Merge pull request #28 from int-brain-lab/alignment_dev

Alignment dev

Author: mayofaulkner

.flake8

@@ -8,4 +8,4 @@ exclude =
     data_exploration_gui/
     launch_phy/
     histology/
-
+    qt_matplotlib.py

atlaselectrophysiology/ephys_atlas_gui.py

@@ -81,6 +81,7 @@ def init_variables(self):
         self.scale_regions = np.empty((0, 1))
         self.slice_lines = []
         self.slice_items = []
+        self.probe_bounds = []
 
         # Variables to keep track of popup plots
         self.cluster_popups = []
@@ -905,7 +906,7 @@ def plot_line(self, data):
             self.set_axis(self.fig_line, 'bottom', label=data['xaxis'])
             self.line_plots.append(line)
 
-    def plot_probe(self, data):
+    def plot_probe(self, data, bounds=None):
         """
         Plots a 2D image with probe geometry
         param data: dictionary of data to plot
@@ -925,9 +926,11 @@ def plot_probe(self, data):
         else:
             [self.fig_probe.removeItem(plot) for plot in self.probe_plots]
             [self.fig_probe_cb.removeItem(cbar) for cbar in self.probe_cbars]
+            [self.fig_probe.removeItem(line) for line in self.probe_bounds]
             self.set_axis(self.fig_probe_cb, 'top', pen='w')
             self.probe_plots = []
             self.probe_cbars = []
+            self.probe_bounds = []
             color_bar = cb.ColorBar(data['cmap'])
             lut = color_bar.getColourMap()
             for img, scale, offset in zip(data['img'], data['scale'], data['offset']):
@@ -936,18 +939,24 @@ def plot_probe(self, data):
                 image.translate(offset[0], offset[1])
                 image.scale(scale[0], scale[1])
                 image.setLookupTable(lut)
-                image.setLevels((data['level'][0], data['level'][1]))
+                image.setLevels((data['levels'][0], data['levels'][1]))
                 self.fig_probe.addItem(image)
                 self.probe_plots.append(image)
 
-            cbar = color_bar.makeColourBar(20, 5, self.fig_probe_cb, min=data['level'][0],
-                                           max=data['level'][1], label=data['title'], lim=True)
+            cbar = color_bar.makeColourBar(20, 5, self.fig_probe_cb, min=data['levels'][0],
+                                           max=data['levels'][1], label=data['title'], lim=True)
             self.fig_probe_cb.addItem(cbar)
             self.probe_cbars.append(cbar)
 
             self.fig_probe.setXRange(min=data['xrange'][0], max=data['xrange'][1], padding=0)
             self.fig_probe.setYRange(min=self.probe_tip - self.probe_extra,
                                      max=self.probe_top + self.probe_extra, padding=self.pad)
+            if bounds is not None:
+                # add some infinite line stuff
+                for bound in bounds:
+                    line = pg.InfiniteLine(pos=bound, angle=0, pen='w')
+                    self.fig_probe.addItem(line)
+                    self.probe_bounds.append(line)
 
     def plot_image(self, data):
         """
@@ -975,6 +984,7 @@ def plot_image(self, data):
 
             image = pg.ImageItem()
             image.setImage(data['img'])
+            image.translate(data['offset'][0], data['offset'][1])
             image.scale(data['scale'][0], data['scale'][1])
             cmap = data.get('cmap', [])
             if cmap:
@@ -1107,10 +1117,14 @@ def data_button_pressed(self):
                 'LF')
             self.img_lfp_data, self.probe_lfp_data = self.plotdata.get_lfp_spectrum_data()
             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
 
+            self.init_menubar()
+
         # Initialise checked plots
         self.img_init.setChecked(True)
         self.line_init.setChecked(True)
@@ -1174,6 +1188,8 @@ def filter_unit_pressed(self, type):
         self.img_corr_data = self.plotdata.get_correlation_data_img()
         self.img_fr_data = self.plotdata.get_fr_img()
         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.img_init.setChecked(True)
         self.line_init.setChecked(True)
         self.probe_init.setChecked(True)
@@ -1527,7 +1543,11 @@ def display_qc_options(self):
     def qc_button_clicked(self):
         align_qc = self.align_qc.currentText()
         ephys_qc = self.ephys_qc.currentText()
-        ephys_desc = self.ephys_desc.currentText()
+        ephys_desc = []
+        for button in self.desc_buttons.buttons():
+            if button.isChecked():
+                ephys_desc.append(button.text())
+
         self.loaddata.upload_dj(align_qc, ephys_qc, ephys_desc)
         self.complete_button_pressed()
 

atlaselectrophysiology/ephys_gui_setup.py

@@ -16,7 +16,6 @@ def init_layout(self, main_window, offline=False):
         main_widget = QtWidgets.QWidget()
         self.setCentralWidget(main_widget)
 
-        self.init_menubar()
         self.init_interaction_features()
         self.init_figures()
 
@@ -74,6 +73,7 @@ def init_menubar(self):
         img_rmsLFP.triggered.connect(lambda: self.plot_image(self.img_rms_LFPdata))
         img_LFP = QtGui.QAction('LFP Spectrum', self, checkable=True, checked=False)
         img_LFP.triggered.connect(lambda: self.plot_image(self.img_lfp_data))
+
         # Initialise with firing rate 2D plot
         self.img_init = img_fr
 
@@ -102,6 +102,14 @@ def init_menubar(self):
         img_options.addAction(scatter_amp)
         self.img_options_group.addAction(scatter_amp)
 
+        stim_type = list(self.img_stim_data.keys())
+        for stim in stim_type:
+            img = QtGui.QAction(stim, self, checkable=True, checked=False)
+            img.triggered.connect(lambda checked, item=stim: self.plot_image(
+                                  self.img_stim_data[item]))
+            img_options.addAction(img)
+            self.img_options_group.addAction(img)
+
         # LINE PLOTS MENU BAR
         # Define all 1D line plot options
         line_fr = QtGui.QAction('Firing Rate', self, checkable=True, checked=True)
@@ -128,6 +136,7 @@ def init_menubar(self):
         probe_rmsAP.triggered.connect(lambda: self.plot_probe(self.probe_rms_APdata))
         probe_rmsLFP = QtGui.QAction('rms LFP', self, checkable=True, checked=False)
         probe_rmsLFP.triggered.connect(lambda: self.plot_probe(self.probe_rms_LFPdata))
+
         # Initialise with rms of AP probe plot
         self.probe_init = probe_rmsAP
 
@@ -152,6 +161,14 @@ def init_menubar(self):
             probe_options.addAction(probe)
             self.probe_options_group.addAction(probe)
 
+        sub_types = list(self.probe_rfmap.keys())
+        for sub in sub_types:
+            probe = QtGui.QAction(f'RF Map - {sub}', self, checkable=True, checked=False)
+            probe.triggered.connect(lambda checked, item=sub: self.plot_probe(
+                                    self.probe_rfmap[item], bounds=self.rfmap_boundaries))
+            probe_options.addAction(probe)
+            self.probe_options_group.addAction(probe)
+
         # SLICE PLOTS MENU BAR
         # Define all coronal slice plot options
         slice_hist_rd = QtGui.QAction('Histology Red', self, checkable=True, checked=True)
@@ -462,10 +479,23 @@ def init_interaction_features(self):
             ephys_qc_label = QtGui.QLabel("QC for ephys recording")
             self.ephys_qc = QtGui.QComboBox()
             self.ephys_qc.addItems(["Pass", "Warning", "Critical"])
-            ephys_desc_label = QtGui.QLabel("Describe problem with recording")
-            self.ephys_desc = QtGui.QComboBox()
-            self.ephys_desc.addItems(["None", "Noise and artifact", "Drift", "Poor neural yield",
-                                      "Brain Damage", "Other"])
+
+            self.desc_buttons = QtWidgets.QButtonGroup()
+            self.desc_group = QtWidgets.QGroupBox("Describe problem with recording")
+            self.desc_layout = QtWidgets.QVBoxLayout()
+            self.desc_layout.setSpacing(5)
+            self.desc_buttons.setExclusive(False)
+            options = ["Noise and artifact", "Drift", "Poor neural yield", "Brain Damage", "Other"]
+            for i, val in enumerate(options):
+
+                button = QtWidgets.QCheckBox(val)
+                button.setCheckState(QtCore.Qt.Unchecked)
+
+                self.desc_buttons.addButton(button, id=i)
+                self.desc_layout.addWidget(button)
+
+            self.desc_group.setLayout(self.desc_layout)
+
             self.qc_dialog = QtGui.QDialog(self)
             self.qc_dialog.setWindowTitle('QC assessment')
             self.qc_dialog.resize(300, 150)
@@ -480,8 +510,7 @@ def init_interaction_features(self):
             dialog_layout.addWidget(self.align_qc)
             dialog_layout.addWidget(ephys_qc_label)
             dialog_layout.addWidget(self.ephys_qc)
-            dialog_layout.addWidget(ephys_desc_label)
-            dialog_layout.addWidget(self.ephys_desc)
+            dialog_layout.addWidget(self.desc_group)
             dialog_layout.addWidget(buttonBox)
             self.qc_dialog.setLayout(dialog_layout)
 
@@ -727,3 +756,17 @@ def closeEvent(self, event):
 
     def leaveEvent(self, event):
         self.moved.emit()
+
+
+class CheckableComboBox(QtGui.QComboBox):
+    def __init__(self):
+        super(CheckableComboBox, self).__init__()
+        self.view().pressed.connect(self.handleItemPressed)
+        self.setModel(QtGui.QStandardItemModel(self))
+
+    def handleItemPressed(self, index):
+        item = self.model().itemFromIndex(index)
+        if item.checkState() == QtCore.Qt.Checked:
+            item.setCheckState(QtCore.Qt.Unchecked)
+        else:
+            item.setCheckState(QtCore.Qt.Checked)

atlaselectrophysiology/load_data.py

@@ -8,6 +8,7 @@
 from pathlib import Path
 import alf.io
 import glob
+import os
 from atlaselectrophysiology.load_histology import download_histology_data, tif2nrrd
 
 ONE_BASE_URL = "https://alyx.internationalbrainlab.org"
@@ -48,6 +49,7 @@ def __init__(self, one=None, brain_atlas=None, testing=False, probe_id=None):
         self.allen_id = None
         self.cluster_chns = None
         self.resolved = None
+        self.alyx_str = None
 
     def get_subjects(self):
         """
@@ -210,7 +212,12 @@ def get_data(self):
             '_iblqc_ephysTimeRms.timestamps',
             '_iblqc_ephysSpectralDensity.freqs',
             '_iblqc_ephysSpectralDensity.power',
-            '_iblqc_ephysSpectralDensity.amps'
+            '_iblqc_ephysSpectralDensity.amps',
+            '_ibl_passiveGabor.table',
+            '_ibl_passivePeriods.intervalsTable',
+            '_ibl_passiveRFM.frames',
+            '_ibl_passiveRFM.times',
+            '_ibl_passiveStims.table'
         ]
 
         print(self.subj)
@@ -223,6 +230,11 @@ def get_data(self):
 
         alf_path = Path(self.sess_path, 'alf', self.probe_label)
         ephys_path = Path(self.sess_path, 'raw_ephys_data', self.probe_label)
+
+        cluster_file_old = alf_path.joinpath('clusters.metrics.csv')
+        if cluster_file_old.exists():
+            os.remove(cluster_file_old)
+
         try:
             self.chn_coords = np.load(Path(alf_path, 'channels.localCoordinates.npy'))
             self.chn_depths = self.chn_coords[:, 1]
@@ -364,14 +376,17 @@ def upload_data(self, xyz_channels, channels=True):
 
         return channel_upload
 
-    def update_alignments(self, feature, track, key_info=None):
+    def update_alignments(self, feature, track, key_info=None, user_eval=None):
         if not key_info:
             user = self.one._par.ALYX_LOGIN
             date = datetime.now().replace(microsecond=0).isoformat()
-            data = {date + '_' + user: [feature.tolist(), track.tolist()]}
+            data = {date + '_' + user: [feature.tolist(), track.tolist(), self.alyx_str]}
         else:
             user = key_info[20:]
-            data = {key_info: [feature.tolist(), track.tolist()]}
+            if user_eval:
+                data = {key_info: [feature.tolist(), track.tolist(), user_eval]}
+            else:
+                data = {key_info: [feature.tolist(), track.tolist()]}
 
         old_user = [key for key in self.alignments.keys() if user in key]
         # Only delete duplicated if trajectory is not resolved
@@ -392,20 +407,27 @@ def update_json(self, json_data):
     def upload_dj(self, align_qc, ephys_qc, ephys_desc):
         # Upload qc results to datajoint table
         user = self.one._par.ALYX_LOGIN
-        if ephys_desc == 'None':
-            ephys_desc = None
+        if len(ephys_desc) == 0:
+            ephys_desc_str = 'None'
+            ephys_dj_str = None
+        else:
+            ephys_desc_str = ", ".join(ephys_desc)
+            ephys_dj_str = ephys_desc_str
+
         self.qc.insert1(dict(probe_insertion_uuid=self.probe_id, user_name=user,
-                        alignment_qc=align_qc, ephys_qc=ephys_qc, ephys_qc_description=ephys_desc),
+                             alignment_qc=align_qc, ephys_qc=ephys_qc,
+                             ephys_qc_description=ephys_dj_str),
                         allow_direct_insert=True, replace=True)
+        self.alyx_str = ephys_qc.upper() + ': ' + ephys_desc_str
 
     def update_qc(self, upload_alyx=True, upload_flatiron=True):
         # if resolved just update the alignment_number
-
         align_qc = AlignmentQC(self.probe_id, one=self.one, brain_atlas=self.brain_atlas)
         align_qc.load_data(prev_alignments=self.alignments, xyz_picks=self.xyz_picks,
                            depths=self.chn_depths, cluster_chns=self.cluster_chns)
         results = align_qc.run(update=True, upload_alyx=upload_alyx,
                                upload_flatiron=upload_flatiron)
+        align_qc.update_experimenter_evaluation(prev_alignments=self.alignments)
 
         self.resolved = results['alignment_resolved']