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
- XNATpy Tutorial
- XNAT REST API
- Installation
- Connecting to a server
- Low level REST directives
- Exploring your xnat server
- Looping over data
- 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
- 0.5.3 - 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
xnat
Packagesession
ModuleBaseXNATSession
BaseXNATSession.clearcache()
BaseXNATSession.create_object()
BaseXNATSession.delete()
BaseXNATSession.download()
BaseXNATSession.download_stream()
BaseXNATSession.download_zip()
BaseXNATSession.experiments
BaseXNATSession.get()
BaseXNATSession.get_json()
BaseXNATSession.head()
BaseXNATSession.interface
BaseXNATSession.plugins
BaseXNATSession.post()
BaseXNATSession.prearchive
BaseXNATSession.projects
BaseXNATSession.put()
BaseXNATSession.scan_types
BaseXNATSession.scanners
BaseXNATSession.services
BaseXNATSession.session_expiration_time
BaseXNATSession.subjects
BaseXNATSession.upload()
BaseXNATSession.upload_file()
BaseXNATSession.upload_stream()
BaseXNATSession.upload_string()
BaseXNATSession.url_for()
BaseXNATSession.users
BaseXNATSession.xnat_build_info
BaseXNATSession.xnat_uptime
BaseXNATSession.xnat_version
XNATSession
default_update_func()
core
ModuleCustomVariableDef
CustomVariableGroup
CustomVariableMap
XNATBaseListing
XNATBaseListing.caching
XNATBaseListing.clearcache()
XNATBaseListing.data
XNATBaseListing.data_maps
XNATBaseListing.delete_item_from_cache()
XNATBaseListing.delete_item_from_listings()
XNATBaseListing.key_map
XNATBaseListing.listing
XNATBaseListing.logger
XNATBaseListing.non_unique_keys
XNATBaseListing.sanitize_name()
XNATBaseListing.uri
XNATBaseListing.xnat_session
XNATBaseObject
XNATBaseObject.DEFAULT_SEARCH_FIELDS
XNATBaseObject.FROM_SEARCH_URI
XNATBaseObject.SECONDARY_LOOKUP_FIELD
XNATBaseObject.cache_id
XNATBaseObject.caching
XNATBaseObject.clearcache()
XNATBaseObject.create_cache_id()
XNATBaseObject.data
XNATBaseObject.del_()
XNATBaseObject.delete()
XNATBaseObject.external_uri()
XNATBaseObject.fieldname
XNATBaseObject.fulldata
XNATBaseObject.fulluri
XNATBaseObject.get()
XNATBaseObject.get_object()
XNATBaseObject.id
XNATBaseObject.logger
XNATBaseObject.mset()
XNATBaseObject.parent
XNATBaseObject.set()
XNATBaseObject.uri
XNATBaseObject.xnat_session
XNATBaseObject.xpath
XNATListing
XNATNestedObject
XNATObject
XNATSimpleListing
XNATSubListing
XNATSubObject
caching()
inspect
Moduleprearchive
ModulePrearchive
PrearchiveFile
PrearchiveScan
PrearchiveSession
PrearchiveSession.archive()
PrearchiveSession.autoarchive
PrearchiveSession.cli_str()
PrearchiveSession.data
PrearchiveSession.delete()
PrearchiveSession.download()
PrearchiveSession.folder_name
PrearchiveSession.fulldata
PrearchiveSession.id
PrearchiveSession.label
PrearchiveSession.lastmod
PrearchiveSession.move()
PrearchiveSession.name
PrearchiveSession.prevent_anon
PrearchiveSession.prevent_auto_commit
PrearchiveSession.project
PrearchiveSession.rebuild()
PrearchiveSession.scan_date
PrearchiveSession.scan_time
PrearchiveSession.scans
PrearchiveSession.status
PrearchiveSession.subject
PrearchiveSession.tag
PrearchiveSession.timestamp
PrearchiveSession.uploaded
PrearchiveSession.xpath
services
ModuleDicomBoxImportRequest
DicomBoxImportRequest.cleanup_after_import
DicomBoxImportRequest.created
DicomBoxImportRequest.enabled
DicomBoxImportRequest.id
DicomBoxImportRequest.project_id
DicomBoxImportRequest.session_path
DicomBoxImportRequest.status
DicomBoxImportRequest.subject_id
DicomBoxImportRequest.timestamp
DicomBoxImportRequest.username
Services
TokenResult
users
Modulemixin
ModuleAbstractResource
AbstractResource.SECONDARY_LOOKUP_FIELD
AbstractResource.cache_id
AbstractResource.create_cache_id()
AbstractResource.data
AbstractResource.data_dir
AbstractResource.download()
AbstractResource.download_dir()
AbstractResource.file_count
AbstractResource.file_size
AbstractResource.files
AbstractResource.fulldata
AbstractResource.parent_obj
AbstractResource.refresh_catalog()
AbstractResource.upload()
AbstractResource.upload_data()
AbstractResource.upload_dir()
DerivedData
ExperimentData
ExperimentData.DEFAULT_SEARCH_FIELDS
ExperimentData.FROM_SEARCH_URI
ExperimentData.SECONDARY_LOOKUP_FIELD
ExperimentData.activate()
ExperimentData.cache_id
ExperimentData.cli_str()
ExperimentData.create_cache_id()
ExperimentData.data_dir
ExperimentData.label
ExperimentData.quarantine()
ExperimentData.status
ImageScanData
ImageSessionData
InvestigatorData
ProjectData
ProjectData.FROM_SEARCH_URI
ProjectData.SECONDARY_LOOKUP_FIELD
ProjectData.cache_id
ProjectData.cli_str()
ProjectData.create_cache_id()
ProjectData.create_resource()
ProjectData.data_dir
ProjectData.download_dir()
ProjectData.experiments
ProjectData.files
ProjectData.fulluri
ProjectData.parent
ProjectData.project
ProjectData.resources
ProjectData.subjects
ProjectData.users
SubjectAssessorData
SubjectData
- Generated XSD classes
XSD Classes
DocumentationAbstractDemographicData
AbstractProtocol
AbstractResource
AbstractResourceTags
AbstractStatistics
AbstractSubjectMetadata
AddField
AddFieldString
AddIDString
AdditionalStatisticsDouble
Algorithm
AliasString
ComputationData
ContrastBolus
CrScanData
CrSessionData
CtScanData
CtScanDataDcmvalidation
CtScanDataParameters
CtScanDataParameters.acquisition_number
CtScanDataParameters.collection_diameter
CtScanDataParameters.collimation_width
CtScanDataParameters.contrast_bolus
CtScanDataParameters.convolution_kernel
CtScanDataParameters.ct_divol
CtScanDataParameters.derivation
CtScanDataParameters.distance_source_to_detector
CtScanDataParameters.distance_source_to_patient
CtScanDataParameters.estimated_dose_saving
CtScanDataParameters.exposure
CtScanDataParameters.exposure_time
CtScanDataParameters.filter
CtScanDataParameters.focal_spots
CtScanDataParameters.fov
CtScanDataParameters.gantry_tilt
CtScanDataParameters.generator_power
CtScanDataParameters.image_type
CtScanDataParameters.kvp
CtScanDataParameters.options
CtScanDataParameters.orientation
CtScanDataParameters.pitch_factor
CtScanDataParameters.rescale
CtScanDataParameters.rotation_direction
CtScanDataParameters.subject_position
CtScanDataParameters.table_feed_per_rotation
CtScanDataParameters.table_height
CtScanDataParameters.table_speed
CtScanDataParameters.voxel_res
CtScanDataParameters.xray_tube_current
CtScanDataParametersCollimationwidth
CtScanDataParametersDerivation
CtScanDataParametersEstimateddosesaving
CtScanDataParametersFov
CtScanDataParametersRescale
CtScanDataParametersVoxelres
CtSessionData
DatatypeProtocol
DcmValidationString
DelayInteger
DemographicData
DemographicData.age
DemographicData.birth_weight
DemographicData.dob
DemographicData.education
DemographicData.education_desc
DemographicData.employment
DemographicData.ethnicity
DemographicData.gender
DemographicData.gestational_age
DemographicData.handedness
DemographicData.height
DemographicData.post_menstrual_age
DemographicData.race
DemographicData.race2
DemographicData.race3
DemographicData.race4
DemographicData.race5
DemographicData.race6
DemographicData.ses
DemographicData.weight
DemographicData.yob
DemographicDataHeight
DemographicDataWeight
DerivationString
DerivedData
DicomCodedValue
DicomSeries
DicomSeriesDimensions
DicomSeriesImageset
DicomSeriesVoxelres
DoseFloat
Dx3DCraniofacialScanData
Dx3DCraniofacialSessionData
DxScanData
DxSessionData
EcatValidationString
EcgScanData
EcgSessionData
EegScanData
EegScanDataChannels
EegScanDataParameters
EegScanDataParametersDatarecord
EegScanDataSoftwarefiltersimpedances
EegScanDataSoftwarefiltersimpedancesImpedance
EegSessionData
EegSessionDataSamplinginterval
EegSessionDataSamplingrate
EpsScanData
EpsSessionData
EsScanData
EsSessionData
EstimatedDoseSavingFloat
EsvScanData
EsvSessionData
ExperimentData
ExperimentData.acquisition_site
ExperimentData.custom_variables
ExperimentData.date
ExperimentData.delay
ExperimentData.duration
ExperimentData.fields
ExperimentData.investigator
ExperimentData.note
ExperimentData.original
ExperimentData.project
ExperimentData.protocol
ExperimentData.resources
ExperimentData.sharing
ExperimentData.time
ExperimentData.validation
ExperimentData.version
ExperimentData.visit
ExperimentData.visit_id
ExperimentDataDelay
ExperimentDataFields
ExperimentDataSharing
FieldDefinitionGroup
FieldDefinitionGroupFields
FieldDefinitionGroupFieldsFieldPossiblevalues
FieldString
FileData
FileData.SECONDARY_LOOKUP_FIELD
FileData.cat_id
FileData.collection
FileData.data
FileData.data_path
FileData.delete()
FileData.digest
FileData.download()
FileData.download_stream()
FileData.file_content
FileData.file_format
FileData.file_size
FileData.file_tags
FileData.fulldata
FileData.id
FileData.name
FileData.open()
FileData.parent
FileData.path
FileData.size
GenericData
GmScanData
GmSessionData
GmvScanData
GmvSessionData
HdScanData
HdSessionData
HeightFloat
ImageAssessorData
ImageResource
ImageResourceDimensions
ImageResourceSeries
ImageResourceSeriesDimensions
ImageResourceSeriesVoxelres
ImageResourceVoxelres
ImageScanData
ImageScanData.condition
ImageScanData.documentation
ImageScanData.file
ImageScanData.frames
ImageScanData.image_session_id
ImageScanData.modality
ImageScanData.note
ImageScanData.operator
ImageScanData.project
ImageScanData.quality
ImageScanData.scanner
ImageScanData.series_class
ImageScanData.series_description
ImageScanData.sharing
ImageScanData.start_date
ImageScanData.start_time
ImageScanData.type
ImageScanData.uid
ImageScanData.validation
ImageScanDataScanner
ImageScanDataSharing
ImageSessionData
ImageSessionData.assessors
ImageSessionData.dcm_accession_number
ImageSessionData.dcm_patient_birth_date
ImageSessionData.dcm_patient_id
ImageSessionData.dcm_patient_name
ImageSessionData.dcm_patient_weight
ImageSessionData.modality
ImageSessionData.operator
ImageSessionData.prearchive_path
ImageSessionData.reconstructions
ImageSessionData.regions
ImageSessionData.scanner
ImageSessionData.scans
ImageSessionData.session_type
ImageSessionData.study_id
ImageSessionData.uid
ImageSessionDataScanner
IntermediateFloat
InvestigatorData
IoScanData
IoSessionData
IsotopeString
LONGVARCHAR
LabelString
MegScanData
MegSessionData
MgScanData
MgSessionData
MrAssessorData
MrQcScanData
MrScanData
MrScanDataDcmvalidation
MrScanDataParameters
MrScanDataParameters.acq_time
MrScanDataParameters.acq_type
MrScanDataParameters.add_param
MrScanDataParameters.coil
MrScanDataParameters.coil_elements
MrScanDataParameters.delta_te
MrScanDataParameters.diffusion
MrScanDataParameters.dti_acq_count
MrScanDataParameters.echo_spacing
MrScanDataParameters.flip
MrScanDataParameters.fov
MrScanDataParameters.image_type
MrScanDataParameters.in_plane_phase_encoding
MrScanDataParameters.matrix
MrScanDataParameters.orientation
MrScanDataParameters.origin
MrScanDataParameters.partitions
MrScanDataParameters.phase_encoding_direction
MrScanDataParameters.pixel_bandwidth
MrScanDataParameters.pmc
MrScanDataParameters.readout_sample_spacing
MrScanDataParameters.scan_options
MrScanDataParameters.scan_sequence
MrScanDataParameters.seq_variant
MrScanDataParameters.sequence
MrScanDataParameters.subject_position
MrScanDataParameters.te
MrScanDataParameters.ti
MrScanDataParameters.tr
MrScanDataParameters.voxel_res
MrScanDataParametersDiffusion
MrScanDataParametersFov
MrScanDataParametersInplanephaseencoding
MrScanDataParametersMatrix
MrScanDataParametersVoxelres
MrSessionData
MrsScanData
NmScanData
NmSessionData
OpScanData
OpSessionData
OptScanData
OptScanDataDcmvalidation
OptScanDataParameters
OptScanDataParametersFov
OptScanDataParametersVoxelres
OptSessionData
OtherDicomScanData
OtherDicomSessionData
OtherQcScanData
PVisitData
PetAssessorData
PetQcScanData
PetQcScanData.acceptable_voxel_size
PetQcScanData.acquisition
PetQcScanData.bottom_cutoff
PetQcScanData.correct_filters
PetQcScanData.correct_iterations_and_subsets
PetQcScanData.correct_reconstruction_algorithm
PetQcScanData.correct_slice_thickness
PetQcScanData.processing_errors
PetQcScanData.qc_outcome
PetQcScanData.qc_outcome_reason
PetQcScanData.reason_frames_unacceptable
PetQcScanData.reconstruction_algorithm_used
PetQcScanData.top_cutoff
PetQcScanData.unacceptable_frames
PetScanData
PetScanDataEcatvalidation
PetScanDataParameters
PetScanDataParameters.acq_type
PetScanDataParameters.add_param
PetScanDataParameters.annotation
PetScanDataParameters.bed_position
PetScanDataParameters.bin_size
PetScanDataParameters.data_type
PetScanDataParameters.dimensions
PetScanDataParameters.ecat_calibration_factor
PetScanDataParameters.facility
PetScanDataParameters.file_type
PetScanDataParameters.filter
PetScanDataParameters.filter_code
PetScanDataParameters.frames
PetScanDataParameters.gate_duration
PetScanDataParameters.mt_1_1
PetScanDataParameters.mt_1_2
PetScanDataParameters.mt_1_3
PetScanDataParameters.mt_1_4
PetScanDataParameters.mt_2_1
PetScanDataParameters.mt_2_2
PetScanDataParameters.mt_2_3
PetScanDataParameters.mt_2_4
PetScanDataParameters.mt_3_1
PetScanDataParameters.mt_3_2
PetScanDataParameters.mt_3_3
PetScanDataParameters.mt_3_4
PetScanDataParameters.num_accepted_beats
PetScanDataParameters.num_angles
PetScanDataParameters.num_gates
PetScanDataParameters.num_planes
PetScanDataParameters.num_relements
PetScanDataParameters.offset
PetScanDataParameters.orientation
PetScanDataParameters.original_file_name
PetScanDataParameters.pixel_size
PetScanDataParameters.plane_separation
PetScanDataParameters.processing_code
PetScanDataParameters.r_wave_offset
PetScanDataParameters.recon_type
PetScanDataParameters.recon_views
PetScanDataParameters.recon_zoom
PetScanDataParameters.resolution
PetScanDataParameters.rfilter
PetScanDataParameters.scatter_type
PetScanDataParameters.system_type
PetScanDataParameters.transaxial_fov
PetScanDataParameters.zfilter
PetScanDataParameters.zrotation_angle
PetScanDataParametersDimensions
PetScanDataParametersFilter
PetScanDataParametersFrames
PetScanDataParametersFramesFrame
PetScanDataParametersOffset
PetScanDataParametersPixelsize
PetScanDataParametersResolution
PetScanDataParametersRfilter
PetScanDataParametersZfilter
PetSessionData
PetSessionData.blood_glucose
PetSessionData.blood_glucose_time
PetSessionData.blood_glucose_units
PetSessionData.patient_id
PetSessionData.patient_name
PetSessionData.stabilization
PetSessionData.start_time
PetSessionData.start_time_injection
PetSessionData.start_time_scan
PetSessionData.study_type
PetSessionData.tracer
PetSessionDataTracer
PetSessionDataTracerDose
PetSessionDataTracerIntermediate
PetSessionDataTracerIsotope
PetSessionDataTracerTotalmass
PetmrSessionData
PetmrSessionData.blood_glucose
PetmrSessionData.blood_glucose_time
PetmrSessionData.blood_glucose_units
PetmrSessionData.coil
PetmrSessionData.field_strength
PetmrSessionData.marker
PetmrSessionData.patient_id
PetmrSessionData.patient_name
PetmrSessionData.stabilization
PetmrSessionData.start_time
PetmrSessionData.start_time_injection
PetmrSessionData.start_time_scan
PetmrSessionData.study_type
PetmrSessionData.tracer
PetmrSessionDataTracer
PetmrSessionDataTracer.dose
PetmrSessionDataTracer.intermediate
PetmrSessionDataTracer.isotope
PetmrSessionDataTracer.name
PetmrSessionDataTracer.specific_activity
PetmrSessionDataTracer.start_time
PetmrSessionDataTracer.total_mass
PetmrSessionDataTracer.transmissions
PetmrSessionDataTracer.transmissions_starttime
PetmrSessionDataTracerDose
PetmrSessionDataTracerIntermediate
PetmrSessionDataTracerIsotope
PetmrSessionDataTracerTotalmass
PossibleValueString
ProjectData
ProjectDataAliases
ProjectDataFields
ProjectParticipant
PublicationResource
QcAssessmentData
QcAssessmentDataScans
QcAssessmentDataScansScanSliceqc
QcManualAssessorData
QcManualAssessorData.comments
QcManualAssessorData.incidental_findings
QcManualAssessorData.pass_
QcManualAssessorData.payable
QcManualAssessorData.rater
QcManualAssessorData.rescan
QcManualAssessorData.resolvable
QcManualAssessorData.retrain
QcManualAssessorData.scans
QcManualAssessorData.stereotactic_marker
QcScanData
QcScanDataFields
QcScanDataRating
RatingString
ReconstructedImageData
ReconstructedImageData.base_scan_type
ReconstructedImageData.computations
ReconstructedImageData.id
ReconstructedImageData.image_session_id
ReconstructedImageData.in_
ReconstructedImageData.in_scans
ReconstructedImageData.out
ReconstructedImageData.parameters
ReconstructedImageData.provenance
ReconstructedImageData.type
RegionResource
RegionResourceCreator
RegionResourceSubregionlabels
Resource
ResourceCatalog
ResourceSeries
RfScanData
RfSessionData
RtImageScanData
RtSessionData
SamplingIntervalFloat
SamplingRateFloat
ScScanData
ScannerString
SegScanData
ShareString
SmScanData
SmSessionData
SrScanData
SrSessionData
StatisticsData
StatisticsDataAddfield
StatisticsDataAdditionalstatistics
StudyProtocol
StudyProtocolAcqconditions
StudyProtocolImagesessiontypes
StudyProtocolSubjectgroups
StudyProtocolSubjectvariables
SubjectAssessorData
SubjectData
SubjectDataAddid
SubjectDataFields
SubjectMetadata
SubjectVariablesData
SubjectVariablesDataVariables
TagString
TotalMassFloat
UsScanData
UsSessionData
ValidationData
VariableString
VoiceAudioScanData
VolumetricRegion
VolumetricRegionSubregions
WeightFloat
XNATNestedObjectMixin
XNATObjectMixin
XNATSubObjectMixin
Xa3DScanData
Xa3DSessionData
XaScanData
XaScanDataParameters
XaScanDataParametersFov
XaScanDataParametersPixelres
XaSessionData
XcScanData
XcSessionData
XcvScanData
XcvSessionData
current_session()