Axes: show the confirmation at once and make it faster; image type moves to Channels (v0.5.2 owner feedback)

CHANGELOG.md

@@ -8,6 +8,32 @@ v0.5.1: no run before v0.5.1 is read.)
 
 ## Unreleased
 
+**Owner feedback on the v0.5.2 Colab test (12 November 2026)**
+
+- **Axes: the confirmation is seen at once.** The instant **Confirm these axes** or
+  **Confirm axis roles** (or **Change axis roles**) is clicked, the button is greyed out and
+  says *Working…*, and the progress line of the folder check appears under it before any of
+  the work: *Working…*, then the 5 parts of the confirmation with a bar (n of 5, what it does
+  now). Both clear when it is done.
+  If something fails part-way, the button is given back and the error is said in red where
+  it is seen (under **Confirm axis roles** once the one-click card has gone), with the full
+  report in *Technical details*; nothing stays on *Working…*.
+- **Axes: the confirmation is faster.** It read every channel of every folder's first image for
+  the per-folder image-type rows, which are folded under *Set per folder…* (28 folders of
+  3 × 2048² images: 93 plane reads, 84 of them for those rows), and rebuilt the pairing editor
+  of Design for pictures the stepper never shows. The rows now read their pictures only once
+  opened, and the editor is not rebuilt there: 9 plane reads instead of 93 (about 72 MiB read
+  instead of 744 MiB) and 1,037 widgets built instead of 1,439 on the same data. Nothing
+  validated changed.
+- **The image type moved from Axes to Channels.** It is proposed at the quick scan, display
+  only, from the headers (the shown image's before the folder check, every header after it;
+  nothing is recorded there), and confirmed on Channels, first on the page, since it decides
+  whether the channels are R, G and B or the stains. The rules are unchanged: recorded only by
+  a click, pre-filled only when every header agrees, per folder when they differ, **Use for all
+  folders**, and folders of different types refused (`R_HETEROGENEOUS_LAYOUT_NOT_ENABLED`). The
+  Axes step is done once the roles are confirmed; the Channels step needs the image type. The
+  published files are unchanged for the same answers.
+
 **Parent-label (grouped) masks** (MorphoBricks-Spec PR #28, merge `69a58b3`: ADR 0001 PL1,
 experiment-v1 §4.5, §4.5a-§4.5c, §7, §8; ADR 0002 resolver contract version 2)
 

docs/colab-release-check.md

@@ -40,11 +40,18 @@ release PR moves both together and records the pair in `RELEASE_CALLS` of
 7. - [ ] **Images:** paste the Drive paths (experiment, masks, output); **Browse…** says it
    cannot open here and offers **Copy path**. **Scan the folders** shows the folders and an
    example picture with a progress line; **Looks right: read all image headers** shows its
-   progress (done of total, time left) and the result.
+   progress (done of total, time left) and the result. The image type (separate channels or
+   colour RGB) is shown from the headers, display only: "nothing is recorded here".
 8. - [ ] **Axes:** one row per dimension with its role, the example redrawn when a role changes,
-   the pixel size in one line, the image type in one line (**Use for all folders**). The roles
-   are confirmed only by the click.
-9. - [ ] **Channels:** name the stains, then tag each folder's channels.
+   the pixel size in one line; no image type. The roles are confirmed only by the click. The
+   instant **Confirm these axes** (or **Confirm axis roles**) is clicked, the button is greyed
+   out and says **Working…**, and a progress bar under it counts the parts done (n of 5, what
+   it does now); both clear when the roles are confirmed.
+9. - [ ] **Channels:** first the image type in one line, pre-filled only when every header
+   agrees and recorded only by **Use for all folders** (or each folder under **Set per
+   folder…**; folders of different types are refused, `R_HETEROGENEOUS_LAYOUT_NOT_ENABLED`);
+   then name the stains (none for colour RGB: its channels are R, G and B) and tag each
+   folder's channels.
 10. - [ ] **Masks:** **Check the masks** runs with progress; each mask type can be described.
     **Describe the masks** is greyed out, with its reason, until a run exists.
 11. - [ ] **Design:** the grid of conditions by biological repeats; **Looks right: confirm the

docs/contract.md

@@ -590,7 +590,7 @@ plan N34); this brick suggests it, asks for it after the axis roles, and records
 | Types | `fluorescence` (any number of channels, every pixel type) and `rgb` (exactly three channels of an integer pixel type, the rule of the normalization brick's `check_rgb`). |
 | RGB samples | A TIFF image is stored as RGB colour when its first series has the photometric interpretation RGB with three samples per pixel (`tifffile` axis `S`; `TiffMetadata.rgb_samples`). RGB with an alpha sample, several grey samples and OME-Zarr images are not. |
 | Suggestion | `rgb` when every analysed image is stored as RGB colour, the confirmed C role is on its samples axis, and `rgb` is possible; `fluorescence` otherwise. `review_image_type` gives the suggestion, why, and why `rgb` is not possible (from the headers and the confirmed axis roles; no pixels are read). |
-| Confirmation | Never applied without the user's confirmation. The notebook asks in step 2 once the axis roles are confirmed, with the suggestion preselected and a **Yes, this is the right image type** button; `rgb` cannot be chosen, with the reason shown, when it is not possible. Changing the axis roles or the folder asks again. Step 3 runs only once the type is confirmed. The command line takes `--image-type`, or uses the suggestion and prints it. |
+| Confirmation | Never applied without the user's confirmation. The notebook proposes it at the quick scan (display only, from the headers; nothing is recorded there) and asks on the Channels step once the axis roles are confirmed (owner, 12 November 2026), pre-filled only when every header agrees and recorded only by a click (**Use for all folders**, or each folder); folders of different types are refused (`R_HETEROGENEOUS_LAYOUT_NOT_ENABLED`). Changing the axis roles or the folder asks again. The run takes the type the saved description states. The command line takes `--image-type`, or uses the suggestion and prints it. |
 | Run | `run_experiment(..., image_type=...)` records the type and `channels_from_rgb_samples` in the manifest (§9). `rgb` for images that cannot be RGB is the error `rgb_not_possible`; any other value raises `ValueError`. Without a type the manifest records null. |
 | Outputs | `plane_histograms.csv` and `experiment_design.csv` do not depend on the type: a plane of an RGB image is one row with channels C0, C1 and C2, as for any image. Changing the type on a later run reads no image again. |
 

notebooks/MorphoBricks_Preprocessing.ipynb

@@ -395,8 +395,8 @@
     "The app has seven steps, one on screen at a time; move with **Next** or click a step in the strip at the top:\n",
     "\n",
     "1. **Images**: give the experiment folder (masks and output are optional), click **Scan the folders**, look at the example image, then **Looks right: read all image headers**.\n",
-    "2. **Axes**: what each image dimension is, the pixel size, and the image type (separate stains or colour).\n",
-    "3. **Channels**: name what you stained, then tag each folder's channels.\n",
+    "2. **Axes**: what each image dimension is, and the pixel size.\n",
+    "3. **Channels**: confirm the image type (separate stains or colour), name what you stained, then tag each folder's channels.\n",
     "4. **Masks**: say what each mask type is (nothing to do without masks). After the run, come back here for **Describe the masks** if later bricks use the masks.\n",
     "5. **Design**: conditions, biological repeats and comparisons in one grid; **Looks right: confirm the design**.\n",
     "6. **Check and save**: read your experiment in words and save it.\n",

src/morphobricks_preprocessing/notebook_axes_quick.py

@@ -50,8 +50,11 @@ def _build_quick_axes(self) -> None:
             tooltip="The example looks right: use these roles for every image",
             main=True,
         )
-        self.quick_confirm.on_click(lambda _: self._confirm_quick_axes())
-        self.quick_card = widgets.VBox([self.quick_text, self.quick_confirm, self.quick_caption])
+        self.quick_confirm.on_click(lambda _: self._quick_clicked())
+        self.quick_progress = widgets.HTML()  # Working…, then the parts done (owner, 12 Nov)
+        self.quick_card = widgets.VBox(
+            [self.quick_text, self.quick_confirm, self.quick_progress, self.quick_caption]
+        )
         ui.set_visible(self.quick_card, False)
 
     # What can be offered -------------------------------------------------------------------
@@ -178,6 +181,21 @@ def _headers_changed_line(self) -> list[str]:
 
     # The click ---------------------------------------------------------------------------
 
+    def _quick_clicked(self) -> None:
+        """*Confirm these axes*: working at once, then the parts of the confirmation."""
+        self._working(self.quick_confirm, self.quick_progress, self._confirm_quick_axes)
+
+    def _after_working(self, button: widgets.Button) -> None:
+        super()._after_working(button)
+        if button is getattr(self, "quick_confirm", None):
+            self._refresh_quick_axes(drawn=True)  # its state, from the roles and the example
+
+    def _failure_line(self, progress: widgets.HTML) -> widgets.HTML:
+        """Say a failure of *Confirm these axes* under *Confirm axis roles* once its card hides."""
+        if progress is getattr(self, "quick_progress", None) and not ui.is_visible(self.quick_card):
+            return self.confirm_progress
+        return super()._failure_line(progress)
+
     def _confirm_quick_axes(self) -> bool:
         """Confirm the offered roles: the preview checked, then the roles, as the role boxes do.
 

src/morphobricks_preprocessing/notebook_axis_preview.py

@@ -3,6 +3,10 @@
 from __future__ import annotations
 
 import html
+import traceback
+from collections.abc import Callable
+
+import ipywidgets as widgets
 
 from . import notebook_style as ui
 from .axes import AxisMapping, axis_name, file_mapping_for
@@ -17,10 +21,90 @@
 from .preview import PreviewRefused, check_unchanged, checked_fingerprint
 from .validation import plural
 
+WORKING = "Working…"
+"""What a confirmation button says, and its progress line first, the instant it is clicked."""
+CONFIRM_STEPS = (
+    "Checking the roles against every image",
+    "Redrawing the example with these roles",
+    "Reading the pixel sizes",
+    "Preparing the run",
+    "Preparing Channels, Masks and Check and save",
+)
+"""The parts of *Confirm axis roles* (or of taking it back), in order, for its progress bar."""
+
 
 class _AxisPreview:
     """Step 2's preview, the confirmation of the axis roles and the image type."""
 
+    # The click, shown at once ------------------------------------------------------------
+
+    def _confirm_clicked(self) -> None:
+        """*Confirm axis roles* (or *Change axis roles*): working at once, then the parts."""
+        self._working(self.confirm_button, self.confirm_progress, self._toggle_confirmation)
+
+    def _working(
+        self, button: widgets.Button, progress: widgets.HTML, action: Callable[[], object]
+    ) -> object:
+        """Run ``action`` behind a disabled button and a progress line drawn before it starts.
+
+        Owner (12 November 2026): the click must show at once that something happens. The
+        button is disabled and says *Working…*, and the line under it shows *Working…* before
+        any of the work; the parts of the work then advance its bar
+        (:meth:`_confirm_step`). The widgets' state is sent to the page as it is set, so the
+        line is seen while the work runs. Afterwards the line is cleared and the button given
+        back the state the answers give it (:meth:`_after_working`). A disabled button does
+        nothing. An unexpected failure part-way gives the button back too, and says what
+        failed where it is seen (:meth:`_failure_line`), the full report in Technical details.
+        """
+        if button.disabled:
+            return None
+        saved = (button.description, button.icon)
+        self._busy(button, WORKING)
+        self._working_on = button  # it stays disabled, saying Working…, until the end
+        wait = self._confirm_wait = Wait(progress)
+        wait.start(WORKING, len(CONFIRM_STEPS))
+        failed: str = ""
+        try:
+            return action()
+        except Exception as exc:  # unexpected failures still get a readable message
+            self.log.lines.append(traceback.format_exc())
+            failed = ui.status(
+                "error",
+                "The confirmation stopped because of an unexpected problem.",
+                [
+                    f"{type(exc).__name__}: {exc}",
+                    "Open Technical details for the full report. Click the button again; "
+                    "once the roles are confirmed, Change axis roles takes them back.",
+                ],
+            )
+            return None
+        finally:
+            self._confirm_wait = self._working_on = None
+            progress.value = ""
+            button.description, button.icon = saved
+            button.disabled = False
+            try:
+                self._after_working(button)
+            finally:
+                if failed:
+                    self._failure_line(progress).value = failed
+                    self._show_log()
+
+    def _failure_line(self, progress: widgets.HTML) -> widgets.HTML:
+        """Return the line that says a failure: the click's own, where it is seen."""
+        return progress
+
+    def _after_working(self, button: widgets.Button) -> None:
+        """Give the confirmation buttons back the state the step's answers give them."""
+        self._confirm_words(self.confirmed_mapping is not None)
+        self._update_confirm_button()
+
+    def _confirm_step(self, index: int) -> None:
+        """Advance the progress of a confirmation to part ``index`` (0-based), when one shows."""
+        wait = getattr(self, "_confirm_wait", None)
+        if wait is not None:
+            wait.phase(CONFIRM_STEPS[index], len(CONFIRM_STEPS), index)
+
     def _fill_preview_files(self) -> None:
         """List the images that fit the roles in the preview dropdown."""
         files = [
@@ -211,13 +295,14 @@ def _preview_header(self):  # noqa: ANN202
     def _toggle_confirmation(self) -> None:
         """Confirm the roles shown (or take the confirmation back) and update what follows."""
         if self.confirmed_mapping is None:
-            if self.confirm_button.disabled:
+            if self._confirm_blockers():  # what disables the button (it shows Working… now)
                 return
             self.confirmed_mapping = self._current_mapping()
         else:
             self.confirmed_mapping = None
         locked = self.confirmed_mapping is not None
         self._set_locked(locked)
+        self._confirm_step(0)
         if locked:
             roles = [
                 f"{axis_name(a)} → {r}"
@@ -256,11 +341,17 @@ def _toggle_confirmation(self) -> None:
             self.confirmed_status.value = ""
             # The image type depends on the channels the roles give.
             self._close_image_type()
+            self._confirm_step(1)
             self._mapping_changed()
         self._update_confirm_button()
+        if locked:
+            self._confirm_step(1)
         self._render_preview_if_shown()
+        self._confirm_step(2)
         self._show_calibration()
+        self._confirm_step(3)
         self._refresh_run_step()
+        self._confirm_step(4)
         self._refresh_channels()
 
     def _open_image_type(self) -> None:
@@ -350,6 +441,12 @@ def _set_locked(self, locked: bool) -> None:
             dropdown.disabled = locked
         self.missing_as_singleton.disabled = locked
         self._gate_preview_tick()
+        self._confirm_words(locked)
+
+    def _confirm_words(self, locked: bool) -> None:
+        """Say *Confirm axis roles*, or *Change axis roles* once they are confirmed."""
+        if getattr(self, "_working_on", None) is self.confirm_button:
+            return  # it says Working… until the work is done (:meth:`_working`)
         self.confirm_button.description = " Change axis roles" if locked else " Confirm axis roles"
         self.confirm_button.icon = "pencil" if locked else "check"
         self.confirm_button.button_style = "warning" if locked else "success"

src/morphobricks_preprocessing/notebook_axis_step.py

@@ -50,6 +50,7 @@ def _build_axis_step(self) -> None:
             tooltip="Use these roles for every image of the experiment",
             main=True,
         )
+        self.confirm_progress = widgets.HTML()  # Working…, then the parts done (owner, 12 Nov)
         self.confirm_blocker = widgets.HTML()
         self.confirmed_status = widgets.HTML()
         self.axis_next = widgets.HTML()
@@ -59,7 +60,7 @@ def _build_axis_step(self) -> None:
         for slider in self.preview_sliders.values():
             slider.observe(lambda _: self._render_preview_if_shown(), names="value")
         self.preview_checked.observe(lambda _: self._update_confirm_button())
-        self.confirm_button.on_click(lambda _: self._toggle_confirmation())
+        self.confirm_button.on_click(lambda _: self._confirm_clicked())
         self._build_image_type_card()
 
     def _build_missing_card(self) -> None:
@@ -204,9 +205,10 @@ def _refresh_axis_step(self) -> None:
             self.convert_card,
             self.axis_sizes_slot,
             self.confirm_button,
+            self.confirm_progress,
             self.confirm_blocker,
             self.confirmed_status,
-            self.image_type_card,
+            # No image type here (owner, 12 November 2026): it is confirmed on Channels.
             self.axis_next,
         ]
         self._fill_preview_files()
@@ -393,6 +395,8 @@ def _mapping_changed(self) -> None:
 
     def _update_confirm_button(self) -> None:
         """Enable *Confirm axis roles* when nothing blocks it; say beside it what does."""
+        if getattr(self, "_working_on", None) is self.confirm_button:
+            return  # disabled, saying Working…, until the work is done
         if self.confirmed_mapping is not None:
             self.confirm_button.disabled = False
             self.confirm_blocker.value = ""

src/morphobricks_preprocessing/notebook_channels_grid.py

@@ -416,11 +416,11 @@ def _block_text(self, units: Sequence[UnitLayout], colour: bool, apart: bool) ->
     def _type_text(self, layout: UnitLayout) -> str:
         """Say the image-type answer of a colour block, as the image-type page gave it."""
         if self.types.saved(layout.key) == "rgb":
-            where = "" if self.place_types else " (Axes)"
+            where = "" if self.place_types else " (Image type, above)"
             return f"Answered colour (RGB){where}: its channels are R, G and B, nothing to tag."
         if self.place_types:
             return "Colour is pre-ticked from the header: confirm it with the button below."
-        return "Colour is pre-ticked from the header: confirm it on Axes (Image type)."
+        return "Colour is pre-ticked from the header: confirm it under Image type, above."
 
     def _pending(self, layout: UnitLayout) -> bool:
         """Return True when the unit shows a proposal not saved yet.