camacq package

Control microscope through client server program.

Subpackages

• camacq.data package
• camacq.helper package
  • Submodules
  • camacq.helper.template module
• camacq.plugins package
  • Subpackages
    • camacq.plugins.api package
    • camacq.plugins.automations package
      • Submodules
      • camacq.plugins.automations.event module
    • camacq.plugins.leica package
      • Submodules
      • camacq.plugins.leica.command module
      • camacq.plugins.leica.helper module
    • camacq.plugins.sample package
      • Submodules
      • camacq.plugins.sample.helper module
  • Submodules
  • camacq.plugins.rename_image module

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: camacq.util.dotdict

Represent an action type.

clear() → None. Remove all items from D.

copy() → a shallow copy of D

fromkeys()

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

get()

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() → (k, v), remove and return some (key, value) pair as a

2-tuple; but raise KeyError if D is empty.

setdefault()

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: camacq.event.Event

An event fired when camacq has started.

data

event_type = 'camacq_start_event'

class camacq.control.CamAcqStopEvent(data=None)

Bases: camacq.event.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: camacq.exceptions.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: camacq.exceptions.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: camacq.exceptions.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: camacq.exceptions.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()

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

get()

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() → (k, v), remove and return some (key, value) pair as a

2-tuple; but raise KeyError if D is empty.

setdefault()

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