spacr.import_examples

Import’s test data: one set of fields, written in every format and naming.

A small set of fields from the toxo_mito example plate, converted into the container formats spaCR reads and renamed into every filename convention Mask’s metadata_type offers, published together with their masks and a measurements database. Importing any variant should give back exactly the wells, fields and channels the fields started as, and the manifest says what those are.

Published contents: IMPORT_EXAMPLE_REPO holds one archive. Inside it, under import_example/:

• variants/<key>/plate1/ – the same twelve planes (wells E01 and E02, fields 9 and 10, three channels, cropped from the toxo_mito plate) written once per variant: once per filename convention, once as Zeiss CZI, once as OME-TIFF and once as an ImageJ TIFF stack;

• variants/<key>/masks/{cell,nucleus,pathogen}/ – the Mask run’s label images for exactly those fields, named the way that variant names images;

• variants/<key>/measurements.db – the Measure rows of exactly the cells in those masks, keyed by that variant’s own file names, as a collaborator’s table would be;

• reference/measurements.db – the same rows as spaCR wrote them;

• variants/nikon_nd2 and variants/leica_lif – public sample files, because no open library writes ND2 or LIF. They are third-party images under CC BY 4.0, with no masks, and they go through the Format Converter;

• manifest.csv – one row per image file stating its actual well, field, channel, z and t. It is the last member of the archive, so an interrupted transfer leaves no manifest and the set reads as absent.

The variant registry is defined in this module, not in the archive. IMPORT_VARIANTS is what the Import screen offers before anything is downloaded, and what tools/build_import_example.py writes. Using one list for both keeps every button pointing at a folder the archive contains.

This module imports nothing from Qt, so the round-trip test and the builder can use it headless.

Classes

ImportVariant

One way the same fields were written, and how Import reads it back.

Functions

import_example_folder(→ pathlib.Path)	Where the unpacked set lives.
import_variant(→ ImportVariant)	The variant called key.
is_present(→ bool)	Whether a complete copy of the set -- or of one variant -- is here.
manifest_rows(→ List[Dict[str, str]])	Every row of the set's manifest.csv.
variant_inputs(→ Dict[str, object])	What the chooser fills in for one variant.

Module Contents

class spacr.import_examples.ImportVariant

One way the same fields were written, and how Import reads it back.

Parameters:

• key – the folder under variants/ and the chooser’s route key.

• label – the button text.

• route – 'import' for the Import screen itself (images, masks and a measurement table), 'convert' for the Format Converter (images only).

• metadata_type – the filename convention to parse by, or 'auto' for folders and tokens.

• custom_regex – the pattern, for metadata_type='custom'.

• file_format – what the image files are, in words.

• example – one image path from the variant, relative to its plate1 folder, so the chooser can show what the names look like before anything is downloaded.

• note – anything the reader should know about this variant.

property description: str

The paragraph the chooser shows on hover.

spacr.import_examples.import_example_folder(plate_folder: pathlib.Path | None = None) → pathlib.Path

Where the unpacked set lives.

Parameters:

plate_folder – the shared example plate the archive unpacks into; spacr.example_archives.example_plate_folder() when omitted.

Returns:

<plate folder>/import_example. Not created here.

spacr.import_examples.import_variant(key: str) → ImportVariant

The variant called key.

Parameters:

key – a key from IMPORT_VARIANTS.

Raises:

KeyError – naming the keys that exist.

spacr.import_examples.is_present(root, key: str | None = None) → bool

Whether a complete copy of the set – or of one variant – is here.

Parameters:

• root – the unpacked import_example folder.

• key – one variant, or every variant when omitted.

Returns:

True only when the manifest exists and every file it lists for the variant(s) is on disk. A partly unpacked set reads as absent, so it is downloaded again.

spacr.import_examples.manifest_rows(root) → List[Dict[str, str]]

Every row of the set’s manifest.csv.

Parameters:

root – the unpacked import_example folder.

Returns:

the rows, or [] when there is no readable manifest.

spacr.import_examples.variant_inputs(root, key: str) → Dict[str, object]

What the chooser fills in for one variant.

Parameters:

• root – the unpacked import_example folder.

• key – the variant.

Returns:

images (the plate1 folder), masks ({object: folder} for the import route, empty for the converter), measurements (the table, or ''), metadata_type and custom_regex.