leicacam package¶

Control Leica microscopes with python.

class leicacam.CAM(*args, **kwargs)[source]¶

Bases: leicacam.cam.BaseCAM

Driver for LASAF Computer Assisted Microscopy.

autofocus_scan()[source]¶: Start the autofocus job.

close()[source]¶: Close the socket.

connect()[source]¶: Connect to LASAF through a CAM-socket.

disable(slide=0, wellx=1, welly=1, fieldx=1, fieldy=1)[source]¶: Disable a given scan field.

disable_all()[source]¶: Disable all scan fields.

enable(slide=0, wellx=1, welly=1, fieldx=1, fieldy=1)[source]¶: Enable a given scan field.

enable_all()[source]¶: Enable all scan fields.

flush()[source]¶: Flush incoming socket messages.

get_information(about='stage')[source]¶: Get information about given keyword. Defaults to stage.

load_template(filename='{ScanningTemplate}leicacam.xml')[source]¶

Load scanning template from filename.

Template needs to exist in database, otherwise it will not load.

Parameters: filename (str) – Filename to template to load. Filename may contain path also, in such case, the basename will be used. ‘.xml’ will be stripped from the filename if it exists because of a bug; LASAF implicit add ‘.xml’. If ‘{ScanningTemplate}’ is omitted, it will be added.
Returns: Response from LASAF in an ordered dict.
Return type: collections.OrderedDict

Example

>>> # load {ScanningTemplate}leicacam.xml
>>> cam.load_template('leicacam')

>>> # load {ScanningTemplate}leicacam.xml
>>> cam.load_template('{ScanningTemplate}leicacam')

>>> # load {ScanningTemplate}leicacam.xml
>>> cam.load_template('/path/to/{ScanningTemplate}leicacam.xml')

pause_scan()[source]¶: Pause the matrix scan.

receive()[source]¶: Receive message from socket interface as list of OrderedDict.

save_template(filename='{ScanningTemplate}leicacam.xml')[source]¶: Save scanning template to filename.

send(commands)[source]¶

Send commands to LASAF through CAM-socket.

Parameters: commands (list of tuples or bytes string) – Commands as a list of tuples or a bytes string. cam.prefix is allways prepended before sending.
Returns: Bytes sent.
Return type: int

Example

>>> # send list of tuples
>>> cam.send([('cmd', 'enableall'), ('value', 'true')])

>>> # send bytes string
>>> cam.send(b'/cmd:enableall /value:true')

start_scan()[source]¶: Start the matrix scan.

stop_scan()[source]¶: Stop the matrix scan.

wait_for(cmd, value=None, timeout=60)[source]¶

Hang until command is received.

If value is supplied, it will hang until cmd:value is received.

Parameters

cmd (string) – Command to wait for in bytestring from microscope CAM interface. If value is falsy, value of received command does not matter.
value (string) – Wait until cmd:value is received.
timeout (int) – Minutes to wait for command. If timeout is reached, an empty OrderedDict will be returned.

Returns

Last received messsage or empty message if timeout is reached.

Return type

collections.OrderedDict

Submodules¶

leicacam.async_cam module¶

Provide an interface using asyncio to the CAM server.

class leicacam.async_cam.AsyncCAM(*args, loop=None, **kwargs)[source]¶

Bases: leicacam.cam.BaseCAM

Driver for LASAF Computer Assisted Microscopy using asyncio.

close()[source]¶: Close stream.

async connect()[source]¶: Connect to LASAF through a CAM-socket.

async receive()[source]¶: Receive message from socket interface as list of OrderedDict.

async send(commands)[source]¶

Send commands to LASAF through CAM-socket.

Parameters: commands (list of tuples or bytes string) – Commands as a list of tuples or a bytes string. cam.prefix is allways prepended before sending.
Returns: Bytes sent.
Return type: int

Example

>>> # send list of tuples
>>> await cam.send([('cmd', 'enableall'), ('value', 'true')])

>>> # send bytes string
>>> await cam.send(b'/cmd:enableall /value:true')

async wait_for(cmd, value=None, timeout=60)[source]¶

Hang until command is received.

If value is supplied, it will hang until cmd:value is received.

Parameters

cmd (string) – Command to wait for in bytestring from microscope CAM interface. If value is falsy, value of received command does not matter.
value (string) – Wait until cmd:value is received.
timeout (int) – Minutes to wait for command. If timeout is reached, an empty OrderedDict will be returned.

Returns

Last received messsage or empty message if timeout is reached.

Return type

collections.OrderedDict

leicacam.cam module¶

Provide an interface to the CAM server.

class leicacam.cam.BaseCAM(host='127.0.0.1', port=8895)[source]¶

Bases: object

Base driver for LASAF Computer Assisted Microscopy.

class leicacam.cam.CAM(*args, **kwargs)[source]¶

Bases: leicacam.cam.BaseCAM

Driver for LASAF Computer Assisted Microscopy.

autofocus_scan()[source]¶: Start the autofocus job.

close()[source]¶: Close the socket.

connect()[source]¶: Connect to LASAF through a CAM-socket.

disable(slide=0, wellx=1, welly=1, fieldx=1, fieldy=1)[source]¶: Disable a given scan field.

disable_all()[source]¶: Disable all scan fields.

enable(slide=0, wellx=1, welly=1, fieldx=1, fieldy=1)[source]¶: Enable a given scan field.

enable_all()[source]¶: Enable all scan fields.

flush()[source]¶: Flush incoming socket messages.

get_information(about='stage')[source]¶: Get information about given keyword. Defaults to stage.

load_template(filename='{ScanningTemplate}leicacam.xml')[source]¶

Load scanning template from filename.

Template needs to exist in database, otherwise it will not load.

Parameters: filename (str) – Filename to template to load. Filename may contain path also, in such case, the basename will be used. ‘.xml’ will be stripped from the filename if it exists because of a bug; LASAF implicit add ‘.xml’. If ‘{ScanningTemplate}’ is omitted, it will be added.
Returns: Response from LASAF in an ordered dict.
Return type: collections.OrderedDict

Example

>>> # load {ScanningTemplate}leicacam.xml
>>> cam.load_template('leicacam')

>>> # load {ScanningTemplate}leicacam.xml
>>> cam.load_template('{ScanningTemplate}leicacam')

>>> # load {ScanningTemplate}leicacam.xml
>>> cam.load_template('/path/to/{ScanningTemplate}leicacam.xml')

pause_scan()[source]¶: Pause the matrix scan.

receive()[source]¶: Receive message from socket interface as list of OrderedDict.

save_template(filename='{ScanningTemplate}leicacam.xml')[source]¶: Save scanning template to filename.

send(commands)[source]¶

Send commands to LASAF through CAM-socket.

Parameters: commands (list of tuples or bytes string) – Commands as a list of tuples or a bytes string. cam.prefix is allways prepended before sending.
Returns: Bytes sent.
Return type: int

Example

>>> # send list of tuples
>>> cam.send([('cmd', 'enableall'), ('value', 'true')])

>>> # send bytes string
>>> cam.send(b'/cmd:enableall /value:true')

start_scan()[source]¶: Start the matrix scan.

stop_scan()[source]¶: Stop the matrix scan.

wait_for(cmd, value=None, timeout=60)[source]¶

Hang until command is received.

If value is supplied, it will hang until cmd:value is received.

Parameters

cmd (string) – Command to wait for in bytestring from microscope CAM interface. If value is falsy, value of received command does not matter.
value (string) – Wait until cmd:value is received.
timeout (int) – Minutes to wait for command. If timeout is reached, an empty OrderedDict will be returned.

Returns

Last received messsage or empty message if timeout is reached.

Return type

collections.OrderedDict

leicacam.cam.bytes_as_dict(msg)[source]¶

Parse CAM message to OrderedDict based on format /key:val.

Parameters: msg (bytes) – Sequence of /key:val.
Returns: With /key:val => dict[key] = val.
Return type: collections.OrderedDict

leicacam.cam.check_messages(msgs, cmd, value=None)[source]¶

Check if specific message is present.

Parameters

cmd (string) – Command to check for in bytestring from microscope CAM interface. If value is falsy, value of received command does not matter.
value (string) – Check if cmd:value is received.

Returns

Correct messsage or None if no correct message if found.

Return type

collections.OrderedDict

leicacam.cam.logger(function)[source]¶: Decorate passed in function and log message to module logger.

leicacam.cam.tuples_as_bytes(cmds)[source]¶

Format list of tuples to CAM message with format /key:val.

Parameters: cmds (list of tuples) – List of commands as tuples.
Returns: Sequence of /key:val.
Return type: bytes

Example

>>> tuples_as_bytes([('cmd', 'val'), ('cmd2', 'val2')])
b'/cmd:val /cmd2:val2'

leicacam.cam.tuples_as_dict(_list)[source]¶

Translate a list of tuples to OrderedDict with key and val as strings.

Parameters: _list (list of tuples) –
Returns
Return type: collections.OrderedDict

Example

>>> tuples_as_dict([('cmd', 'val'), ('cmd2', 'val2')])
OrderedDict([('cmd', 'val'), ('cmd2', 'val2')])