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minor code-cleanup
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@dietzc
dietzc committed Oct 25, 2015
1 parent 8eb477a commit a65762e
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Showing 2 changed files with 71 additions and 123 deletions.
179 changes: 66 additions & 113 deletions org.knime.knip.cellprofiler/src/org/knime/knip/cellprofiler/CellProfilerInstance.java
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Original file line number Diff line number Diff line change
Expand Up @@ -67,8 +67,7 @@ public class CellProfilerInstance {

private boolean closed = false;

private IKnimeBridge m_knimeBridge = new KnimeBridgeFactory()
.newKnimeBridge();
private IKnimeBridge m_knimeBridge = new KnimeBridgeFactory().newKnimeBridge();

private int m_port;

Expand All @@ -83,20 +82,19 @@ public class CellProfilerInstance {
* @throws ZMQException
* @throws PipelineException
*/
public CellProfilerInstance() throws IOException, ZMQException,
ProtocolException, URISyntaxException, PipelineException {
public CellProfilerInstance()
throws IOException, ZMQException, ProtocolException, URISyntaxException, PipelineException {
// Do some error checks on the configured module path
final String[] cellProfilerCommand = CellProfilerPreferencePage
.getCellProfilerCommand();
final String[] cellProfilerCommand = CellProfilerPreferencePage.getCellProfilerCommand();

// Get a free port for communication with CellProfiler
m_port = getFreePort();
// Start CellProfiler

final String param = "--knime-bridge-address=tcp://127.0.0.1:" + m_port;
final ProcessBuilder processBuilder = cellProfilerCommand[0].isEmpty() ? new ProcessBuilder(
cellProfilerCommand[1], param) : new ProcessBuilder(
cellProfilerCommand[0], cellProfilerCommand[1], param);
final ProcessBuilder processBuilder = cellProfilerCommand[0].isEmpty()
? new ProcessBuilder(cellProfilerCommand[1], param)
: new ProcessBuilder(cellProfilerCommand[0], cellProfilerCommand[1], param);

m_cellProfilerProcess = processBuilder.start();

Expand All @@ -107,10 +105,9 @@ public CellProfilerInstance() throws IOException, ZMQException,
m_knimeBridge.connect(new URI("tcp://127.0.0.1:" + m_port));
}

public void loadPipeline(final String pipelineFile) throws ZMQException,
PipelineException, ProtocolException, IOException {
m_knimeBridge.loadPipeline(FileUtils.readFileToString(new File(
pipelineFile)));
public void loadPipeline(final String pipelineFile)
throws ZMQException, PipelineException, ProtocolException, IOException {
m_knimeBridge.loadPipeline(FileUtils.readFileToString(new File(pipelineFile)));
m_knimeBridge.cleanPipeline();
}

Expand All @@ -125,13 +122,11 @@ public String[] getInputParameters() {
/**
* @return Spec of the output produced by the pipeline.
*/
public static DataTableSpec getOutputSpec(final DataTableSpec inSpec,
final Pair<String, String>[] imageColumns,
public static DataTableSpec getOutputSpec(final DataTableSpec inSpec, final Pair<String, String>[] imageColumns,
final List<String> objectNames) {
// Passing null to createColumnRearranger will cause an NPE if we use it
// for more than the spec
return createColumnRearranger(inSpec, imageColumns, null, objectNames)
.createSpec();
return createColumnRearranger(inSpec, imageColumns, null, objectNames).createSpec();
}

/**
Expand All @@ -152,68 +147,51 @@ public static DataTableSpec getOutputSpec(final DataTableSpec inSpec,
* @throws ZMQException
* @throws CanceledExecutionException
*/
public BufferedDataTable execute(ExecutionContext exec,
BufferedDataTable inputTable, Pair<String, String>[] imageColumns,
List<String> objectNames) throws IOException, ZMQException,
CellProfilerException, PipelineException, ProtocolException,
CanceledExecutionException {
ColumnRearranger colRearranger = createColumnRearranger(
inputTable.getDataTableSpec(), imageColumns, m_knimeBridge,
objectNames);
public BufferedDataTable execute(ExecutionContext exec, BufferedDataTable inputTable,
Pair<String, String>[] imageColumns, List<String> objectNames) throws IOException, ZMQException,
CellProfilerException, PipelineException, ProtocolException, CanceledExecutionException {
ColumnRearranger colRearranger = createColumnRearranger(inputTable.getDataTableSpec(), imageColumns,
m_knimeBridge, objectNames);
return exec.createColumnRearrangeTable(inputTable, colRearranger, exec);
}

private static CellProfilerCell[] createCellProfilerContentCell(
final String parentKey, final IKnimeBridge knimeBridge) {
private static CellProfilerCell[] createCellProfilerContentCell(final String parentKey,
final IKnimeBridge knimeBridge) {

final List<String> measurementNames = knimeBridge.getResultTableNames();
final CellProfilerCell[] cells = new CellProfilerCell[measurementNames
.size()];
final CellProfilerCell[] cells = new CellProfilerCell[measurementNames.size()];

int i = 0;
for (String measurementName : measurementNames) {
CellProfilerMeasurementTable measurement = new CellProfilerMeasurementTable(
parentKey);
for (IFeatureDescription featureDescription : knimeBridge
.getFeatures(measurementName)) {
CellProfilerMeasurementTable measurement = new CellProfilerMeasurementTable(parentKey);
for (IFeatureDescription featureDescription : knimeBridge.getFeatures(measurementName)) {
if (featureDescription.getType().equals(Double.class)) {
double[] values = knimeBridge
.getDoubleMeasurements((IFeatureDescription) featureDescription);
measurement.addDoubleFeature(featureDescription.getName(),
values);
double[] values = knimeBridge.getDoubleMeasurements((IFeatureDescription) featureDescription);
measurement.addDoubleFeature(featureDescription.getName(), values);
} else if (featureDescription.getType().equals(Float.class)) {
float[] values = knimeBridge
.getFloatMeasurements((IFeatureDescription) featureDescription);
measurement.addFloatFeature(featureDescription.getName(),
values);
float[] values = knimeBridge.getFloatMeasurements((IFeatureDescription) featureDescription);
measurement.addFloatFeature(featureDescription.getName(), values);
} else if (featureDescription.getType().equals(Integer.class)) {
int[] values = knimeBridge
.getIntMeasurements((IFeatureDescription) featureDescription);
measurement.addIntegerFeature(featureDescription.getName(),
values);
int[] values = knimeBridge.getIntMeasurements((IFeatureDescription) featureDescription);
measurement.addIntegerFeature(featureDescription.getName(), values);
} else if (featureDescription.getType().equals(String.class)) {
String value = knimeBridge
.getStringMeasurement((IFeatureDescription) featureDescription);
measurement.addStringFeature(featureDescription.getName(),
value);
String value = knimeBridge.getStringMeasurement((IFeatureDescription) featureDescription);
measurement.addStringFeature(featureDescription.getName(), value);
}
}

cells[i++] = new CellProfilerCell(new CellProfilerContent(
parentKey, measurement,
measurementName.equals(KBConstants.IMAGE)));
cells[i++] = new CellProfilerCell(
new CellProfilerContent(parentKey, measurement, measurementName.equals(KBConstants.IMAGE)));
}

return cells;
}

private void startStreamListener(final InputStream stream,
final boolean error) {
private void startStreamListener(final InputStream stream, final boolean error) {
new Thread(new Runnable() {
@Override
public void run() {
BufferedReader in = new BufferedReader(new InputStreamReader(
stream));
BufferedReader in = new BufferedReader(new InputStreamReader(stream));
String line = null;
try {
while ((line = in.readLine()) != null) {
Expand Down Expand Up @@ -279,19 +257,16 @@ public List<String> getObjectNames() {
return m_knimeBridge.getResultTableNames();
}

private static ColumnRearranger createColumnRearranger(
final DataTableSpec inSpec,
final Pair<String, String>[] imageColumns,
final IKnimeBridge knimeBridge, final List<String> objectNames) {
private static ColumnRearranger createColumnRearranger(final DataTableSpec inSpec,
final Pair<String, String>[] imageColumns, final IKnimeBridge knimeBridge, final List<String> objectNames) {

final ColumnRearranger rearranger = new ColumnRearranger(inSpec);
final DataColumnSpec[] colSpecs = new DataColumnSpec[objectNames.size()];
int k = 0;
for (final String colName : objectNames) {
final String columnName = DataTableSpec.getUniqueColumnName(inSpec,
"CellProfiler Measurement: [" + colName + "]");
colSpecs[k++] = new DataColumnSpecCreator(columnName,
CellProfilerCell.TYPE).createSpec();
colSpecs[k++] = new DataColumnSpecCreator(columnName, CellProfilerCell.TYPE).createSpec();
}

final int[] colIndexes = new int[imageColumns.length];
Expand All @@ -305,86 +280,65 @@ private static ColumnRearranger createColumnRearranger(
@Override
public DataCell[] getCells(final DataRow row) {
try {
return createCells(row, inSpec, imageColumns, colIndexes,
knimeBridge);
} catch (ZMQException | ProtocolException
| CellProfilerException | PipelineException e) {
return createCells(row, inSpec, imageColumns, colIndexes, knimeBridge);
} catch (ZMQException | ProtocolException | CellProfilerException | PipelineException e) {
throw new RuntimeException(e.getMessage(), e);
}
}

@SuppressWarnings({ "rawtypes", "unchecked" })
private <T extends RealType<T>> DataCell[] createCells(
final DataRow row, final DataTableSpec inSpec,
final Pair<String, String>[] imageColumns,
final int[] colIndexes, final IKnimeBridge knimeBridge)
throws ProtocolException, ZMQException,
CellProfilerException, PipelineException {
private <T extends RealType<T>> DataCell[] createCells(final DataRow row, final DataTableSpec inSpec,
final Pair<String, String>[] imageColumns, final int[] colIndexes, final IKnimeBridge knimeBridge)
throws ProtocolException, ZMQException, CellProfilerException, PipelineException {
boolean group = false;
Map<String, ImgPlus<?>> images = new HashMap<String, ImgPlus<?>>();
for (int i = 0; i < colIndexes.length; i++) {
final DataCell cell = row.getCell(colIndexes[i]);
if(cell.isMissing()){

if (cell.isMissing()) {
images = null;
break;
}

final ImgPlusValue<T> value = (ImgPlusValue<T>) cell;

if (m_reference == null || m_reference[i] == null) {
m_reference = new Interval[colIndexes.length];
m_reference[i] = value.getImgPlus();
} else if (!Intervals.equalDimensions(m_reference[i],
value.getImgPlus())) {
throw new IllegalStateException(
"All images in one column must have the same dimensionality!");
} else if (!Intervals.equalDimensions(m_reference[i], value.getImgPlus())) {
throw new IllegalStateException("All images in one column must have the same dimensionality!");
}

// convert to floats
final RandomAccessibleInterval<FloatType> converted = Converters
.convert((RandomAccessibleInterval<T>) value
.getImgPlus(),
new FloatConverter<T>(value.getImgPlus()),
new FloatType());

if (converted.numDimensions() == 2
|| (converted.numDimensions() == 3 && value
.getImgPlus().axis(2).type()
.equals(Axes.CHANNEL))) {
final RandomAccessibleInterval<FloatType> converted = Converters.convert(
(RandomAccessibleInterval<T>) value.getImgPlus(), new FloatConverter<T>(value.getImgPlus()),
new FloatType());

if (converted.numDimensions() == 2 || (converted.numDimensions() == 3
&& value.getImgPlus().axis(2).type().equals(Axes.CHANNEL))) {
try {
images.put(
imageColumns[i].getFirst(),
images.put(imageColumns[i].getFirst(),
new ImgPlus(
new ImgView<FloatType>(
converted,
value.getImgPlus()
.factory()
.imgFactory(
new FloatType())),
new ImgView<FloatType>(converted,
value.getImgPlus().factory().imgFactory(new FloatType())),
value.getImgPlus()));
} catch (IncompatibleTypeException e) {
throw new RuntimeException(e);
}
} else {
try {
images.put(
imageColumns[i].getFirst(),
images.put(imageColumns[i].getFirst(),
new ImgPlus(
new ImgView<FloatType>(
converted,
value.getImgPlus()
.factory()
.imgFactory(
new FloatType())),
new ImgView<FloatType>(converted,
value.getImgPlus().factory().imgFactory(new FloatType())),
value.getImgPlus()));
} catch (IncompatibleTypeException e) {
throw new RuntimeException(e);
}
group = true;
}
}

if (images != null) {
if (group) {
knimeBridge.runGroup(images);
Expand All @@ -393,12 +347,12 @@ private <T extends RealType<T>> DataCell[] createCells(
}

return createCellProfilerContentCell(row.getKey().getString(), knimeBridge);
} else {
KNIPGateway.log().warn("Detected missing cell in Row " + row.getKey() + "! Therefore, we create a datarow with missing cells, too.");
final DataCell[] missingCells = new DataCell[objectNames.size()];
Arrays.fill(missingCells, DataType.getMissingCell());
return missingCells;
}
KNIPGateway.log().warn("Detected missing cell in Row " + row.getKey()
+ "! Therefore, we create a datarow with missing cells, too.");
final DataCell[] missingCells = new DataCell[objectNames.size()];
Arrays.fill(missingCells, DataType.getMissingCell());
return missingCells;
}

/**
Expand All @@ -408,8 +362,7 @@ private <T extends RealType<T>> DataCell[] createCells(
*
* @param <T>
*/
class FloatConverter<T extends RealType<T>> implements
Converter<T, FloatType> {
class FloatConverter<T extends RealType<T>> implements Converter<T, FloatType> {

private final double max;
private final double min;
Expand Down
15 changes: 5 additions & 10 deletions ...er/src/org/knime/knip/cellprofiler/nodes/pipelineexecutor/PipelineExecutorNodeConfig.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -40,8 +40,7 @@ public class PipelineExecutorNodeConfig {
* @throws InvalidSettingsException
* If the settings are invalid.
*/
public void loadConfig(NodeSettingsRO settings)
throws InvalidSettingsException {
public void loadConfig(NodeSettingsRO settings) throws InvalidSettingsException {
m_pipelineFile = settings.getString(PIPELINE_FILE_CFG);
m_imageColumns = settings.getStringArray(IMAGE_COLUMNS_CFG);
m_inputParameters = settings.getStringArray(INPUT_PARAMETERS_CFG);
Expand All @@ -56,10 +55,8 @@ public void loadConfig(NodeSettingsRO settings)
*/
public void loadConfigInDialog(NodeSettingsRO settings) {
m_pipelineFile = settings.getString(PIPELINE_FILE_CFG, "");
m_imageColumns = settings.getStringArray(IMAGE_COLUMNS_CFG,
new String[0]);
m_inputParameters = settings.getStringArray(INPUT_PARAMETERS_CFG,
new String[0]);
m_imageColumns = settings.getStringArray(IMAGE_COLUMNS_CFG, new String[0]);
m_inputParameters = settings.getStringArray(INPUT_PARAMETERS_CFG, new String[0]);
m_objectNames = settings.getStringArray(OBJECT_NAMES_CONFIG, new String[0]);
}

Expand Down Expand Up @@ -127,16 +124,14 @@ public void setInputParameters(final String[] inputParameters) {
public List<String> getObjectNames() {
if (m_objectNames == null)
return null;
else
return Arrays.asList(m_objectNames);
return Arrays.asList(m_objectNames);
}

/**
* @param objectNames
* number of measurement outputs of this pipeline
*/
public void setObjectNames(final List<String> objectNames) {
this.m_objectNames = objectNames
.toArray(new String[objectNames.size()]);
this.m_objectNames = objectNames.toArray(new String[objectNames.size()]);
}
}

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