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clemens-vonschwerin-knime
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Support for new python2 extension points added
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‎org.knime.knip.knimepython/META-INF/MANIFEST.MF‎

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@@ -20,7 +20,8 @@ Require-Bundle: org.knime.base;bundle-version="2.11.0",
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scijava-common;bundle-version="2.37.0",
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imagej-common;bundle-version="0.12.1",
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scifio-bf-compat;bundle-version="1.11.0",
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org.knime.python.nodes;bundle-version="3.0.0"
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org.knime.python.nodes;bundle-version="3.0.0",
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org.knime.python2;bundle-version="3.3.0"
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Bundle-RequiredExecutionEnvironment: JavaSE-1.8
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Bundle-ClassPath: .
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Export-Package: org.knime.knip.knimepython

‎org.knime.knip.knimepython/plugin.xml‎

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@@ -30,4 +30,21 @@
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path="templates/">
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</folder>
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</extension>
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<extension
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point="org.knime.python2.typeextension.knimetopython">
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<type
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id="org.knime.knip.knimepython.ImgPlus"
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java-serializer-factory="org.knime.knip.knimepython2.ImgPlusSerializerFactory"
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python-deserializer="py/KNIPImageDeserializer.py">
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</type>
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</extension>
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<extension
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point="org.knime.python2.typeextension.pythontoknime">
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<type
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id="org.knime.knip.knimepython.type2"
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java-deserializer-factory="org.knime.knip.knimepython2.ImgPlusDeserializerFactory"
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python-serializer="py/KNIPImageSerializer.py"
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python-type-identifier="KNIPImage.KNIPImage">
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</type>
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</extension>
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</plugin>

‎org.knime.knip.knimepython/py/KNIPImage.py‎

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Original file line numberDiff line numberDiff line change
@@ -2,5 +2,5 @@
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class KNIPImage:
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# data is ndarray
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def __init__(self, array):
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self.array = array
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self.array = array
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‎org.knime.knip.knimepython/src/org/knime/knip/knimepython2/ImgPlusDeserializerFactory.java‎

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@@ -0,0 +1,92 @@
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package org.knime.knip.knimepython2;
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import java.io.IOException;
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import org.knime.core.data.DataCell;
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import org.knime.core.data.filestore.FileStoreFactory;
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import org.knime.knip.base.data.img.ImgPlusCell;
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import org.knime.knip.base.data.img.ImgPlusCellFactory;
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import org.knime.knip.io.ScifioGateway;
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import org.knime.python2.typeextension.Deserializer;
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import org.knime.python2.typeextension.DeserializerFactory;
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import io.scif.Format;
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import io.scif.FormatException;
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import io.scif.Metadata;
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import io.scif.Parser;
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import io.scif.Reader;
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import io.scif.config.SCIFIOConfig;
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import io.scif.img.ImgOpener;
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import io.scif.io.RandomAccessInputStream;
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import net.imagej.ImgPlus;
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public class ImgPlusDeserializerFactory extends DeserializerFactory {
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/**
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* ImgOpener to read ImgPlus from stream
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*/
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private ImgOpener m_imgOpener;
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private SCIFIOConfig m_scifioConfig;
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public ImgPlusDeserializerFactory() {
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super(ImgPlusCell.TYPE);
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m_imgOpener = new ImgOpener(ScifioGateway.getSCIFIO().context());
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m_scifioConfig = new SCIFIOConfig();
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m_scifioConfig.groupableSetGroupFiles(false);
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m_scifioConfig.imgOpenerSetComputeMinMax(false);
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}
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@Override
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public Deserializer createDeserializer() {
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return new Deserializer() {
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private final Format m_format;
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private final Parser m_parser;
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{
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try {
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m_format = ScifioGateway.getSCIFIO().format().getFormat(".tif");
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m_parser = m_format.createParser();
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} catch (FormatException e) {
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throw new RuntimeException(e);
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}
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}
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@SuppressWarnings({ "rawtypes", "unchecked" })
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@Override
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public DataCell deserialize(final byte[] bytes, final FileStoreFactory fileStoreFactory)
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throws IOException {
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final ImgPlusCellFactory factory = new ImgPlusCellFactory(fileStoreFactory);
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// TODO this hack should be removed in the future, as soon as
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// filename bug is resolved
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// We have to set the filename as a NPE would be thrown
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// otherwise
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final RandomAccessInputStream stream = new RandomAccessInputStream(
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ScifioGateway.getSCIFIO().getContext(), bytes) {
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@Override
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public String getFileName() {
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return "";
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}
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};
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try {
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final Metadata metadata = m_parser.parse(stream, m_scifioConfig);
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metadata.setSource(stream);
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final Reader reader = m_format.createReader();
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reader.setMetadata(metadata);
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reader.setSource(stream, m_scifioConfig);
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return factory.createCell((ImgPlus) m_imgOpener.openImgs(reader, m_scifioConfig).get(0));
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} catch (final Exception e) {
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throw new RuntimeException(e);
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}
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}
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};
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}
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}
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‎org.knime.knip.knimepython/src/org/knime/knip/knimepython2/ImgPlusSerializerFactory.java‎

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@@ -0,0 +1,163 @@
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package org.knime.knip.knimepython2;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import org.knime.knip.base.data.img.ImgPlusValue;
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import org.knime.knip.io.ScifioGateway;
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import org.knime.knip.knimepython.TypeUtils;
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import org.knime.python2.typeextension.Serializer;
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import org.knime.python2.typeextension.SerializerFactory;
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import io.scif.DefaultImageMetadata;
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import io.scif.DefaultMetadata;
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import io.scif.FormatException;
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import io.scif.ImageMetadata;
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import io.scif.Metadata;
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import io.scif.Translator;
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import io.scif.Writer;
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import io.scif.config.SCIFIOConfig;
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import io.scif.img.ImgIOException;
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import io.scif.img.ImgSaver;
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import io.scif.img.SCIFIOImgPlus;
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import io.scif.io.ByteArrayHandle;
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import io.scif.io.RandomAccessOutputStream;
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import net.imagej.ImgPlus;
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import net.imagej.axis.Axes;
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import net.imagej.axis.CalibratedAxis;
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public class ImgPlusSerializerFactory extends SerializerFactory<ImgPlusValue>{
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/**
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* ImgSaver to write ImgPlus to stream as tif
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*/
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private ImgSaver m_saver;
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/**
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* SCIFIO config to read/write images
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*/
41+
private SCIFIOConfig m_scifioConfig;
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/**
44+
* Constructor
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*/
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public ImgPlusSerializerFactory() {
47+
super(ImgPlusValue.class);
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m_saver = new ImgSaver(ScifioGateway.getSCIFIO().getContext());
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m_scifioConfig = new SCIFIOConfig();
50+
m_scifioConfig.groupableSetGroupFiles(false);
51+
m_scifioConfig.imgOpenerSetComputeMinMax(false);
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}
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@Override
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public Serializer<? extends ImgPlusValue<?>> createSerializer() {
56+
57+
return new Serializer<ImgPlusValue<?>>() {
58+
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private final Writer m_writer;
60+
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{
62+
try {
63+
m_writer = ScifioGateway.format().getWriterByExtension(".tif");
64+
} catch (FormatException e) {
65+
throw new RuntimeException(e);
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}
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}
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@Override
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public byte[] serialize(final ImgPlusValue<?> value) throws IOException {
71+
final ImgPlus<?> imgPlus = TypeUtils.converted(value.getImgPlus());
72+
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try {
74+
final ByteArrayHandle handle = new ByteArrayHandle();
75+
populateMeta(m_writer, imgPlus, m_scifioConfig, 0);
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// HACK Corresponds to filename
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m_writer.getMetadata().setDatasetName("");
78+
m_writer.setDest(new RandomAccessOutputStream(handle), 0);
79+
80+
m_saver.saveImg(m_writer, imgPlus.getImg(), m_scifioConfig);
81+
82+
m_writer.close();
83+
84+
return handle.getBytes();
85+
} catch (Exception e) {
86+
e.printStackTrace();
87+
throw new RuntimeException(
88+
"Could not serialize image. Possible reasons: Unsupported image type, dimensionality of the image,...");
89+
}
90+
}
91+
};
92+
}
93+
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/**
95+
* This method is copied from SCIFIO
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*
97+
* FIXME/TODO: Remove when method available in SCIFIO (see
98+
* https://github.com/scifio/scifio/issues/233)
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*
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* Uses the provided {@link SCIFIOImgPlus} to populate the minimum metadata
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* fields necessary for writing.
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*
103+
* @param imageIndex
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*/
105+
private void populateMeta(final Writer w, final ImgPlus<?> img, final SCIFIOConfig config, final int imageIndex)
106+
throws FormatException, IOException, ImgIOException {
107+
108+
final Metadata meta = w.getFormat().createMetadata();
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// Get format-specific metadata
111+
Metadata imgMeta = ScifioGateway.getSCIFIO().imgUtil().makeSCIFIOImgPlus(img).getMetadata();
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113+
final List<ImageMetadata> imageMeta = new ArrayList<ImageMetadata>();
114+
115+
if (imgMeta == null) {
116+
imgMeta = new DefaultMetadata();
117+
imgMeta.createImageMetadata(1);
118+
imageMeta.add(imgMeta.get(0));
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} else {
120+
for (int i = 0; i < imgMeta.getImageCount(); i++) {
121+
imageMeta.add(new DefaultImageMetadata());
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}
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}
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// Create Img-specific ImageMetadatas
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final int pixelType = ScifioGateway.getSCIFIO().imgUtil().makeType(img.firstElement());
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// TODO is there some way to consolidate this with the isCompressible
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// method?
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final CalibratedAxis[] axes = new CalibratedAxis[img.numDimensions()];
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img.axes(axes);
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final long[] axisLengths = new long[img.numDimensions()];
134+
img.dimensions(axisLengths);
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for (int i = 0; i < imageMeta.size(); i++) {
137+
final ImageMetadata iMeta = imageMeta.get(i);
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iMeta.populate(img.getName(), Arrays.asList(axes), axisLengths, pixelType, true, false, false, false, true);
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// Adjust for RGB information
141+
if (img.getCompositeChannelCount() > 1) {
142+
if (config.imgSaverGetWriteRGB()) {
143+
iMeta.setPlanarAxisCount(3);
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}
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iMeta.setAxisType(2, Axes.CHANNEL);
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// Split Axes.CHANNEL if necessary
147+
if (iMeta.getAxisLength(Axes.CHANNEL) > img.getCompositeChannelCount()) {
148+
iMeta.addAxis(Axes.get("Channel-planes", false),
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iMeta.getAxisLength(Axes.CHANNEL) / img.getCompositeChannelCount());
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iMeta.setAxisLength(Axes.CHANNEL, img.getCompositeChannelCount());
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}
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}
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}
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// Translate to the output metadata
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final Translator t = ScifioGateway.getSCIFIO().translator().findTranslator(imgMeta, meta, false);
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t.translate(imgMeta, imageMeta, meta);
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w.setMetadata(meta);
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}
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}

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