spacr.host_pathogen_preview

Read-only, bounded field previews using the Host–Pathogen analysis engine.

Functions

preview_field(settings, field, *[, planes, ...])

Analyze one measured field without modifying source or result files.

preview_fields(settings, *[, limit])

List at most limit measured fields, in stable source/identity order.

Module Contents

spacr.host_pathogen_preview.preview_field(settings, field, *, planes=None, image_channel=0, row_limit=100000)[source]

Analyze one measured field without modifying source or result files.

Parameters:

  • settings – current Host–Pathogen settings, shared with the full run.

  • field – one record returned by preview_fields().

  • planes – optional explicit host/vacuole/parasite mask plane indices. Missing entries use a valid merged-plane manifest; absent metadata never silently chooses mask planes. A negative index disables that overlay.

  • image_channel – intensity plane shown as grayscale, display-only.

  • row_limit – refuse fields exceeding this many rows in any input table.

Returns:

real analysis tables, display image/masks and explicit image notes. Infection denominators cover this field only, including uninfected hosts.

spacr.host_pathogen_preview.preview_fields(settings, *, limit=50)[source]

List at most limit measured fields, in stable source/identity order.

Parameters:

  • settings – Host–Pathogen settings; src is a project, database or list.

  • limit – positive maximum number of fields offered by the preview.

Returns:

field records and a boolean saying whether additional fields exist. Database connections are read-only; no migration or analysis is written.