physion 1.2.2__tar.gz → 2.0__tar.gz

{physion-1.2.2/src/physion.egg-info → physion-2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: physion
-Version: 1.2.2
+Version: 2.0
 Summary: Vision Physiology Software
 Author-email: Yann Zerlaut <yann.zerlaut@icm-institute.org>, Mai-An Nguyen <mai-an.nguyen@icm-institute.org>, Laura Sofia Gonzalez <laura.gonzalez@icm-institute.org>
 Project-URL: Homepage, https://github.com/yzerlaut/physion
@@ -29,11 +29,21 @@ Requires-Dist: opencv-contrib-python-headless
 Requires-Dist: ffmpeg-python
 Requires-Dist: pyqt5
 Requires-Dist: openpyxl
-Requires-Dist: open-ephys-python-tools>=1.0
-Requires-Dist: spikeinterface[full]
-Requires-Dist: probeinterface
-Requires-Dist: elephant==1.0.0
-Requires-Dist: neo==0.14.4
+Requires-Dist: h5py
+Requires-Dist: hdmf
+Requires-Dist: pillow
+Requires-Dist: python-dateutil
+Requires-Dist: requests
+Provides-Extra: ephys
+Requires-Dist: open-ephys-python-tools>=1.0; extra == "ephys"
+Requires-Dist: spikeinterface[full]; extra == "ephys"
+Requires-Dist: probeinterface; extra == "ephys"
+Requires-Dist: elephant==1.0.0; extra == "ephys"
+Requires-Dist: neo==0.14.4; extra == "ephys"
+Provides-Extra: acquisition
+Requires-Dist: nidaqmx; extra == "acquisition"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
 Dynamic: license-file
 
 <!--             ** Build Instructions **              -->
@@ -71,6 +81,11 @@ Then either install:
 - the [Pypi build](https://pypi.org/project/physion/) with:
 ```
 pip install physion
+```
+  with optional dependencies for electrophysiology (spike sorting, LFP, ephys notebooks) and/or for acquisition setups:
+```
+pip install "physion[ephys]"
+pip install "physion[ephys,acquisition]"
 ```
 - from source with:
 ```

{physion-1.2.2 → physion-2.0}/README.md

@@ -33,6 +33,11 @@ Then either install:
 - the [Pypi build](https://pypi.org/project/physion/) with:
 ```
 pip install physion
+```
+  with optional dependencies for electrophysiology (spike sorting, LFP, ephys notebooks) and/or for acquisition setups:
+```
+pip install "physion[ephys]"
+pip install "physion[ephys,acquisition]"
 ```
 - from source with:
 ```

{physion-1.2.2 → physion-2.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "physion"
-version = "1.2.2"
+version = "2.0"
 authors = [
   { name="Yann Zerlaut", email="yann.zerlaut@icm-institute.org" },
   { name="Mai-An Nguyen", email="mai-an.nguyen@icm-institute.org" },
@@ -32,12 +32,32 @@ dependencies = [
     "ffmpeg-python",
     "pyqt5",
     "openpyxl",
+    # imported directly (previously only installed through other packages)
+    "h5py",
+    "hdmf",
+    "pillow",
+    "python-dateutil",
+    "requests",
+]
+
+[project.optional-dependencies]
+# electrophysiology: spike sorting, LFP, "Ephys-Analysis" and "CSD-Analysis" notebooks
+ephys = [
     "open-ephys-python-tools>=1.0",
     "spikeinterface[full]",
     "probeinterface",
     "elephant==1.0.0",
     "neo==0.14.4",
 ]
+# acquisition setups (camera SDKs: see docs/install/acquisition.md)
+acquisition = [
+    "nidaqmx",
+]
+test = ["pytest"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py"]  # the other scripts of tests/ are not collected
 
 [tool.setuptools.packages.find]
 where = ["src"]
@@ -45,6 +65,8 @@ where = ["src"]
 "physion.acquisition.protocols" = ["*.json"]
 "physion.acquisition.configs" = ["*.json"]
 "physion.acquisition" = ["DataTable.xlsx"]
+"physion.utils" = ["*.mplstyle"]
+"physion.visual_stim" = ["NI_bank/*.jpg"]
 
 [project.urls]
 "Homepage" = "https://github.com/yzerlaut/physion"

physion-2.0/src/physion/acquisition/__init__.py

@@ -0,0 +1,43 @@
+from . import settings, tools, run
+
+MODALITIES = ['NIDAQ',
+              'FaceCamera',
+              'RigCamera',
+              'ImagingCamera',
+              'Neuropixels',
+              'CaImaging',
+              'onlyDemo']
+
+EXPERIMENTERS = {
+    '':{'folder':''},
+    'Adrianna Nozownik':{
+        'folder':'Adrianna'
+        },
+    'Cibele Martins Pinho':{
+        'folder':'Cibele'
+        },
+    'Dhanasak Dhanasobhon':{
+        'folder':'Taddy'
+        },
+    'Joana Lourenco':{
+        'folder':'Joana'
+        },
+    'Laura Sofia Gonzalez':{
+        'folder':'Sofia'
+        },
+    'Nathan Mallet':{
+        'folder':'Nathan'
+        },
+    'Pan Sally Zhang':{
+        'folder':'Sally'
+        },
+    'Nelson Rebola':{
+        'folder':'Nelson'
+        },
+    'Valentin Ritou':{
+        'folder':'Valentin'
+        },
+    'Yann Zerlaut':{
+        'folder':'Yann'
+        },
+}

{physion-1.2.2 → physion-2.0}/src/physion/acquisition/gui.py

@@ -25,6 +25,7 @@ def multimodal(self,
     self.config = None
     self.subject, self.protocol = None, {}
     self.MODALITIES = MODALITIES
+    self.EXPERIMENTERS = EXPERIMENTERS
 
     ##########################################
     ######## Multiprocessing quantities  #####
@@ -55,13 +56,7 @@ def multimodal(self,
 
     # ========================================================
     #------------------- SIDE PANELS FIRST -------------------
-    # folder box
-    self.add_side_widget(tab.layout,
-            QtWidgets.QLabel('data folder:'))
-    self.folderBox = QtWidgets.QComboBox(self)
-    self.folderBox.addItems(FOLDERS.keys())
-    self.add_side_widget(tab.layout, self.folderBox)
-    self.add_side_widget(tab.layout, QtWidgets.QLabel(' '))
+    # -------------------------------------------------------
     self.add_side_widget(tab.layout, QtWidgets.QLabel(' '))
     # -------------------------------------------------------
     self.add_side_widget(tab.layout,
@@ -100,7 +95,7 @@ def multimodal(self,
     # self.add_side_widget(tab.layout, self.saveSetB)
 
     self.buildNWB = QtWidgets.QPushButton('plot NIdaq of last', self)
-    self.buildNWB.clicked.connect(plot_NIdaq_of_last)
+    self.buildNWB.clicked.connect(lambda: plot_NIdaq_of_last(self))
     self.add_side_widget(tab.layout, self.buildNWB)
 
     # ========================================================
@@ -124,10 +119,11 @@ def multimodal(self,
                          ip, self.side_wdgt_length+1, 
                          1, int(width/2))
     self.experimenterBox = QtWidgets.QComboBox(self)
-    self.experimenterBox.addItems(EXPERIMENTERS)
+    self.experimenterBox.addItems(self.EXPERIMENTERS.keys())
     tab.layout.addWidget(self.experimenterBox,\
                          ip, self.side_wdgt_length+int(width/2)+1, 
                          1, int(width/2))
+    self.experimenterBox.activated.connect(self.update_config)
     ip+=1
     # -
     tab.layout.addWidget(\
@@ -144,7 +140,7 @@ def multimodal(self,
     ip+=1
     # -
     tab.layout.addWidget(\
-        QtWidgets.QLabel(40*' '+'** Visual Protocol **'+40*' ', self),
+        QtWidgets.QLabel(40*' '+'** Stimulation Protocol **'+40*' ', self),
                          ip, self.side_wdgt_length, 
                          1, width)
     ip+=1
@@ -155,18 +151,6 @@ def multimodal(self,
                          ip, self.side_wdgt_length+1, 
                          1, width)
     ip+=1
-    # -
-    # tab.layout.addWidget(\
-    #     QtWidgets.QLabel(40*' '+'** Rec. Settings **'+40*' ', self),
-    #                      ip, self.side_wdgt_length, 
-    #                      1, width)
-    # ip+=1
-    # # -
-    # self.recordingBox = QtWidgets.QComboBox(self)
-    # tab.layout.addWidget(self.recordingBox,\
-    #                      ip, self.side_wdgt_length+1, 
-    #                      1, width)
-    # ip+=1
 
     # image panels layout:
     self.winImg = pg.GraphicsLayoutWidget()
@@ -175,12 +159,31 @@ def multimodal(self,
                          self.nWidgetRow-ip, 
                          self.nWidgetCol-self.side_wdgt_length)
     # image choice box
-    self.imgButton = QtWidgets.QComboBox()
-    self.imgButton.addItems([' *pick camera* ', 'FaceCamera', 'RigCamera', 'ImagingCamera'])
-    tab.layout.addWidget(self.imgButton,
+    tab.layout.addWidget(\
+        QtWidgets.QLabel('  =>  live :   ', self),
+                         ip, self.nWidgetCol-2,
+                         1, 2)
+    ip+=1
+    self.liveFaceButton = QtWidgets.QPushButton('Face')
+    self.liveFaceButton.setCheckable(True)
+    tab.layout.addWidget(self.liveFaceButton,\
                          ip, self.nWidgetCol-2,
                          1, 2)
-    # FaceCamera panel
+    ip+=1
+    self.liveRigButton = QtWidgets.QPushButton('Rig')
+    self.liveRigButton.setCheckable(True)
+    tab.layout.addWidget(self.liveRigButton,\
+                         ip, self.nWidgetCol-2,
+                         1, 2)
+    ip+=1
+    self.liveImagingButton = QtWidgets.QPushButton('Imaging')
+    self.liveImagingButton.setCheckable(True)
+    tab.layout.addWidget(self.liveImagingButton,\
+                         ip, self.nWidgetCol-2,
+                         1, 2)
+    ip+=1
+
+    # FaceCamera/RigCamera/Imaging panel
     self.pFace = self.winImg.addViewBox(lockAspect=True,
                         invertY=True, border=[1, 1, 1])
     self.pCamImg = pg.ImageItem(np.ones((10,12))*50)
@@ -220,12 +223,13 @@ def multimodal(self,
         self.runButton.setEnabled(False)
         self.stopButton.setEnabled(False)
 
-def plot_NIdaq_of_last():
-    # last folder
+def plot_NIdaq_of_last(self):
+    # last folder (in the experimenter subfolder)
+    root_data_folder = os.path.join(\
+                os.path.expanduser('~'), 'DATA',
+                    self.EXPERIMENTERS[self.experimenterBox.currentText()]['folder'])
     folder = last_datafolder_in_dayfolder(\
-                # day_folder(FOLDERS[list(FOLDERS.keys())[0]]))
-                # day_folder(FOLDERS[self.folderBox.currentText()])
-                day_folder(os.path.expanduser('~/DATA')))
+                day_folder(root_data_folder))
     print()
     print('[ ] loading NIdaq data of recording: ', folder)
     print()

{physion-1.2.2 → physion-2.0}/src/physion/acquisition/run.py

@@ -6,9 +6,9 @@ from PyQt5 import QtCore
 
 from physion.utils.files import get_latest_file
 from physion.acquisition.tools import find_line_props,\
-        check_gui_to_init_metadata, set_filename_and_folder, stimulus_movies_folder
-from physion.acquisition import recordings
-
+        check_gui_to_init_metadata, set_filename_and_folder
+from physion.opto import stim as opto_stim
+from physion.ephys.synch import sequence as ephysSynch
 from physion.visual_stim.main import build_stim as build_VisualStim
 from physion.visual_stim.show import init_stimWindows
 
@@ -42,8 +42,12 @@ except ModuleNotFoundError:
 def init_VisualStim(self):
 
     movie_folder = \
-        os.path.join(stimulus_movies_folder,
-                     self.protocolBox.currentText())
+        os.path.join(
+            os.path.expanduser('~'),
+            'visualStim-protocols', self.EXPERIMENTERS[\
+                        self.experimenterBox.currentText()\
+                                        ]['folder'], 
+            self.protocolBox.currentText())
 
     with open(\
             os.path.join(movie_folder,
@@ -160,7 +164,7 @@ def run(self):
             #  -- find channel
             props = find_line_props(digital_line_labels,
                                     'ephys-synch-signal')
-            sequence = recordings.ephysSynch(self.max_time, freq=props['freq'])
+            sequence = ephysSynch(self.max_time, freq=props['freq'])
             digital_output_steps += [{'channel':props['chan'], 'onset':e, 'duration':0.1}\
                                                     for e in sequence[:-1]]
 
@@ -168,27 +172,22 @@ def run(self):
             props = find_line_props(digital_line_labels,
                                     '2P-start-stop-trigger')
             
-            ###### EXTRACT THE DELAY FROM THE METADATA:  "2P-start-stop-trigger-with-0.1s-delay"
-
             digital_output_steps += [\
                 {'channel':props['chan'], 'onset':self.metadata['2P']['onset-delay'], 'duration':0.1},
                 {'channel':props['chan'], 'onset':self.max_time - self.metadata['2P']['offset-advance'], 'duration':0.1}]
             
-            ## --- old code using analog outputs --- 
-            # def trigger2P(t):
-            #     array = np.zeros(len(t), dtype=float)
-            #     array[(t>=TwoP_trigger_delay) & (t<(TwoP_trigger_delay+TwoP_pulse_length))] = 1.
-            #     return 5.*array 
-            # analog_output_funcs.append(recordings.trigger2P)
 
         if self.stim is not None:
-            #  means WITH VisualStim -- find channel
+            #  means WITH VisualStim -- find channel --> TTL for stim onsets
             props = find_line_props(digital_line_labels,
                                     'visual-stim-episode-start')
             digital_output_steps += [{'channel':props['chan'], 'onset':e, 'duration':0.05}\
                                         for e in self.stim.experiment['time_start']]
 
+        ################################################################################
+        ##### ---> from here: WHAT IS THIS ?
         if (len(analog_output_labels)>0) and ('trigger-delay' in analog_output_labels[0]):
+            print('analog output trigger delay ... ')
             trigger_delay = float(analog_output_labels[0].split('trigger-delay-')[1].split('s')[0])
             def delayedTrigger(t):
                 array = np.zeros(len(t), dtype=float)
@@ -197,6 +196,7 @@ def run(self):
             analog_output_funcs.append(delayedTrigger)
 
         if (len(analog_output_labels)>1) and ('square-wave-TTL' in analog_output_labels[1]):
+            print('analog output square wave TTL ...')
             period = 1./2./float(analog_output_labels[1].split('square-wave-TTL-')[1].split('Hz')[0])
             def squareTTL(t):
                 array = np.zeros(len(t), dtype=float)
@@ -206,25 +206,14 @@ def run(self):
                     tt+=2*period
                 return 5.*array 
             analog_output_funcs.append(squareTTL)
+        ##### ---> end: WHAT IS THIS ?           TO BE REMOVED IF NOT USED...
+        ################################################################################
+
+        if 'Opto-stim' in self.protocol:
 
-        if 'Opto' in self.protocolBox.currentText():
-            ## -------------------------------------------------- ##
-            ## --------- OPTOGENETIC STEP STIMULATION !!! ------- ##
-            ##          the protocol name should have the suffix  ##
-            ##          of the form +1sPrePost, +0.5sPrePost, ... ##
-            ## -------------------------------------------------- ##
-            prepost_duration = float(self.protocolBox.currentText().split('+')[1].split('sPrePost')[0])
-            #  means WITH VisualStim -- find channel
-            props = find_line_props(\
-                self.metadata['NIdaq']['digital-outputs']['line-labels'],
-                                    'LED-optogenetics-activation')
-            digital_output_steps += [{'channel':props['chan'], 
-                                      'onset':e-prepost_duration, 
-                                      'duration':d+2*prepost_duration}\
-                                        for e, d, r in zip(\
-                                            self.stim.experiment['time_start'],
-                                            self.stim.experiment['time_duration'],
-                                            self.stim.experiment['repeat']) if (r%2==1)]
+            digital_output_steps += opto_stim.TTL_signal(self.stim, 
+                                                         self.metadata,
+                                                         self.protocol['Opto-stim'])
 
         if self.metadata['NIDAQ']:
 
@@ -437,19 +426,19 @@ def run_update(self):
 
     # ----- online visualization here -----
     if (self.FaceCamera_process is not None) and\
-                    (self.imgButton.currentText()=='FaceCamera'):
+                    (self.liveFaceButton.isChecked()):
         image = np.load(get_latest_file(\
                 os.path.join(str(self.datafolder.get()), 'FaceCamera-imgs')))
         self.pCamImg.setImage(image.T)
 
     elif (self.RigCamera_process is not None) and\
-                    (self.imgButton.currentText()=='RigCamera'):
+                    (self.liveRigButton.isChecked()):
         image = np.load(get_latest_file(\
                 os.path.join(str(self.datafolder.get()), 'RigCamera-imgs')))
         self.pCamImg.setImage(image.T)
 
     elif (self.ImagingCamera_process is not None) and\
-                    (self.imgButton.currentText()=='ImagingCamera'):
+                    (self.liveImagingButton.isChecked()):
         image = np.load(get_latest_file(\
                 os.path.join(str(self.datafolder.get()), 'ImagingCamera-imgs')))
         self.pCamImg.setImage(image.T)

{physion-1.2.2 → physion-2.0}/src/physion/acquisition/settings.py

@@ -24,7 +24,20 @@ def get_config_list(self):
 
 def update_config(self):
 
-    if self.configBox.currentText()!='':
+    if hasattr(self, 'experimenterBox'):
+        experimenter = self.experimenterBox.currentText()
+    else:
+        experimenter = ''
+
+    config = self.configBox.currentText()
+    if hasattr(self, 'EXPERIMENTERS'):
+        protocol_folder = os.path.join(os.path.expanduser('~'),
+                                'visualStim-protocols',
+                                self.EXPERIMENTERS[experimenter]['folder'])
+    else:
+        protocol_folder = ''
+
+    if config!='':
 
         # first read the new config
         fn = os.path.join(base_path, 'configs',
@@ -32,14 +45,21 @@ def update_config(self):
         with open(fn) as f:
             self.config = json.load(f)
 
+
         if hasattr(self, 'protocolBox'):
             # now update protocols
-            if self.config['protocols']=='all':
-                self.protocol_list = [f for f in os.listdir(os.path.join(base_path,
-                                        'protocols', 'movies')) if\
-                                            ((f!='_') and not ('DS' in f) and not ('._' in f))]
+
+            if os.path.isdir(protocol_folder):
+
+                self.protocol_list = [f for f in os.listdir(protocol_folder)\
+                                       if ((f!='_') and not ('DS' in f) and not ('._' in f))]
+
             else:
-                self.protocol_list = self.config['protocols']
+                print()
+                print(' no "visualStim-protocols" found in ~/visualStim-protocol/%s' % experimenter)
+                print()
+                self.protocol_list = []
+
             self.protocolBox.clear()
             self.protocolBox.addItems(['None']+self.protocol_list)
 
@@ -52,9 +72,6 @@ def update_config(self):
                 and not self.stopButton.isEnabled():
             self.runButton.setEnabled(True)
 
-     # now update screen 
-        # if 'Screen' in self.config:
-            # self.screenBox.setCurrentText(self.config['Screen'])
 
 def save_settings(self):
 

{physion-1.2.2 → physion-2.0}/src/physion/acquisition/tools.py

@@ -6,17 +6,13 @@ base_path = str(pathlib.Path(__file__).resolve().parents[0])
 from physion.utils.files0 import generate_datafolders, get_date, get_time
 from physion.utils.paths import FOLDERS
 
-stimulus_movies_folder = os.path.join(base_path, 
-                                      'protocols', 'movies')
-
 def set_filename_and_folder(self):
 
     self.date, self.time = get_date(), get_time()
-    if hasattr(self, 'folderBox'):
-        self.root_data_folder = FOLDERS[self.folderBox.currentText()]
-    else:
-        self.root_data_folder = os.path.join(\
-                            os.path.expanduser('~'), 'DATA')
+
+    self.root_data_folder = os.path.join(\
+                os.path.expanduser('~'), 'DATA', 
+                    self.EXPERIMENTERS[self.experimenterBox.currentText()]['folder'])
 
     self.date_time_folder = generate_datafolders(\
                                     self.root_data_folder,
@@ -70,9 +66,15 @@ def check_gui_to_init_metadata(self):
                 'subject_ID':self.subjectBox.text()}
 
     if self.protocolBox.currentText()!='None':
-        fn = os.path.join(stimulus_movies_folder,
-                          self.protocolBox.currentText(), 
+        fn = os.path.join(
+                os.path.expanduser('~'),
+                'visualStim-protocols',
+                self.EXPERIMENTERS[\
+                            self.experimenterBox.currentText()\
+                                            ]['folder'], 
+                self.protocolBox.currentText(),
                           'protocol.json')
+
         with open(fn) as f:
             self.protocol = json.load(f)
     else:

{physion-1.2.2 → physion-2.0}/src/physion/analysis/dataframe.py

@@ -329,6 +329,14 @@ def NWB_to_dataframe(nwbfile,
 
 ############################################################################
 
+def episode_value(data, key, i):
+    """
+    value of the stimulus quantity "key" for episode "i" as a scalar
+        (older files store the episode quantities with shape (episodes, 1))
+    """
+    return float(np.ravel(data.nwbfile.stimulus[key].data[i])[0])
+
+
 def build_stim_specific_array(data, index_cond, time, 
                               normalize=False):
 
@@ -338,11 +346,11 @@ def build_stim_specific_array(data, index_cond, time,
     for i in np.flatnonzero(index_cond):
 
         if i<data.nwbfile.stimulus['time_start_realigned'].num_samples:
-            tstart = data.nwbfile.stimulus['time_start_realigned'].data[i]
-            tstop = data.nwbfile.stimulus['time_stop_realigned'].data[i]
+            tstart = episode_value(data, 'time_start_realigned', i)
+            tstop = episode_value(data, 'time_stop_realigned', i)
             
 
-            t_cond = (time>=float(tstart)) & (time<float(tstop))
+            t_cond = (time>=tstart) & (time<tstop)
             array[t_cond] = True
 
     # TO BE FIXED
@@ -382,7 +390,7 @@ def build_timelag_set_of_stim_specific_arrays(data, DF, index_cond,
 
     Nframe_pre = max([1, int(pre_interval/DF.dt)]) # at least one frame
     Nframe_post = int(post_interval/DF.dt)
-    Nframe_stim = int(np.min([data.nwbfile.stimulus['time_duration'].data[i]\
+    Nframe_stim = int(np.min([episode_value(data, 'time_duration', i)\
             for i in np.flatnonzero(index_cond)])/DF.dt)
 
 
@@ -394,8 +402,8 @@ def build_timelag_set_of_stim_specific_arrays(data, DF, index_cond,
     for i in np.flatnonzero(index_cond):
 
         if i<data.nwbfile.stimulus['time_start_realigned'].num_samples:
-            tstart = data.nwbfile.stimulus['time_start_realigned'].data[i]
-            tstop = data.nwbfile.stimulus['time_stop_realigned'].data[i]
+            tstart = episode_value(data, 'time_start_realigned', i)
+            tstop = episode_value(data, 'time_stop_realigned', i)
 
             iT0 = np.argmin((DF['time']-tstart)**2)
            

{physion-1.2.2 → physion-2.0}/src/physion/analysis/episodes/build.py

@@ -32,6 +32,7 @@ class EpisodeData:
         'neuropil',
         'dFoF',
         'spikes',
+        'firing',
         'LFP',
         'MUA'
     """
@@ -205,7 +206,7 @@ class EpisodeData:
                     QUANTITY_VALUES.append(getattr(full_data, quantity))
                     QUANTITY_TIMES.append(getattr(full_data, 't_%s' % quantity))
                     QUANTITIES.append(quantity)
-                except BaseException as be:
+                except Exception as be:
                     print()
                     print(be)
                     print()
@@ -250,7 +251,7 @@ class EpisodeData:
                                         kind=interpolation)
                         RESPS.append(func(self.t))
 
-                except BaseException as be:
+                except (ValueError, IndexError) as be:
 
                     success=False # we switch this off to remove the episode in all modalities
                     if self.verbose:
@@ -269,7 +270,7 @@ class EpisodeData:
                 for key in full_data.nwbfile.stimulus.keys():
                     try:
                         getattr(self, key).append(full_data.nwbfile.stimulus[key].data[iEp,0])
-                    except BaseException as be:
+                    except (IndexError, ValueError, TypeError) as be:
                         pass # we skip thise variable
 
         # transform stim params to np.array

physion-2.0/src/physion/analysis/modalities/__init__.py

@@ -0,0 +1,12 @@
+"""
+the modalities of the NWB files, read by physion.analysis.read_NWB.Data
+
+one module per modality, each one defining the methods (has_X, build_X, ...)
+of a "mixin" class inherited by the Data class
+"""
+from .visual_stim import VisualStimMixin
+from .locomotion import LocomotionMixin
+from .facecamera import FaceCameraMixin
+from .opto import OptoMixin
+from .ophys import OphysMixin
+from .ephys import EphysMixin