rahix/openflexure-microscope-server
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Get UI working for background detector things

Browse source
This commit is contained in:
Julian Stirling 2026-01-13 19:05:24 +00:00
parent 44860bf777
commit 3e8874188e
5 changed files with 70 additions and 38 deletions
Download patch file Download diff file Expand all files Collapse all files

42
src/openflexure_microscope_server/things/background_detect.py
View file

@ -13,6 +13,8 @@ from pydantic import BaseModel
import labthings_fastapi as lt
from openflexure_microscope_server.ui import PropertyControl, property_control_for
SettingsType = TypeVar("SettingsType", bound=BaseModel)
BackgroundType = TypeVar("BackgroundType", bound=BaseModel)
@ -32,6 +34,8 @@ class ChannelBlankError(RuntimeError):
class BackgroundDetectAlgorithm(lt.Thing):
"""The base class for defining background detect algorithms."""
display_name: str = lt.property(default="Base Detector", readonly=True)
@lt.property
def ready(self) -> bool:
"""Whether the background detector is ready."""
@ -59,6 +63,13 @@ class BackgroundDetectAlgorithm(lt.Thing):
"Each background detect algorithm must implement an set_background method."
)
@lt.property
def settings_ui(self) -> list[PropertyControl]:
"""A list of PropertyControl objects to create the settings in the UI."""
raise NotImplementedError(
"Each background detect algorithm must implement an settings_ui method."
)
class ColourChannelDetectLUV(BackgroundDetectAlgorithm):
"""Compare images with a known background in LUV colourspace.
@ -68,6 +79,8 @@ class ColourChannelDetectLUV(BackgroundDetectAlgorithm):
intuitive way.
"""
display_name: str = lt.property(default="Colour Channel (LUV)", readonly=True)
background_means: Optional[list[float]] = lt.setting(default=None, readonly=True)
"""The mean of each channel in the colourspace."""
background_stds: Optional[list[float]] = lt.setting(default=None, readonly=True)
@ -91,10 +104,20 @@ class ColourChannelDetectLUV(BackgroundDetectAlgorithm):
image to be labeled as containing sample.
"""
@lt.property
def settings_ui(self) -> list[PropertyControl]:
"""A list of PropertyControl objects to create the settings in the UI."""
return [
property_control_for(self, "channel_tolerance", label="Channel Tolerance"),
property_control_for(
self, "min_sample_coverage", label="Sample Coverage Required (%)"
),
]
@lt.property
def ready(self) -> bool:
"""Whether the background detector is ready."""
return not (self.background_means is None or self.background_stds is None)
return self.background_means is not None and self.background_stds is not None
def background_mask(self, image: np.ndarray) -> np.ndarray:
"""Calculate a binary image, showing whether each pixel is background.
@ -180,6 +203,8 @@ class ChannelDeviationLUV(BackgroundDetectAlgorithm):
to the median standard deviation for a grid of background images.
"""
display_name: str = lt.property(default="Channel Deviation (LUV)", readonly=True)
background_stds: Optional[list[float]] = lt.setting(default=None, readonly=True)
"""The standard deviation of each channel in the colourspace."""
@ -203,6 +228,21 @@ class ChannelDeviationLUV(BackgroundDetectAlgorithm):
image to be labeled as containing sample.
"""
@lt.property
def settings_ui(self) -> list[PropertyControl]:
"""A list of PropertyControl objects to create the settings in the UI."""
return [
property_control_for(self, "channel_tolerance", label="Channel Tolerance"),
property_control_for(
self, "min_sample_coverage", label="Sample Coverage Required (%)"
),
]
@lt.property
def ready(self) -> bool:
"""Whether the background detector is ready."""
return self.background_stds is not None
def get_sample_coverage(self, image: np.ndarray) -> float:
"""Return the percentage of the input image that is background.

7
src/openflexure_microscope_server/things/camera/__init__.py
View file

@ -173,6 +173,10 @@ class BaseCamera(lt.Thing):
dictionary in this function. Configuration will be added at a later date.
"""
super().__init__(thing_server_interface)
# Default is never updated but is used if the value set from settings is
# incorrect. In the future a better way to set defaults for thing slot mappings
# would be ideal.
self._default_detector = "bg_channel_deviations_luv"
self._detector_name = "bg_channel_deviations_luv"
def __enter__(self) -> Self:
@ -591,6 +595,9 @@ class BaseCamera(lt.Thing):
@property
def active_detector(self) -> BackgroundDetectAlgorithm:
"""The active background detector instance."""
if self.detector_name not in self.background_detectors:
self.logger.warning(f"No detector named {self.detector_name}")
self.detector_name = self._default_detector
return self.background_detectors[self.detector_name]
@lt.action

2
src/openflexure_microscope_server/things/camera/simulation.py
View file

@ -181,7 +181,7 @@ class SimulatedCamera(BaseCamera):
@lt.property
def calibration_required(self) -> bool:
"""Whether the camera needs calibrating."""
return not self.background_detector_status.ready
return not self.active_detector.ready
def generate_sprites(self) -> None:
"""Generate sprites to populate the image."""

2
src/openflexure_microscope_server/things/smart_scan.py
View file

@ -234,7 +234,7 @@ class SmartScanThing(lt.Thing):
self._csm.assert_calibration()
if self.skip_background:
if not self._cam.background_detector_status.ready:
if not self._cam.active_detector.ready:
raise RuntimeError(
"Background is not set: you need to calibrate background detection."
)

55
webapp/src/components/tabContentComponents/backgroundDetectComponents/paneBackgroundDetect.vue
View file

@ -5,18 +5,13 @@
<li>
<a class="uk-accordion-title" href="#">Configure</a>
<div class="uk-accordion-content">
<h4 v-if="backgroundDetectorName" class="detector-name">
{{ backgroundDetectorName }}
<h4 v-if="backgroundDetectorDisplayName" class="detector-name">
{{ backgroundDetectorDisplayName }}
</h4>
<input-from-schema
v-if="backgroundDetectorStatus"
v-model="backgroundDetectorStatus.settings"
:data-schema="backgroundDetectorStatus.settings_schema"
label=""
:animate="animate"
@requestUpdate="readSettings"
@sendValue="writeSettings"
@animationShown="resetAnimate"
<server-specified-property-control
v-for="(setting, index) in backgroundDetectorSettings"
:key="'detector_setting' + index"
:property-data="setting"
/>
</div>
</li>
@ -51,33 +46,26 @@
<script>
import ActionButton from "../../labThingsComponents/actionButton.vue";
import InputFromSchema from "../../labThingsComponents/inputFromSchema.vue";
import ServerSpecifiedPropertyControl from "../../labThingsComponents/serverSpecifiedPropertyControl.vue";
export default {
components: {
ActionButton,
InputFromSchema,
ServerSpecifiedPropertyControl,
},
data() {
return {
backgroundDetectorStatus: undefined,
ready: false,
backgroundDetectorName: undefined,
backgroundDetectorDisplayName: undefined,
backgroundDetectorSettings: [],
animate: false,
};
},
computed: {
ready() {
const status = this.backgroundDetectorStatus;
return status && status.ready === true;
},
},
async created() {
this.backgroundDetectorStatus = await this.readThingProperty(
"camera",
"background_detector_status",
);
this.readSettings();
},
methods: {
@ -95,18 +83,15 @@ export default {
},
readSettings: async function () {
this.backgroundDetectorName = await this.readThingProperty("camera", "detector_name");
this.backgroundDetectorStatus = await this.readThingProperty(
"camera",
"background_detector_status",
this.ready = await this.readThingProperty(this.backgroundDetectorName, "ready");
this.backgroundDetectorSettings = await this.readThingProperty(
this.backgroundDetectorName,
"settings_ui",
);
this.backgroundDetectorDisplayName = await this.readThingProperty(
this.backgroundDetectorName,
"display_name",
);
},
writeSettings: async function (requestedValue) {
await this.invokeAction("camera", "update_detector_settings", { data: requestedValue });
this.animate = true;
this.readSettings();
},
resetAnimate: function () {
this.animate = false;
},
},
};