"""The modules folded onto Mask Generation: Timelapse, and OPS.
Two kinds of fold are used here, and they change this screen differently.
Timelapse is a settings fold: switching it on mounts its categories on Mask's
own form and sets the pipeline gate the run reads, so its switch belongs on the
masthead strip beside the heading. OPS is a page fold: it has 63 settings of
its own and its own run entry point, none of which is
`preprocess_generate_masks`, so switching it on puts it on this screen's page
strip instead and its switch sits in the actions row beside the Live and 3D
buttons, in the same format. See :data:`CATEGORY_FOLDS`, :data:`PAGE_FOLDS` and
:func:`install_ops_switch`.
Spatial Mask Generation (alpha, F534) is a page fold of the same kind: its
Spatial switch sits beside OPS and opens the ``spatial_masks`` settings
page, which segments a whole Xenium or Visium HD slide in overlapping tiles.
Both are :class:`~spacr.qt.screens.map_barcodes.PageFold` instances; see
:func:`install_spatial_masks_switch`.
The Timelapse switch enables ``timelapse=True`` for the standard mask
pipeline and displays the additional time-series and tracking settings on the
Mask form. Settings files created for the Timelapse module remain compatible;
:func:`sync_folds` restores the switch state from the pipeline gate.
The integrated tracking preview evaluates object linkage across frames,
whereas the standard Mask preview evaluates segmentation of an individual
field. Motility analysis remains under Measure because it quantifies existing
masks and writes measurements rather than generating masks.
Category mounting and fold-state synchronization are shared with the other
host screens through :mod:`spacr.qt.screens.map_barcodes`.
"""
from __future__ import annotations
import logging
import os
from typing import Dict, Optional, Sequence, Tuple
from PySide6.QtCore import QObject
from PySide6.QtWidgets import QWidget
from ..widgets.fold_strip import (
FoldStrip, mark_folded_categories, mark_folded_sections,
)
from .map_barcodes import (
CategoryFoldSet, PageFold, _gate_alpha, build_settings_screen,
hide_as_page, install_page_fold, page_fold, register_page_fold,
)
LOG = logging.getLogger(__name__)
#: Registry key of the screen this module hangs its strip on.
HOST_KEY = "mask"
#: Registry keys of the modules folded into it.
#:
#: TRACKING ONLY. Timelapse belongs here because it is segmentation with a
#: time axis: it assigns one identity to a mask across frames, and it
#: overlaps this host's settings almost entirely.
#:
#: The Motility Assay does not. It reads finished masks and WRITES A
#: MEASUREMENTS TABLE -- per-cell rows and per-track velocities into
#: measurements/measurements.db -- which is Measure's job description with
#: a time axis rather than this one's. It folds onto Measure.
#: OPS IS FOLDED HERE TOO, AND IT IS NOT A SETTINGS CATEGORY. Optical
#: pooled screening was folded onto Align & Stitch when it was built,
#: because it is stitching; it is reached from Mask Generation instead,
#: because segmentation is what the plate it stitches is acquired for and
#: this is the screen a user of it is already on. It opens a page of its
#: own rather than mounting categories on this form -- its 63 settings and
#: its own run entry point are not `preprocess_generate_masks` -- so it is
#: in :data:`PAGE_FOLDS` below and not in :data:`FOLD_GATES`.
FOLDED_APPS: Tuple[str, ...] = ("timelapse", "ops")
#: The folds that ARE settings categories on this screen's own form.
#:
#: This is what the masthead strip is built from and what
#: :class:`~spacr.qt.screens.map_barcodes.CategoryFoldSet` mounts. Every
#: key here needs a row in :data:`FOLD_GATES`, because switching one on is
#: exactly setting its gate.
CATEGORY_FOLDS: Tuple[str, ...] = ("timelapse",)
#: The folds that open a page of their own instead.
#:
#: A page fold has no gate and no mounted categories, so it is not on the
#: strip: it is a switch in the actions row, beside Live and the dimension
#: switches, and switching it on puts the module on this screen's page
#: strip. See :func:`install_ops_switch`.
PAGE_FOLDS: Tuple[str, ...] = ("ops", "spatial_masks")
#: Name, sentence and maturity for a fold with no registry row to carry
#: them. Moved here with the fold itself, from `align.FOLD_FALLBACK`.
#:
#: ALPHA, HONESTLY. The engine has run end to end on two wells of one real
#: plate, A1 and A2, and matched the hand-driven run on A1; nothing wider
#: than that, and it does not place the phenotype images at all. A user
#: opening this should know it is new.
FOLD_FALLBACK: Dict[str, Tuple[str, str, str]] = {
"ops": (
"OPS",
"For optical pooled screening: stitch each well of the sequencing "
"acquisition, segment its nuclei and decode their barcodes.",
"alpha"),
}
#: ``key -> the settings the pipeline reads to decide it should do this``.
#:
#: These are the seam. :func:`spacr.core.preprocess_generate_masks` groups
#: a plate into time stacks when ``timelapse`` is true, and
#: the same function calls :func:`spacr.timelapse.automated_motility_assay`
#: once per plate, after every mask is merged, when ``timelapse and motility_analysis`` are both true -- so switching a
#: fold on is exactly setting its gate, and no new pipeline path is
#: involved.
#:
FOLD_GATES: Dict[str, Tuple[str, ...]] = {
"timelapse": ("timelapse",),
}
#: ``key -> the folds it cannot run without``. Nothing here needs another
#: fold on today; the table stays because the mechanism reads it and a
#: second gated fold would otherwise arrive with no place to say so.
FOLD_IMPLIES: Dict[str, Tuple[str, ...]] = {}
#: ``key -> the categories on THIS screen's OWN form that are its settings``.
#:
#: The fold mounts the categories Mask Generation does not already offer,
#: and those are marked from the fold itself. This table is for the other
#: half: the time-axis settings Mask Generation has always drawn itself,
#: which are Timelapse's subject however early they were written. Marking
#: them says the same thing the mounted cards say -- these belong to the
#: module the switch on the masthead turns on -- rather than leaving one
#: half of a module's settings attributed and the other half anonymous.
FOLD_CATEGORIES: Dict[str, Tuple[str, ...]] = {
"timelapse": ("Time Axes & Tracking (Beta)",),
}
[docs]
def fold_set(screen: QWidget) -> Optional[CategoryFoldSet]:
"""The set of category folds installed on ``screen``, or None.
:param screen: the module screen to inspect.
"""
folds = getattr(screen, "_category_folds", None)
return folds if isinstance(folds, CategoryFoldSet) else None
class _OfferedPreview(QObject):
"""A folded module's preview panel, offered while its switch is on.
A ``QObject`` parented to the card, with a bound-method slot, rather
than a closure hung off the button: a closure capturing the preview
would keep it alive through the switch that is supposed to own it.
Off is stronger than merely hidden. Switching the fold off unchecks
the preview's toggle as well as hiding it, so the card cannot stay on
screen showing tracks for a run that is no longer tracking.
:param host: the screen offering the preview. Its ``card`` is the
QObject parent -- not the host itself, which is what the note above
means about not keeping it alive through the switch that owns it.
"""
def __init__(self, host) -> None:
"""Parent to the host's CARD, not the host. See the class note."""
super().__init__(host.card)
self._host = host
def set_offered(self, on: bool) -> None:
"""Show or hide the toggle, and close the card when hiding it."""
on = bool(on)
try:
if not on:
self._host.toggle.setChecked(False)
self._host.card.setVisible(False)
self._host.toggle.setVisible(on)
except RuntimeError:
LOG.debug("the folded preview is gone", exc_info=True)
[docs]
def fold_previews(screen: QWidget) -> Dict[str, object]:
"""The folded previews attached to ``screen``, keyed by folded app.
:param screen: the module screen to inspect; a screen with no folded
previews gives an empty dict.
"""
return dict(getattr(screen, "_fold_previews", {}) or {})
def _offer_fold_previews(screen: QWidget,
folds: CategoryFoldSet,
strip: FoldStrip) -> Dict[str, _OfferedPreview]:
"""Attach each mounted fold's own preview panel, hidden behind its switch.
A module whose preview is its whole reason for a runtime panel loses
it the day its row is dropped, because nothing builds its screen any
more. Attaching it to the host is what keeps the capability, and
hiding it behind the switch is what stops Mask Generation growing a
track preview for a run with no time axis in it.
Guarded per fold: a preview that cannot be built costs that one
panel, never the strip.
"""
from ..preview_registry import attach_folded
offered: Dict[str, _OfferedPreview] = {}
for key in folds.order:
button = strip.button_for(key)
if button is None:
continue
try:
host = attach_folded(screen, key)
except Exception:
LOG.debug("Could not attach %s's preview to %s", key, HOST_KEY,
exc_info=True)
continue
if host is None:
continue
watcher = _OfferedPreview(host)
button.toggled.connect(watcher.set_offered)
watcher.set_offered(button.isChecked())
offered[key] = watcher
return offered
[docs]
def mark_fold_sources(screen: QWidget) -> Dict[str, Tuple[str, ...]]:
"""Mark settings categories with their folded module icons.
Both mounted categories and host categories listed in
:data:`FOLD_CATEGORIES` are marked. Repeated calls are idempotent, and a
missing icon does not interrupt screen construction.
:param screen: Host module screen.
:returns: Mapping from folded application keys to marked category titles.
"""
marked: Dict[str, Tuple[str, ...]] = {}
folds = fold_set(screen)
for key, fold in (folds.folds.items() if folds is not None else ()):
try:
titles = mark_folded_sections(key, getattr(fold, "sections", ()))
except Exception:
LOG.debug("Could not mark %s's mounted categories", key,
exc_info=True)
continue
if titles:
marked[key] = titles
try:
own = mark_folded_categories(
getattr(screen, "_settings_sections", ()) or (), FOLD_CATEGORIES)
except Exception:
LOG.debug("Could not mark %s's own folded categories", HOST_KEY,
exc_info=True)
own = {}
for key, titles in own.items():
marked[key] = marked.get(key, ()) + titles
return marked
#: The folder the example plate is written into, under the same cache the
#: example screen already uses, so one directory holds everything spaCR
#: fetched or made for a user who wanted something to press Run on.
EXAMPLE_PLATE_DIRNAME = "mask_example_plate"
#: The button, and what it says it does.
EXAMPLE_BUTTON_TEXT = "Load the example images…"
EXAMPLE_BUTTON_TOOLTIP = (
"Generate a reproducible example microscopy plate in the spaCR cache, "
"then fill this form with its folder, channels, and acquisition settings. "
"This operation does not require a network connection.")
[docs]
def example_plate_folder() -> str:
"""Return the cache directory used for the example microscopy plate."""
from ...example_data import cache_folder
return os.path.join(cache_folder(), EXAMPLE_PLATE_DIRNAME)
[docs]
def load_the_example_images(screen: QWidget,
folder: str = "") -> Dict[str, object]:
"""Generate an example plate and apply its settings to Mask Generation.
The reproducible synthetic fields follow the filename and channel layout
expected by the default pipeline. A summary of written images, applied
settings, and unavailable controls is displayed in the screen console.
:param screen: Mask Generation screen.
:param folder: Output directory. Defaults to
:func:`example_plate_folder`.
:returns: Result containing ``folder``, ``images``, ``written``,
``applied``, ``filled``, and ``unplaced``. Returns an empty mapping if
the plate could not be written.
"""
from ..synthetic import demo_settings, generate_mask_demo
dst = str(folder or example_plate_folder())
try:
before = set(os.listdir(dst)) if os.path.isdir(dst) else set()
except OSError:
before = set()
try:
layout = generate_mask_demo(dst)
except Exception as error: # noqa: BLE001
LOG.debug("Could not write the example plate", exc_info=True)
_say(screen, f"The example plate could not be written to {dst}: "
f"{error}\n")
return {}
images = [str(path) for path in layout.image_files]
written = [path for path in images
if os.path.basename(path) not in before]
settings = demo_settings("mask", str(layout.src))
applied = int(screen.apply_settings_dict(settings) or 0)
widgets = getattr(getattr(screen, "_settings_model", None), "_widgets", {})
filled = sorted(key for key in settings if key in widgets)
unplaced = sorted(key for key in settings if key not in widgets)
notes = layout.notes or {}
channels = ", ".join(str(c) for c in notes.get("channels", ()))
said = (f"Example plate ready: {len(images)} image(s) in {dst} "
f"({len(written)} written now, {len(images) - len(written)} "
f"already there) — {notes.get('n_fields', 0)} field(s), "
f"channels {channels}.\n"
f"src is now {dst}, and {applied} setting(s) on this form were "
f"filled from the plate: {', '.join(filled)}.\n")
if unplaced:
said += (f"{len(unplaced)} of the plate's settings have no control on "
f"this form and were not filled: {', '.join(unplaced)}.\n")
_say(screen, said)
return {"folder": dst, "images": images, "written": written,
"applied": applied, "filled": filled, "unplaced": unplaced}
def _say(screen: QWidget, text: str) -> None:
"""Put ``text`` in the screen's console, if it has one."""
console = getattr(screen, "_console", None)
if console is None or not hasattr(console, "append_stdout"):
return
try:
console.append_stdout(text)
except Exception: # noqa: BLE001
LOG.debug("Could not write to the console", exc_info=True)
def _install_organize_button(screen: QWidget):
"""Add "Organize images…" above the source-directory setting.
It opens the organizer in its images-only mode; once the images are
moved into one Yokogawa-named folder, ``src`` and ``metadata_type``
are set to read it. Idempotent.
:param screen: Host module screen.
:returns: Installed button, or ``None`` when the screen has no
source-directory section.
"""
from PySide6.QtWidgets import QPushButton
from ..i18n import tr
if getattr(screen, "app_key", None) != HOST_KEY:
return None
existing = getattr(screen, "_organize_images_button", None)
if existing is not None:
return existing
widget = getattr(getattr(screen, "_settings_model", None),
"_widgets", {}).get("src")
if widget is None:
return None
section = next((c for c in getattr(screen, "_settings_sections", ()) or ()
if hasattr(c, "add_prose") and c.isAncestorOf(widget)),
None)
if section is None:
return None
button = QPushButton(tr("Organize images…"))
button.setObjectName("MaskOrganizeImagesButton")
button.setToolTip(tr(
"Arrange intensity images from any folder structure or naming, "
"single- or multi-channel, into the folder Mask Generation reads, "
"and point src at it. Same popup as Make Masks' Organize for "
"Measure."))
button.clicked.connect(lambda _checked=False: _open_organize(screen))
section.add_prose(button, at_top=True)
screen._organize_images_button = button
return button
def _open_organize(screen: QWidget):
"""Open the images-only organizer for ``screen``.
:param screen: the Mask Generation screen.
:returns: the popup.
"""
from ..widgets.organize_for_measure import _open_and_organize
model = getattr(screen, "_settings_model", None)
try:
source = str((model.collect() or {}).get("src") or "")
except Exception:
source = ""
return _open_and_organize(
screen, "images", source if os.path.isdir(source) else "",
done=lambda *args: _on_organized(screen, *args))
def _on_organized(screen: QWidget, error, result, plan, target_layout) -> bool:
"""Point the form at the organised folder, or say why it failed.
:param screen: the Mask Generation screen.
:param error: the exception the move raised, or None.
:param result: the :class:`spacr.channel_sorting.ApplyResult`.
:param plan: the applied plan.
:param target_layout: the layout written.
:returns: whether the form now reads the folder.
"""
from .. import prefs
from ..i18n import tr
from ..widgets.organize_for_measure import _mask_generation_settings
if error is not None or result is None:
_say(screen, tr("Organizing failed: {error}. Every move made before "
"the failure is listed in the manifest.",
error=str(error)) + "\n")
return False
if target_layout != "mask":
return False
screen.apply_settings_dict(_mask_generation_settings(plan))
prefs.push_recent_source(HOST_KEY, result.dest)
_say(screen, tr("Moved {moved} file(s) into {dest}; src now reads it. "
"Every move is in {manifest}.", moved=result.moved,
dest=result.dest, manifest=result.manifest) + "\n")
return True
#: The registry key of the page fold, so the switch and the declaration
#: cannot drift apart.
OPS_KEY: str = PAGE_FOLDS[0]
#: What the switch says. AN ACRONYM, DELIBERATELY UNEXPANDED: "optical
#: pooled screening" does not fit the actions row beside Live, and OPS is
#: what the field calls it.
OPS_TOGGLE_TEXT = "OPS"
#: What it says on hover. The full name is here, where there is room for
#: it, together with the maturity -- the button is the only place a user
#: meets this module, and it is alpha.
OPS_TOGGLE_TOOLTIP = (
"Show or hide the optical pooled screening page: stitch each well of "
"the sequencing acquisition, segment its nuclei and decode their "
"barcodes. Alpha: two wells of one real plate have been run through "
"it so far."
)
def _build_ops(host_window: Optional[QWidget]) -> QWidget:
"""OPS's own screen: the settings-driven module, unchanged."""
return build_settings_screen(OPS_KEY, host_window)
class _OpsPage(PageFold):
"""Mask Generation's OPS switch and the page it opens.
:class:`~spacr.qt.screens.map_barcodes.PageFold` for the key ``"ops"``,
whose behaviour this class was before it was made general: the screen
behind the page is built once and kept, the page strip's own close mark
puts the switch back, and a module that cannot be built leaves the
switch off.
:param screen: the Mask Generation screen the switch sits on.
:param switch: the actions-row toggle.
"""
def __init__(self, screen: QWidget, switch) -> None:
"""Record the switch and how to build the page, building neither."""
super().__init__(screen, switch, OPS_KEY, _build_ops)
[docs]
def ops_page(screen: QWidget) -> Optional["_OpsPage"]:
"""The OPS switch installed on ``screen``, or None.
:param screen: the module screen to inspect.
"""
page = getattr(screen, "_ops_page", None)
return page if isinstance(page, _OpsPage) else None
[docs]
def install_ops_switch(screen: QWidget, switch) -> Optional["_OpsPage"]:
"""Wire an actions-row switch to the OPS page.
Idempotent: a second call on the same screen returns the first
installation and connects nothing further.
:param screen: the Mask Generation screen.
:param switch: the toggle to connect.
:returns: the installation, or None when this is not the host screen.
"""
if getattr(screen, "app_key", None) != HOST_KEY or switch is None:
return None
existing = ops_page(screen)
if existing is not None:
return existing
page = _OpsPage(screen, switch)
register_page_fold(screen, page)
screen._ops_page = page
return page
[docs]
SPATIAL_MASKS_KEY: str = PAGE_FOLDS[1]
"""The registry key of the page Mask Generation's Spatial switch opens."""
"""What Mask Generation's Spatial switch says on hover."""
[docs]
def spatial_masks_page(screen: QWidget) -> Optional[PageFold]:
"""The Spatial Mask Generation switch installed on ``screen``, or None.
:param screen: the module screen to inspect.
"""
return page_fold(screen, SPATIAL_MASKS_KEY)
[docs]
def install_spatial_masks_switch(screen: QWidget,
switch) -> Optional[PageFold]:
"""Wire Mask Generation's actions-row Spatial switch to its page.
The switch is alpha: it is named for the alpha gate here and hidden at
once unless Preferences -> Show alpha features is on.
:param screen: the Mask Generation screen.
:param switch: the toggle to connect.
:returns: the installation, or None when this is not the host screen.
"""
if getattr(screen, "app_key", None) != HOST_KEY or switch is None:
return None
switch.setObjectName("MaskSpatialSwitch")
fold = install_page_fold(screen, switch, HOST_KEY, SPATIAL_MASKS_KEY)
_gate_alpha(switch)
return fold
[docs]
def install_folds(screen: QWidget) -> Optional[FoldStrip]:
"""Put Mask Generation's fold switches on ``screen``'s masthead.
And the example-plate button on its form: this is the one walk that
reaches this screen from outside, so everything hung on Mask Generation
is hung here. See :func:`install_example_data_button`.
Idempotent, and errors are not raised, so a failure leaves the screen
without its switches rather than stopping it from opening.
:param screen: the host module's screen.
:returns: the strip, or None when this screen cannot carry one -- it
is not the host, it has no masthead, one is already installed, or
no folded module had a category of its own to add.
"""
if getattr(screen, "app_key", None) != HOST_KEY:
return None
try:
install_example_data_button(screen)
except Exception:
LOG.debug("Could not install the example-plate button on %s", HOST_KEY,
exc_info=True)
try:
_install_organize_button(screen)
except Exception:
LOG.debug("Could not install the organize button on %s", HOST_KEY,
exc_info=True)
existing = getattr(screen, "_fold_strip", None)
if isinstance(existing, FoldStrip):
return existing
header = getattr(screen, "_header", None)
if header is None or not hasattr(header, "add_trailing"):
return None
try:
folds = CategoryFoldSet(
screen,
{key: FOLD_GATES[key] for key in CATEGORY_FOLDS},
implies=FOLD_IMPLIES,
)
if not folds.mount():
return None
strip = folds.build_strip(header)
if strip is None:
return None
header.add_trailing(strip)
except Exception:
LOG.debug("Could not build the fold strip for %s", HOST_KEY,
exc_info=True)
return None
screen._category_folds = folds
screen._fold_strip = strip
screen._fold_previews = _offer_fold_previews(screen, folds, strip)
mark_fold_sources(screen)
return strip
[docs]
def sync_folds(screen: QWidget,
settings: Dict[str, object]) -> Sequence[str]:
"""Move the switches to match a settings dict that was just applied.
The tracking and assay CONTROLS take their values through the ordinary bulk
apply, because they are ordinary controls on this form. Their gates are not
controls -- the switch is -- so a Timelapse settings file would otherwise
fill in every tracking setting and leave tracking off.
Safe to call on any screen: one that has no category folds returns an
empty tuple.
:param screen: the screen the settings were applied to.
:param settings: the dict that was applied.
:returns: the folded keys the settings switched on.
"""
folds = fold_set(screen)
if folds is None:
return ()
try:
return folds.sync_from_settings(settings)
except Exception:
LOG.debug("Could not sync the folds from the applied settings",
exc_info=True)
return ()