Update session variables

README.md

@@ -38,7 +38,7 @@ This is Open Source software. We use the `GNU General Public License version 3 <
 
 1. Duplicate *user_settings.py.template* and save it as *user_settings.py*
 
-        Define the SERIAL_PORT attribute with your machine serial port where Bpod is connected to
+        Define the PYBPOD_SERIAL_PORT attribute with your machine serial port where Bpod is connected to
         Define the API_LOG_LEVEL with logging.DEBUG if you want detailed logging for the API
 
 2. On the project root folder run:

docs/source/about/about.rst

@@ -31,13 +31,12 @@ Maintenance team
 
 The current and past members of the **pybpod-api** team.
 
-* `@cajomferro <https://github.com/cajomferro/>`_ Carlos Mão de Ferro
-* `@JBauto <https://github.com/JBauto>`_ João Baúto
 * `@UmSenhorQualquer <https://github.com/UmSenhorQualquer/>`_ Ricardo Ribeiro
+* `@sergio-copedo <https://bitbucket.org/sergio-copeto/>`_ Sérgio Copeto
 
 Questions?
 ==========
-If you have any questions or want to report a problem with this library please fill a issue `here <https://bitbucket.org/fchampalimaud/pybpod-api/issues>`_.
+If you have any questions or want to report a problem with this library please fill a issue `here <https://bitbucket.org/fchampalimaud/pybpod/issues>`_.
 
 
 .. Changes log

docs/source/getting_started/installing.rst

@@ -1,4 +1,4 @@
-.. pybpodapi documentation master file, created by
+ .. pybpodapi documentation master file, created by
    sphinx-quickstart on Wed Jan 18 09:35:10 2017.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
@@ -9,26 +9,21 @@
 Installing
 **********
 
+.. note::
+
+    To install the **full pybpod package**, please follow the instructions located @ `Pybpod <http://pybpod.readthedocs.org>`_.
+
+
 .. warning::
    This project uses Python 3!
 
-Download project
+Clone the project from Bitbucket
 ================
 
-
-Option A. Clone project from Bitbucket:
----------------------------------------
-
 ::
 
     git clone https://bitbucket.org/fchampalimaud/pybpod-api
 
-
-Option B. Download zip
-----------------------
-
-https://bitbucket.org/fchampalimaud/pybpod-api/get/master.zip
-
 Install files
 =============
 
@@ -45,27 +40,25 @@ Settings file
 
 ::
 
-	# list of python libraries to interfaces bpod modules. 
-	PYBPOD_API_MODULES = [
-		'pybpod_rotaryencoder_module'
-	]
-
-	# folder where the bpod output files are be saved
-	WORKSPACE_PATH 	= 'BPOD-WORKSPACE'
-
-	# name of the session file
-	PROTOCOL_NAME	= now()  
-
-	# serial port settings
-	BAUDRATE 		= 1312500
-	SYNC_CHANNEL	= 255
-	SYNC_MODE		= 1
-	SERIAL_PORT = '/dev/ttyACM0'
-
-	# enable or disable bpod ports
-	BPOD_BNC_PORTS_ENABLED 		= [True, True]
-	BPOD_WIRED_PORTS_ENABLED 	= [True, True]
-	BPOD_BEHAVIOR_PORTS_ENABLED	= [True, True, True, True, True, True, True, True]
-
-
-
+    # list of python libraries to interfaces bpod modules. 
+    PYBPOD_API_MODULES = [
+        'pybpod_rotaryencoder_module'
+    ]
+
+    PYBPOD_SERIAL_PORT = '/dev/ttyACM0'  # serial port settings
+    PYBPOD_NET_PORT    = '' # network port to receive remote commands like softcodes.
+
+    # enable or disable bpod ports
+    BPOD_BNC_PORTS_ENABLED      = [True, True]
+    BPOD_WIRED_PORTS_ENABLED    = [True, True]
+    BPOD_BEHAVIOR_PORTS_ENABLED = [True, True, True, True, True, True, True, True]
+
+    PYBPOD_PROTOCOL     = '' # Executed protocol
+    PYBPOD_CREATOR      = '' # Name of the user
+    PYBPOD_PROJECT      = '' # Name of the project
+    PYBPOD_EXPERIMENT   = '' # Name of the experiment
+    PYBPOD_BOARD        = '' # Board name
+    PYBPOD_SETUP        = '' # Setup name
+    PYBPOD_SESSION      = '' # Name of the session file
+    PYBPOD_SESSION_PATH = '' # Folder where the bpod output files are be saved
+    PYBPOD_SUBJECTS     = [] # List of subjects to be saved in the session file.

docs/source/getting_started/running.rst

@@ -23,11 +23,11 @@ Example of  *'examples/user_settings.py'*  file:
 
 	PYBPOD_API_LOG_LEVEL = None
 	
-	WORKSPACE_PATH  = 'BPOD-WORKSPACE'
+	PYBPOD_SESSION_PATH  = 'SESSION-WORKSPACE'
 
-	# if you do not define the next variable, the PROTOCOL_NAME 
+	# if you do not define the next variable, the PYBPOD_SESSION 
 	# will assume the current datetime value.
-	PROTOCOL_NAME   = 'PROTOCOL-NAME' 
+	PYBPOD_SESSION = 'SESSION-NAME' 
 
 	SERIAL_PORT   = '/dev/ttyACM0'
 

docs/source/index.rst

@@ -16,7 +16,7 @@ Welcome to pybpod-api's documentation!
 
 What is pybpod-api?
 ===================
-**pybpod-api** is a Python library that enables communication with the latest `Bpod device <https://sanworks.io/shop/viewproduct?productID=1011>`_ version. You can use it directly as a CLI (Command Line Interface) or use your favorite GUI to interact with it.
+**pybpod-api** is a Python library that enables communication with the latest `Bpod device <https://sanworks.io/shop/viewproduct?productID=1011>`_ version. You can use it directly as a CLI (Command Line Interface) or use your favorite `GUI <http://pybpod.readthedocs.io>`_ to interact with it.
 
 This library is maintained by a team of SW developers at the `Champalimaud Foundation <http://research.fchampalimaud.org>`_. Please find more information on section :ref:`Project Info <project-info-label>`.
 
@@ -43,7 +43,7 @@ Python is one of the most popular programming languages today `[1] <https://pypl
 
 Questions?
 ==========
-If you have any questions or want to report a problem with this library please fill in an issue `here <https://bitbucket.org/fchampalimaud/pybpod-api/issues>`_.
+If you have any questions or want to report a problem with this library please fill in an issue `here <https://bitbucket.org/fchampalimaud/pybpod/issues>`_.
 
 .. high level toc tree
 

examples/user_settings.py

@@ -5,14 +5,10 @@
 PYBPOD_API_LOG_FILE  = 'pybpod-api.log'
 
 
-PYBPOD_SESSION_PATH 	= 'PYBPOD_SESSION_PATH'
-
-PYBPOD_SESSION 	= datetime.datetime.fromtimestamp(time.time()).strftime('%Y-%m-%d %H:%M:%S')
-
-SERIAL_PORT 	= '/dev/ttyACM0'
-#SERIAL_PORT 	= '/dev/tty.usbmodem3174431'
-
+PYBPOD_SESSION_PATH = 'PYBPOD_SESSION_PATH'
+PYBPOD_SESSION 		= datetime.datetime.fromtimestamp(time.time()).strftime('%Y-%m-%d %H:%M:%S')
 
+PYBPOD_SERIAL_PORT 	= '/dev/ttyACM0'
 
 BPOD_BNC_PORTS_ENABLED 		= [True, True]
 BPOD_WIRED_PORTS_ENABLED 	= [True, True]

pybpodapi/bpod/bpod_base.py

@@ -60,11 +60,11 @@ class ChannelNames(ChannelName):     pass
     def __init__(self, serial_port=None, sync_channel=None, sync_mode=None, net_port=None):
         self._session = self.create_session()
 
-        self.serial_port    = serial_port    if serial_port     is not None else settings.SERIAL_PORT
-        self.baudrate       = settings.BAUDRATE
-        self.sync_channel   = sync_channel   if sync_channel    is not None else settings.SYNC_CHANNEL
-        self.sync_mode      = sync_mode      if sync_mode       is not None else settings.SYNC_MODE
-        self.net_port       = net_port       if net_port        is not None else settings.NET_PORT
+        self.serial_port    = serial_port    if serial_port     is not None else settings.PYBPOD_SERIAL_PORT
+        self.baudrate       = settings.PYBPOD_BAUDRATE
+        self.sync_channel   = sync_channel   if sync_channel    is not None else settings.PYBPOD_SYNC_CHANNEL
+        self.sync_mode      = sync_mode      if sync_mode       is not None else settings.PYBPOD_SYNC_MODE
+        self.net_port       = net_port       if net_port        is not None else settings.PYBPOD_NET_PORT
         self._hardware      = Hardware()    # type: Hardware
         self.bpod_modules   = None          # type: BpodModules
         self.bpod_start_timestamp = None
@@ -73,21 +73,21 @@ def __init__(self, serial_port=None, sync_channel=None, sync_mode=None, net_port
 
         self.session_timestamps = [] #Store the session timestamps in case bpod is using live_timestamps
 
-
         self._hardware.sync_channel = self.sync_channel  # 255 = no sync, otherwise set to a hardware channel number
         self._hardware.sync_mode    = self.sync_mode    # 0 = flip logic every trial, 1 = every state
 
-        self.session += SessionInfo( self.session.INFO_SERIAL_PORT, self.serial_port )
-        if self.net_port:
-            self.session += SessionInfo( self.session.INFO_NET_PORT,    self.net_port )
-
-        self.session += SessionInfo(self.session.INFO_CREATOR_NAME, settings.PYBPOD_CREATOR)
-        self.session += SessionInfo(self.session.INFO_PROJECT_NAME, settings.PYBPOD_PROJECT)
+        self.session += SessionInfo(self.session.INFO_SERIAL_PORT,     self.serial_port )
+        self.session += SessionInfo(self.session.INFO_PROTOCOL_NAME,   settings.PYBPOD_PROTOCOL)
+        self.session += SessionInfo(self.session.INFO_CREATOR_NAME,    settings.PYBPOD_CREATOR)
+        self.session += SessionInfo(self.session.INFO_PROJECT_NAME,    settings.PYBPOD_PROJECT)
         self.session += SessionInfo(self.session.INFO_EXPERIMENT_NAME, settings.PYBPOD_EXPERIMENT)
-        self.session += SessionInfo(self.session.INFO_BOARD_NAME, settings.PYBPOD_BOARD)
-        self.session += SessionInfo(self.session.INFO_SETUP_NAME, settings.PYBPOD_SETUP)
+        self.session += SessionInfo(self.session.INFO_BOARD_NAME,      settings.PYBPOD_BOARD)
+        self.session += SessionInfo(self.session.INFO_SETUP_NAME,      settings.PYBPOD_SETUP)
         self.session += SessionInfo(self.session.INFO_BPODGUI_VERSION, settings.PYBPOD_BPODGUI_VERSION)
 
+        if self.net_port:
+            self.session += SessionInfo( self.session.INFO_NET_PORT, self.net_port )
+
         for subject_name in settings.PYBPOD_SUBJECTS: 
             self.session += SessionInfo(self.session.INFO_SUBJECT_NAME, subject_name)
 
@@ -147,8 +147,8 @@ def open(self):
         if firmware_version > int(settings.TARGET_BPOD_FIRMWARE_VERSION):
             raise BpodErrorException('Error: Future firmware detected. Please update the Bpod python software.')
 
-        self._hardware.firmware_version     = firmware_version
-        self._hardware.machine_type         = machine_type
+        self._hardware.firmware_version = firmware_version
+        self._hardware.machine_type     = machine_type
         #########################################################
 
 
@@ -576,6 +576,14 @@ def __update_timestamps(self, sma, state_change_indexes):
         trial_end_timestamp, discrepancy    = self._bpodcom_read_timestamps()
         current_trial.trial_end_timestamp   = trial_end_timestamp
 
+        self.session += SessionInfo(
+            self.session.INFO_TRIAL_BPODTIME,
+            trial_end_timestamp-self.trial_start_timestamp, 
+            start_time=self.trial_start_timestamp,
+            end_time  =trial_end_timestamp
+        )
+
+
         if discrepancy>1:
             self.session += WarningMessage( "Bpod missed hardware update deadline(s) on the past trial by ~{milliseconds}ms".format(milliseconds=discrepancy) )
 

pybpodapi/bpod/bpod_com_protocol.py

@@ -215,6 +215,8 @@ def _bpodcom_hardware_description(self, hardware):
         outputs = self._arcom.read_char_array(array_len=n_outputs)  # type: list(str)
         logger.debug("Read outputs: %s", outputs)
 
+        print('max_states', max_states)
+        print('----------------------')
         hardware.max_states         = max_states
         hardware.cycle_period       = cycle_period
         hardware.max_serial_events  = max_serial_events

pybpodapi/bpod/bpod_io.py

@@ -29,7 +29,7 @@ def __init__(self, serial_port=None, workspace_path=None, session_name=None, syn
 
         self.session += SessionInfo("This is a PYBPOD file. Find more info at http://pybpod.readthedocs.io")
         self.session += SessionInfo( Session.INFO_BPODAPI_VERSION, pybpodapi.__version__)
-        self.session += SessionInfo( Session.INFO_PYBPOD_SESSION_NAME,    self.session_name )
+        self.session += SessionInfo( Session.INFO_SESSION_NAME,    self.session_name )
         self.session += SessionInfo( Session.INFO_SESSION_STARTED,  self.session.start_timestamp )
 
     def create_session(self):

pybpodapi/com/messaging/session_info.py

@@ -15,16 +15,17 @@ class SessionInfo(BaseMessage):
 	MESSAGE_TYPE_ALIAS = 'INFO'
 	MESSAGE_COLOR 	   = (150,150,255)
 
-	def __init__(self, infoname, infovalue=None):
-		super(SessionInfo, self).__init__(infoname)
+	def __init__(self, infoname, infovalue=None, start_time=None, end_time=None):
+		super(SessionInfo, self).__init__(infoname, host_timestamp=start_time)
 		self._infovalue = infovalue
+		self._endtime   = end_time
 
 	def tolist(self):
 		return [
 			self.MESSAGE_TYPE_ALIAS, 
 			self.pc_timestamp,
 			self.host_timestamp,
-			None,
+			self._endtime,
 			self.content,
 			self._infovalue
 		]

pybpodapi/com/messaging/state_occurrence.py

@@ -37,7 +37,7 @@ def tolist(self):
 			self.start_timestamp,
 			self.end_timestamp,
 			self.content,
-			None
+			self.end_timestamp-self.start_timestamp
 		]
 
 	@classmethod

pybpodapi/session.py

@@ -65,13 +65,14 @@ class Session(object):
     MSGTYPE_WARNING  = 'warning'
     MSGTYPE_STATE    = 'STATE'
 
-    INFO_PYBPOD_SESSION_NAME   = 'PROTOCOL-NAME'
+    INFO_SESSION_NAME = 'SESSION-NAME'
     INFO_SESSION_STARTED = 'SESSION-STARTED'
     INFO_SESSION_ENDED   = 'SESSION-ENDED'
     INFO_SERIAL_PORT     = 'SERIAL-PORT'
     INFO_NET_PORT        = 'NET-PORT'
     INFO_BPODAPI_VERSION = 'BPOD-API-VERSION'
 
+    INFO_PROTOCOL_NAME   = 'PROTOCOL-NAME'
     INFO_CREATOR_NAME    = 'CREATOR-NAME'
     INFO_PROJECT_NAME    = 'PROJECT-NAME'
     INFO_EXPERIMENT_NAME = 'EXPERIMENT-NAME'
@@ -80,6 +81,8 @@ class Session(object):
     INFO_SUBJECT_NAME    = 'SUBJECT-NAME'
     INFO_BPODGUI_VERSION = 'BPOD-GUI-VERSION'
 
+    INFO_TRIAL_BPODTIME = 'TRIAL-BPOD-TIME'
+
 
     def __init__(self, path=None):
         self.ostdout = sys.stdout

pybpodapi/settings.py

@@ -23,26 +23,25 @@
 #TARGET_BPOD_FIRMWARE_VERSION = "17" # 0.9
 TARGET_BPOD_FIRMWARE_VERSION  = "21"  
 
-SERIAL_PORT     = None
-NET_PORT        = None
-BAUDRATE        = 1312500
-SYNC_CHANNEL    = 255
-SYNC_MODE       = 1
+PYBPOD_SERIAL_PORT  = None
+PYBPOD_NET_PORT     = None
+PYBPOD_BAUDRATE     = 1312500
+PYBPOD_SYNC_CHANNEL = 255
+PYBPOD_SYNC_MODE    = 1
 
 
 BPOD_BNC_PORTS_ENABLED      = [True, True]
 BPOD_WIRED_PORTS_ENABLED    = [True, True]
 BPOD_BEHAVIOR_PORTS_ENABLED = [True, True, True, True, True, True, True, True]
 
-#SERIAL_PORT = '/dev/ttyACM0'
-
+PYBPOD_SERIAL_PORT = ''
 
+PYBPOD_PROTOCOL         = ''
 PYBPOD_CREATOR          = ''
 PYBPOD_PROJECT          = ''
 PYBPOD_EXPERIMENT       = ''
 PYBPOD_BOARD            = ''
 PYBPOD_SETUP            = ''
-PYBPOD_TASK             = ''
 PYBPOD_SESSION          = ''
 PYBPOD_SESSION_PATH     = ''
 PYBPOD_BPODGUI_VERSION  = ''