napari_track_edit.example_data

Attributes

logger

ZENODO_RAW_URL

ZENODO_LABELS_URL

CTC_URL_TEMPLATE

HELA_CROP

ZENODO_ARRAYS

CTC_ARRAYS

ReportHook

SAMPLE_TRACKS

Classes

SampleTracks

Example tracks shown in the welcome widget, with their raw data.

Functions

user_data_dir(→ pathlib.Path)

The platformdirs "user data dir", where all example data is cached. Created if

_ensure_dataset(→ pathlib.Path)

Return the path to a dataset's zarr, downloading the dataset first if it

_zenodo_raw_layer(→ napari.types.LayerData)

The membrane intensity layer of a zenodo dataset zarr.

_ctc_raw_layer(→ napari.types.LayerData)

The 01 training intensity layer of a CTC dataset zarr.

Mouse_Embryo_Membrane(→ list[napari.types.LayerData])

Loads the Mouse Embryo Membrane raw data and segmentation data from

Fluo_N2DL_HeLa(→ list[napari.types.LayerData])

Loads the Fluo-N2DL-HeLa 01 training raw data and silver truth from

Fluo_N2DL_HeLa_crop(→ list[napari.types.LayerData])

Loads the Fluo-N2DL-HeLa 01 training raw data and silver truth from

read_zenodo_dataset(→ list[napari.types.LayerData])

Read a zenodo dataset (assumes pre-downloaded)

read_ctc_dataset(→ list[napari.types.LayerData])

Read a CTC dataset from a zarr (assumes pre-downloaded and converted)

_download_dir(→ collections.abc.Iterator[pathlib.Path])

A fresh scratch directory next to the output, deleted afterwards. Downloads

download_zenodo_dataset(→ None)

Download a sample dataset from zenodo doi and unzip it, then delete the zip. Then convert the tiffs to

download_ctc_dataset(→ None)

Download a dataset from the Cell Tracking Challenge

convert_4d_arr_to_zarr(→ None)

Convert 4D tiff file to zarr array. Deletes the tiff after conversion.

convert_to_zarr(→ None)

Convert a directory of tiff files to a zarr array. Deletes tiffs after conversion.

Fluo_N2DL_HeLa_crop_raw(→ napari.types.LayerData)

Loads only the cropped raw data of Fluo-N2DL-HeLa (see Fluo_N2DL_HeLa_crop),

Mouse_Embryo_Membrane_raw(→ napari.types.LayerData)

Loads only the raw data of Mouse_Embryo_Membrane, downloading the dataset

_drive_download_url(→ str)

Direct-download URL for a Google Drive file (skips the preview page).

sample_tracks_path(→ pathlib.Path)

Return the local path to the example tracks geff with the given name,

raw_data_is_downloaded(→ bool)

Whether the raw data belonging to a sample is already on disk, so that

download_zipped_store(→ None)

Download a zip holding a store named like the output, and unpack it there.

Module Contents

napari_track_edit.example_data.logger
napari_track_edit.example_data.ZENODO_RAW_URL = 'https://zenodo.org/records/13903500/files/imaging.zip'
napari_track_edit.example_data.ZENODO_LABELS_URL = 'https://zenodo.org/records/13903500/files/segmentation.zip'
napari_track_edit.example_data.CTC_URL_TEMPLATE = 'http://data.celltrackingchallenge.net/training-datasets/{ds_name}.zip'
napari_track_edit.example_data.HELA_CROP
napari_track_edit.example_data.ZENODO_ARRAYS = ('01_membrane', '01_labels')
napari_track_edit.example_data.CTC_ARRAYS = ('01', '01_ST')
napari_track_edit.example_data.ReportHook
napari_track_edit.example_data.user_data_dir() → pathlib.Path

The platformdirs “user data dir”, where all example data is cached. Created if it does not exist yet.

napari_track_edit.example_data._ensure_dataset(ds_name: str, data_dir: pathlib.Path, download: collections.abc.Callable[[], None], arrays: tuple[str, ...]) → pathlib.Path

Return the path to a dataset’s zarr, downloading the dataset first if it is not there yet. A zarr missing any of the expected arrays (left behind by an interrupted download in older versions) is deleted and downloaded again.

Parameters:

  • ds_name (str) – Dataset name, the zarr is named after it

  • data_dir (Path) – The directory the dataset is cached in

  • download (Callable[[], None]) – Fetches and converts the dataset

  • arrays (tuple[str, ...]) – Names of the arrays the zarr must contain

Returns:

Path to the zarr holding the dataset

Return type:

Path

napari_track_edit.example_data._zenodo_raw_layer(ds_zarr: pathlib.Path) → napari.types.LayerData

The membrane intensity layer of a zenodo dataset zarr.

napari_track_edit.example_data._ctc_raw_layer(ds_zarr: pathlib.Path, crop_region: bool) → napari.types.LayerData

The 01 training intensity layer of a CTC dataset zarr.

napari_track_edit.example_data.Mouse_Embryo_Membrane() → list[napari.types.LayerData]

Loads the Mouse Embryo Membrane raw data and segmentation data from the appdir “user data dir”. Will download it from the Zenodo DOI if not present.

Returns:

An image layer of raw data and a segmentation labels

layer

Return type:

list[LayerData]

napari_track_edit.example_data.Fluo_N2DL_HeLa() → list[napari.types.LayerData]

Loads the Fluo-N2DL-HeLa 01 training raw data and silver truth from the appdir “user data dir”. Will download it from the CTC and convert it to zarr if it is not present already.

Returns:

An image layer of 01 training raw data and a labels

layer of 01 training silver truth labels

Return type:

list[LayerData]

napari_track_edit.example_data.Fluo_N2DL_HeLa_crop() → list[napari.types.LayerData]

Loads the Fluo-N2DL-HeLa 01 training raw data and silver truth from the appdir “user data dir”. Will download it from the CTC and convert it to zarr if it is not present already.

Returns:

An image layer of 01 training raw data and a labels

layer of 01 training silver truth labels

Return type:

list[LayerData]

napari_track_edit.example_data.read_zenodo_dataset(ds_name: str, raw_name: str, label_name: str, data_dir: pathlib.Path) → list[napari.types.LayerData]

Read a zenodo dataset (assumes pre-downloaded) and returns a list of layer data for making napari layers

Parameters:

  • ds_name (str) – name to give to the dataset

  • raw_name (str) – name of the file that points to the intensity data

  • label_name (str) – name of the file that points to the segmentation data

  • data_dir (Path) – Path to the directory containing the images

Returns:

An image layer of raw data and a segmentation labels

layer

Return type:

list[LayerData]

napari_track_edit.example_data.read_ctc_dataset(ds_name: str, data_dir: pathlib.Path, crop_region=False) → list[napari.types.LayerData]

Read a CTC dataset from a zarr (assumes pre-downloaded and converted) and returns a list of layer data for making napari layers

Parameters:

  • ds_name (str) – Dataset name

  • data_dir (Path) – Path to the directory containing the zarr

Returns:

An image layer of 01 training raw data and a labels

layer of 01 training silver truth labels

Return type:

list[LayerData]

napari_track_edit.example_data._download_dir(output: pathlib.Path) → collections.abc.Iterator[pathlib.Path]

A fresh scratch directory next to the output, deleted afterwards. Downloads are unpacked and converted there and only moved to the output once complete, so an interrupted download is not mistaken for existing data.

napari_track_edit.example_data.download_zenodo_dataset(ds_name: str, raw_name: str, label_name: str, data_dir: pathlib.Path, reporthook: ReportHook | None = None) → None

Download a sample dataset from zenodo doi and unzip it, then delete the zip. Then convert the tiffs to zarrs for the first training set consisting of 3D membrane intensity images and segmentation.

Parameters:

  • ds_name (str) – Name to give to the dataset

  • raw_name (str) – Name of the file that contains the intensity data

  • label_name (str) – Name of the file that contains the label data

  • data_dir (Path) – The directory in which to store the data.

  • reporthook (ReportHook | None) – Called with the download progress.

napari_track_edit.example_data.download_ctc_dataset(ds_name: str, data_dir: pathlib.Path, reporthook: ReportHook | None = None) → None

Download a dataset from the Cell Tracking Challenge and unzip it, then delete the zip. Then convert the tiffs to zarrs for the first training set images and silver truth.

Parameters:

  • ds_name (str) – Dataset name, according to the CTC

  • data_dir (Path) – The directory in which to store the data.

  • reporthook (ReportHook | None) – Called with the download progress.

napari_track_edit.example_data.convert_4d_arr_to_zarr(tiff_file: pathlib.Path, zarr_path: pathlib.Path, zarr_group: str, relabel: bool = False) → None

Convert 4D tiff file to zarr array. Deletes the tiff after conversion.

Parameters:

  • tiff_file – Path to the 4D tiff file

  • zarr_path – Path to the zarr store to write to

  • zarr_group – Name of the array within the zarr store

  • relabel – If True, relabel segmentations to be unique across time

napari_track_edit.example_data.convert_to_zarr(tiff_path: pathlib.Path, zarr_path: pathlib.Path, zarr_group: str, relabel: bool = False) → None

Convert a directory of tiff files to a zarr array. Deletes tiffs after conversion.

Parameters:

  • tiff_path – Path to directory containing tiff files (one per time point)

  • zarr_path – Path to the zarr store to write to

  • zarr_group – Name of the array within the zarr store

  • relabel – If True, relabel segmentations to be unique across time

napari_track_edit.example_data.Fluo_N2DL_HeLa_crop_raw(reporthook: ReportHook | None = None) → napari.types.LayerData

Loads only the cropped raw data of Fluo-N2DL-HeLa (see Fluo_N2DL_HeLa_crop), downloading the dataset first if it is not present.

Parameters:

reporthook (ReportHook | None) – Called with the download progress.

Returns:

An image layer of the cropped 01 training raw data

Return type:

LayerData

napari_track_edit.example_data.Mouse_Embryo_Membrane_raw(reporthook: ReportHook | None = None) → napari.types.LayerData

Loads only the raw data of Mouse_Embryo_Membrane, downloading the dataset first if it is not present.

Parameters:

reporthook (ReportHook | None) – Called with the download progress.

Returns:

An image layer of the membrane raw data

Return type:

LayerData

class napari_track_edit.example_data.SampleTracks

Bases: NamedTuple

Example tracks shown in the welcome widget, with their raw data.

url: str
store_name: str
raw_name: str
raw_zarr: str
raw_size: str
load_raw: collections.abc.Callable[..., napari.types.LayerData]
napari_track_edit.example_data._drive_download_url(file_id: str) → str

Direct-download URL for a Google Drive file (skips the preview page).

napari_track_edit.example_data.SAMPLE_TRACKS: dict[str, SampleTracks]
napari_track_edit.example_data.sample_tracks_path(name: str, reporthook: ReportHook | None = None) → pathlib.Path

Return the local path to the example tracks geff with the given name, downloading it from Google Drive into the appdir “user data dir” first if it is not present yet.

Parameters:

  • name (str) – A key of SAMPLE_TRACKS

  • reporthook (ReportHook | None) – Called with the download progress.

Returns:

Path to the geff store

Return type:

Path

napari_track_edit.example_data.raw_data_is_downloaded(name: str) → bool

Whether the raw data belonging to a sample is already on disk, so that clicking the sample does not trigger a large download unannounced.

Parameters:

name (str) – A key of SAMPLE_TRACKS

Returns:

True if the zarr holding the raw data exists

Return type:

bool

napari_track_edit.example_data.download_zipped_store(url: str, output: pathlib.Path, reporthook: ReportHook | None = None) → None

Download a zip holding a store named like the output, and unpack it there.

The zip is downloaded and unpacked next to the output, and only moved into place once complete, so an interrupted download is not mistaken for existing data.

Parameters:

  • url (str) – Download url of the zip

  • output (Path) – Path to put the store at. The zip must contain a directory with the same name.

  • reporthook (ReportHook | None) – Called with the download progress.