cosplay package¶

Submodules¶

cosplay.cli module¶

cosplay.cli.main()¶: Process arguments and pass them to server.main.

cosplay.cli.return_parser()¶: Return argparse argument parser.

cosplay.dump_mem module¶

From Dave Hylands’ json-ipc/dump_mem.py ( https://github.com/dhylands/json-ipc.git ). Provides the dump_mem function, which dumps memory in hex/ASCII.

cosplay.dump_mem.dump_mem(buf, prefix='', address=0, line_width=16, show_ascii=True, show_addr=True, log=<function print_>)¶: Dumps out a hex/ASCII representation of the given buffer.

cosplay.dump_mem.hexlify(buf)¶

cosplay.dump_mem.print_(s)¶

Print string s.

In Python 2, print is not a function. This function makes it possible to use it like one.

cosplay.pkt module¶

This file is based on Dave Hylands’ json-ipc/json_pkt.py ( https://github.com/dhylands/json-ipc.git ).

class cosplay.pkt.Packet(serial_port, show_packets=False)¶

ANS_no = 0¶

ANS_yes = 1¶

INS_ask_user = 3¶

INS_check_for_sequences_on_server = 2¶

INS_send_sequences = 4¶

STATE_EOT = 8¶

STATE_ETX = 6¶

STATE_LEN_0 = 1¶

STATE_LEN_1 = 2¶

STATE_LRC = 7¶

STATE_PAYLOAD = 5¶

STATE_SOH = 0¶

STATE_STX = 4¶

STATE_TYPE = 3¶

process_byte(byte)¶

Process a single byte. Return an object when one is successfully parsed, otherwise return None.

Parameters:	byte (bytes object / bytearray) – Input byte. For MicroPython and Python 3 this should be a bytes object. In Python 2 a bytearray should be used.
Returns:	out – Returns object if package is successfully parsed, otherwise returns None.
Return type:	2d array / string / int

receive(time_out=0)¶

Try to receive an object.

This function tries to receive an object until time_out. If a byte is received, time_out becomes obsolete and the function times out if no more bytes are received for 1s. Returns None upon time out.

Parameters:	time_out (int) – Approximate time in ms until return if no bytes are received. If time_out = 0, the function never times out.
Returns:	out – Received object or None in case of time out.
Return type:	object

send(obj)¶

Convert a Python object into its string representation and then send it using the ‘serial_port’ passed in the constructor.

Parameters:	obj (list, string or int) – object that is send via ‘serial_port’

cosplay.pkt.lrc(str)¶: Return longitudinal redundancy checksum.

cosplay.serial_port module¶

Based on Dave Hylands’ json-ipc/serial_port.py (https://github.com/dhylands/json-ipc.git). This module implements the SerialPort class, which allows the host to talk to another device using a serial like interface over a UART.

class cosplay.serial_port.SerialPort¶

Bases: object

Implements a PySerial port.

close_serial()¶: Close serial connection if it is open.

connect_serial(port, baud=115200)¶

Try to connect to serial port.

This function tries to connect to a serial port named port.

Parameters:	port (string) – name of port (e.g. /dev/ttyACM0)
Returns:	True if connection could be established, otherwise False.
Return type:	bool

is_byte_available()¶: Check if byte can be read from serial port.

read_byte()¶

Read a byte from the serial port.

Returns:	Value of byte.
Return type:	int

write(data)¶

Write data to the serial port.

Parameters:	data (string / bytearray) – Data to write.

cosplay.serial_port.autoscan()¶

Check all serial ports to see if they are MicroPython devices.

Checks serial ports until it finds a port with matching VID:PID for a MicroPython board.

Returns:	Full device name/path. None if no MicroPython device was found.
Return type:	string

cosplay.serial_port.is_micropython_usb_device(port)¶

Check a USB device to see if it looks like a MicroPython device.

Parameters:	port (serial.tools.list_ports object) – Port to check.
Returns:	True if device connected to ‘port’ looks like a MicroPython device, False otherwise.
Return type:	bool

cosplay.server module¶

cosplay.server.ask_user()¶

Ask user whether sequences on server or microcontroller shall be used.

Returns:	True if sequences on server shall be used, False otherwise.
Return type:	bool

cosplay.server.check_for_sequences(sequences_arg=None)¶

Try to find sequences.

This function returns a list of paths to all files ending with ‘.tsv’ in sequence_arg. Shell-style wildcards can be used. sequences_arg can be directories, files or a mixture of both. Directories are searched non-recursively on the first level. If no sequence_arg is specified, the default location of COSgen is used.

Parameters:	sequences_arg (string, optional) – Path to sequence files, can be None.
Returns:	List of paths to sequence files. None if no sequences were found.
Return type:	list

cosplay.server.connect(port_name=None)¶

Establish connection to pyboard.

This function tries to connect to port_name. If port_name is None, tries to connect to the first serial port with a maching VID:PID for the MicroPython Pyboard.

Parameters:	port_name (string, optional) – Name of port the microcontroller is connected to. If None, tries to automatically detected port and connect. Default is None.
Returns:	port – Port object that is connected. None if no connection could be establish.
Return type:	cosplay.serial_port.SerialPort object

cosplay.server.find_current_scan_dir(vendor, storage_root=None)¶

Find directory of current scan.

This function finds the scan directory with the most recent inode change time of the fid file.

Parameters:	vendor (string) – Name of the MRI vendor, currently only Bruker is supported.
Returns:	Path to current scan directory.
Return type:	string

cosplay.server.listdir_nohidden(path)¶

List all entries in path excluding hidden ones.

This function implements the same functionality as os.listdir but ignores hidden entires.

Parameters:	path (string) – Path to directory
Returns:	List of all non-hidden entries in the directory.
Return type:	list

cosplay.server.main(verbose, vendor, port_name, sequences, storage_path=None, storage_root=None)¶

Main function running on server.

This function constantly tries to receive data from pyboard. It acts according to the instructions received from the board. Exit this function by pressing CTRL-C.

Parameters:	verbose (int) – Verbosity level. vendor (string) – Vendor of the MRI scanner. port_name (string) – Port name. sequences (string) – Path to sequences (can include wildcards). storage_path (string) – String to storage location for delivered sequences.

cosplay.server.process_message(obj, error_msgs)¶

Add obj to error_msgs if it is an error message.

Parameters:	obj (string) – Input message. error_msgs (string) – Already accumulated error messages.
Returns:	updated error_msgs
Return type:	string

cosplay.server.save_sequence(obj, storage_path, error_msgs, vendor, verbose=0, storage_root=None)¶

Save sequence in storage_path.

This function saves a sequence and error messages in two separate files. If storage_path is None, the files are saved in the most recent scan directory (see ‘find_current_scan_dir’).

Parameters:

obj (2d matrix) – Sequence.
storage_path (string) – Path to directory, where files shall be stored. If it is None, the most recent scan directory is used.
error_msgs (string) – String containing error messages. Is stored in same directory as the sequence.
vendor (string) – Name of MRI vendor.
verbose (int, optional) – If ‘verbose’ is larger than 1, the sequence is printed to the screen. Default is 0.

cosplay.server.send_sequences(sequences_paths, pkt, verbose)¶

Send sequences to microcontroller.

Parameters:	sequences_paths (list) – List of paths (strings) to sequences that are sent. pkt (cosplay.pkt Packet object) – Object that sends the sequences. verbose (int) – If larger than 1, print path to every sequence sent. If larger than 2, print every sequence sent.

cosplay.server.signal_handler_end_program(signal, frame)¶

cosplay.tsv module¶

cosplay.tsv.cast(s)¶

Cast string to float if possible.

This functions casts a string to float if possible and returns the string otherwise.

Parameters:	s (string) – Input strings
Returns:	Float number of string input s, if possible, s otherwise.
Return type:	float or string

cosplay.tsv.dump(matrix, file_obj)¶

Serialize matrix as a tsv formatted stream to file_obj.

This function converts a matrix into a tsv formatted string and stores it in a file.

Parameters:	matrix (2d array) – Input matrix. file_obj (file_obj) – A .write()-supporting file-like object.

cosplay.tsv.dumps(matrix)¶

Serialize matrix to a tsv formatted string.

Parameters:	matrix (2d array) – Input matrix.
Returns:	tsv formatted string.
Return type:	string

cosplay.tsv.load(file_obj)¶

Load BIDS sequence tsv file [BIDS].

This function converts a BIDS sequence tsv file to a matrix.

Parameters:	file_obj (file object) – File object of BIDS sequence tsv file [BIDS].
Returns:	First line contains names for columns. First columns contains event numbers.
Return type:	2d array

cosplay.tsv.loads(s)¶

Convert tsv formatted string into matrix.

This function converts a ‘Brain Image Data Structure’ [BIDS] sequence tsv string into a matrix.

Parameters:	s (string) – String form BIDS sequence tsv file[BIDS].
Returns:	First line contains names for columns. First columns contains event numbers.
Return type:	2d array

[BIDS]

Brain Imaging Data Structure Specification (http://bids.neuroimaging.io/bids_spec1.0.1.pdf)