diff --git a/src/openflexure_microscope_server/things/auto_recentre_stage.py b/src/openflexure_microscope_server/things/auto_recentre_stage.py index 45a8cae5..0e46e97b 100644 --- a/src/openflexure_microscope_server/things/auto_recentre_stage.py +++ b/src/openflexure_microscope_server/things/auto_recentre_stage.py @@ -61,7 +61,6 @@ class RecentringThing(Thing): stage.position["z"] - height_min < dz / 5 or height_max - stage.position["z"] < dz / 5 ): - print(heights) attempts += 1 else: repeat = False @@ -111,8 +110,6 @@ class RecentringThing(Thing): focused_pos[direction] = [list(stage.position.values())] moves = +1 - print(centre) - stage.move_absolute(x=centre[0], y=centre[1], z=centre[2]) steps = 0 all_heights = [] diff --git a/src/openflexure_microscope_server/things/settings_manager.py b/src/openflexure_microscope_server/things/settings_manager.py index 24ed8052..7514d7f1 100644 --- a/src/openflexure_microscope_server/things/settings_manager.py +++ b/src/openflexure_microscope_server/things/settings_manager.py @@ -102,6 +102,11 @@ class SettingsManager(Thing): self.thing_settings["microscope_id"] = str(uuid4()) return UUID(self.thing_settings["microscope_id"]) + @thing_property + def hostname(self) -> str: + """The hostname of the microscope, as reported by its operating system.""" + return gethostname() + @thing_action def get_things_state(self, metadata_getter: GetThingStates) -> Mapping: """Metadata summarising the current state of all Things in the server""" @@ -119,7 +124,7 @@ class SettingsManager(Thing): @property def thing_state(self) -> Mapping: state = { - "hostname": gethostname(), + "hostname": self.hostname, "microscope-uuid": str(self.microscope_id), } metadata = self.external_metadata diff --git a/src/openflexure_microscope_server/things/smart_scan.py b/src/openflexure_microscope_server/things/smart_scan.py index d7f11ab4..51a44b44 100644 --- a/src/openflexure_microscope_server/things/smart_scan.py +++ b/src/openflexure_microscope_server/things/smart_scan.py @@ -1,4 +1,5 @@ import shutil +import zipfile import threading from typing import Mapping, Optional import cv2 @@ -312,6 +313,9 @@ DOWNLOADABLE_SCAN_FILES = ( class JPEGBlob(BlobOutput): media_type = "image/jpeg" +class ZipBlob(BlobOutput): + media_type = "application/zip" + class SmartScanThing(Thing): def __init__(self, path_to_openflexure_stitch: str): self._script = path_to_openflexure_stitch @@ -425,6 +429,11 @@ class SmartScanThing(Thing): r = cam.grab_jpeg() arr = np.array(Image.open(r.open())) + if csm.image_resolution is None: + raise RuntimeError( + "Camera-stage mapping is not calibrated. This is required before " + "scans can be carried out." + ) if list(arr.shape[:2]) != [int(i) for i in csm.image_resolution]: logger.error( f"Images are, by default, {arr.shape[:2]}, but the CSM was " @@ -564,9 +573,9 @@ class SmartScanThing(Thing): positions.append(loc[:2]) names.append(name) + if not self.preview_stitch_running(): + self.preview_stitch_start(images_folder) if self.stitch_automatically: - if not self.preview_stitch_running(): - self.preview_stitch_start(images_folder) if not self.correlate_running(): self.correlate_start(images_folder, overlap=overlap) @@ -593,15 +602,17 @@ class SmartScanThing(Thing): except InvocationCancelledError: logger.error("Stopping scan because it was cancelled.") except NotEnoughFreeSpaceError as e: - logger.exception( + logger.error( f"Stopping scan to avoid filling up the disk: {e}", + exc_info=e, ) raise e except Exception as e: - logger.exception( + logger.error( f"The scan stopped because of an error: {e}", "We will attempt to stitch and archive the images acquired " - "so far." + "so far.", + exc_info=e, ) raise e finally: @@ -614,18 +625,13 @@ class SmartScanThing(Thing): logger.info("Waiting for background processes to finish...") self.preview_stitch_wait() self.correlate_wait() - logger.info("Stitching final image (may take some time)...") try: if scan_folder and self.stitch_automatically: + logger.info("Stitching final image (may take some time)...") self.stitch_scan(logger, os.path.basename(scan_folder), overlap=overlap) except SubprocessError as e: - logger.exception(f"Stitching failed: {e}") - logger.info("Creating zip archive of images (may take some time)...") - if images_folder and os.path.isdir(images_folder): - shutil.make_archive( - os.path.join(scan_folder, "images"), "zip", images_folder - ) - + logger.error(f"Stitching failed: {e}", exc_info=e) + @thing_property def max_range(self) -> int: """The maximum distance from the centre of the scan before we break""" @@ -777,12 +783,17 @@ class SmartScanThing(Thing): @thing_property def latest_preview_stitch_time(self) -> Optional[datetime]: - """The modification time of the latest preview image""" - fpath = self.latest_preview_stitch_path - if not os.path.exists(fpath): + """The modification time of the latest preview image + + This will return `null` if there is no preview image to return. + """ + try: + fpath = self.latest_preview_stitch_path + if os.path.exists(fpath): + return os.path.getmtime(fpath) + except IOError: return None - else: - return os.path.getmtime(fpath) + return None @fastapi_endpoint( "get", @@ -868,4 +879,33 @@ class SmartScanThing(Thing): """Generate a stitched image based on stage position metadata""" images_folder = self.images_folder(scan_name=scan_name) self.run_subprocess(logger, [self._script, "--stitching_mode", "all", "--minimum_overlap", f"{overlap*0.9}", images_folder]) + + @thing_action + def create_zip_of_scan(self, logger: InvocationLogger, scan_name: Optional[str]=None) -> ZipBlob: + """Generate a zip file that can be downloaded, with all the scan files in it.""" + images_folder = self.images_folder(scan_name=scan_name) + scan_folder = self.scan_folder_path(scan_name=scan_name) + if scan_folder != os.path.dirname(images_folder) or os.path.basename(images_folder) != "images": + logger.error( + "There is a problem with filenames, the archive may be incorrect." + f"scan_folder: {scan_folder}, images_folder: {images_folder}." + ) + if not os.path.isdir(images_folder): + raise FileNotFoundError(f"Tried to make a zip archive of {images_folder} but it does not exist.") + logger.info("Creating zip archive of images (may take some time)...") + shutil.make_archive( + os.path.join(scan_folder, "images"), + "zip", + scan_folder, + "images/", + logger=logger + ) + zip_fname = os.path.join(scan_folder, "images.zip") + # Promote key files to the top level of the zip + with zipfile.ZipFile(zip_fname, mode="a") as zip: + for fname in ["stitched_from_stage.jpg", "stitched.jpg"]: + fpath = os.path.join(images_folder, fname) + if os.path.exists(fpath): + zip.write(fpath, arcname=fname) + return ZipBlob.from_file(zip_fname) diff --git a/webapp/src/App.vue b/webapp/src/App.vue index e1234a92..2dfbe3d0 100644 --- a/webapp/src/App.vue +++ b/webapp/src/App.vue @@ -321,6 +321,13 @@ export default { ); } } + try { + let hostname = await this.readThingProperty("settings", "hostname"); + this.$store.commit("changeMicroscopeHostname", hostname); + document.title = `OpenFlexure Microscope: ${hostname}`; + } catch { + this.$store.commit("changeMicroscopeHostname", null); + } this.$store.commit("setConnected"); this.$store.commit("setErrorMessage", null); } catch (error) { diff --git a/webapp/src/components/tabContentComponents/aboutComponents/statusPane.vue b/webapp/src/components/tabContentComponents/aboutComponents/statusPane.vue index 63d12f02..3a6b5288 100644 --- a/webapp/src/components/tabContentComponents/aboutComponents/statusPane.vue +++ b/webapp/src/components/tabContentComponents/aboutComponents/statusPane.vue @@ -2,11 +2,23 @@
+
+ Microscope hostname: +
+ {{ $store.state.microscopeHostname }} +
API origin:
{{ $store.state.origin }}
+
@@ -71,13 +83,18 @@