Examples with Editable org.dcm4che3.img.util.Editable used on opensource projects

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Example 1 with Editable

use of org.dcm4che3.img.util.Editable in project karnak by OsiriX-Foundation.

the class ForwardService method transferOther.

public void transferOther(ForwardDicomNode fwdNode, WebForwardDestination destination, Attributes copy, Params p) throws IOException {
    Attributes attributesToSend = new Attributes();
    Attributes attributesOriginal = new Attributes();
    try {
        List<AttributeEditor> editors = destination.getDicomEditors();
        DicomStowRS stow = destination.getStowrsSingleFile();
        var syntax = new AdaptTransferSyntax(p.getTsuid(), destination.getOutputTransferSyntax(p.getTsuid()));
        if (syntax.getRequested().equals(p.getTsuid()) && editors.isEmpty()) {
            attributesToSend = copy;
            attributesOriginal.addAll(copy);
            stow.uploadDicom(copy, syntax.getRequested());
        } else {
            AttributeEditorContext context = new AttributeEditorContext(p.getTsuid(), fwdNode, null);
            Attributes attributes = new Attributes(copy);
            attributesToSend = attributes;
            attributesOriginal.addAll(attributes);
            editors.forEach(e -> e.apply(attributes, context));
            if (context.getAbort() == Abort.FILE_EXCEPTION) {
                throw new AbortException(context.getAbort(), context.getAbortMessage());
            } else if (context.getAbort() == Abort.CONNECTION_EXCEPTION) {
                throw new AbortException(context.getAbort(), "DICOM associtation abort. " + context.getAbortMessage());
            }
            BytesWithImageDescriptor desc = ImageAdapter.imageTranscode(attributes, syntax, context);
            if (desc == null) {
                stow.uploadDicom(attributes, syntax.getOriginal());
            } else {
                Editable<PlanarImage> editable = transformImage(attributes, context);
                stow.uploadPayload(ImageAdapter.preparePlayload(attributes, syntax, desc, editable));
            }
            progressNotify(destination, p.getIuid(), p.getCuid(), false, 0);
            monitor(fwdNode.getId(), destination.getId(), attributesOriginal, attributesToSend, true, null);
        }
    } catch (HttpException httpException) {
        if (httpException.getStatusCode() != 409) {
            progressNotify(destination, p.getIuid(), p.getCuid(), true, 0);
            monitor(fwdNode.getId(), destination.getId(), attributesOriginal, attributesToSend, false, httpException.getMessage());
            throw new AbortException(Abort.FILE_EXCEPTION, "DICOMWeb forward", httpException);
        } else {
            progressNotify(destination, p.getIuid(), p.getCuid(), false, 0);
            monitor(fwdNode.getId(), destination.getId(), attributesOriginal, attributesToSend, true, null);
            LOGGER.debug("File already present in destination");
        }
    } catch (AbortException e) {
        progressNotify(destination, p.getIuid(), p.getCuid(), true, 0);
        monitor(fwdNode.getId(), destination.getId(), attributesOriginal, attributesToSend, false, e.getMessage());
        if (e.getAbort() == Abort.CONNECTION_EXCEPTION) {
            throw e;
        }
    } catch (IOException e) {
        progressNotify(destination, p.getIuid(), p.getCuid(), true, 0);
        monitor(fwdNode.getId(), destination.getId(), attributesOriginal, attributesToSend, false, e.getMessage());
        throw e;
    } catch (Exception e) {
        progressNotify(destination, p.getIuid(), p.getCuid(), true, 0);
        monitor(fwdNode.getId(), destination.getId(), attributesOriginal, attributesToSend, false, e.getMessage());
        LOGGER.error(ERROR_WHEN_FORWARDING, e);
    }
}
Also used : Attributes(org.dcm4che3.data.Attributes) IOException(java.io.IOException) HttpException(org.weasis.dicom.web.HttpException) AbortException(org.karnak.backend.exception.AbortException) IOException(java.io.IOException) AttributeEditorContext(org.weasis.dicom.param.AttributeEditorContext) AttributeEditor(org.weasis.dicom.param.AttributeEditor) HttpException(org.weasis.dicom.web.HttpException) AdaptTransferSyntax(org.dcm4che3.img.stream.ImageAdapter.AdaptTransferSyntax) BytesWithImageDescriptor(org.dcm4che3.img.stream.BytesWithImageDescriptor) DicomStowRS(org.weasis.dicom.web.DicomStowRS) PlanarImage(org.weasis.opencv.data.PlanarImage) AbortException(org.karnak.backend.exception.AbortException)

Example 2 with Editable

use of org.dcm4che3.img.util.Editable in project karnak by OsiriX-Foundation.

the class ForwardService method transfer.

public List<File> transfer(ForwardDicomNode sourceNode, DicomForwardDestination destination, Attributes copy, Params p) throws IOException {
    StoreFromStreamSCU streamSCU = destination.getStreamSCU();
    DicomInputStream in = null;
    List<File> files;
    Attributes attributesOriginal = new Attributes();
    Attributes attributesToSend = new Attributes();
    try {
        if (!streamSCU.isReadyForDataTransfer()) {
            throw new IllegalStateException("Association not ready for transfer.");
        }
        DataWriter dataWriter;
        String cuid = p.getCuid();
        String iuid = p.getIuid();
        String tsuid = p.getTsuid();
        var syntax = new AdaptTransferSyntax(tsuid, streamSCU.selectTransferSyntax(cuid, destination.getOutputTransferSyntax(tsuid)));
        List<AttributeEditor> editors = destination.getDicomEditors();
        if (copy == null && editors.isEmpty() && syntax.getRequested().equals(tsuid)) {
            dataWriter = new InputStreamDataWriter(p.getData());
            attributesToSend = new DicomInputStream(p.getData()).readDataset();
            attributesOriginal.addAll(attributesToSend);
        } else {
            AttributeEditorContext context = new AttributeEditorContext(tsuid, sourceNode, streamSCU.getRemoteDicomNode());
            in = new DicomInputStream(p.getData(), tsuid);
            in.setIncludeBulkData(IncludeBulkData.URI);
            Attributes attributes = in.readDataset();
            attributesOriginal.addAll(attributes);
            attributesToSend = attributes;
            if (copy != null) {
                copy.addAll(attributes);
            }
            if (!editors.isEmpty()) {
                editors.forEach(e -> e.apply(attributes, context));
                iuid = attributes.getString(Tag.SOPInstanceUID);
                cuid = attributes.getString(Tag.SOPClassUID);
            }
            if (context.getAbort() == Abort.FILE_EXCEPTION) {
                if (p.getData() instanceof PDVInputStream) {
                    ((PDVInputStream) p.getData()).skipAll();
                }
                throw new AbortException(context.getAbort(), context.getAbortMessage());
            } else if (context.getAbort() == Abort.CONNECTION_EXCEPTION) {
                if (p.getAs() != null) {
                    p.getAs().abort();
                }
                throw new AbortException(context.getAbort(), "DICOM association abort: " + context.getAbortMessage());
            }
            BytesWithImageDescriptor desc = ImageAdapter.imageTranscode(attributes, syntax, context);
            Editable<PlanarImage> editable = transformImage(attributes, context);
            dataWriter = ImageAdapter.buildDataWriter(attributes, syntax, editable, desc);
        }
        streamSCU.cstore(cuid, iuid, p.getPriority(), dataWriter, syntax.getSuitable());
        progressNotify(destination, p.getIuid(), p.getCuid(), false, streamSCU.getNumberOfSuboperations());
        monitor(sourceNode.getId(), destination.getId(), attributesOriginal, attributesToSend, true, null);
    } catch (AbortException e) {
        progressNotify(destination, p.getIuid(), p.getCuid(), true, streamSCU.getNumberOfSuboperations());
        monitor(sourceNode.getId(), destination.getId(), attributesOriginal, attributesToSend, false, e.getMessage());
        if (e.getAbort() == Abort.CONNECTION_EXCEPTION) {
            throw e;
        }
    } catch (IOException e) {
        progressNotify(destination, p.getIuid(), p.getCuid(), true, streamSCU.getNumberOfSuboperations());
        monitor(sourceNode.getId(), destination.getId(), attributesOriginal, attributesToSend, false, e.getMessage());
        throw e;
    } catch (Exception e) {
        if (e instanceof InterruptedException) {
            Thread.currentThread().interrupt();
        }
        progressNotify(destination, p.getIuid(), p.getCuid(), true, streamSCU.getNumberOfSuboperations());
        monitor(sourceNode.getId(), destination.getId(), attributesOriginal, attributesToSend, false, e.getMessage());
        LOGGER.error(ERROR_WHEN_FORWARDING, e);
    } finally {
        streamSCU.triggerCloseExecutor();
        files = cleanOrGetBulkDataFiles(in, copy == null);
    }
    return files;
}
Also used : StoreFromStreamSCU(org.weasis.dicom.util.StoreFromStreamSCU) Attributes(org.dcm4che3.data.Attributes) IOException(java.io.IOException) DicomInputStream(org.dcm4che3.io.DicomInputStream) HttpException(org.weasis.dicom.web.HttpException) AbortException(org.karnak.backend.exception.AbortException) IOException(java.io.IOException) InputStreamDataWriter(org.dcm4che3.net.InputStreamDataWriter) AttributeEditorContext(org.weasis.dicom.param.AttributeEditorContext) AttributeEditor(org.weasis.dicom.param.AttributeEditor) AdaptTransferSyntax(org.dcm4che3.img.stream.ImageAdapter.AdaptTransferSyntax) BytesWithImageDescriptor(org.dcm4che3.img.stream.BytesWithImageDescriptor) File(java.io.File) PlanarImage(org.weasis.opencv.data.PlanarImage) DataWriter(org.dcm4che3.net.DataWriter) InputStreamDataWriter(org.dcm4che3.net.InputStreamDataWriter) PDVInputStream(org.dcm4che3.net.PDVInputStream) AbortException(org.karnak.backend.exception.AbortException)

Example 3 with Editable

use of org.dcm4che3.img.util.Editable in project karnak by OsiriX-Foundation.

the class ForwardService method transfer.

public List<File> transfer(ForwardDicomNode fwdNode, WebForwardDestination destination, Attributes copy, Params p) throws IOException {
    DicomInputStream in = null;
    List<File> files;
    Attributes attributesToSend = new Attributes();
    Attributes attributesOriginal = new Attributes();
    try {
        List<AttributeEditor> editors = destination.getDicomEditors();
        DicomStowRS stow = destination.getStowrsSingleFile();
        var syntax = new AdaptTransferSyntax(p.getTsuid(), destination.getOutputTransferSyntax(p.getTsuid()));
        if (syntax.getRequested().equals(p.getTsuid()) && copy == null && editors.isEmpty()) {
            Attributes fmi = Attributes.createFileMetaInformation(p.getIuid(), p.getCuid(), syntax.getRequested());
            try (InputStream stream = p.getData()) {
                attributesToSend = new DicomInputStream(p.getData()).readDataset();
                attributesOriginal.addAll(attributesToSend);
                stow.uploadDicom(stream, fmi);
            } catch (HttpException httpException) {
                if (httpException.getStatusCode() != 409) {
                    throw new AbortException(Abort.FILE_EXCEPTION, httpException.getMessage());
                } else {
                    LOGGER.debug("File already present in destination");
                }
            }
        } else {
            AttributeEditorContext context = new AttributeEditorContext(p.getTsuid(), fwdNode, null);
            in = new DicomInputStream(p.getData(), p.getTsuid());
            in.setIncludeBulkData(IncludeBulkData.URI);
            Attributes attributes = in.readDataset();
            attributesToSend = attributes;
            attributesOriginal.addAll(attributes);
            if (copy != null) {
                copy.addAll(attributes);
            }
            if (!editors.isEmpty()) {
                editors.forEach(e -> e.apply(attributes, context));
            }
            if (context.getAbort() == Abort.FILE_EXCEPTION) {
                if (p.getData() instanceof PDVInputStream) {
                    ((PDVInputStream) p.getData()).skipAll();
                }
                throw new AbortException(context.getAbort(), context.getAbortMessage());
            } else if (context.getAbort() == Abort.CONNECTION_EXCEPTION) {
                if (p.getAs() != null) {
                    p.getAs().abort();
                }
                throw new AbortException(context.getAbort(), "STOW-RS abort: " + context.getAbortMessage());
            }
            BytesWithImageDescriptor desc = ImageAdapter.imageTranscode(attributes, syntax, context);
            if (desc == null) {
                stow.uploadDicom(attributes, syntax.getOriginal());
            } else {
                Editable<PlanarImage> editable = transformImage(attributes, context);
                stow.uploadPayload(ImageAdapter.preparePlayload(attributes, syntax, desc, editable));
            }
        }
        progressNotify(destination, p.getIuid(), p.getCuid(), false, 0);
        monitor(fwdNode.getId(), destination.getId(), attributesOriginal, attributesToSend, true, null);
    } catch (AbortException e) {
        progressNotify(destination, p.getIuid(), p.getCuid(), true, 0);
        monitor(fwdNode.getId(), destination.getId(), attributesOriginal, attributesToSend, false, e.getMessage());
        if (e.getAbort() == Abort.CONNECTION_EXCEPTION) {
            throw e;
        }
    } catch (IOException e) {
        progressNotify(destination, p.getIuid(), p.getCuid(), true, 0);
        monitor(fwdNode.getId(), destination.getId(), attributesOriginal, attributesToSend, false, e.getMessage());
        throw e;
    } catch (Exception e) {
        progressNotify(destination, p.getIuid(), p.getCuid(), true, 0);
        monitor(fwdNode.getId(), destination.getId(), attributesOriginal, attributesToSend, false, e.getMessage());
        LOGGER.error(ERROR_WHEN_FORWARDING, e);
    } finally {
        files = cleanOrGetBulkDataFiles(in, copy == null);
    }
    return files;
}
Also used : PDVInputStream(org.dcm4che3.net.PDVInputStream) DicomInputStream(org.dcm4che3.io.DicomInputStream) InputStream(java.io.InputStream) Attributes(org.dcm4che3.data.Attributes) IOException(java.io.IOException) DicomInputStream(org.dcm4che3.io.DicomInputStream) HttpException(org.weasis.dicom.web.HttpException) AbortException(org.karnak.backend.exception.AbortException) IOException(java.io.IOException) AttributeEditorContext(org.weasis.dicom.param.AttributeEditorContext) AttributeEditor(org.weasis.dicom.param.AttributeEditor) HttpException(org.weasis.dicom.web.HttpException) AdaptTransferSyntax(org.dcm4che3.img.stream.ImageAdapter.AdaptTransferSyntax) BytesWithImageDescriptor(org.dcm4che3.img.stream.BytesWithImageDescriptor) File(java.io.File) DicomStowRS(org.weasis.dicom.web.DicomStowRS) PlanarImage(org.weasis.opencv.data.PlanarImage) AbortException(org.karnak.backend.exception.AbortException) PDVInputStream(org.dcm4che3.net.PDVInputStream)

Example 4 with Editable

use of org.dcm4che3.img.util.Editable in project karnak by OsiriX-Foundation.

the class ForwardService method transformImage.

private static Editable<PlanarImage> transformImage(Attributes attributes, AttributeEditorContext context) {
    MaskArea m = context.getMaskArea();
    boolean defacing = LangUtil.getEmptytoFalse(context.getProperties().getProperty(Defacer.APPLY_DEFACING));
    if (m != null || defacing) {
        return img -> {
            PlanarImage image = img;
            if (defacing) {
                image = Defacer.apply(attributes, image);
            }
            if (m != null) {
                image = MaskArea.drawShape(image.toMat(), m);
            }
            return image;
        };
    }
    return null;
}
Also used : AttributeEditor(org.weasis.dicom.param.AttributeEditor) HttpException(org.weasis.dicom.web.HttpException) DataWriter(org.dcm4che3.net.DataWriter) AttributeEditorContext(org.weasis.dicom.param.AttributeEditorContext) UID(org.dcm4che3.data.UID) Attributes(org.dcm4che3.data.Attributes) BytesWithImageDescriptor(org.dcm4che3.img.stream.BytesWithImageDescriptor) ForwardDestination(org.karnak.backend.dicom.ForwardDestination) AbortException(org.karnak.backend.exception.AbortException) LoggerFactory(org.slf4j.LoggerFactory) Autowired(org.springframework.beans.factory.annotation.Autowired) ArrayList(java.util.ArrayList) ImageAdapter(org.dcm4che3.img.stream.ImageAdapter) Service(org.springframework.stereotype.Service) ApplicationEventPublisher(org.springframework.context.ApplicationEventPublisher) WebForwardDestination(org.karnak.backend.dicom.WebForwardDestination) InputStreamDataWriter(org.dcm4che3.net.InputStreamDataWriter) StoreFromStreamSCU(org.weasis.dicom.util.StoreFromStreamSCU) TransferStatusEntity(org.karnak.backend.data.entity.TransferStatusEntity) FileUtil(org.weasis.core.util.FileUtil) DicomOutputData(org.dcm4che3.img.DicomOutputData) Editable(org.dcm4che3.img.util.Editable) PDVInputStream(org.dcm4che3.net.PDVInputStream) LangUtil(org.weasis.core.util.LangUtil) PlanarImage(org.weasis.opencv.data.PlanarImage) Logger(org.slf4j.Logger) Params(org.karnak.backend.dicom.Params) IncludeBulkData(org.dcm4che3.io.DicomInputStream.IncludeBulkData) DataWriterAdapter(org.dcm4che3.net.DataWriterAdapter) DicomStowRS(org.weasis.dicom.web.DicomStowRS) Set(java.util.Set) AdaptTransferSyntax(org.dcm4che3.img.stream.ImageAdapter.AdaptTransferSyntax) IOException(java.io.IOException) Status(org.dcm4che3.net.Status) ProgressStatus(org.weasis.dicom.util.ServiceUtil.ProgressStatus) File(java.io.File) TransferMonitoringEvent(org.karnak.backend.model.event.TransferMonitoringEvent) Association(org.dcm4che3.net.Association) List(java.util.List) ForwardDicomNode(org.karnak.backend.dicom.ForwardDicomNode) Tag(org.dcm4che3.data.Tag) ServiceUtil(org.weasis.dicom.util.ServiceUtil) DicomInputStream(org.dcm4che3.io.DicomInputStream) DicomForwardDestination(org.karnak.backend.dicom.DicomForwardDestination) Abort(org.weasis.dicom.param.AttributeEditorContext.Abort) Defacer(org.karnak.backend.dicom.Defacer) MaskArea(org.dcm4che3.img.op.MaskArea) InputStream(java.io.InputStream) MaskArea(org.dcm4che3.img.op.MaskArea) PlanarImage(org.weasis.opencv.data.PlanarImage)

Example 5 with Editable

use of org.dcm4che3.img.util.Editable in project karnak by OsiriX-Foundation.

the class ForwardService method transferOther.

public void transferOther(ForwardDicomNode fwdNode, DicomForwardDestination destination, Attributes copy, Params p) throws IOException {
    StoreFromStreamSCU streamSCU = destination.getStreamSCU();
    Attributes attributesToSend = new Attributes();
    Attributes attributesOriginal = new Attributes();
    try {
        if (!streamSCU.isReadyForDataTransfer()) {
            throw new IllegalStateException("Association not ready for transfer.");
        }
        DataWriter dataWriter;
        String tsuid = p.getTsuid();
        String iuid = p.getIuid();
        String cuid = p.getCuid();
        var syntax = new AdaptTransferSyntax(tsuid, streamSCU.selectTransferSyntax(cuid, destination.getOutputTransferSyntax(tsuid)));
        List<AttributeEditor> editors = destination.getDicomEditors();
        if (editors.isEmpty() && syntax.getRequested().equals(tsuid)) {
            dataWriter = new DataWriterAdapter(copy);
            attributesOriginal.addAll(copy);
            attributesToSend = copy;
        } else {
            AttributeEditorContext context = new AttributeEditorContext(tsuid, fwdNode, streamSCU.getRemoteDicomNode());
            Attributes attributes = new Attributes(copy);
            attributesOriginal.addAll(attributes);
            attributesToSend = attributes;
            if (!editors.isEmpty()) {
                editors.forEach(e -> e.apply(attributes, context));
                iuid = attributes.getString(Tag.SOPInstanceUID);
                cuid = attributes.getString(Tag.SOPClassUID);
            }
            if (context.getAbort() == Abort.FILE_EXCEPTION) {
                throw new AbortException(context.getAbort(), context.getAbortMessage());
            } else if (context.getAbort() == Abort.CONNECTION_EXCEPTION) {
                throw new AbortException(context.getAbort(), "DICOM association abort. " + context.getAbortMessage());
            }
            BytesWithImageDescriptor desc = ImageAdapter.imageTranscode(attributes, syntax, context);
            Editable<PlanarImage> editable = transformImage(attributes, context);
            dataWriter = ImageAdapter.buildDataWriter(attributes, syntax, editable, desc);
        }
        streamSCU.cstore(cuid, iuid, p.getPriority(), dataWriter, syntax.getSuitable());
        progressNotify(destination, p.getIuid(), p.getCuid(), false, streamSCU.getNumberOfSuboperations());
        monitor(fwdNode.getId(), destination.getId(), attributesOriginal, attributesToSend, true, null);
    } catch (AbortException e) {
        progressNotify(destination, p.getIuid(), p.getCuid(), true, streamSCU.getNumberOfSuboperations());
        monitor(fwdNode.getId(), destination.getId(), attributesOriginal, attributesToSend, false, e.getMessage());
        if (e.getAbort() == Abort.CONNECTION_EXCEPTION) {
            throw e;
        }
    } catch (IOException e) {
        progressNotify(destination, p.getIuid(), p.getCuid(), true, streamSCU.getNumberOfSuboperations());
        monitor(fwdNode.getId(), destination.getId(), attributesOriginal, attributesToSend, false, e.getMessage());
        throw e;
    } catch (Exception e) {
        if (e instanceof InterruptedException) {
            Thread.currentThread().interrupt();
        }
        progressNotify(destination, p.getIuid(), p.getCuid(), true, streamSCU.getNumberOfSuboperations());
        monitor(fwdNode.getId(), destination.getId(), attributesOriginal, attributesToSend, false, e.getMessage());
        LOGGER.error(ERROR_WHEN_FORWARDING, e);
    } finally {
        streamSCU.triggerCloseExecutor();
    }
}
Also used : StoreFromStreamSCU(org.weasis.dicom.util.StoreFromStreamSCU) Attributes(org.dcm4che3.data.Attributes) IOException(java.io.IOException) DataWriterAdapter(org.dcm4che3.net.DataWriterAdapter) HttpException(org.weasis.dicom.web.HttpException) AbortException(org.karnak.backend.exception.AbortException) IOException(java.io.IOException) AttributeEditorContext(org.weasis.dicom.param.AttributeEditorContext) AttributeEditor(org.weasis.dicom.param.AttributeEditor) AdaptTransferSyntax(org.dcm4che3.img.stream.ImageAdapter.AdaptTransferSyntax) BytesWithImageDescriptor(org.dcm4che3.img.stream.BytesWithImageDescriptor) PlanarImage(org.weasis.opencv.data.PlanarImage) DataWriter(org.dcm4che3.net.DataWriter) InputStreamDataWriter(org.dcm4che3.net.InputStreamDataWriter) AbortException(org.karnak.backend.exception.AbortException)

Aggregations

Attributes (org.dcm4che3.data.Attributes)6 IOException (java.io.IOException)5 BytesWithImageDescriptor (org.dcm4che3.img.stream.BytesWithImageDescriptor)5 AdaptTransferSyntax (org.dcm4che3.img.stream.ImageAdapter.AdaptTransferSyntax)5 AbortException (org.karnak.backend.exception.AbortException)5 AttributeEditor (org.weasis.dicom.param.AttributeEditor)5 AttributeEditorContext (org.weasis.dicom.param.AttributeEditorContext)5 HttpException (org.weasis.dicom.web.HttpException)5 PlanarImage (org.weasis.opencv.data.PlanarImage)5 File (java.io.File)3 DicomInputStream (org.dcm4che3.io.DicomInputStream)3 DataWriter (org.dcm4che3.net.DataWriter)3 InputStreamDataWriter (org.dcm4che3.net.InputStreamDataWriter)3 PDVInputStream (org.dcm4che3.net.PDVInputStream)3 StoreFromStreamSCU (org.weasis.dicom.util.StoreFromStreamSCU)3 InputStream (java.io.InputStream)2 ArrayList (java.util.ArrayList)2 DataWriterAdapter (org.dcm4che3.net.DataWriterAdapter)2 DicomStowRS (org.weasis.dicom.web.DicomStowRS)2 Color (java.awt.Color)1
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