Reference documentation¶

The Interface class¶

class pyxnat.core.Interface(server=None, user=None, password=None, cachedir='/tmp', config=None, anonymous=False)¶

Main entry point to access a XNAT server.

>>> central = Interface(server='http://central.xnat.org:8080',
                        user='login',
                        password='pwd',
                        cachedir='/tmp'
                        )

Or with config file:

>>> central = Interface(config='/home/me/.xnat.cfg')

Or for interactive use:

>>> central = Interface('http://central.xnat.org')

Note

The interactive mode is activated whenever an argument within server, user or password is missing. In interactive mode pyxnat tries to check the validity of the connection parameters.

Or anonymously (unauthenticated):

>>> central = Interface('http://central.xnat.org', anonymous=True)

Attributes :

_mode: online | offline :

Online or offline mode

_memtimeout: float :

Lifespan of in-memory cache

load_config(location)¶

Loads a configuration file and replaces current connection parameters.

Note

This method raises NotImplementedError for an anonymous interface.

Parameters :

location: string :

Configuration file path.

save_config(location)¶

Saves current configuration - including password - in a file.

Warning

Since the password is saved as well, make sure the file is saved at a safe location with appropriate permissions.

Note

This method raises NotImplementedError for an anonymous interface.

Parameters :

location: string :

Destination config file.

The Select class¶

class pyxnat.core.select.Select(interface)¶

Data selection interface. Callable object that indicates the data to be returned to the user.

Examples

Select with a path:

>>> interface.select('/projects/myproj/subjects').get()

Select with a datatype:

>>> columns = ['xnat:subjectData/PROJECT',
               'xnat:subjectData/SUBJECT_ID'
               ]
>>> criteria = [('xnat:subjectData/SUBJECT_ID', 'LIKE', '*'),
                'AND'
                ]
>>> interface.select('xnat:subjectData', columns
            ).where(criteria)

__call__(datatype_or_path, columns=[])¶

Select clause to specify what type of data is to be returned.

Parameters :

datatype_or_path: string :

Can either be a resource path or a datatype:

when a path, REST resources are returned, the columns argument is useless.

when a datatype, a search Object is returned, the columns argument has to be specified.

columns: list :

List of fieldtypes e.g. xnat:subjectData/SUBJECT_ID Datatype and columns are used to specify the search table that has to be returned. Use the method where on the Search object to trigger a search on the database.

project(ID)¶

Access a particular project.

Parameters :

ID: string :

ID of the project.

projects(id_filter='*')¶

Returns the list of all visible projects for the server.

Parameters :

id_filter: string :

Name pattern to filter the returned projects.

The Inspect class¶

class pyxnat.core.help.Inspector(interface)¶

Database introspection interface.

assessor_types()¶: Returns the datatypes used at the assessor level in this database.

See also

Inspector.set_autolearn

assessor_values(experiment_type, project=None)¶

Look for the values at the assessor level for a given experiment type in the database.

Note

The experiment type should be one of Inspector.experiment_types()

Warning

Depending on the number of elements the operation may take a while.

Parameters :

datatype: string :

An experiment type.

project: string :

Optional. Restrict operation to a project.

datatypes(pattern='*', fields_pattern=None)¶

Discovers the datatypes and datafields of the database.

Parameters :

pattern: string :

Pattern for the datatype. May include wildcards.

fields_pattern: string :

Pattern for the datafields – may include wildcards.

If specified, datafields will be returned instead of datatypes.

Returns :

list : datatypes or datafields depending on the argument usage.

experiment_types()¶: Returns the datatypes used at the experiment level in this database.

See also

Inspector.set_autolearn

experiment_values(datatype, project=None)¶

Look for the values a the experiment level for a given datatype in the database.

Note

The datatype should be one of Inspector.experiment_types()

Parameters :

datatype: string :

An experiment type.

project: string :

Optional. Restrict operation to a project.

project: string :

Optional. Restrict operation to a project.

field_values(field_name)¶: Look for the values a specific datafield takes in the database.

project_values()¶: Look for the values a the project level in the database.

Note

Is equivalent to interface.select.projects().get()

reconstruction_types()¶: Returns the datatypes used at the reconstruction level in this database.

See also

Inspector.set_autolearn

reconstruction_values(experiment_type, project=None)¶

Look for the values at the reconstruction level for a given experiment type in the database.

Note

The experiment type should be one of Inspector.experiment_types()

Warning

Depending on the number of elements the operation may take a while.

Parameters :

datatype: string :

An experiment type.

project: string :

Optional. Restrict operation to a project.

scan_types()¶: Returns the datatypes used at the scan level in this database.

See also

Inspector.set_autolearn

scan_values(experiment_type, project=None)¶

Look for the values at the scan level for a given experiment type in the database.

Note

The experiment type should be one of Inspector.experiment_types()

Warning

Depending on the number of elements the operation may take a while.

Parameters :

datatype: string :

An experiment type.

project: string :

Optional. Restrict operation to a project.

set_autolearn(auto=None, tick=None)¶

Once in a while queries will persist additional information on the server. This information is available through the following methods of this class:

experiment_types

assessor_types

scan_types

reconstruction_types

It is also transparently used in insert operations.

Parameters :

auto: boolean :

True to enable auto learn. False to disable.

tick: int :

Every ‘tick’ seconds, if a query is issued, additional information will be persisted.

See also

EObject.insert

structure()¶: Displays the keywords structure used in XNAT REST API.

subject_values(project=None)¶: Look for the values a the subject level in the database.

Note

Is equivalent to interface.select(‘//subjects’).get()

The SearchManager class¶

class pyxnat.core.search.SearchManager(interface)¶

Search interface. Handles operations to save and get back searches on the server.

Examples

>>> row = 'xnat:subjectData'
>>> columns = ['xnat:subjectData/PROJECT',
               'xnat:subjectData/SUBJECT_ID'
               ]
>>> criteria = [('xnat:subjectData/SUBJECT_ID', 'LIKE', '*'),
                'AND'
                ]
>>> interface.manage.search.save('mysearch', row, columns,
                                 criteria, sharing='public',
                                 description='my first search'
                                 )

delete(name)¶: Removes the search from the server.

delete_template(name)¶: Deletes a search template.

get(name, out_format='results')¶

Returns the results of the query saved on the XNAT server or the query itself to know what it does.

Parameters :

name: string :

Name of the saved search. An exception is raised if the name does not exist.

out_format: string :

Can take the following values:

results to download the results of the search

xml to download the XML document defining the search

query to get the pyxnat representation of the search

get_template(name, as_xml=False)¶

Get a saved template, either as an xml document, or as a pyxnat representation, with the keys to be used in the template between the parentheses in %()s.

Parameters :

name: str :

Name under which the template is saved

as_xml: boolean :

If True returns an XML document, else return a list of constraints. Defaults to False.

save(name, row, columns, constraints, sharing='private', description='')¶

Saves a query on the XNAT server.

Parameters :

name: string :

Name of the query displayed on the Web Interface and used to get back the results.

row: string :

Datatype from Interface.inspect.datatypes(). Usually xnat:subjectData

columns: list :

List of data fields from Interface.inspect.datatypes(‘*’, ‘*’)

constraints: list :

See also: Search.where()

sharing: string | list :

Define by whom the query is visible. If sharing is a string it may be either private or public. Otherwise a list of valid logins for the XNAT server from Interface.users().

See also

Search.where

save_template(name, row=None, columns=[], constraints=[], sharing='private', description='')¶

Define and save a search template. Same as the save method, but the values in the constraints are used as keywords for value replacement when using the template.

Parameters :

name: string :

Name under which the template is save in XNAT. A ‘template_‘ is prepended to the name so that it appear clearly as a template on the web interface.

row: string :

Datatype from Interface.inspect.datatypes(). Usually xnat:subjectData

columns: list :

List of data fields from Interface.inspect.datatypes(‘*’, ‘*’)

constraints: list :

See also: Search.where(), values are keywords for the template

sharing: string | list :

Define by whom the query is visible. If sharing is a string it may be either private or public. Otherwise a list of valid logins for the XNAT server from Interface.users().

saved(with_description=False)¶: Returns the names of accessible saved search on the server.

saved_templates(with_description=False)¶: Returns the names of accessible saved search templates on the server.

use_template(name, values)¶

Parameters :

name: string :

Name of the template.

values: dict :

Values to put in the template, get the valid keys using the get_template method.

Examples

>>> interface.manage.search.use_template(name,
              {'subject_id':'ID',
               'age':'32'
               })

The Search class¶

class pyxnat.core.search.Search(row, columns, interface)¶

Define constraints to make a complex search on the database.

This Search is available at different places throughout the API:

>>> interface.select(DATA_SELECTION).where(QUERY)
>>> interface.manage.search.save('name', TABLE_DEFINITION, QUERY)

Examples

>>> query = [('xnat:subjectData/SUBJECT_ID', 'LIKE', '%'),
             ('xnat:projectData/ID', '=', 'my_project'),
             [('xnat:subjectData/AGE', '>', '14'),
               'AND'
              ],
             'OR'
            ]

where(constraints=None, template=None, query=None)¶

Triggers the search.

Parameters :

contraints: list :

A query is an unordered list that contains

1 or more constraints

0 or more sub-queries (lists as this one)

1 comparison method between the constraints

(‘AND’ or ‘OR’)

A constraint is an ordered tuple that contains

1 valid searchable_type/searchable_field

1 operator among ‘=’, ‘<’, ‘>’, ‘<=’, ‘>=’, ‘LIKE’

Returns :

results: JsonTable object :

An table-like object containing the results. It is basically a list of dictionaries that has additional helper methods.

The EObject class¶

class pyxnat.core.resources.EObject(uri, interface)¶

Generic Object for an element URI.

children(show_names=True)¶

Returns the children levels of this element.

Parameters :

show_name: boolean :

If True returns a list of strings. If False returns a collection object referencing all child objects of this elements.

Examples

>>> subject_object.children()
['experiments', 'resources']
>>> subject_object.children(False)
<Collection Object> 170976556

create(**params)¶

Creates the element if it does not exists. Any non-existing ancestor will be created as well.

Warning

An element resource both have an ID and a label that can be used to access it. At the moment, XNAT REST API defines the label when creating an element, but not the ID, which is generated. It means that the name given to a resource may not appear when listing the resources because the IDs will appear, not the labels.

Note

To set up additional variables for the element at its creation it is possible to use shortcuts defined in the XNAT REST documentation or xpath in the schema:

element.create(ID=’theid’)

subject.create(**{‘xnat:subjectData/ID’:’theid’})

Parameters :

params: keywords :

Specify the datatype of the element resource and of any ancestor that may need to be created. The keywords correspond to the levels in the REST hierarchy, see Interface.inspect.architecture()

If an element is created with no specified type:

if its name matches a naming convention, this type will be used

else a default type is defined in the schema module

To give the ID the same value as the label use use_label=True e.g element.create(use_label=True)

See also

EObject.id, EObject.label, EObject.datatype

Examples

>>> interface.select('/project/PROJECT/subject'
                     '/SUBJECT/experiment/EXP/scan/SCAN'
            ).create(experiments='xnat:mrSessionData', 
                     scans='xnat:mrScanData'
                     )

datatype()¶

Returns the type defined in the XNAT schema for this element resource.

EObject possible xsi types

Project xnat:projectData

Subject xnat:subjectData

Experiment xnat:mrSessionData xnat:petSessionData

delete(delete_files=True)¶

Deletes an element resource.

Parameters :

delete_files: boolean :

Tells if files attached to the element resources are removed as well from the server filesystem.

exists(consistent=False)¶: Test whether an element resource exists.

get()¶: Retrieves the XML document corresponding to this element.

id()¶: Returns the element resource id.

insert(**params)¶

Creates the element if it does not exists. Any non-existing ancestor will be created as well.

Warning

An element resource both have an ID and a label that can be used to access it. At the moment, XNAT REST API defines the label when creating an element, but not the ID, which is generated. It means that the name given to a resource may not appear when listing the resources because the IDs will appear, not the labels.

Note

To set up additional variables for the element at its creation it is possible to use shortcuts defined in the XNAT REST documentation or xpath in the schema:

element.create(ID=’theid’)

subject.create(**{‘xnat:subjectData/ID’:’theid’})

Parameters :

params: keywords :

Specify the datatype of the element resource and of any ancestor that may need to be created. The keywords correspond to the levels in the REST hierarchy, see Interface.inspect.architecture()

If an element is created with no specified type:

if its name matches a naming convention, this type will be used

else a default type is defined in the schema module

To give the ID the same value as the label use use_label=True e.g element.create(use_label=True)

See also

EObject.id, EObject.label, EObject.datatype

Examples

>>> interface.select('/project/PROJECT/subject'
                     '/SUBJECT/experiment/EXP/scan/SCAN'
            ).create(experiments='xnat:mrSessionData', 
                     scans='xnat:mrScanData'
                     )

label()¶: Returns the element resource label.

tag(name)¶: Tag the element.

untag(name)¶: Remove a tag for the element.

The CObject class¶

class pyxnat.core.resources.CObject(cbase, interface, pattern='*', nested=None, id_header='ID', columns=[], filters={})¶

Generic Object for a collection resource.

A collection resource is a list of element resources. There is however several ways to obtain such a list:

a collection URI e.g. /REST/projects

a list of element URIs

a list of collections

e.g. /REST/projects/ONE/subjects AND /REST/projects/TWO/subjects

a list of element objects

a list a collection objects

Collections objects built in different ways share the same behavior:

they behave as iterators, which enables a lazy access to the data
they always yield EObjects
they can be nested with any other collection

Examples

No access to the data:

>>> interface.select.projects()
<Collection Object> 173667084

Lazy access to the data:

>>> for project in interface.select.projects():
>>>     print project

Nesting:

>>> for subject in interface.select.projects().subjects():
>>>     print subject

fetchall(*args)¶

Returns every element.

Warning

If a collection needs to issue thousands of queries it may be better to access the resources within a for-loop.

Parameters :

args: strings :

Specify the information to return for the elements within ID, label and Object.

Any combination of ID, label and obj is valid, if more than one is given, a list of tuple is returned instead of a list.

fetchone()¶: Returns the first element of the collection.

first()¶: Returns the first element of the collection.

get(*args)¶

Returns every element.

Warning

If a collection needs to issue thousands of queries it may be better to access the resources within a for-loop.

Parameters :

args: strings :

Specify the information to return for the elements within ID, label and Object.

Any combination of ID, label and obj is valid, if more than one is given, a list of tuple is returned instead of a list.

tag(name)¶: Tag the collection.

untag(name)¶: Remove the tag from the collection.

where(constraints=None, template=None, query=None)¶

Only the element objects whose subject that are matching the constraints will be returned. It means that it is not possible to use this method on an element that is not linked to a subject, such as a project.

See also

search.Search

Examples

The where clause should be on the first select:

>>> for experiment in interface.select('//experiments'
         ).where([('atest/FIELD', '=', 'value'), 'AND']):
>>>      print experiment

Do NOT do this:

>>> for experiment in interface.select('//experiments'):
        for assessor in experiment.assessors(
            ).where([('atest/FIELD', '=', 'value'), 'AND']):
>>>         print assessor

Or this:

>>> for project in interface.select('//projects'
        ).where([('atest/FIELD', '=', 'value'), 'AND']):
>>>     print project

The Project class¶

class pyxnat.core.resources.Project(uri, interface)¶

accessibility()¶: Gets project accessibility.

add_custom_variables(custom_variables, allow_data_deletion=False)¶

Adds a custom variable to a specified group

Parameters :

custom_variables: a dictionary :

allow_data_deletion : a boolean

Examples

>>> variables = {'Subjects' : {'newgroup' : {'foo' : 'string', 'bar' : 'int'}}}
>>> project.add_custom_variables(variables)

add_user(login, role='member')¶

Adds a user to the project. The user must already exist on the server.

Parameters :

login: string :

Valid username for the XNAT database.

role: owner | member | collaborator :

The user level for this project:

owner: read and write access, as well as administrative privileges such as adding and removing users.

member: read access and can create new resources but not remove them.

collaborator: read access only.

collaborators()¶: Gets collaborator of this project.

current_arc()¶: Gets project current archive folder on the server.

get_custom_variables()¶

Retrieves custom variables as a dictionary

It has the format {studyProtocol: { setname : {field: type, ...}}}

last_modified()¶

Gets the last modified dates for all the project subjects.

If any element related to a subject changes, experiment, variable, scan, image etc... the date will be changed.

members()¶: Gets members of this project.

owners()¶: Gets owners of this project.

prearchive_code()¶: Gets project prearchive code.

quarantine_code()¶: Gets project quarantine code.

remove_user(login)¶

Removes a user from the project.

Parameters :

login: string :

Valid username for the XNAT database.

set_accessibility(accessibility='protected')¶

Sets project accessibility.

Note

Write access is given or not by the user level for a specific project.

Parameters :

accessibility: public | protected | private :

Sets the project accessibility:

public: the project is visible and provides read access for anyone.

protected: the project is visible by anyone but the data is accessible for allowed users only.

private: the project is visible by allowed users only.

set_prearchive_code(code)¶

Sets project prearchive code.

Parameters :	code: 0 to 4 :

set_quarantine_code(code)¶

Sets project quarantine code.

Parameters :	code: 0 to 1 :

set_subfolder_in_current_arc(subfolder)¶: Changes project current archive subfolder on the server.

user_role(login)¶

Gets the user level of the user for this project.

Parameters :

login: string :

A user of the project.

Returns :

string : owner | member | collaborator

users()¶: Gets all registered users for this project.

The File class¶

class pyxnat.core.resources.File(uri, interface)¶

EObject for files stored in XNAT.

attributes()¶

Files attributes include:

URI
Name
Size in bytes
path (relative to the parent resource)
file_tags
file_format
file_content

Returns :	dict : a dictionnary with the file attributes

content()¶: Gets the file content description.

create(src, format='U', content='U', tags='U', **datatypes)¶

Uploads a file to XNAT.

Parameters :

src: string :

Location of the local file to upload or the actual content to upload.

format: string :

Optional parameter to specify the file format. Defaults to ‘U’.

content: string :

Optional parameter to specify the file content. Defaults to ‘U’.

tags: string :

Optional parameter to specify tags for the file. Defaults to ‘U’.

delete()¶: Deletes the file on the server.

format()¶: Gets the file format.

get(dest=None, force_default=False)¶

Downloads the file to the cache directory.

Note

The default cache path is computed like this: path_to_cache/md5(uri + query_string)_filename

Parameters :

dest: string | None :

If None a default path in the cache folder is automatically computed.

Else the file is downloaded at the requested location.

force_default: boolean :

Has no effect if the file is downloaded for the first time

If the file was previously download with a custom path, calling get() will remember the custom location unless:

another custom location is set in dest

force_default is set to True and the file will be moved to the cache

Returns :

string : the file location.

get_copy(dest=None)¶

Downloads the file to the cache directory but creates a copy at the specified location.

Parameters :

dest: string | None :

file path for the copy

if None a copy is created at a default location based on the file URI on the server

Returns :

string : the copy location.

insert(src, format='U', content='U', tags='U', **datatypes)¶

Uploads a file to XNAT.

Parameters :

src: string :

Location of the local file to upload or the actual content to upload.

format: string :

Optional parameter to specify the file format. Defaults to ‘U’.

content: string :

Optional parameter to specify the file content. Defaults to ‘U’.

tags: string :

Optional parameter to specify tags for the file. Defaults to ‘U’.

labels()¶: Gets the file labels.

last_modified()¶: Gets the file last-modified date.

put(src, format='U', content='U', tags='U', **datatypes)¶

Uploads a file to XNAT.

Parameters :

src: string :

Location of the local file to upload or the actual content to upload.

format: string :

Optional parameter to specify the file format. Defaults to ‘U’.

content: string :

Optional parameter to specify the file content. Defaults to ‘U’.

tags: string :

Optional parameter to specify tags for the file. Defaults to ‘U’.

size()¶: Gets the file size.

The Attributes class¶

class pyxnat.core.attributes.EAttrs(eobj)¶

Accessor class to resource fields.

Help to retrieve the attributes paths relevant to this element::

>>> subject.attrs()
['xnat:subjectData/sharing', 
 'xnat:subjectData/sharing/share',
 'xnat:subjectData/resources',
 ...
 'xnat:subjectData/experiments/experiment'
 ]

All paths are not valid but they give an indication of what is available. To retrieve the paths, the corresponding schemas must be downloaded first through the schema management interface in order to be parsed:

>>> interface.manage.schemas.add('xnat.xsd')
>>> interface.manage.schemas.add('myschema/myschema.xsd')

get(path)¶

Get an attribute value.

Note

The value is always returned in a Python string. It must be explicitly casted or transformed if needed.

Parameters :

path: string :

The xpath of the attribute relative to the element.

Returns :

A string containing the value. :

mget(paths)¶

Set multiple attributes at once.

It is more efficient to use this method instead of multiple times the get() method when getting more than one attribute because only a single HTTP call is issued to the server.

Parameters :

paths: list :

List of attributes’ paths.

Returns :

list: ordered list of values (in the order of the :

requested paths) :

mset(dict_attrs)¶

Set multiple attributes at once.

It is more efficient to use this method instead of multiple times the set() method when setting more than one attribute because only a single HTTP call is issued to the server.

Parameters :

dict_attrs: dict :

The dict of key values to set. It follows the same principles as the single set() method.

set(path, value)¶

Set an attribute.

Parameters :

path: string :

The xpath of the attribute relative to the element.

value: string :

The attribute’s value. Note that the python type is always a string but the content of the value must match what is defined in the schema.

e.g. an element defined as a float in the schema must be given a string containing a number, a valid date must follow the ISO 8601 which is the standard representation for dates and times established by the W3C.

The Provenance class¶

class pyxnat.core.provenance.Provenance(eobject)¶

Class to annotate processed data with provenance information. The following parameters are available:

program

program_version

program_arguments

timestamp

cvs

user

machine

platform

platform_version

compiler

compiler_version

Examples

>>> prov = {'program':'young',
            'timestamp':'2011-03-01T12:01:01.897987', 
            'user':'angus', 
            'machine':'war', 
            'platform':'linux',
            }
>>> element.provenance.set(prov)
>>> element.provenance.get()
>>> element.delete()

delete()¶: Removes the provenance attached to this object.

Warning

doesn’t work because of a bug with the allowDataDeletion flag in XNAT

get()¶

Gets all the provenance information for that object.

Returns :	A list of dicts. :

set(process_steps, overwrite=False)¶

Set provenance information for the data within this element.

Note

If some required parameters are not provided, theses parameters will be extracted from the current machine and set automatically. Those parameters are:

machine

platform

timestamp

user

Warning

overwrite option doesn’t work because of a bug with the allowDataDeletion flag in XNAT

Parameters :

process_steps: list or dict :

dict or list of dicts to define the processing steps of the data. The minimum set of information to give is: program, timestamp, user, machine and platform. More keywords in the class documentation.

overwrite: boolean :

If False the process_steps are added to the existing ones. Else the processing steps overwrite any existing provenance.

The Users class¶

class pyxnat.core.users.Users(interface)¶

Database user management interface. It is used to retrieve information on users registered on a server.

Note

At the moment user creation and deletion is not supported through the REST API but it will be at some point.

See also

Project.users, Project.add_user, Project.remove_user

Examples

>>> interface.manage.users()
['list_of_users']
>>> interface.manage.users.firstname('nosetests')
'nose'

email(login)¶: Returns the email of the user.

firstname(login)¶: Returns the firstname of the user.

id(login)¶: Returns the id of the user.

lastname(login)¶: Returns the lastname of the user.

resources()¶: Returns the resources of the user.

The Inspector class¶

class pyxnat.core.help.Inspector(interface)

Database introspection interface.

assessor_types(): Returns the datatypes used at the assessor level in this database.

See also

Inspector.set_autolearn

assessor_values(experiment_type, project=None)

Look for the values at the assessor level for a given experiment type in the database.

Note

The experiment type should be one of Inspector.experiment_types()

Warning

Depending on the number of elements the operation may take a while.

Parameters :

datatype: string :

An experiment type.

project: string :

Optional. Restrict operation to a project.

datatypes(pattern='*', fields_pattern=None)

Discovers the datatypes and datafields of the database.

Parameters :

pattern: string :

Pattern for the datatype. May include wildcards.

fields_pattern: string :

Pattern for the datafields – may include wildcards.

If specified, datafields will be returned instead of datatypes.

Returns :

list : datatypes or datafields depending on the argument usage.

experiment_types(): Returns the datatypes used at the experiment level in this database.

See also

Inspector.set_autolearn

experiment_values(datatype, project=None)

Look for the values a the experiment level for a given datatype in the database.

Note

The datatype should be one of Inspector.experiment_types()

Parameters :

datatype: string :

An experiment type.

project: string :

Optional. Restrict operation to a project.

project: string :

Optional. Restrict operation to a project.

field_values(field_name): Look for the values a specific datafield takes in the database.

project_values(): Look for the values a the project level in the database.

Note

Is equivalent to interface.select.projects().get()

reconstruction_types(): Returns the datatypes used at the reconstruction level in this database.

See also

Inspector.set_autolearn

reconstruction_values(experiment_type, project=None)

Look for the values at the reconstruction level for a given experiment type in the database.

Note

The experiment type should be one of Inspector.experiment_types()

Warning

Depending on the number of elements the operation may take a while.

Parameters :

datatype: string :

An experiment type.

project: string :

Optional. Restrict operation to a project.

scan_types(): Returns the datatypes used at the scan level in this database.

See also

Inspector.set_autolearn

scan_values(experiment_type, project=None)

Look for the values at the scan level for a given experiment type in the database.

Note

The experiment type should be one of Inspector.experiment_types()

Warning

Depending on the number of elements the operation may take a while.

Parameters :

datatype: string :

An experiment type.

project: string :

Optional. Restrict operation to a project.

set_autolearn(auto=None, tick=None)

Once in a while queries will persist additional information on the server. This information is available through the following methods of this class:

experiment_types

assessor_types

scan_types

reconstruction_types

It is also transparently used in insert operations.

Parameters :

auto: boolean :

True to enable auto learn. False to disable.

tick: int :

Every ‘tick’ seconds, if a query is issued, additional information will be persisted.

See also

EObject.insert

structure(): Displays the keywords structure used in XNAT REST API.

subject_values(project=None): Look for the values a the subject level in the database.

Note

Is equivalent to interface.select(‘//subjects’).get()

The CacheManager class¶

class pyxnat.core.cache.CacheManager(interface)¶

Management interface for the cache.

It provides a few methods to::

evaluate the size a the cache
check if there is space left on the disk
clear the cache
define cache usage parameters

available_disk(path=None, unit='bytes')¶: Available disk on partition. Default location is cache folder.

clear()¶: Clears all files tracked by pyxnat.

disk_ready(path=None, ready_ratio=90.0)¶: Checks the status of the disk. Basically if there is enough space left. The default location is cache dir.

set_usage(mode=None, expiration=1.0)¶

Customize cache usage.

Parameters :

mode: string :

‘online’ or ‘offline’:

online will always query the server to have up to date data.

offline will only try to query the server if the data is not cached.

expiration: float :

Relevant only to online mode. The cache has an expiration mechanism. If two queries on the same resource are issued under the specified value, the cache will be used and the server will not be requested.

size(unit='bytes')¶

Returns the amount of space taken by the cache.

Parameters :

unit: str :

unit in which to return the size can be bytes (default), mega or giga

Returns :

size: float :

total_disk(path=None, unit='bytes')¶: Total disk on partition. Default location is cache folder.

used_disk(path=None, unit='bytes')¶: Used disk on partition. Default location is cache folder.

The SchemaManager class¶

class pyxnat.core.manage.SchemaManager(interface)¶

Management interface for XNAT schemas.

The aim is to provide a minimal set of functionalities to parse and look at XNAT schemas.

add(url)¶

Loads an additional schema.

Parameters :

url: str :

url of the schema relative to the server.

e.g. for http://central.xnat.org/schemas/xnat/xnat.xsd give schemas/xnat/xnat.xsd or even only xnat.xsd

remove(name)¶: Removes a schema.

Reference documentation¶

The Interface class¶

The Select class¶

The Inspect class¶

The SearchManager class¶

The Search class¶

The EObject class¶

The CObject class¶

The Project class¶

The File class¶

The Attributes class¶

The Provenance class¶

The Users class¶

The Inspector class¶

The CacheManager class¶

The SchemaManager class¶

Table Of Contents

This Page

EObject	possible xsi types
Project	xnat:projectData
Subject	xnat:subjectData
Experiment	xnat:mrSessionData xnat:petSessionData

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Reference documentation¶

The Interface class¶

The Select class¶

The Inspect class¶

The SearchManager class¶

The Search class¶

The EObject class¶

The CObject class¶

The Project class¶

The File class¶

The Attributes class¶

The Provenance class¶

The Users class¶

The Inspector class¶

The CacheManager class¶

The SchemaManager class¶

Table Of Contents

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