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author
Gabriel Einsdorf
committed
ImgreaderTable code cleanup
1 parent a75c9da commit f9cc77a

2 files changed

Lines changed: 53 additions & 61 deletions

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‎org.knime.knip.io/src/org/knime/knip/io/nodes/imgreader2/readfrominput/ImgReaderTableNodeModel.java‎

Lines changed: 46 additions & 48 deletions
Original file line numberDiff line numberDiff line change
@@ -47,10 +47,16 @@
4747
package org.knime.knip.io.nodes.imgreader2.readfrominput;
4848

4949
import java.util.ArrayList;
50-
import java.util.Iterator;
5150
import java.util.List;
5251
import java.util.concurrent.atomic.AtomicBoolean;
5352

53+
import net.imglib2.img.ImgFactory;
54+
import net.imglib2.img.array.ArrayImgFactory;
55+
import net.imglib2.img.cell.CellImgFactory;
56+
import net.imglib2.img.planar.PlanarImgFactory;
57+
import net.imglib2.type.NativeType;
58+
import net.imglib2.type.numeric.RealType;
59+
5460
import org.knime.core.data.DataColumnSpec;
5561
import org.knime.core.data.DataColumnSpecCreator;
5662
import org.knime.core.data.DataRow;
@@ -79,13 +85,6 @@
7985
import org.knime.knip.io.nodes.imgreader2.ColumnCreationMode;
8086
import org.knime.knip.io.nodes.imgreader2.MetadataMode;
8187

82-
import net.imglib2.img.ImgFactory;
83-
import net.imglib2.img.array.ArrayImgFactory;
84-
import net.imglib2.img.cell.CellImgFactory;
85-
import net.imglib2.img.planar.PlanarImgFactory;
86-
import net.imglib2.type.NativeType;
87-
import net.imglib2.type.numeric.RealType;
88-
8988
/**
9089
* This Node reads images.
9190
*
@@ -127,9 +126,9 @@ public ImgReaderTableNodeModel() {
127126
}
128127

129128
@Override
130-
protected DataTableSpec[] configure(DataTableSpec[] inSpecs) throws InvalidSettingsException {
129+
protected DataTableSpec[] configure(final DataTableSpec[] inSpecs) throws InvalidSettingsException {
131130

132-
int imgIdx = getPathColIdx(inSpecs[0]);
131+
final int imgIdx = getPathColIdx(inSpecs[0]);
133132
if (-1 == imgIdx) {
134133
throw new InvalidSettingsException("A string column must be selected!");
135134
}
@@ -138,32 +137,28 @@ protected DataTableSpec[] configure(DataTableSpec[] inSpecs) throws InvalidSetti
138137
}
139138

140139
@Override
141-
protected BufferedDataTable[] execute(BufferedDataTable[] inData, ExecutionContext exec) throws Exception {
140+
protected BufferedDataTable[] execute(final BufferedDataTable[] inData, final ExecutionContext exec)
141+
throws Exception {
142142

143143
// boolean for exceptions and file format
144144
final AtomicBoolean encounteredExceptions = new AtomicBoolean(false);
145145

146-
int imgIdx = getPathColIdx(inData[0].getDataTableSpec());
147-
ReadImgTableFunction<T> rifp = createImgTableFunction(exec, inData[0].getDataTableSpec(),
146+
final int imgIdx = getPathColIdx(inData[0].getDataTableSpec());
147+
final ReadImgTableFunction<T> rifp = createImgTableFunction(exec, inData[0].getDataTableSpec(),
148148
Long.valueOf(inData[0].size()).intValue());
149149

150-
BufferedDataContainer bdc = exec.createDataContainer(getOutspec(inData[0].getDataTableSpec(), imgIdx));
151-
152-
Iterator<DataRow> iterator = inData[0].iterator();
153-
while (iterator.hasNext()) {
154-
rifp.apply(iterator.next()).forEachOrdered(dataRow -> {
150+
final BufferedDataContainer bdc = exec.createDataContainer(getOutspec(inData[0].getDataTableSpec(), imgIdx));
155151

152+
for (final DataRow x : inData[0]) {
153+
rifp.apply(x).forEachOrdered(dataRow -> {
156154
if (dataRow.getSecond().isPresent()) {
157155
encounteredExceptions.set(true);
158156
LOGGER.warn("Encountered exception while reading image: " + dataRow.getFirst().getKey()
159157
+ "! view log for more info.");
160158
LOGGER.debug("Encountered exception while reading image:", dataRow.getSecond().get());
161159
}
162-
163160
bdc.addRowToTable(dataRow.getFirst());
164-
165161
});
166-
167162
exec.checkCanceled();
168163
}
169164

@@ -186,14 +181,15 @@ public StreamableOperator createStreamableOperator(final PartitionInfo partition
186181
final PortObjectSpec[] inSpecs) throws InvalidSettingsException {
187182
return new StreamableOperator() {
188183
@Override
189-
public void runFinal(PortInput[] inputs, PortOutput[] outputs, ExecutionContext exec) throws Exception {
190-
RowInput in = (RowInput) inputs[0];
191-
RowOutput out = (RowOutput) outputs[0];
184+
public void runFinal(final PortInput[] inputs, final PortOutput[] outputs, final ExecutionContext exec)
185+
throws Exception {
186+
final RowInput in = (RowInput) inputs[0];
187+
final RowOutput out = (RowOutput) outputs[0];
192188

193189
// boolean for exceptions and file format
194190
final AtomicBoolean encounteredExceptions = new AtomicBoolean(false);
195191

196-
ReadImgTableFunction<T> readImgFunction = createImgTableFunction(exec, in.getDataTableSpec(), 1);
192+
final ReadImgTableFunction<T> readImgFunction = createImgTableFunction(exec, in.getDataTableSpec(), 1);
197193

198194
DataRow row;
199195
while ((row = in.poll()) != null) {
@@ -207,7 +203,7 @@ public void runFinal(PortInput[] inputs, PortOutput[] outputs, ExecutionContext
207203

208204
try {
209205
out.push(result.getFirst());
210-
} catch (Exception exc) {
206+
} catch (final Exception exc) {
211207
encounteredExceptions.set(true);
212208
LOGGER.warn("Couldn't push row " + result.getFirst().getKey() + " into output stream.");
213209
LOGGER.debug("Encountered exception when trying to push result: ", exc);
@@ -237,21 +233,22 @@ public OutputPortRole[] getOutputPortRoles() {
237233
return new OutputPortRole[] { OutputPortRole.DISTRIBUTED };
238234
}
239235

240-
private DataTableSpec getOutspec(DataTableSpec spec, int imgIdx) {
241-
MetadataMode metadataMode = EnumUtils.valueForName(m_metadataModeModel.getStringValue(), MetadataMode.values());
236+
private DataTableSpec getOutspec(final DataTableSpec spec, final int imgIdx) {
237+
final MetadataMode metadataMode = EnumUtils.valueForName(m_metadataModeModel.getStringValue(),
238+
MetadataMode.values());
242239

243-
boolean readImage = (metadataMode == MetadataMode.NO_METADATA || metadataMode == MetadataMode.APPEND_METADATA)
244-
? true : false;
245-
boolean readMetadata = (metadataMode == MetadataMode.APPEND_METADATA
240+
final boolean readImage = (metadataMode == MetadataMode.NO_METADATA
241+
|| metadataMode == MetadataMode.APPEND_METADATA) ? true : false;
242+
final boolean readMetadata = (metadataMode == MetadataMode.APPEND_METADATA
246243
|| metadataMode == MetadataMode.METADATA_ONLY) ? true : false;
247244

248245
DataTableSpec outSpec;
249246
// new table
250-
ColumnCreationMode columnCreationMode = ColumnCreationMode.fromString(m_colCreationMode.getStringValue());
247+
final ColumnCreationMode columnCreationMode = ColumnCreationMode.fromString(m_colCreationMode.getStringValue());
251248
if (columnCreationMode == ColumnCreationMode.NEW_TABLE) {
252249

253-
DataColumnSpec imgSpec = new DataColumnSpecCreator("Image", ImgPlusCell.TYPE).createSpec();
254-
DataColumnSpec omeSpec = new DataColumnSpecCreator("OME-XML Metadata", XMLCell.TYPE).createSpec();
250+
final DataColumnSpec imgSpec = new DataColumnSpecCreator("Image", ImgPlusCell.TYPE).createSpec();
251+
final DataColumnSpec omeSpec = new DataColumnSpecCreator("OME-XML Metadata", XMLCell.TYPE).createSpec();
255252

256253
if (readImage && readMetadata) {
257254
outSpec = new DataTableSpec(imgSpec, omeSpec);
@@ -265,14 +262,14 @@ private DataTableSpec getOutspec(DataTableSpec spec, int imgIdx) {
265262
// append
266263
else if (columnCreationMode == ColumnCreationMode.APPEND) {
267264

268-
DataColumnSpec imgSpec = new DataColumnSpecCreator(
265+
final DataColumnSpec imgSpec = new DataColumnSpecCreator(
269266
DataTableSpec.getUniqueColumnName(spec, "Image" + m_colSuffix.getStringValue()), ImgPlusCell.TYPE)
270267
.createSpec();
271-
DataColumnSpec omeSpec = new DataColumnSpecCreator(
268+
final DataColumnSpec omeSpec = new DataColumnSpecCreator(
272269
DataTableSpec.getUniqueColumnName(spec, "OME-XML Metadata" + m_colSuffix.getStringValue()),
273270
XMLCell.TYPE).createSpec();
274271

275-
List<DataColumnSpec> list = new ArrayList<>();
272+
final List<DataColumnSpec> list = new ArrayList<>();
276273
for (int i = 0; i < spec.getNumColumns(); i++) {
277274
list.add(spec.getColumnSpec(i));
278275
}
@@ -290,14 +287,14 @@ else if (columnCreationMode == ColumnCreationMode.APPEND) {
290287
}
291288
// replace
292289
else if (columnCreationMode == ColumnCreationMode.REPLACE) {
293-
DataColumnSpec imgSpec = new DataColumnSpecCreator(
290+
final DataColumnSpec imgSpec = new DataColumnSpecCreator(
294291
DataTableSpec.getUniqueColumnName(spec, "Image" + m_colSuffix.getStringValue()), ImgPlusCell.TYPE)
295292
.createSpec();
296-
DataColumnSpec omeSpec = new DataColumnSpecCreator(
293+
final DataColumnSpec omeSpec = new DataColumnSpecCreator(
297294
DataTableSpec.getUniqueColumnName(spec, "OME-XML Metadata" + m_colSuffix.getStringValue()),
298295
XMLCell.TYPE).createSpec();
299296

300-
List<DataColumnSpec> list = new ArrayList<>();
297+
final List<DataColumnSpec> list = new ArrayList<>();
301298
for (int i = 0; i < spec.getNumColumns(); i++) {
302299
list.add(spec.getColumnSpec(i));
303300
}
@@ -338,15 +335,16 @@ private int getPathColIdx(final DataTableSpec inSpec) throws InvalidSettingsExce
338335
return imgColIndex;
339336
}
340337

341-
private ReadImgTableFunction<T> createImgTableFunction(ExecutionContext exec, DataTableSpec inSpec, int rowCount)
342-
throws InvalidSettingsException {
338+
private ReadImgTableFunction<T> createImgTableFunction(final ExecutionContext exec, final DataTableSpec inSpec,
339+
final int rowCount) throws InvalidSettingsException {
343340

344-
int imgIdx = getPathColIdx(inSpec);
341+
final int imgIdx = getPathColIdx(inSpec);
345342

346-
MetadataMode metadataMode = EnumUtils.valueForName(m_metadataModeModel.getStringValue(), MetadataMode.values());
347-
boolean readImage = (metadataMode == MetadataMode.NO_METADATA || metadataMode == MetadataMode.APPEND_METADATA)
348-
? true : false;
349-
boolean readMetadata = (metadataMode == MetadataMode.APPEND_METADATA
343+
final MetadataMode metadataMode = EnumUtils.valueForName(m_metadataModeModel.getStringValue(),
344+
MetadataMode.values());
345+
final boolean readImage = (metadataMode == MetadataMode.NO_METADATA
346+
|| metadataMode == MetadataMode.APPEND_METADATA) ? true : false;
347+
final boolean readMetadata = (metadataMode == MetadataMode.APPEND_METADATA
350348
|| metadataMode == MetadataMode.METADATA_ONLY) ? true : false;
351349

352350
// create ImgFactory
@@ -372,7 +370,7 @@ private ReadImgTableFunction<T> createImgTableFunction(ExecutionContext exec, Da
372370
}
373371

374372
// create image function
375-
ReadImgTableFunction<T> rifp = new ReadImgTableFunction<>(exec, rowCount, m_planeSelect, readImage,
373+
final ReadImgTableFunction<T> rifp = new ReadImgTableFunction<>(exec, rowCount, m_planeSelect, readImage,
376374
readMetadata, m_readAllMetaDataModel.getBooleanValue(), m_checkFileFormat.getBooleanValue(),
377375
m_isGroupFiles.getBooleanValue(), seriesSelectionFrom, seriesSelectionTo, imgFac,
378376
ColumnCreationMode.fromString(m_colCreationMode.getStringValue()), imgIdx,

‎org.knime.knip.io/src/org/knime/knip/io/nodes/imgreader2/readfrominput/ReadImgTableFunction.java‎

Lines changed: 7 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,6 @@
11
package org.knime.knip.io.nodes.imgreader2.readfrominput;
22

33
import java.io.IOException;
4-
import java.net.URI;
54
import java.net.URISyntaxException;
65
import java.net.URL;
76
import java.nio.file.InvalidPathException;
@@ -13,6 +12,11 @@
1312
import java.util.stream.IntStream;
1413
import java.util.stream.Stream;
1514

15+
import net.imglib2.img.Img;
16+
import net.imglib2.img.ImgFactory;
17+
import net.imglib2.type.NativeType;
18+
import net.imglib2.type.numeric.RealType;
19+
1620
import org.knime.core.data.DataCell;
1721
import org.knime.core.data.DataRow;
1822
import org.knime.core.data.RowKey;
@@ -26,11 +30,6 @@
2630
import org.knime.knip.io.nodes.imgreader2.ColumnCreationMode;
2731
import org.knime.knip.io.nodes.imgreader2.URLUtil;
2832

29-
import net.imglib2.img.Img;
30-
import net.imglib2.img.ImgFactory;
31-
import net.imglib2.type.NativeType;
32-
import net.imglib2.type.numeric.RealType;
33-
3433
/**
3534
* {@link Function} to read an {@link Img}, OME-XML Metadata or both from a file
3635
* path.
@@ -68,10 +67,8 @@ public Stream<Pair<DataRow, Optional<Throwable>>> apply(DataRow input) {
6867
String path;
6968
int numSeries;
7069
try {
71-
URI uri = URLUtil.encode(t);
72-
URL url = uri.toURL();
73-
74-
// check if its an internet address;
70+
URL url = URLUtil.encode(t).toURL();
71+
// check if its an remote address;
7572
if (url.getProtocol().equalsIgnoreCase("HTTP") || url.getProtocol().equalsIgnoreCase("FTP")
7673
|| url.getProtocol().equalsIgnoreCase("HTTPS")) {
7774
path = url.toURI().toString();
@@ -115,9 +112,6 @@ public Stream<Pair<DataRow, Optional<Throwable>>> apply(DataRow input) {
115112
* @param readFiles
116113
* the {@link List} of read {@link Img}s, with {@link Optional}
117114
* {@link Exception}s.
118-
* @param columnSelectionMode
119-
* the column selection mode see
120-
* {@link ImgReaderTableNodeModel#COL_CREATION_MODES}
121115
* @param inputColumnIndex
122116
* the column index of the path.
123117
* @return a {@link Stream} with the output {@link DataRow}s.

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