HealthImaging examples using SDK for C++

Code for the CMakeLists.txt CMake file.

# Set the minimum required version of CMake for this project.
cmake_minimum_required(VERSION 3.13)

# Set the AWS service components used by this project.
set(SERVICE_COMPONENTS medical-imaging)

# Set this project's name.
project("hello_health-imaging")

# Set the C++ standard to use to build this target.
# At least C++ 11 is required for the AWS SDK for C++.
set(CMAKE_CXX_STANDARD 11)

# Use the MSVC variable to determine if this is a Windows build.
set(WINDOWS_BUILD ${MSVC})

if (WINDOWS_BUILD) # Set the location where CMake can find the installed libraries for the AWS SDK.
    string(REPLACE ";" "/aws-cpp-sdk-all;" SYSTEM_MODULE_PATH "${CMAKE_SYSTEM_PREFIX_PATH}/aws-cpp-sdk-all")
    list(APPEND CMAKE_PREFIX_PATH ${SYSTEM_MODULE_PATH})
endif ()

# Find the AWS SDK for C++ package.
find_package(AWSSDK REQUIRED COMPONENTS ${SERVICE_COMPONENTS})

if (WINDOWS_BUILD)
    # Copy relevant AWS SDK for C++ libraries into the current binary directory for running and debugging.

    # set(BIN_SUB_DIR "/Debug") # If you are building from the command line, you may need to uncomment this
    # and set the proper subdirectory to the executable location.

    AWSSDK_CPY_DYN_LIBS(SERVICE_COMPONENTS "" ${CMAKE_CURRENT_BINARY_DIR} ${BIN_SUB_DIR})
endif ()

add_executable(${PROJECT_NAME}
        hello_health_imaging.cpp)

target_link_libraries(${PROJECT_NAME}
        ${AWSSDK_LINK_LIBRARIES})

Code for the hello_health_imaging.cpp source file.

#include <aws/core/Aws.h>
#include <aws/medical-imaging/MedicalImagingClient.h>
#include <aws/medical-imaging/model/ListDatastoresRequest.h>

#include <iostream>

/*
 *  A "Hello HealthImaging" starter application which initializes an AWS HealthImaging (HealthImaging) client
 *  and lists the HealthImaging data stores in the current account.
 *
 *  main function
 *
 *  Usage: 'hello_health-imaging'
 *
 */
#include <aws/core/auth/AWSCredentialsProviderChain.h>
#include <aws/core/platform/Environment.h>

int main(int argc, char **argv) {
    (void) argc;
    (void) argv;
    Aws::SDKOptions options;
    //   Optional: change the log level for debugging.
    //   options.loggingOptions.logLevel = Aws::Utils::Logging::LogLevel::Debug;

    Aws::InitAPI(options); // Should only be called once.
    {
        Aws::Client::ClientConfiguration clientConfig;
        // Optional: Set to the AWS Region (overrides config file).
        // clientConfig.region = "us-east-1";

        Aws::MedicalImaging::MedicalImagingClient medicalImagingClient(clientConfig);
        Aws::MedicalImaging::Model::ListDatastoresRequest listDatastoresRequest;

        Aws::Vector<Aws::MedicalImaging::Model::DatastoreSummary> allDataStoreSummaries;
        Aws::String nextToken; // Used for paginated results.
        do {
            if (!nextToken.empty()) {
                listDatastoresRequest.SetNextToken(nextToken);
            }
            Aws::MedicalImaging::Model::ListDatastoresOutcome listDatastoresOutcome =
                    medicalImagingClient.ListDatastores(listDatastoresRequest);
            if (listDatastoresOutcome.IsSuccess()) {
                const Aws::Vector<Aws::MedicalImaging::Model::DatastoreSummary> &dataStoreSummaries =
                        listDatastoresOutcome.GetResult().GetDatastoreSummaries();
                allDataStoreSummaries.insert(allDataStoreSummaries.cend(),
                                             dataStoreSummaries.cbegin(),
                                             dataStoreSummaries.cend());
                nextToken = listDatastoresOutcome.GetResult().GetNextToken();
            }
            else {
                std::cerr << "ListDatastores error: "
                          << listDatastoresOutcome.GetError().GetMessage() << std::endl;
                break;
            }
        } while (!nextToken.empty());

        std::cout << allDataStoreSummaries.size() << " HealthImaging data "
                  << ((allDataStoreSummaries.size() == 1) ?
                      "store was retrieved." : "stores were retrieved.") << std::endl;

        for (auto const &dataStoreSummary: allDataStoreSummaries) {
            std::cout << "  Datastore: " << dataStoreSummary.GetDatastoreName()
                      << std::endl;
            std::cout << "  Datastore ID: " << dataStoreSummary.GetDatastoreId()
                      << std::endl;
        }
    }

    Aws::ShutdownAPI(options); // Should only be called once.
    return 0;
}

//! Routine which deletes an AWS HealthImaging image set.
/*!
  \param dataStoreID: The HealthImaging data store ID.
  \param imageSetID: The image set ID.
  \param clientConfig: Aws client configuration.
  \return bool: Function succeeded.
  */
bool AwsDoc::Medical_Imaging::deleteImageSet(
        const Aws::String &dataStoreID, const Aws::String &imageSetID,
        const Aws::Client::ClientConfiguration &clientConfig) {
    Aws::MedicalImaging::MedicalImagingClient client(clientConfig);
    Aws::MedicalImaging::Model::DeleteImageSetRequest request;
    request.SetDatastoreId(dataStoreID);
    request.SetImageSetId(imageSetID);
    Aws::MedicalImaging::Model::DeleteImageSetOutcome outcome = client.DeleteImageSet(
            request);
    if (outcome.IsSuccess()) {
        std::cout << "Successfully deleted image set " << imageSetID
                  << " from data store " << dataStoreID << std::endl;
    }
    else {
        std::cerr << "Error deleting image set " << imageSetID << " from data store "
                  << dataStoreID << ": " <<
                  outcome.GetError().GetMessage() << std::endl;
    }

    return outcome.IsSuccess();
}

//! Routine which gets a HealthImaging DICOM import job's properties.
/*!
  \param dataStoreID: The HealthImaging data store ID.
  \param importJobID: The DICOM import job ID
  \param clientConfig: Aws client configuration.
  \return GetDICOMImportJobOutcome: The import job outcome.
*/
Aws::MedicalImaging::Model::GetDICOMImportJobOutcome
AwsDoc::Medical_Imaging::getDICOMImportJob(const Aws::String &dataStoreID,
                                           const Aws::String &importJobID,
                                           const Aws::Client::ClientConfiguration &clientConfig) {
    Aws::MedicalImaging::MedicalImagingClient client(clientConfig);
    Aws::MedicalImaging::Model::GetDICOMImportJobRequest request;
    request.SetDatastoreId(dataStoreID);
    request.SetJobId(importJobID);
    Aws::MedicalImaging::Model::GetDICOMImportJobOutcome outcome = client.GetDICOMImportJob(
            request);
    if (!outcome.IsSuccess()) {
        std::cerr << "GetDICOMImportJob error: "
                  << outcome.GetError().GetMessage() << std::endl;
    }

    return outcome;
}

//! Routine which downloads an AWS HealthImaging image frame.
/*!
  \param dataStoreID: The HealthImaging data store ID.
  \param imageSetID: The image set ID.
  \param frameID: The image frame ID.
  \param jphFile: File to store the downloaded frame.
  \param clientConfig: Aws client configuration.
  \return bool: Function succeeded.
*/
bool AwsDoc::Medical_Imaging::getImageFrame(const Aws::String &dataStoreID,
                                            const Aws::String &imageSetID,
                                            const Aws::String &frameID,
                                            const Aws::String &jphFile,
                                            const Aws::Client::ClientConfiguration &clientConfig) {
    Aws::MedicalImaging::MedicalImagingClient client(clientConfig);

    Aws::MedicalImaging::Model::GetImageFrameRequest request;
    request.SetDatastoreId(dataStoreID);
    request.SetImageSetId(imageSetID);

    Aws::MedicalImaging::Model::ImageFrameInformation imageFrameInformation;
    imageFrameInformation.SetImageFrameId(frameID);
    request.SetImageFrameInformation(imageFrameInformation);

    Aws::MedicalImaging::Model::GetImageFrameOutcome outcome = client.GetImageFrame(
            request);

    if (outcome.IsSuccess()) {
        std::cout << "Successfully retrieved image frame." << std::endl;
        auto &buffer = outcome.GetResult().GetImageFrameBlob();

        std::ofstream outfile(jphFile, std::ios::binary);
        outfile << buffer.rdbuf();
    }
    else {
        std::cout << "Error retrieving image frame." << outcome.GetError().GetMessage()
                  << std::endl;

    }

    return outcome.IsSuccess();
}

Utility function to get image set metadata.

//! Routine which gets a HealthImaging image set's metadata.
/*!
  \param dataStoreID: The HealthImaging data store ID.
  \param imageSetID: The HealthImaging image set ID.
  \param versionID: The HealthImaging image set version ID, ignored if empty.
  \param outputFilePath: The path where the metadata will be stored as gzipped json.
  \param clientConfig: Aws client configuration.
  \\return bool: Function succeeded.
*/
bool AwsDoc::Medical_Imaging::getImageSetMetadata(const Aws::String &dataStoreID,
                                                  const Aws::String &imageSetID,
                                                  const Aws::String &versionID,
                                                  const Aws::String &outputFilePath,
                                                  const Aws::Client::ClientConfiguration &clientConfig) {
    Aws::MedicalImaging::Model::GetImageSetMetadataRequest request;
    request.SetDatastoreId(dataStoreID);
    request.SetImageSetId(imageSetID);
    if (!versionID.empty()) {
        request.SetVersionId(versionID);
    }
    Aws::MedicalImaging::MedicalImagingClient client(clientConfig);
    Aws::MedicalImaging::Model::GetImageSetMetadataOutcome outcome = client.GetImageSetMetadata(
            request);
    if (outcome.IsSuccess()) {
        std::ofstream file(outputFilePath, std::ios::binary);
        auto &metadata = outcome.GetResult().GetImageSetMetadataBlob();
        file << metadata.rdbuf();
    }
    else {
        std::cerr << "Failed to get image set metadata: "
                  << outcome.GetError().GetMessage() << std::endl;
    }

    return outcome.IsSuccess();
}

Get image set metadata without version.

        if (AwsDoc::Medical_Imaging::getImageSetMetadata(dataStoreID, imageSetID, "", outputFilePath, clientConfig))
        {
            std::cout << "Successfully retrieved image set metadata." << std::endl;
            std::cout << "Metadata stored in: " << outputFilePath << std::endl;
        }

Get image set metadata with version.

        if (AwsDoc::Medical_Imaging::getImageSetMetadata(dataStoreID, imageSetID, versionID, outputFilePath, clientConfig))
        {
            std::cout << "Successfully retrieved image set metadata." << std::endl;
            std::cout << "Metadata stored in: " << outputFilePath << std::endl;
        }

The utility function for searching image sets.

//! Routine which searches for image sets based on defined input attributes.
/*!
  \param dataStoreID: The HealthImaging data store ID.
  \param searchCriteria: A search criteria instance.
  \param imageSetResults: Vector to receive the image set IDs.
  \param clientConfig: Aws client configuration.
  \return bool: Function succeeded.
  */
bool AwsDoc::Medical_Imaging::searchImageSets(const Aws::String &dataStoreID,
                                              const Aws::MedicalImaging::Model::SearchCriteria &searchCriteria,
                                              Aws::Vector<Aws::String> &imageSetResults,
                                              const Aws::Client::ClientConfiguration &clientConfig) {
    Aws::MedicalImaging::MedicalImagingClient client(clientConfig);
    Aws::MedicalImaging::Model::SearchImageSetsRequest request;
    request.SetDatastoreId(dataStoreID);
    request.SetSearchCriteria(searchCriteria);

    Aws::String nextToken; // Used for paginated results.
    bool result = true;
    do {
        if (!nextToken.empty()) {
            request.SetNextToken(nextToken);
        }

        Aws::MedicalImaging::Model::SearchImageSetsOutcome outcome = client.SearchImageSets(
                request);
        if (outcome.IsSuccess()) {
            for (auto &imageSetMetadataSummary: outcome.GetResult().GetImageSetsMetadataSummaries()) {
                imageSetResults.push_back(imageSetMetadataSummary.GetImageSetId());
            }

            nextToken = outcome.GetResult().GetNextToken();
        }
        else {
            std::cout << "Error: " << outcome.GetError().GetMessage() << std::endl;
            result = false;
        }
    } while (!nextToken.empty());

    return result;
}

Use case #1: EQUAL operator.

        Aws::Vector<Aws::String> imageIDsForPatientID;
        Aws::MedicalImaging::Model::SearchCriteria searchCriteriaEqualsPatientID;
        Aws::Vector<Aws::MedicalImaging::Model::SearchFilter> patientIDSearchFilters = {
                Aws::MedicalImaging::Model::SearchFilter().WithOperator(Aws::MedicalImaging::Model::Operator::EQUAL)
                .WithValues({Aws::MedicalImaging::Model::SearchByAttributeValue().WithDICOMPatientId(patientID)})
        };

        searchCriteriaEqualsPatientID.SetFilters(patientIDSearchFilters);
        bool result = AwsDoc::Medical_Imaging::searchImageSets(dataStoreID,
                                                               searchCriteriaEqualsPatientID,
                                                               imageIDsForPatientID,
                                                               clientConfig);
        if (result) {
            std::cout << imageIDsForPatientID.size() << " image sets found for the patient with ID '"
            <<  patientID << "'." << std::endl;
            for (auto &imageSetResult : imageIDsForPatientID) {
                std::cout << "  Image set with ID '" << imageSetResult << std::endl;
            }
        }

Use case #2: BETWEEN operator using DICOMStudyDate and DICOMStudyTime.

         Aws::MedicalImaging::Model::SearchByAttributeValue useCase2StartDate;
        useCase2StartDate.SetDICOMStudyDateAndTime(Aws::MedicalImaging::Model::DICOMStudyDateAndTime()
        .WithDICOMStudyDate("19990101")
        .WithDICOMStudyTime("000000.000"));

        Aws::MedicalImaging::Model::SearchByAttributeValue useCase2EndDate;
        useCase2EndDate.SetDICOMStudyDateAndTime(Aws::MedicalImaging::Model::DICOMStudyDateAndTime()
        .WithDICOMStudyDate(Aws::Utils::DateTime(std::chrono::system_clock::now()).ToLocalTimeString("%Y%m%d"))
        .WithDICOMStudyTime("000000.000"));

        Aws::MedicalImaging::Model::SearchFilter useCase2SearchFilter;
        useCase2SearchFilter.SetValues({useCase2StartDate, useCase2EndDate});
        useCase2SearchFilter.SetOperator(Aws::MedicalImaging::Model::Operator::BETWEEN);

        Aws::MedicalImaging::Model::SearchCriteria useCase2SearchCriteria;
        useCase2SearchCriteria.SetFilters({useCase2SearchFilter});

        Aws::Vector<Aws::String> usesCase2Results;
        result = AwsDoc::Medical_Imaging::searchImageSets(dataStoreID,
                                                          useCase2SearchCriteria,
                                                          usesCase2Results,
                                                          clientConfig);
        if (result) {
            std::cout << usesCase2Results.size() << " image sets found for between 1999/01/01 and present."
                      <<  std::endl;
            for (auto &imageSetResult : usesCase2Results) {
                std::cout << "  Image set with ID '" << imageSetResult << std::endl;
            }
        }

Use case #3: BETWEEN operator using createdAt. Time studies were previously persisted.

        Aws::MedicalImaging::Model::SearchByAttributeValue useCase3StartDate;
        useCase3StartDate.SetCreatedAt(Aws::Utils::DateTime("20231130T000000000Z",Aws::Utils::DateFormat::ISO_8601_BASIC));

        Aws::MedicalImaging::Model::SearchByAttributeValue useCase3EndDate;
        useCase3EndDate.SetCreatedAt(Aws::Utils::DateTime(std::chrono::system_clock::now()));

        Aws::MedicalImaging::Model::SearchFilter useCase3SearchFilter;
        useCase3SearchFilter.SetValues({useCase3StartDate, useCase3EndDate});
        useCase3SearchFilter.SetOperator(Aws::MedicalImaging::Model::Operator::BETWEEN);

        Aws::MedicalImaging::Model::SearchCriteria useCase3SearchCriteria;
        useCase3SearchCriteria.SetFilters({useCase3SearchFilter});

        Aws::Vector<Aws::String> usesCase3Results;
        result = AwsDoc::Medical_Imaging::searchImageSets(dataStoreID,
                                                          useCase3SearchCriteria,
                                                          usesCase3Results,
                                                          clientConfig);
        if (result) {
            std::cout << usesCase3Results.size() << " image sets found for created between 2023/11/30 and present."
                      <<  std::endl;
            for (auto &imageSetResult : usesCase3Results) {
                std::cout << "  Image set with ID '" << imageSetResult << std::endl;
            }
        }

Use case #4: EQUAL operator on DICOMSeriesInstanceUID and BETWEEN on updatedAt and sort response in ASC order on updatedAt field.

        Aws::MedicalImaging::Model::SearchByAttributeValue useCase4StartDate;
        useCase4StartDate.SetUpdatedAt(Aws::Utils::DateTime("20231130T000000000Z",Aws::Utils::DateFormat::ISO_8601_BASIC));

        Aws::MedicalImaging::Model::SearchByAttributeValue useCase4EndDate;
        useCase4EndDate.SetUpdatedAt(Aws::Utils::DateTime(std::chrono::system_clock::now()));

        Aws::MedicalImaging::Model::SearchFilter useCase4SearchFilterBetween;
        useCase4SearchFilterBetween.SetValues({useCase4StartDate, useCase4EndDate});
        useCase4SearchFilterBetween.SetOperator(Aws::MedicalImaging::Model::Operator::BETWEEN);

        Aws::MedicalImaging::Model::SearchByAttributeValue seriesInstanceUID;
        seriesInstanceUID.SetDICOMSeriesInstanceUID(dicomSeriesInstanceUID);

        Aws::MedicalImaging::Model::SearchFilter useCase4SearchFilterEqual;
        useCase4SearchFilterEqual.SetValues({seriesInstanceUID});
        useCase4SearchFilterEqual.SetOperator(Aws::MedicalImaging::Model::Operator::EQUAL);

        Aws::MedicalImaging::Model::SearchCriteria useCase4SearchCriteria;
        useCase4SearchCriteria.SetFilters({useCase4SearchFilterBetween, useCase4SearchFilterEqual});

        Aws::MedicalImaging::Model::Sort useCase4Sort;
        useCase4Sort.SetSortField(Aws::MedicalImaging::Model::SortField::updatedAt);
        useCase4Sort.SetSortOrder(Aws::MedicalImaging::Model::SortOrder::ASC);

        useCase4SearchCriteria.SetSort(useCase4Sort);

        Aws::Vector<Aws::String> usesCase4Results;
        result = AwsDoc::Medical_Imaging::searchImageSets(dataStoreID,
                                                          useCase4SearchCriteria,
                                                          usesCase4Results,
                                                          clientConfig);
        if (result) {
            std::cout << usesCase4Results.size() << " image sets found for EQUAL operator "
            << "on DICOMSeriesInstanceUID and BETWEEN on updatedAt and sort response\n"
            <<  "in ASC order on updatedAt field." <<  std::endl;
            for (auto &imageSetResult : usesCase4Results) {
                std::cout << "  Image set with ID '" << imageSetResult << std::endl;
            }
        }

//! Routine which starts a HealthImaging import job.
/*!
  \param dataStoreID: The HealthImaging data store ID.
  \param inputBucketName: The name of the Amazon S3 bucket containing the DICOM files.
  \param inputDirectory: The directory in the S3 bucket containing the DICOM files.
  \param outputBucketName: The name of the S3 bucket for the output.
  \param outputDirectory: The directory in the S3 bucket to store the output.
  \param roleArn: The ARN of the IAM role with permissions for the import.
  \param importJobId: A string to receive the import job ID.
  \param clientConfig: Aws client configuration.
  \return bool: Function succeeded.
  */
bool AwsDoc::Medical_Imaging::startDICOMImportJob(
        const Aws::String &dataStoreID, const Aws::String &inputBucketName,
        const Aws::String &inputDirectory, const Aws::String &outputBucketName,
        const Aws::String &outputDirectory, const Aws::String &roleArn,
        Aws::String &importJobId,
        const Aws::Client::ClientConfiguration &clientConfig) {
    Aws::MedicalImaging::MedicalImagingClient medicalImagingClient(clientConfig);
    Aws::String inputURI = "s3://" + inputBucketName + "/" + inputDirectory + "/";
    Aws::String outputURI = "s3://" + outputBucketName + "/" + outputDirectory + "/";
    Aws::MedicalImaging::Model::StartDICOMImportJobRequest startDICOMImportJobRequest;
    startDICOMImportJobRequest.SetDatastoreId(dataStoreID);
    startDICOMImportJobRequest.SetDataAccessRoleArn(roleArn);
    startDICOMImportJobRequest.SetInputS3Uri(inputURI);
    startDICOMImportJobRequest.SetOutputS3Uri(outputURI);

    Aws::MedicalImaging::Model::StartDICOMImportJobOutcome startDICOMImportJobOutcome = medicalImagingClient.StartDICOMImportJob(
            startDICOMImportJobRequest);

    if (startDICOMImportJobOutcome.IsSuccess()) {
        importJobId = startDICOMImportJobOutcome.GetResult().GetJobId();
    }
    else {
        std::cerr << "Failed to start DICOM import job because "
                  << startDICOMImportJobOutcome.GetError().GetMessage() << std::endl;
    }

    return startDICOMImportJobOutcome.IsSuccess();
}

Create an Amazon CloudFormation stack with the necessary resources.

    Aws::String inputBucketName;
    Aws::String outputBucketName;
    Aws::String dataStoreId;
    Aws::String roleArn;
    Aws::String stackName;

    if (askYesNoQuestion(
            "Would you like to let this workflow create the resources for you? (y/n) ")) {
        stackName = askQuestion(
                "Enter a name for the AWS CloudFormation stack to create. ");
        Aws::String dataStoreName = askQuestion(
                "Enter a name for the HealthImaging datastore to create. ");

        Aws::Map<Aws::String, Aws::String> outputs = createCloudFormationStack(
                stackName,
                dataStoreName,
                clientConfiguration);

        if (!retrieveOutputs(outputs, dataStoreId, inputBucketName, outputBucketName,
                             roleArn)) {
            return false;
        }

        std::cout << "The following resources have been created." << std::endl;
        std::cout << "A HealthImaging datastore with ID: " << dataStoreId << "."
                  << std::endl;
        std::cout << "An Amazon S3 input bucket named: " << inputBucketName << "."
                  << std::endl;
        std::cout << "An Amazon S3 output bucket named: " << outputBucketName << "."
                  << std::endl;
        std::cout << "An IAM role with the ARN: " << roleArn << "." << std::endl;
        askQuestion("Enter return to continue.", alwaysTrueTest);
    }
    else {
        std::cout << "You have chosen to use preexisting resources:" << std::endl;
        dataStoreId = askQuestion(
                "Enter the data store ID of the HealthImaging datastore you wish to use: ");
        inputBucketName = askQuestion(
                "Enter the name of the S3 input bucket you wish to use: ");
        outputBucketName = askQuestion(
                "Enter the name of the S3 output bucket you wish to use: ");
        roleArn = askQuestion(
                "Enter the ARN for the IAM role with the proper permissions to import a DICOM series: ");
    }

Copy DICOM files to the Amazon S3 import bucket.

    std::cout
            << "This workflow uses DICOM files from the National Cancer Institute Imaging Data\n"
            << "Commons (IDC) Collections." << std::endl;
    std::cout << "Here is the link to their website." << std::endl;
    std::cout << "https://registry.opendata.aws/nci-imaging-data-commons/" << std::endl;
    std::cout << "We will use DICOM files stored in an S3 bucket managed by the IDC."
              << std::endl;
    std::cout
            << "First one of the DICOM folders in the IDC collection must be copied to your\n"
               "input S3 bucket."
            << std::endl;
    std::cout << "You have the choice of one of the following "
              << IDC_ImageChoices.size() << " folders to copy." << std::endl;

    int index = 1;
    for (auto &idcChoice: IDC_ImageChoices) {
        std::cout << index << " - " << idcChoice.mDescription << std::endl;
        index++;
    }
    int choice = askQuestionForIntRange("Choose DICOM files to import: ", 1, 4);

    Aws::String fromDirectory = IDC_ImageChoices[choice - 1].mDirectory;
    Aws::String inputDirectory = "input";

    std::cout << "The files in the directory '" << fromDirectory << "' in the bucket '"
              << IDC_S3_BucketName << "' will be copied " << std::endl;
    std::cout << "to the folder '" << inputDirectory << "/" << fromDirectory
              << "' in the bucket '" << inputBucketName << "'." << std::endl;
    askQuestion("Enter return to start the copy.", alwaysTrueTest);

    if (!AwsDoc::Medical_Imaging::copySeriesBetweenBuckets(
            IDC_S3_BucketName,
            fromDirectory,
            inputBucketName,
            inputDirectory, clientConfiguration)) {
        std::cerr << "This workflow will exit because of an error." << std::endl;
        cleanup(stackName, dataStoreId, clientConfiguration);
        return false;
    }

Import the DICOM files to the Amazon S3 data store.

bool AwsDoc::Medical_Imaging::startDicomImport(const Aws::String &dataStoreID,
                                               const Aws::String &inputBucketName,
                                               const Aws::String &inputDirectory,
                                               const Aws::String &outputBucketName,
                                               const Aws::String &outputDirectory,
                                               const Aws::String &roleArn,
                                               Aws::String &importJobId,
                                               const Aws::Client::ClientConfiguration &clientConfiguration) {
    bool result = false;
    if (startDICOMImportJob(dataStoreID, inputBucketName, inputDirectory,
                            outputBucketName, outputDirectory, roleArn, importJobId,
                            clientConfiguration)) {
        std::cout << "DICOM import job started with job ID " << importJobId << "."
                  << std::endl;
        result = waitImportJobCompleted(dataStoreID, importJobId, clientConfiguration);
        if (result) {
            std::cout << "DICOM import job completed." << std::endl;

        }
    }

    return result;
}

//! Routine which starts a HealthImaging import job.
/*!
  \param dataStoreID: The HealthImaging data store ID.
  \param inputBucketName: The name of the Amazon S3 bucket containing the DICOM files.
  \param inputDirectory: The directory in the S3 bucket containing the DICOM files.
  \param outputBucketName: The name of the S3 bucket for the output.
  \param outputDirectory: The directory in the S3 bucket to store the output.
  \param roleArn: The ARN of the IAM role with permissions for the import.
  \param importJobId: A string to receive the import job ID.
  \param clientConfig: Aws client configuration.
  \return bool: Function succeeded.
  */
bool AwsDoc::Medical_Imaging::startDICOMImportJob(
        const Aws::String &dataStoreID, const Aws::String &inputBucketName,
        const Aws::String &inputDirectory, const Aws::String &outputBucketName,
        const Aws::String &outputDirectory, const Aws::String &roleArn,
        Aws::String &importJobId,
        const Aws::Client::ClientConfiguration &clientConfig) {
    Aws::MedicalImaging::MedicalImagingClient medicalImagingClient(clientConfig);
    Aws::String inputURI = "s3://" + inputBucketName + "/" + inputDirectory + "/";
    Aws::String outputURI = "s3://" + outputBucketName + "/" + outputDirectory + "/";
    Aws::MedicalImaging::Model::StartDICOMImportJobRequest startDICOMImportJobRequest;
    startDICOMImportJobRequest.SetDatastoreId(dataStoreID);
    startDICOMImportJobRequest.SetDataAccessRoleArn(roleArn);
    startDICOMImportJobRequest.SetInputS3Uri(inputURI);
    startDICOMImportJobRequest.SetOutputS3Uri(outputURI);

    Aws::MedicalImaging::Model::StartDICOMImportJobOutcome startDICOMImportJobOutcome = medicalImagingClient.StartDICOMImportJob(
            startDICOMImportJobRequest);

    if (startDICOMImportJobOutcome.IsSuccess()) {
        importJobId = startDICOMImportJobOutcome.GetResult().GetJobId();
    }
    else {
        std::cerr << "Failed to start DICOM import job because "
                  << startDICOMImportJobOutcome.GetError().GetMessage() << std::endl;
    }

    return startDICOMImportJobOutcome.IsSuccess();
}


//! Routine which waits for a DICOM import job to complete.
/*!
 * @param dataStoreID: The HealthImaging data store ID.
 * @param importJobId: The import job ID.
 * @param clientConfiguration : Aws client configuration.
 * @return  bool: Function succeeded.
 */
bool AwsDoc::Medical_Imaging::waitImportJobCompleted(const Aws::String &datastoreID,
                                                     const Aws::String &importJobId,
                                                     const Aws::Client::ClientConfiguration &clientConfiguration) {

    Aws::MedicalImaging::Model::JobStatus jobStatus = Aws::MedicalImaging::Model::JobStatus::IN_PROGRESS;
    while (jobStatus == Aws::MedicalImaging::Model::JobStatus::IN_PROGRESS) {
        std::this_thread::sleep_for(std::chrono::seconds(1));

        Aws::MedicalImaging::Model::GetDICOMImportJobOutcome getDicomImportJobOutcome = getDICOMImportJob(
                datastoreID, importJobId,
                clientConfiguration);

        if (getDicomImportJobOutcome.IsSuccess()) {
            jobStatus = getDicomImportJobOutcome.GetResult().GetJobProperties().GetJobStatus();

            std::cout << "DICOM import job status: " <<
                      Aws::MedicalImaging::Model::JobStatusMapper::GetNameForJobStatus(
                              jobStatus) << std::endl;
        }
        else {
            std::cerr << "Failed to get import job status because "
                      << getDicomImportJobOutcome.GetError().GetMessage() << std::endl;
            return false;
        }
    }

    return jobStatus == Aws::MedicalImaging::Model::JobStatus::COMPLETED;
}

//! Routine which gets a HealthImaging DICOM import job's properties.
/*!
  \param dataStoreID: The HealthImaging data store ID.
  \param importJobID: The DICOM import job ID
  \param clientConfig: Aws client configuration.
  \return GetDICOMImportJobOutcome: The import job outcome.
*/
Aws::MedicalImaging::Model::GetDICOMImportJobOutcome
AwsDoc::Medical_Imaging::getDICOMImportJob(const Aws::String &dataStoreID,
                                           const Aws::String &importJobID,
                                           const Aws::Client::ClientConfiguration &clientConfig) {
    Aws::MedicalImaging::MedicalImagingClient client(clientConfig);
    Aws::MedicalImaging::Model::GetDICOMImportJobRequest request;
    request.SetDatastoreId(dataStoreID);
    request.SetJobId(importJobID);
    Aws::MedicalImaging::Model::GetDICOMImportJobOutcome outcome = client.GetDICOMImportJob(
            request);
    if (!outcome.IsSuccess()) {
        std::cerr << "GetDICOMImportJob error: "
                  << outcome.GetError().GetMessage() << std::endl;
    }

    return outcome;
}

Get image sets created by the DICOM import job.

bool
AwsDoc::Medical_Imaging::getImageSetsForDicomImportJob(const Aws::String &datastoreID,
                                                       const Aws::String &importJobId,
                                                       Aws::Vector<Aws::String> &imageSets,
                                                       const Aws::Client::ClientConfiguration &clientConfiguration) {
    Aws::MedicalImaging::Model::GetDICOMImportJobOutcome getDicomImportJobOutcome = getDICOMImportJob(
            datastoreID, importJobId, clientConfiguration);
    bool result = false;
    if (getDicomImportJobOutcome.IsSuccess()) {
        auto outputURI = getDicomImportJobOutcome.GetResult().GetJobProperties().GetOutputS3Uri();
        Aws::Http::URI uri(outputURI);
        const Aws::String &bucket = uri.GetAuthority();
        Aws::String key = uri.GetPath();

        Aws::S3::S3Client s3Client(clientConfiguration);
        Aws::S3::Model::GetObjectRequest objectRequest;
        objectRequest.SetBucket(bucket);
        objectRequest.SetKey(key + "/" + IMPORT_JOB_MANIFEST_FILE_NAME);

        auto getObjectOutcome = s3Client.GetObject(objectRequest);
        if (getObjectOutcome.IsSuccess()) {
            auto &data = getObjectOutcome.GetResult().GetBody();

            std::stringstream stringStream;
            stringStream << data.rdbuf();

            try {
                // Use JMESPath to extract the image set IDs.
                // https://jmespath.org/specification.html
                std::string jmesPathExpression = "jobSummary.imageSetsSummary[].imageSetId";
                jsoncons::json doc = jsoncons::json::parse(stringStream.str());

                jsoncons::json imageSetsJson = jsoncons::jmespath::search(doc,
                                                                          jmesPathExpression);\
                for (auto &imageSet: imageSetsJson.array_range()) {
                    imageSets.push_back(imageSet.as_string());
                }

                result = true;
            }
            catch (const std::exception &e) {
                std::cerr << e.what() << '\n';
            }

        }
        else {
            std::cerr << "Failed to get object because "
                      << getObjectOutcome.GetError().GetMessage() << std::endl;
        }

    }
    else {
        std::cerr << "Failed to get import job status because "
                  << getDicomImportJobOutcome.GetError().GetMessage() << std::endl;
    }

    return result;
}

Get image frame information for image sets.

bool AwsDoc::Medical_Imaging::getImageFramesForImageSet(const Aws::String &dataStoreID,
                                                        const Aws::String &imageSetID,
                                                        const Aws::String &outDirectory,
                                                        Aws::Vector<ImageFrameInfo> &imageFrames,
                                                        const Aws::Client::ClientConfiguration &clientConfiguration) {
    Aws::String fileName = outDirectory + "/" + imageSetID + "_metadata.json.gzip";
    bool result = false;
    if (getImageSetMetadata(dataStoreID, imageSetID, "", // Empty string for version ID.
                            fileName, clientConfiguration)) {
        try {
            std::string metadataGZip;
            {
                std::ifstream inFileStream(fileName.c_str(), std::ios::binary);
                if (!inFileStream) {
                    throw std::runtime_error("Failed to open file " + fileName);
                }

                std::stringstream stringStream;
                stringStream << inFileStream.rdbuf();
                metadataGZip = stringStream.str();
            }
            std::string metadataJson = gzip::decompress(metadataGZip.data(),
                                                        metadataGZip.size());
            // Use JMESPath to extract the image set IDs.
            // https://jmespath.org/specification.html
            jsoncons::json doc = jsoncons::json::parse(metadataJson);
            std::string jmesPathExpression = "Study.Series.*.Instances[].*[]";
            jsoncons::json instances = jsoncons::jmespath::search(doc,
                                                                  jmesPathExpression);
            for (auto &instance: instances.array_range()) {
                jmesPathExpression = "DICOM.RescaleSlope";
                std::string rescaleSlope = jsoncons::jmespath::search(instance,
                                                                      jmesPathExpression).to_string();
                jmesPathExpression = "DICOM.RescaleIntercept";
                std::string rescaleIntercept = jsoncons::jmespath::search(instance,
                                                                          jmesPathExpression).to_string();

                jmesPathExpression = "ImageFrames[][]";
                jsoncons::json imageFramesJson = jsoncons::jmespath::search(instance,
                                                                            jmesPathExpression);

                for (auto &imageFrame: imageFramesJson.array_range()) {
                    ImageFrameInfo imageFrameIDs;
                    imageFrameIDs.mImageSetId = imageSetID;
                    imageFrameIDs.mImageFrameId = imageFrame.find(
                            "ID")->value().as_string();
                    imageFrameIDs.mRescaleIntercept = rescaleIntercept;
                    imageFrameIDs.mRescaleSlope = rescaleSlope;
                    imageFrameIDs.MinPixelValue = imageFrame.find(
                            "MinPixelValue")->value().as_string();
                    imageFrameIDs.MaxPixelValue = imageFrame.find(
                            "MaxPixelValue")->value().as_string();

                    jmesPathExpression = "max_by(PixelDataChecksumFromBaseToFullResolution, &Width).Checksum";
                    jsoncons::json checksumJson = jsoncons::jmespath::search(imageFrame,
                                                                             jmesPathExpression);
                    imageFrameIDs.mFullResolutionChecksum = checksumJson.as_integer<uint32_t>();

                    imageFrames.emplace_back(imageFrameIDs);
                }
            }

            result = true;
        }
        catch (const std::exception &e) {
            std::cerr << "getImageFramesForImageSet failed because " << e.what()
                      << std::endl;
        }
    }

    return result;
}

//! Routine which gets a HealthImaging image set's metadata.
/*!
  \param dataStoreID: The HealthImaging data store ID.
  \param imageSetID: The HealthImaging image set ID.
  \param versionID: The HealthImaging image set version ID, ignored if empty.
  \param outputFilePath: The path where the metadata will be stored as gzipped json.
  \param clientConfig: Aws client configuration.
  \\return bool: Function succeeded.
*/
bool AwsDoc::Medical_Imaging::getImageSetMetadata(const Aws::String &dataStoreID,
                                                  const Aws::String &imageSetID,
                                                  const Aws::String &versionID,
                                                  const Aws::String &outputFilePath,
                                                  const Aws::Client::ClientConfiguration &clientConfig) {
    Aws::MedicalImaging::Model::GetImageSetMetadataRequest request;
    request.SetDatastoreId(dataStoreID);
    request.SetImageSetId(imageSetID);
    if (!versionID.empty()) {
        request.SetVersionId(versionID);
    }
    Aws::MedicalImaging::MedicalImagingClient client(clientConfig);
    Aws::MedicalImaging::Model::GetImageSetMetadataOutcome outcome = client.GetImageSetMetadata(
            request);
    if (outcome.IsSuccess()) {
        std::ofstream file(outputFilePath, std::ios::binary);
        auto &metadata = outcome.GetResult().GetImageSetMetadataBlob();
        file << metadata.rdbuf();
    }
    else {
        std::cerr << "Failed to get image set metadata: "
                  << outcome.GetError().GetMessage() << std::endl;
    }

    return outcome.IsSuccess();
}

Download, decode and verify image frames.

bool AwsDoc::Medical_Imaging::downloadDecodeAndCheckImageFrames(
        const Aws::String &dataStoreID,
        const Aws::Vector<ImageFrameInfo> &imageFrames,
        const Aws::String &outDirectory,
        const Aws::Client::ClientConfiguration &clientConfiguration) {

    Aws::Client::ClientConfiguration clientConfiguration1(clientConfiguration);
    clientConfiguration1.executor = Aws::MakeShared<Aws::Utils::Threading::PooledThreadExecutor>(
            "executor", 25);
    Aws::MedicalImaging::MedicalImagingClient medicalImagingClient(
            clientConfiguration1);

    Aws::Utils::Threading::Semaphore semaphore(0, 1);
    std::atomic<size_t> count(imageFrames.size());

    bool result = true;
    for (auto &imageFrame: imageFrames) {
        Aws::MedicalImaging::Model::GetImageFrameRequest getImageFrameRequest;
        getImageFrameRequest.SetDatastoreId(dataStoreID);
        getImageFrameRequest.SetImageSetId(imageFrame.mImageSetId);

        Aws::MedicalImaging::Model::ImageFrameInformation imageFrameInformation;
        imageFrameInformation.SetImageFrameId(imageFrame.mImageFrameId);
        getImageFrameRequest.SetImageFrameInformation(imageFrameInformation);

        auto getImageFrameAsyncLambda = [&semaphore, &result, &count, imageFrame, outDirectory](
                const Aws::MedicalImaging::MedicalImagingClient *client,
                const Aws::MedicalImaging::Model::GetImageFrameRequest &request,
                Aws::MedicalImaging::Model::GetImageFrameOutcome outcome,
                const std::shared_ptr<const Aws::Client::AsyncCallerContext> &context) {

                if (!handleGetImageFrameResult(outcome, outDirectory, imageFrame)) {
                    std::cerr << "Failed to download and convert image frame: "
                              << imageFrame.mImageFrameId << " from image set: "
                              << imageFrame.mImageSetId << std::endl;
                    result = false;
                }

                count--;
                if (count <= 0) {

                    semaphore.ReleaseAll();
                }
        }; // End of 'getImageFrameAsyncLambda' lambda.

        medicalImagingClient.GetImageFrameAsync(getImageFrameRequest,
                                                getImageFrameAsyncLambda);
    }

    if (count > 0) {
        semaphore.WaitOne();
    }

    if (result) {
        std::cout << imageFrames.size() << " image files were downloaded."
                  << std::endl;
    }

    return result;
}

bool AwsDoc::Medical_Imaging::decodeJPHFileAndValidateWithChecksum(
        const Aws::String &jphFile,
        uint32_t crc32Checksum) {
    opj_image_t *outputImage = jphImageToOpjBitmap(jphFile);
    if (!outputImage) {
        return false;
    }

    bool result = true;
    if (!verifyChecksumForImage(outputImage, crc32Checksum)) {
        std::cerr << "The checksum for the image does not match the expected value."
                  << std::endl;
        std::cerr << "File :" << jphFile << std::endl;
        result = false;
    }

    opj_image_destroy(outputImage);

    return result;
}

opj_image *
AwsDoc::Medical_Imaging::jphImageToOpjBitmap(const Aws::String &jphFile) {
    opj_stream_t *inFileStream = nullptr;
    opj_codec_t *decompressorCodec = nullptr;
    opj_image_t *outputImage = nullptr;
    try {
        std::shared_ptr<opj_dparameters> decodeParameters = std::make_shared<opj_dparameters>();
        memset(decodeParameters.get(), 0, sizeof(opj_dparameters));

        opj_set_default_decoder_parameters(decodeParameters.get());

        decodeParameters->decod_format = 1; // JP2 image format.
        decodeParameters->cod_format = 2; // BMP image format.

        std::strncpy(decodeParameters->infile, jphFile.c_str(),
                     OPJ_PATH_LEN);

        inFileStream = opj_stream_create_default_file_stream(
                decodeParameters->infile, true);
        if (!inFileStream) {
            throw std::runtime_error(
                    "Unable to create input file stream for file '" + jphFile + "'.");
        }

        decompressorCodec = opj_create_decompress(OPJ_CODEC_JP2);
        if (!decompressorCodec) {
            throw std::runtime_error("Failed to create decompression codec.");
        }

        int decodeMessageLevel = 1;
        if (!setupCodecLogging(decompressorCodec, &decodeMessageLevel)) {
            std::cerr << "Failed to setup codec logging." << std::endl;
        }

        if (!opj_setup_decoder(decompressorCodec, decodeParameters.get())) {
            throw std::runtime_error("Failed to setup decompression codec.");
        }
        if (!opj_codec_set_threads(decompressorCodec, 4)) {
            throw std::runtime_error("Failed to set decompression codec threads.");
        }

        if (!opj_read_header(inFileStream, decompressorCodec, &outputImage)) {
            throw std::runtime_error("Failed to read header.");
        }

        if (!opj_decode(decompressorCodec, inFileStream,
                        outputImage)) {
            throw std::runtime_error("Failed to decode.");
        }

        if (DEBUGGING) {
            std::cout << "image width : " << outputImage->x1 - outputImage->x0
                      << std::endl;
            std::cout << "image height : " << outputImage->y1 - outputImage->y0
                      << std::endl;
            std::cout << "number of channels: " << outputImage->numcomps
                      << std::endl;
            std::cout << "colorspace : " << outputImage->color_space << std::endl;
        }

    } catch (const std::exception &e) {
        std::cerr << e.what() << std::endl;
        if (outputImage) {
            opj_image_destroy(outputImage);
            outputImage = nullptr;
        }
    }
    if (inFileStream) {
        opj_stream_destroy(inFileStream);
    }
    if (decompressorCodec) {
        opj_destroy_codec(decompressorCodec);
    }

    return outputImage;
}

//! Template function which converts a planar image bitmap to an interleaved image bitmap and
//! then verifies the checksum of the bitmap.
/*!
 * @param image: The OpenJPEG image struct.
 * @param crc32Checksum: The CRC32 checksum.
 * @return  bool: Function succeeded.
 */
template<class myType>
bool verifyChecksumForImageForType(opj_image_t *image, uint32_t crc32Checksum) {
    uint32_t width = image->x1 - image->x0;
    uint32_t height = image->y1 - image->y0;
    uint32_t numOfChannels = image->numcomps;

    // Buffer for interleaved bitmap.
    std::vector<myType> buffer(width * height * numOfChannels);

    // Convert planar bitmap to interleaved bitmap.
    for (uint32_t channel = 0; channel < numOfChannels; channel++) {
        for (uint32_t row = 0; row < height; row++) {
            uint32_t fromRowStart = row / image->comps[channel].dy * width /
                                    image->comps[channel].dx;
            uint32_t toIndex = (row * width) * numOfChannels + channel;

            for (uint32_t col = 0; col < width; col++) {
                uint32_t fromIndex = fromRowStart + col / image->comps[channel].dx;

                buffer[toIndex] = static_cast<myType>(image->comps[channel].data[fromIndex]);

                toIndex += numOfChannels;
            }
        }
    }

    // Verify checksum.
    boost::crc_32_type crc32;
    crc32.process_bytes(reinterpret_cast<char *>(buffer.data()),
                        buffer.size() * sizeof(myType));

    bool result = crc32.checksum() == crc32Checksum;
    if (!result) {
        std::cerr << "verifyChecksumForImage, checksum mismatch, expected - "
                  << crc32Checksum << ", actual - " << crc32.checksum()
                  << std::endl;
    }

    return result;
}

//! Routine which verifies the checksum of an OpenJPEG image struct.
/*!
 * @param image: The OpenJPEG image struct.
 * @param crc32Checksum: The CRC32 checksum.
 * @return  bool: Function succeeded.
 */
bool AwsDoc::Medical_Imaging::verifyChecksumForImage(opj_image_t *image,
                                                     uint32_t crc32Checksum) {
    uint32_t channels = image->numcomps;
    bool result = false;
    if (0 < channels) {
        // Assume the precision is the same for all channels.
        uint32_t precision = image->comps[0].prec;
        bool signedData = image->comps[0].sgnd;
        uint32_t bytes = (precision + 7) / 8;

        if (signedData) {
            switch (bytes) {
                case 1 :
                    result = verifyChecksumForImageForType<int8_t>(image,
                                                                   crc32Checksum);
                    break;
                case 2 :
                    result = verifyChecksumForImageForType<int16_t>(image,
                                                                    crc32Checksum);
                    break;
                case 4 :
                    result = verifyChecksumForImageForType<int32_t>(image,
                                                                    crc32Checksum);
                    break;
                default:
                    std::cerr
                            << "verifyChecksumForImage, unsupported data type, signed bytes - "
                            << bytes << std::endl;
                    break;
            }
        }
        else {
            switch (bytes) {
                case 1 :
                    result = verifyChecksumForImageForType<uint8_t>(image,
                                                                    crc32Checksum);
                    break;
                case 2 :
                    result = verifyChecksumForImageForType<uint16_t>(image,
                                                                     crc32Checksum);
                    break;
                case 4 :
                    result = verifyChecksumForImageForType<uint32_t>(image,
                                                                     crc32Checksum);
                    break;
                default:
                    std::cerr
                            << "verifyChecksumForImage, unsupported data type, unsigned bytes - "
                            << bytes << std::endl;
                    break;
            }
        }

        if (!result) {
            std::cerr << "verifyChecksumForImage, error bytes " << bytes
                      << " signed "
                      << signedData << std::endl;
        }
    }
    else {
        std::cerr << "'verifyChecksumForImage', no channels in the image."
                  << std::endl;
    }
    return result;
}

Clean up resources.

bool AwsDoc::Medical_Imaging::cleanup(const Aws::String &stackName,
                                      const Aws::String &dataStoreId,
                                      const Aws::Client::ClientConfiguration &clientConfiguration) {
    bool result = true;

    if (!stackName.empty() && askYesNoQuestion(
            "Would you like to delete the stack " + stackName + "? (y/n)")) {
        std::cout << "Deleting the image sets in the stack." << std::endl;
        result &= emptyDatastore(dataStoreId, clientConfiguration);
        printAsterisksLine();
        std::cout << "Deleting the stack." << std::endl;
        result &= deleteStack(stackName, clientConfiguration);
    }
    return result;
}

bool AwsDoc::Medical_Imaging::emptyDatastore(const Aws::String &datastoreID,
                                             const Aws::Client::ClientConfiguration &clientConfiguration) {

    Aws::MedicalImaging::Model::SearchCriteria emptyCriteria;
    Aws::Vector<Aws::String> imageSetIDs;
    bool result = false;
    if (searchImageSets(datastoreID, emptyCriteria, imageSetIDs,
                        clientConfiguration)) {
        result = true;
        for (auto &imageSetID: imageSetIDs) {
            result &= deleteImageSet(datastoreID, imageSetID, clientConfiguration);
        }
    }

    return result;
}