws FormatException,
// exist on disk - they are defined purely by their file name - so they're
// good for testing.
final String sampleImage =
- "8bit-signed&pixelType=int8&lengths=50,50,3,5,7&axes=X,Y,Z,Channel,Time.fake";
-
+ "8bit-unsigned&pixelType=uint8&lengths=50,50,3,5,7&axes=X,Y,Z,Channel,Time.fake";
+
+ // We use the {@link LocationService} to resolve our input image to a {@link Location}.
+ // a Location identifies where the data resides, without necessarily specifying
+ // how to access that data.
+ Location location = scifio.location().resolve(sampleImage);
+
// This method checks the Context used by our SCIFIO instance for all its
// known format plugins, and returns an io.scif.Reader capable of opening
// the specified image's planes.
- final Reader reader = scifio.initializer().initializeReader(sampleImage);
+ final Reader reader = scifio.initializer().initializeReader(location);
// ------------------------------------------------------------------------
// COMPARISON WITH BIO-FORMATS 4.X
diff --git a/core/src/main/java/io/scif/tutorials/core/T1bReadingTilesBad.java b/core/src/main/java/io/scif/tutorials/core/T1bReadingTilesBad.java
index 83cd993..734603b 100644
--- a/core/src/main/java/io/scif/tutorials/core/T1bReadingTilesBad.java
+++ b/core/src/main/java/io/scif/tutorials/core/T1bReadingTilesBad.java
@@ -23,6 +23,8 @@
import java.io.IOException;
+import org.scijava.io.location.Location;
+
/**
* WARNING: this code intentionally fails. For functional code, see
* {@link T1cReadingTilesGood}.
@@ -43,11 +45,15 @@ public static void main(final String... args) throws FormatException,
final SCIFIO scifio = new SCIFIO();
// This time we're going to set up an imageID with planes that won't fit
- // in a byte array.
- final String hugeImage = "hugePlane&lengths=70000,80000.fake";
+ // in a byte array.
+ // For the rest of these tutorials, we will use the {@link TestImgLocation.Builder}
+ // to build fake images for us and return their Location. This is in contrast to creating
+ // a fake image as a String and then resolving its Location with LocationService like
+ // we did in T1aIntroToSCIFIO.
+ Location hugeImageLocation = FakeTutorialImages.hugeImage();
// We initialize a reader as we did before
- final Reader reader = scifio.initializer().initializeReader(hugeImage);
+ final Reader reader = scifio.initializer().initializeReader(hugeImageLocation);
// Now we'll try the naive thing, and just open all the planes in this
// dataset.
diff --git a/core/src/main/java/io/scif/tutorials/core/T1cReadingTilesGood.java b/core/src/main/java/io/scif/tutorials/core/T1cReadingTilesGood.java
index 77b969c..0c8bfd6 100644
--- a/core/src/main/java/io/scif/tutorials/core/T1cReadingTilesGood.java
+++ b/core/src/main/java/io/scif/tutorials/core/T1cReadingTilesGood.java
@@ -27,6 +27,8 @@
import java.io.IOException;
import java.util.Arrays;
+import org.scijava.io.location.Location;
+
import net.imagej.axis.Axes;
import net.imglib2.FinalInterval;
import net.imglib2.Interval;
@@ -47,11 +49,11 @@ public static void main(final String... args) throws FormatException,
final SCIFIO scifio = new SCIFIO();
// This time we're going to set up an image with planes that won't fit
- // in a 2GB byte array.
- final String hugeImage = "hugePlane&lengths=70000,80000.fake";
-
+ // in a 2GB byte array and get its Location again.
+ Location hugeImageLocation = FakeTutorialImages.hugeImage();
+
// We initialize a reader as we did before
- final Reader reader = scifio.initializer().initializeReader(hugeImage);
+ final Reader reader = scifio.initializer().initializeReader(hugeImageLocation);
// In T1b we saw that the naive use of the API to open planes doesn't
// work when the individual planes are too large.
diff --git a/core/src/main/java/io/scif/tutorials/core/T1dSavingImagePlanes.java b/core/src/main/java/io/scif/tutorials/core/T1dSavingImagePlanes.java
index c041960..93bed5d 100644
--- a/core/src/main/java/io/scif/tutorials/core/T1dSavingImagePlanes.java
+++ b/core/src/main/java/io/scif/tutorials/core/T1dSavingImagePlanes.java
@@ -21,10 +21,14 @@
import io.scif.Reader;
import io.scif.SCIFIO;
import io.scif.Writer;
-import io.scif.io.Location;
+import io.scif.io.location.TestImgLocation;
import java.io.File;
import java.io.IOException;
+import java.net.URISyntaxException;
+
+import org.scijava.io.location.Location;
+import org.scijava.io.location.LocationService;
/**
* Tutorial demonstrating use of the Writer component.
@@ -34,31 +38,35 @@
public class T1dSavingImagePlanes {
public static void main(final String... args) throws FormatException,
- IOException
+ IOException, URISyntaxException
{
// In this tutorial, we're going to make our .fake sample image
- // "real". If you look at the FakeFormat source code, you'll notice that
+ // "real". If you look at the TestImgFormat source code, you'll notice that
// it doesn't have a functional Writer, so we'll have to translate
// to a different Format that can write our fake planes to disk.
final SCIFIO scifio = new SCIFIO();
- final String sampleImage =
- "8bit-signed&pixelType=int8&lengths=50,50,3,5,7&axes=X,Y,Z,Channel,Time.fake";
+
+ // Create a fake image and get its Location.
+ Location sampleImageLocation = FakeTutorialImages.sampleImage();
// We'll need a path to write to. By making it a ".png" we are locking in
// the final format of the file on disk.
final String outPath = "SCIFIOTutorial.png";
+
+ // We can resolve this Location in the same way as T1aIntroToSCIFIO
+ Location outLoction = scifio.location().resolve(outPath);
// Clear the file if it already exists.
- final Location l = new Location(scifio.getContext(), outPath);
- if (l.exists()) l.delete();
+ File f = new File(outPath);
+ if (f.exists()) f.delete();
// We'll need a reader for the input image
- final Reader reader = scifio.initializer().initializeReader(sampleImage);
+ final Reader reader = scifio.initializer().initializeReader(sampleImageLocation);
// .. and a writer for the output path
final Writer writer =
- scifio.initializer().initializeWriter(sampleImage, outPath);
+ scifio.initializer().initializeWriter(sampleImageLocation, outLoction);
// Note that these initialize methods are used for convenience.
// Initializing a reader and a writer requires that you set the source
diff --git a/core/src/main/java/io/scif/tutorials/core/T2aUntypedComponents.java b/core/src/main/java/io/scif/tutorials/core/T2aUntypedComponents.java
index bc598b5..2a6debf 100644
--- a/core/src/main/java/io/scif/tutorials/core/T2aUntypedComponents.java
+++ b/core/src/main/java/io/scif/tutorials/core/T2aUntypedComponents.java
@@ -26,6 +26,8 @@
import java.io.IOException;
+import org.scijava.io.location.Location;
+
/**
* Demonstrates how individual components can be used together instead of the
* convenience methods in the T1 tutorials. This is for more advanced SCIFIO
@@ -44,8 +46,9 @@ public static void main(final String... args) throws FormatException,
// As always, we create a context and sample image path first.
final SCIFIO scifio = new SCIFIO();
- final String sampleImage =
- "8bit-signed&pixelType=int8&lengths=50,50,3,5,7&axes=X,Y,Z,Channel,Time.fake";
+
+ // Create a fake image and get its Location.
+ Location sampleImageLocation = FakeTutorialImages.sampleImage();
// This time we'll get a handle on the Format itself, which will allow us
// to create the additional components. scifio.format() contains several
@@ -53,12 +56,12 @@ public static void main(final String... args) throws FormatException,
// NB: This implicitly invokes an io.scif.Checker component to determine
// format compatibility. These can also be used individually, e.g. if
// given a list of Formats to test.
- final Format format = scifio.format().getFormat(sampleImage);
+ final Format format = scifio.format().getFormat(sampleImageLocation);
// Typically the first thing we want to do, after confirming we have a
// Format that can support an image, is parse the Metadata of that image.
final Parser parser = format.createParser();
- final Metadata meta = parser.parse(sampleImage);
+ final Metadata meta = parser.parse(sampleImageLocation);
System.out.println("Metadata = " + meta);
// Metadata is used by other components, such as Readers, Writers, and
diff --git a/core/src/main/java/io/scif/tutorials/core/T2bTypedComponents.java b/core/src/main/java/io/scif/tutorials/core/T2bTypedComponents.java
index da4f2d1..d8cdff5 100644
--- a/core/src/main/java/io/scif/tutorials/core/T2bTypedComponents.java
+++ b/core/src/main/java/io/scif/tutorials/core/T2bTypedComponents.java
@@ -20,12 +20,15 @@
import io.scif.ByteArrayPlane;
import io.scif.FormatException;
import io.scif.SCIFIO;
-import io.scif.formats.FakeFormat;
-import io.scif.formats.FakeFormat.Parser;
-import io.scif.formats.FakeFormat.Reader;
+
+import io.scif.formats.TestImgFormat;
+import io.scif.formats.TestImgFormat.Parser;
+import io.scif.formats.TestImgFormat.Reader;
import java.io.IOException;
+import org.scijava.io.location.Location;
+
/**
* In {@link T2aUntypedComponents} we looked at using the general,
* interface-level SCIFIO components. Now we'll look at how to get access
@@ -42,21 +45,21 @@ public static void main(final String... args) throws FormatException,
// if we know exactly what kind of image we're working with?
final SCIFIO scifio = new SCIFIO();
- final String sampleImage =
- "8bit-unsigned&pixelType=uint8&indexed=true&planarDims=3&lengths=50,50,3&axes=X,Y,Channel.fake";
+
+ Location sampleImageLocation = FakeTutorialImages.sampleIndexedImage();
// This time, since we know we have a .fake image, we'll get a handle to the
// Fake format.
- final FakeFormat fakeFormat =
- scifio.format().getFormatFromClass(FakeFormat.class);
+ final TestImgFormat fakeFormat =
+ scifio.format().getFormatFromClass(TestImgFormat.class);
// Two important points here:
// 1 - getformatFromClass is overloaded. You can use any component's class
// and get back the corresponding Format.
- // 2 - we didn't invoke the FakeFormat's constructor.
- // new FakeFormat() would have given us a Format instance with no context.
- // new FakeFormat(scifio) would have given us a Format with the correct
- // context, but wouldn't update the context's FakeFormat singleton. So it
+ // 2 - we didn't invoke the TestImgFormat's constructor.
+ // new TestImgFormat() would have given us a Format instance with no context.
+ // new TestImgFormat(scifio) would have given us a Format with the correct
+ // context, but wouldn't update the context's TestImgFormat singleton. So it
// would basically be an orphan Format instance.
// Formats have no state, so as long as you want a Format that was
// discovered as a plugin, you should access it via the desired context. We
@@ -65,16 +68,16 @@ public static void main(final String... args) throws FormatException,
// Formats provide access to all other components, and with a typed Format
// you can create typed components:
- final FakeFormat.Reader reader = (Reader) fakeFormat.createReader();
- final FakeFormat.Parser parser = (Parser) fakeFormat.createParser();
+ final TestImgFormat.Reader reader = (Reader) fakeFormat.createReader();
+ final TestImgFormat.Parser parser = (Parser) fakeFormat.createParser();
// Now that we have typed components, we can guarantee the return type
// for many methods, and access type-specific API:
- final FakeFormat.Metadata meta = parser.parse(sampleImage);
+ final TestImgFormat.Metadata meta = parser.parse(sampleImageLocation);
// getColorTable isn't a part of the Metadata API, but since
- // FakeFormat.Metadata implements HasColorTable, we have access to this
+ // TestImgFormat.Metadata implements HasColorTable, we have access to this
// method.
System.out.println("Color table: " + meta.getColorTable(0, 0));
diff --git a/core/src/main/java/io/scif/tutorials/core/T3aCustomFormats.java b/core/src/main/java/io/scif/tutorials/core/T3aCustomFormats.java
index 02efffe..c231d07 100644
--- a/core/src/main/java/io/scif/tutorials/core/T3aCustomFormats.java
+++ b/core/src/main/java/io/scif/tutorials/core/T3aCustomFormats.java
@@ -33,17 +33,19 @@
import io.scif.Plane;
import io.scif.SCIFIO;
import io.scif.config.SCIFIOConfig;
-import io.scif.io.RandomAccessInputStream;
-import io.scif.io.RandomAccessOutputStream;
import io.scif.services.FormatService;
import java.io.IOException;
+import java.net.URISyntaxException;
import java.util.Arrays;
import java.util.List;
import net.imagej.axis.Axes;
import net.imglib2.Interval;
+import org.scijava.io.handle.DataHandle;
+import org.scijava.io.location.Location;
+import org.scijava.io.location.LocationService;
import org.scijava.plugin.Plugin;
/**
@@ -181,7 +183,7 @@ public static class Parser extends AbstractParser {
// In this method we populate the given Metadata object
@Override
- public void typedParse(final RandomAccessInputStream stream,
+ public void typedParse(final DataHandle handle,
final Metadata meta, final SCIFIOConfig config) throws IOException,
FormatException
{
@@ -337,9 +339,9 @@ public void writePlane(int imageIndex, long planeIndex, Plane plane,
final Metadata meta = getMetadata();
System.out.println("Metadata = " + meta);
- // This stream is the destination image to write to.
- final RandomAccessOutputStream stream = getStream();
- System.out.println("Stream = " + stream);
+ // This data handle is the destination image to write to.
+ final DataHandle dataHandle = getHandle();
+ System.out.println("DataHandle = " + dataHandle);
// The given Plane object is the source plane to write
final byte[] bytes = plane.getBytes();
@@ -450,7 +452,7 @@ protected void translateImageMetadata(final List source,
// *** END OF SAMPLE FORMAT ***
// This method is provided simply to confirm the format is discovered
- public static void main(final String... args) throws FormatException {
+ public static void main(final String... args) throws FormatException, URISyntaxException {
// ------------------------------------------------------------------------
// COMPARISON WITH BIO-FORMATS 4.X
// In Bio-Formats 4.X, adding support for a new format required modifying
@@ -470,9 +472,12 @@ public static void main(final String... args) throws FormatException {
// ... and a sample image path:
final String sampleImage = "notAnImage.scifiosmpl";
+ // Resolving the Location of this image.
+ Location location = scifio.location().resolve(sampleImage);
+
// As SampleFormat below was annotated as a @Plugin it should be available
// to our context:
- final Format format = scifio.format().getFormat(sampleImage);
+ final Format format = scifio.format().getFormat(location);
// Verify that we found the format plugin
System.out.println("SampleFormat found via FormatService: " +
diff --git a/core/src/main/java/io/scif/tutorials/core/T3bTranslatingMetadata.java b/core/src/main/java/io/scif/tutorials/core/T3bTranslatingMetadata.java
index e73993e..0a074db 100644
--- a/core/src/main/java/io/scif/tutorials/core/T3bTranslatingMetadata.java
+++ b/core/src/main/java/io/scif/tutorials/core/T3bTranslatingMetadata.java
@@ -24,11 +24,12 @@
import io.scif.Metadata;
import io.scif.SCIFIO;
import io.scif.Translator;
-import io.scif.formats.FakeFormat;
+import io.scif.formats.TestImgFormat;
import java.io.IOException;
import java.util.List;
+import org.scijava.io.location.Location;
import org.scijava.plugin.Plugin;
/**
@@ -55,13 +56,13 @@ public static void main(final String... args) throws FormatException,
// As usual, we start by creating a SCIFIO and our trusty sample image.
final SCIFIO scifio = new SCIFIO();
- final String sampleImage =
- "8bit-unsigned&pixelType=uint8&indexed=true&planarDims=3&lengths=50,50,3&axes=X,Y,Channel.fake";
+
+ Location sampleImageLocation = FakeTutorialImages.sampleIndexedImage();
// First let's get a handle on a compatible Format, and parse the sample
// image's Metadata
- final Format format = scifio.format().getFormat(sampleImage);
- final Metadata input = format.createParser().parse(sampleImage);
+ final Format format = scifio.format().getFormat(sampleImageLocation);
+ final Metadata input = format.createParser().parse(sampleImageLocation);
// Now that we have some Metadata, let's find the MischeviousTranslator we
// defined below.
@@ -79,7 +80,7 @@ public static void main(final String... args) throws FormatException,
// To try the MischeviousTranslator out, let's get another copy
// of this image's Metadata.
- final Metadata output = format.createParser().parse(sampleImage);
+ final Metadata output = format.createParser().parse(sampleImageLocation);
// Then we translate
t.translate(input, output);
@@ -116,7 +117,7 @@ public static void main(final String... args) throws FormatException,
*/
@Plugin(type = Translator.class)
public static class MischeviousTranslator extends
- AbstractTranslator
+ AbstractTranslator
{
// -- Translator API methods --
@@ -129,7 +130,7 @@ public static class MischeviousTranslator extends
*/
@Override
protected void translateImageMetadata(final List source,
- final FakeFormat.Metadata dest)
+ final TestImgFormat.Metadata dest)
{
// Here we would put our translation implementation, as in T3a.
System.out.println("Translating source: " + source + " to dest: " + dest);
@@ -137,12 +138,12 @@ protected void translateImageMetadata(final List source,
@Override
public Class source() {
- return FakeFormat.Metadata.class;
+ return TestImgFormat.Metadata.class;
}
@Override
public Class dest() {
- return FakeFormat.Metadata.class;
+ return TestImgFormat.Metadata.class;
}
}
}
diff --git a/ome/pom.xml b/ome/pom.xml
index 2b0d33c..810a464 100644
--- a/ome/pom.xml
+++ b/ome/pom.xml
@@ -6,7 +6,6 @@
io.scif
pom-scifio-tutorials
1.0.0-SNAPSHOT
-
io.scif
diff --git a/ome/src/main/java/io/scif/tutorials/ome/T1OpeningOMEXML.java b/ome/src/main/java/io/scif/tutorials/ome/T1OpeningOMEXML.java
index 84c40dd..3841027 100644
--- a/ome/src/main/java/io/scif/tutorials/ome/T1OpeningOMEXML.java
+++ b/ome/src/main/java/io/scif/tutorials/ome/T1OpeningOMEXML.java
@@ -23,8 +23,12 @@
import io.scif.ome.OMEMetadata;
import io.scif.tutorials.core.T1dSavingImagePlanes;
+import java.net.URISyntaxException;
import java.io.IOException;
+import org.scijava.io.location.Location;
+import org.scijava.io.location.LocationService;
+
import loci.common.xml.XMLTools;
/**
@@ -35,7 +39,7 @@
public class T1OpeningOMEXML {
public static void main(final String... args) throws FormatException,
- IOException
+ IOException, URISyntaxException
{
// Creation of OME-XML metadata in SCIFIO is accomplished via translation.
// The OME-XML component is essentially a collection of translators, from
@@ -44,12 +48,15 @@ public static void main(final String... args) throws FormatException,
// translator to OME-XML. Luckily we already have a tutorial which creates a
// PNG image for us:
T1dSavingImagePlanes.main();
+
+ // We'll need a context for discovering formats and translators
+ final SCIFIO scifio = new SCIFIO();
// Now we can reference the image we wrote via this path:
final String samplePNG = "SCIFIOTutorial.png";
-
- // We'll need a context for discovering formats and translators
- final SCIFIO scifio = new SCIFIO();
+
+ // We can get the location of our samplePNG
+ Location location = scifio.location().resolve(samplePNG);
// This is the Metadata object we will translate to OMEXML Metadata;
Metadata meta = null;
@@ -57,7 +64,7 @@ public static void main(final String... args) throws FormatException,
// Since we are not going to be reading or writing any planes in this
// tutorial, we only need to populate the Metadata. To help us out, there
// is a very convenint method in the SCIFIO initializer:
- meta = scifio.initializer().parseMetadata(samplePNG);
+ meta = scifio.initializer().parseMetadata(location);
// Now that we have our source Metadata, we will need OME-XML Metadata to
// translate to:
diff --git a/pom.xml b/pom.xml
index f209478..0ab9bed 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
org.scijava
pom-scijava
- 26.0.0
+ 35.1.1