catpy package

Submodules

catpy.client module

class catpy.client.CatmaidClient(base_url, token=None, auth_name=None, auth_pass=None, project_id=None)

Bases: object

Python object handling authentication, request pooling etc. for requests made to a CATMAID server.

Methods

fetch(relative_url[, method, data, raw])	Interact with the CATMAID server in a manner very similar to the javascript CATMAID.fetch API.
from_json(path[, with_project_id])	Return a CatmaidClient instance with credentials matching those in a JSON file.
get(relative_url[, params, raw])	Get data from a running instance of CATMAID.
post(relative_url[, data, raw])	Post data to a running instance of CATMAID.
set_api_token(token)	Set CatmaidClient to use the given API token in place.
set_http_auth(username, password)	Set HTTP authorization for CatmaidClient in place.

fetch(relative_url, method='GET', data=None, raw=False)

Interact with the CATMAID server in a manner very similar to the javascript CATMAID.fetch API.

Parameters:

relative_url : str or tuple of str

URL to send the request to, relative to the base_url. If a tuple is passed, its elements will be joined with ‘/’.

method: {‘GET’, ‘POST’}, optional

HTTP method to use (the default is ‘GET’)

data: dict or str, optional

JSON-like key/value data to be included in the request as a payload (defaults to empty)

raw: bool, optional

Whether to return the response as a string (defaults to returning a dict)

Returns:

dict or str

Data returned from CATMAID: type depends on the ‘raw’ parameter.

classmethod from_json(path, with_project_id=True)

Return a CatmaidClient instance with credentials matching those in a JSON file. Should have the property base_url as a minimum.

If HTTP authentication is required, should have the properties auth_name and auth_pass.

If you intend to use an authorized CATMAID account (required for some endpoints), should have the property token.

Can optionally include the property project_id.

Parameters:

path : str

Path to the JSON credentials file

with_project_id : bool

Whether to look for the project_id field (it can be set later on the returned CatmaidClient instance)

Returns:

CatmaidClient

Instance of the API, authenticated with

get(relative_url, params=None, raw=False)

Get data from a running instance of CATMAID.

Parameters:

relative_url : str or tuple of str

URL to send the request to, relative to the base_url. If a tuple is passed, its elements will be joined with ‘/’.

params: dict or str, optional

JSON-like key/value data to be included in the get URL (defaults to empty)

raw: bool, optional

Whether to return the response as a string (defaults to returning a dict)

Returns:

dict or str

Data returned from CATMAID: type depends on the ‘raw’ parameter.

post(relative_url, data=None, raw=False)

Post data to a running instance of CATMAID.

Parameters:

relative_url : str or tuple of str

URL to send the request to, relative to the base_url. If a tuple is passed, its elements will be joined with ‘/’.

data: dict or str, optional

JSON-like key/value data to be included in the request as a payload (defaults to empty)

raw: bool, optional

Whether to return the response as a string (defaults to returning a dict)

Returns:

dict or str

Data returned from CATMAID: type depends on the ‘raw’ parameter.

set_api_token(token)

Set CatmaidClient to use the given API token in place.

Parameters:

token : str

API token associated with your CATMAID account

Returns:

CatmaidClient

Reference to the same, now-authenticated CatmaidClient instance

set_http_auth(username, password)

Set HTTP authorization for CatmaidClient in place.

Parameters:

username : str

HTTP authorization username

password : str

HTTP authorization password

Returns:

CatmaidClient

Reference to the same, now-authenticated CatmaidClient instance

class catpy.client.CoordinateTransformer(resolution=None, translation=None)

Bases: object

Methods

from_catmaid(catmaid_client, stack_id)	Return a CoordinateTransformer for a particular CATMAID stack.
project_to_stack(project_coords)	Take a point in project space and transform it into stack space.
project_to_stack_array(arr[, dims])	Take an array of points in project space and transform them into stack space.
project_to_stack_coord(dim, project_coord)
stack_to_project(stack_coords)	Take a point in stack space and transform it into project space.
stack_to_project_array(arr[, dims])	Take an array of points in stack space and transform them into project space.
stack_to_project_coord(dim, stack_coord)

classmethod from_catmaid(catmaid_client, stack_id)

Return a CoordinateTransformer for a particular CATMAID stack.

Parameters:

catmaid_client : CatmaidClient

Authenticated instance of CatmaidClient

stack_id : int

Returns:

CoordinateTransformer

project_to_stack(project_coords)

Take a point in project space and transform it into stack space.

Parameters:

project_coords : dict

x, y, and/or z coordinates in project / real space

Returns:

dict

coordinates transformed into stack / voxel space

project_to_stack_array(arr, dims='xyz')

Take an array of points in project space and transform them into stack space.

Parameters:

arr : array-like

M by N array containing M coordinates in project / real space in N dimensions

dims : str

Order of dimensions in columns, default ‘xyz’

Returns:

np.ndarray

M by N array containing M coordinates in stack / voxel space in N dimensions

project_to_stack_coord(dim, project_coord)

stack_to_project(stack_coords)

Take a point in stack space and transform it into project space.

Parameters:

stack_coords : dict

x, y, and/or z coordinates in stack / voxel space

Returns:

dict

coordinates transformed into project / real space

stack_to_project_array(arr, dims='xyz')

Take an array of points in stack space and transform them into project space.

Parameters:

arr : array-like

M by N array containing M coordinates in stack / voxel space in N dimensions

dims : array-like or str

Order of dimensions in columns, default (x, y, z)

Returns:

np.ndarray

M by N array containing M coordinates in project / real space in N dimensions

stack_to_project_coord(dim, stack_coord)

catpy.client.make_url(base_url, *args)

Given any number of URL components, join them as if they were a path regardless of trailing and prepending slashes

Examples

>>> make_url('google.com', 'mail')
'google.com/mail'

>>> make_url('google.com/', '/mail')
'google.com/mail'

Module contents