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Dynamic UI for scan workflows

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This commit is contained in:
Julian Stirling 2026-01-16 12:18:54 +00:00
parent 2a3a54b936
commit 21b779a4a5
4 changed files with 157 additions and 66 deletions
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3
ofm_config_simulation.json
View file

@ -8,7 +8,8 @@
"smart_scan": {
"class": "openflexure_microscope_server.things.smart_scan:SmartScanThing",
"kwargs": {
"scans_folder": "./openflexure/scans/"
"scans_folder": "./openflexure/scans/",
"default_workflow": "histo_scan_workflow"
}
},
"histo_scan_workflow": "openflexure_microscope_server.things.scan_workflows:HistoScanWorkflow",

44
src/openflexure_microscope_server/things/scan_workflows.py
View file

@ -33,6 +33,7 @@ from openflexure_microscope_server.things.background_detect import (
)
from openflexure_microscope_server.things.camera import BaseCamera
from openflexure_microscope_server.things.camera_stage_mapping import CameraStageMapper
from openflexure_microscope_server.ui import PropertyControl, property_control_for
SettingModelType = TypeVar("SettingModelType", bound=BaseModel)
@ -44,6 +45,11 @@ class ScanWorkflow(Generic[SettingModelType], lt.Thing):
scan planning, acquisition routine.
"""
display_name: str = lt.property(default="Base Workflow", readonly=True)
ui_blurb: str = lt.property(
default="If you see this message, something is wrong.", readonly=True
)
_settings_model: type[SettingModelType]
# All workflows must have a set class for scan planning
@ -106,6 +112,13 @@ class ScanWorkflow(Generic[SettingModelType], lt.Thing):
"Each specific ScanWorkflow must implement an acquisition routine"
)
@lt.property
def settings_ui(self) -> list[PropertyControl]:
"""A list of PropertyControl objects to create the settings in the scan tab."""
raise NotImplementedError(
"Each scan workflow must implement a settings_ui method."
)
class HistoScanSettingsModel(BaseModel):
"""The settings for a scan with the HistoScanWorkflow.
@ -129,6 +142,16 @@ class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
the centre position, scanning only where it detects sample.
"""
display_name: str = lt.property(default="Histo Scan", readonly=True)
ui_blurb: str = lt.property(
default=(
"This scan workflow is optimised for scanning H&E stained biopsies. It"
"spirals out from the starting location, scanning only where it detects"
"sample. It also works well for many other flat, well-featured samples."
),
readonly=True,
)
_settings_model = HistoScanSettingsModel
_planner_cls: type[ScanPlanner] = SmartSpiral
# Thing Slots
@ -428,3 +451,24 @@ class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
focus_height = None
return imaged, focus_height
@lt.property
def settings_ui(self) -> list[PropertyControl]:
"""A list of PropertyControl objects to create the settings in the scan tab."""
return [
property_control_for(self, "overlap", label="Image Overlap (0.1-0.7)"),
property_control_for(
self, "skip_background", label="Detect and Skip Empty Fields "
),
property_control_for(
self, "stack_images_to_save", label="Images in Stack to Save"
),
property_control_for(
self,
"stack_min_images_to_test",
label="Minimum number of images to test for focus",
),
property_control_for(self, "stack_dz", label="Stack dz (steps)"),
property_control_for(self, "autofocus_dz", label="Autofocus Range (steps)"),
property_control_for(self, "max_range", label="Maximum Distance (steps)"),
]

47
src/openflexure_microscope_server/things/smart_scan.py
View file

@ -1,8 +1,8 @@
"""The core sample scanning functionality for the OpenFlexure Microscope.
SmartScan provides sample scanning functionality including automatic background
detection (via the ``CameraThing``) and automatic path planning via
`scan_planners`. It manages the directories of past scans via `scan_directories`.
SmartScan provides sample scanning functionality. This functionality can be customised
by different ``ScanWorkflow`` Things which control the path planning and acquisition
routines. It manages the directories of past scans via `scan_directories`.
It also controls external processes for live stitching composite images, and
the creation of the final stitched images.
"""
@ -20,6 +20,7 @@ from typing import (
Mapping,
Optional,
ParamSpec,
Self,
TypeVar,
)
@ -30,10 +31,11 @@ from pydantic import BaseModel, PlainSerializer
import labthings_fastapi as lt
from openflexure_microscope_server import scan_directories, stitching
from openflexure_microscope_server.utilities import coerce_thing_selector
# Things
from .camera import BaseCamera
from .scan_workflows import HistoScanWorkflow, ScanWorkflow
from .scan_workflows import ScanWorkflow
from .stage import BaseStage
T = TypeVar("T")
@ -127,10 +129,13 @@ class SmartScanThing(lt.Thing):
_cam: BaseCamera = lt.thing_slot()
_stage: BaseStage = lt.thing_slot()
_workflow: HistoScanWorkflow = lt.thing_slot()
_all_workflows: Mapping[str, ScanWorkflow] = lt.thing_slot()
def __init__(
self, thing_server_interface: lt.ThingServerInterface, scans_folder: str
self,
thing_server_interface: lt.ThingServerInterface,
scans_folder: str,
default_workflow: Optional[str],
) -> None:
"""Initialise a SmartScanThing saving to and loading from the input directory.
@ -141,6 +146,36 @@ class SmartScanThing(lt.Thing):
super().__init__(thing_server_interface)
self._scan_dir_manager = scan_directories.ScanDirectoryManager(scans_folder)
self._scan_lock = threading.Lock()
self._default_workflow = default_workflow
self._workflow_name: Optional[str] = None
def __enter__(self) -> Self:
"""Open hardware connection when the Thing context manager is opened."""
self._workflow_name = coerce_thing_selector(
thing_mapping=self._all_workflows,
selected=self.workflow_name,
default=self._default_workflow,
)
return self
# Note that the default detector name is set at init. This is over written if
# setting is loaded from disk.
@lt.setting
def workflow_name(self) -> Optional[str]:
"""The name of the scan workflow selector."""
return self._workflow_name
@workflow_name.setter
def _set_workflow_name(self, name: str) -> None:
"""Validate and set workflow_name."""
if name not in self._all_workflows:
self.logger.warning(f"{name} is not a valid scan workflow name.")
self._workflow_name = name
@property
def _workflow(self) -> ScanWorkflow:
"""The active scan workflow object."""
return self._all_workflows[self.workflow_name]
_ongoing_scan: Optional[scan_directories.ScanDirectory] = None

129
webapp/src/components/tabContentComponents/slideScanContent.vue
View file

@ -1,51 +1,32 @@
<template>
<div uk-grid class="uk-height-1-1 uk-margin-remove uk-padding-remove">
<div class="control-component uk-padding-small">
<div v-show="!scanning" class="uk-padding-small">
<div v-show="!scanning" v-observe-visibility="visibilityChanged" class="uk-padding-small">
<ul uk-accordion="multiple: true">
<li>
<a class="uk-accordion-title" href="#">Configure</a>
<a class="uk-accordion-title" href="#">Scan Settings</a>
<div class="uk-accordion-content">
<h4 v-if="workflowDisplayName" class="workflow-name">
{{ workflowDisplayName }}
</h4>
<p class="workflow-blurb">{{ workflowBlurb }}</p>
<div
v-for="(setting, index) in workflowSettings"
:key="'detector_setting' + index"
class="uk-margin"
>
<server-specified-property-control :property-data="setting" />
</div>
</div>
</li>
<li class="uk-open">
<a class="uk-accordion-title" href="#">Stitching Settings</a>
<div class="uk-accordion-content">
<div class="uk-margin">
<propertyControl
thing-name="smart_scan"
property-name="max_range"
label="Maximum Distance (steps)"
/>
</div>
<div class="uk-margin">
<propertyControl
thing-name="smart_scan"
property-name="autofocus_dz"
label="Autofocus Range (steps)"
/>
</div>
<div class="uk-margin">
<propertyControl
thing-name="autofocus"
property-name="stack_dz"
label="Stack dz (steps)"
/>
</div>
<div class="uk-margin">
<propertyControl
thing-name="autofocus"
property-name="stack_images_to_save"
label="Images in Stack to Save"
/>
</div>
<div class="uk-margin">
<propertyControl
thing-name="autofocus"
property-name="stack_min_images_to_test"
label="Minimum number of images to test for focus"
/>
</div>
<div class="uk-margin">
<propertyControl
thing-name="smart_scan"
property-name="overlap"
label="Image Overlap (0-1)"
property-name="stitch_automatically"
label="Automatically Stitch Images Together"
/>
</div>
<div class="uk-margin">
@ -57,25 +38,6 @@
</div>
</div>
</li>
<li class="uk-open">
<a class="uk-accordion-title" href="#">Scan Settings</a>
<div class="uk-accordion-content">
<div class="uk-margin">
<propertyControl
thing-name="smart_scan"
property-name="skip_background"
label="Detect and Skip Empty Fields"
/>
</div>
<div class="uk-margin">
<propertyControl
thing-name="smart_scan"
property-name="stitch_automatically"
label="Automatically Stitch Images Together"
/>
</div>
</div>
</li>
</ul>
<label class="uk-form-label" for="form-stacked-text">Sample ID</label>
<div class="uk-form-controls">
@ -149,6 +111,7 @@
<script>
import streamDisplay from "./streamContent.vue";
import propertyControl from "../labThingsComponents/propertyControl.vue";
import ServerSpecifiedPropertyControl from "../labThingsComponents/serverSpecifiedPropertyControl.vue";
import actionLogDisplay from "../labThingsComponents/actionLogDisplay.vue";
import actionProgressBar from "../labThingsComponents/actionProgressBar.vue";
import MiniStreamDisplay from "../genericComponents/miniStreamDisplay.vue";
@ -160,6 +123,7 @@ export default {
components: {
streamDisplay,
propertyControl,
ServerSpecifiedPropertyControl,
actionLogDisplay,
actionProgressBar,
MiniStreamDisplay,
@ -177,6 +141,10 @@ export default {
log: [],
lastStitchedImage: null,
scan_name: "",
workflowName: undefined,
workflowSettings: [],
workflowDisplayName: undefined,
workflowBlurb: undefined,
};
},
@ -189,12 +157,49 @@ export default {
},
},
async created() {
this.readSettings();
},
methods: {
visibilityChanged(isVisible) {
if (isVisible) {
this.readSettings();
}
},
async readSettings() {
this.workflowName = await this.readThingProperty("smart_scan", "workflow_name");
if (this.workflowName) {
this.ready = await this.readThingProperty(this.workflowName, "ready");
this.workflowSettings = await this.readThingProperty(this.workflowName, "settings_ui");
console.log(this.workflowSettings);
this.workflowDisplayName = await this.readThingProperty(this.workflowName, "display_name");
this.workflowBlurb = await this.readThingProperty(this.workflowName, "ui_blurb");
}
},
onScanError: function (error) {
this.scanRunning = false;
this.modalError(error);
},
correlateCurrentScan() {},
/**
* Transition the UI into "scanning" mode and begin polling for scan updates.
*
* IMPORTANT:
* This method does NOT start a scan on the server.
*
* The <ActionButton> component is responsible for:
* - initiating the scan action on the backend when the user clicks the button
* - detecting and resuming an already-running scan when the page loads
*
* As a result, this method may be invoked in two cases:
* 1. Immediately after the user clicks "Start Smart Scan"
* 2. Automatically on page load if <ActionButton> detects an ongoing scan
*
* This function only:
* - updates local UI state to reflect that scanning is in progress
* - clears any previous preview image
* - starts the polling loop that fetches scan progress and preview images
*/
startScanning() {
this.lastStitchedImage = null;
this.scanning = true;
@ -233,4 +238,10 @@ export default {
.control-component {
width: 33%;
}
.workflow-name {
margin-bottom: 0.5rem;
}
.workflow-blurb {
color: #a2a2a2;
}
</style>