Merge pull request #92 from catalystneuro/electrodes_mapping

Electrodes mapping

ecogvis/ecogvis.py

@@ -33,6 +33,7 @@
 from ecogvis.functions.save_to_nwb import SaveToNWBDialog
 from ecogvis.functions.nwb_copy_file import nwb_copy_file
 
+
 annotationAdd_ = False
 annotationDel_ = False
 annotationColor_ = 'red'
@@ -178,9 +179,6 @@ def init_gui(self):
         action_del_badchannel = QAction('Del Bad Channel', self)
         channels_tools_menu.addAction(action_del_badchannel)
         action_del_badchannel.triggered.connect(self.del_badchannel)
-        action_save_badchannel = QAction('Save Bad Channels', self)
-        channels_tools_menu.addAction(action_save_badchannel)
-        action_save_badchannel.triggered.connect(self.save_badchannel)
         action_spectral_decomposition = QAction('Spectral Decomposition', self)
         toolsMenu.addAction(action_spectral_decomposition)
         action_spectral_decomposition.triggered.connect(self.spectral_decomposition)
@@ -251,8 +249,6 @@ def init_gui(self):
         self.push3_1.clicked.connect(self.add_badchannel)
         self.push3_2 = QPushButton('Del')
         self.push3_2.clicked.connect(self.del_badchannel)
-        self.push3_3 = QPushButton('Save')
-        self.push3_3.clicked.connect(self.save_badchannel)
 
         # Get channel by brain region
         self.push4_0 = QPushButton('Select regions')
@@ -284,7 +280,6 @@ def init_gui(self):
         grid1.addWidget(qlabelBadChannels, 4, 0, 1, 6)
         grid1.addWidget(self.push3_1, 5, 0, 1, 2)
         grid1.addWidget(self.push3_2, 5, 2, 1, 2)
-        grid1.addWidget(self.push3_3, 5, 4, 1, 2)
         grid1.addWidget(self.push4_0, 6, 0, 1, 3)
         grid1.addWidget(self.push5_0, 6, 3, 1, 3)
         grid1.addWidget(self.push6_0, 7, 0, 1, 3)
@@ -576,10 +571,6 @@ def del_badchannel(self):
             except Exception as ex:
                 print(str(ex))
 
-    def save_badchannel(self):
-        """Saves bad channels to file."""
-        self.model.BadChannelSave()
-
     def spectral_decomposition(self):
         """Opens Spectral decomposition dialog."""
         w = SpectralChoiceDialog(self)
@@ -755,7 +746,7 @@ def ChannelSelect(self):
         self.reset_buttons()
         # Dialog to choose channels from specific brain regions
         w = SelectChannelsDialog(self.model.all_regions, self.model.regions_mask)
-        all_locs = self.model.nwb.electrodes['location'][:]
+        all_locs = self.model.nwb.electrodes['location'][self.model.electrical_series_channel_ids]
         self.model.channels_mask = np.zeros(len(all_locs))
         for loc in w.choices:
             self.model.channels_mask += all_locs == np.array(loc)

ecogvis/functions/nwb_copy_file.py

@@ -266,10 +266,10 @@ def copy_obj(obj_old, nwb_old, nwb_new):
 
     # ElectricalSeries --------------------------------------------------------
     if type(obj_old) is ElectricalSeries:
-        nChannels = len(obj_old.electrodes.table['x'].data)
-        elecs_region = nwb_new.electrodes.create_region(
+        region = np.array(obj_old.electrodes.table.id[:])[obj_old.electrodes.data[:]].tolist()
+        elecs_region = nwb_new.create_electrode_table_region(
             name='electrodes',
-            region=np.arange(nChannels).tolist(),
+            region=region,
             description=''
         )
         els = ElectricalSeries(
@@ -297,7 +297,6 @@ def copy_obj(obj_old, nwb_old, nwb_new):
             'Expected precisely one electrical series, got %i!' %
             len(obj_old.electrical_series))
         els = list(obj_old.electrical_series.values())[0]
-        nChannels = els.data.shape[1]
 
         ####
         # first check for a table among the new file's data_interfaces
@@ -308,9 +307,10 @@ def copy_obj(obj_old, nwb_old, nwb_new):
             LFP_dynamic_table = nwb_new.electrodes
         ####
 
+        region = np.array(els.electrodes.table.id[:])[els.electrodes.data[:]].tolist()
         elecs_region = LFP_dynamic_table.create_region(
             name='electrodes',
-            region=[i for i in range(nChannels)],
+            region=region,
             description=els.electrodes.description
         )
 

ecogvis/functions/subFunctions.py

@@ -73,15 +73,17 @@ def __init__(self, par, htk_config=None):
         self.tbin_signal = 1 / self.fs_signal  # time bin duration [seconds]
         self.nBins = self.source.data.shape[0]     # total number of bins
         self.min_window_bins = 10                   # minimum number of bins to plot
-        self.nChTotal = self.source.data.shape[1]     # total number of channels
-        self.allChannels = np.arange(0, self.nChTotal)  # array with all channels
+        # all electricalseries channels ids
+        self.all_channels_ids = self.source.electrodes.table.id[:]
+        self.electrical_series_channel_ids = np.array(self.all_channels_ids)[self.source.electrodes.data[:]].tolist()
+        self.n_channels_total = len(self.electrical_series_channel_ids)     # total number of channels
 
         # Get Brain regions present in current file
-        self.all_regions = list(set(list(self.nwb.electrodes['location'][:])))
+        self.all_regions = list(set(list(self.nwb.electrodes['location'][self.electrical_series_channel_ids])))
         self.all_regions.sort()
         self.regions_mask = [True] * len(self.all_regions)
 
-        self.channels_mask = np.ones(len(self.nwb.electrodes['location'][:]))
+        self.channels_mask = np.ones(len(self.regions_mask))
         self.channels_mask_ind = np.where(self.channels_mask)[0]
 
         self.h = []
@@ -93,7 +95,7 @@ def __init__(self, par, htk_config=None):
 
         # Channels to show
         self.firstCh = int(self.parent.qline1.text())
-        self.lastCh = min(self.nChTotal, int(self.parent.qline0.text()))
+        self.lastCh = min(self.n_channels_total, int(self.parent.qline0.text()))
         self.parent.qline0.setText(str(self.lastCh))
         self.nChToShow = self.lastCh - self.firstCh + 1
         self.selectedChannels = np.arange(self.firstCh - 1, self.lastCh)
@@ -102,9 +104,10 @@ def __init__(self, par, htk_config=None):
 
         # List of bad channels
         if 'bad' in self.nwb.electrodes:
-            self.badChannels = np.where(self.nwb.electrodes['bad'][:])[0].tolist()
+            aux_mask = self.nwb.electrodes[self.electrical_series_channel_ids]['bad']
+            self.bad_channels_ids = list(self.nwb.electrodes[self.electrical_series_channel_ids][aux_mask].index)
         else:
-            self.badChannels = []
+            self.bad_channels_ids = []
 
         # Load invalid intervals from NWB file
         self.allIntervals = []
@@ -249,7 +252,8 @@ def TimeSeries_plotter(self):
         # Iterate over chosen channels, plot one at a time
         nrows, ncols = np.shape(plotData)
         for i in range(nrows):
-            if self.selectedChannels[i] in self.badChannels:
+            elec_index = self.source.electrodes[int(self.selectedChannels[i])].index[0]
+            if elec_index in self.bad_channels_ids:
                 plt2.plot(timebaseGuiUnits, plotData[i], pen=pg.mkPen((220, 0, 0), width=1.2))
             else:
                 c = pg.mkPen((0, 120, 0), width=1.2)
@@ -258,7 +262,7 @@ def TimeSeries_plotter(self):
                 plt2.plot(timebaseGuiUnits, plotData[i], pen=c)
         plt2.setLabel('bottom', 'Time', units='sec')
         plt2.setLabel('left', 'Channel #')
-        labels = [str(ch + 1) for ch in self.selectedChannels]
+        labels = [str(self.electrical_series_channel_ids[ch]) for ch in self.selectedChannels]
         ticks = list(zip(self.scaleVec, labels))
         plt2.getAxis('left').setTicks([ticks])
         plt2.setXRange(timebaseGuiUnits[0], timebaseGuiUnits[-1], padding=0.003)
@@ -414,11 +418,11 @@ def time_scroll(self, scroll=0):
     def channel_Scroll_Up(self, opt='unit'):
         """Updates the channels to be plotted. Buttons: ^, ^^ """
         # Test upper limit
-        if self.lastCh < self.nChTotal:
+        if self.lastCh < self.n_channels_total:
             if opt == 'unit':
                 step = 1
             elif opt == 'page':
-                step = np.minimum(self.nChToShow, self.nChTotal - self.lastCh)
+                step = np.minimum(self.nChToShow, self.n_channels_total - self.lastCh)
             # Add +1 to first and last channels
             self.firstCh += step
             self.lastCh += step
@@ -454,15 +458,15 @@ def nChannels_Displayed(self):
         if self.firstCh < 1:
             self.firstCh = 1
 
-        if self.firstCh > self.nChTotal:
-            self.firstCh = self.nChTotal
-            self.lastCh = self.nChTotal
+        if self.firstCh > self.n_channels_total:
+            self.firstCh = self.n_channels_total
+            self.lastCh = self.n_channels_total
 
         if self.lastCh < 1:
             self.lastCh = self.firstCh
 
-        if self.lastCh > self.nChTotal:
-            self.lastCh = self.nChTotal
+        if self.lastCh > self.n_channels_total:
+            self.lastCh = self.n_channels_total
 
         if self.lastCh - self.firstCh < 1:
             self.lastCh = self.firstCh
@@ -733,10 +737,11 @@ def BadChannelAdd(self, ch_list):
         ch_list : list of integers
             List of indices of channels to be marked as 'bad'.
         """
+        # Update list of bad electrodes ids
         for ch in ch_list:
-            if ch not in self.badChannels:
-                self.badChannels.append(ch)
-        self.refreshScreen()
+            if ch not in self.bad_channels_ids:
+                self.bad_channels_ids.append(ch)
+        self.update_bad_channels()
 
     def BadChannelDel(self, ch_list):
         """
@@ -747,28 +752,32 @@ def BadChannelDel(self, ch_list):
         ch_list : list of integers
             List of indices of channels to be un-marked as 'bad'.
         """
+        # Update list of bad electrodes ids
         for ch in ch_list:
-            if ch in self.badChannels:
-                self.badChannels.remove(ch)
-        self.refreshScreen()
+            if ch in self.bad_channels_ids:
+                self.bad_channels_ids.remove(ch)
+        self.update_bad_channels()
+
+    def update_bad_channels(self):
+        """Updates list of bad channels after add or del"""
+        # List of electrodes IDs
+        elecs_ids = list(self.nwb.electrodes.id[:])
+        is_bad_list = [False] * len(elecs_ids)
+        for i, id in enumerate(elecs_ids):
+            if id in self.bad_channels_ids:
+                is_bad_list[i] = True
+
+        if 'bad' not in self.nwb.electrodes:
+            self.nwb.add_electrode_column(
+                name='bad',
+                description='electrode identified as too noisy',
+                data=is_bad_list,
+            )
+        else:
+            self.nwb.electrodes['bad'].data[:] = is_bad_list
 
-    def BadChannelSave(self):
-        """Saves list of bad channels in current NWB file."""
-        buttonReply = QMessageBox.question(None, ' ', 'Save Bad Channels on current NWB file?',
-                                           QMessageBox.No | QMessageBox.Yes)
-        if buttonReply == QMessageBox.Yes:
-            # Modify current list of bad channels
-            aux = [False] * self.nChTotal
-            for ind in self.badChannels:
-                aux[ind] = True
-            if 'bad' not in self.nwb.electrodes:
-                self.nwb.add_electrode_column(
-                    name='bad',
-                    description='electrode identified as too noisy',
-                    data=aux,
-                )
-            else:
-                self.nwb.electrodes['bad'].data[:] = aux
+        # Refresh screen
+        self.refreshScreen()
 
     def DrawMarkTime(self, position):
         """Marks temporary reference line when adding a new interval."""