Mercurial > hg > orthanc
changeset 4713:8866981e2f58
merge
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 23 Jun 2021 14:33:46 +0200 |
| parents | bad8935cd5f2 (diff) dbb1a90c4df4 (current diff) |
| children | 8ffe2fdb541f |
| files | NEWS OrthancFramework/Resources/Patches/curl-7.57.0-cmake.patch OrthancFramework/Resources/Patches/curl-7.64.0-cmake.patch |
| diffstat | 5 files changed, 133 insertions(+), 57 deletions(-) [+] |
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--- a/NEWS Tue Jun 22 10:40:08 2021 +0200 +++ b/NEWS Wed Jun 23 14:33:46 2021 +0200 @@ -41,6 +41,7 @@ - GET /patients/{id}/module, GET /patients/{id}/patient-module - GET /series/{id}/module, GET /studies/{id}/module, GET /instances/{id}/module - POST /tools/find +* "/studies/{id}/split" accepts "Instances" parameter to split instances instead of series Maintenance -----------
--- a/OrthancServer/Sources/OrthancRestApi/OrthancRestAnonymizeModify.cpp Tue Jun 22 10:40:08 2021 +0200 +++ b/OrthancServer/Sources/OrthancRestApi/OrthancRestAnonymizeModify.cpp Wed Jun 23 14:33:46 2021 +0200 @@ -50,6 +50,24 @@ "Starting with Orthanc 1.9.4, paths to subsequences can be provided using the "\ "same syntax as the `dcmodify` command-line tool (wildcards are supported as well)." + +static const char* const CONTENT = "Content"; +static const char* const FORCE = "Force"; +static const char* const INSTANCES = "Instances"; +static const char* const INTERPRET_BINARY_TAGS = "InterpretBinaryTags"; +static const char* const KEEP = "Keep"; +static const char* const KEEP_PRIVATE_TAGS = "KeepPrivateTags"; +static const char* const KEEP_SOURCE = "KeepSource"; +static const char* const PARENT = "Parent"; +static const char* const PRIVATE_CREATOR = "PrivateCreator"; +static const char* const REMOVE = "Remove"; +static const char* const REPLACE = "Replace"; +static const char* const RESOURCES = "Resources"; +static const char* const SERIES = "Series"; +static const char* const TAGS = "Tags"; +static const char* const TRANSCODE = "Transcode"; + + namespace Orthanc { // Modification of DICOM instances ------------------------------------------ @@ -66,23 +84,23 @@ { // Check out "DicomModification::ParseModifyRequest()" call.GetDocumentation() - .SetRequestField("Transcode", RestApiCallDocumentation::Type_String, + .SetRequestField(TRANSCODE, RestApiCallDocumentation::Type_String, "Transcode the DICOM instances to the provided DICOM transfer syntax: " "https://book.orthanc-server.com/faq/transcoding.html", false) - .SetRequestField("Force", RestApiCallDocumentation::Type_Boolean, + .SetRequestField(FORCE, RestApiCallDocumentation::Type_Boolean, "Allow the modification of tags related to DICOM identifiers, at the risk of " "breaking the DICOM model of the real world", false) .SetRequestField("RemovePrivateTags", RestApiCallDocumentation::Type_Boolean, "Remove the private tags from the DICOM instances (defaults to `false`)", false) - .SetRequestField("Replace", RestApiCallDocumentation::Type_JsonObject, + .SetRequestField(REPLACE, RestApiCallDocumentation::Type_JsonObject, "Associative array to change the value of some DICOM tags in the DICOM instances. " INFO_SUBSEQUENCES, false) - .SetRequestField("Remove", RestApiCallDocumentation::Type_JsonListOfStrings, + .SetRequestField(REMOVE, RestApiCallDocumentation::Type_JsonListOfStrings, "List of tags that must be removed from the DICOM instances. " INFO_SUBSEQUENCES, false) - .SetRequestField("Keep", RestApiCallDocumentation::Type_JsonListOfStrings, + .SetRequestField(KEEP, RestApiCallDocumentation::Type_JsonListOfStrings, "Keep the original value of the specified tags, to be chosen among the `StudyInstanceUID`, " "`SeriesInstanceUID` and `SOPInstanceUID` tags. Avoid this feature as much as possible, " "as this breaks the DICOM model of the real world.", false) - .SetRequestField("PrivateCreator", RestApiCallDocumentation::Type_String, + .SetRequestField(PRIVATE_CREATOR, RestApiCallDocumentation::Type_String, "The private creator to be used for private tags in `Replace`", false); } @@ -91,21 +109,21 @@ { // Check out "DicomModification::ParseAnonymizationRequest()" call.GetDocumentation() - .SetRequestField("Force", RestApiCallDocumentation::Type_Boolean, + .SetRequestField(FORCE, RestApiCallDocumentation::Type_Boolean, "Allow the modification of tags related to DICOM identifiers, at the risk of " "breaking the DICOM model of the real world", false) .SetRequestField("DicomVersion", RestApiCallDocumentation::Type_String, "Version of the DICOM standard to be used for anonymization. Check out " "configuration option `DeidentifyLogsDicomVersion` for possible values.", false) - .SetRequestField("KeepPrivateTags", RestApiCallDocumentation::Type_Boolean, + .SetRequestField(KEEP_PRIVATE_TAGS, RestApiCallDocumentation::Type_Boolean, "Keep the private tags from the DICOM instances (defaults to `false`)", false) - .SetRequestField("Replace", RestApiCallDocumentation::Type_JsonObject, + .SetRequestField(REPLACE, RestApiCallDocumentation::Type_JsonObject, "Associative array to change the value of some DICOM tags in the DICOM instances. " INFO_SUBSEQUENCES, false) - .SetRequestField("Remove", RestApiCallDocumentation::Type_JsonListOfStrings, + .SetRequestField(REMOVE, RestApiCallDocumentation::Type_JsonListOfStrings, "List of additional tags to be removed from the DICOM instances. " INFO_SUBSEQUENCES, false) - .SetRequestField("Keep", RestApiCallDocumentation::Type_JsonListOfStrings, + .SetRequestField(KEEP, RestApiCallDocumentation::Type_JsonListOfStrings, "List of DICOM tags whose value must not be destroyed by the anonymization. " INFO_SUBSEQUENCES, false) - .SetRequestField("PrivateCreator", RestApiCallDocumentation::Type_String, + .SetRequestField(PRIVATE_CREATOR, RestApiCallDocumentation::Type_String, "The private creator to be used for private tags in `Replace`", false); } @@ -253,7 +271,6 @@ modification.SetLevel(DetectModifyLevel(modification)); - static const char* TRANSCODE = "Transcode"; if (request.isMember(TRANSCODE)) { std::string s = SerializationToolbox::ReadString(request, TRANSCODE); @@ -305,7 +322,6 @@ static void SetKeepSource(CleaningInstancesJob& job, const Json::Value& body) { - static const char* KEEP_SOURCE = "KeepSource"; if (body.isMember(KEEP_SOURCE)) { job.SetKeepSource(SerializationToolbox::ReadBoolean(body, KEEP_SOURCE)); @@ -337,7 +353,6 @@ job->SetOrigin(call); SetKeepSource(*job, body); - static const char* TRANSCODE = "Transcode"; if (body.isMember(TRANSCODE)) { job->SetTranscode(SerializationToolbox::ReadString(body, TRANSCODE)); @@ -377,7 +392,7 @@ const Json::Value& body) { std::set<std::string> resources; - SerializationToolbox::ReadSetOfStrings(resources, body, "Resources"); + SerializationToolbox::ReadSetOfStrings(resources, body, RESOURCES); SubmitModificationJob(modification, isAnonymization, call, body, ResourceType_Instance /* arbitrary value, unused */, @@ -426,7 +441,7 @@ call.GetDocumentation() .SetTag("System") .SetSummary("Modify a set of resources") - .SetRequestField("Resources", RestApiCallDocumentation::Type_JsonListOfStrings, + .SetRequestField(RESOURCES, RestApiCallDocumentation::Type_JsonListOfStrings, "List of the Orthanc identifiers of the patients/studies/series/instances of interest.", true) .SetDescription("Start a job that will modify all the DICOM patients, studies, series or instances " "whose identifiers are provided in the `Resources` field.") @@ -484,7 +499,7 @@ call.GetDocumentation() .SetTag("System") .SetSummary("Anonymize a set of resources") - .SetRequestField("Resources", RestApiCallDocumentation::Type_JsonListOfStrings, + .SetRequestField(RESOURCES, RestApiCallDocumentation::Type_JsonListOfStrings, "List of the Orthanc identifiers of the patients/studies/series/instances of interest.", true) .SetDescription("Start a job that will anonymize all the DICOM patients, studies, series or instances " "whose identifiers are provided in the `Resources` field.") @@ -638,16 +653,16 @@ } else if (content[i].type() == Json::objectValue) { - if (!content[i].isMember("Content")) + if (!content[i].isMember(CONTENT)) { throw OrthancException(ErrorCode_CreateDicomNoPayload); } - payload = &content[i]["Content"]; + payload = &content[i][CONTENT]; - if (content[i].isMember("Tags")) + if (content[i].isMember(TAGS)) { - InjectTags(*dicom, content[i]["Tags"], decodeBinaryTags, privateCreator, force); + InjectTags(*dicom, content[i][TAGS], decodeBinaryTags, privateCreator, force); } } @@ -689,13 +704,7 @@ static void CreateDicomV2(RestApiPostCall& call, const Json::Value& request) { - static const char* const CONTENT = "Content"; - static const char* const FORCE = "Force"; - static const char* const INTERPRET_BINARY_TAGS = "InterpretBinaryTags"; - static const char* const PARENT = "Parent"; - static const char* const PRIVATE_CREATOR = "PrivateCreator"; static const char* const SPECIFIC_CHARACTER_SET_2 = "SpecificCharacterSet"; - static const char* const TAGS = "Tags"; static const char* const TYPE = "Type"; static const char* const VALUE = "Value"; @@ -769,7 +778,7 @@ // Choose the same encoding as the parent resource { - static const char* SPECIFIC_CHARACTER_SET = "0008,0005"; + static const char* const SPECIFIC_CHARACTER_SET = "0008,0005"; if (siblingTags.isMember(SPECIFIC_CHARACTER_SET)) { @@ -948,25 +957,25 @@ .SetTag("System") .SetSummary("Create one DICOM instance") .SetDescription("Create one DICOM instance, and store it into Orthanc") - .SetRequestField("Tags", RestApiCallDocumentation::Type_JsonObject, + .SetRequestField(TAGS, RestApiCallDocumentation::Type_JsonObject, "Associative array containing the tags of the new instance to be created", true) - .SetRequestField("Content", RestApiCallDocumentation::Type_String, + .SetRequestField(CONTENT, RestApiCallDocumentation::Type_String, "This field can be used to embed an image (pixel data) or a PDF inside the created DICOM instance. " "The PNG image, the JPEG image or the PDF file must be provided using their " "[data URI scheme encoding](https://en.wikipedia.org/wiki/Data_URI_scheme). " "This field can possibly contain a JSON array, in which case a DICOM series is created " "containing one DICOM instance for each item in the `Content` field.", false) - .SetRequestField("Parent", RestApiCallDocumentation::Type_String, + .SetRequestField(PARENT, RestApiCallDocumentation::Type_String, "If present, the newly created instance will be attached to the parent DICOM resource " "whose Orthanc identifier is contained in this field. The DICOM tags of the parent " "modules in the DICOM hierarchy will be automatically copied to the newly created instance.", false) - .SetRequestField("InterpretBinaryTags", RestApiCallDocumentation::Type_Boolean, + .SetRequestField(INTERPRET_BINARY_TAGS, RestApiCallDocumentation::Type_Boolean, "If some value in the `Tags` associative array is formatted according to some " "[data URI scheme encoding](https://en.wikipedia.org/wiki/Data_URI_scheme), " "whether this value is decoded to a binary value or kept as such (`true` by default)", false) - .SetRequestField("PrivateCreator", RestApiCallDocumentation::Type_String, + .SetRequestField(PRIVATE_CREATOR, RestApiCallDocumentation::Type_String, "The private creator to be used for private tags in `Tags`", false) - .SetRequestField("Force", RestApiCallDocumentation::Type_Boolean, + .SetRequestField(FORCE, RestApiCallDocumentation::Type_Boolean, "Avoid the consistency checks for the DICOM tags that enforce the DICOM model of the real-world. " "You can notably use this flag if you need to manually set the tags `StudyInstanceUID`, " "`SeriesInstanceUID`, or `SOPInstanceUID`. Be careful with this feature.", false) @@ -982,7 +991,7 @@ throw OrthancException(ErrorCode_BadRequest); } - if (request.isMember("Tags")) + if (request.isMember(TAGS)) { CreateDicomV2(call, request); } @@ -1007,22 +1016,25 @@ .SetTag("Studies") .SetSummary("Split study") .SetDescription("Start a new job so as to split the DICOM study whose Orthanc identifier is provided in the URL, " - "by taking some of its children series out of it and putting them into a brand new study (this " - "new study is created by setting the `StudyInstanceUID` tag to a random identifier): " + "by taking some of its children series or instances out of it and putting them into a brand new study " + "(this new study is created by setting the `StudyInstanceUID` tag to a random identifier): " "https://book.orthanc-server.com/users/anonymization.html#splitting") .SetUriArgument("id", "Orthanc identifier of the study of interest") - .SetRequestField("Series", RestApiCallDocumentation::Type_JsonListOfStrings, - "The list of series to be separated from the parent study (mandatory option). " - "These series must all be children of the same source study, that is specified in the URI.", true) - .SetRequestField("Replace", RestApiCallDocumentation::Type_JsonObject, + .SetRequestField(SERIES, RestApiCallDocumentation::Type_JsonListOfStrings, + "The list of series to be separated from the parent study. " + "These series must all be children of the same source study, that is specified in the URI.", false) + .SetRequestField(REPLACE, RestApiCallDocumentation::Type_JsonObject, "Associative array to change the value of some DICOM tags in the new study. " "These tags must be part of the \"Patient Module Attributes\" or the \"General Study " "Module Attributes\", as specified by the DICOM 2011 standard in Tables C.7-1 and C.7-3.", false) - .SetRequestField("Remove", RestApiCallDocumentation::Type_JsonListOfStrings, + .SetRequestField(REMOVE, RestApiCallDocumentation::Type_JsonListOfStrings, "List of tags that must be removed in the new study (from the same modules as in the `Replace` option)", false) - .SetRequestField("KeepSource", RestApiCallDocumentation::Type_Boolean, - "If set to `true`, instructs Orthanc to keep a copy of the original series in the source study. " - "By default, the original series are deleted from Orthanc.", false); + .SetRequestField(KEEP_SOURCE, RestApiCallDocumentation::Type_Boolean, + "If set to `true`, instructs Orthanc to keep a copy of the original series/instances in the source study. " + "By default, the original series/instances are deleted from Orthanc.", false) + .SetRequestField(INSTANCES, RestApiCallDocumentation::Type_JsonListOfStrings, + "The list of instances to be separated from the parent study. " + "These instances must all be children of the same source study, that is specified in the URI.", false); return; } @@ -1040,19 +1052,40 @@ std::unique_ptr<SplitStudyJob> job(new SplitStudyJob(context, study)); job->SetOrigin(call); - std::vector<std::string> series; - SerializationToolbox::ReadArrayOfStrings(series, request, "Series"); + bool ok = false; + if (request.isMember(SERIES)) + { + std::vector<std::string> series; + SerializationToolbox::ReadArrayOfStrings(series, request, SERIES); + + for (size_t i = 0; i < series.size(); i++) + { + job->AddSourceSeries(series[i]); + ok = true; + } + } - for (size_t i = 0; i < series.size(); i++) + if (request.isMember(INSTANCES)) { - job->AddSourceSeries(series[i]); + std::vector<std::string> instances; + SerializationToolbox::ReadArrayOfStrings(instances, request, INSTANCES); + + for (size_t i = 0; i < instances.size(); i++) + { + job->AddSourceInstance(instances[i]); + ok = true; + } } + + if (!ok) + { + throw OrthancException(ErrorCode_BadRequest, "Both the \"Series\" and the \"Instances\" fields are missing"); + } job->AddTrailingStep(); SetKeepSource(*job, request); - static const char* REMOVE = "Remove"; if (request.isMember(REMOVE)) { if (request[REMOVE].type() != Json::arrayValue) @@ -1073,7 +1106,6 @@ } } - static const char* REPLACE = "Replace"; if (request.isMember(REPLACE)) { if (request[REPLACE].type() != Json::objectValue) @@ -1114,10 +1146,10 @@ .SetDescription("Start a new job so as to move some DICOM series into the DICOM study whose Orthanc identifier " "is provided in the URL: https://book.orthanc-server.com/users/anonymization.html#merging") .SetUriArgument("id", "Orthanc identifier of the study of interest") - .SetRequestField("Resources", RestApiCallDocumentation::Type_JsonListOfStrings, + .SetRequestField(RESOURCES, RestApiCallDocumentation::Type_JsonListOfStrings, "The list of DICOM resources (patients, studies, series, and/or instances) to be merged " "into the study of interest (mandatory option)", true) - .SetRequestField("KeepSource", RestApiCallDocumentation::Type_Boolean, + .SetRequestField(KEEP_SOURCE, RestApiCallDocumentation::Type_Boolean, "If set to `true`, instructs Orthanc to keep a copy of the original resources in their source study. " "By default, the original resources are deleted from Orthanc.", false); return; @@ -1138,7 +1170,7 @@ job->SetOrigin(call); std::vector<std::string> resources; - SerializationToolbox::ReadArrayOfStrings(resources, request, "Resources"); + SerializationToolbox::ReadArrayOfStrings(resources, request, RESOURCES); for (size_t i = 0; i < resources.size(); i++) {
--- a/OrthancServer/Sources/ServerJobs/MergeStudyJob.h Tue Jun 22 10:40:08 2021 +0200 +++ b/OrthancServer/Sources/ServerJobs/MergeStudyJob.h Wed Jun 23 14:33:46 2021 +0200 @@ -59,6 +59,10 @@ void AddSourceStudyInternal(const std::string& study); + // Make setter methods private to prevent incorrect calls + using SetOfInstancesJob::AddParentResource; + using SetOfInstancesJob::AddInstance; + protected: virtual bool HandleInstance(const std::string& instance) ORTHANC_OVERRIDE;
--- a/OrthancServer/Sources/ServerJobs/SplitStudyJob.cpp Tue Jun 22 10:40:08 2021 +0200 +++ b/OrthancServer/Sources/ServerJobs/SplitStudyJob.cpp Wed Jun 23 14:33:46 2021 +0200 @@ -192,6 +192,17 @@ } + static void RegisterSeries(std::map<std::string, std::string>& target, + const std::string& series) + { + // Generate a target SeriesInstanceUID for this series + if (target.find(series) == target.end()) + { + target[series] = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series); + } + } + + void SplitStudyJob::AddSourceSeries(const std::string& series) { std::string parent; @@ -208,8 +219,7 @@ } else { - // Generate a target SeriesInstanceUID for this series - seriesUidMap_[series] = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series); + RegisterSeries(seriesUidMap_, series); // Add all the instances of the series as to be processed std::list<std::string> instances; @@ -224,6 +234,29 @@ } + void SplitStudyJob::AddSourceInstance(const std::string& instance) + { + std::string study, series; + + if (IsStarted()) + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + else if (!GetContext().GetIndex().LookupParent(series, instance, ResourceType_Series) || + !GetContext().GetIndex().LookupParent(study, series, ResourceType_Study) || + study != sourceStudy_) + { + throw OrthancException(ErrorCode_UnknownResource, + "This instance does not belong to the study to be split: " + instance); + } + else + { + RegisterSeries(seriesUidMap_, series); + AddInstance(instance); + } + } + + bool SplitStudyJob::LookupTargetSeriesUid(std::string& uid, const std::string& series) const {
--- a/OrthancServer/Sources/ServerJobs/SplitStudyJob.h Tue Jun 22 10:40:08 2021 +0200 +++ b/OrthancServer/Sources/ServerJobs/SplitStudyJob.h Wed Jun 23 14:33:46 2021 +0200 @@ -60,6 +60,10 @@ void CheckAllowedTag(const DicomTag& tag) const; void Setup(); + + // Make setter methods private to prevent incorrect calls + using SetOfInstancesJob::AddParentResource; + using SetOfInstancesJob::AddInstance; protected: virtual bool HandleInstance(const std::string& instance) ORTHANC_OVERRIDE; @@ -88,6 +92,8 @@ void AddSourceSeries(const std::string& series); + void AddSourceInstance(const std::string& instance); // New in Orthanc 1.9.4 + bool LookupTargetSeriesUid(std::string& uid, const std::string& series) const;