diff --git a/CHANGELOG.md b/CHANGELOG.md index 451f27a27..07978501e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,11 @@ Changelog ========= +8.24.3 +------ +* fix: create the `raw_ephys_data` folder even if there are no probes (when running behavior sessions on ephys rig) +* move some Qt related code to `iblqt` repository + 8.24.2 ------ * make Frame2TTL validation more robust diff --git a/docs/source/faq.rst b/docs/source/faq.rst index 8a98a9134..5138b23bc 100644 --- a/docs/source/faq.rst +++ b/docs/source/faq.rst @@ -121,3 +121,32 @@ Frame2TTL Look for a voltage step in Frame2TTL's output when the calibration routine switches from dark to light. #. If you *do* see the change in the TTL signal, the Bpod might be faulty. Try using a different Bpod unit. #. If you do *not* see the voltage step, the Frame2TTL might be faulty. Try using a different Frame2TTL unit. + + +Move a mouse onto a previous training stage +=========================================== +Training phases enfold according to an automated procedure, see the `mouse training protocol on Figshare `_ for a description of these phases. + +However, it is possible that one wants to overwrite the automated progression, and bring back an animal onto a previous +training stage. + +In this case: + +1. Select the training protocol on the GUI +2. Select the wanted training phase manually + + + .. figure:: img/training_phase_manual_update.png + :width: 100% + :class: with-border + + Select the training phase manually using the arrows. + +On the next day of training, the "automatic" criteria will be computed assuming the training phase last used, i.e. +the one you manually selected in this instance. + +For example, if you have a mouse on Training Phase 5, and move it manually to Phase 4 (which can be useful when +trying to debias an animal), the next session on "automatic" mode will compute the stage progression from stage 4, +and disregard the fact that the mouse was on Phase 5 beforehand. diff --git a/docs/source/img/training_phase_manual_update.png b/docs/source/img/training_phase_manual_update.png new file mode 100644 index 000000000..8d88207bb Binary files /dev/null and b/docs/source/img/training_phase_manual_update.png differ diff --git a/docs/source/reference_developer_guide.rst b/docs/source/reference_developer_guide.rst index a5a6e24db..87e7027f3 100644 --- a/docs/source/reference_developer_guide.rst +++ b/docs/source/reference_developer_guide.rst @@ -139,4 +139,4 @@ To write the documentation: To release the documentation onto the `website `_: * Wait for the next release, or -* Manually trigger the GitHub action by clicking "Run Workflow" (select ``master``) `here `_ +* Manually trigger the GitHub action by clicking "Run Workflow" (select ``iblrigv8dev``) `here `_ diff --git a/iblrig/__init__.py b/iblrig/__init__.py index 60f029c22..a7fb4293c 100644 --- a/iblrig/__init__.py +++ b/iblrig/__init__.py @@ -6,7 +6,7 @@ # 5) git tag the release in accordance to the version number below (after merge!) # >>> git tag 8.15.6 # >>> git push origin --tags -__version__ = '8.24.2' +__version__ = '8.24.3' from iblrig.version_management import get_detailed_version_string diff --git a/iblrig/base_tasks.py b/iblrig/base_tasks.py index 0833b3955..d2a11c311 100644 --- a/iblrig/base_tasks.py +++ b/iblrig/base_tasks.py @@ -1215,7 +1215,7 @@ def __init__(self, *_, remote_rigs=None, **kwargs): if isinstance(remote_rigs, list): # For now we flatten to list of remote rig names but could permit list of (name, URI) tuples remote_rigs = list(filter(None, flatten(remote_rigs))) - all_remote_rigs = net.get_remote_devices(iblrig_settings=kwargs.get('iblrig_settings', None)) + all_remote_rigs = net.get_remote_devices(iblrig_settings=kwargs.get('iblrig_settings')) if not set(remote_rigs).issubset(all_remote_rigs.keys()): raise ValueError('Selected remote rigs not in remote rigs list') remote_rigs = {k: v for k, v in all_remote_rigs.items() if k in remote_rigs} diff --git a/iblrig/gui/tab_data.py b/iblrig/gui/tab_data.py index b2274e3f6..d9cb85e6a 100644 --- a/iblrig/gui/tab_data.py +++ b/iblrig/gui/tab_data.py @@ -17,7 +17,7 @@ ) from PyQt5.QtWidgets import QHeaderView, QStyledItemDelegate, QWidget -from iblrig.gui.tools import DataFrameTableModel +from iblqt.core import DataFrameTableModel from iblrig.gui.ui_tab_data import Ui_TabData from iblrig.path_helper import get_local_and_remote_paths from iblrig.transfer_experiments import CopyState, SessionCopier @@ -79,7 +79,7 @@ def __init__(self, *args, **kwargs): # create empty DataFrameTableModel data = pd.DataFrame(None, index=[], columns=[c.name for c in COLUMNS]) - self.tableModel = DataFrameTableModel(df=data) + self.tableModel = DataFrameTableModel(dataFrame=data) # create filter proxy & assign it to view self.tableProxy = QSortFilterProxyModel() diff --git a/iblrig/gui/tools.py b/iblrig/gui/tools.py index 50180120c..6cf1db920 100644 --- a/iblrig/gui/tools.py +++ b/iblrig/gui/tools.py @@ -9,17 +9,12 @@ from shutil import disk_usage from typing import Any -import numpy as np -import pandas as pd from PyQt5 import QtGui from PyQt5.QtCore import ( - QAbstractTableModel, - QModelIndex, QObject, QRunnable, Qt, QThreadPool, - QVariant, pyqtProperty, pyqtSignal, pyqtSlot, @@ -223,144 +218,6 @@ def run(self) -> None: self.signals.finished.emit() -class DataFrameTableModel(QAbstractTableModel): - def __init__(self, *args, df: pd.DataFrame, **kwargs): - super().__init__(*args, **kwargs) - self._dataFrame = df - - def dataFrame(self): - return self._dataFrame - - def setDataFrame(self, data_frame: pd.DataFrame): - self.beginResetModel() - self._dataFrame = data_frame.copy() - self.endResetModel() - - dataFrame = pyqtProperty(pd.DataFrame, fget=dataFrame, fset=setDataFrame) - - def headerData(self, section, orientation, role=...): - """ - Get the header data for the specified section. - - Parameters - ---------- - section : int - The section index. - orientation : Qt.Orientation - The orientation of the header. - role : int, optional - The role of the header data. - - Returns - ------- - QVariant - The header data. - """ - if role == Qt.DisplayRole: - if orientation == Qt.Horizontal: - return str(self._dataFrame.columns[section]) - else: - return str(self._dataFrame.index[section]) - - def rowCount(self, parent=...): - """ - Get the number of rows in the model. - - Parameters - ---------- - parent : QModelIndex, optional - The parent index. - - Returns - ------- - int - The number of rows. - """ - if isinstance(parent, QModelIndex) and parent.isValid(): - return 0 - return self.dataFrame.shape[0] - - def columnCount(self, parent=...): - """ - Get the number of columns in the model. - - Parameters - ---------- - parent : QModelIndex, optional - The parent index. - - Returns - ------- - int - The number of columns. - """ - if isinstance(parent, QModelIndex) and parent.isValid(): - return 0 - return self.dataFrame.shape[1] - - def data(self, index, role=...): - """ - Get the data for the specified index. - - Parameters - ---------- - index : QModelIndex - The index of the data. - role : int, optional - The role of the data. - - Returns - ------- - QVariant - The data for the specified index. - """ - if index.isValid(): - row = self._dataFrame.index[index.row()] - col = self._dataFrame.columns[index.column()] - dat = self._dataFrame.iloc[row][col] - if role == Qt.DisplayRole: - if isinstance(dat, np.generic): - return dat.item() - return dat - return QVariant() - - def sort(self, column, order=...): - """ - Sort the data based on the specified column and order. - - Parameters - ---------- - column : int - The column index to sort by. - order : Qt.SortOrder, optional - The sort order. - """ - self.layoutAboutToBeChanged.emit() - col_name = self._dataFrame.columns.values[column] - self._dataFrame.sort_values(by=col_name, ascending=order == Qt.AscendingOrder, inplace=True) - self._dataFrame.reset_index(inplace=True, drop=True) - self.layoutChanged.emit() - - def setData(self, index, value, role=Qt.DisplayRole): - """ - Set data at the specified index with the given value. - - Parameters - ---------- - index : QModelIndex - The index where the data will be set. - value : Any - The new value to be set at the specified index. - role : int, optional - The role of the data. Default is Qt.DisplayRole. - """ - if index.isValid(): - row = self._dataFrame.index[index.row()] - col = self._dataFrame.columns[index.column()] - self._dataFrame.at[row, col] = value - self.dataChanged.emit(index, index, [role]) - - class RemoteDevicesListView(QListView): def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) diff --git a/iblrig/test/test_hardware_mixins.py b/iblrig/test/test_hardware_mixins.py index f89d7bb5a..1fcfae39f 100644 --- a/iblrig/test/test_hardware_mixins.py +++ b/iblrig/test/test_hardware_mixins.py @@ -109,12 +109,12 @@ def test_rotary_encoder_mixin(self): 'RotaryEncoder1_3', 'RotaryEncoder1_4', ] - assert { + assert session.device_rotary_encoder.THRESHOLD_EVENTS == { -35: 'RotaryEncoder1_1', 35: 'RotaryEncoder1_2', -2: 'RotaryEncoder1_3', 2: 'RotaryEncoder1_4', - } == session.device_rotary_encoder.THRESHOLD_EVENTS + } with self.assertRaises(ValueError): RotaryEncoderMixin.start_mixin_rotary_encoder(session) diff --git a/iblrig/test/test_transfers.py b/iblrig/test/test_transfers.py index 4a82be0f6..edfdae5e8 100644 --- a/iblrig/test/test_transfers.py +++ b/iblrig/test/test_transfers.py @@ -6,6 +6,9 @@ from pathlib import Path from unittest import mock +from packaging import version + +import ibllib import iblrig.commands import iblrig.path_helper import iblrig.raw_data_loaders @@ -228,6 +231,52 @@ def test_behavior_ephys_video_copy(self): self.assertEqual(set(final_experiment_description['devices']['cameras'].keys()), {'left'}) self.assertEqual(set(final_experiment_description['sync'].keys()), {'nidq'}) + # Requires recent change to ibllib test fixture code supporting no probe ephys recording files + @unittest.skipIf(version.parse(ibllib.__version__) < version.parse('2.39'), 'ibllib < 2.39') + def test_ephys_no_probe(self): + """Test copying a session at ephys rig when no probes were used (DAQ only).""" + # First create a behavior session + task_kwargs = copy.deepcopy(self.session_kwargs) + task_kwargs['hardware_settings'].update( + { + 'device_cameras': None, + 'MAIN_SYNC': False, # this is quite important for ephys sessions + } + ) + session = _create_behavior_session(kwargs=task_kwargs, ntrials=50) + folder_session_ephys = Path(self.td.name).joinpath('ephys', 'Subjects', *session.paths.SESSION_FOLDER.parts[-3:]) + + # Create an ephys acquisition + n_probes = 0 + # SpikeGLX then saves these files into the session folder + populate_raw_spikeglx(folder_session_ephys, model='3B', n_probes=n_probes) + + # Test the copiers + sc = BehaviorCopier(session_path=session.paths.SESSION_FOLDER, remote_subjects_folder=session.paths.REMOTE_SUBJECT_FOLDER) + self.assertEqual('.status_pending', sc.glob_file_remote_copy_status().suffix) + self.assertEqual(1, sc.state) + sc.copy_collections() + self.assertEqual(2, sc.state) + self.assertEqual('.status_complete', sc.glob_file_remote_copy_status().suffix) + sc.copy_collections() + self.assertEqual(2, sc.state) + sc.finalize_copy(number_of_expected_devices=None) + self.assertEqual(2, sc.state) # here we still don't have all devices so we stay in state 2 + + ec = EphysCopier(session_path=folder_session_ephys, remote_subjects_folder=session.paths.REMOTE_SUBJECT_FOLDER) + self.assertEqual(0, ec.state) + ec.initialize_experiment() + self.assertEqual(1, ec.state) + self.assertIn('sync', ec.experiment_description) + ec.copy_collections() + self.assertEqual(2, ec.state) + # this time it's all there and we move on + ec.finalize_copy(number_of_expected_devices=None) + self.assertEqual(3, ec.state) + final_experiment_description = session_params.read_params(ec.remote_session_path) + self.assertEqual(1, len(final_experiment_description['tasks'])) + self.assertEqual(set(final_experiment_description['sync'].keys()), {'nidq'}) + def test_copy_snapshots(self): """Test copy of snapshots folder(s).""" # Create without task data diff --git a/iblrig/transfer_experiments.py b/iblrig/transfer_experiments.py index 97f8fdcef..c4d3ef266 100644 --- a/iblrig/transfer_experiments.py +++ b/iblrig/transfer_experiments.py @@ -553,8 +553,9 @@ def initialize_experiment(self, acquisition_description=None, nprobes=None, main self._experiment_description = acquisition_description super().initialize_experiment(acquisition_description=acquisition_description, **kwargs) # once the session folders have been initialized, create the probe folders + (ephys_path := self.session_path.joinpath('raw_ephys_data')).mkdir(exist_ok=True) for n in range(nprobes): - 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