XNAT Python Client#
A new XNAT client that exposes XNAT objects/functions as python objects/functions.
The XNAT Python client is open-source (licensed under the Apache 2.0 license) and hosted on gitlab at https://gitlab.com/radiology/infrastructure/xnatpy
The official documentation can be found at xnat.readthedocs.org
To install from pypi simply use:
pip install xnat
There is also a conda package available:
conda install -c conda-forge xnat
Alternatively, you can get yourself a copy of the source code:
git clone https://gitlab.com/radiology/infrastructure/xnatpy
Note
This is NOT pyxnat, but a new module which is not as mature but uses a different philisophy for the user interface. Pyxnat is located at: https://pyxnat.github.io/pyxnat
XNAT Client Documentation#
- Introduction
- Manual
- XNAT REST API
- Installation
- Connecting to a server
- Low level REST directives
- Exploring your xnat server
- Looping over data
- Mapping function
- Selecting an object based on its uri
- Downloading data
- Custom variables
- Getting external urls of an object
- Importing data into XNAT
- Prearchive
- Searching
- Object creation
- Accessing XNAT files as local files (partial read)
- Accessing DICOM headers of scan
- Re-using XNAT jsession
- Example scripts
- Command-line interface
- Changelog
- 0.6.0 - 2024-05-14
- 0.5.3 - 2023-12-04
- 0.5.2 - 2023-10-02
- 0.5.1 - 2023-03-30
- 0.5.0 - 2023-02-27
- 0.4.3 - 2022-10-31
- 0.4.2 - 2022-04-07
- 0.4.1 - 2022-02-22
- 0.4.0 - 2022-01-27
- 0.3.28 - 2021-10-28
- 0.3.27 - 2021-09-29
- 0.3.26 - 2021-04-16
- 0.3.25 - 2020-09-24
- 0.3.24 - 2020-06-19
- 0.3.23 - 2020-06-19
- 0.3.22 - 2020-02-26
- 0.3.21 - 2019-10-09
- 0.3.20 - 2019-10-09
- 0.3.19 - 2019-09-20
- 0.3.18 - 2019-06-06
- 0.3.17 - 2019-04-04
- 0.3.16 - 2019-03-28
- 0.3.14 - 2019-02-22
- 0.3.13 - 2019-01-07
- 0.3.12 - 2019-01-03
- 0.3.11 - 2018-11-12
- 0.3.10 - 2018-08-31
- 0.3.9 - 2018-07-02
- 0.3.8 - 2018-06-04
- 0.3.7 - 2018-03-12
- 0.3.6 - 2018-03-09
- 0.3.5 - 2018-01-02
- 0.3.4 - 2017-11-13
- 0.3.3 - 2017-10-18
- 0.3.2 - 2017-10-15
- 0.3.1 - 2017-09-04
- 0.3.0 - 2017-08-17
- 0.2.3 - 2017-04-03
- Code reference
xnatPackagesessionModuleBaseXNATSessionBaseXNATSession.clearcache()BaseXNATSession.create_object()BaseXNATSession.delete()BaseXNATSession.download()BaseXNATSession.download_stream()BaseXNATSession.download_zip()BaseXNATSession.experimentsBaseXNATSession.get()BaseXNATSession.get_json()BaseXNATSession.head()BaseXNATSession.interfaceBaseXNATSession.pluginsBaseXNATSession.post()BaseXNATSession.prearchiveBaseXNATSession.projectsBaseXNATSession.put()BaseXNATSession.scan_typesBaseXNATSession.scannersBaseXNATSession.servicesBaseXNATSession.session_expiration_timeBaseXNATSession.subjectsBaseXNATSession.upload()BaseXNATSession.upload_file()BaseXNATSession.upload_stream()BaseXNATSession.upload_string()BaseXNATSession.url_for()BaseXNATSession.usersBaseXNATSession.xnat_build_infoBaseXNATSession.xnat_uptimeBaseXNATSession.xnat_version
XNATSessiondefault_update_func()
coreModuleCustomVariableDefCustomVariableGroupCustomVariableMapXNATBaseListingXNATBaseListing.cachingXNATBaseListing.clearcache()XNATBaseListing.dataXNATBaseListing.data_mapsXNATBaseListing.delete_item_from_cache()XNATBaseListing.delete_item_from_listings()XNATBaseListing.key_mapXNATBaseListing.listingXNATBaseListing.loggerXNATBaseListing.non_unique_keysXNATBaseListing.sanitize_name()XNATBaseListing.uriXNATBaseListing.xnat_session
XNATBaseObjectXNATBaseObject.DEFAULT_SEARCH_FIELDSXNATBaseObject.FROM_SEARCH_URIXNATBaseObject.SECONDARY_LOOKUP_FIELDXNATBaseObject.cache_idXNATBaseObject.cachingXNATBaseObject.clearcache()XNATBaseObject.create_cache_id()XNATBaseObject.dataXNATBaseObject.del_()XNATBaseObject.delete()XNATBaseObject.external_uri()XNATBaseObject.fieldnameXNATBaseObject.fulldataXNATBaseObject.fulluriXNATBaseObject.get()XNATBaseObject.get_object()XNATBaseObject.idXNATBaseObject.loggerXNATBaseObject.mset()XNATBaseObject.parentXNATBaseObject.set()XNATBaseObject.uriXNATBaseObject.xnat_sessionXNATBaseObject.xpath
XNATListingXNATNestedObjectXNATObjectXNATSimpleListingXNATSubListingXNATSubObjectcaching()
inspectModuleprearchiveModulePrearchivePrearchiveFilePrearchiveScanPrearchiveSessionPrearchiveSession.archive()PrearchiveSession.autoarchivePrearchiveSession.cli_str()PrearchiveSession.dataPrearchiveSession.delete()PrearchiveSession.download()PrearchiveSession.folder_namePrearchiveSession.fulldataPrearchiveSession.idPrearchiveSession.labelPrearchiveSession.lastmodPrearchiveSession.move()PrearchiveSession.namePrearchiveSession.prevent_anonPrearchiveSession.prevent_auto_commitPrearchiveSession.projectPrearchiveSession.rebuild()PrearchiveSession.scan_datePrearchiveSession.scan_timePrearchiveSession.scansPrearchiveSession.statusPrearchiveSession.subjectPrearchiveSession.tagPrearchiveSession.timestampPrearchiveSession.uploadedPrearchiveSession.xpath
servicesModuleDicomBoxImportRequestDicomBoxImportRequest.cleanup_after_importDicomBoxImportRequest.createdDicomBoxImportRequest.enabledDicomBoxImportRequest.idDicomBoxImportRequest.project_idDicomBoxImportRequest.session_pathDicomBoxImportRequest.statusDicomBoxImportRequest.subject_idDicomBoxImportRequest.timestampDicomBoxImportRequest.username
ServicesTokenResult
usersModulemixinModuleAbstractResourceAbstractResource.SECONDARY_LOOKUP_FIELDAbstractResource.cache_idAbstractResource.create_cache_id()AbstractResource.dataAbstractResource.data_dirAbstractResource.download()AbstractResource.download_dir()AbstractResource.file_countAbstractResource.file_sizeAbstractResource.filesAbstractResource.fulldataAbstractResource.parent_objAbstractResource.refresh_catalog()AbstractResource.upload()AbstractResource.upload_data()AbstractResource.upload_dir()
DerivedDataExperimentDataExperimentData.DEFAULT_SEARCH_FIELDSExperimentData.FROM_SEARCH_URIExperimentData.SECONDARY_LOOKUP_FIELDExperimentData.activate()ExperimentData.cache_idExperimentData.cli_str()ExperimentData.create_cache_id()ExperimentData.data_dirExperimentData.labelExperimentData.mapping_iter()ExperimentData.quarantine()ExperimentData.status
FilterFunctionsImageScanDataImageSessionDataInvestigatorDataProjectDataProjectData.FROM_SEARCH_URIProjectData.SECONDARY_LOOKUP_FIELDProjectData.cache_idProjectData.cli_str()ProjectData.create_cache_id()ProjectData.create_resource()ProjectData.data_dirProjectData.download_dir()ProjectData.experimentsProjectData.filesProjectData.fulluriProjectData.map()ProjectData.mapping_iter()ProjectData.parentProjectData.projectProjectData.resourcesProjectData.subjectsProjectData.users
SubjectAssessorDataSubjectData
- Generated XSD classes
XSD ClassesDocumentationAbstractDemographicDataAbstractProjectAssetAbstractProtocolAbstractResourceAbstractResourceTagsAbstractStatisticsAbstractSubjectMetadataAddFieldAddFieldStringAddIDStringAdditionalStatisticsDoubleAlgorithmAliasStringComputationDataContrastBolusCrScanDataCrSessionDataCtQcScanDataCtScanDataCtScanDataDcmvalidationCtScanDataParametersCtScanDataParameters.acquisition_numberCtScanDataParameters.add_paramCtScanDataParameters.collection_diameterCtScanDataParameters.collimation_widthCtScanDataParameters.contrast_bolusCtScanDataParameters.convolution_kernelCtScanDataParameters.ct_divolCtScanDataParameters.derivationCtScanDataParameters.distance_source_to_detectorCtScanDataParameters.distance_source_to_patientCtScanDataParameters.estimated_dose_savingCtScanDataParameters.exposureCtScanDataParameters.exposure_timeCtScanDataParameters.filterCtScanDataParameters.focal_spotsCtScanDataParameters.fovCtScanDataParameters.gantry_tiltCtScanDataParameters.generator_powerCtScanDataParameters.image_typeCtScanDataParameters.kvpCtScanDataParameters.optionsCtScanDataParameters.orientationCtScanDataParameters.pitch_factorCtScanDataParameters.rescaleCtScanDataParameters.rotation_directionCtScanDataParameters.subject_positionCtScanDataParameters.table_feed_per_rotationCtScanDataParameters.table_heightCtScanDataParameters.table_speedCtScanDataParameters.voxel_resCtScanDataParameters.xray_tube_current
CtScanDataParametersCollimationwidthCtScanDataParametersDerivationCtScanDataParametersEstimateddosesavingCtScanDataParametersFovCtScanDataParametersRescaleCtScanDataParametersVoxelresCtSessionDataDatatypeProtocolDcmValidationStringDelayIntegerDemographicDataDemographicData.ageDemographicData.birth_weightDemographicData.dobDemographicData.educationDemographicData.education_descDemographicData.employmentDemographicData.ethnicityDemographicData.genderDemographicData.gestational_ageDemographicData.handednessDemographicData.heightDemographicData.post_menstrual_ageDemographicData.raceDemographicData.race2DemographicData.race3DemographicData.race4DemographicData.race5DemographicData.race6DemographicData.sesDemographicData.weightDemographicData.yob
DemographicDataHeightDemographicDataWeightDerivationStringDerivedDataDicomCodedValueDicomSeriesDicomSeriesDimensionsDicomSeriesImagesetDicomSeriesVoxelresDoseFloatDx3DCraniofacialScanDataDx3DCraniofacialSessionDataDxScanDataDxSessionDataEcatValidationStringEcgScanDataEcgSessionDataEegScanDataEegScanDataChannelsEegScanDataParametersEegScanDataParametersDatarecordEegScanDataSoftwarefiltersimpedancesEegScanDataSoftwarefiltersimpedancesImpedanceEegSessionDataEegSessionDataSamplingintervalEegSessionDataSamplingrateEpsScanDataEpsSessionDataEsScanDataEsSessionDataEstimatedDoseSavingFloatEsvScanDataEsvSessionDataExperimentDataExperimentData.acquisition_siteExperimentData.custom_variablesExperimentData.dateExperimentData.delayExperimentData.durationExperimentData.fieldsExperimentData.investigatorExperimentData.noteExperimentData.originalExperimentData.projectExperimentData.protocolExperimentData.resourcesExperimentData.sharingExperimentData.timeExperimentData.validationExperimentData.versionExperimentData.visitExperimentData.visit_id
ExperimentDataDelayExperimentDataFieldsExperimentDataSharingFieldDefinitionGroupFieldDefinitionGroupFieldsFieldDefinitionGroupFieldsFieldPossiblevaluesFieldStringFileDataFileData.SECONDARY_LOOKUP_FIELDFileData.cat_idFileData.collectionFileData.dataFileData.data_pathFileData.delete()FileData.digestFileData.download()FileData.download_stream()FileData.file_contentFileData.file_formatFileData.file_sizeFileData.file_tagsFileData.fulldataFileData.idFileData.nameFileData.open()FileData.parentFileData.pathFileData.size
GenericDataGmScanDataGmSessionDataGmvScanDataGmvSessionDataHdScanDataHdSessionDataHeightFloatImageAssessorDataImageResourceImageResourceDimensionsImageResourceSeriesImageResourceSeriesDimensionsImageResourceSeriesVoxelresImageResourceVoxelresImageScanDataImageScanData.body_part_examinedImageScanData.conditionImageScanData.documentationImageScanData.fileImageScanData.framesImageScanData.image_session_idImageScanData.modalityImageScanData.noteImageScanData.operatorImageScanData.projectImageScanData.protocol_nameImageScanData.qualityImageScanData.requested_procedure_descriptionImageScanData.scannerImageScanData.series_classImageScanData.series_descriptionImageScanData.sharingImageScanData.start_dateImageScanData.start_timeImageScanData.typeImageScanData.uidImageScanData.validation
ImageScanDataScannerImageScanDataSharingImageSessionDataImageSessionData.assessorsImageSessionData.dcm_accession_numberImageSessionData.dcm_patient_birth_dateImageSessionData.dcm_patient_idImageSessionData.dcm_patient_nameImageSessionData.dcm_patient_weightImageSessionData.modalityImageSessionData.operatorImageSessionData.prearchive_pathImageSessionData.reconstructionsImageSessionData.regionsImageSessionData.scannerImageSessionData.scansImageSessionData.session_typeImageSessionData.study_idImageSessionData.uid
ImageSessionDataScannerIntermediateFloatInvestigatorDataIoScanDataIoSessionDataIsotopeStringJsonbLONGVARCHARLabelStringMegScanDataMegSessionDataMgScanDataMgSessionDataMrAssessorDataMrQcScanDataMrScanDataMrScanDataDcmvalidationMrScanDataParametersMrScanDataParameters.acq_timeMrScanDataParameters.acq_typeMrScanDataParameters.add_paramMrScanDataParameters.coilMrScanDataParameters.coil_elementsMrScanDataParameters.delta_teMrScanDataParameters.diffusionMrScanDataParameters.dti_acq_countMrScanDataParameters.echo_spacingMrScanDataParameters.flipMrScanDataParameters.fovMrScanDataParameters.image_typeMrScanDataParameters.in_plane_phase_encodingMrScanDataParameters.matrixMrScanDataParameters.orientationMrScanDataParameters.originMrScanDataParameters.partitionsMrScanDataParameters.phase_encoding_directionMrScanDataParameters.pixel_bandwidthMrScanDataParameters.pmcMrScanDataParameters.readout_sample_spacingMrScanDataParameters.scan_optionsMrScanDataParameters.scan_sequenceMrScanDataParameters.seq_variantMrScanDataParameters.sequenceMrScanDataParameters.subject_positionMrScanDataParameters.teMrScanDataParameters.tiMrScanDataParameters.trMrScanDataParameters.voxel_res
MrScanDataParametersDiffusionMrScanDataParametersFovMrScanDataParametersInplanephaseencodingMrScanDataParametersMatrixMrScanDataParametersVoxelresMrSessionDataMrsScanDataNmScanDataNmSessionDataOpScanDataOpSessionDataOptScanDataOptScanDataDcmvalidationOptScanDataParametersOptScanDataParametersFovOptScanDataParametersVoxelresOptSessionDataOtherDicomScanDataOtherDicomSessionDataOtherQcScanDataPVisitDataPetAssessorDataPetQcScanDataPetQcScanData.acceptable_voxel_sizePetQcScanData.acquisitionPetQcScanData.bottom_cutoffPetQcScanData.correct_filtersPetQcScanData.correct_iterations_and_subsetsPetQcScanData.correct_reconstruction_algorithmPetQcScanData.correct_slice_thicknessPetQcScanData.processing_errorsPetQcScanData.qc_outcomePetQcScanData.qc_outcome_reasonPetQcScanData.reason_frames_unacceptablePetQcScanData.reconstruction_algorithm_usedPetQcScanData.top_cutoffPetQcScanData.unacceptable_frames
PetScanDataPetScanDataEcatvalidationPetScanDataParametersPetScanDataParameters.acq_typePetScanDataParameters.add_paramPetScanDataParameters.annotationPetScanDataParameters.bed_positionPetScanDataParameters.bin_sizePetScanDataParameters.data_typePetScanDataParameters.dimensionsPetScanDataParameters.ecat_calibration_factorPetScanDataParameters.facilityPetScanDataParameters.file_typePetScanDataParameters.filterPetScanDataParameters.filter_codePetScanDataParameters.framesPetScanDataParameters.gate_durationPetScanDataParameters.mt_1_1PetScanDataParameters.mt_1_2PetScanDataParameters.mt_1_3PetScanDataParameters.mt_1_4PetScanDataParameters.mt_2_1PetScanDataParameters.mt_2_2PetScanDataParameters.mt_2_3PetScanDataParameters.mt_2_4PetScanDataParameters.mt_3_1PetScanDataParameters.mt_3_2PetScanDataParameters.mt_3_3PetScanDataParameters.mt_3_4PetScanDataParameters.num_accepted_beatsPetScanDataParameters.num_anglesPetScanDataParameters.num_gatesPetScanDataParameters.num_planesPetScanDataParameters.num_relementsPetScanDataParameters.offsetPetScanDataParameters.orientationPetScanDataParameters.original_file_namePetScanDataParameters.pixel_sizePetScanDataParameters.plane_separationPetScanDataParameters.processing_codePetScanDataParameters.r_wave_offsetPetScanDataParameters.recon_typePetScanDataParameters.recon_viewsPetScanDataParameters.recon_zoomPetScanDataParameters.resolutionPetScanDataParameters.rfilterPetScanDataParameters.scatter_typePetScanDataParameters.system_typePetScanDataParameters.transaxial_fovPetScanDataParameters.zfilterPetScanDataParameters.zrotation_angle
PetScanDataParametersDimensionsPetScanDataParametersFilterPetScanDataParametersFramesPetScanDataParametersFramesFramePetScanDataParametersOffsetPetScanDataParametersPixelsizePetScanDataParametersResolutionPetScanDataParametersRfilterPetScanDataParametersZfilterPetSessionDataPetSessionData.blood_glucosePetSessionData.blood_glucose_timePetSessionData.blood_glucose_unitsPetSessionData.patient_idPetSessionData.patient_namePetSessionData.stabilizationPetSessionData.start_timePetSessionData.start_time_injectionPetSessionData.start_time_scanPetSessionData.study_typePetSessionData.tracer
PetSessionDataTracerPetSessionDataTracerDosePetSessionDataTracerIntermediatePetSessionDataTracerIsotopePetSessionDataTracerTotalmassPetmrSessionDataPetmrSessionData.blood_glucosePetmrSessionData.blood_glucose_timePetmrSessionData.blood_glucose_unitsPetmrSessionData.coilPetmrSessionData.field_strengthPetmrSessionData.markerPetmrSessionData.patient_idPetmrSessionData.patient_namePetmrSessionData.stabilizationPetmrSessionData.start_timePetmrSessionData.start_time_injectionPetmrSessionData.start_time_scanPetmrSessionData.study_typePetmrSessionData.tracer
PetmrSessionDataTracerPetmrSessionDataTracer.dosePetmrSessionDataTracer.intermediatePetmrSessionDataTracer.isotopePetmrSessionDataTracer.namePetmrSessionDataTracer.specific_activityPetmrSessionDataTracer.start_timePetmrSessionDataTracer.total_massPetmrSessionDataTracer.transmissionsPetmrSessionDataTracer.transmissions_starttime
PetmrSessionDataTracerDosePetmrSessionDataTracerIntermediatePetmrSessionDataTracerIsotopePetmrSessionDataTracerTotalmassPossibleValueStringProjectDataProjectDataAliasesProjectDataFieldsProjectParticipantPublicationResourceQcAssessmentDataQcAssessmentDataScansQcAssessmentDataScansScanSliceqcQcManualAssessorDataQcManualAssessorData.commentsQcManualAssessorData.incidental_findingsQcManualAssessorData.pass_QcManualAssessorData.payableQcManualAssessorData.protocolQcManualAssessorData.protocol_commentsQcManualAssessorData.raterQcManualAssessorData.rescanQcManualAssessorData.resolvableQcManualAssessorData.retrainQcManualAssessorData.scansQcManualAssessorData.stereotactic_marker
QcScanDataQcScanDataFieldsQcScanDataRatingRatingStringReconstructedImageDataReconstructedImageData.base_scan_typeReconstructedImageData.computationsReconstructedImageData.idReconstructedImageData.image_session_idReconstructedImageData.in_ReconstructedImageData.in_scansReconstructedImageData.outReconstructedImageData.parametersReconstructedImageData.provenanceReconstructedImageData.type
RegionResourceRegionResourceCreatorRegionResourceSubregionlabelsResourceResourceCatalogResourceSeriesRfScanDataRfSessionDataRgScanDataRgSessionDataRtImageScanDataRtSessionDataSamplingIntervalFloatSamplingRateFloatScScanDataScannerStringSegScanDataShareStringSmScanDataSmSessionDataSrScanDataSrSessionDataStatisticsDataStatisticsDataAddfieldStatisticsDataAdditionalstatisticsStudyProtocolStudyProtocolAcqconditionsStudyProtocolImagesessiontypesStudyProtocolSubjectgroupsStudyProtocolSubjectvariablesSubjectAssessorDataSubjectDataSubjectDataAddidSubjectDataFieldsSubjectMetadataSubjectVariablesDataSubjectVariablesDataVariablesTagStringTotalMassFloatUsScanDataUsSessionDataValidationDataVariableStringVoiceAudioScanDataVolumetricRegionVolumetricRegionSubregionsWeightFloatXNATNestedObjectMixinXNATObjectMixinXNATSubObjectMixinXa3DScanDataXa3DSessionDataXaScanDataXaScanDataParametersXaScanDataParametersFovXaScanDataParametersPixelresXaSessionDataXcScanDataXcSessionDataXcvScanDataXcvSessionDatacurrent_session()