camacq package

Control microscope through client server program.

Subpackages

Submodules

camacq.bootstrap module

Configure and set up control center.

async camacq.bootstrap.setup_dict(center, config)

Set up control center from config dict.

Parameters:

config (dict) – The config dict.

Returns:

Return the Center instance.

Return type:

Center instance

async camacq.bootstrap.setup_file(config_file, cmd_args)

Set up control center from config file and command line args.

Parameters:

  • config_file (str) – The path to the configuration YAML file.

  • cmd_args (dict) – The dict with the command line arguments.

Returns:

Return the Center instance.

Return type:

Center instance

camacq.config module

Handle the config file.

camacq.config.create_default_config(config_dir)

Create a default config file in given configuration directory.

Parameters:

config_dir (pathlib.Path) – The path to the configuration directory.

Returns:

Return path to new configuration file if success, None if failed.

Return type:

pathlib.Path

camacq.config.ensure_config_exists(config_dir)

Ensure configuration file exists in the configuration directory.

Create a default configuration file if needed.

Parameters:

config_dir (pathlib.Path) – The path to the configuration directory.

Returns:

Return path to the configuration file.

Return type:

pathlib.Path

camacq.config.find_config_file(config_dir)

Find the configuration file in the configuration directory.

Parameters:

config_dir (pathlib.Path) – The path to the configuration directory.

Returns:

Return path to the configuration file if found, None if not found.

Return type:

pathlib.Path

camacq.config.get_default_config_dir()

Get the default configuration directory based on OS.

Returns:

Return the path to the configuration directory.

Return type:

str

camacq.config.load_config_file(path)

Parse a YAML configuration file.

Parameters:

path (pathlib.Path) – The path to the configuration YAML file.

Returns:

Return a dict with the configuration contents.

Return type:

dict

camacq.const module

Store common constants.

camacq.control module

Control the microscope.

class camacq.control.Action(action_type, action_id, func, schema)

Bases: object

Represent an action.

class camacq.control.ActionType

Bases: dotdict

Represent an action type.

clear() → None.  Remove all items from D.
copy() → a shallow copy of D
fromkeys(value=None, /)

Create a new dictionary with keys from iterable and values set to value.

get(key, default=None, /)

Return the value for key if key is in the dictionary, else default.

items() → a set-like object providing a view on D's items
keys() → a set-like object providing a view on D's keys
pop(k[, d]) → v, remove specified key and return the corresponding value.

If key is not found, d is returned if given, otherwise KeyError is raised

popitem()

Remove and return a (key, value) pair as a 2-tuple.

Pairs are returned in LIFO (last-in, first-out) order. Raises KeyError if the dict is empty.

setdefault(key, default=None, /)

Insert key with a value of default if key is not in the dictionary.

Return the value for key if key is in the dictionary, else default.

update([E, ]**F) → None.  Update D from dict/iterable E and F.

If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]

values() → an object providing a view on D's values
class camacq.control.ActionsRegistry(center)

Bases: object

Manage all registered actions.

property actions

Return dict of ActionTypes with all registered actions.

Type:

dict

async call(action_type, action_id, **kwargs)

Call an action with optional kwargs.

Parameters:

  • action_type (str) – The name of the module where the action is registered.

  • action_id (str) – The id of the action to call.

  • **kwargs – Arbitrary keyword arguments. These will be passed to the action function when an action is called.

register(action_type, action_id, action_func, schema)

Register an action.

Register actions per module.

Parameters:

  • action_type (str) – The name of the action_type to register the action under.

  • action_id (str) – The id of the action to register.

  • action_func (voluptuous schema) – The function that should be called for the action.

  • action_func – The voluptuous schema that should validate the parameters of the action call.

class camacq.control.CamAcqStartEvent(data=None)

Bases: Event

An event fired when camacq has started.

data
event_type = 'camacq_start_event'
class camacq.control.CamAcqStopEvent(data=None)

Bases: Event

An event fired when camacq is about to stop.

data
event_type = 'camacq_stop_event'
property exit_code

Return the plate instance of the event.

Type:

int

class camacq.control.Center(loop=None)

Bases: object

Represent a control center for the microscope.

Parameters:

loop (asyncio.EventLoop) – The event loop.

loop

Return the event loop.

Type:

asyncio.EventLoop

bus

Return the EventBus instance.

Type:

EventBus instance

samples

Return the Samples instance that holds all the Sample instances.

Type:

Samples instance

actions

Return the ActionsRegistry instance.

Type:

ActionsRegistry instance

data

Return dict that stores data from other modules than control.

Type:

dict

add_executor_job(func, *args)

Schedule a function to be run in the thread pool.

Return a task.

create_task(coro)

Schedule a coroutine on the event loop.

Return a task.

async end(code)

Prepare app for exit.

Parameters:

code (int) – Exit code to return when the app exits.

async start()

Start the app.

async wait_for()

Wait for all pending tasks.

camacq.control.loop_exception_handler(loop, context)

Handle exceptions inside the event loop.

camacq.event module

Hold events.

class camacq.event.Event(data=None)

Bases: object

A base event.

Parameters:

data (dict) – The data of the event.

data

Return the data of the event.

Type:

dict

data
event_type = 'base_event'
class camacq.event.EventBus(center)

Bases: object

Representation of an eventbus.

Parameters:

center (Center instance) – The Center instance.

property event_types

Return all registered event types.

Type:

list

async notify(event)

Notify handlers that an event has fired.

Parameters:

event (Event instance) – An instance of Event or an instance of subclass of Event.

register(event_type, handler)

Register event handler and return a function to remove it.

An event can be a message from the microscope API or an internal event.

Parameters:

  • event_type (str) – A string representing the type of event.

  • handler (callable) – A coroutine function that should accept two parameters, center and event. The first parameter is the Center instance, the second parameter is the Event instance that has fired.

Returns:

Return a function to remove the registered handler.

Return type:

callable

camacq.event.match_event(event, **event_data)

Return True if event attributes match event_data.

camacq.exceptions module

Provide exceptions.

exception camacq.exceptions.CamAcqError

Bases: Exception

Represent the base camacq exception.

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception camacq.exceptions.MissingActionError(action_id)

Bases: CamAcqError

Represent a missing action error.

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception camacq.exceptions.MissingActionTypeError(action_type)

Bases: CamAcqError

Represent a missing action type error.

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception camacq.exceptions.SampleError

Bases: CamAcqError

Represent a sample error.

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception camacq.exceptions.TemplateError(exc)

Bases: CamAcqError

Represent a template error.

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

camacq.image module

Handle images.

class camacq.image.ImageData(path=None, data=None, metadata=None)

Bases: object

Represent the data of an image with path, data, metadata and histogram.

Parameters:

  • path (str) – Path to the image.

  • data (numpy array) – A numpy array with the image data.

  • metadata (dict) – The meta data of the image as a JSON dict.

path

The path to the image.

Type:

str

property data

Return the data of the image.

Setter:

Set the data of the image.

Type:

numpy array

property histogram

Calculate and return image histogram.

Type:

numpy array

property metadata

Return metadata of image.

Setter:

Set the meta data of the image.

Type:

str

save(path=None, data=None, metadata=None)

Save image with image data and optional meta data.

Parameters:

  • path (str) – The path to the image.

  • data (numpy array) – A numpy array with the image data.

  • metadata (dict) – The meta data of the image as a JSON dict.

camacq.image.make_proj(images)

Make a dict of max projections from a dict of channels and paths.

Each channel will make one max projection.

Parameters:

images (dict) – Dict of paths and channel ids.

Returns:

Return a dict of channels that map ImageData objects. Each image object have a max projection as data.

Return type:

dict

camacq.image.read_image(path)

Read a tif image and return the data.

Parameters:

path (str) – The path to the image.

Returns:

Return a numpy array with image data.

Return type:

numpy array

camacq.image.save_image(path, data, description=None)

Save a tif image with image data and meta data.

Parameters:

  • path (str) – The path to the image.

  • data (numpy array) – A numpy array with the image data.

  • description (str) – The description string of the image.

camacq.log module

Handle logging.

camacq.log.check_path(path)

Check that path to config exists and is writable for logging.

Parameters:

path (pathlib.Path) – The path to the log file or log directory.

Returns:

Return True if path exists and is writable.

Return type:

bool

camacq.log.enable_log(config)

Enable logging.

Parameters:

config (dict) – The dict with the configuration.

camacq.util module

Host utils that are not aware of the implementation of camacq.

class camacq.util.dotdict

Bases: dict

Access to dictionary attributes with dot notation.

clear() → None.  Remove all items from D.
copy() → a shallow copy of D
fromkeys(value=None, /)

Create a new dictionary with keys from iterable and values set to value.

get(key, default=None, /)

Return the value for key if key is in the dictionary, else default.

items() → a set-like object providing a view on D's items
keys() → a set-like object providing a view on D's keys
pop(k[, d]) → v, remove specified key and return the corresponding value.

If key is not found, d is returned if given, otherwise KeyError is raised

popitem()

Remove and return a (key, value) pair as a 2-tuple.

Pairs are returned in LIFO (last-in, first-out) order. Raises KeyError if the dict is empty.

setdefault(key, default=None, /)

Insert key with a value of default if key is not in the dictionary.

Return the value for key if key is in the dictionary, else default.

update([E, ]**F) → None.  Update D from dict/iterable E and F.

If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]

values() → an object providing a view on D's values