Merge pull request #33 from int-brain-lab/develop

Develop

Author: mayofaulkner

atlaselectrophysiology/README.md

@@ -130,6 +130,10 @@ be lost once the line is deleted. The reference lines can be hidden/ redisplayed
 Once the alignment is complete, the new locations of the electrode locations can be uploaded to Alyx by pressing the **Upload**
 button or Shift + U. 
 
+Upon upload, a window will pop-up asking to determine 1) the confidence in alignment, 2) the QC (which will label the insertion), 3) the reason for that QC (e.g. Drift and Noise seen in the recording).
+<img width="294" alt="Capture d’écran 2021-03-19 à 11 04 04" src="https://user-images.githubusercontent.com/43007596/112831143-cdaa1480-9093-11eb-8fc2-12fd586e604b.png">
+
+
 ### Additional Features
 #### Session Notes
 If any notes associated with a session have been uploaded to Alyx, these can be displayed as a popup by clicking on

atlaselectrophysiology/create_overview_plots.py

@@ -3,10 +3,12 @@
 import glob
 
 
-def make_overview_plot(folder, sess_info):
+def make_overview_plot(folder, sess_info, save_folder=None):
 
     image_folder = folder
     image_info = sess_info
+    if not save_folder:
+        save_folder = image_folder
 
     def load_image(image_name, ax):
         with image_name as ifile:
@@ -74,6 +76,6 @@ def load_image(image_name, ax):
 
     ax.text(0.5, 0, image_info[:-1], va="center", ha="center", transform=ax.transAxes)
 
-    plt.savefig(image_folder.joinpath(image_info + "overview.png"),
+    plt.savefig(save_folder.joinpath(image_info + "overview.png"),
                 bbox_inches='tight', pad_inches=0)
-    plt.show()
+    plt.show()

atlaselectrophysiology/ephys_atlas_gui.py

@@ -15,19 +15,26 @@
 
 
 class MainWindow(QtWidgets.QMainWindow, ephys_gui.Setup):
-    def __init__(self, offline=False):
+    def __init__(self, offline=False, probe_id=None, one=None):
         super(MainWindow, self).__init__()
 
         self.init_variables()
         self.init_layout(self, offline=offline)
-        if not offline:
+        self.configure = True
+        if not offline and probe_id is None:
             self.loaddata = LoadData()
             self.populate_lists(self.loaddata.get_subjects(), self.subj_list, self.subj_combobox)
+        elif not offline and probe_id is not None:
+            self.loaddata = LoadData(probe_id=probe_id, one=one)
+            self.loaddata.get_info(0)
+            self.feature_prev, self.track_prev = self.loaddata.get_starting_alignment(0)
+            self.data_status=False
+            self.data_button_pressed()
         else:
             self.loaddata = LoadDataLocal()
+
         self.allen = self.loaddata.get_allen_csv()
         self.init_region_lookup(self.allen)
-        self.configure = True
 
     def init_variables(self):
         """
@@ -321,7 +328,7 @@ def set_view(self, view=1, configure=False):
             self.fig_line.update()
             self.fig_probe.update()
 
-    def save_plots(self):
+    def save_plots(self, save_path=None):
         """
         Saves all plots from the GUI into folder
         """
@@ -336,6 +343,9 @@ def save_plots(self):
             image_path_overview = self.alf_path.joinpath('GUI_plots')
             image_path = image_path_overview
 
+        if save_path:
+            image_path_overview = Path(save_path)
+
         os.makedirs(image_path_overview, exist_ok=True)
         os.makedirs(image_path, exist_ok=True)
         # Reset all axis, put view back to 1 and remove any reference lines
@@ -490,7 +500,7 @@ def save_plots(self):
         self.set_font(self.fig_hist_ref, 'bottom', ptsize=8)
         self.set_axis(self.fig_hist_ref, 'bottom', pen='w')
 
-        make_overview_plot(image_path, sess_info)
+        make_overview_plot(image_path, sess_info, save_folder=image_path_overview)
 
     def toggle_plots(self, options_group):
         """
@@ -1130,6 +1140,7 @@ def data_button_pressed(self):
             self.line_fr_data, self.line_amp_data = self.plotdata.get_fr_amp_data_line()
             self.probe_rfmap, self.rfmap_boundaries = self.plotdata.get_rfmap_data()
             self.img_stim_data = self.plotdata.get_passive_events()
+
             self.slice_data = self.loaddata.get_slice_images(self.ephysalign.xyz_samples)
 
             self.data_status = True
@@ -1546,10 +1557,10 @@ def complete_button_pressed_offline(self):
             QtGui.QMessageBox.information(self, 'Status', "Channels locations saved")
         else:
             pass
-            QtGui.QMessageBox.information(self, 'Status', "Channels not saved")
+            QtGui.QMessageBox.warning(self, 'Status', "Channels not saved")
 
     def display_qc_options(self):
-        self.qc_dialog.exec()
+        self.qc_dialog.open()
 
     def qc_button_clicked(self):
         align_qc = self.align_qc.currentText()
@@ -1559,6 +1570,11 @@ def qc_button_clicked(self):
             if button.isChecked():
                 ephys_desc.append(button.text())
 
+        if ephys_qc != 'Pass' and len(ephys_desc) == 0:
+            QtGui.QMessageBox.warning(self, 'Status', "You must select a reason for qc choice")
+            self.display_qc_options()
+            return
+
         self.loaddata.upload_dj(align_qc, ephys_qc, ephys_desc)
         self.complete_button_pressed()
 
@@ -1868,16 +1884,24 @@ def update_string(self):
         self.tot_idx_string.setText(f"Total Index = {self.total_idx}")
 
 
+def viewer(probe_id=None, one=None):
+    # To generate the plot from the command line
+    mainapp = MainWindow(probe_id=probe_id, one=one)
+    mainapp.show()
+    return mainapp
+
+
 if __name__ == '__main__':
 
     import argparse
 
     parser = argparse.ArgumentParser(description='Offline vs online mode')
     parser.add_argument('-o', '--offline', default=False, required=False, help='Offline mode')
+    parser.add_argument('-i', '--insertion', default=None, required=False, help='Insertion mode')
     args = parser.parse_args()
 
     app = QtWidgets.QApplication([])
-    mainapp = MainWindow(offline=args.offline)
+    mainapp = MainWindow(offline=args.offline, probe_id=args.insertion)
     # mainapp = MainWindow(offline=True)
     mainapp.show()
     app.exec_()

atlaselectrophysiology/ephys_gui_setup.py

@@ -201,10 +201,12 @@ def init_menubar(self):
         # Define unit filtering options
         all_units = QtGui.QAction('All', self, checkable=True, checked=True)
         all_units.triggered.connect(lambda: self.filter_unit_pressed('all'))
-        good_units = QtGui.QAction('Good', self, checkable=True, checked=False)
-        good_units.triggered.connect(lambda: self.filter_unit_pressed('good'))
-        mua_units = QtGui.QAction('MUA', self, checkable=True, checked=False)
-        mua_units.triggered.connect(lambda: self.filter_unit_pressed('mua'))
+        good_units = QtGui.QAction('KS good', self, checkable=True, checked=False)
+        good_units.triggered.connect(lambda: self.filter_unit_pressed('KS good'))
+        mua_units = QtGui.QAction('KS mua', self, checkable=True, checked=False)
+        mua_units.triggered.connect(lambda: self.filter_unit_pressed('KS mua'))
+        ibl_units = QtGui.QAction('IBL good', self, checkable=True, checked=False)
+        ibl_units.triggered.connect(lambda: self.filter_unit_pressed('IBL good'))
         # Initialise with all units being shown
         self.unit_init = all_units
 
@@ -219,6 +221,8 @@ def init_menubar(self):
         unit_filter_options_group.addAction(good_units)
         unit_filter_options.addAction(mua_units)
         unit_filter_options_group.addAction(mua_units)
+        unit_filter_options.addAction(ibl_units)
+        unit_filter_options_group.addAction(ibl_units)
 
         # FIT OPTIONS MENU BAR
         # Define all possible keyboard shortcut interactions for GUI

atlaselectrophysiology/load_data.py

@@ -51,6 +51,10 @@ def __init__(self, one=None, brain_atlas=None, testing=False, probe_id=None):
         self.resolved = None
         self.alyx_str = None
 
+        if probe_id is not None:
+            self.sess = self.one.alyx.rest('trajectories', 'list', provenance='Histology track',
+                                           probe_insertion=probe_id)
+
     def get_subjects(self):
         """
         Finds all subjects that have a histology track trajectory registered
@@ -87,8 +91,8 @@ def get_sessions(self, idx):
         :return session: list of sessions associated with subject, displayed as date + probe
         :type: list of strings
         """
-        self.subj = self.subjects[idx]
-        sess_idx = [i for i, e in enumerate(self.subj_with_hist) if e == self.subj]
+        subj = self.subjects[idx]
+        sess_idx = [i for i, e in enumerate(self.subj_with_hist) if e == subj]
         self.sess = [self.sess_with_hist[idx] for idx in sess_idx]
         session = [(sess['session']['start_time'][:10] + ' ' + sess['probe_name']) for sess in
                    self.sess]
@@ -111,6 +115,7 @@ def get_info(self, idx):
         self.probe_id = self.sess[idx]['probe_insertion']
         self.lab = self.sess[idx]['session']['lab']
         self.eid = self.sess[idx]['session']['id']
+        self.subj = self.sess[idx]['session']['subject']
 
         return self.get_previous_alignments()
 
@@ -215,16 +220,21 @@ def get_data(self):
             '_iblqc_ephysSpectralDensity.amps',
             '_ibl_passiveGabor.table',
             '_ibl_passivePeriods.intervalsTable',
-            '_ibl_passiveRFM.frames',
+            '_iblrig_RFMapStim.raw',
             '_ibl_passiveRFM.times',
-            '_ibl_passiveStims.table'
+            '_ibl_passiveStims.table',
+            '_iblrig_RFMapStim.raw'
         ]
 
         print(self.subj)
         print(self.probe_label)
         print(self.date)
         print(self.eid)
 
+        # dsets = self.one.alyx.rest('datasets', 'list', probe_insertion=self.probe_id)
+        # dsets_int = [d for d in dsets if d['dataset_type'] in dtypes]
+        # _ = self.one.download_datasets(dsets_int)
+
         _ = self.one.load(self.eid, dataset_types=dtypes, download_only=True)
         self.sess_path = self.one.path_from_eid(self.eid)
 

atlaselectrophysiology/plot_data.py

@@ -3,7 +3,7 @@
 import numpy as np
 import alf.io
 from brainbox.processing import bincount2D
-from brainbox.population import xcorr
+from brainbox.population.decode import xcorr
 from brainbox.task import passive
 import scipy
 from PyQt5 import QtGui
@@ -58,8 +58,19 @@ def __init__(self, alf_path, ephys_path):
             self.lfp_data_status = False
 
         try:
-            self.rf_map = alf.io.load_object(self.alf_path.parent, object='passiveRFM',
-                                             namespace='ibl')
+            rf_map_times = alf.io.load_object(self.alf_path.parent, object='passiveRFM',
+                                              namespace='ibl')
+            # This needs to go into brainbox!!
+            rf_map_frames_path = (self.alf_path.parent.parent.
+                                  joinpath('raw_passive_data', '_iblrig_RFMapStim.raw.bin'))
+            rf_map_frames = np.fromfile(rf_map_frames_path, dtype="uint8")
+            y_pix, x_pix = 15, 15
+            frames = np.transpose(np.reshape(rf_map_frames, [y_pix, x_pix, -1], order="F"),
+                                  [2, 1, 0])
+
+            self.rf_map = dict()
+            self.rf_map['times'] = rf_map_times['times']
+            self.rf_map['frames'] = frames
             if len(self.rf_map) == 2:
                 self.rfmap_data_status = True
             else:
@@ -94,15 +105,27 @@ def __init__(self, alf_path, ephys_path):
     def filter_units(self, type):
         if type == 'all':
             self.spike_idx = np.arange(self.spikes['clusters'].size)
-            # Filter for nans in depths and also in amps
-            self.kp_idx = np.where(~np.isnan(self.spikes['depths'][self.spike_idx]) &
-                                   ~np.isnan(self.spikes['amps'][self.spike_idx]))[0]
 
-        else:
-            clust = np.where(self.clusters.metrics.ks2_label == type)
+        elif type == 'KS good':
+            clust = np.where(self.clusters.metrics.ks2_label == 'good')
+            self.spike_idx = np.where(np.isin(self.spikes['clusters'], clust))[0]
+
+        elif type == 'KS mua':
+            clust = np.where(self.clusters.metrics.ks2_label == 'mua')
             self.spike_idx = np.where(np.isin(self.spikes['clusters'], clust))[0]
-            self.kp_idx = np.where(~np.isnan(self.spikes['depths'][self.spike_idx]) & ~np.isnan(
-                self.spikes['amps'][self.spike_idx]))[0]
+
+        elif type == 'IBL good':
+            try:
+                clust = np.where(self.clusters.metrics.label == 1)
+                self.spike_idx = np.where(np.isin(self.spikes['clusters'], clust))[0]
+            except Exception:
+                print('IBL metrics not implemented will return ks good units instead')
+                clust = np.where(self.clusters.metrics.ks2_label == 'good')
+                self.spike_idx = np.where(np.isin(self.spikes['clusters'], clust))[0]
+
+        # Filter for nans in depths and also in amps
+        self.kp_idx = np.where(~np.isnan(self.spikes['depths'][self.spike_idx]) &
+                               ~np.isnan(self.spikes['amps'][self.spike_idx]))[0]
 
 # Plots that require spike and cluster data
     def get_depth_data_scatter(self):
@@ -477,7 +500,7 @@ def get_rfmap_data(self):
             (rf_map_times, rf_map_pos,
              rf_stim_frames) = passive.get_on_off_times_and_positions(self.rf_map)
 
-            rf_map, depths = \
+            rf_map, _ = \
                 passive.get_rf_map_over_depth(rf_map_times, rf_map_pos, rf_stim_frames,
                                               self.spikes['times'][self.spike_idx][self.kp_idx],
                                               self.spikes['depths'][self.spike_idx][self.kp_idx],
@@ -491,6 +514,8 @@ def get_rfmap_data(self):
             xscale = 1
             levels = np.quantile(np.c_[img['on'], img['off']], [0, 1])
 
+            depths = np.linspace(0, 3840, len(rfs_svd['on']) + 1)
+
             sub_type = ['on', 'off']
             for sub in sub_type:
                 sub_data = {sub: {

atlasview/atlasview.py

@@ -208,7 +208,7 @@ def replace_image_layer(self, index, **kwargs):
 
 class PgImageController:
     """
-    Abstract class that implements mapping from axes to voxels for any window.
+    Abstract class that implements mapping fr`om axes to voxels for any window.
     Not instantiated directly.
     """
     def __init__(self, win, res=25):