Merge branch 'postdlc_local' into develop

Author: juhuntenburg

brainbox/behavior/dlc.py

@@ -350,11 +350,12 @@ def plot_wheel_position(wheel_position, wheel_time, trials_df):
 
     plt.axvline(x=0, linestyle='--', c='k', label='stimOn')
     plt.axhline(y=-0.26, linestyle='--', c='g', label='reward')
+    plt.axhline(y=0.26, linestyle='--', c='g', label='reward')
     plt.ylim([-0.27, 0.27])
     plt.xlabel('time [sec]')
-    plt.ylabel('wheel position [rad]')
+    plt.ylabel('wheel position diff to first value [rad]')
     plt.legend(loc='center right')
-    plt.title('Wheel position')
+    plt.title('Wheel position trial avg\n(and individual trials)')
     plt.tight_layout()
 
     return plt.gca()
@@ -406,7 +407,7 @@ def plot_lick_hist(lick_times, trials_df):
     plt.plot(times, pd.DataFrame.from_dict(dict(zip(correct.index, incorrect.values))).mean(axis=1),
              c='gray', label='incorrect trial')
     plt.axvline(x=0, label='feedback', linestyle='--', c='purple')
-    plt.title('Lick events')
+    plt.title('Lick events trial avg')
     plt.xlabel('time [sec]')
     plt.ylabel('lick events [a.u.]')
     plt.legend(loc='lower right')
@@ -479,7 +480,7 @@ def plot_motion_energy_hist(camera_dict, trials_df):
     plt.xlabel('time [sec]')
     plt.axvline(x=0, label='stimOn', linestyle='--', c='k')
     plt.legend(loc='lower right')
-    plt.title('Motion Energy')
+    plt.title('Motion Energy trial avg\n(+/- std)')
     if len(missing_data) > 0:
         ax = plt.gca()
         ax.text(.95, .35, f"Data incomplete for\n{' and '.join(missing_data)} camera", color='r', fontsize=10,
@@ -523,7 +524,7 @@ def plot_speed_hist(dlc_df, cam_times, trials_df, feature='paw_r', cam='left', l
     plt.plot(times, pd.DataFrame.from_dict(dict(zip(incorrect.index, incorrect.values))).mean(axis=1),
              c='gray', label='incorrect trial')
     plt.axvline(x=0, label='stimOn', linestyle='--', c='r')
-    plt.title(f'{feature.split("_")[0].capitalize()} speed ({cam} cam)')
+    plt.title(f'{feature.capitalize()} speed trial avg\n({cam.upper()} cam)')
     plt.xticks([-0.5, 0, 0.5, 1, 1.5])
     plt.xlabel('time [sec]')
     plt.ylabel('speed [px/sec]')
@@ -559,8 +560,8 @@ def plot_pupil_diameter_hist(pupil_diameter, cam_times, trials_df, cam='left'):
         plt.plot(times, pupil_mean, label=align_to.split("_")[0], color=color)
         plt.fill_between(times, pupil_mean + pupil_std, pupil_mean - pupil_std, color=color, alpha=0.5)
     plt.axvline(x=0, linestyle='--', c='k')
-    plt.title(f'Pupil diameter ({cam} cam)')
+    plt.title(f'Pupil diameter trial avg\n({cam.upper()} cam)')
     plt.xlabel('time [sec]')
     plt.xticks([-0.5, 0, 0.5, 1, 1.5])
-    plt.ylabel('pupil diameter [px]')
+    plt.ylabel('z-scored smoothed pupil diameter [px]')
     plt.legend(loc='lower right', title='aligned to')

ibllib/pipes/ephys_preprocessing.py

@@ -1055,9 +1055,6 @@ def _run(self, cams=None, overwrite=False):
 class EphysPostDLC(tasks.Task):
     """
     The post_dlc task takes dlc traces as input and computes useful quantities, as well as qc.
-
-    For creating the full dlc_qc_plot, several other inputs are required that can be found in the docstring of
-    :py:func:ibllib.plots.figures.dlc_qc_plot
     """
     io_charge = 90
     level = 3
@@ -1067,11 +1064,28 @@ class EphysPostDLC(tasks.Task):
                                  ('_ibl_rightCamera.dlc.pqt', 'alf', True),
                                  ('_ibl_rightCamera.times.npy', 'alf', True),
                                  ('_ibl_leftCamera.times.npy', 'alf', True),
-                                 ('_ibl_bodyCamera.times.npy', 'alf', True)],
+                                 ('_ibl_bodyCamera.times.npy', 'alf', True),
+                                 # the following are required for the DLC plot only
+                                 # they are not strictly required, some plots just might be skipped
+                                 # In particular the raw videos don't need to be downloaded as they can be streamed
+                                 ('_iblrig_bodyCamera.raw.mp4', 'raw_video_data', False),
+                                 ('_iblrig_leftCamera.raw.mp4', 'raw_video_data', False),
+                                 ('_iblrig_rightCamera.raw.mp4', 'raw_video_data', False),
+                                 ('rightROIMotionEnergy.position.npy', 'alf', False),
+                                 ('leftROIMotionEnergy.position.npy', 'alf', False),
+                                 ('bodyROIMotionEnergy.position.npy', 'alf', False),
+                                 ('_ibl_trials.choice.npy', 'alf', False),
+                                 ('_ibl_trials.feedbackType.npy', 'alf', False),
+                                 ('_ibl_trials.feedback_times.npy', 'alf', False),
+                                 ('_ibl_trials.stimOn_times.npy', 'alf', False),
+                                 ('_ibl_wheel.position.npy', 'alf', False),
+                                 ('_ibl_wheel.timestamps.npy', 'alf', False),
+                                 ],
                  # More files are required for all panels of the DLC QC plot to function
                  'output_files': [('_ibl_leftCamera.features.pqt', 'alf', True),
                                   ('_ibl_rightCamera.features.pqt', 'alf', True),
-                                  ('licks.times.npy', 'alf', True)]
+                                  ('licks.times.npy', 'alf', True),
+                                  ('dlc_qc_plot.png', 'snapshot', False)]
                  }
 
     def _run(self, overwrite=False, run_qc=True, plot_qc=True):
@@ -1080,7 +1094,7 @@ def _run(self, overwrite=False, run_qc=True, plot_qc=True):
         (dlc_qc_plot.png) is not returned, but saved in session_path/snapshots and uploaded to Alyx as a note.
 
         :param overwrite: bool, whether to recompute existing output files (default is False).
-                          Note that the dlc_qc_plot will be computed even if overwrite = False
+                          Note that the dlc_qc_plot will be (re-)computed even if overwrite = False
         :param run_qc: bool, whether to run the DLC QC (default is True)
         :param plot_qc: book, whether to create the dlc_qc_plot (default is True)
 
@@ -1092,7 +1106,7 @@ def _run(self, overwrite=False, run_qc=True, plot_qc=True):
         else:
             if exist and overwrite:
                 _logger.warning('EphysPostDLC outputs exist and overwrite=True, overwriting existing outputs.')
-            # Find all available dlc traces and dlc times
+            # Find all available dlc files
             dlc_files = list(Path(self.session_path).joinpath('alf').glob('_ibl_*Camera.dlc.*'))
             for dlc_file in dlc_files:
                 _logger.debug(dlc_file)
@@ -1177,7 +1191,7 @@ def _run(self, overwrite=False, run_qc=True, plot_qc=True):
                 fig_path = self.session_path.joinpath('snapshot', 'dlc_qc_plot.png')
                 if not fig_path.parent.exists():
                     fig_path.parent.mkdir(parents=True, exist_ok=True)
-                fig = dlc_qc_plot(self.one.path2eid(self.session_path), one=self.one)
+                fig = dlc_qc_plot(self.session_path, one=self.one)
                 fig.savefig(fig_path)
                 fig.clf()
                 snp = ReportSnapshot(self.session_path, session_id, one=self.one)

ibllib/pipes/tasks.py

@@ -81,6 +81,9 @@ def run(self, **kwargs):
         # if taskid of one properties are not available, local run only without alyx
         use_alyx = self.one is not None and self.taskid is not None
         if use_alyx:
+            # check that alyx user is logged in
+            if not self.one.alyx.is_logged_in:
+                self.one.alyx.authenticate()
             tdict = self.one.alyx.rest('tasks', 'partial_update', id=self.taskid,
                                        data={'status': 'Started'})
             self.log = ('' if not tdict['log'] else tdict['log'] +