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
|
|
@ -13,6 +13,7 @@ import time
|
|||
from datetime import datetime
|
||||
from subprocess import SubprocessError
|
||||
from typing import (
|
||||
Annotated,
|
||||
Any,
|
||||
Callable,
|
||||
Concatenate,
|
||||
|
|
@ -24,16 +25,14 @@ from typing import (
|
|||
|
||||
from fastapi import HTTPException
|
||||
from fastapi.responses import FileResponse
|
||||
from pydantic import BaseModel
|
||||
from pydantic import BaseModel, PlainSerializer
|
||||
|
||||
import labthings_fastapi as lt
|
||||
|
||||
from openflexure_microscope_server import scan_directories, stitching
|
||||
|
||||
# Things
|
||||
from .autofocus import AutofocusThing, StackParams
|
||||
from .camera import BaseCamera
|
||||
from .camera_stage_mapping import CameraStageMapper
|
||||
from .scan_workflows import HistoScanWorkflow, ScanWorkflow
|
||||
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