Spikeinterface view

src/viewephys/gui.py

@@ -111,8 +111,10 @@ def on_horizontalSliderReleased(self):
             if not self.cbs[k].isChecked():
                 continue
             if k == 'destripe':
-                data = fcn_destripe(x=data, fs=self.sr.fs, channel_labels=True, h=self.sr.geometry, neuropixel_version=self.sr.major_version)
-            self.viewers[k] = viewephys(data, self.sr.fs, channels=self.sr.geometry, title=k, t0=t0 * T_SCALAR, t_scalar=T_SCALAR, a_scalar=A_SCALAR)
+                data = fcn_destripe(x=data, fs=self.sr.fs, channel_labels=True, h=self.sr.geometry,
+                                    neuropixel_version=self.sr.major_version)
+            self.viewers[k] = viewephys(data, self.sr.fs, channels=self.sr.geometry, title=k,
+                                        t0=t0 * T_SCALAR, t_scalar=T_SCALAR, a_scalar=A_SCALAR)
 
     def closeEvent(self, event):
         for k in self.viewers:
@@ -121,6 +123,96 @@ def closeEvent(self, event):
                 ev.close()
         self.close()
 
+# =------
+
+class SpikeInterfaceViewer(QtWidgets.QMainWindow):
+    def __init__(self, recording, save_path_picks=None, *args, **kwargs):
+        """
+        :param parent:
+        :param sr: ibllib.io.spikeglx.Reader instance
+        """
+        super(SpikeInterfaceViewer, self).__init__(*args, *kwargs)
+        self.settings = QtCore.QSettings('int-brain-lab', 'SpikeInterfaceViewer')
+        uic.loadUi(Path(__file__).parent.joinpath('nav_file.ui'), self)
+        self.setWindowIcon(QtGui.QIcon(str(Path(__file__).parent.joinpath('viewephys.svg'))))
+        self.horizontalSlider.setMinimum(0)
+        self.horizontalSlider.setSingleStep(1)
+        self.horizontalSlider.setTickInterval(10)
+        self.horizontalSlider.sliderReleased.connect(self.on_horizontalSliderReleased)
+        self.horizontalSlider.valueChanged.connect(self.on_horizontalSliderValueChanged)
+        self.label_smin.setText('0')
+        self.show()
+        self.viewers = {'recording': None}
+        # self.cbs = {'butterworth': self.cb_butterworth_ap, 'destripe': self.cb_destripe_ap}
+        self.recording = recording
+        # Set save path for picks
+        if save_path_picks is None:
+            save_path_picks = Path(__file__).parent.joinpath('picks.csv')  # This will save into the viewephys folder
+        elif save_path_picks.suffix != '.csv':
+            raise ValueError('Extension of save file must be .csv')
+        self.save_path_picks = save_path_picks
+        self.set_recording()
+
+    def set_recording(self, *args, **kwargs):
+        # enable and set slider
+        num_samples = self.recording.get_num_samples()
+        fs = self.recording.sampling_frequency
+        total_duration = self.recording.get_total_duration()
+        num_channel = self.recording.get_num_channels()
+        self.horizontalSlider.setMaximum(int(np.floor(num_samples / NSAMP_CHUNK)))
+        tmax = np.floor(num_samples / NSAMP_CHUNK) * NSAMP_CHUNK / fs
+
+        self.label_smax.setText(f"{tmax:0.2f}s")
+        tlabel = f'{total_duration} seconds long \n' \
+                 f'{fs} Hz Sampling Frequency \n' \
+                 f'{num_channel} Channels'
+        self.label.setText(tlabel)
+        first = 0  # first sample
+        self.horizontalSlider.setValue(first)
+        self.horizontalSlider.setEnabled(True)
+        self.on_horizontalSliderReleased()
+
+        for k in self.viewers:
+            # Propagate save path to each view
+            self.viewers[k].save_path_picks = self.save_path_picks
+            self.viewers[k].current_sample0 = first
+            # TODO make sure picks df remain across views
+            # Load if exists
+            if self.save_path_picks.exists():
+                df = pd.read_csv(self.save_path_picks)
+                self.viewers[k].ctrl.model.pickspikes.load_df(df)
+                self.viewers[k].update_pick_scatter()
+
+
+    def on_horizontalSliderValueChanged(self):
+        tcur = self.horizontalSlider.value() * NSAMP_CHUNK / self.recording.sampling_frequency
+        self.label_sval.setText(f"{tcur:0.2f}s")
+
+    def on_horizontalSliderReleased(self):
+        first = int(float(self.horizontalSlider.value()) * NSAMP_CHUNK)
+        last = first + int(NSAMP_CHUNK)
+        data = self.recording.get_traces(start_frame=first, end_frame=last).T
+
+        t0 = first / self.recording.sampling_frequency * 0
+        # TODO if t0 is not zero the sliders bugs and does not lead to display change (empty)
+
+        for k in self.viewers:
+            self.viewers[k] = viewephys(data, self.recording.sampling_frequency,
+                                        channels=None, title=k,
+                                        t0=t0 * T_SCALAR, t_scalar=T_SCALAR, a_scalar=A_SCALAR)
+            self.viewers[k].current_sample0 = first
+            self.viewers[k].update_pick_scatter()
+
+
+    def closeEvent(self, event):
+        for k in self.viewers:
+            ev = self.viewers[k]
+            if ev is not None:
+                ev.close()
+        self.close()
+
+#-----
+
 
 class PickSpikes():
 
@@ -134,6 +226,7 @@ def init_df(self, nrow=0):
             'trace': np.zeros(nrow, dtype=np.int32) * -1,
             'amp': np.zeros(nrow, dtype=np.int32),
             'group': np.zeros(nrow, dtype=np.int32),
+            'sample0': np.zeros(nrow, dtype=np.int32)
         })
         return init_df
 
@@ -151,19 +244,20 @@ def load_df(self, df):
 
         if isinstance(df, pd.DataFrame):
             # check all keys are in
-            indxmissing = np.where(~df.columns.isin(default_df.columns))[0]
+            indxmissing = np.where(~default_df.columns.isin(df.columns))[0]
             if len(indxmissing) > 0:
                 raise ValueError(f'df does not contain column {default_df.columns[indxmissing]}')
             self.update_pick(df)
         else:
             raise ValueError('df input is not pd.DataFrame')
 
-    def new_row_frompick(self, sample=None, trace=None, amp=None, group=None):
+    def new_row_frompick(self, sample=None, trace=None, amp=None, group=None, sample0=None):
         new_row = self.init_df(nrow=1)
         new_row['sample'] = sample
         new_row['trace'] = trace
         new_row['amp'] = amp
         new_row['group'] = group
+        new_row['sample0'] = sample0
         return new_row
 
     def add_spike(self, new_row):
@@ -184,14 +278,18 @@ def remove_spike(self, indx_remove):
             df_updated = df_updated.reset_index(drop=True)
             self.update_pick(df_updated)
 
-
     def indx_select(self, sample, trace, s_range=0.5 * 30000, tr_range=3):
         iclose = np.where(np.logical_and(
             np.abs(self.picks['sample'] - sample) <= (s_range + 1),
             np.abs(self.picks['trace'] - trace) <= (tr_range + 1)
         ))[0]
         return iclose
 
+    def save_picks(self, save_path):
+        self.picks.to_csv(save_path, index=False)
+        # chose format CSV output
+
+
 class EphysViewer(EasyQC):
     keyPressed = QtCore.pyqtSignal(int)
 
@@ -202,6 +300,8 @@ def __init__(self, *args, **kwargs):
         self.menufile.setEnabled(True)
         self.settings = QtCore.QSettings('int-brain-lab', 'EphysViewer')
         self.header_curves = {}
+        self.current_sample0 = 0
+        self.save_path_picks = None
         # menus handling
         # menu pick
         self.menupick = self.menuBar().addMenu('&Pick')
@@ -278,6 +378,18 @@ def on_key_picking_mode(self, key):
         match key:
             case QtCore.Qt.Key.Key_Space:
                 self.ctrl.model.pick_group += 1
+            case QtCore.Qt.Key.Key_S:
+                print(f"Saved picks to: {self.save_path_picks}")
+                self.ctrl.model.pickspikes.save_picks(self.save_path_picks)
+
+    def update_pick_scatter(self):
+        # updates scatter plot with only picks from T0
+        df = self.ctrl.model.pickspikes.picks
+        df_local_picks = df.loc[df["sample0"] == self.current_sample0]
+
+        self.ctrl.add_scatter(df_local_picks['sample'] * self.ctrl.model.si,
+                              df_local_picks['trace'],
+                              label='_picks', rgb=PICK_COLOR)
 
     def mouseClickPickingEvent(self, event):
         """
@@ -294,6 +406,8 @@ def mouseClickPickingEvent(self, event):
             return
         TR_RANGE = 3
         S_RANGE = int(0.5 / self.ctrl.model.si)
+        # TODO modify s_range so it is scaled according to zoom,
+        #  otherwise can be hard to delete when zoomed out
         qxy = self.imageItem_seismic.mapFromScene(event.scenePos())
         s, tr = (qxy.x(), qxy.y())
         # if event.buttons() == QtCore.Qt.MiddleButton:
@@ -331,13 +445,11 @@ def mouseClickPickingEvent(self, event):
             group = 0  # TODO group
             # Create new row
             new_row = self.ctrl.model.pickspikes.new_row_frompick(
-                sample=tmax, trace=xmax, amp=amp, group=group)
+                sample=tmax, trace=xmax, amp=amp, group=group, sample0=self.current_sample0)
             self.ctrl.model.pickspikes.add_spike(new_row=new_row)
 
         # updates scatter plot
-        self.ctrl.add_scatter(self.ctrl.model.pickspikes.picks['sample'] * self.ctrl.model.si,
-                              self.ctrl.model.pickspikes.picks['trace'],
-                              label='_picks', rgb=PICK_COLOR)
+        self.update_pick_scatter()
 
     def save_current_plot(self, filename):
         """

src/viewephys/picks.csv

@@ -0,0 +1,4 @@
+sample,trace,amp,group,sample0
+2717,297,26411326.0,0,330000
+3612,296,-75356264.0,0,330000
+3991,297,-64742784.0,0,330000

src/viewephys/raster.py

@@ -15,7 +15,7 @@
 import one.alf.io as alfio
 from one.alf.files import get_session_path
 import spikeglx
-from ibldsp import voltage, utils
+from ibldsp import voltage
 from iblatlas.atlas import BrainRegions
 
 from viewephys.gui import viewephys, SNS_PALETTE
@@ -181,9 +181,10 @@ def show_ephys(self, t0, tlen=.4):
         sos = scipy.signal.butter(**butter_kwargs, output='sos')
         butt = scipy.signal.sosfiltfilt(sos, raw)
         destripe = voltage.destripe(raw, fs=self.data.sr.fs, channel_labels=True)
-        self.eqc_raw = viewephys(butt, self.data.sr.fs, channels=self.data.channels, br=self.data.br, title='butt', t0=t0, t_scalar=1)
-        self.eqc_des = viewephys(destripe, self.data.sr.fs, channels=self.data.channels, br=self.data.br, title='destripe', t0=t0, t_scalar=1)
-        stripes_noise = 20 * np.log10(np.median(utils.rms(butt - destripe)))
+        self.eqc_raw = viewephys(butt, self.data.sr.fs, channels=self.data.channels,
+                                 br=self.data.br, title='butt', t0=t0, t_scalar=1)
+        self.eqc_des = viewephys(destripe, self.data.sr.fs, channels=self.data.channels,
+                                 br=self.data.br, title='destripe', t0=t0, t_scalar=1)
         eqc_xrange = [t0 + tlen / 2 - 0.01, t0 + tlen / 2 + 0.01]
         self.eqc_des.viewBox_seismic.setXRange(*eqc_xrange)
         self.eqc_raw.viewBox_seismic.setXRange(*eqc_xrange)

src/viewephys/spike_interface.ui

@@ -0,0 +1,153 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>MainWindow</class>
+ <widget class="QMainWindow" name="MainWindow">
+  <property name="enabled">
+   <bool>true</bool>
+  </property>
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>785</width>
+    <height>295</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Spike Interface Viewer</string>
+  </property>
+  <widget class="QWidget" name="centralwidget">
+   <layout class="QGridLayout" name="gridLayout">
+    <item row="4" column="0">
+     <widget class="QSlider" name="horizontalSlider">
+      <property name="enabled">
+       <bool>false</bool>
+      </property>
+      <property name="orientation">
+       <enum>Qt::Horizontal</enum>
+      </property>
+     </widget>
+    </item>
+    <item row="0" column="0">
+     <widget class="QFrame" name="frame">
+      <property name="frameShape">
+       <enum>QFrame::StyledPanel</enum>
+      </property>
+      <property name="frameShadow">
+       <enum>QFrame::Raised</enum>
+      </property>
+      <layout class="QGridLayout" name="gridLayout_2">
+       <item row="0" column="1">
+        <widget class="QLabel" name="label">
+         <property name="text">
+          <string>Dataset Info</string>
+         </property>
+         <property name="alignment">
+          <set>Qt::AlignCenter</set>
+         </property>
+        </widget>
+       </item>
+       <item row="1" column="1">
+        <spacer name="horizontalSpacer">
+         <property name="orientation">
+          <enum>Qt::Horizontal</enum>
+         </property>
+         <property name="sizeHint" stdset="0">
+          <size>
+           <width>40</width>
+           <height>20</height>
+          </size>
+         </property>
+        </spacer>
+       </item>
+       <item row="1" column="0">
+        <widget class="QComboBox" name="uiComboProcessing">
+         <property name="minimumSize">
+          <size>
+           <width>160</width>
+           <height>0</height>
+          </size>
+         </property>
+        </widget>
+       </item>
+      </layout>
+     </widget>
+    </item>
+    <item row="5" column="0">
+     <widget class="QFrame" name="frame_2">
+      <property name="maximumSize">
+       <size>
+        <width>16777215</width>
+        <height>40</height>
+       </size>
+      </property>
+      <property name="frameShape">
+       <enum>QFrame::StyledPanel</enum>
+      </property>
+      <property name="frameShadow">
+       <enum>QFrame::Raised</enum>
+      </property>
+      <layout class="QHBoxLayout" name="horizontalLayout">
+       <item>
+        <widget class="QLabel" name="label_smin">
+         <property name="text">
+          <string>smin</string>
+         </property>
+        </widget>
+       </item>
+       <item>
+        <widget class="QLabel" name="label_sval">
+         <property name="text">
+          <string>sval</string>
+         </property>
+         <property name="alignment">
+          <set>Qt::AlignCenter</set>
+         </property>
+        </widget>
+       </item>
+       <item>
+        <widget class="QLabel" name="label_smax">
+         <property name="text">
+          <string>smax</string>
+         </property>
+         <property name="alignment">
+          <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
+         </property>
+        </widget>
+       </item>
+      </layout>
+     </widget>
+    </item>
+   </layout>
+  </widget>
+  <widget class="QMenuBar" name="menubar">
+   <property name="geometry">
+    <rect>
+     <x>0</x>
+     <y>0</y>
+     <width>785</width>
+     <height>22</height>
+    </rect>
+   </property>
+   <widget class="QMenu" name="menuFile">
+    <property name="title">
+     <string>File</string>
+    </property>
+   </widget>
+   <addaction name="menuFile"/>
+  </widget>
+  <widget class="QStatusBar" name="statusbar"/>
+  <action name="actionopen">
+   <property name="text">
+    <string>open</string>
+   </property>
+  </action>
+  <action name="actionopen_live_recording">
+   <property name="text">
+    <string>open live recording</string>
+   </property>
+  </action>
+ </widget>
+ <resources/>
+ <connections/>
+</ui>