From 7f8bf95604cba65591eaf87688c1ebbf9fc09048 Mon Sep 17 00:00:00 2001 From: owinter Date: Thu, 17 Oct 2024 11:37:21 +0100 Subject: [PATCH 1/5] load jsonable from iblrig available to all installs --- CHANGELOG.md | 6 ++++++ iblutil/__init__.py | 2 +- iblutil/io/jsonable.py | 35 +++++++++++++++++++++++++++++++++++ 3 files changed, 42 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 47a8d2e..77f3600 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,12 @@ * Minor releases (X.1.X) are new features such as added functions or small changes that don't cause major compatibility issues. * Major releases (1.X.X) are major new features or changes that break backward compatibility in a big way. +## [Latest](https://github.com/int-brain-lab/iblutil/commits/main) [1.14.0] + +### Added + +- io.jsonable.load_task_jsonable: read and format iblrig raw data to a trials table Dataframe and a list of raw Bpod trials + ## [Latest](https://github.com/int-brain-lab/iblutil/commits/main) [1.13.0] ### Added diff --git a/iblutil/__init__.py b/iblutil/__init__.py index 84c54b7..e4f2ad4 100644 --- a/iblutil/__init__.py +++ b/iblutil/__init__.py @@ -1 +1 @@ -__version__ = '1.13.0' +__version__ = '1.14.0' diff --git a/iblutil/io/jsonable.py b/iblutil/io/jsonable.py index 01fe55f..0c4fbad 100644 --- a/iblutil/io/jsonable.py +++ b/iblutil/io/jsonable.py @@ -1,4 +1,8 @@ import json +from pathlib import Path +from typing import Any + +import pandas as pd def read(file): @@ -21,3 +25,34 @@ def write(file, data): def append(file, data): _write(file, data, 'a') + + +def load_task_jsonable(jsonable_file: str | Path, offset: int | None = None) -> tuple[pd.DataFrame, list[Any]]: + """ + Reads in a task data jsonable file and returns a trials dataframe and a bpod data list. + + Parameters + ---------- + - jsonable_file (str): full path to jsonable file. + - offset (int or None): The offset to start reading from (default: None). + + Returns + ------- + - tuple: A tuple containing: + - trials_table (pandas.DataFrame): A DataFrame with the trial info in the same format as the Session trials table. + - bpod_data (list): timing data for each trial + """ + trials_table = [] + with open(jsonable_file) as f: + if offset is not None: + f.seek(offset, 0) + for line in f: + trials_table.append(json.loads(line)) + + # pop-out the bpod data from the table + bpod_data = [] + for td in trials_table: + bpod_data.append(td.pop('behavior_data')) + + trials_table = pd.DataFrame(trials_table) + return trials_table, bpod_data From 6772f1854f25b8fe42276dd85e40471263c7254e Mon Sep 17 00:00:00 2001 From: Miles Wells Date: Thu, 17 Oct 2024 16:58:20 +0300 Subject: [PATCH 2/5] one.util.Listable -> iblutil.util.Listable --- CHANGELOG.md | 3 ++- iblutil/io/jsonable.py | 4 ++-- iblutil/util.py | 7 ++++++- tests/test_util.py | 12 ++++++++++++ 4 files changed, 22 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 77f3600..abab176 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,8 @@ ### Added -- io.jsonable.load_task_jsonable: read and format iblrig raw data to a trials table Dataframe and a list of raw Bpod trials +- io.jsonable.load_task_jsonable: read and format iblrig raw data to a trials table Dataframe and a list of raw Bpod trials +- util.Listable: returns a typing class that is the union of input class and a sequence thereof ## [Latest](https://github.com/int-brain-lab/iblutil/commits/main) [1.13.0] diff --git a/iblutil/io/jsonable.py b/iblutil/io/jsonable.py index 0c4fbad..b965023 100644 --- a/iblutil/io/jsonable.py +++ b/iblutil/io/jsonable.py @@ -1,6 +1,6 @@ import json from pathlib import Path -from typing import Any +from typing import Any, List, Tuple import pandas as pd @@ -27,7 +27,7 @@ def append(file, data): _write(file, data, 'a') -def load_task_jsonable(jsonable_file: str | Path, offset: int | None = None) -> tuple[pd.DataFrame, list[Any]]: +def load_task_jsonable(jsonable_file: str | Path, offset: int | None = None) -> Tuple[pd.DataFrame, List[Any]]: """ Reads in a task data jsonable file and returns a trials dataframe and a bpod data list. diff --git a/iblutil/util.py b/iblutil/util.py index ac9d4bf..6eecbf3 100644 --- a/iblutil/util.py +++ b/iblutil/util.py @@ -7,7 +7,7 @@ import copy import logging import sys -from typing import Union, Iterable +from typing import Union, Iterable, Sequence import numpy as np @@ -23,6 +23,11 @@ 'CRITICAL': 'bold_purple'} +def Listable(t): + """Return a typing.Union if the input and sequence of input.""" + return Union[t, Sequence[t]] + + class Bunch(dict): """A subclass of dictionary with an additional dot syntax.""" diff --git a/tests/test_util.py b/tests/test_util.py index c46c31e..3fd5aa9 100644 --- a/tests/test_util.py +++ b/tests/test_util.py @@ -1,5 +1,6 @@ import unittest import types +import typing from pathlib import Path import tempfile import logging @@ -230,5 +231,16 @@ def test_ensure_list(self): self.assertEqual([x], util.ensure_list(x, exclude_type=(np.ndarray))) +class TestListable(unittest.TestCase): + """Test Listable typing class.""" + + def test_listable(self): + """Test listable type from given class.""" + listable = util.Listable(str) + self.assertIs(listable, typing.Union[str, typing.Sequence[str]]) + listable = util.Listable(dict) + self.assertIs(listable, typing.Union[dict, typing.Sequence[dict]]) + + if __name__ == '__main__': unittest.main(exit=False) From 45b4bd6cbc238c779e5afeb4280acdea353fe952 Mon Sep 17 00:00:00 2001 From: owinter Date: Thu, 17 Oct 2024 15:18:21 +0100 Subject: [PATCH 3/5] add test jsonable - move test folder inside package for pip installed --- MANIFEST.ini | 1 + {tests => iblutil/tests}/__init__.py | 0 .../tests/fixtures/task_data_short.jsonable | 2 ++ {tests => iblutil/tests}/test_io.py | 23 +++++++++++++++++++ {tests => iblutil/tests}/test_net.py | 0 {tests => iblutil/tests}/test_numerical.py | 0 {tests => iblutil/tests}/test_spacers.py | 0 {tests => iblutil/tests}/test_util.py | 0 8 files changed, 26 insertions(+) create mode 100644 MANIFEST.ini rename {tests => iblutil/tests}/__init__.py (100%) create mode 100644 iblutil/tests/fixtures/task_data_short.jsonable rename {tests => iblutil/tests}/test_io.py (90%) rename {tests => iblutil/tests}/test_net.py (100%) rename {tests => iblutil/tests}/test_numerical.py (100%) rename {tests => iblutil/tests}/test_spacers.py (100%) rename {tests => iblutil/tests}/test_util.py (100%) diff --git a/MANIFEST.ini b/MANIFEST.ini new file mode 100644 index 0000000..f5ca296 --- /dev/null +++ b/MANIFEST.ini @@ -0,0 +1 @@ +recursive-include tests/fixtures * diff --git a/tests/__init__.py b/iblutil/tests/__init__.py similarity index 100% rename from tests/__init__.py rename to iblutil/tests/__init__.py diff --git a/iblutil/tests/fixtures/task_data_short.jsonable b/iblutil/tests/fixtures/task_data_short.jsonable new file mode 100644 index 0000000..1991c7c --- /dev/null +++ b/iblutil/tests/fixtures/task_data_short.jsonable @@ -0,0 +1,2 @@ +{"block_num": 0, "block_trial_num": 0, "contrast": 0.25, "position": -35.0, "quiescent_period": 0.4878452636429898, "response_side": -1, "response_time": 11.527400000000002, "reward_amount": 0.0, "reward_valve_time": NaN, "stim_angle": 0.0, "stim_freq": 0.1, "stim_gain": 4.0, "stim_phase": 5.026547158268823, "stim_probability_left": 0.5, "stim_reverse": false, "stim_sigma": 7.0, "trial_correct": false, "trial_num": 0, "omit_feedback": false, "choice_delay": 2.3499999999999996, "behavior_data": {"Bpod start timestamp": 21.073711, "Trial start timestamp": 21.073711, "Trial end timestamp": 40.815813, "States timestamps": {"trial_start": [[0, 2.7767]], "delay_initiation": [[2.7767, 2.7768]], "reset_rotary_encoder": [[2.7768, 2.7769]], "quiescent_period": [[2.7769, 3.2647]], "stim_on": [[3.2647, 3.3647]], "interactive_delay": [[3.3647, 3.3648000000000002]], "play_tone": [[3.3648000000000002, 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14.514600000000002, 14.631200000000002, 14.698, 14.747800000000002, 15.931000000000001, 16.1145, 16.1476, 16.1811, 16.2144, 16.247500000000002, 16.281000000000002, 16.3144, 16.3477, 16.381, 16.4143, 16.4477, 16.5309, 16.6143], "RotaryEncoder1_4": [1.8142], "RotaryEncoder1_3": [3.0733], "RotaryEncoder1_1": [16.5612]}}} diff --git a/tests/test_io.py b/iblutil/tests/test_io.py similarity index 90% rename from tests/test_io.py rename to iblutil/tests/test_io.py index 474f984..f69b01a 100644 --- a/tests/test_io.py +++ b/iblutil/tests/test_io.py @@ -220,5 +220,28 @@ def tearDown(self) -> None: os.unlink(self.tfile.name) +class TestLoadTaskData(unittest.TestCase): + def test_load_task_jsonable(self): + jsonable_file = Path(__file__).parent.joinpath('fixtures', 'task_data_short.jsonable') + trials_table, bpod_data = jsonable.load_task_jsonable(jsonable_file) + assert trials_table.shape[0] == 2 + assert len(bpod_data) == 2 + + def test_load_task_jsonable_partial(self): + jsonable_file = Path(__file__).parent.joinpath('fixtures', 'task_data_short.jsonable') + with open(jsonable_file) as fp: + fp.readline() + offset = fp.tell() + trials_table, bpod_data = jsonable.load_task_jsonable(jsonable_file, offset=offset) + + trials_table_full, bpod_data_full = jsonable.load_task_jsonable(jsonable_file) + for c in trials_table.columns: + if not np.isnan(trials_table[c][0]): + np.testing.assert_equal(trials_table_full[c].values[-1], trials_table[c][0]) + + assert bpod_data_full[-1] == bpod_data[0] + + + if __name__ == '__main__': unittest.main(exit=False, verbosity=2) diff --git a/tests/test_net.py b/iblutil/tests/test_net.py similarity index 100% rename from tests/test_net.py rename to iblutil/tests/test_net.py diff --git a/tests/test_numerical.py b/iblutil/tests/test_numerical.py similarity index 100% rename from tests/test_numerical.py rename to iblutil/tests/test_numerical.py diff --git a/tests/test_spacers.py b/iblutil/tests/test_spacers.py similarity index 100% rename from tests/test_spacers.py rename to iblutil/tests/test_spacers.py diff --git a/tests/test_util.py b/iblutil/tests/test_util.py similarity index 100% rename from tests/test_util.py rename to iblutil/tests/test_util.py From aa323340b99d2b8cf57cb8938ba42f33b76921db Mon Sep 17 00:00:00 2001 From: owinter Date: Thu, 17 Oct 2024 15:49:16 +0100 Subject: [PATCH 4/5] flake --- iblutil/tests/test_io.py | 1 - 1 file changed, 1 deletion(-) diff --git a/iblutil/tests/test_io.py b/iblutil/tests/test_io.py index f69b01a..4c2b6fe 100644 --- a/iblutil/tests/test_io.py +++ b/iblutil/tests/test_io.py @@ -242,6 +242,5 @@ def test_load_task_jsonable_partial(self): assert bpod_data_full[-1] == bpod_data[0] - if __name__ == '__main__': unittest.main(exit=False, verbosity=2) From 4b31571e924258bc484516e7806b0fa089650bd9 Mon Sep 17 00:00:00 2001 From: Miles Wells Date: Mon, 21 Oct 2024 16:51:09 +0300 Subject: [PATCH 5/5] typing; docstring formatting --- iblutil/io/jsonable.py | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/iblutil/io/jsonable.py b/iblutil/io/jsonable.py index b965023..6a1a4fe 100644 --- a/iblutil/io/jsonable.py +++ b/iblutil/io/jsonable.py @@ -1,5 +1,4 @@ import json -from pathlib import Path from typing import Any, List, Tuple import pandas as pd @@ -27,20 +26,23 @@ def append(file, data): _write(file, data, 'a') -def load_task_jsonable(jsonable_file: str | Path, offset: int | None = None) -> Tuple[pd.DataFrame, List[Any]]: +def load_task_jsonable(jsonable_file, offset: int = None) -> Tuple[pd.DataFrame, List[Any]]: """ Reads in a task data jsonable file and returns a trials dataframe and a bpod data list. Parameters ---------- - - jsonable_file (str): full path to jsonable file. - - offset (int or None): The offset to start reading from (default: None). + jsonable_file : str, pathlib.Path + Full path to jsonable file. + offset : int + The offset to start reading from (default: None). Returns ------- - - tuple: A tuple containing: - - trials_table (pandas.DataFrame): A DataFrame with the trial info in the same format as the Session trials table. - - bpod_data (list): timing data for each trial + pandas.DataFrame + A DataFrame with the trial info in the same format as the Session trials table. + list + Timing data for each trial. """ trials_table = [] with open(jsonable_file) as f: