From c01a251a135ebdf32788664f3719f03b05ee0b48 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 12 Dec 2024 04:55:51 +0000 Subject: [PATCH 01/12] ci: version bump [skip actions] --- src/foraging_gui/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/foraging_gui/__init__.py b/src/foraging_gui/__init__.py index 18683c510..ceae0e561 100644 --- a/src/foraging_gui/__init__.py +++ b/src/foraging_gui/__init__.py @@ -1,3 +1,3 @@ -__version__ = "1.6.11" +__version__ = "1.6.12" From 05d0c9c6bb6cc1f0cd36c8081328c92059e3e93a Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 12 Dec 2024 05:05:46 +0000 Subject: [PATCH 02/12] ci: version bump [skip actions] --- src/foraging_gui/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/foraging_gui/__init__.py b/src/foraging_gui/__init__.py index ceae0e561..0a6b5300e 100644 --- a/src/foraging_gui/__init__.py +++ b/src/foraging_gui/__init__.py @@ -1,3 +1,3 @@ -__version__ = "1.6.12" +__version__ = "1.6.13" From 98e46a8069a4c1bc828d2d0c07c907cb090084e4 Mon Sep 17 00:00:00 2001 From: XX-Yin <109394934+XX-Yin@users.noreply.github.com> Date: Wed, 11 Dec 2024 21:09:30 -0800 Subject: [PATCH 03/12] Revert "Fix 1155 waterlog post session weight" --- src/foraging_gui/Foraging.py | 19 +++++++++++++------ tash | 31 ------------------------------- 2 files changed, 13 insertions(+), 37 deletions(-) delete mode 100644 tash diff --git a/src/foraging_gui/Foraging.py b/src/foraging_gui/Foraging.py index 5b02a87f7..5d33b0721 100644 --- a/src/foraging_gui/Foraging.py +++ b/src/foraging_gui/Foraging.py @@ -1361,15 +1361,14 @@ def _AddWaterLogResult(self, session: Session): # extract software information logging.info('Extracting software information from first data stream') - software = session.stimulus_epochs[0].software[0] + software = session.data_streams[0].software[0] # create model logging.info('Creating SlimsWaterlogResult based on session information.') model = models.SlimsWaterlogResult( mouse_pk=mouse.pk, date=session.session_start_time, - weight_g=session.animal_weight_post, - operator=self.behavior_session_model.experimenter[0], + weight_g=session.animal_weight_prior, water_earned_ml=water['water_in_session_foraging'], water_supplement_delivered_ml=water['water_after_session'], water_supplement_recommended_ml=None, @@ -3187,7 +3186,7 @@ def _Open(self,open_last = False,input_file = ''): self.stage_widget.movement_page_view.lineEdit_y1.setText(str(last_positions['y1'])) self.stage_widget.movement_page_view.lineEdit_y2.setText(str(last_positions['y2'])) self.stage_widget.movement_page_view.lineEdit_z.setText(str(last_positions['z'])) - self.move_aind_stage() + threading.Thread(target=self.move_aind_stage).start() elif 'B_NewscalePositions' in Obj.keys() and len(Obj['B_NewscalePositions']) != 0: # cross compatibility for mice run on older version of code. last_positions = Obj['B_NewscalePositions'][-1] self.current_stage.move_absolute_3d(float(last_positions[0]), @@ -3232,8 +3231,16 @@ def move_aind_stage(self): """ Move all axis of stage in stage widget """ - positions = self.stage_widget.movement_page_view.get_positions_from_line_edit() - self.stage_widget.movement_page_view.signal_position_change.emit(positions) + # save current positions since stage widget will reset once returnPressed in emitted + axes = ['x', 'y1', 'y2', 'z'] + textboxes = [getattr(self.stage_widget.movement_page_view, f'lineEdit_{axis}') for axis in axes] + positions = [textbox.text() for textbox in textboxes] + for textbox, position in zip(textboxes, positions): + textbox.setText(position) + textbox.returnPressed.emit() + time.sleep(1) # allow worker to initialize + while self.stage_widget.stage_model.move_thread.isRunning(): + time.sleep(.1) def _LoadVisualization(self): '''To visulize the training when loading a session''' diff --git a/tash b/tash deleted file mode 100644 index 343951745..000000000 --- a/tash +++ /dev/null @@ -1,31 +0,0 @@ -[1mdiff --git a/src/foraging_gui/Foraging.py b/src/foraging_gui/Foraging.py[m -[1mindex 122706fe..b9a37510 100644[m -[1m--- a/src/foraging_gui/Foraging.py[m -[1m+++ b/src/foraging_gui/Foraging.py[m -[36m@@ -9,7 +9,7 @@[m [mimport math[m - import logging[m - from hashlib import md5[m - [m -[31m-import logging_loki[m -[32m+[m[32m#import logging_loki[m - import socket[m - import harp[m - import threading[m -[36m@@ -25,7 +25,7 @@[m [mfrom aind_slims_api import models[m - import serial[m - import numpy as np[m - import pandas as pd[m -[31m-from pykeepass import PyKeePass[m -[32m+[m[32m#from pykeepass import PyKeePass[m - from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar[m - from scipy.io import savemat, loadmat[m - from PyQt5.QtWidgets import QApplication, QMainWindow, QMessageBox, QSizePolicy[m -[36m@@ -252,6 +252,8 @@[m [mclass Window(QMainWindow):[m - def _show_disk_space(self):[m - '''Show the disk space of the current computer'''[m - total, used, free = shutil.disk_usage(self.default_saveFolder)[m -[32m+[m[32m used = 450*1024**3[m -[32m+[m[32m free = total-used[m - self.diskspace.setText(f"Used space: {used/1024**3:.2f}GB Free space: {free/1024**3:.2f}GB")[m - self.DiskSpaceProgreeBar.setValue(int(used/total*100))[m - if free/1024**3 < 100 or used/total > 0.9:[m From 36e83aea8e5a2d0dc9b4ae66fd2130433217c16c Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 12 Dec 2024 05:09:59 +0000 Subject: [PATCH 04/12] ci: version bump [skip actions] --- src/foraging_gui/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/foraging_gui/__init__.py b/src/foraging_gui/__init__.py index 0a6b5300e..9b52ff8dd 100644 --- a/src/foraging_gui/__init__.py +++ b/src/foraging_gui/__init__.py @@ -1,3 +1,3 @@ -__version__ = "1.6.13" +__version__ = "1.6.14" From 8df9cab9cfe66309b93c4cb7a59398eefcedd83a Mon Sep 17 00:00:00 2001 From: XX-Yin <109394934+XX-Yin@users.noreply.github.com> Date: Wed, 11 Dec 2024 21:11:43 -0800 Subject: [PATCH 05/12] Revert "fix stream" --- src/foraging_gui/GenerateMetadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/foraging_gui/GenerateMetadata.py b/src/foraging_gui/GenerateMetadata.py index d4fbfd71c..f46abd9ab 100644 --- a/src/foraging_gui/GenerateMetadata.py +++ b/src/foraging_gui/GenerateMetadata.py @@ -569,7 +569,7 @@ def _combine_data_streams(self): self.data_streams = self.ophys_streams elif self.ophys_streams != []: # add the ophys streams to the high speed camera streams - self.data_streams[0].stream_modalities = self.data_streams[0].stream_modalities + self.ophys_streams[0].stream_modalities + self.data_streams.stream_modalities = self.data_streams[0].stream_modalities + self.ophys_streams[0].stream_modalities self.data_streams[0].stream_start_time=min(self.data_streams[0].stream_start_time,self.ophys_streams[0].stream_start_time) self.data_streams[0].stream_end_time=max(self.data_streams[0].stream_end_time,self.ophys_streams[0].stream_end_time) self.data_streams[0].daq_names = self.data_streams[0].daq_names + self.ophys_streams[0].daq_names From 2b53103c84950ffef7b8a6edbc54d8c327d65f6d Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 12 Dec 2024 05:12:15 +0000 Subject: [PATCH 06/12] ci: version bump [skip actions] --- src/foraging_gui/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/foraging_gui/__init__.py b/src/foraging_gui/__init__.py index 9b52ff8dd..450109dc7 100644 --- a/src/foraging_gui/__init__.py +++ b/src/foraging_gui/__init__.py @@ -1,3 +1,3 @@ -__version__ = "1.6.14" +__version__ = "1.6.15" From 1bb13751f4c3975ec5c36561f433f5cd3498793e Mon Sep 17 00:00:00 2001 From: Xinxin Yin <yinxx15@tsinghua.org.cn> Date: Wed, 11 Dec 2024 23:41:55 -0800 Subject: [PATCH 07/12] change to warning --- src/foraging_gui/Foraging.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/foraging_gui/Foraging.py b/src/foraging_gui/Foraging.py index 5d33b0721..a0bf230b0 100644 --- a/src/foraging_gui/Foraging.py +++ b/src/foraging_gui/Foraging.py @@ -2257,7 +2257,7 @@ def _ShowRewardPairs(self): self.ShowRewardPairs_2.setText(self.ShowRewardPairs.text()) except Exception as e: # Catch the exception and log error information - logging.error(traceback.format_exc()) + logging.warning(traceback.format_exc()) def closeEvent(self, event): # stop the current session first From fff439518639ae1a48ff4e7571a18e8a1ce479aa Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 12 Dec 2024 07:45:39 +0000 Subject: [PATCH 08/12] ci: version bump [skip actions] --- src/foraging_gui/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/foraging_gui/__init__.py b/src/foraging_gui/__init__.py index 450109dc7..22b8bd4f6 100644 --- a/src/foraging_gui/__init__.py +++ b/src/foraging_gui/__init__.py @@ -1,3 +1,3 @@ -__version__ = "1.6.15" +__version__ = "1.6.16" From 27c41077600e204f02c349eafef0834f49218938 Mon Sep 17 00:00:00 2001 From: XX-Yin <109394934+XX-Yin@users.noreply.github.com> Date: Wed, 11 Dec 2024 23:56:32 -0800 Subject: [PATCH 09/12] fixed a typo --- src/foraging_gui/GenerateMetadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/foraging_gui/GenerateMetadata.py b/src/foraging_gui/GenerateMetadata.py index f46abd9ab..d4fbfd71c 100644 --- a/src/foraging_gui/GenerateMetadata.py +++ b/src/foraging_gui/GenerateMetadata.py @@ -569,7 +569,7 @@ def _combine_data_streams(self): self.data_streams = self.ophys_streams elif self.ophys_streams != []: # add the ophys streams to the high speed camera streams - self.data_streams.stream_modalities = self.data_streams[0].stream_modalities + self.ophys_streams[0].stream_modalities + self.data_streams[0].stream_modalities = self.data_streams[0].stream_modalities + self.ophys_streams[0].stream_modalities self.data_streams[0].stream_start_time=min(self.data_streams[0].stream_start_time,self.ophys_streams[0].stream_start_time) self.data_streams[0].stream_end_time=max(self.data_streams[0].stream_end_time,self.ophys_streams[0].stream_end_time) self.data_streams[0].daq_names = self.data_streams[0].daq_names + self.ophys_streams[0].daq_names From 4ca4f2869212baeda16d07ba736036e1130453ff Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 12 Dec 2024 07:56:56 +0000 Subject: [PATCH 10/12] ci: version bump [skip actions] --- src/foraging_gui/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/foraging_gui/__init__.py b/src/foraging_gui/__init__.py index 22b8bd4f6..c2d56b6b7 100644 --- a/src/foraging_gui/__init__.py +++ b/src/foraging_gui/__init__.py @@ -1,3 +1,3 @@ -__version__ = "1.6.16" +__version__ = "1.6.17" From 4715b61a09b72684f25f5dd3c5d8540ed1694cec Mon Sep 17 00:00:00 2001 From: XX-Yin <109394934+XX-Yin@users.noreply.github.com> Date: Wed, 11 Dec 2024 23:58:55 -0800 Subject: [PATCH 11/12] Revert "Revert "Fix 1155 waterlog post session weight"" --- src/foraging_gui/Foraging.py | 19 ++++++------------- tash | 31 +++++++++++++++++++++++++++++++ 2 files changed, 37 insertions(+), 13 deletions(-) create mode 100644 tash diff --git a/src/foraging_gui/Foraging.py b/src/foraging_gui/Foraging.py index a0bf230b0..894857408 100644 --- a/src/foraging_gui/Foraging.py +++ b/src/foraging_gui/Foraging.py @@ -1361,14 +1361,15 @@ def _AddWaterLogResult(self, session: Session): # extract software information logging.info('Extracting software information from first data stream') - software = session.data_streams[0].software[0] + software = session.stimulus_epochs[0].software[0] # create model logging.info('Creating SlimsWaterlogResult based on session information.') model = models.SlimsWaterlogResult( mouse_pk=mouse.pk, date=session.session_start_time, - weight_g=session.animal_weight_prior, + weight_g=session.animal_weight_post, + operator=self.behavior_session_model.experimenter[0], water_earned_ml=water['water_in_session_foraging'], water_supplement_delivered_ml=water['water_after_session'], water_supplement_recommended_ml=None, @@ -3186,7 +3187,7 @@ def _Open(self,open_last = False,input_file = ''): self.stage_widget.movement_page_view.lineEdit_y1.setText(str(last_positions['y1'])) self.stage_widget.movement_page_view.lineEdit_y2.setText(str(last_positions['y2'])) self.stage_widget.movement_page_view.lineEdit_z.setText(str(last_positions['z'])) - threading.Thread(target=self.move_aind_stage).start() + self.move_aind_stage() elif 'B_NewscalePositions' in Obj.keys() and len(Obj['B_NewscalePositions']) != 0: # cross compatibility for mice run on older version of code. last_positions = Obj['B_NewscalePositions'][-1] self.current_stage.move_absolute_3d(float(last_positions[0]), @@ -3231,16 +3232,8 @@ def move_aind_stage(self): """ Move all axis of stage in stage widget """ - # save current positions since stage widget will reset once returnPressed in emitted - axes = ['x', 'y1', 'y2', 'z'] - textboxes = [getattr(self.stage_widget.movement_page_view, f'lineEdit_{axis}') for axis in axes] - positions = [textbox.text() for textbox in textboxes] - for textbox, position in zip(textboxes, positions): - textbox.setText(position) - textbox.returnPressed.emit() - time.sleep(1) # allow worker to initialize - while self.stage_widget.stage_model.move_thread.isRunning(): - time.sleep(.1) + positions = self.stage_widget.movement_page_view.get_positions_from_line_edit() + self.stage_widget.movement_page_view.signal_position_change.emit(positions) def _LoadVisualization(self): '''To visulize the training when loading a session''' diff --git a/tash b/tash new file mode 100644 index 000000000..343951745 --- /dev/null +++ b/tash @@ -0,0 +1,31 @@ +[1mdiff --git a/src/foraging_gui/Foraging.py b/src/foraging_gui/Foraging.py[m +[1mindex 122706fe..b9a37510 100644[m +[1m--- a/src/foraging_gui/Foraging.py[m +[1m+++ b/src/foraging_gui/Foraging.py[m +[36m@@ -9,7 +9,7 @@[m [mimport math[m + import logging[m + from hashlib import md5[m + [m +[31m-import logging_loki[m +[32m+[m[32m#import logging_loki[m + import socket[m + import harp[m + import threading[m +[36m@@ -25,7 +25,7 @@[m [mfrom aind_slims_api import models[m + import serial[m + import numpy as np[m + import pandas as pd[m +[31m-from pykeepass import PyKeePass[m +[32m+[m[32m#from pykeepass import PyKeePass[m + from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar[m + from scipy.io import savemat, loadmat[m + from PyQt5.QtWidgets import QApplication, QMainWindow, QMessageBox, QSizePolicy[m +[36m@@ -252,6 +252,8 @@[m [mclass Window(QMainWindow):[m + def _show_disk_space(self):[m + '''Show the disk space of the current computer'''[m + total, used, free = shutil.disk_usage(self.default_saveFolder)[m +[32m+[m[32m used = 450*1024**3[m +[32m+[m[32m free = total-used[m + self.diskspace.setText(f"Used space: {used/1024**3:.2f}GB Free space: {free/1024**3:.2f}GB")[m + self.DiskSpaceProgreeBar.setValue(int(used/total*100))[m + if free/1024**3 < 100 or used/total > 0.9:[m From f6de3470a14a3ed256e6e0a3d034aeda9c47f66f Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 12 Dec 2024 07:59:25 +0000 Subject: [PATCH 12/12] ci: version bump [skip actions] --- src/foraging_gui/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/foraging_gui/__init__.py b/src/foraging_gui/__init__.py index c2d56b6b7..3e4631852 100644 --- a/src/foraging_gui/__init__.py +++ b/src/foraging_gui/__init__.py @@ -1,3 +1,3 @@ -__version__ = "1.6.17" +__version__ = "1.6.18"