First working interation of ScanWorkflows. Needs a tidy
This commit is contained in:
Julian Stirling
parent
adab5bae24
commit
665622a802
6 changed files with 173 additions and 149 deletions
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@ -8,12 +8,11 @@ import shutil
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import threading
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import zipfile
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from datetime import datetime, timedelta
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from typing import Annotated, Any, Mapping, Optional, Self
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from typing import Any, Mapping, Optional, Self
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from pydantic import (
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BaseModel,
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ConfigDict,
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PlainSerializer,
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ValidationError,
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field_serializer,
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field_validator,
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@ -60,56 +59,20 @@ class StitchingData(BaseModel):
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"""The overlap between adjacent images as a fraction of the image size."""
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def _coerce_lecacy_scan_data(data: dict) -> dict:
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"""Coerce any scan data from before version 2 into the version 2 format."""
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# Before the current version no schema_version was set
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if "schema_version" in data:
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return data
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class BaseScanData(BaseModel):
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"""Data about a scan not including workflow specific data.
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if "correlation_resize" and "overlap" in data:
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correlation_resize = data.pop("correlation_resize")
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# Note we don't pop overlap is a setting for the legacy workflow as well
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# as a stitching setting.
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# This is done because in future workflows the stitching overlap may be a
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# directly set setting or something that is calculated from other settings.
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overlap = data["overlap"]
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data["stitching_settings"] = StitchingData(
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correlation_resize=correlation_resize,
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overlap=overlap,
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)
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else:
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data["stitching_settings"] = None
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For including workflow specific data see also:
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# Add any legacy workflow settings that are found
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legacy_keys = [
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"overlap",
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"max_dist",
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"dx",
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"dy",
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"autofocus_dz",
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"autofocus_on",
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"skip_background",
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]
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workflow_settings = {}
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for key in legacy_keys:
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if key in data:
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workflow_settings[key] = data.pop(key)
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* ActiveScanData which subclasses this including the BaseModel used by the
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ScanWorkflow
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* HistoricScanData which has the workflow specific data loaded as a dictionary.
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data["workflow"] = "Legacy"
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data["workflow_settings"] = workflow_settings
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return data
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# This is a dictionary of a PyDantic model. It allows ScanData to hold arbitrary
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# workflow settings models during a scan.
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AnyModelOrDict = Annotated[
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dict | BaseModel,
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PlainSerializer(lambda v: v.model_dump(), return_type=dict),
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]
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class ScanData(BaseModel):
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"""Data about a scan to be saved to a JSON file in the directory.
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Sepearating historic and active data allows workflows to use any BaseModel for its
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settings, but for the data to be reloaded even if that model has updated or is not
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available. Historic scan data loaded from disk is used for stitching and for
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creating a ScanInfo object for communicating with the UI. These uses are clearly
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typed by this model.
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This serialises into a human readable format where possible with
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@ -153,31 +116,14 @@ class ScanData(BaseModel):
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This should be set with ``set_final_data()`` to ensure duration is set.
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"""
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workflow: str
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"""The class name of the workflow Thing."""
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workflow_settings: AnyModelOrDict
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"""The settings for this workflow."""
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stitching_settings: Optional[StitchingData]
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"""The data needed to stitch a scan.
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Set to None for types of scan that cannot be stitched.
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"""
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def set_final_data(self, result: str) -> None:
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"""Set the final data for the scan, scan duration is automatically calculated.
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:param result: A string describing the result.
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"""
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self.duration = datetime.now() - self.start_time
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self.scan_result = result
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@model_validator(mode="before")
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@classmethod
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def coerce_legacy(cls, data: dict) -> dict:
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"""Coerce any legacy data."""
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return _coerce_lecacy_scan_data(data)
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workflow: str
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"""The class name of the workflow Thing."""
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@model_validator(mode="after")
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def validate_schema_version(self) -> Self:
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@ -238,6 +184,53 @@ class ScanData(BaseModel):
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return "Unknown" if value is None else value
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class HistoricScanData(BaseScanData):
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workflow_settings: dict
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"""A dictionary of the settings for the workflow that was used workflow."""
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@model_validator(mode="before")
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@classmethod
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def coerce_legacy(cls, data: dict) -> dict:
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"""Coerce any legacy data."""
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r"""Coerce any scan data from before version 2 into the version 2 format."""
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# Before the current version no schema_version was set
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if "schema_version" in data:
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return data
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if "correlation_resize" and "overlap" in data:
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correlation_resize = data.pop("correlation_resize")
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# Note we don't pop overlap is a setting for the legacy workflow as well
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# as a stitching setting.
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# This is done because in future workflows the stitching overlap may be a
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# directly set setting or something that is calculated from other settings.
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overlap = data["overlap"]
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data["stitching_settings"] = StitchingData(
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correlation_resize=correlation_resize,
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overlap=overlap,
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)
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else:
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data["stitching_settings"] = None
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# Add any legacy workflow settings that are found
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legacy_keys = [
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"overlap",
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"max_dist",
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"dx",
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"dy",
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"autofocus_dz",
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"autofocus_on",
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"skip_background",
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]
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workflow_settings = {}
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for key in legacy_keys:
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if key in data:
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workflow_settings[key] = data.pop(key)
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data["workflow"] = "Legacy"
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data["workflow_settings"] = workflow_settings
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return data
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class ScanDirectoryManager:
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"""A class for managing interactions with scan directories."""
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@ -565,10 +558,10 @@ class ScanDirectory:
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except (json.decoder.JSONDecodeError, IOError):
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return None
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def get_scan_data(self) -> Optional[ScanData]:
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"""Return the scan data from the json file as a ScanData model.
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def get_scan_data(self) -> Optional[HistoricScanData]:
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"""Return the scan data from the json file as a HistoricScanData model.
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:return: The data as a ScanData model or None if it couldn't be loaded or
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:return: The data as a HistoricScanData model or None if it couldn't be loaded or
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valdiated.
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"""
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data_dict = self.get_scan_data_dict()
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@ -576,7 +569,7 @@ class ScanDirectory:
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LOGGER.warning(f"Could not load scan data for {self.name}.")
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return None
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try:
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return ScanData(**data_dict)
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return HistoricScanData(**data_dict)
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except ValidationError:
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LOGGER.warning(f"Could not validate scan data for {self.name}.")
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return None
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@ -627,7 +620,7 @@ class ScanDirectory:
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files.append(os.path.relpath(full_path, self.dir_path))
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return files
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def save_scan_data(self, scan_data: ScanData) -> None:
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def save_scan_data(self, scan_data: BaseScanData) -> None:
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"""Save the scan data for this scan to disk."""
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if self.scan_data_path is None:
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raise FileNotFoundError(
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@ -218,9 +218,11 @@ class FinalStitcher(BaseStitcher):
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if not known enter None. A value will be chosen from the scan_data_dict, or
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set to a default value if no value is available in the scan_data.
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:param stitch_tiff: Whether to stitch a pyramidal TIFF.
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:param scan_data_dict: The ScanData for this scan as a dictionary. This is used
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to read/calculate overlap and correlation_resize if they are not provided.
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:param scan_data_dict: The HistoricScanData for this scan as a dictionary. This
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is used to read/calculate overlap and correlation_resize if they are not
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provided.
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"""
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# TODO ^fix the above historic data
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self.logger = logger
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overlap, correlation_resize = self._process_inputs(
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overlap=overlap,
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@ -1,4 +1,11 @@
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from typing import Mapping, Optional
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from __future__ import annotations
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from typing import (
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Generic,
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Mapping,
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Optional,
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TypeVar,
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)
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from pydantic import BaseModel
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@ -16,16 +23,21 @@ from openflexure_microscope_server.things.autofocus import (
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from openflexure_microscope_server.things.background_detect import (
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ChannelDeviationLUV,
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)
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from openflexure_microscope_server.things.camera import BaseCamera
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from openflexure_microscope_server.things.camera_stage_mapping import CameraStageMapper
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SettingModelType = TypeVar("SettingModelType", bound=BaseModel)
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class ScanWorkflow(lt.Thing):
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class ScanWorkflow(Generic[SettingModelType], lt.Thing):
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"""A base class for all Scanworkflows.
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Scan workflows set the behaviour of a scan, inclduing the background detection,
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scan planning, aquisition routine.
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"""
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_settings_model: type[SettingModelType]
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# All workdlows must have a set class for scan planning
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_planner_cls: type[ScanPlanner]
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@ -50,11 +62,13 @@ class ScanWorkflow(lt.Thing):
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"Each specific ScanWorkflow must implement a ready property."
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)
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# TODO should be a model
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def all_settings(self, images_dir: str) -> tuple[dict, Optional[StitchingData]]:
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def all_settings(
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self, images_dir: str
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) -> tuple[SettingModelType, Optional[StitchingData]]:
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"""Return the scan settings and the stitching settings.
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- The specific settings for this scan workflow are returned as a dict.
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- The specific settings for this scan workflow are returned as a Base Model of
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the type set when defining the class.
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- Stitiching settings are returned either as a StitchingData object or None
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is returned if it is not possible to stitch the scan.
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"""
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@ -62,18 +76,20 @@ class ScanWorkflow(lt.Thing):
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"Each specific ScanWorkflow must implement a `all_settings`. method."
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)
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def pre_scan_routine(self, settings: dict) -> None:
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def pre_scan_routine(self, settings: SettingModelType) -> None:
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raise NotImplementedError(
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"Each specific ScanWorkflow must implement a pre-scan routine."
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)
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def new_scan_planner(self, settings: dict, position: Mapping[str, int]) -> None:
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def new_scan_planner(
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self, settings: SettingModelType, position: Mapping[str, int]
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) -> ScanPlanner:
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raise NotImplementedError(
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"Each specific ScanWorkflow must implement a ``new_scan_planner`` method."
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)
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def aquisition_routine(
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self, settings: dict, xyz_pos: tuple[int, int, int]
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self, settings: SettingModelType, xyz_pos: tuple[int, int, int]
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) -> tuple[bool, Optional[int]]:
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raise NotImplementedError(
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"Each specific ScanWorkflow must implement an aquisition routine"
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@ -83,8 +99,8 @@ class ScanWorkflow(lt.Thing):
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class HistoScanSettingsModel(BaseModel):
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"""The settings including needed for running a HistoScan.
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This includes settings caluclated when starting. This will be serialised in
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ScanData.
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This includes settings caluclated when starting. This will be held by smart scan
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during a scan and serialised to disk.
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"""
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overlap: float
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@ -92,14 +108,16 @@ class HistoScanSettingsModel(BaseModel):
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dx: int
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dy: int
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skip_background: bool
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smart_stack_prarams: SmartStackParams
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smart_stack_params: SmartStackParams
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class HistoScanWorkflow(ScanWorkflow):
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class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
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_settings_model = HistoScanSettingsModel
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_planner_cls: type[ScanPlanner] = SmartSpiral
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# Thing Slots
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_background_detector: ChannelDeviationLUV = lt.thing_slot()
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_cam: BaseCamera = lt.thing_slot()
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_csm: CameraStageMapper = lt.thing_slot()
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_planner_cls: type[ScanPlanner] = SmartSpiral
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_autofocus: AutofocusThing = lt.thing_slot()
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# Scan settings
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@ -147,7 +165,8 @@ class HistoScanWorkflow(ScanWorkflow):
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* 200 for 20x
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"""
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# noqa, scan_name is unused but is needed for equivalence with other workflows.
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# The noqa statment is because scan_name is unused but is needed for equivalence
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# with other workflows that may want to validate the scan name.
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def check_before_start(self, scan_name: str) -> None: # noqa: ARG002
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"""Before starting a scan, check that background and camera-stage-mapping are set.
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@ -191,12 +210,13 @@ class HistoScanWorkflow(ScanWorkflow):
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correlation_resize=STITCHING_RESOLUTION[0] / self.save_resolution[0],
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)
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dx, dy = self._calc_displacement_from_test_image(self.overlap)
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dx, dy = self._calc_displacement_from_overlap(self.overlap)
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self.logger.info(
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f"Based on an overlap of {self.overlap}, the stage will make steps of "
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f"{dx}, {dy}"
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)
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# TODO: set a min on the property
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autofocus_dz = self.autofocus_dz
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if autofocus_dz == 0:
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self.logger.info("Running scan without autofocus")
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@ -207,7 +227,7 @@ class HistoScanWorkflow(ScanWorkflow):
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)
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autofocus_dz = 0
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smart_stack_prarams = self.create_smart_stack_params(
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smart_stack_params = self.create_smart_stack_params(
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images_dir=images_dir,
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autofocus_dz=autofocus_dz,
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save_resolution=self.save_resolution,
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@ -219,9 +239,8 @@ class HistoScanWorkflow(ScanWorkflow):
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dx=dx,
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dy=dy,
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skip_background=self.skip_background,
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smart_stack_prarams=smart_stack_prarams,
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smart_stack_params=smart_stack_params,
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)
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autofocus_dz = (autofocus_dz,)
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return scan_settings, stitching_settings
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@ -233,7 +252,9 @@ class HistoScanWorkflow(ScanWorkflow):
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:returns: (dx, dy) - the x and y displacements in steps
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"""
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csm_image_res = [int(i) for i in self._csm.image_resolution]
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csm_image_res = self._csm.image_resolution
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if csm_image_res is None:
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raise RuntimeError("CSM not set. Scan shouldn't have progresses this far.")
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# Calculate displacements in image coordinates
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dx_img = csm_image_res[1] * (1 - overlap)
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@ -320,11 +341,13 @@ class HistoScanWorkflow(ScanWorkflow):
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)
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def pre_scan_routine(self, settings: HistoScanSettingsModel) -> None:
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self._autofocus.looping_autofocus(dz=settings.autofocus_dz, start="centre")
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self._autofocus.looping_autofocus(
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dz=settings.smart_stack_params.autofocus_dz, start="centre"
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)
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def new_scan_planner(
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self, settings: HistoScanSettingsModel, position: Mapping[str, int]
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) -> None:
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) -> ScanPlanner:
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# The initial plan for the scan should be a single x,y position. All future
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# moves will be planned around this point. In future, route planner could
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# have multiple starting positions, each of which will be visited before the
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@ -349,7 +372,11 @@ class HistoScanWorkflow(ScanWorkflow):
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"""
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# If skipping background, take an image to check if current field of view is background
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if settings.skip_background:
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capture_image, bg_message = self._cam.image_is_sample()
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image_array = self._cam.grab_as_array(stream_name="lores")
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capture_image, bg_message = self._background_detector.image_is_sample(
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image_array
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)
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del image_array
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if not capture_image:
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msg = f"Skipping {xyz_pos} as it is {bg_message}."
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@ -358,7 +385,8 @@ class HistoScanWorkflow(ScanWorkflow):
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save_on_failure = settings.skip_background
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focused, focused_height = self._autofocus.run_smart_stack(
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focus_height: Optional[int]
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focused, focus_height = self._autofocus.run_smart_stack(
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stack_parameters=settings.smart_stack_params,
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save_on_failure=save_on_failure,
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)
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@ -368,6 +396,6 @@ class HistoScanWorkflow(ScanWorkflow):
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# run_smart_stage always returns a focus height for the sharpest image even
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# if it failed to find a good focus. Set to None if not focussed.
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if not focused:
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focused_height = None
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focus_height = None
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return imaged, focused_height
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return imaged, focus_height
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|
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@ -13,6 +13,7 @@ import time
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from datetime import datetime
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from subprocess import SubprocessError
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from typing import (
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Annotated,
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Any,
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Callable,
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Concatenate,
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@ -24,16 +25,14 @@ from typing import (
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from fastapi import HTTPException
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from fastapi.responses import FileResponse
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from pydantic import BaseModel
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from pydantic import BaseModel, PlainSerializer
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import labthings_fastapi as lt
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from openflexure_microscope_server import scan_directories, stitching
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# Things
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from .autofocus import AutofocusThing, StackParams
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from .camera import BaseCamera
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from .camera_stage_mapping import CameraStageMapper
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from .scan_workflows import HistoScanWorkflow, ScanWorkflow
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from .stage import BaseStage
|
||||
|
||||
|
|
@ -41,6 +40,26 @@ T = TypeVar("T")
|
|||
P = ParamSpec("P")
|
||||
|
||||
|
||||
# This allows ActiveScanData to hold arbitrary workflow settings models during a scan.
|
||||
AnyModel = Annotated[
|
||||
BaseModel,
|
||||
PlainSerializer(lambda value: value.model_dump(), return_type=dict),
|
||||
]
|
||||
|
||||
|
||||
class ActiveScanData(scan_directories.BaseScanData):
|
||||
workflow_settings: AnyModel
|
||||
"""The settings for the ongoing workflow."""
|
||||
|
||||
def set_final_data(self, result: str) -> None:
|
||||
"""Set the final data for the scan, scan duration is automatically calculated.
|
||||
|
||||
:param result: A string describing the result.
|
||||
"""
|
||||
self.duration = datetime.now() - self.start_time
|
||||
self.scan_result = result
|
||||
|
||||
|
||||
class ScanListInfo(BaseModel):
|
||||
"""The information to be sent to the Scan List tab."""
|
||||
|
||||
|
|
@ -99,9 +118,7 @@ class SmartScanThing(lt.Thing):
|
|||
past scans.
|
||||
"""
|
||||
|
||||
_autofocus: AutofocusThing = lt.thing_slot()
|
||||
_cam: BaseCamera = lt.thing_slot()
|
||||
_csm: CameraStageMapper = lt.thing_slot()
|
||||
_stage: BaseStage = lt.thing_slot()
|
||||
_workflow: HistoScanWorkflow = lt.thing_slot()
|
||||
|
||||
|
|
@ -118,19 +135,6 @@ class SmartScanThing(lt.Thing):
|
|||
self._scan_dir_manager = scan_directories.ScanDirectoryManager(scans_folder)
|
||||
self._scan_lock = threading.Lock()
|
||||
|
||||
# Variables set by the scan
|
||||
_stack_params: Optional[StackParams] = None
|
||||
|
||||
@property
|
||||
def stack_params(self) -> StackParams:
|
||||
"""The parameters for z-stacking during the onging scan.
|
||||
|
||||
Only read this property is a scan is ongoing or it will raise an error.
|
||||
"""
|
||||
if self._stack_params is None:
|
||||
raise RuntimeError("Cannot get stack parameters as they are not set.")
|
||||
return self._stack_params
|
||||
|
||||
_ongoing_scan: Optional[scan_directories.ScanDirectory] = None
|
||||
|
||||
@property
|
||||
|
|
@ -143,11 +147,11 @@ class SmartScanThing(lt.Thing):
|
|||
raise ScanNotRunningError("Cannot get ongoing scan if scan is not running.")
|
||||
return self._ongoing_scan
|
||||
|
||||
_scan_data: Optional[scan_directories.ScanData] = None
|
||||
_scan_data: Optional[ActiveScanData] = None
|
||||
|
||||
@property
|
||||
def scan_data(self) -> scan_directories.ScanData:
|
||||
"""The ScanData object jolding information about the of the ongoing scan.
|
||||
def scan_data(self) -> ActiveScanData:
|
||||
"""The ActiveScanData object holding information about the of the ongoing scan.
|
||||
|
||||
Only read this property is a scan is ongoing or it will raise an error.
|
||||
"""
|
||||
|
|
@ -157,18 +161,6 @@ class SmartScanThing(lt.Thing):
|
|||
|
||||
_preview_stitcher: Optional[stitching.PreviewStitcher] = None
|
||||
|
||||
@property
|
||||
def preview_stitcher(self) -> stitching.PreviewStitcher:
|
||||
"""The PreviewStitcher object for stitching live previews.
|
||||
|
||||
Only read this property is a scan is ongoing or it will raise an error.
|
||||
"""
|
||||
if self._preview_stitcher is None:
|
||||
raise ScanNotRunningError(
|
||||
"No preview stitcher agailable as scan is not running."
|
||||
)
|
||||
return self._preview_stitcher
|
||||
|
||||
_latest_scan_name: Optional[str] = None
|
||||
|
||||
@lt.property
|
||||
|
|
@ -218,7 +210,6 @@ class SmartScanThing(lt.Thing):
|
|||
self._scan_lock.release()
|
||||
# Ensure any PreviewStitcher created cannot be reused.
|
||||
self._preview_stitcher = None
|
||||
self._stack_params = None
|
||||
|
||||
# Remove any scan folders containing zero images.
|
||||
self.purge_empty_scans()
|
||||
|
|
@ -248,7 +239,7 @@ class SmartScanThing(lt.Thing):
|
|||
return (next_point[0], next_point[1], z_estimate)
|
||||
|
||||
@_scan_running
|
||||
def _collect_scan_data(self, workflow: ScanWorkflow) -> scan_directories.ScanData:
|
||||
def _collect_scan_data(self, workflow: ScanWorkflow) -> ActiveScanData:
|
||||
"""Collect and return the data for this scan so it cannot be changed mid-scan."""
|
||||
# Record starting position so it can be returned to at end of scan.
|
||||
starting_position = self._stage.position
|
||||
|
|
@ -266,7 +257,7 @@ class SmartScanThing(lt.Thing):
|
|||
auto_stitch = self.stitch_automatically and stitching_settings is not None
|
||||
|
||||
# Fix scan parameters in case UI is updated during scan.
|
||||
return scan_directories.ScanData(
|
||||
return ActiveScanData(
|
||||
scan_name=self.ongoing_scan.name,
|
||||
starting_position=starting_position,
|
||||
start_time=datetime.now(),
|
||||
|
|
@ -290,13 +281,13 @@ class SmartScanThing(lt.Thing):
|
|||
@_scan_running
|
||||
def _manage_stitching_threads(self) -> None:
|
||||
"""Manage the stitching threads, starting them if needed and not already running."""
|
||||
if self.scan_data.stitching_settings is None:
|
||||
if self._preview_stitcher is None:
|
||||
# This scan can't stitch.
|
||||
return
|
||||
# Assume 4 images means at least one offset in x and y, making the stitching
|
||||
# well constrained.
|
||||
if self.scan_data.image_count > 3 and not self.preview_stitcher.running:
|
||||
self.preview_stitcher.start()
|
||||
if self.scan_data.image_count > 3 and not self._preview_stitcher.running:
|
||||
self._preview_stitcher.start()
|
||||
|
||||
@_scan_running
|
||||
def _run_scan(self, workflow: ScanWorkflow) -> None:
|
||||
|
|
@ -309,7 +300,8 @@ class SmartScanThing(lt.Thing):
|
|||
try:
|
||||
self._cam.start_streaming(main_resolution=(3280, 2464))
|
||||
self._scan_data = self._collect_scan_data(workflow)
|
||||
workflow.pre_scan_routine(self._scan_data)
|
||||
|
||||
workflow.pre_scan_routine(self._scan_data.workflow_settings)
|
||||
self.ongoing_scan.save_scan_data(self._scan_data)
|
||||
images_dir = self.ongoing_scan.images_dir
|
||||
# Type narrowing
|
||||
|
|
@ -317,11 +309,16 @@ class SmartScanThing(lt.Thing):
|
|||
raise RuntimeError(
|
||||
"Couldn't run scan, images directory was not created."
|
||||
)
|
||||
self._preview_stitcher = stitching.PreviewStitcher(
|
||||
images_dir,
|
||||
overlap=self.scan_data.overlap,
|
||||
correlation_resize=self.scan_data.correlation_resize,
|
||||
)
|
||||
|
||||
# If stitching settings are None then this type of scan can't be stitched
|
||||
if self.scan_data.stitching_settings is not None:
|
||||
# Settings exist, so create preview stitcher
|
||||
stitching_settings = self.scan_data.stitching_settings
|
||||
self._preview_stitcher = stitching.PreviewStitcher(
|
||||
images_dir,
|
||||
overlap=stitching_settings.overlap,
|
||||
correlation_resize=stitching_settings.correlation_resize,
|
||||
)
|
||||
|
||||
# This is the main loop of the scan!
|
||||
self._main_scan_loop(workflow)
|
||||
|
|
@ -386,6 +383,7 @@ class SmartScanThing(lt.Thing):
|
|||
if focus_height is None:
|
||||
focused = False
|
||||
else:
|
||||
focused = True
|
||||
current_pos_xyz = (new_pos_xyz[0], new_pos_xyz[1], focus_height)
|
||||
|
||||
route_planner.mark_location_visited(
|
||||
|
|
@ -426,17 +424,18 @@ class SmartScanThing(lt.Thing):
|
|||
|
||||
self.logger.info("Waiting for background processes to finish...")
|
||||
|
||||
# Actually check the sticher exists rather than using self.preview_sticher as
|
||||
# Check the sticher exists rather than using self.preview_sticher as
|
||||
# this method can be called during exception handling.
|
||||
if self._preview_stitcher is not None:
|
||||
self._preview_stitcher.wait()
|
||||
|
||||
if self.scan_data.stitch_automatically:
|
||||
stitching_settings = self.scan_data.stitching_settings
|
||||
if self.scan_data.stitch_automatically and stitching_settings is not None:
|
||||
self.logger.info("Stitching final image (may take some time)...")
|
||||
self.stitch_scan(
|
||||
scan_name=self.ongoing_scan.name,
|
||||
correlation_resize=self.scan_data.correlation_resize,
|
||||
overlap=self.scan_data.overlap,
|
||||
correlation_resize=stitching_settings.correlation_resize,
|
||||
overlap=stitching_settings.overlap,
|
||||
)
|
||||
|
||||
@lt.endpoint(
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue