Notebook: tags per header block, colour pictures, one-click axes (PR 17b-1)

AGENTS.md

@@ -182,7 +182,8 @@ src/morphobricks_preprocessing/
                     the confirmed AxisReview; no channel axis guessed), mask_thumbnail, PreviewCache;
                     preview_render.py display_panel (float32 after the reduction, percentile contrast
                     of the finite values; flat / no-finite / non-finite shown as such), stdlib PNG,
-                    strip_png, mask_overlay_png (declared representation only)
+                    strip_png, mask_overlay_png (declared representation only),
+                    colour_composite (an RGB image as one colour picture, display only)
   planes.py         plane-by-plane reader (iter_planes, read_plane, read_sample_plane), table rows as
                     XYC planes whose channels are read one at a time (iter_xyc_planes, XycPlane),
                     memory estimate,
@@ -309,6 +310,8 @@ src/morphobricks_preprocessing/
                             composition of the cards below); notebook_stepper.py the strip, Back/Next
                             and the overview; notebook_step_states.py each step's done/one-line state
   notebook_names.py         the names card's rows (conditions on step 4, replicates on step 5)
+  notebook_axes_quick.py    the stepper's one-click Confirm these axes (Q3, PR 17b)
+  notebook_channels_rows.py the tag grid's folder rows: pictures (colour for RGB), Enlarge
   notebook_folder.py        step 1: folder, check, issues, labels (_FolderStep)
   notebook_design.py        step 1: the experiment design card (_DesignCard)
   notebook_axis_step.py     step 2: role dropdowns, axis check, missing-axes card (_AxisStep)

CHANGELOG.md

@@ -8,6 +8,24 @@ are in [docs/plan.md](docs/plan.md) §12. Upgrading from v0.3: see the
 
 ## Unreleased
 
+- **Notebook: tags per header block, colour pictures, one-click axes (PR 17b-1).** *Tag channels*
+  shows folders whose image headers are identical, exactly (channel count, every raw header name
+  present and equal, colour flag), as one block tagged once for all its folders (owner decision Q5),
+  with every folder's pictures below for checking; a header lacking a channel name, other names or
+  other saved tags keep folders apart, and **Tag this folder on its own** takes one out. A block
+  answer writes the same per-folder answers into the draft as tagging one folder at a time (tested on
+  the draft bytes). The colour pre-tick is confirmed only on *Image type*; *Tag channels* restates
+  it. A colour (RGB) folder is drawn as one colour picture (channel 1 red, 2 green, 3 blue, each with
+  its own percentile contrast; display only) on *Tag channels*, *Image type* (which now has a picture
+  per folder), the pairing and *Check and save*: `preview_render.colour_composite`,
+  `Thumbnails.colour`. The axes step offers complete, unambiguous roles (no axis message, every image
+  naming its axes, nothing missing to state) with a preview and one **Confirm these axes** click,
+  which records what the two clicks of the role boxes record (owner decision Q3); an unchanged reopen
+  offers the earlier run's roles and then opens its next open step. Pixel sizes say *uncalibrated*
+  on the chip and in the summary when no physical size is found. Replicate IDs are shown in natural
+  order (`rep2` before `rep10`, the folder breaking a tie) in the run plots and legends, the
+  replicate blocks, the names rows and the short names: display only. Texts no longer name the old
+  steps 1-4 (the results page, the design card, the mask step, the design messages).
 - **Described runs with several layouts report `R_HETEROGENEOUS_LAYOUT_NOT_ENABLED` first (#245).**
   The run lists it before the axis review's issues, and the arrangement issues
   (`inconsistent_mapping`, `missing_axes`, `ambiguous_missing_axes`) no longer advise exporting the

docs/user_guide.md

@@ -416,6 +416,11 @@ results or comparing another grouping.
      **Axes checked: they are correct for every image**. Changing a role afterwards asks
      you to check the preview again.
      The confirmed roles are locked until you click **Change axis roles**.
+   - In the shipped notebook (one step at a time), when the suggested roles leave nothing
+     to ask (no axis message, every image names its axes, no missing axis to state), the
+     *Axes* step shows them with a preview and one **Confirm these axes** button; it records
+     the same two answers. A reopened experiment whose folders did not change offers the
+     roles of its earlier run. The role boxes stay under **Look closer, or change the roles**.
    - If some images lack a dimension the others have (often a single channel), a yellow box
      lists them; press **Yes, they have a single plane there** if that is the case.
      Once you confirm the axis roles, this resolves the missing-axis error for step 3.

pyproject.toml

@@ -139,9 +139,11 @@ baseline = "tools/code_rules_baseline.json"
 "morphobricks_preprocessing.mask_record" = "io"
 "morphobricks_preprocessing.run_labels" = "io"
 "morphobricks_preprocessing.notebook_axes" = "ui"
+"morphobricks_preprocessing.notebook_axes_quick" = "ui"
 "morphobricks_preprocessing.notebook_channel_thumbs" = "ui"
 "morphobricks_preprocessing.notebook_channels" = "ui"
 "morphobricks_preprocessing.notebook_channels_grid" = "ui"
+"morphobricks_preprocessing.notebook_channels_rows" = "ui"
 "morphobricks_preprocessing.notebook_channels_labels" = "ui"
 "morphobricks_preprocessing.notebook_channels_type" = "ui"
 "morphobricks_preprocessing.notebook_channels_view" = "ui"

src/morphobricks_preprocessing/dataset.py

@@ -370,7 +370,7 @@ def _missing_issues(balance: BalanceTable) -> list[ValidationIssue]:
             ],
             "No action needed if a repeat was not acquired for every condition. If the "
             "same repeat has a different folder name in another condition, pair the "
-            "folders in the experiment design (step 1 of the notebook, or the "
+            "folders in the experiment design (Replicates in the notebook, or the "
             "repeat_group column of experiment_design.csv).",
         )
     ]

src/morphobricks_preprocessing/description_review.py

@@ -17,6 +17,7 @@
 from .design import DesignRow, ExperimentDesign
 from .draft import Draft
 from .draft_answers import ConditionAnswer, DraftAnswers, RepeatAnswer, UnitKey
+from .notebook_values import natural_key
 
 SINGLE = "single"
 
@@ -96,10 +97,17 @@ def _members(applied: Draft, label: str, answers: DraftAnswers) -> tuple[MemberV
 
 
 def replicates(applied: Draft, answers: DraftAnswers) -> tuple[ReplicateView, ...]:
-    """Return every replicate with its folders, their channels and the labels some lack."""
+    """Return every replicate with its folders, their channels and the labels some lack.
+
+    In natural order of the replicate ID (``rep2`` before ``rep10``), the folder label breaking
+    a tie: for display only.
+    """
     every = sorted({c for unit in answers.units.values() for c in unit.channels if c is not None})
     out = []
-    for label, repeat in sorted(applied.repeats.items()):
+    shown = sorted(
+        applied.repeats.items(), key=lambda i: (natural_key(i[1].id.confirmed or i[0]), i[0])
+    )
+    for label, repeat in shown:
         members = _members(applied, label, answers)
         units = [u for m in members for u in m.units]
         present = sorted({c for u in units for c in u.channels if c is not None})
@@ -135,7 +143,7 @@ def short_names(applied: Draft, answers: DraftAnswers) -> list[tuple[str, tuple[
         ("Channels", set(answers.channels)),
         ("Masks", set(answers.masks)),
     ]
-    return [(title, tuple(sorted(ids))) for title, ids in kinds if ids]
+    return [(title, tuple(sorted(ids, key=natural_key))) for title, ids in kinds if ids]
 
 
 def unit_text(key: UnitKey) -> str:

src/morphobricks_preprocessing/design.py

@@ -465,8 +465,8 @@ def design_issues(design: ExperimentDesign) -> list[ValidationIssue]:
                 "A repeat group is one biological repeat across the conditions, so it can "
                 f"hold only one folder of each condition: {described}.",
                 [_folder(row) for g in design.conflicts for row in design.members(g)],
-                "Move one of the folders into another repeat group in the experiment design "
-                "(step 1, or the repeat_group column of experiment_design.csv).",
+                "Move one of the folders into another repeat group (Replicates in the "
+                "notebook, or the repeat_group column of experiment_design.csv).",
             )
         )
     unconfirmed = [g for g in design.unconfirmed_groups if g not in design.conflicts]
@@ -484,7 +484,7 @@ def design_issues(design: ExperimentDesign) -> list[ValidationIssue]:
                 "that the biological repeats were prepared and acquired under the same "
                 "circumstances, so that they are comparable.",
                 [_folder(row) for g in unconfirmed for row in design.members(g)],
-                "Confirm the biological repeats in step 1 of the notebook, with the design "
+                "Confirm the biological repeats in the notebook, with the design "
                 "command (--confirm), or by setting confirmed to true in experiment_design.csv.",
             )
         )
@@ -592,7 +592,7 @@ def read_confirmed_design(
     """
     path = Path(path)
     rerun = (
-        "Run step 1 of the preprocessing brick on this experiment (it pairs and confirms the "
+        "Check this experiment in the preprocessing notebook (it pairs and confirms the "
         "biological repeats), then run the preprocessing brick again."
     )
     if not path.is_file():
@@ -720,7 +720,7 @@ def load_design(
                 exc,
                 "Correct the file where the message says (a spreadsheet program may have "
                 f"rewritten a date such as 2026-10-26 as 26/10/2026; dates are {DATE_FORMAT}). "
-                "Answering the questions again in step 1 of the notebook also replaces it; "
+                "Answering the questions again in the notebook also replaces it; "
                 "nothing replaces it without an answer.",
             ) from exc
     return reconcile_design(previous, repeats)

src/morphobricks_preprocessing/notebook_axes_quick.py

@@ -0,0 +1,184 @@
+"""*Confirm these axes*: the axes step in one click, when nothing about the axes is open.
+
+Owner decision Q3 (UX proposal 2026-11-09): when the suggested roles are complete and nothing
+in them is uncertain, the axes step shows them with a preview and one **Confirm these axes**
+button; the role boxes are folded under *Look closer, or change the roles*. On a reopened
+experiment whose folders are unchanged, the roles the earlier run recorded are the ones offered,
+so a reopening no longer stops on the axes.
+
+Nothing is confirmed without the click. The click records exactly what the two clicks of the
+role boxes record (the preview checked, then the roles confirmed), through the same code. The
+roles are offered only when the axis review finds no message at all, every readable image fits
+them with no missing axis to state, and every image names its axes in its header (a plain
+stack only when the earlier run's confirmation still covers it unchanged); otherwise the role
+boxes are shown open, as before.
+"""
+
+from __future__ import annotations
+
+import html
+from pathlib import Path
+
+import ipywidgets as widgets
+
+from . import notebook_style as ui
+from .axes import AxisMapping, axis_name
+from .axis_check import ConfirmedAxes
+from .axis_review import review_axes
+from .fingerprint import unchanged_confirmation
+
+DETAILS_OPEN, DETAILS_CLOSED = " Hide the role boxes", " Look closer, or change the roles"
+
+
+class _QuickAxes:
+    """The one-click confirmation card of the stepper's axes step."""
+
+    def _build_quick_axes(self) -> None:
+        """Build the card (hidden until roles can be offered) and the fold of the role boxes."""
+        self._quick_offer: AxisMapping | None = None
+        self._quick_filling = False
+        # The check whose recorded roles were offered: once offered, a role the user changes is
+        # theirs, and the recorded roles are not put back into the boxes.
+        self._quick_seeded: object | None = None
+        self.quick_text = widgets.HTML()
+        self.quick_image = widgets.Image(format="png", layout=widgets.Layout(max_width="420px"))
+        ui.set_visible(self.quick_image, False)
+        self.quick_caption = widgets.HTML()
+        self.quick_confirm = ui.button(
+            " Confirm these axes",
+            style="success",
+            icon="check",
+            tooltip="The preview looks right: use these roles for every image",
+            main=True,
+        )
+        self.quick_confirm.on_click(lambda _: self._confirm_quick_axes())
+        self.quick_card = ui.card(
+            "Suggested axes",
+            [
+                self.quick_text,
+                widgets.HBox([self.quick_image]),
+                self.quick_caption,
+                self.quick_confirm,
+            ],
+            visible=False,
+        )
+        self.axes_details = ui.button(DETAILS_CLOSED, style="info", icon="sliders")
+        self.axes_details.on_click(lambda _: self._toggle_axes_details())
+        ui.set_visible(self.axes_details, False)
+
+    def _toggle_axes_details(self) -> None:
+        shown = not ui.is_visible(self.axis_box)
+        ui.set_visible(self.axis_box, shown)
+        self.axes_details.description = DETAILS_OPEN if shown else DETAILS_CLOSED
+
+    # What can be offered -------------------------------------------------------------------
+
+    def _saved_axes(self) -> AxisMapping | ConfirmedAxes | None:
+        """Return the roles the earlier run recorded, on a reopening with unchanged folders."""
+        state = self._published() if self.preflight is not None else None
+        recorded = getattr(self, "_recorded", None)
+        if state is None or state.changed or recorded is None or recorded.mapping is None:
+            return None
+        root = Path(self.preflight.discovery.root)
+        saved = unchanged_confirmation(recorded.mapping, root)
+        roles = saved.mapping if isinstance(saved, ConfirmedAxes) else saved
+        if self.mapping is None or roles.axes != self.mapping.axes:
+            return None
+        edited = roles.roles != self.mapping.roles and self._quick_seeded is self.preflight
+        return None if edited else saved
+
+    def _quick_mapping(self) -> AxisMapping | None:
+        """Return the roles to offer for one click, or None when the role boxes are needed."""
+        pre = self.preflight
+        if pre is None or self.mapping is None or not self.role_dropdowns:
+            return None
+        saved = self._saved_axes()
+        covered: set[str] = set()
+        if isinstance(saved, ConfirmedAxes):
+            covered, saved = set(saved.files), saved.mapping
+        mapping = saved or self.mapping
+        review = review_axes(pre.metadata, mapping, missing_as_singleton=False)
+        readable = [f for f in pre.metadata.files if f.readable]
+        if (
+            review.issues
+            or len(review.file_mappings) != len(readable)
+            or any(m.singleton_roles for m in review.file_mappings.values())
+            or not set(review.confirmed_files) <= covered
+        ):
+            return None
+        return mapping
+
+    # Showing -----------------------------------------------------------------------------
+
+    def _refresh_quick_axes(self) -> None:
+        """Offer the roles for one click, or show the role boxes open."""
+        if getattr(self, "quick_card", None) is None or self._quick_filling:
+            return
+        offer = None if self.confirmed_mapping is not None else self._quick_mapping()
+        self._quick_offer = offer
+        if offer is not None and self._saved_axes() is not None:
+            self._quick_seeded = self.preflight  # the recorded roles go into the boxes once
+        ui.set_visible(self.quick_card, offer is not None)
+        ui.set_visible(self.axes_details, offer is not None)
+        ui.set_visible(self.axis_box, offer is None)
+        self.axes_details.description = DETAILS_CLOSED
+        if offer is None:
+            return
+        if offer.roles != self.mapping.roles:
+            self._quick_filling = True  # the recorded roles fill the boxes, as other inputs
+            try:
+                for box, role in zip(self.role_dropdowns, offer.roles, strict=True):
+                    box.value = role or "-"
+            finally:
+                self._quick_filling = False
+        self.quick_text.value = self._quick_text(offer)
+        self.show_preview()
+        self.quick_image.value = self.preview_image.value
+        ui.set_visible(self.quick_image, bool(self.preview_image.value))
+        self.quick_caption.value = self.preview_caption.value
+
+    def _quick_text(self, offer: AxisMapping) -> str:
+        """Return what the card says: the roles, where they come from, what the click does."""
+        roles = ", ".join(
+            f"{html.escape(axis_name(axis))} → {role}"
+            for axis, role in zip(offer.axes, offer.roles, strict=True)
+            if role is not None
+        )
+        source = (
+            "the roles the earlier run of this experiment recorded"
+            if self._saved_axes() is not None
+            else "the roles every image header names"
+        )
+        return ui.status(
+            "info",
+            f"Suggested: {roles}.",
+            [
+                f"These are {source}; the axis check finds nothing to ask about them.",
+                "Look at the preview: if it looks like a normal image of your sample, confirm. "
+                "Nothing is confirmed until you click.",
+            ],
+            raw=True,
+        )
+
+    # The click ---------------------------------------------------------------------------
+
+    def _confirm_quick_axes(self) -> bool:
+        """Confirm the offered roles: the preview checked, then the roles, as the role boxes do.
+
+        Returns
+        -------
+        bool
+            True when the roles are now confirmed.
+        """
+        offer = self._quick_offer
+        if offer is None or self.confirmed_mapping is not None:
+            return False
+        if self._current_mapping() != offer:
+            self._refresh_quick_axes()
+            return False
+        self.preview_checked.set(True)  # the user's click says the preview looks right
+        self._toggle_confirmation()
+        return self.confirmed_mapping is not None
+
+
+__all__ = ["DETAILS_CLOSED", "DETAILS_OPEN", "_QuickAxes"]