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NDI-matlab
NDI-matlab
- Home
- Installation
- Tutorials
  Tutorials
  - 1 The NDI model
    1 The NDI model
    
    1.1 Introduction
    
    1.2 Real world vocabulary
  - 2 Analzying your first electrophysiology experiment with NDI
    2 Analzying your first electrophysiology experiment with NDI
    
    2.1 Reading an example dataset
    
    2.2 Automating data reading with NDI
    
    2.3 Using apps to analyze data (example - spike sorting)
    
    2.4 Analyzing spiking responses and tuning curve properties
    
    2.5 Searching NDI databases
  - 3 Tutorials for new coders or new Matlab users
    3 Tutorials for new coders or new Matlab users
    
    3.1 Newbie version of your first electrophysiology experiment with NDI
  - 7 Writing your own apps and calculators
    7 Writing your own apps and calculators
    
    7.2 Writing short calculations
  - Planned
    Planned
    
    4. Case studies in reading data in NDI
    
    5. Making your own data pipeline in NDI
    
    6. Making your own analysis app that uses NDI
    
    7. Submitting your data to an archive
    
    8. Search and analyze NDI databases on the web
- Document reference
  Document reference
  - animalsubject
  - app
  - base
  - dataset_session_info
  - demoNDI
  - element
  - element_epoch
  - epochclocktimes
  - epochid
  - mock
  - oneepoch
  - projectvar
  - session
  - subject
  - subjectmeasurement
  - treatment
  - apps
    apps
    
    calculators
    calculators
    
    simple_calc
    
    tuningcurve_calc
    
    jrclust
    jrclust
    
    jrclust_clusters
    
    markgarbage
    markgarbage
    
    valid_interval
    
    spikeextractor
    spikeextractor
    
    spike_extraction_parameters
    
    spike_extraction_parameters_modification
    
    spikewaves
    
    spikesorter
    spikesorter
    
    sorting_parameters
    
    spike_clusters
    
    vhlab_voltage2firingrate
    vhlab_voltage2firingrate
    
    binnedspikeratevm
    
    vmneuralresponseresiduals
    
    vmspikefilteringparameters
    
    vmspikefit
    
    vmspikesummary
  - daq
    daq
    
    daqmetadatareader
    
    daqreader
    
    daqreader_ndr
    
    daqsystem
    
    filenavigator
    
    syncgraph
    
    syncrule
  - data
    data
    
    binaryseries_parameters
    
    fitcurve
    
    ngrid
  - ingestion
    ingestion
    
    daqmetadatareader_epochdata_ingested
    
    daqreader_epochdata_ingested
    
    daqreader_mfdaq_epochdata_ingested
    
    epochfiles_ingested
    
    metadata_editor
    
    syncrule_mapping
  - metadata
    metadata
    
    openminds
    
    openminds_element
    
    openminds_stimulus
    
    openminds_subject
  - neuron
    neuron
    
    neuron_extracellular
  - probe
    probe
    
    electrode_offset_voltage
    
    probe_location
  - stimulus
    stimulus
    
    control_stimulus_ids
    
    stimulus_bath
    
    stimulus_parameter
    
    stimulus_parameter_table
    
    stimulus_presentation
    
    stimulus_response
    
    stimulus_response_scalar
    
    stimulus_response_scalar_parameters
    
    stimulus_response_scalar_parameters_basic
    
    stimulus_tuningcurve
    
    vision
    vision
    
    oridir
    oridir
    
    orientation_direction_tuning
- Code reference
  Code reference
  - ndi_Init
  - ndi_install
  - ndi PACKAGE
    ndi PACKAGE
    
    ndi.app
    
    ndi.cache
    
    ndi.calculator
    
    ndi.database
    
    ndi.dataset
    
    ndi.document
    
    ndi.documentservice
    
    ndi.element
    
    ndi.epoch
    
    ndi.filesep
    
    ndi.ido
    
    ndi.neuron
    
    ndi.pipeline
    
    ndi.probe
    
    ndi.query
    
    ndi.session
    
    ndi.subject
    
    ndi.toolboxdir
    
    ndi.validate
    
    ndi.version
    
    app PACKAGE
    app PACKAGE
    
    ndi.app.appdoc
    
    ndi.app.markgarbage
    
    ndi.app.oridirtuning
    
    ndi.app.spikeextractor
    
    ndi.app.spikesorter
    
    stimulus PACKAGE
    stimulus PACKAGE
    
    ndi.app.stimulus.decoder
    
    ndi.app.stimulus.tuning_response
    
    calc PACKAGE
    calc PACKAGE
    
    example PACKAGE
    example PACKAGE
    
    ndi.calc.example.simple
    
    stimulus PACKAGE
    stimulus PACKAGE
    
    ndi.calc.stimulus.tuningcurve
    
    cloud PACKAGE
    cloud PACKAGE
    
    ndi.cloud.authenticate
    
    ndi.cloud.uilogin
    
    api PACKAGE
    api PACKAGE
    
    ndi.cloud.api.url
    
    auth PACKAGE
    auth PACKAGE
    
    ndi.cloud.api.auth.change_password
    
    ndi.cloud.api.auth.login
    
    ndi.cloud.api.auth.logout
    
    ndi.cloud.api.auth.resend_confirmation
    
    ndi.cloud.api.auth.reset_password
    
    ndi.cloud.api.auth.verify_user
    
    datasets PACKAGE
    datasets PACKAGE
    
    ndi.cloud.api.datasets.bulk_delete_documents
    
    ndi.cloud.api.datasets.create_dataset
    
    ndi.cloud.api.datasets.create_dataset_branch
    
    ndi.cloud.api.datasets.delete_dataset
    
    ndi.cloud.api.datasets.get_branches
    
    ndi.cloud.api.datasets.get_dataset
    
    ndi.cloud.api.datasets.get_file_collection_upload_url
    
    ndi.cloud.api.datasets.get_file_details
    
    ndi.cloud.api.datasets.get_file_upload_url
    
    ndi.cloud.api.datasets.get_published
    
    ndi.cloud.api.datasets.get_raw_file_upload_url
    
    ndi.cloud.api.datasets.get_unpublished
    
    ndi.cloud.api.datasets.list_datasets
    
    ndi.cloud.api.datasets.publish_dataset
    
    ndi.cloud.api.datasets.submit_dataset
    
    ndi.cloud.api.datasets.unpublish_dataset
    
    ndi.cloud.api.datasets.update_dataset
    
    documents PACKAGE
    documents PACKAGE
    
    ndi.cloud.api.documents.add_document
    
    ndi.cloud.api.documents.add_document_as_file
    
    ndi.cloud.api.documents.delete_document
    
    ndi.cloud.api.documents.get_bulk_download_url
    
    ndi.cloud.api.documents.get_bulk_upload_url
    
    ndi.cloud.api.documents.get_document
    
    ndi.cloud.api.documents.list_dataset_documents
    
    ndi.cloud.api.documents.update_document
    
    files PACKAGE
    files PACKAGE
    
    ndi.cloud.api.files.get_file_details
    
    ndi.cloud.api.files.get_file_upload_url
    
    ndi.cloud.api.files.get_raw_file_upload_url
    
    ndi.cloud.api.files.put_files
    
    users PACKAGE
    users PACKAGE
    
    ndi.cloud.api.users.create_user
    
    ndi.cloud.api.users.get_user
    
    download PACKAGE
    download PACKAGE
    
    ndi.cloud.download.dataset
    
    ndi.cloud.download.dataset_documents
    
    ndi.cloud.download.download_document_collection
    
    ndi.cloud.download.jsons2documents
    
    ndi.cloud.download.set_file_info
    
    internal PACKAGE
    internal PACKAGE
    
    ndi.cloud.internal.decode_jwt
    
    ndi.cloud.internal.get_active_token
    
    ndi.cloud.internal.get_token_expiration
    
    ndi.cloud.internal.get_uploaded_document_ids
    
    ndi.cloud.internal.get_uploaded_file_ids
    
    ndi.cloud.internal.get_weboptions_with_auth_header
    
    upload PACKAGE
    upload PACKAGE
    
    ndi.cloud.upload.create_cloud_metadata_struct
    
    ndi.cloud.upload.new_dataset
    
    ndi.cloud.upload.scan_for_upload
    
    ndi.cloud.upload.update_cloud_metadata
    
    ndi.cloud.upload.update_cloud_metadata_struct
    
    ndi.cloud.upload.upload_document_collection
    
    ndi.cloud.upload.upload_to_NDI_cloud
    
    ndi.cloud.upload.zip_documents_for_upload
    
    ndi.cloud.upload.zip_for_upload
    
    old FOLDER
    old FOLDER
    
    ndi.cloud.upload/old.test_upload
    
    ndi.cloud.upload/old.test_upload_old
    
    ndi.cloud.upload/old.upload_dataset_database
    
    ndi.cloud.upload/old.upload_to_NDI_cloud_bulk
    
    common PACKAGE
    common PACKAGE
    
    ndi.common.PathConstants
    
    ndi.common.assertDIDInstalled
    
    ndi.common.getCache
    
    ndi.common.getDatabaseHierarchy
    
    ndi.common.getLogger
    
    daq PACKAGE
    daq PACKAGE
    
    ndi.daq.daqsystemstring
    
    ndi.daq.metadatareader
    
    ndi.daq.reader
    
    ndi.daq.system
    
    metadatareader PACKAGE
    metadatareader PACKAGE
    
    ndi.daq.metadatareader.NewStimStims
    
    ndi.daq.metadatareader.NielsenLabStims
    
    reader PACKAGE
    reader PACKAGE
    
    ndi.daq.reader.mfdaq
    
    mfdaq PACKAGE
    mfdaq PACKAGE
    
    ndi.daq.reader.mfdaq.blackrock
    
    ndi.daq.reader.mfdaq.cedspike2
    
    ndi.daq.reader.mfdaq.intan
    
    ndi.daq.reader.mfdaq.ndr
    
    ndi.daq.reader.mfdaq.spikegadgets
    
    system PACKAGE
    system PACKAGE
    
    ndi.daq.system.mfdaq
    
    premature FOLDER
    premature FOLDER
    
    ndi.daq/premature.ndi_daqsystem_image
    
    ndi.daq/premature.ndi_daqsystem_image_tiffstack
    
    ndi.daq/premature.ndi_image
    
    ndi.daq/premature.ndi_image_tiffstack
    
    data PACKAGE
    data PACKAGE
    
    ndi.data.evaluate_fitcurve
    
    database PACKAGE
    database PACKAGE
    
    ndi.database.binarydoc
    
    ndi.database.ingestion_help
    
    app PACKAGE
    app PACKAGE
    
    dataset_viewer PACKAGE
    dataset_viewer PACKAGE
    
    utility PACKAGE
    utility PACKAGE
    
    ndi.database.app.dataset_viewer.utility.listLocalDatasets
    
    ndi.database.app.dataset_viewer.utility.listRemoteDatasets
    
    fun PACKAGE
    fun PACKAGE
    
    ndi.database.fun.copy_session_to_dataset
    
    ndi.database.fun.copydocfile2temp
    
    ndi.database.fun.createGenBankControlledVocabulary
    
    ndi.database.fun.createNIFbrainareas
    
    ndi.database.fun.create_new_database
    
    ndi.database.fun.database2json
    
    ndi.database.fun.databasehierarchyinit
    
    ndi.database.fun.dataset_metadata
    
    ndi.database.fun.docs2graph
    
    ndi.database.fun.docs_from_ids
    
    ndi.database.fun.extract_docs_files
    
    ndi.database.fun.find_ingested_docs
    
    ndi.database.fun.findallantecedents
    
    ndi.database.fun.findalldependencies
    
    ndi.database.fun.finddocs_elementEpochType
    
    ndi.database.fun.finddocs_missing_dependencies
    
    ndi.database.fun.lookup_uberon_term
    
    ndi.database.fun.ndi_document2ndi_object
    
    ndi.database.fun.ndicloud_ontology_lookup
    
    ndi.database.fun.openMINDSobj2ndi_document
    
    ndi.database.fun.openMINDSobj2struct
    
    ndi.database.fun.opendatabase
    
    ndi.database.fun.plotinteractivedocgraph
    
    ndi.database.fun.projectvardef
    
    ndi.database.fun.queryNCIm
    
    ndi.database.fun.readGenBankNames
    
    ndi.database.fun.readGenBankNodes
    
    ndi.database.fun.read_presentation_time_structure
    
    ndi.database.fun.readtablechar
    
    ndi.database.fun.uberon_ontology_lookup
    
    ndi.database.fun.write_presentation_time_structure
    
    ndi.database.fun.writetablechar
    
    implementations PACKAGE
    implementations PACKAGE
    
    binarydoc PACKAGE
    binarydoc PACKAGE
    
    ndi.database.implementations.binarydoc.matfid
    
    database PACKAGE
    database PACKAGE
    
    ndi.database.implementations.database.didsqlite
    
    ndi.database.implementations.database.matlabdumbjsondb
    
    ndi.database.implementations.database.matlabdumbjsondb2
    
    fun PACKAGE
    fun PACKAGE
    
    ndi.database.implementations.fun.doc2ingesteddbfilename
    
    ndi.database.implementations.fun.expell
    
    ndi.database.implementations.fun.expell_plan
    
    ndi.database.implementations.fun.ingest
    
    ndi.database.implementations.fun.ingest_plan
    
    internal PACKAGE
    internal PACKAGE
    
    ndi.database.internal.list_binary_files
    
    metadata PACKAGE
    metadata PACKAGE
    
    ndi.database.metadata.table2treatment
    
    metadata_app PACKAGE
    metadata_app PACKAGE
    
    checker PACKAGE
    checker PACKAGE
    
    ndi.database.metadata_app.checker.subject
    
    class PACKAGE
    class PACKAGE
    
    ndi.database.metadata_app.class.Affiliation
    
    ndi.database.metadata_app.class.AffiliationData
    
    ndi.database.metadata_app.class.AuthorData
    
    ndi.database.metadata_app.class.DatasetData
    
    ndi.database.metadata_app.class.DatasetVersionData
    
    ndi.database.metadata_app.class.DeviceType
    
    ndi.database.metadata_app.class.Electrode
    
    ndi.database.metadata_app.class.ElectrodeArray
    
    ndi.database.metadata_app.class.License
    
    ndi.database.metadata_app.class.MiscellaneousProbe
    
    ndi.database.metadata_app.class.Organization
    
    ndi.database.metadata_app.class.Pipette
    
    ndi.database.metadata_app.class.Probe
    
    ndi.database.metadata_app.class.ProbeData
    
    ndi.database.metadata_app.class.Species
    
    ndi.database.metadata_app.class.SpeciesData
    
    ndi.database.metadata_app.class.Strain
    
    ndi.database.metadata_app.class.Subject
    
    ndi.database.metadata_app.class.SubjectData
    
    ndi.database.metadata_app.class.test
    
    fun PACKAGE
    fun PACKAGE
    
    ndi.database.metadata_app.fun.SearchSpecies
    
    ndi.database.metadata_app.fun.checkValidRORID
    
    ndi.database.metadata_app.fun.expandDropDownItems
    
    ndi.database.metadata_app.fun.generateShortName
    
    ndi.database.metadata_app.fun.getCCByLicences
    
    ndi.database.metadata_app.fun.getOpenMindsInstances
    
    ndi.database.metadata_app.fun.getOpenmindsInstanceFile
    
    ndi.database.metadata_app.fun.getOrcId
    
    ndi.database.metadata_app.fun.getOrcIdSearchUrl
    
    ndi.database.metadata_app.fun.getPublicationTitleFromDoi
    
    ndi.database.metadata_app.fun.getPubmedIdFromDoi
    
    ndi.database.metadata_app.fun.getRequiredFields
    
    ndi.database.metadata_app.fun.getRorId
    
    ndi.database.metadata_app.fun.getRorIdSearchUrl
    
    ndi.database.metadata_app.fun.getSpeciesInfo
    
    ndi.database.metadata_app.fun.loadExperimentalApproach
    
    ndi.database.metadata_app.fun.loadInstancesToListBox
    
    ndi.database.metadata_app.fun.loadInstancesToTreeCheckbox
    
    ndi.database.metadata_app.fun.loadOpenMindsInstanceCatalog
    
    ndi.database.metadata_app.fun.loadProbes
    
    ndi.database.metadata_app.fun.loadSubjects
    
    ndi.database.metadata_app.fun.loadTechniquesEmployed
    
    ndi.database.metadata_app.fun.loadUnits
    
    ndi.database.metadata_app.fun.loadUserInstanceCatalog
    
    ndi.database.metadata_app.fun.loadUserInstances
    
    ndi.database.metadata_app.fun.mustBeValidDate
    
    ndi.database.metadata_app.fun.parseOpenMINDSAtID
    
    ndi.database.metadata_app.fun.readExistingMetadata
    
    ndi.database.metadata_app.fun.resolveRelatedPublication
    
    ndi.database.metadata_app.fun.saveUserInstances
    
    ndi.database.metadata_app.fun.save_dataset_docs
    
    ndi.database.metadata_app.fun.submit_dataset
    
    metadata_ds_core PACKAGE
    metadata_ds_core PACKAGE
    
    ndi.database.metadata_ds_core.Contents
    
    ndi.database.metadata_ds_core.check_metadata_cloud_inputs
    
    ndi.database.metadata_ds_core.check_metadata_inputs
    
    ndi.database.metadata_ds_core.convertDatasetInfoToDocument
    
    ndi.database.metadata_ds_core.convertDocumentToDatasetInfo
    
    ndi.database.metadata_ds_core.convertFormDataToDocuments
    
    ndi.database.metadata_ds_core.load_author_from_ndidocument
    
    ndi.database.metadata_ds_core.metadata_to_json
    
    ndi.database.metadata_ds_core.ndidataset2metadataeditorstruct
    
    ndi.database.metadata_ds_core.saveEditor2Doc
    
    dataset PACKAGE
    dataset PACKAGE
    
    ndi.dataset.dir
    
    docs PACKAGE
    docs PACKAGE
    
    ndi.docs.all_documents2markdown
    
    ndi.docs.build
    
    ndi.docs.calcbuild
    
    ndi.docs.concatenateFiles
    
    ndi.docs.document2markdown
    
    ndi.docs.schemastructure2docstructure
    
    element PACKAGE
    element PACKAGE
    
    ndi.element.downsample
    
    ndi.element.missingepochs
    
    ndi.element.oneepoch
    
    ndi.element.oneepoch_bkup
    
    ndi.element.timeseries
    
    epoch PACKAGE
    epoch PACKAGE
    
    ndi.epoch.epochprobemap
    
    ndi.epoch.epochprobemap_daqsystem
    
    ndi.epoch.epochrange
    
    ndi.epoch.epochset
    
    ndi.epoch.findepochnode
    
    epochset PACKAGE
    epochset PACKAGE
    
    ndi.epoch.epochset.param
    
    example PACKAGE
    example PACKAGE
    
    fun PACKAGE
    fun PACKAGE
    
    ndi.example.fun.element2spiketimes
    
    ndi.example.fun.find_epochids_with_temperature
    
    ndi.example.fun.getEarlyEyeOpening
    
    ndi.example.fun.get_unique_bath_components
    
    ndi.example.fun.mfdaqsysepoch2timetablestruct
    
    ndi.example.fun.probe2elements
    
    ndi.example.fun.probe2spiketimes
    
    tutorial PACKAGE
    tutorial PACKAGE
    
    ndi.example.tutorial.plottreeshrewdata
    
    ndi.example.tutorial.tutorial_02_01
    
    ndi.example.tutorial.tutorial_02_02
    
    ndi.example.tutorial.tutorial_02_03
    
    ndi.example.tutorial.tutorial_02_04
    
    ndi.example.tutorial.tutorial_02_05
    
    file PACKAGE
    file PACKAGE
    
    ndi.file.navigator
    
    ndi.file.pfilemirror
    
    ndi.file.temp_fid
    
    ndi.file.temp_name
    
    navigator PACKAGE
    navigator PACKAGE
    
    ndi.file.navigator.epochdir
    
    type PACKAGE
    type PACKAGE
    
    ndi.file.type.mfdaq_epoch_channel
    
    fun PACKAGE
    fun PACKAGE
    
    ndi.fun.assertAddonOnPath
    
    ndi.fun.channelname2prefixnumber
    
    ndi.fun.check_Matlab_toolboxes
    
    ndi.fun.console
    
    ndi.fun.convertoldnsd2ndi
    
    ndi.fun.debuglog
    
    ndi.fun.errlog
    
    ndi.fun.find_calc_directories
    
    ndi.fun.plot_extracellular_spikeshapes
    
    ndi.fun.pseudorandomint
    
    ndi.fun.run_Linux_checks
    
    ndi.fun.stimulustemporalfrequency
    
    ndi.fun.syslog
    
    ndi.fun.timestamp
    
    calc PACKAGE
    calc PACKAGE
    
    ndi.fun.calc.stimulus_tuningcurve_log
    
    plot PACKAGE
    plot PACKAGE
    
    ndi.fun.plot.multichan
    
    stimulus PACKAGE
    stimulus PACKAGE
    
    ndi.fun.stimulus.f0_f1_responses
    
    ndi.fun.stimulus.tuning_curve_to_response_type
    
    gui PACKAGE
    gui PACKAGE
    
    ndi.gui.Data
    
    ndi.gui.Icon
    
    ndi.gui.Lab
    
    ndi.gui.docViewer
    
    ndi.gui.gui
    
    ndi.gui.gui_v2
    
    component PACKAGE
    component PACKAGE
    
    ndi.gui.component.CommandWindowProgressMonitor
    
    ndi.gui.component.NDIProgressBar
    
    abstract PACKAGE
    abstract PACKAGE
    
    ndi.gui.component.abstract.ProgressMonitor
    
    internal PACKAGE
    internal PACKAGE
    
    ndi.gui.component.internal.AsynchProgressTracker
    
    ndi.gui.component.internal.ProgressTracker
    
    event PACKAGE
    event PACKAGE
    
    ndi.gui.component.internal.event.MessageUpdatedEventData
    
    ndi.gui.component.internal.event.ProgressUpdatedEventData
    
    utility PACKAGE
    utility PACKAGE
    
    ndi.gui.utility.centerFigure
    
    mock PACKAGE
    mock PACKAGE
    
    ndi.mock.ctest
    
    fun PACKAGE
    fun PACKAGE
    
    ndi.mock.fun.clear
    
    ndi.mock.fun.stimulus_presentation
    
    ndi.mock.fun.stimulus_response
    
    ndi.mock.fun.subject_stimulator_neuron
    
    probe PACKAGE
    probe PACKAGE
    
    ndi.probe.timeseries
    
    fun PACKAGE
    fun PACKAGE
    
    ndi.probe.fun.getProbeTypeMap
    
    ndi.probe.fun.initProbeTypeMap
    
    ndi.probe.fun.probestruct2probe
    
    timeseries PACKAGE
    timeseries PACKAGE
    
    ndi.probe.timeseries.mfdaq
    
    ndi.probe.timeseries.stimulator
    
    session PACKAGE
    session PACKAGE
    
    ndi.session.dir
    
    ndi.session.empty_id
    
    ndi.session.mock
    
    ndi.session.sessiontable
    
    setup PACKAGE
    setup PACKAGE
    
    ndi.setup.angeluccilab
    
    ndi.setup.dbkatzlab
    
    ndi.setup.lab
    
    ndi.setup.marderlab
    
    ndi.setup.vhlab
    
    ndi.setup.yangyangwang
    
    conv PACKAGE
    conv PACKAGE
    
    gluckman PACKAGE
    gluckman PACKAGE
    
    ndi.setup.conv.gluckman.binepochprobemap
    
    ndi.setup.conv.gluckman.channelname2probename
    
    ndi.setup.conv.gluckman.channelnames2daqsystemstrings
    
    marder PACKAGE
    marder PACKAGE
    
    ndi.setup.conv.marder.abf2probetable
    
    ndi.setup.conv.marder.abfepochprobemap
    
    ndi.setup.conv.marder.abfprobetable2probemap
    
    ndi.setup.conv.marder.channelname2probename
    
    ndi.setup.conv.marder.channelnames2daqsystemstrings
    
    ndi.setup.conv.marder.channelnametable2probename
    
    ndi.setup.conv.marder.demo
    
    ndi.setup.conv.marder.makeVoltageOffsets
    
    ndi.setup.conv.marder.makesubjects
    
    ndi.setup.conv.marder.marderbath
    
    ndi.setup.conv.marder.marderprobe2uberon
    
    ndi.setup.conv.marder.mixtureStr2mixtureTable
    
    ndi.setup.conv.marder.plot_epoch
    
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ndi.setup.daq.system.listDaqSystemNames

  listDaqSystemNames - List names of pre-configured DAQ systems for a lab

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