camacq.plugins.leica package

Leica microscope API specific modules.

class camacq.plugins.leica.LeicaApi(center, config, client)

Bases: 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.

class camacq.plugins.leica.LeicaCommandEvent(data=None)

Bases: CommandEvent

Leica CommandEvent class.

property command

Return the command string.

data

event_type = 'leica_command_event'

class camacq.plugins.leica.LeicaImageEvent(data=None)

Bases: 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

class camacq.plugins.leica.LeicaStartCommandEvent(data=None)

Bases: StartCommandEvent, LeicaCommandEvent

Leica StartCommandEvent class.

property command

Return the command string.

data

event_type = 'leica_start_command_event'

class camacq.plugins.leica.LeicaStopCommandEvent(data=None)

Bases: StopCommandEvent, LeicaCommandEvent

Leica StopCommandEvent class.

property command

Return the command string.

data

event_type = 'leica_stop_command_event'

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.

Submodules

camacq.plugins.leica.command module

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.

camacq.plugins.leica.helper module

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