Merge branch 'dev'

Author: ThomasAkam

com/data_logger.py

@@ -21,18 +21,20 @@ def set_state_machine(self, sm_info):
                            in self.sm_info['analog_inputs'].items()}
         self.analog_files = {ai['ID']: None for ai in self.sm_info['analog_inputs'].values()}
 
-    def open_data_file(self, data_dir, experiment_name, subject_ID, datetime_now=None):
+    def open_data_file(self, data_dir, experiment_name, setup_ID, subject_ID, datetime_now=None):
         '''Open data file and write header information.'''
         self.data_dir = data_dir
         self.experiment_name = experiment_name
         self.subject_ID = subject_ID
+        self.setup_ID = setup_ID
         if datetime_now is None: datetime_now = datetime.now()
         file_name = os.path.join(self.subject_ID + datetime_now.strftime('-%Y-%m-%d-%H%M%S') + '.txt')
         self.file_path = os.path.join(self.data_dir, file_name)
         self.data_file = open(self.file_path, 'w', newline = '\n')
         self.data_file.write('I Experiment name  : {}\n'.format(self.experiment_name))
         self.data_file.write('I Task name : {}\n'.format(self.sm_info['name']))
         self.data_file.write('I Task file hash : {}\n'.format(self.sm_info['task_hash']))
+        self.data_file.write('I Setup ID : {}\n'.format(self.setup_ID))
         self.data_file.write('I Subject ID : {}\n'.format(self.subject_ID))
         self.data_file.write('I Start date : ' + datetime_now.strftime('%Y/%m/%d %H:%M:%S') + '\n\n')
         self.data_file.write('S {}\n\n'.format(json.dumps(self.sm_info['states'])))
@@ -45,7 +47,7 @@ def copy_task_file(self, data_dir, tasks_dir, dir_name='task_files'):
         if not os.path.exists(exp_tasks_dir):
             os.mkdir(exp_tasks_dir)
         task_file_path = os.path.join(tasks_dir, self.sm_info['name']+'.py')
-        task_save_name = self.sm_info['name']+'_{}.py'.format(self.sm_info['task_hash'])
+        task_save_name = os.path.split(self.sm_info['name'])[1] +'_{}.py'.format(self.sm_info['task_hash'])
         if not task_save_name in os.listdir(exp_tasks_dir):
             copyfile(task_file_path, os.path.join(exp_tasks_dir, task_save_name))
 

com/pycboard.py

@@ -278,10 +278,12 @@ def load_hardware_definition(self, hwd_path=os.path.join(dirs['config'], 'hardwa
         else:
             self.print('Hardware definition file not found.') 
 
-    def setup_state_machine(self, sm_name, sm_dir=dirs['tasks'], uploaded=False):
+    def setup_state_machine(self, sm_name, sm_dir=None, uploaded=False):
         '''Transfer state machine descriptor file sm_name.py from folder sm_dir
         to board. Instantiate state machine object as state_machine on pyboard.'''
         self.reset()
+        if sm_dir is None:
+            sm_dir = dirs['tasks']
         sm_path = os.path.join(sm_dir, sm_name + '.py')
         if uploaded:
             self.print('\nResetting task. ', end='')
@@ -350,7 +352,10 @@ def process_data(self):
             new_byte = self.serial.read(1)  
             if new_byte == b'A': # Analog data, 13 byte header + variable size content.
                 data_header = self.serial.read(13)
-                typecode      = data_header[0:1].decode()             
+                typecode      = data_header[0:1].decode() 
+                if typecode not in ('b','B','h','H','l','L'):
+                    new_data.append(('!','bad typecode A'))
+                    continue   
                 ID            = int.from_bytes(data_header[1:3], 'little')
                 sampling_rate = int.from_bytes(data_header[3:5], 'little')
                 data_len      = int.from_bytes(data_header[5:7], 'little')

data/.gitignore

@@ -1,3 +1,3 @@
-# Ignore all contents of data folder except .gitignore needed to ensure folder is version controlled.
+# Ignore all contents of folder except .gitignore needed to ensure folder is version controlled.
 *
 !.gitignore

experiments/.gitignore

@@ -0,0 +1,3 @@
+# Ignore all contents of folder except .gitignore needed to ensure folder is version controlled.
+*
+!.gitignore

experiments/.hgempty

@@ -96,18 +96,22 @@ def __init__(self):
         # Go to readthedocs
         documentation_action= QtGui.QAction("&Documentation", self)
         documentation_action.triggered.connect(self.view_docs)
+        documentation_action.setIcon(QtGui.QIcon("gui/icons/book.svg"))
         help_menu.addAction(documentation_action)
         # Go to Google forum
         forum_action= QtGui.QAction("&Forum", self)
         forum_action.triggered.connect(self.view_forum)
+        forum_action.setIcon(QtGui.QIcon("gui/icons/google-groups.svg")) #https://iconscout.com/icon/google-groups-1
         help_menu.addAction(forum_action)
         # Go to GitHub Repository
         github_action= QtGui.QAction("&GitHub Repository", self)
         github_action.triggered.connect(self.view_github)
+        github_action.setIcon(QtGui.QIcon("gui/icons/github.svg")) #https://simpleicons.org/?q=github
         help_menu.addAction(github_action)
         # Keyboard shortcuts dialog.
         shortcuts_action = QtGui.QAction("&Keyboard shortcuts", self)
         shortcuts_action.triggered.connect(self.shortcuts_dialog.show)
+        shortcuts_action.setIcon(QtGui.QIcon("gui/icons/keyboard.svg"))
         help_menu.addAction(shortcuts_action)
 
         self.show()
@@ -127,10 +131,19 @@ def view_forum(self):
     def view_github(self):
         QtGui.QDesktopServices.openUrl(QtCore.QUrl("https://github.com/pyControl/pyControl"))
 
+    def get_task_file_list(self):
+        '''Return list of .py files in tasks folder and subfolders in format:
+        subdir_1/subdir_2/task_file_name.py'''
+        task_files = []
+        for (dirpath, dirnames, filenames) in os.walk(dirs['tasks']):
+            task_files += [os.path.join(dirpath, file).split(dirs['tasks'])[1][1:-3]
+                           for file in filenames if file.endswith('.py')]
+        return task_files
+
     def refresh(self):
         '''Called regularly when framework not running.'''
         # Scan task folder.
-        tasks = [t.split('.')[0] for t in os.listdir(dirs['tasks']) if t[-3:] == '.py']
+        tasks = self.get_task_file_list()
         self.available_tasks_changed = tasks != self.available_tasks
         if self.available_tasks_changed:    
             self.available_tasks = tasks