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

Send more data back from smart scan to enable if a zip was created

Browse source
This commit is contained in:
Julian Stirling 2026-07-02 14:40:34 +01:00
parent 1aed597f9c
commit 18e3978134
4 changed files with 78 additions and 15 deletions
Download patch file Download diff file Expand all files Collapse all files

52
src/openflexure_microscope_server/things/smart_scan.py
View file

@ -17,6 +17,7 @@ from typing import (
Any,
Callable,
Concatenate,
Literal,
Mapping,
Optional,
ParamSpec,
@ -52,6 +53,15 @@ AnyModel = Annotated[
]
class LiveScanDetails(BaseModel):
"""Details of ongoing scan used for the UI."""
name: str
stitch_timestamp: Optional[float] = None
image_count: int = 0
scan_phase: Literal["Setup", "Scanning", "Stitching", "Complete"] = "Setup"
class ActiveScanData(scan_directories.BaseScanData):
"""A model for the scan data during an ongoing scan.
@ -277,12 +287,21 @@ class SmartScanThing(OFMThing):
_preview_stitcher: Optional[stitching.PreviewStitcher] = None
_latest_scan_name: Optional[str] = None
_latest_scan_live_details: Optional[LiveScanDetails] = None
@lt.property
def latest_scan_name(self) -> Optional[str]:
"""The name of the last scan to be started."""
return self._latest_scan_name
def latest_scan_live_details(self) -> Optional[LiveScanDetails]:
"""The details of any ongoing scan, or the previous scan if no san ongoing."""
if self._latest_scan_live_details is None:
return None
# Update image count and stitch timestamp if scan is ongoing.
if self._scan_data is not None:
self._latest_scan_live_details.image_count = self._scan_data.image_count
# Use walrus operator to not need to read filesystem timestamp twice
if (stitch_time := self.latest_preview_stitch_time) is not None:
self._latest_scan_live_details.stitch_timestamp = stitch_time
return self._latest_scan_live_details
@lt.action
def sample_scan(self, scan_name: str = "") -> None:
@ -306,7 +325,9 @@ class SmartScanThing(OFMThing):
workflow.check_before_start(scan_name)
self._ongoing_scan = self._scan_dir_manager.new_scan_dir(scan_name)
self._latest_scan_name = self.ongoing_scan.name
self._latest_scan_live_details = LiveScanDetails(
name=self.ongoing_scan.name
)
self._run_scan(workflow)
# Save any final messages.
self._ongoing_scan.save_scan_log(self)
@ -328,6 +349,12 @@ class SmartScanThing(OFMThing):
# Reraise so the action reports as cancelled if stitching is cancelled.
raise e
finally:
# Save some final details but not set to the base model until after
# resetting valued and unlocking just in case somehow pydantic errors.
if self._scan_data is not None:
final_image_count = self._scan_data.image_count
if self._preview_stitcher is not None:
last_timestamp = self.latest_preview_stitch_time
# However the scan finishes, unset all variables and release lock
self._ongoing_scan = None
self._scan_data = None
@ -335,6 +362,11 @@ class SmartScanThing(OFMThing):
# Ensure any PreviewStitcher created cannot be reused.
self._preview_stitcher = None
# Set the final details so they persist until the next scan
self._latest_scan_live_details.image_count = final_image_count
self._latest_scan_live_details.stitch_timestamp = last_timestamp
self._latest_scan_live_details.scan_phase = "Complete"
# Remove any scan folders containing zero images.
self.purge_empty_scans()
@ -449,6 +481,7 @@ class SmartScanThing(OFMThing):
correlation_resize=stitching_settings.correlation_resize,
)
self._latest_scan_live_details.scan_phase = "Scanning"
# This is the main loop of the scan!
self._main_scan_loop(workflow)
self._save_final_scan_data(scan_result="success")
@ -553,6 +586,7 @@ class SmartScanThing(OFMThing):
@_scan_running
def _perform_final_stitch(self) -> None:
"""Update the scan zip and perform final stitch of the data."""
self._latest_scan_live_details.scan_phase = "Stitching"
if self.scan_data.image_count <= 1:
self.logger.info("Not performing a stitch as not enough images captured")
return
@ -676,14 +710,16 @@ class SmartScanThing(OFMThing):
@property
def latest_preview_stitch_path(self) -> Optional[str]:
"""The path of the latest preview stitched image, or None if not available."""
if self.latest_scan_name is None:
if self._latest_scan_live_details is None:
return None
return self._scan_dir_manager.get_file_path_from_img_dir(
scan_name=self.latest_scan_name, filename="preview.jpg", check_exists=True
scan_name=self._latest_scan_live_details.name,
filename="preview.jpg",
check_exists=True,
)
@lt.property
@property
def latest_preview_stitch_time(self) -> Optional[float]:
"""The modification time of the latest preview image, to allow live updating.

2
tests/unit_tests/test_smart_scan.py
View file

@ -92,7 +92,7 @@ def test_initial_properties(entered_smart_scan_thing):
"""
smart_scan_thing = entered_smart_scan_thing
assert smart_scan_thing._scan_dir_manager.base_dir == SCAN_DIR
assert smart_scan_thing.latest_scan_name is None
assert smart_scan_thing.latest_scan_live_details is None
@dataclass

2
webapp/src/components/tabContentComponents/actionTab.vue
View file

@ -134,7 +134,7 @@ export default {
},
},
emits: ["closeTask", "completed", "actionStartedExternally"],
emits: ["closeTask", "completed", "finished", "actionStartedExternally"],
data() {
return {

35
webapp/src/components/tabContentComponents/slideScanContent.vue
View file

@ -39,7 +39,7 @@
<div class="uk-width-1-1 uk-flex uk-flex-center">
<div class="uk-width-2-3">
<action-button
v-if="scanComplete"
v-if="scanComplete && imageCount >= 1"
thing="smart_scan"
action="download_zip"
submit-label="Download ZIP"
@ -51,7 +51,10 @@
/>
</div>
</div>
<div class="uk-margin-left info-headings">
<h3 v-if="scanning" class="uk-margin-left">Scan ID: {{ lastScanName }}</h3>
<h3 v-if="scanning" class="uk-margin-left">Images captured: {{ imageCount }}</h3>
</div>
</template>
</actionTab>
</template>
@ -79,6 +82,8 @@ export default {
taskId: null,
taskUrl: null,
lastStitchedImage: null,
imageCount: null,
scanPhase: null,
scanComplete: false,
scan_name: "",
// This adds the parent name as value for prop streamId
@ -123,6 +128,8 @@ export default {
startScanning(id, url) {
this.lastStitchedImage = null;
this.lastScanName = null;
this.imageCount = 0;
this.scanPhase = null;
this.taskId = id;
this.taskUrl = url;
this.scanComplete = false;
@ -135,17 +142,27 @@ export default {
this.taskId = null;
this.taskUrl = null;
this.lastStitchedImage = null;
this.imageCount = null;
this.scanPhase = null;
this.scanComplete = false;
},
async pollScan() {
if (!this.scanComplete) {
// while the scan is running
let mtime = await this.readThingProperty("smart_scan", "latest_preview_stitch_time", true);
let scanDetails = await this.readThingProperty(
"smart_scan",
"latest_scan_live_details",
true,
);
this.lastScanName = scanDetails.name;
let mtime = scanDetails.stitch_timestamp;
this.imageCount = scanDetails.image_count;
this.scanPhase = scanDetails.scan_phase;
if (mtime !== null) {
this.lastStitchedImage = `${this.baseUri}/smart_scan/latest_preview_stitch.jpg?t=${mtime}`;
}
this.lastScanName = await this.readThingProperty("smart_scan", "latest_scan_name", true);
setTimeout(this.pollScan, 1000); // keep rescheduling until it's stopped
}
},
@ -163,4 +180,14 @@ export default {
};
</script>
<style scoped></style>
<style scoped>
.info-headings h3 {
margin-top: 20px;
margin-bottom: 5px;
}
/* If one heading follows another don't have a large top margin. */
.info-headings h3 + h3 {
margin-top: 5px;
}
</style>