plexora 0.0.1__py3-none-any.whl

plexora/plugins/roi/__init__.py

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+"""Regions of interest: shapes the user draws on the image.
+
+An ROI is an annotation in image space, not a property of the cell table. That
+one decision is what the rest of this plugin follows from: drawing works on a
+project that is nothing but an image, the geometry is stored in full-resolution
+image pixels, and CSV/AnnData/SpatialData are destinations you can export to
+rather than the thing being edited.
+
+Deliberately NOT here: what the cells inside a region express, or anything else
+that needs the marker matrix. Building that into the annotation engine is what
+would make drawing a box conditional on having imported one -- see Requires()
+below, which requires nothing.
+
+WHICH cells fall inside a region is the one exception, and it stays on the right
+side of the line because it is opt-in in both directions: the table is offered
+rather than demanded, and "Map to cells" only exists once one is there.
+
+Kept import-light, like every descriptor module: this is imported whenever the
+plugin is activated, and building the Blueprint (which pulls in the geometry and
+adapter code) is left to the factory.
+"""
+
+from plexora.api.plugin import Plugin, Requires
+
+VERSION = "20260822_roi_figure_bridge"
+
+
+def _blueprint():
+    from plexora.plugins.roi.server.routes import roi_bp
+
+    return roi_bp
+
+
+PLUGIN = Plugin(
+    name="roi",
+    label="ROI",
+    version=VERSION,
+    blueprint_factory=_blueprint,
+    # Templates are namespaced by plugin name, so two plugins can both ship a
+    # "panel.html" without colliding in Flask's shared template lookup.
+    panels={"tool_panel_slot": "roi/panel.html"},
+    # Listed in dependency order for reading, not because the browser needs it:
+    # every cross-file reference is inside a method or a constructor, and
+    # toolLoader awaits all six before anything is activated, so the bindings
+    # resolve whatever sequence they arrive in. What DOES matter is that all six
+    # are here -- one omitted is a plugin that loads and does nothing, which is
+    # what plexora/plugins/roi/tests/test_roi_boot.py exists to catch.
+    scripts=(
+        "roiApi.js",
+        "roiGeometry.js",
+        "roiState.js",
+        "roiRenderer.js",
+        "roiTools.js",
+        "roiSidebarController.js",
+        # Answers Figure Builder's two capture/restore events. A listener
+        # nobody dispatches to never fires, so this costs a build without
+        # that plugin nothing -- and neither plugin imports the other.
+        "roiFigureBridge.js",
+    ),
+    styles=("roi.css",),
+    # Nothing REQUIRED, and that is still the whole point. Drawing a region
+    # needs the image and nothing else -- no table, no segmentation, no marker
+    # split, no column roles. A project that is one OME-TIFF and nothing more
+    # can annotate, which is the case a table requirement would have silently
+    # ruled out.
+    #
+    # What is new is the optional tier. Requiring nothing also meant SAYING
+    # nothing: a user never found out that attaching their cells is what lets
+    # ROI annotations be written back onto them, because the tool opened
+    # straight into the panel and the connection was invisible. These four are
+    # offered exactly once (Requires.optional_missing_from), and skipping them
+    # is a real answer that is never re-asked.
+    #
+    # Ordering is the framework's, not ours: the two files come first, and the
+    # column questions are held back until a table exists to ask them about --
+    # "which column holds the cell id" has no answers before then.
+    #
+    # `excluded_image_kinds` keeps its default of ('rgb',): the flat quick-view
+    # path returns from main.js's init() before any plugin is activated, so a
+    # tool offered there could never come up.
+    requires=Requires(
+        optional=("table", "segmentation", "role:image_id", "role:cell_id"),
+    ),
+    # Shown instead of core's generic subtitle, because the generic one says
+    # Plexora filled these in from the data -- true of a form full of guesses to
+    # confirm, false twice over for a form where nothing was guessed and nothing
+    # is required. Core cannot word this; only the plugin knows what the offer
+    # buys.
+    intro=("None of these are needed to draw ROIs. Adding cell-level data is "
+           "what lets Plexora write ROI annotations back onto your cells."),
+    # ROI draws its own overlay above the image and never colours cells. Claiming
+    # the cell layer would evict whichever plugin legitimately holds it (the
+    # shader has one range table) in exchange for nothing.
+    owns_cell_layer=False,
+)

plexora/plugins/roi/server/__init__.py

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+"""Server half of the ROI plugin.
+
+`routes` is the Flask surface, `repository` owns persistence and the revision
+check, `operations` applies one edit to the state, `geometry`/`schema` say what
+a valid annotation is, and `geojson`/`adapters` are the export formats. Nothing
+here imports `data_model` -- everything about the project comes through
+`plexora.api`.
+"""