List of usage examples for org.apache.commons.beanutils ConvertUtils convert
public static Object convert(String values[], Class clazz)
Convert an array of specified values to an array of objects of the specified class (if possible).
For more details see ConvertUtilsBean.
From source file:uk.ac.diamond.scisoft.ncd.passerelle.actors.forkjoin.NcdSectorIntegrationForkJoinTransformer.java
@Override protected long[] getResultDataShape() { int[] areaShape = (int[]) ConvertUtils .convert(Arrays.copyOfRange(frames, frames.length - dimension, frames.length), int[].class); areaData = ROIProfile.area(areaShape, Dataset.FLOAT32, mask, intSector, doRadial, doAzimuthal, doFast); int areaDataRank = areaData[0].getRank(); int[] areaDataShape = areaData[0].getShape(); int secRank = frames.length - dimension + 1; long[] secFrames = Arrays.copyOf(frames, secRank); secFrames[secRank - 1] = areaDataShape[areaDataRank - 1]; return secFrames; }
From source file:uk.ac.diamond.scisoft.ncd.passerelle.actors.forkjoin.NcdSectorIntegrationForkJoinTransformer.java
@Override protected void writeAxisData() throws HDF5Exception { Dataset qaxis = calculateQaxisDataset(); long[] qaxisShape = (long[]) ConvertUtils.convert(qaxis.getShape(), long[].class); UnitFormat unitFormat = UnitFormat.getUCUMInstance(); String units = "a.u."; String axisName = "indecies"; if (axisUnit != null) { units = unitFormat.format(axisUnit); axisName = "q"; }//ww w . jav a2s . co m int[] qaxisRank = new int[] { qaxis.getRank() }; resultAxisDataID = NcdNexusUtils.makeaxis(resultGroupID, axisName, HDF5Constants.H5T_NATIVE_FLOAT, qaxisShape, qaxisRank, 1, units); int filespace_id = H5.H5Dget_space(resultAxisDataID); int type_id = H5.H5Dget_type(resultAxisDataID); int memspace_id = H5.H5Screate_simple(qaxis.getRank(), qaxisShape, null); H5.H5Sselect_all(filespace_id); H5.H5Dwrite(resultAxisDataID, type_id, memspace_id, filespace_id, HDF5Constants.H5P_DEFAULT, qaxis.getBuffer()); H5.H5Sclose(filespace_id); H5.H5Sclose(memspace_id); H5.H5Tclose(type_id); if (qaxis.hasErrors()) { long[] qaxisShapeError = (long[]) ConvertUtils.convert(qaxis.getShape(), long[].class); resultAxisErrorsID = NcdNexusUtils.makedata(resultGroupID, axisName + "_errors", HDF5Constants.H5T_NATIVE_DOUBLE, qaxisShapeError, false, units); filespace_id = H5.H5Dget_space(resultAxisErrorsID); type_id = H5.H5Dget_type(resultAxisErrorsID); memspace_id = H5.H5Screate_simple(qaxis.getRank(), qaxisShapeError, null); H5.H5Sselect_all(filespace_id); H5.H5Dwrite(resultAxisErrorsID, type_id, memspace_id, filespace_id, HDF5Constants.H5P_DEFAULT, qaxis.getError().getBuffer()); H5.H5Sclose(filespace_id); H5.H5Sclose(memspace_id); H5.H5Tclose(type_id); } if (doAzimuthal) { writeAzimuthalAxisData(); } }
From source file:uk.ac.diamond.scisoft.ncd.passerelle.actors.forkjoin.NcdSectorIntegrationForkJoinTransformer.java
private void writeAzimuthalAxisData() throws HDF5Exception { Dataset azAxis = calculateAzimuthalAxisDataset(); long[] azAxisShape = (long[]) ConvertUtils.convert(azAxis.getShape(), long[].class); String units = azAxis.getName(); String axisName = "direction"; int[] azAxisRank = new int[] { azAxis.getRank() }; azimuthalAxisID = NcdNexusUtils.makeaxis(resultGroupID, axisName, HDF5Constants.H5T_NATIVE_DOUBLE, azAxisShape, azAxisRank, 1, units); int filespace_id = H5.H5Dget_space(azimuthalAxisID); int type_id = H5.H5Dget_type(azimuthalAxisID); int memspace_id = H5.H5Screate_simple(azAxis.getRank(), azAxisShape, null); H5.H5Sselect_all(filespace_id);/*from w w w .jav a2s. com*/ H5.H5Dwrite(azimuthalAxisID, type_id, memspace_id, filespace_id, HDF5Constants.H5P_DEFAULT, azAxis.getBuffer()); H5.H5Sclose(filespace_id); H5.H5Sclose(memspace_id); H5.H5Tclose(type_id); }
From source file:uk.ac.diamond.scisoft.ncd.passerelle.actors.forkjoin.NcdSectorIntegrationForkJoinTransformer.java
private void writeMaskMetadata(int datagroup_id) throws HDF5LibraryException, NullPointerException, HDF5Exception { long[] maskShape = (long[]) ConvertUtils.convert(mask.getShape(), long[].class); int mask_id = NcdNexusUtils.makedata(datagroup_id, "mask", HDF5Constants.H5T_NATIVE_INT8, maskShape, false, "pixels"); int filespace_id = H5.H5Dget_space(mask_id); int type = H5.H5Dget_type(mask_id); int memspace_id = H5.H5Screate_simple(mask.getRank(), maskShape, null); H5.H5Sselect_all(filespace_id);/*from w w w . j a v a2s. c o m*/ H5.H5Dwrite(mask_id, type, memspace_id, filespace_id, HDF5Constants.H5P_DEFAULT, (DatasetUtils.cast(mask, Dataset.INT8)).getBuffer()); H5.H5Sclose(filespace_id); H5.H5Sclose(memspace_id); H5.H5Tclose(type); H5.H5Dclose(mask_id); }
From source file:uk.ac.diamond.scisoft.ncd.passerelle.actors.forkjoin.NcdSelectionForkJoinTransformer.java
@Override protected long[] getResultDataShape() { selectedShape = Arrays.copyOf(frames, frames.length - dimension); indexList = NcdDataUtils.createSliceList(format, (int[]) ConvertUtils.convert(selectedShape, int[].class)); for (int i = 0; i < selectedShape.length; i++) { selectedShape[i] = indexList.get(i).length; }// w ww . j a v a 2 s. c o m long[] imageSize = Arrays.copyOfRange(frames, frames.length - dimension, frames.length); long[] resultDataShape = ArrayUtils.addAll(selectedShape, imageSize); return resultDataShape; }
From source file:uk.ac.diamond.scisoft.ncd.passerelle.actors.NcdAbstractDataTransformer.java
@Override protected void doInitialize() throws InitializationException { super.doInitialize(); try {/*from w w w . java2 s .co m*/ enabled = ((BooleanToken) isEnabled.getToken()).booleanValue(); if (!enabled) { return; } dimension = ((IntToken) dimensionParam.getToken()).intValue(); entryGroupID = ((IntToken) entryGroupParam.getToken()).intValue(); processingGroupID = ((IntToken) processingGroupParam.getToken()).intValue(); int[][] framesMatrix = ((IntMatrixToken) framesParam.getToken()).intMatrix(); if (framesMatrix == null || framesMatrix.length != 1) { throw new InitializationException(ErrorCode.ACTOR_INITIALISATION_ERROR, "Invalid data shape", this, null); } frames = (long[]) ConvertUtils.convert(framesMatrix[0], long[].class); int gridDimension = frames.length - dimension; if (gridDimension < 0) { throw new InitializationException(ErrorCode.ACTOR_INITIALISATION_ERROR, "Data shape incompatible with the specified dimension", this, null); } if (gridDimension > 0) { grid = Arrays.copyOf(framesMatrix[0], gridDimension); } else { grid = null; } } catch (IllegalActionException e) { throw new InitializationException(ErrorCode.ACTOR_INITIALISATION_ERROR, "Error initializing NCD actor", this, e); } }
From source file:uk.ac.diamond.scisoft.ncd.passerelle.actors.NcdNormalisationTransformer.java
@Override protected void process(ActorContext ctxt, ProcessRequest request, ProcessResponse response) throws ProcessingException { ManagedMessage receivedMsg = request.getMessage(input); if (!enabled) { response.addOutputMessage(output, receivedMsg); return;/*w w w. j ava 2 s. com*/ } NcdProcessingSliceObject receivedObject; int filespaceID = -1; int typeID = -1; int memspaceID = -1; try { receivedObject = (NcdProcessingSliceObject) receivedMsg.getBodyContent(); lock = receivedObject.getLock(); SliceSettings sliceData = receivedObject.getSliceData(); Dataset data = receivedObject.getData(); Dataset qaxis = receivedObject.getAxis(); Normalisation nm = new Normalisation(); nm.setCalibChannel(normChannel); if (absScaling != null) { nm.setNormvalue(absScaling); } int[] dataShape = data.getShape(); data = NcdDataUtils.flattenGridData(data, dimension); Dataset errors = data.getErrorBuffer(); SliceSettings calibrationSliceParams = new SliceSettings(sliceData); calibrationSliceParams.setFrames(framesCal); Dataset dataCal = NcdNexusUtils.sliceInputData(calibrationSliceParams, calibrationIDs); Dataset calibngd = NcdDataUtils.flattenGridData(dataCal, 1); Object[] myobj = nm.process(data.getBuffer(), errors.getBuffer(), calibngd.getBuffer(), data.getShape()[0], data.getShape(), calibngd.getShape()); float[] mydata = (float[]) myobj[0]; double[] myerrors = (double[]) myobj[1]; Dataset myres = new FloatDataset(mydata, dataShape); myres.setErrorBuffer(new DoubleDataset(myerrors, dataShape)); int selectID = -1; int writeID = -1; lock.lock(); long[] frames = sliceData.getFrames(); long[] start_pos = (long[]) ConvertUtils.convert(sliceData.getStart(), long[].class); int sliceDim = sliceData.getSliceDim(); int sliceSize = sliceData.getSliceSize(); long[] start = Arrays.copyOf(start_pos, frames.length); long[] block = Arrays.copyOf(frames, frames.length); Arrays.fill(block, 0, sliceData.getSliceDim(), 1); block[sliceDim] = Math.min(frames[sliceDim] - start_pos[sliceDim], sliceSize); long[] count = new long[frames.length]; Arrays.fill(count, 1); filespaceID = H5.H5Dget_space(normDataID); typeID = H5.H5Dget_type(normDataID); memspaceID = H5.H5Screate_simple(block.length, block, null); selectID = H5.H5Sselect_hyperslab(filespaceID, HDF5Constants.H5S_SELECT_SET, start, block, count, block); if (selectID < 0) { throw new HDF5Exception("Failed to allocate space fro writing Normalisation data"); } writeID = H5.H5Dwrite(normDataID, typeID, memspaceID, filespaceID, HDF5Constants.H5P_DEFAULT, mydata); if (writeID < 0) { throw new HDF5Exception("Failed to write Normalisation data into the results file"); } NcdNexusUtils.closeH5idList(new ArrayList<Integer>(Arrays.asList(memspaceID, typeID, filespaceID))); filespaceID = H5.H5Dget_space(normErrorsID); typeID = H5.H5Dget_type(normErrorsID); memspaceID = H5.H5Screate_simple(block.length, block, null); selectID = H5.H5Sselect_hyperslab(filespaceID, HDF5Constants.H5S_SELECT_SET, start, block, count, block); if (selectID < 0) { throw new HDF5Exception("Failed to allocate space for writing Normalisation error data"); } writeID = H5.H5Dwrite(normErrorsID, typeID, memspaceID, filespaceID, HDF5Constants.H5P_DEFAULT, myres.getError().getBuffer()); if (writeID < 0) { throw new HDF5Exception("Failed to write Normalisation error data into the results file"); } ManagedMessage outputMsg = createMessageFromCauses(receivedMsg); NcdProcessingSliceObject obj = new NcdProcessingSliceObject(myres, qaxis, sliceData, lock); outputMsg.setBodyContent(obj, "application/octet-stream"); response.addOutputMessage(output, outputMsg); } catch (MessageException e) { throw new ProcessingException(ErrorCode.ACTOR_EXECUTION_ERROR, e.getMessage(), this, e.getCause()); } catch (HDF5LibraryException e) { throw new ProcessingException(ErrorCode.ACTOR_EXECUTION_ERROR, e.getMessage(), this, e.getCause()); } catch (HDF5Exception e) { throw new ProcessingException(ErrorCode.ACTOR_EXECUTION_ERROR, e.getMessage(), this, e.getCause()); } finally { if (lock != null && lock.isHeldByCurrentThread()) { lock.unlock(); } try { NcdNexusUtils.closeH5idList(new ArrayList<Integer>(Arrays.asList(memspaceID, typeID, filespaceID))); } catch (HDF5LibraryException e) { throw new ProcessingException(ErrorCode.ACTOR_EXECUTION_ERROR, e.getMessage(), this, e.getCause()); } } }
From source file:uk.ac.diamond.scisoft.ncd.rcp.reduction.NcdLazyDataReductionTest.java
@Test public void testLazyBackgroundSubtraction() throws HDF5Exception { LazyBackgroundSubtraction lazyBackgroundSubtraction = new LazyBackgroundSubtraction(); int nxsFile = H5.H5Fopen(filename, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); int entry_id = H5.H5Gopen(nxsFile, "entry1", HDF5Constants.H5P_DEFAULT); int processing_group_id = H5.H5Gopen(entry_id, "results", HDF5Constants.H5P_DEFAULT); DataSliceIdentifiers[] ids = NcdNexusUtilsTest.readDataId(bgFile, testDatasetName, "data", "errors"); DataSliceIdentifiers bgIds = ids[0]; H5.H5Sget_simple_extent_dims(bgIds.dataspace_id, bgShape, null); int[] bgShape_int = (int[]) ConvertUtils.convert(bgShape, int[].class); lazyBackgroundSubtraction.setBgScale((double) scaleBg); SliceSettings bgSliceParams = new SliceSettings(bgShape, 0, bgShape_int[0]); int[] start = new int[] { 0, 0, 0, 0 }; bgSliceParams.setStart(start);//w ww. jav a 2 s . co m Dataset bgData = NcdNexusUtils.sliceInputData(bgSliceParams, bgIds); int bgFrames = bgShape_int[0] * bgShape_int[1]; bgData = bgData.sum(0).sum(0).idivide(bgFrames); DataSliceIdentifiers bgErrorIds = ids[1]; Dataset bgError = NcdNexusUtils.sliceInputData(bgSliceParams, bgErrorIds); bgError = bgError.ipower(2).sum(0).sum(0).idivide(bgFrames); bgData.setErrorBuffer(bgError); lazyBackgroundSubtraction.setBgFile(bgFile); lazyBackgroundSubtraction.setBgDetector(testDatasetName); lazyBackgroundSubtraction.setBgScale((double) scaleBg); SliceSettings slice = new SliceSettings(shape, 0, (int) shape[0]); slice.setStart(new int[] { 0, 0, 0, 0, 0 }); lazyBackgroundSubtraction.configure(dim, shape, processing_group_id); Dataset outData = lazyBackgroundSubtraction.execute(dim, data, bgData, slice, lock); Dataset outErrors = outData.getError(); for (int h = 0; h < shape[0]; h++) for (int g = 0; g < shape[1]; g++) for (int k = 0; k < shape[2]; k++) { for (int i = 0; i < imageShape[0]; i++) for (int j = 0; j < imageShape[1]; j++) { float value = outData.getFloat(h, g, k, i, j); double error = outErrors.getDouble(h, g, k, i, j); float expected = g * shape[2] + k + (1.0f - scaleBg) * (i * imageShape[1] + j) - scaleBg * (bgShape_int[1] - 1) / 2.0f; double expectederr = Math .sqrt(g * shape[2] + k + (1.0 + scaleBg * scaleBg) * (i * imageShape[1] + j) + scaleBg * scaleBg * (bgShape_int[1] - 1.0) / 2.0); assertEquals(String.format("Test background subtraction frame for (%d, %d, %d, %d, %d)", h, g, k, i, j), expected, value, 1e-4 * Math.abs(expected)); assertEquals(String.format( "Test background subtraction frame error for (%d, %d, %d, %d, %d)", h, g, k, i, j), expectederr, error, 1e-4 * Math.abs(expectederr)); } } }
From source file:uk.ac.diamond.scisoft.ncd.rcp.reduction.NcdLazyDataReductionTest.java
@Test public void testLazyAverage() throws Exception { int nxsFile = H5.H5Fopen(filename, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); int entry_id = H5.H5Gopen(nxsFile, "entry1", HDF5Constants.H5P_DEFAULT); int processing_group_id = H5.H5Gopen(entry_id, "results", HDF5Constants.H5P_DEFAULT); DataSliceIdentifiers[] ids = NcdNexusUtilsTest.readDataId(filename, testDatasetName, "data", "errors"); DataSliceIdentifiers input_ids = ids[0]; long[] lstart = new long[] { 0, 0, 0, 0, 0 }; long[] count = new long[] { 1, 1, 1, 1, 1 }; input_ids.setSlice(lstart, shape, count, shape); DataSliceIdentifiers input_errors_ids = ids[1]; input_errors_ids.setSlice(lstart, shape, count, shape); LazyAverage lazyAverage = new LazyAverage(); lazyAverage.setAverageIndices(new int[] { 1, 3 }); lazyAverage.configure(dim, (int[]) ConvertUtils.convert(shape, int[].class), processing_group_id, 100); lazyAverage.execute(input_ids, input_errors_ids); long[] shapeRes = new long[] { 1, shape[1], 1, imageShape[0], imageShape[1] }; SliceSettings resultsSlice = new SliceSettings(shapeRes, 0, (int) shapeRes[0]); int[] start = new int[] { 0, 0, 0, 0, 0 }; resultsSlice.setStart(start);//from w w w . ja va2 s .c om Dataset outDataset = NcdNexusUtils.sliceInputData(resultsSlice, input_ids); Dataset outErrors = NcdNexusUtils.sliceInputData(resultsSlice, input_errors_ids); Dataset dataErrors = data.getErrorBuffer(); for (int k = 0; k < shape[1]; k++) { for (int i = 0; i < imageShape[0]; i++) { for (int j = 0; j < imageShape[1]; j++) { start = new int[] { 0, k, 0, i, j }; int[] stop = new int[] { (int) shape[0], k + 1, (int) shape[2], i + 1, j + 1 }; Dataset dataSlice = data.getSlice(start, stop, null); Dataset errorsSlice = dataErrors.getSlice(start, stop, null); double value = outDataset.getDouble(0, k, 0, i, j); double errors = outErrors.getDouble(0, k, 0, i, j); double expected = (Double) dataSlice.sum() / (shape[0] * shape[2]); double expectederrors = Math.sqrt((Double) errorsSlice.sum()) / (shape[0] * shape[2]); // This check fails for higher accuracy settings assertEquals(String.format("Test average frame for (%d, %d, %d)", k, i, j), expected, value, 1e-6 * expected); assertEquals(String.format("Test average frame errors for (%d, %d, %d)", k, i, j), expectederrors, errors, 1e-6 * expectederrors); } } } }
From source file:uk.ac.diamond.scisoft.ncd.rcp.utils.NcdNexusUtilsTest.java
public void testSliceInputData(int sliceDim, int sliceBatch, int frameStart) throws HDF5Exception { int[] start = new int[] { 0, 0, 0, 0 }; start[sliceDim] = frameStart;/* ww w .j a v a2 s .com*/ int[] stop = Arrays.copyOf(frames, frames.length); Arrays.fill(stop, 0, sliceDim + 1, 1); stop[sliceDim] = Math.min(frameStart + sliceBatch, frames[sliceDim]); int[] step = new int[] { 1, 1, 1, 1 }; IDataset data = lazyDataset.getSlice(start, stop, step); DataSliceIdentifiers dr_id = readDataId(inputPath, detector, "data", null)[0]; long[] frames_long = (long[]) ConvertUtils.convert(frames, long[].class); SliceSettings drSlice = new SliceSettings(frames_long, sliceDim, sliceBatch); drSlice.setStart(start); Dataset result = NcdNexusUtils.sliceInputData(drSlice, dr_id); for (int idx = 0; idx < data.getShape()[0]; idx++) for (int frame = 0; frame < data.getShape()[1]; frame++) { start = new int[] { idx, frame, 0, 0 }; stop = new int[] { idx + 1, frame + 1, image[0], image[1] }; Dataset testResult = result.getSlice(start, stop, null); Dataset testData = (Dataset) data.getSlice(start, stop, null); float valResult = testResult.max().floatValue(); float valData = testData.max().floatValue(); float acc = (float) Math.max(1e-6 * Math.abs(Math.sqrt(valResult * valResult + valData * valData)), 1e-10); assertArrayEquals(String.format("Data slicing test for frame (%d, %d) has failed.", idx, frame), (float[]) testResult.getBuffer(), (float[]) testData.getBuffer(), acc); } }