From 81f67053b038261f2a59d914bdac849774d671d9 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Thu, 15 Feb 2024 15:28:01 +0000 Subject: [PATCH] Update documentation --- _autosummary/brainbox.behavior.dlc.html | 17 +- _autosummary/brainbox.behavior.html | 2 +- _autosummary/brainbox.behavior.training.html | 2 +- _autosummary/brainbox.io.one.html | 34 +- _autosummary/iblatlas.genomics.agea.html | 14 +- _autosummary/iblatlas.genomics.html | 93 +++- _autosummary/iblatlas.genomics.merfish.html | 227 +++++++++ _autosummary/iblatlas.html | 2 +- _autosummary/iblatlas.plots.html | 4 +- _autosummary/iblatlas.regions.html | 142 ++++++ _autosummary/ibllib.atlas.atlas.html | 40 ++ _autosummary/ibllib.ephys.ephysqc.html | 2 +- .../ibllib.io.extractors.ephys_passive.html | 8 +- _autosummary/ibllib.io.flags.html | 4 +- _autosummary/ibllib.misc.html | 4 + _autosummary/ibllib.misc.misc.html | 5 +- _autosummary/ibllib.misc.qt.html | 218 ++++++++ _autosummary/ibllib.oneibl.html | 4 +- _autosummary/ibllib.pipes.base_tasks.html | 56 ++- _autosummary/ibllib.pipes.behavior_tasks.html | 165 +++++- .../ibllib.pipes.ephys_preprocessing.html | 23 +- _autosummary/ibllib.pipes.ephys_tasks.html | 4 +- .../ibllib.pipes.mesoscope_tasks.html | 7 +- _autosummary/ibllib.pipes.misc.html | 2 +- _autosummary/ibllib.pipes.tasks.html | 10 +- .../ibllib.pipes.training_preprocessing.html | 11 + _autosummary/ibllib.pipes.video_tasks.html | 4 +- _autosummary/ibllib.qc.alignment_qc.html | 2 + .../ibllib.qc.base.SIGN_OFF_CATEGORIES.html | 2 + _autosummary/ibllib.qc.base.html | 2 + _autosummary/ibllib.qc.camera.html | 6 +- _autosummary/ibllib.qc.critical_reasons.html | 2 + _autosummary/ibllib.qc.dlc.html | 8 +- _autosummary/ibllib.qc.html | 12 +- _autosummary/ibllib.qc.qcplots.html | 4 +- _autosummary/ibllib.qc.task_extractors.html | 16 +- _autosummary/ibllib.qc.task_metrics.html | 17 +- .../ibllib.qc.task_qc_viewer.ViewEphysQC.html | 314 ++++++++++++ _autosummary/ibllib.qc.task_qc_viewer.html | 192 +++++++ .../ibllib.qc.task_qc_viewer.task_qc.html | 300 +++++++++++ _autosummary/ibllib.tests.fixtures.utils.html | 26 + _autosummary/ibllib.tests.html | 4 +- _autosummary/ibllib.tests.qc.html | 3 + .../ibllib.tests.qc.test_alignment_qc.html | 26 +- .../ibllib.tests.qc.test_task_metrics.html | 4 +- ....tests.qc.test_task_qc_viewer.MOCK_QT.html | 201 ++++++++ .../ibllib.tests.qc.test_task_qc_viewer.html | 242 +++++++++ _autosummary/ibllib.tests.test_atlas.html | 4 +- .../ibllib.tests.test_base_tasks.html | 6 + _autosummary/ibllib.tests.test_tasks.html | 10 +- ...xternal_Working_with_ibllib_atlas_10_1.png | Bin 54038 -> 54038 bytes ...external_Working_with_ibllib_atlas_7_1.png | Bin 168026 -> 168026 bytes ..._atlas_circular_pyramidal_flatmap_10_1.png | Bin 136735 -> 136735 bytes ..._atlas_circular_pyramidal_flatmap_17_0.png | Bin 240779 -> 240779 bytes ..._atlas_circular_pyramidal_flatmap_18_0.png | Bin 175716 -> 175716 bytes ..._atlas_circular_pyramidal_flatmap_19_0.png | Bin 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_modules/ibllib/pipes/local_server.html | 7 +- _modules/ibllib/pipes/tasks.html | 6 +- .../ibllib/pipes/training_preprocessing.html | 53 +- _modules/ibllib/qc/qcplots.html | 3 +- _modules/ibllib/qc/task_extractors.html | 16 +- _modules/ibllib/qc/task_metrics.html | 3 + .../ibllib/qc/task_qc_viewer/ViewEphysQC.html | 370 ++++++++++++++ .../ibllib/qc/task_qc_viewer/task_qc.html | 474 ++++++++++++++++++ _modules/ibllib/tests/fixtures/utils.html | 43 ++ .../ibllib/tests/qc/test_alignment_qc.html | 24 +- _modules/ibllib/tests/qc/test_base_qc.html | 8 +- .../tests/qc/test_critical_reasons.html | 10 +- .../ibllib/tests/qc/test_task_qc_viewer.html | 267 ++++++++++ _modules/ibllib/tests/test_base_tasks.html | 35 +- _modules/ibllib/tests/test_ephys.html | 2 +- _modules/ibllib/tests/test_pipes.html | 6 +- _modules/ibllib/tests/test_plots.html | 7 +- _modules/index.html | 9 +- genindex.html | 319 ++++++++++-- .../Working with ibllib atlas.ipynb | 98 ++-- .../atlas_circular_pyramidal_flatmap.html | 4 +- .../atlas_circular_pyramidal_flatmap.ipynb | 98 ++-- .../atlas_dorsal_cortex_flatmap.ipynb | 82 +-- .../atlas_genomics_load_merfish.html | 189 +++++++ .../atlas_genomics_load_merfish.ipynb | 86 ++++ notebooks_external/atlas_mapping.html | 11 +- notebooks_external/atlas_mapping.ipynb | 218 ++++---- .../atlas_plotting_points_on_slice.html | 11 +- .../atlas_plotting_points_on_slice.ipynb | 66 +-- .../atlas_plotting_scalar_on_slice.html | 2 +- .../atlas_plotting_scalar_on_slice.ipynb | 98 ++-- notebooks_external/atlas_swanson_flatmap.html | 12 +- .../atlas_swanson_flatmap.ipynb | 106 ++-- .../atlas_working_with_ibllib_atlas.ipynb | 282 +++++------ notebooks_external/data_download.html | 333 +----------- notebooks_external/data_download.ipynb | 114 ++--- .../data_release_behavior.ipynb | 2 +- .../data_release_brainwidemap.ipynb | 2 +- .../data_release_repro_ephys.ipynb | 2 +- ...data_release_spikesorting_benchmarks.ipynb | 2 +- notebooks_external/data_structure.ipynb | 2 +- notebooks_external/docs_wheel_moves.html | 15 +- notebooks_external/docs_wheel_moves.ipynb | 138 ++--- notebooks_external/loading_ephys_data.ipynb | 50 +- .../loading_multi_photon_imaging_data.ipynb | 2 +- notebooks_external/loading_passive_data.ipynb | 10 +- .../loading_raw_audio_data.ipynb | 10 +- .../loading_raw_ephys_data.html | 271 +++++++++- .../loading_raw_ephys_data.ipynb | 58 +-- .../loading_raw_mesoscope_data.ipynb | 10 +- .../loading_raw_video_data.ipynb | 50 +- .../loading_spike_waveforms.ipynb | 34 +- .../loading_spikesorting_data.html | 11 +- .../loading_spikesorting_data.ipynb | 74 +-- notebooks_external/loading_trials_data.html | 18 +- notebooks_external/loading_trials_data.ipynb | 58 +-- notebooks_external/loading_video_data.html | 11 +- notebooks_external/loading_video_data.ipynb | 50 +- notebooks_external/loading_wheel_data.ipynb | 34 +- notebooks_external/one_quickstart.html | 227 +-------- notebooks_external/one_quickstart.ipynb | 74 +-- objects.inv | Bin 68654 -> 71040 bytes py-modindex.html | 35 ++ searchindex.js | 2 +- 175 files changed, 6136 insertions(+), 1740 deletions(-) create mode 100644 _autosummary/iblatlas.genomics.merfish.html create mode 100644 _autosummary/ibllib.misc.qt.html create mode 100644 _autosummary/ibllib.qc.task_qc_viewer.ViewEphysQC.html create mode 100644 _autosummary/ibllib.qc.task_qc_viewer.html create mode 100644 _autosummary/ibllib.qc.task_qc_viewer.task_qc.html create mode 100644 _autosummary/ibllib.tests.qc.test_task_qc_viewer.MOCK_QT.html create mode 100644 _autosummary/ibllib.tests.qc.test_task_qc_viewer.html create mode 100644 _images/notebooks_external_atlas_genomics_load_merfish_1_0.png create mode 100644 _modules/iblatlas/genomics/merfish.html create mode 100644 _modules/ibllib/misc/qt.html create mode 100644 _modules/ibllib/qc/task_qc_viewer/ViewEphysQC.html create mode 100644 _modules/ibllib/qc/task_qc_viewer/task_qc.html create mode 100644 _modules/ibllib/tests/qc/test_task_qc_viewer.html create mode 100644 notebooks_external/atlas_genomics_load_merfish.html create mode 100644 notebooks_external/atlas_genomics_load_merfish.ipynb diff --git a/_autosummary/brainbox.behavior.dlc.html b/_autosummary/brainbox.behavior.dlc.html index 758d8f0d..b95f3cce 100644 --- a/_autosummary/brainbox.behavior.dlc.html +++ b/_autosummary/brainbox.behavior.dlc.html @@ -145,7 +145,7 @@

brainbox.behavior.dlc

-

Set of functions to deal with dlc data

+

Set of functions to deal with dlc data.

Functions

@@ -173,12 +173,7 @@ - + @@ -187,7 +182,7 @@ - + @@ -228,7 +223,8 @@
likelihood_threshold(dlc, threshold=0.9)[source]
-

Set dlc points with likelihood less than threshold to nan

+

Set dlc points with likelihood less than threshold to nan.

+

FIXME Add unit test.

Parameters:
    @@ -245,7 +241,8 @@
    get_speed(dlc, dlc_t, camera, feature='paw_r')[source]
    -
    +

    FIXME Document and add unit test!

    +
    Parameters:

    • dlc – dlc pqt table

      • diff --git a/_autosummary/brainbox.behavior.html b/_autosummary/brainbox.behavior.html index f01ae046..a35fabf6 100644 --- a/_autosummary/brainbox.behavior.html +++ b/_autosummary/brainbox.behavior.html @@ -148,7 +148,7 @@

Compute sniff times from the nose tip

get_speed

-
param dlc:
-

dlc pqt table

-
-
-

FIXME Document and add unit test!

get_speed_for_features

Wrapper to compute speed for a number of dlc features and add them to dlc table

likelihood_threshold

Set dlc points with likelihood less than threshold to nan

Set dlc points with likelihood less than threshold to nan.

plot_lick_hist

Plots histogramm of lick events aligned to feedback time, separate for correct and incorrect trials

- + diff --git a/_autosummary/brainbox.behavior.training.html b/_autosummary/brainbox.behavior.training.html index 4a4e9fd1..e42f91c6 100644 --- a/_autosummary/brainbox.behavior.training.html +++ b/_autosummary/brainbox.behavior.training.html @@ -280,7 +280,7 @@
-class TrainingStatus(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
+class TrainingStatus(value)[source]

Bases: IntFlag

Standard IBL training criteria.

Enumeration allows for comparisons between training status.

diff --git a/_autosummary/brainbox.io.one.html b/_autosummary/brainbox.io.one.html index 00c717e9..e6b85f29 100644 --- a/_autosummary/brainbox.io.one.html +++ b/_autosummary/brainbox.io.one.html @@ -509,7 +509,7 @@
-class SpikeSortingLoader(one: One = None, atlas: None = None, pid: str = None, eid: str = '', pname: str = '', session_path: Path = '', collections: list = None, datasets: list = None, files: dict = None, raw_data_files: list = None, collection: str = '', histology: str = '', spike_sorter: str = 'pykilosort', spike_sorting_path: Path = None, _sync: dict = None)[source]
+class SpikeSortingLoader(one: One | None = None, atlas: None = None, pid: str | None = None, eid: str = '', pname: str = '', session_path: Path = '', collections: list | None = None, datasets: list | None = None, files: dict | None = None, raw_data_files: list | None = None, collection: str = '', histology: str = '', spike_sorter: str = 'pykilosort', spike_sorting_path: Path | None = None, _sync: dict | None = None)[source]

Bases: object

Object that will load spike sorting data for a given probe insertion. This class can be instantiated in several manners @@ -832,7 +832,7 @@

-class SessionLoader(one: ~one.api.One = None, session_path: ~pathlib.Path = '', eid: str = '', data_info: ~pandas.core.frame.DataFrame = <factory>, trials: ~pandas.core.frame.DataFrame = <factory>, wheel: ~pandas.core.frame.DataFrame = <factory>, pose: dict = <factory>, motion_energy: dict = <factory>, pupil: ~pandas.core.frame.DataFrame = <factory>)[source]
+class SessionLoader(one: ~one.api.One | None = None, session_path: ~pathlib.Path = '', eid: str = '', data_info: ~pandas.core.frame.DataFrame = <factory>, trials: ~pandas.core.frame.DataFrame = <factory>, wheel: ~pandas.core.frame.DataFrame = <factory>, pose: dict = <factory>, motion_energy: dict = <factory>, pupil: ~pandas.core.frame.DataFrame = <factory>)[source]

Bases: object

Object to load session data for a give session in the recommended way.

@@ -1093,6 +1093,36 @@ property probes
+
+
+data_info: DataFrame
+
+ +
+
+trials: DataFrame
+
+ +
+
+wheel: DataFrame
+
+ +
+
+pose: dict
+
+ +
+
+motion_energy: dict
+
+ +
+
+pupil: DataFrame
+
+
diff --git a/_autosummary/iblatlas.genomics.agea.html b/_autosummary/iblatlas.genomics.agea.html index ef7b18cc..1491b254 100644 --- a/_autosummary/iblatlas.genomics.agea.html +++ b/_autosummary/iblatlas.genomics.agea.html @@ -26,7 +26,7 @@ - + @@ -95,7 +95,10 @@
  • iblatlas.atlas
  • iblatlas.flatmaps
  • iblatlas.genomics
  • iblatlas.plots
    • @@ -136,12 +139,7 @@

    iblatlas.genomics.agea

    -
    -
    [1] E. S. Lein et al., “Genome-wide atlas of gene expression in the adult mouse brain,”

    Nature, vol. 445, no. 7124, Art. no. 7124, Jan. 2007, doi: 10.1038/nature05453.

    -
    -
    [2] L. Ng et al., “An anatomic gene expression atlas of the adult mouse brain,”

    Nat Neurosci, vol. 12, no. 3, Art. no. 3, Mar. 2009, doi: 10.1038/nn.2281.

    -
    -
    +

    A package for loading 4345 formatted and registered gene expression volumes

    Functions

    brainbox.behavior.dlc

    Set of functions to deal with dlc data

    Set of functions to deal with dlc data.

    brainbox.behavior.training

    Computing and testing IBL training status criteria.

    @@ -180,7 +178,7 @@
    diff --git a/_autosummary/iblatlas.genomics.html b/_autosummary/iblatlas.genomics.html index 55434650..f195b08f 100644 --- a/_autosummary/iblatlas.genomics.html +++ b/_autosummary/iblatlas.genomics.html @@ -95,7 +95,10 @@
  • iblatlas.atlas
  • iblatlas.flatmaps
  • iblatlas.genomics
  • iblatlas.plots
    • @@ -135,10 +138,98 @@

    iblatlas.genomics

    +

    A package for working with Allen genomics datasets: AGEA and MERFISH.

    +
    +

    AGEA

    +

    This package provides a way to load the Allen Gene Expression volumes. +The 4345 volumes have been registered and formatted into a binary file.

    +
    +

    agea/ +├── gene-expression.bin +├── gene-expression.pqt +├── image.npy +└── label.npy

    +
    +
      +

    • gene-expression.bin is a float-16 binary file containing the gene expression volumes.

      • +
    +

    In c-order, the dimensions are (4345, 58, 41, 67) that corresponds to (nexperiments, ml, dv, ap) at 200 um. +- gene-expression.pqt is a parquet file describing the 4345 genes corresponding to the +gene expression volumes. +- image.npy: the Allen atlas diffusion imaging volume downsampled at the gene expression resolution +- label.npy: the Allen atlas region label volume downsampled at the gene expression resolution +See the building scripts in ./genomics/gene_expression_scrapping/05-generate-atlas-templates.py

    +
    +
    [1] E. S. Lein et al., “Genome-wide atlas of gene expression in the adult mouse brain,”

    Nature, vol. 445, no. 7124, Art. no. 7124, Jan. 2007, doi: 10.1038/nature05453.

    +
    +
    [2] L. Ng et al., “An anatomic gene expression atlas of the adult mouse brain,”

    Nat Neurosci, vol. 12, no. 3, Art. no. 3, Mar. 2009, doi: 10.1038/nn.2281.

    +
    +
    +
    +
    +

    MERFISH

    +

    Spatially registered cell types from single cell transcriptomics data.

    +

    This package provides a way to load the MERFISH data from the Allen Brain Cell Atlas. +We formatted the original CSV files from the 2023-12-15 release into parquet files for faster loading and smaller hard +drive footprint.

    +
    +

    merfish/ +├── genes.pqt +├── neurotransmitters.pqt +├── classes.pqt +├── subclasses.pqt +├── supertypes.pqt +├── clusters.pqt +├── C57BL6J-638850_cells.pqt +├── Zhuang-ABCA-1_cells.pqt +├── Zhuang-ABCA-2_cells.pqt +├── Zhuang-ABCA-3_cells.pqt +└── Zhuang-ABCA-4_cells.pqt

    +
    +
      +

    • *_cells.pqt: Each dataframe corresponds to a given subject. The concatenation of those 5 dataframes lead to

      • +
    +
    +
    8_879_868, 11 cells with the following columns:
      +

    • ‘brain_section_label’: the label of the brain section (subject and section): “Zhuang-ABCA-1.085”

      • +

    • ‘donor_label’: the label of the subject

      • +
    +
    +
      +

    • ‘neurotransmitter’: neurotransmitter label {<NA>, ‘Glut’, ‘Chol’, ‘GABA-Glyc’, ‘GABA’,’Dopa’,

      • +
    +

    ‘Glut-GABA’, ‘Hist’, ‘Sero’, ‘Nora’} +- ‘class’: direct index of the class record in df_classes +- ‘subclass’: direct index of the subclass record in df_subclasses +- ‘supertype’: direct index of the supertype record in df_supertypes +- ‘cluster’: direct index of the cluster record in df_clusters +- ‘x’, ‘y’, ‘z’: coordinates of the cell in IBL space (see: iblatlas.atlas.AllenAtlas) +- ‘Allen_id’: allen region unique identifier

    +
    +
    +
    +

    The cells are classified hierarchically, from high level to low level: classes, subclasses, supertypes and clusters. +- df_classes: a dataframe of classes (35, 3), where each record corresponds to a single class +- df_subclasses: a dataframe of subclasses (339, 4), where each record corresponds to a single subclass +- df_supertypes: a dataframe of supertypes (1202, 4), where each record corresponds to a single supertype +- df_clusters: a dataframe of clusters (5323, 5), where each record corresponds to a single cluster

    +

    Additional metadata: +- df_neurotransmitters: a dataframe of neurotransmitters (9, 2), index is the neurotransmitter label +- df_genes: a dataframe of genes (1122), this could be used in conjunction with raw gene expressions data (not implemented)

    +
    +
    [1] Z. Yao et al., “A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain,”

    Nature, vol. 624, no. 7991, Art. no. 7991, Dec. 2023, doi: 10.1038/s41586-023-06812-z.

    +
    +
    [2] M. Zhang et al., “Molecularly defined and spatially resolved cell atlas of the whole mouse brain,”

    Nature, vol. 624, no. 7991, Art. no. 7991, Dec. 2023, doi: 10.1038/s41586-023-06808-9.

    +
    +
    +
    - + + + +

    iblatlas.genomics.agea

    [1] E. S. Lein et al., “Genome-wide atlas of gene expression in the adult mouse brain,”

    A package for loading 4345 formatted and registered gene expression volumes

    iblatlas.genomics.merfish
    diff --git a/_autosummary/iblatlas.genomics.merfish.html b/_autosummary/iblatlas.genomics.merfish.html new file mode 100644 index 00000000..72b3e8f4 --- /dev/null +++ b/_autosummary/iblatlas.genomics.merfish.html @@ -0,0 +1,227 @@ + + + + + + + iblatlas.genomics.merfish — IBL Library documentation + + + + + + + + + + + + + + + + + + + + + + + + +
    + + +
    + +
    +
    +
    + +
    +
    +
    +
    + +
    +

    iblatlas.genomics.merfish

    +

    Functions

    + + + + + + + + + +

    int2rgb

    One liner to convert rgba values stored as integer in dataframes

    load

    Reads in the Allen gene expression experiments tables

    +
    +
    +load(folder_cache=None)[source]
    +

    Reads in the Allen gene expression experiments tables

    +
    +
    Parameters:
    +

    folder_cache –

    +
    +
    Returns:
    +

    +
    +
    +

    df_cells: a dataframe of cells (8_879_868, 11), where each record corresponds to a single cell +df_classes: a dataframe of classes (35, 3), where each record corresponds to a single class +df_subclasses: a dataframe of subclasses (339, 4), where each record corresponds to a single subclass +df_supertypes: a dataframe of supertypes (1202, 4), where each record corresponds to a single supertype +df_clusters: a dataframe of clusters (5323, 5), where each record corresponds to a single cluster +df_genes: a dataframe of genes (1672, 4), where each record corresponds to a single gene +df_neurotransmitters: a dataframe of neurotransmitters (9, 2), where each record corresponds to a single

    +
    +

    neurotransmitter

    +
    +
    + +
    +
    +int2rgb(array, dtype=None)[source]
    +

    One liner to convert rgba values stored as integer in dataframes

    +
    +
    Parameters:
    +
      +

    • array – rgba column of a dataframe or slice of the column

      • +

    • dtype – optional, if int will return the uint8 view from 0-255 else will return floats from 0-1

      • +
    +
    +
    Returns:
    +

    +
    +
    +
    + +
    + + +
    +
    + +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/_autosummary/iblatlas.html b/_autosummary/iblatlas.html index 0a3e2a77..bd49e1da 100644 --- a/_autosummary/iblatlas.html +++ b/_autosummary/iblatlas.html @@ -373,7 +373,7 @@

    Remote files

    iblatlas.genomics

    -

    +

    A package for working with Allen genomics datasets: AGEA and MERFISH.

    iblatlas.plots

    Module that has convenience plotting functions for 2D atlas slices and flatmaps.

    diff --git a/_autosummary/iblatlas.plots.html b/_autosummary/iblatlas.plots.html index e905f1a7..326aff37 100644 --- a/_autosummary/iblatlas.plots.html +++ b/_autosummary/iblatlas.plots.html @@ -27,7 +27,7 @@ - + @@ -608,7 +608,7 @@
    diff --git a/_autosummary/iblatlas.regions.html b/_autosummary/iblatlas.regions.html index 1d870a0a..8d009741 100644 --- a/_autosummary/iblatlas.regions.html +++ b/_autosummary/iblatlas.regions.html @@ -191,6 +191,77 @@

    Terminology_BrainRegions

    Mouse Brain in Stereotaxic Coordinates (MBSC).

    Paxinos G, and Franklin KBJ (2012). The Mouse Brain in Stereotaxic Coordinates, 4th edition (Elsevier Academic Press).

    +
    +
    +id: ndarray
    +

    A str array of verbose brain region names.

    +
    +
    Type:
    +

    numpy.array

    +
    +
    +
    + +
    +
    +name: object
    +

    A str array of brain region acronyms.

    +
    +
    Type:
    +

    numpy.array

    +
    +
    +
    + +
    +
    +acronym: object
    +

    A, (n, 3) uint8 array of brain region RGB colour values.

    +
    +
    Type:
    +

    numpy.array

    +
    +
    +
    + +
    +
    +rgb: uint8
    +

    An unsigned integer array indicating the number of degrees removed from root.

    +
    +
    Type:
    +

    numpy.array

    +
    +
    +
    + +
    +
    +level: ndarray
    +

    An integer array of parent brain region IDs.

    +
    +
    Type:
    +

    numpy.array

    +
    +
    +
    + +
    +
    +parent: ndarray
    +

    The position within the flattened graph.

    +
    +
    Type:
    +

    numpy.array

    +
    +
    +
    + +
    +
    +order: uint16
    +
    +
    @@ -203,6 +274,77 @@

    Terminology +
    +id: ndarray
    +

    A str array of verbose brain region names.

    +
    +
    Type:
    +

    numpy.array

    +
    +
    +

    + +
    +
    +name: object
    +

    A str array of brain region acronyms.

    +
    +
    Type:
    +

    numpy.array

    +
    +
    +
    + +
    +
    +acronym: object
    +

    A, (n, 3) uint8 array of brain region RGB colour values.

    +
    +
    Type:
    +

    numpy.array

    +
    +
    +
    + +
    +
    +rgb: uint8
    +

    An unsigned integer array indicating the number of degrees removed from root.

    +
    +
    Type:
    +

    numpy.array

    +
    +
    +
    + +
    +
    +level: ndarray
    +

    An integer array of parent brain region IDs.

    +
    +
    Type:
    +

    numpy.array

    +
    +
    +
    + +
    +
    +parent: ndarray
    +

    The position within the flattened graph.

    +
    +
    Type:
    +

    numpy.array

    +
    +
    +
    + +
    +
    +order: uint16
    +
    +
    compute_hierarchy()[source]
    diff --git a/_autosummary/ibllib.atlas.atlas.html b/_autosummary/ibllib.atlas.atlas.html index bd77f96e..21635024 100644 --- a/_autosummary/ibllib.atlas.atlas.html +++ b/_autosummary/ibllib.atlas.atlas.html @@ -209,6 +209,16 @@ 
    >>> trj = Trajectory.fit(xyz)
    +
    +
    +vector: ndarray
    +
    + +
    +
    +point: ndarray
    +
    +
    @@ -217,6 +227,36 @@

    Bases: Insertion

    Defines an ephys probe insertion in 3D coordinate. IBL conventions.

    To instantiate, use the static methods: Insertion.from_track and Insertion.from_dict.

    +
    +
    +x: float
    +
    + +
    +
    +y: float
    +
    + +
    +
    +z: float
    +
    + +
    +
    +phi: float
    +
    + +
    +
    +theta: float
    +
    + +
    +
    +depth: float
    +
    +
    diff --git a/_autosummary/ibllib.ephys.ephysqc.html b/_autosummary/ibllib.ephys.ephysqc.html index 3ed0407d..fdc47c16 100644 --- a/_autosummary/ibllib.ephys.ephysqc.html +++ b/_autosummary/ibllib.ephys.ephysqc.html @@ -196,7 +196,7 @@
    -run(update: bool = False, overwrite: bool = True, stream: bool = None, **kwargs) -> (<class 'str'>, <class 'dict'>)[source]
    +run(update: bool = False, overwrite: bool = True, stream: bool | None = None, **kwargs) -> (<class 'str'>, <class 'dict'>)[source]

    Run QC on samples of the .ap file, and on the entire file for .lf data if it is present.

    Parameters:
    diff --git a/_autosummary/ibllib.io.extractors.ephys_passive.html b/_autosummary/ibllib.io.extractors.ephys_passive.html index 54227498..fba5d350 100644 --- a/_autosummary/ibllib.io.extractors.ephys_passive.html +++ b/_autosummary/ibllib.io.extractors.ephys_passive.html @@ -173,22 +173,22 @@
    -extract_passive_periods(session_path: str, sync_collection: str = 'raw_ephys_data', sync: dict = None, sync_map: dict = None, tmin=None, tmax=None) → DataFrame[source]
    +extract_passive_periods(session_path: str, sync_collection: str = 'raw_ephys_data', sync: dict | None = None, sync_map: dict | None = None, tmin=None, tmax=None) → DataFrame[source]
    -extract_rfmapping(session_path: str, sync_collection: str = 'raw_ephys_data', task_collection: str = 'raw_passive_data', sync: dict = None, sync_map: dict = None, trfm: array = None) → Tuple[array, array][source]
    +extract_rfmapping(session_path: str, sync_collection: str = 'raw_ephys_data', task_collection: str = 'raw_passive_data', sync: dict | None = None, sync_map: dict | None = None, trfm: array | None = None) → Tuple[array, array][source]
    -extract_task_replay(session_path: str, sync_collection: str = 'raw_ephys_data', task_collection: str = 'raw_passive_data', sync: dict = None, sync_map: dict = None, treplay: array = None) → Tuple[DataFrame, DataFrame][source]
    +extract_task_replay(session_path: str, sync_collection: str = 'raw_ephys_data', task_collection: str = 'raw_passive_data', sync: dict | None = None, sync_map: dict | None = None, treplay: array | None = None) → Tuple[DataFrame, DataFrame][source]
    -extract_replay_debug(session_path: str, sync_collection: str = 'raw_ephys_data', task_collection: str = 'raw_passive_data', sync: dict = None, sync_map: dict = None, treplay: array = None, ax: axes = None) → Tuple[DataFrame, DataFrame][source]
    +extract_replay_debug(session_path: str, sync_collection: str = 'raw_ephys_data', task_collection: str = 'raw_passive_data', sync: dict | None = None, sync_map: dict | None = None, treplay: array | None = None, ax: axes | None = None) → Tuple[DataFrame, DataFrame][source]
    diff --git a/_autosummary/ibllib.io.flags.html b/_autosummary/ibllib.io.flags.html index 3f51da07..81bf0e7a 100644 --- a/_autosummary/ibllib.io.flags.html +++ b/_autosummary/ibllib.io.flags.html @@ -221,7 +221,7 @@
    -write_flag_file(fname, file_list: list = None, clobber=False)[source]
    +write_flag_file(fname, file_list: list | None = None, clobber=False)[source]

    Flag files are *.flag files within a session folder used to schedule some jobs Each line references to a file to extract or register

    @@ -280,7 +280,7 @@
    -create_flags(root_data_folder: str, flags: list, force: bool = False, file_list: list = None) → None[source]
    +create_flags(root_data_folder: str, flags: list, force: bool = False, file_list: list | None = None) → None[source]
    diff --git a/_autosummary/ibllib.misc.html b/_autosummary/ibllib.misc.html index 589758d8..502b2667 100644 --- a/_autosummary/ibllib.misc.html +++ b/_autosummary/ibllib.misc.html @@ -91,6 +91,7 @@
  • ibllib.io
  • ibllib.misc
  • ibllib.oneibl
    • @@ -141,6 +142,9 @@

    ibllib.misc.misc

    +

    ibllib.misc.qt

    +

    PyQt5 helper functions.

    +

    diff --git a/_autosummary/ibllib.misc.misc.html b/_autosummary/ibllib.misc.misc.html index ce84d24c..dd8c39d8 100644 --- a/_autosummary/ibllib.misc.misc.html +++ b/_autosummary/ibllib.misc.misc.html @@ -26,7 +26,7 @@ - + @@ -91,6 +91,7 @@
  • ibllib.io
  • ibllib.misc
  • ibllib.oneibl
    • @@ -167,7 +168,7 @@