sl-shared-assets 1.0.0rc20__py3-none-any.whl → 1.0.0rc22__py3-none-any.whl

sl_shared_assets/suite2p/single_day.pyi

@@ -1,220 +0,0 @@
-from typing import Any
-from pathlib import Path
-from dataclasses import field, dataclass
-
-from _typeshed import Incomplete
-from ataraxis_data_structures import YamlConfig
-
-@dataclass
-class Main:
-    """Stores global parameters that broadly define the suite2p single-day processing configuration."""
-
-    nplanes: int = ...
-    nchannels: int = ...
-    functional_chan: int = ...
-    tau: float = ...
-    force_sktiff: bool = ...
-    fs: float = ...
-    do_bidiphase: bool = ...
-    bidiphase: int = ...
-    bidi_corrected: bool = ...
-    frames_include: int = ...
-    multiplane_parallel: bool = ...
-    parallel_planes: int = ...
-    ignore_flyback: list[int] = field(default_factory=list)
-
-@dataclass
-class FileIO:
-    """Stores general I/O parameters that specify input data location, format, and working and output directories."""
-
-    fast_disk: str = ...
-    delete_bin: bool = ...
-    mesoscan: bool = ...
-    bruker: bool = ...
-    bruker_bidirectional: bool = ...
-    h5py: list[str] = field(default_factory=list)
-    h5py_key: str = ...
-    nwb_file: str = ...
-    nwb_driver: str = ...
-    nwb_series: str = ...
-    save_path0: str = ...
-    save_folder: str = ...
-    data_path: list[str] = field(default_factory=list)
-    look_one_level_down: bool = ...
-    subfolders: list[str] = field(default_factory=list)
-    move_bin: bool = ...
-
-@dataclass
-class Output:
-    """Stores parameters for aggregating and saving the processing results of each plane as a unified directory or
-    file."""
-
-    save_nwb: bool = ...
-    save_mat: bool = ...
-    combined: bool = ...
-    aspect: float = ...
-
-@dataclass
-class Registration:
-    """Stores parameters for rigid registration, which is used to correct motion artifacts between frames by
-    counter-shifting the entire frame."""
-
-    do_registration: bool = ...
-    align_by_chan: int = ...
-    nimg_init: int = ...
-    batch_size: int = ...
-    maxregshift: float = ...
-    smooth_sigma: float = ...
-    smooth_sigma_time: float = ...
-    keep_movie_raw: bool = ...
-    two_step_registration: bool = ...
-    reg_tif: bool = ...
-    reg_tif_chan2: bool = ...
-    th_badframes: float = ...
-    norm_frames: bool = ...
-    force_refImg: bool = ...
-    pad_fft: bool = ...
-    do_regmetrics: bool = ...
-    reg_metric_n_pc: int = ...
-
-@dataclass
-class OnePRegistration:
-    """Stores parameters for additional pre-registration processing used to improve the registration of 1-photon
-    datasets."""
-
-    one_p_reg: bool = ...
-    spatial_hp_reg: int = ...
-    pre_smooth: float = ...
-    spatial_taper: float = ...
-
-@dataclass
-class NonRigid:
-    """Stores parameters for non-rigid registration, which is used to improve motion registration in complex
-    datasets by dividing frames into subregions and shifting each subregion independently of other subregions."""
-
-    nonrigid: bool = ...
-    block_size: list[int] = field(default_factory=Incomplete)
-    snr_thresh: float = ...
-    maxregshiftNR: float = ...
-
-@dataclass
-class ROIDetection:
-    """Stores parameters for cell ROI detection."""
-
-    preclassify: float = ...
-    roidetect: bool = ...
-    sparse_mode: bool = ...
-    spatial_scale: int = ...
-    connected: bool = ...
-    threshold_scaling: float = ...
-    spatial_hp_detect: int = ...
-    max_overlap: float = ...
-    high_pass: int = ...
-    smooth_masks: bool = ...
-    max_iterations: int = ...
-    nbinned: int = ...
-    denoise: bool = ...
-
-@dataclass
-class CellposeDetection:
-    """Stores parameters for the Cellpose algorithm, which can optionally be used to improve cell ROI extraction."""
-
-    anatomical_only: int = ...
-    diameter: int = ...
-    cellprob_threshold: float = ...
-    flow_threshold: float = ...
-    spatial_hp_cp: int = ...
-    pretrained_model: str = ...
-
-@dataclass
-class SignalExtraction:
-    """Stores parameters for extracting fluorescence signals from ROIs and surrounding neuropil regions."""
-
-    neuropil_extract: bool = ...
-    allow_overlap: bool = ...
-    min_neuropil_pixels: int = ...
-    inner_neuropil_radius: int = ...
-    lam_percentile: int = ...
-
-@dataclass
-class SpikeDeconvolution:
-    """Stores parameters for deconvolve fluorescence signals to infer spike trains."""
-
-    spikedetect: bool = ...
-    neucoeff: float = ...
-    baseline: str = ...
-    win_baseline: float = ...
-    sig_baseline: float = ...
-    prctile_baseline: float = ...
-
-@dataclass
-class Classification:
-    """Stores parameters for classifying detected ROIs as real cells or artifacts."""
-
-    soma_crop: bool = ...
-    use_builtin_classifier: bool = ...
-    classifier_path: str = ...
-
-@dataclass
-class Channel2:
-    """Stores parameters for processing the second channel in multichannel datasets."""
-
-    chan2_thres: float = ...
-
-@dataclass
-class SingleDayS2PConfiguration(YamlConfig):
-    """Aggregates all user-addressable parameters of the single-day suite2p pipeline used to discover cell ROIs and
-    extract their fluorescence data.
-
-    This class is used during single-day processing to instruct suite2p on how to process the data. This class is based
-    on the 'default_ops' from the original suite2p package. As part of the suite2p refactoring performed in sl-suite2p
-    package, the 'default_ops' has been replaced with this class instance. Compared to the 'original' ops, it allows
-    saving configuration parameters as a .YAML file, which offers a better way of viewing and editing the parameters and
-    running suite2p pipeline on remote compute servers.
-    """
-
-    main: Main = field(default_factory=Main)
-    file_io: FileIO = field(default_factory=FileIO)
-    output: Output = field(default_factory=Output)
-    registration: Registration = field(default_factory=Registration)
-    one_p_registration: OnePRegistration = field(default_factory=OnePRegistration)
-    non_rigid: NonRigid = field(default_factory=NonRigid)
-    roi_detection: ROIDetection = field(default_factory=ROIDetection)
-    cellpose_detection: CellposeDetection = field(default_factory=CellposeDetection)
-    signal_extraction: SignalExtraction = field(default_factory=SignalExtraction)
-    spike_deconvolution: SpikeDeconvolution = field(default_factory=SpikeDeconvolution)
-    classification: Classification = field(default_factory=Classification)
-    channel2: Channel2 = field(default_factory=Channel2)
-    def to_npy(self, output_directory: Path) -> None:
-        """Saves the managed configuration data as an 'ops.npy' file under the target directory.
-
-        This method is mostly called by internal sl-suite2p functions to translate the user-specified configuration
-        file into the format used by suite2p pipelines.
-
-        Notes:
-            If the target output directory does not exist when this method is called, it will be created.
-
-        Args:
-            output_directory: The path to the directory where the 'ops.npy' file should be saved.
-        """
-    def to_config(self, output_directory: Path) -> None:
-        """Saves the managed configuration data as a 'single_day_s2p_configuration.yaml' file under the target
-        directory.
-
-        This method is typically used to dump the 'default' configuration parameters to disk as a user-editable
-        .yaml file. The user is then expected to modify these parameters as needed, before the class data is loaded and
-        used by the suite2p pipeline.
-
-        Notes:
-            If the target output directory does not exist when this method is called, it will be created.
-
-        Args:
-            output_directory: The path to the directory where the 'single_day_s2p_configuration.yaml' file should be
-            saved.
-        """
-    def to_ops(self) -> dict[str, Any]:
-        """Converts the class instance to a dictionary and returns it to caller.
-
-        This method is mostly called by internal sl-suite2p functions to translate the default configuration parameters
-        to the dictionary format used by suite2p pipelines.
-        """

sl_shared_assets-1.0.0rc20.dist-info/RECORD

@@ -1,40 +0,0 @@
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-sl_shared_assets/data_classes/runtime_data.pyi,sha256=yetdFz29QQyvMmpGTdWGxKSgWAdBZ9zsPM3fluDeDIY,6808
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-sl_shared_assets/server/__init__.py,sha256=nyX6-9ACcrQeRQOCNvBVrWSTHGjRPANIG_u0aq7HPTg,426
-sl_shared_assets/server/__init__.pyi,sha256=7o99f8uf6NuBjMZjNAM1FX69Qbu5uBluRSAyaUWbXOU,263
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-sl_shared_assets/suite2p/multi_day.py,sha256=sjteUROBxx2mAziPv42_qMeP5cqofECvd2HE5WqGjvY,13114
-sl_shared_assets/suite2p/multi_day.pyi,sha256=_kxgHqtsxIG__09YVv-YKEdgClOpTdN0o6fTE1CW4Mo,4315
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-sl_shared_assets/suite2p/single_day.pyi,sha256=UxieE15msb-MPsqnPQr_3CdbYvYLRYfx70M_yYHl-98,7924
-sl_shared_assets/tools/__init__.py,sha256=UWrNfseGupOrY4OK2PgDEJ-Q3LbSrPLC2pfaLm8wYBA,468
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-sl_shared_assets-1.0.0rc20.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-sl_shared_assets-1.0.0rc20.dist-info/RECORD,,

sl_shared_assets-1.0.0rc20.dist-info/entry_points.txt

@@ -1,4 +0,0 @@
-[console_scripts]
-sl-ascend = sl_shared_assets.cli:ascend_tyche_directory
-sl-generate-credentials = sl_shared_assets.cli:generate_server_credentials_file
-sl-replace-root = sl_shared_assets.cli:replace_local_root_directory