Welcome to camacq’s documentation!¶
Contents:
camacq package¶
Control microscope through client server program.
Subpackages¶
camacq.data package¶
Store non python files.
camacq.helper package¶
Helper functions for camacq.
-
camacq.helper.
ensure_dict
(value)¶ Convert None to empty dict.
-
camacq.helper.
get_module
(package, module_name)¶ Return a module from a package.
- Parameters
package (str) – The path to the package.
module_name (str) – The name of the module.
-
camacq.helper.
has_at_least_one_key
(*keys)¶ Validate that at least one key exists.
-
camacq.helper.
register_signals
(center)¶ Register signal handlers.
-
async
camacq.helper.
setup_one_module
(center, config, module)¶ Set up one module or package.
- Returns
Return a task to set up the module or None.
- Return type
asyncio.Task
Submodules¶
camacq.helper.template module¶
Handle templates.
-
camacq.helper.template.
get_env
(center)¶ Get the template environment.
-
camacq.helper.template.
make_template
(center, data)¶ Make templated data.
-
camacq.helper.template.
render_template
(data, variables)¶ Render templated data.
-
camacq.helper.template.
template_next_well_x
(sample, plate_name, x_wells=12, y_wells=8)¶ Return the next well x coordinate for the plate x, y format.
-
camacq.helper.template.
template_next_well_xy
(sample, plate_name, x_wells=12, y_wells=8)¶ Return the next not done well for the given plate x, y format.
-
camacq.helper.template.
template_next_well_y
(sample, plate_name, x_wells=12, y_wells=8)¶ Return the next well x coordinate for the plate x, y format.
camacq.plugins package¶
Handle plugins.
-
camacq.plugins.
get_plugins
()¶ Return a dict of plugin modules.
-
async
camacq.plugins.
setup_module
(center, config)¶ Set up the plugins package.
- Parameters
center (Center instance) – The Center instance.
config (dict) – The config dict.
Subpackages¶
camacq.plugins.api package¶
Microscope API specific modules.
-
class
camacq.plugins.api.
Api
¶ Bases:
object
Represent the microscope API.
-
property
name
¶ Return the name of the API.
-
async
send
(command, **kwargs)¶ Send a command to the microscope API.
- Parameters
command (str) – The command to send.
-
async
send_many
(commands, **kwargs)¶ Send multiple commands to the microscope API.
- Parameters
commands (list) – A list of commands to send.
-
async
start_imaging
()¶ Send a command to the microscope to start the imaging.
-
async
stop_imaging
()¶ Send a command to the microscope to stop the imaging.
-
property
-
class
camacq.plugins.api.
CommandEvent
(data=None)¶ Bases:
camacq.event.Event
An event received from the API.
Notify with this event when a command is received via API.
-
property
command
¶ Return the command string.
- Type
str
-
data
¶
-
event_type
= 'command_event'¶
-
property
-
class
camacq.plugins.api.
ImageEvent
(data=None)¶ Bases:
camacq.event.Event
An event received from the API.
Notify with this event when an image is saved via API.
-
property
channel_id
¶ Return channel id of the image.
- Type
int
-
data
¶
-
event_type
= 'image_event'¶
-
property
field_x
¶ Return x coordinate of the well of the image.
- Type
int
-
property
field_y
¶ Return y coordinate of the well of the image.
- Type
int
-
property
path
¶ Return absolute path to the image.
- Type
str
-
property
plate_name
¶ Return plate name of the image.
- Type
str
-
property
well_x
¶ Return x coordinate of the well of the image.
- Type
int
-
property
well_y
¶ Return y coordinate of the well of the image.
- Type
int
-
property
z_slice_id
¶ Return z index of the image.
- Type
int
-
property
-
class
camacq.plugins.api.
StartCommandEvent
(data=None)¶ Bases:
camacq.plugins.api.CommandEvent
An event received from the API.
Notify with this event when imaging starts via API.
-
property
command
¶ Return the command string.
- Type
str
-
data
¶
-
event_type
= 'start_command_event'¶
-
property
-
class
camacq.plugins.api.
StopCommandEvent
(data=None)¶ Bases:
camacq.plugins.api.CommandEvent
An event received from the API.
Notify with this event when imaging stops via API.
-
property
command
¶ Return the command string.
- Type
str
-
data
¶
-
event_type
= 'stop_command_event'¶
-
property
-
camacq.plugins.api.
register_api
(center, api)¶ Register api.
-
async
camacq.plugins.api.
setup_module
(center, config)¶ Set up the microscope API package.
- Parameters
center (Center instance) – The Center instance.
config (dict) – The config dict.
-
camacq.plugins.api.
validate_commands
(value)¶ Validate a template string via JSON.
camacq.plugins.automations package¶
Handle automations.
-
class
camacq.plugins.automations.
ActionSequence
(center, actions)¶ Bases:
object
Represent a sequence of actions.
-
delay
(seconds, variables, waiting)¶ Delay action sequence.
- Parameters
seconds (float) – A time interval to delay the pending action sequence.
variables (dict) – A dict of template variables.
-
-
class
camacq.plugins.automations.
Automation
(center, name, attach_triggers, cond_func, action_sequence, enabled=True)¶ Bases:
object
Automation class.
-
disable
()¶ Disable automation.
-
enable
()¶ Enable automation.
-
async
trigger
(variables)¶ Run actions of this automation.
-
-
class
camacq.plugins.automations.
TemplateAction
(center, action_conf)¶ Bases:
object
Representation of an action with template data.
-
render
(variables)¶ Render the template with the kwargs for the action.
-
-
camacq.plugins.automations.
make_checker
(condition_type, checks)¶ Return a function to check condition.
-
async
camacq.plugins.automations.
setup_module
(center, config)¶ Set up automations package.
- Parameters
center (Center instance) – The Center instance.
config (dict) – The config dict.
-
camacq.plugins.automations.
template_check
(value)¶ Check if a rendered template string equals true.
If value is not a string, return value as is.
camacq.plugins.leica package¶
Leica microscope API specific modules.
-
class
camacq.plugins.leica.
LeicaApi
(center, config, client)¶ Bases:
camacq.plugins.api.Api
Represent the Leica API.
-
property
name
¶ Return the name of the API.
-
async
receive
(replies)¶ Receive replies from CAM server and fire an event per reply.
- Parameters
replies (list) – A list of replies from the CAM server.
-
async
send
(command, **kwargs)¶ Send a command to the Leica API.
- Parameters
command (list of tuples or string) – The command to send.
-
async
send_many
(commands, **kwargs)¶ Send multiple commands to the microscope API.
- Parameters
commands (list) – A list of commands to send.
-
async
start_imaging
()¶ Send a command to the microscope to start the imaging.
-
async
start_listen
()¶ Receive from the microscope socket.
-
async
stop_imaging
()¶ Send a command to the microscope to stop the imaging.
-
property
-
class
camacq.plugins.leica.
LeicaCommandEvent
(data=None)¶ Bases:
camacq.plugins.api.CommandEvent
Leica CommandEvent class.
-
property
command
¶ Return the command string.
-
data
¶
-
event_type
= 'leica_command_event'¶
-
property
-
class
camacq.plugins.leica.
LeicaImageEvent
(data=None)¶ Bases:
camacq.plugins.api.ImageEvent
Leica ImageEvent class.
-
property
channel_id
¶ Return channel id of the image.
- Type
int
-
data
¶
-
event_type
= 'leica_image_event'¶
-
property
field_x
¶ Return x coordinate of the well of the image.
- Type
int
-
property
field_y
¶ Return y coordinate of the well of the image.
- Type
int
-
property
job_id
¶ Return job id of the image.
- Type
int
-
property
path
¶ Return absolute path to the image.
- Type
str
-
property
plate_name
¶ Return plate name of the image.
- Type
str
-
property
well_x
¶ Return x coordinate of the well of the image.
- Type
int
-
property
well_y
¶ Return y coordinate of the well of the image.
- Type
int
-
property
z_slice_id
¶ Return z index of the image.
- Type
int
-
property
-
class
camacq.plugins.leica.
LeicaStartCommandEvent
(data=None)¶ Bases:
camacq.plugins.api.StartCommandEvent
,camacq.plugins.leica.LeicaCommandEvent
Leica StartCommandEvent class.
-
property
command
¶ Return the command string.
-
data
¶
-
event_type
= 'leica_start_command_event'¶
-
property
-
class
camacq.plugins.leica.
LeicaStopCommandEvent
(data=None)¶ Bases:
camacq.plugins.api.StopCommandEvent
,camacq.plugins.leica.LeicaCommandEvent
Leica StopCommandEvent class.
-
property
command
¶ Return the command string.
-
data
¶
-
event_type
= 'leica_stop_command_event'¶
-
property
-
async
camacq.plugins.leica.
setup_module
(center, config)¶ Set up Leica api package.
- Parameters
center (Center instance) – The Center instance.
config (dict) – The config dict.
Handle commands.
-
camacq.plugins.leica.command.
cam_com
(exp, wellu, wellv, fieldx, fieldy, dxcoord, dycoord)¶ Add a field to the cam list.
Return a list with parts for the cam command.
-
camacq.plugins.leica.command.
camstart_com
(afjob=None, afrange=None, afsteps=None)¶ Start the cam scan with selected AF job and AF settings.
Return a list with parts for the cam command.
-
camacq.plugins.leica.command.
camstop_com
()¶ Stop the cam scan.
Return a list with parts for the cam command.
-
camacq.plugins.leica.command.
del_com
()¶ Delete the cam list.
Return a list with parts for the cam command.
-
camacq.plugins.leica.command.
enable_com
(wellu, wellv, fieldx, fieldy, enable)¶ Enable a field in a well.
Return a list with parts for the cam command.
-
camacq.plugins.leica.command.
gain_com
(exp, num, value)¶ Change the pmt gain in a job.
Return a list with parts for the cam command.
-
camacq.plugins.leica.command.
start
()¶ Start the scan.
Return a list with parts for the cam command.
-
camacq.plugins.leica.command.
stop
()¶ Stop the scan.
Return a list with parts for the cam command.
Helper functions for Leica api.
-
camacq.plugins.leica.helper.
find_image_path
(relpath, root)¶ Parse the relpath from the server to find file path from root.
Convert from windows path to posix path.
- Parameters
relpath (str) – A relative path to the image.
root (str) – Path to directory where path should start.
- Returns
Return path to image.
- Return type
str
-
camacq.plugins.leica.helper.
get_field
(path)¶ Get path to field from image path.
- Parameters
path (string) – Path to image.
- Returns
Return path to field directory of image.
- Return type
str
-
camacq.plugins.leica.helper.
get_imgs
(path, img_type='tif', search='')¶ Get all images below path.
- Parameters
path (string) – Path to directory where to search for images.
img_type (string) – A string representing the image file type extension.
path – A glob pattern string to use in the search.
- Returns
Return paths of all images found.
- Return type
list
-
camacq.plugins.leica.helper.
get_well
(path)¶ Get path to well from image path.
- Parameters
path (string) – Path to image.
- Returns
Return path to well directory of image.
- Return type
str
camacq.plugins.sample package¶
Handle sample state.
-
class
camacq.plugins.sample.
Image
(path, values=None, **kwargs)¶ Bases:
camacq.plugins.sample.ImageContainer
An image with path and position info.
-
property
images
¶ Return a dict with all images for the container.
- Type
dict
-
property
name
¶ Return an identifying name for the container.
- Type
str
-
property
path
¶ Return the path of the image.
- Type
str
-
property
values
¶ Return a dict with the values set for the container.
- Type
dict
-
property
-
class
camacq.plugins.sample.
ImageContainer
¶ Bases:
abc.ABC
A container for images.
-
abstract property
images
¶ Return a dict with all images for the container.
- Type
dict
-
abstract property
name
¶ Return an identifying name for the container.
- Type
str
-
abstract property
values
¶ Return a dict with the values set for the container.
- Type
dict
-
abstract property
-
class
camacq.plugins.sample.
Sample
¶ Bases:
camacq.plugins.sample.ImageContainer
,abc.ABC
Representation of the state of the sample.
-
center
= None¶
-
data
= None¶
-
get_sample
(name, **kwargs)¶ Get an image container of the sample.
- Parameters
name (str) – The name of the container type.
**kwargs – Arbitrary keyword arguments. These will be used to create the id string of the container.
- Returns
Return the found ImageContainer instance.
- Return type
ImageContainer instance
-
abstract property
image_event_type
¶ Return the image event type to listen to for the sample.
- Type
str
-
abstract property
images
¶ Return a dict with all images for the container.
- Type
dict
-
abstract property
name
¶ Return the name of the sample.
- Type
str
-
abstract async
on_image
(center, event)¶ Handle image event for this sample.
-
async
set_sample
(name, values=None, **kwargs)¶ Set an image container of the sample.
- Parameters
name (str) – The name of the container type.
values (dict) – The optional values to set on the container.
**kwargs – Arbitrary keyword arguments. These will be used to create the id string of the container.
- Returns
Return the ImageContainer instance that was updated.
- Return type
ImageContainer instance
-
abstract property
set_sample_schema
¶ Return the validation schema of the set_sample method.
-
abstract property
values
¶ Return a dict with the values set for the container.
- Type
dict
-
-
class
camacq.plugins.sample.
SampleEvent
(data=None)¶ Bases:
camacq.event.Event
An event produced by a sample change event.
-
property
container
¶ Return the container instance of the event.
- Type
ImageContainer instance
-
property
container_name
¶ Return the container name of the event.
- Type
str
-
data
¶
-
event_type
= 'sample_event'¶
-
property
images
¶ Return the container images of the event.
- Type
dict
-
property
values
¶ Return the container values of the event.
- Type
dict
-
property
-
class
camacq.plugins.sample.
SampleImageSetEvent
(data=None)¶ Bases:
camacq.plugins.sample.SampleEvent
An event produced by a new image on the sample.
-
property
container
¶ Return the container instance of the event.
- Type
ImageContainer instance
-
property
container_name
¶ Return the container name of the event.
- Type
str
-
data
¶
-
event_type
= 'sample_image_set_event'¶
-
property
images
¶ Return the container images of the event.
- Type
dict
-
property
values
¶ Return the container values of the event.
- Type
dict
-
property
-
class
camacq.plugins.sample.
Samples
¶ Bases:
camacq.util.dotdict
Hold all samples.
-
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¶
-
-
camacq.plugins.sample.
get_matched_samples
(sample, name, attrs=None, values=None)¶ Return the sample items that match.
-
camacq.plugins.sample.
register_sample
(center, sample)¶ Register sample.
-
async
camacq.plugins.sample.
setup_module
(center, config)¶ Set up sample module.
- Parameters
center (Center instance) – The Center instance.
config (dict) – The config dict.
Submodules¶
camacq.plugins.rename_image module¶
Handle renaming of an image.
-
camacq.plugins.rename_image.
rename_image
(old_path, new_path)¶ Rename image at old_path to new_path.
- Parameters
old_path (str) – The absolute path to the existing image.
new_path (str) – The absolute path to the renamed image.
-
async
camacq.plugins.rename_image.
setup_module
(center, config)¶ Set up image rename plugin.
- Parameters
center (Center instance) – The Center instance.
config (dict) – The config dict.
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.
-
property
-
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¶
-