[feat] save drift corrector images#3487
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Jun 11, 2026
| logging.warning("Shape of data is %s instead of %s", data.shape[::-1], self._res) | ||
|
|
||
| # Save all the drift region scans for offline autocorrelation purposes | ||
| if self._save_images: |
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@pieleric The changes in src/odemis/acq/drift/init.py are made by @yxkdejong. I am not 100% sure if this is what AMOLF needs. Since you have previously written code for the drift corrector, can you tell?
📝 WalkthroughWalkthroughThis PR adds optional drift corrector image saving to SPARC acquisition. A new Sequence DiagramsequenceDiagram
participant User
participant SaveDriftCorrectorImgPlugin
participant DriftCorrector
participant AnchorDriftCorrector
participant AnchoredEstimator
User->>SaveDriftCorrectorImgPlugin: Toggle menu item
SaveDriftCorrectorImgPlugin->>DriftCorrector: Set save_images property
Note over DriftCorrector: Menu state determines<br/>save_images value
DriftCorrector->>AnchorDriftCorrector: Constructor receives<br/>save_images
AnchorDriftCorrector->>AnchoredEstimator: Pass save_images parameter
Note over AnchoredEstimator: Saves anchor scans to disk<br/>during acquire()
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✅ Passed checks (4 passed)
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Actionable comments posted: 5
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⚠️ Outside diff range comments (1)
src/odemis/acq/drift/__init__.py (1)
53-65: 🛠️ Refactor suggestion | 🟠 MajorAdd type hints and fix reStructuredText docstring for
AnchoredEstimator.__init__.In
src/odemis/acq/drift/__init__.py(lines 53-65),__init__has untyped parameters/return and the docstring includes inline type info (e.g.,region (4 floats),max_pixels (int):,follow_drift (bool):). Update the constructor signature with type hints and rewrite the docstring to the required reStructuredText style without inline type annotations.🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@src/odemis/acq/drift/__init__.py` around lines 53 - 65, Update AnchoredEstimator.__init__ to use Python type hints for all parameters (e.g., scanner: Emitter, detector: Detector, region: Sequence[float] or Tuple[float, float, float, float], dwell_time: float, max_pixels: int = MAX_PIXELS, follow_drift: bool = True, save_images: bool = False) and return type None; then replace the inline-typed docstring with reStructuredText style parameter descriptions (use :param scanner:, :type scanner:, :param detector:, :type detector:, :param region:, :type region:, :param dwell_time:, :type dwell_time:, :param max_pixels:, :type max_pixels:, :param follow_drift:, :type follow_drift:, :param save_images:, :type save_images:) and short explanatory text for each parameter, keeping the note about anchor region resizing and follow_drift behavior.
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@plugins/sparc_save_drift_corrector_images.py`:
- Around line 48-52: The menu callback is wired even if
sparc_acq_tab.tab_data_model.driftCorrector may be None, causing runtime errors
when _save_drift_corrector_images uses self._drift_corrector; fix by guarding
when creating the menu: check sparc_acq_tab.tab_data_model.driftCorrector and
only call addMenu (or disable the menu item) if it's not None, and in
_save_drift_corrector_images defensively handle a None self._drift_corrector
(e.g., show a warning and return) so both initialization-time None and later
changes are safe; update references to self._drift_corrector, addMenu,
_save_drift_corrector_images and the source
sparc_acq_tab.tab_data_model.driftCorrector accordingly.
- Around line 30-31: The SaveDriftCorrectorImgPlugin class lacks a class rST
docstring and its methods lack type hints/docstrings; add an rST-style class
docstring to SaveDriftCorrectorImgPlugin describing its purpose, then update
__init(self, microscope, main_app) to include proper type hints for microscope
and main_app (and -> None) and add a short rST docstring describing parameters,
types, and return; also add type hints to _save_drift_corrector_images(self,
menu_item) (typing for menu_item and -> None) and ensure its existing docstring
is converted/expanded to rST param/return sections. Reference the class name
SaveDriftCorrectorImgPlugin and the methods __init__ and
_save_drift_corrector_images when making these changes.
In `@src/odemis/acq/drift/__init__.py`:
- Around line 39-40: Replace os.path and os.makedirs usage for drift image paths
with pathlib.Path: construct DRIFT_IMAGES_DIR using Path(get_picture_folder()) /
"Drift Correction images", ensure directories are created via
Path.mkdir(parents=True, exist_ok=True) where the code currently calls
os.makedirs, and update any image write calls (cv2.imwrite) to pass
str(filename) when filename is a Path object; search for DRIFT_IMAGES_DIR,
get_picture_folder(), and cv2.imwrite in this module to locate the three spots
to change.
In `@src/odemis/acq/leech.py`:
- Around line 155-156: The issue: runtime changes to the plugin's save_images
flag are not propagated to the active AnchoredEstimator because the value is
only copied in series_start(); fix by adding a public setter on
AnchoredEstimator (e.g., set_save_images or update_save_images) and call that
setter wherever the code currently assigns self.save_images into the estimator
(notably in series_start() and the other similar locations around where
save_images is copied), rather than directly mutating a private field; ensure
AnchoredEstimator.acquire() reads the public/internal field the setter updates
so toggles take effect immediately.
- Around line 144-149: Update AnchorDriftCorrector.__init__ to use Python type
hints: annotate parameters as scanner: Emitter, detector: Detector, save_images:
bool = False and add a -> None return annotation; then remove the inline type
markers from the reStructuredText docstring so the :param entries only describe
the parameter purpose (e.g., ":param scanner: A component with a .dwellTime,
.translation, .scale."). Keep the same parameter names and preserve existing
descriptions for scanner, detector, and save_images.
---
Outside diff comments:
In `@src/odemis/acq/drift/__init__.py`:
- Around line 53-65: Update AnchoredEstimator.__init__ to use Python type hints
for all parameters (e.g., scanner: Emitter, detector: Detector, region:
Sequence[float] or Tuple[float, float, float, float], dwell_time: float,
max_pixels: int = MAX_PIXELS, follow_drift: bool = True, save_images: bool =
False) and return type None; then replace the inline-typed docstring with
reStructuredText style parameter descriptions (use :param scanner:, :type
scanner:, :param detector:, :type detector:, :param region:, :type region:,
:param dwell_time:, :type dwell_time:, :param max_pixels:, :type max_pixels:,
:param follow_drift:, :type follow_drift:, :param save_images:, :type
save_images:) and short explanatory text for each parameter, keeping the note
about anchor region resizing and follow_drift behavior.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
ℹ️ Review info
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📒 Files selected for processing (3)
plugins/sparc_save_drift_corrector_images.pysrc/odemis/acq/drift/__init__.pysrc/odemis/acq/leech.py
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| class SaveDriftCorrectorImgPlugin(Plugin): | ||
| name = "Save drift corrector images" |
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Add type hints and rST docstrings to the new SaveDriftCorrectorImgPlugin
File: plugins/sparc_save_drift_corrector_images.py
SaveDriftCorrectorImgPlugin(lines 30-31) is missing a class docstring.__init__(self, microscope, main_app)(lines 36-37) is missing type hints for parameters/return type and has no docstring._save_drift_corrector_images(self, menu_item)(lines 54-62) is missing type hints formenu_itemand the return type (it already has a docstring).
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@plugins/sparc_save_drift_corrector_images.py` around lines 30 - 31, The
SaveDriftCorrectorImgPlugin class lacks a class rST docstring and its methods
lack type hints/docstrings; add an rST-style class docstring to
SaveDriftCorrectorImgPlugin describing its purpose, then update __init(self,
microscope, main_app) to include proper type hints for microscope and main_app
(and -> None) and add a short rST docstring describing parameters, types, and
return; also add type hints to _save_drift_corrector_images(self, menu_item)
(typing for menu_item and -> None) and ensure its existing docstring is
converted/expanded to rST param/return sections. Reference the class name
SaveDriftCorrectorImgPlugin and the methods __init__ and
_save_drift_corrector_images when making these changes.
Source: Coding guidelines
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| self._drift_corrector = sparc_acq_tab.tab_data_model.driftCorrector | ||
| self.addMenu("Help/Development/Save drift corrector images", | ||
| self._save_drift_corrector_images, | ||
| item_kind=wx.ITEM_CHECK, | ||
| pass_menu_item=True) |
There was a problem hiding this comment.
Guard against None drift corrector before wiring the menu callback.
self._drift_corrector is used unconditionally in the callback. If sparc_acq_tab.tab_data_model.driftCorrector is still None at plugin init time, menu interaction will raise at runtime.
Suggested patch
self._drift_corrector = sparc_acq_tab.tab_data_model.driftCorrector
+ if self._drift_corrector is None:
+ logging.debug("Not loading save drift corrector images tool since drift corrector is not initialized.")
+ return
self.addMenu("Help/Development/Save drift corrector images",
self._save_drift_corrector_images,
item_kind=wx.ITEM_CHECK,
pass_menu_item=True)Also applies to: 54-62
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@plugins/sparc_save_drift_corrector_images.py` around lines 48 - 52, The menu
callback is wired even if sparc_acq_tab.tab_data_model.driftCorrector may be
None, causing runtime errors when _save_drift_corrector_images uses
self._drift_corrector; fix by guarding when creating the menu: check
sparc_acq_tab.tab_data_model.driftCorrector and only call addMenu (or disable
the menu item) if it's not None, and in _save_drift_corrector_images defensively
handle a None self._drift_corrector (e.g., show a warning and return) so both
initialization-time None and later changes are safe; update references to
self._drift_corrector, addMenu, _save_drift_corrector_images and the source
sparc_acq_tab.tab_data_model.driftCorrector accordingly.
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| DRIFT_IMAGES_DIR = os.path.join(get_picture_folder(), "Drift Correction images") | ||
|
|
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Use pathlib.Path for the drift-image output path construction.
In src/odemis/acq/drift/__init__.py, replace the os.path/os.makedirs usage at lines 39, 75, and 158 with pathlib.Path (including passing str(filename) to cv2.imwrite).
Suggested patch
-import os
+from pathlib import Path
@@
-DRIFT_IMAGES_DIR = os.path.join(get_picture_folder(), "Drift Correction images")
+DRIFT_IMAGES_DIR = Path(get_picture_folder()) / "Drift Correction images"
@@
- os.makedirs(DRIFT_IMAGES_DIR, exist_ok=True)
+ DRIFT_IMAGES_DIR.mkdir(parents=True, exist_ok=True)
@@
- filename = os.path.join(DRIFT_IMAGES_DIR, f"drift_{self._session_id}_{self._image_counter:05d}.tif")
+ filename = DRIFT_IMAGES_DIR / f"drift_{self._session_id}_{self._image_counter:05d}.tif"
@@
- success = cv2.imwrite(filename, data)
+ success = cv2.imwrite(str(filename), data)🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@src/odemis/acq/drift/__init__.py` around lines 39 - 40, Replace os.path and
os.makedirs usage for drift image paths with pathlib.Path: construct
DRIFT_IMAGES_DIR using Path(get_picture_folder()) / "Drift Correction images",
ensure directories are created via Path.mkdir(parents=True, exist_ok=True) where
the code currently calls os.makedirs, and update any image write calls
(cv2.imwrite) to pass str(filename) when filename is a Path object; search for
DRIFT_IMAGES_DIR, get_picture_folder(), and cv2.imwrite in this module to locate
the three spots to change.
Source: Coding guidelines
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| def __init__(self, scanner, detector, save_images=False): | ||
| """ | ||
| :param scanner: (Emitter) A component with a .dwellTime, .translation, .scale. | ||
| :param detector: (Detector) To acquire the signal. | ||
| :param save_images: (bool) Whether to save drift corrector images. | ||
| """ |
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path = pathlib.Path("src/odemis/acq/leech.py")
text = path.read_text(encoding="utf-8")
# crude extraction: find class AnchorDriftCorrector then next def __init__ block docstring until next def/class at same indent
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if re.search(r"^ {4}(def|class)\s+\w+", lines[k]):
end=k
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PY
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Type-annotate AnchorDriftCorrector.__init__ and fix its reStructuredText docstring parameter formatting.
In src/odemis/acq/leech.py (lines 144-149), AnchorDriftCorrector.__init__(self, scanner, detector, save_images=False) is untyped, and the docstring embeds explicit type markers in :param entries (e.g., (Emitter), (Detector), (bool)). Add Python type hints for parameters (and -> None) and adjust :param text to follow the repo docstring rule (no type info in the docstring).
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@src/odemis/acq/leech.py` around lines 144 - 149, Update
AnchorDriftCorrector.__init__ to use Python type hints: annotate parameters as
scanner: Emitter, detector: Detector, save_images: bool = False and add a ->
None return annotation; then remove the inline type markers from the
reStructuredText docstring so the :param entries only describe the parameter
purpose (e.g., ":param scanner: A component with a .dwellTime, .translation,
.scale."). Keep the same parameter names and preserve existing descriptions for
scanner, detector, and save_images.
Source: Coding guidelines
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| self.save_images = save_images | ||
|
|
There was a problem hiding this comment.
Runtime menu toggles won’t affect the active estimator instance.
save_images is copied into AnchoredEstimator only in series_start(). If the plugin toggles self.save_images during an ongoing series, self._dc_estimator.acquire() still uses the old flag, so behavior won’t change until a new series starts.
Implementation direction
class AnchorDriftCorrector(LeechAcquirer):
@@
def next(self, das):
@@
+ # Keep estimator behavior in sync with runtime UI toggle.
+ if self._dc_estimator is not None and self._dc_estimator._save_images != self.save_images:
+ self._dc_estimator._save_images = self.save_imagesA cleaner variant is adding a public setter on AnchoredEstimator (instead of touching a private field) and calling it here.
Also applies to: 282-287, 347-349
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@src/odemis/acq/leech.py` around lines 155 - 156, The issue: runtime changes
to the plugin's save_images flag are not propagated to the active
AnchoredEstimator because the value is only copied in series_start(); fix by
adding a public setter on AnchoredEstimator (e.g., set_save_images or
update_save_images) and call that setter wherever the code currently assigns
self.save_images into the estimator (notably in series_start() and the other
similar locations around where save_images is copied), rather than directly
mutating a private field; ensure AnchoredEstimator.acquire() reads the
public/internal field the setter updates so toggles take effect immediately.
There was a problem hiding this comment.
Pull request overview
This PR adds an (optional) debug/development capability to persist the anchor ROI frames used by drift correction, so they can be analyzed offline (e.g., autocorrelation).
Changes:
- Adds a
save_imagesflag toAnchorDriftCorrectorand forwards it intodrift.AnchoredEstimator. - Implements image writing in
AnchoredEstimator.acquire()to save each drift-region scan as a TIFF. - Adds a SPARC GUI development plugin to toggle this behavior from the menu.
Reviewed changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 6 comments.
| File | Description |
|---|---|
| src/odemis/acq/leech.py | Adds a save_images option on the drift-corrector leech and passes it into the drift estimator. |
| src/odemis/acq/drift/init.py | Adds optional on-disk saving of anchor ROI frames during drift acquisition. |
| plugins/sparc_save_drift_corrector_images.py | New GUI plugin providing a checkable menu item to enable/disable saving. |
Comments suppressed due to low confidence (1)
src/odemis/acq/drift/init.py:168
- The comment says “we only save the 1st, 2nd and last two images”, but with
save_images=Truethe code now saves every acquired drift image to disk. Please update this comment to reflect the current behavior (the limiting logic below only applies toself.raw).
# TODO: allow to record just every Nth image, and separately record the
# drift after every measurement
# In the mean time, we only save the 1st, 2nd and last two images
if len(self.raw) > 2:
| MIN_RESOLUTION = (20, 20) # sometimes 8x8 works, but it's not reliable enough | ||
| MAX_PIXELS = 128 ** 2 # px | ||
|
|
||
| DRIFT_IMAGES_DIR = os.path.join(get_picture_folder(), "Drift Correction images") |
Contributor
There was a problem hiding this comment.
@nandishjpatel can you look at this comment. You could also leave it completely up to the caller/plugin and add drift_images_dir as an argument to the AnchoredEstimator class
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| self._save_images = save_images | ||
| self._session_id = datetime.datetime.now().strftime("%Y%m%d_%H%M%S") | ||
| self._image_counter = 0 | ||
|
|
||
| if self._save_images: | ||
| os.makedirs(DRIFT_IMAGES_DIR, exist_ok=True) |
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| # Save all the drift region scans for offline autocorrelation purposes | ||
| if self._save_images: | ||
| filename = os.path.join(DRIFT_IMAGES_DIR, f"drift_{self._session_id}_{self._image_counter:05d}.tif") | ||
| self._image_counter += 1 | ||
|
|
||
| success = cv2.imwrite(filename, data) | ||
| if not success: | ||
| logging.warning("Failed to save drift image %s", filename) |
| self._detector = detector | ||
| self._dc_estimator = None | ||
| self._period_acq = None # number of acq left until next drift correction is performed | ||
| self.save_images = save_images |
| self.roi.value, | ||
| self.dwellTime.value) | ||
| self.dwellTime.value, | ||
| save_images=self.save_images) |
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| if checked: | ||
| self._drift_corrector.save_images = True | ||
| logging.debug("Save drift corrector images checked, will acquire drift corrector images") | ||
| else: | ||
| self._drift_corrector.save_images = False | ||
| logging.debug("Save drift corrector images unchecked, will not acquire drift corrector images") |
tepals
requested changes
Jun 11, 2026
| MIN_RESOLUTION = (20, 20) # sometimes 8x8 works, but it's not reliable enough | ||
| MAX_PIXELS = 128 ** 2 # px | ||
|
|
||
| DRIFT_IMAGES_DIR = os.path.join(get_picture_folder(), "Drift Correction images") |
Contributor
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@nandishjpatel can you look at this comment. You could also leave it completely up to the caller/plugin and add drift_images_dir as an argument to the AnchoredEstimator class
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