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Starting to refactor smart scan to rely on class variables

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This commit is contained in:
Julian Stirling 2025-04-09 22:44:02 +01:00
parent ff1184d453
commit 70e7a21a29
2 changed files with 287 additions and 264 deletions
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549
src/openflexure_microscope_server/things/smart_scan.py
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@ -121,43 +121,6 @@ def distance_to_site(current, next):
return np.sqrt((next[1] - current[1]) ** 2 + (next[0] - current[0]) ** 2)
def scale_csm(csm_matrix, calibration_width, img_width):
"Account for a calibration width that may differ from image width"
scale = img_width / calibration_width # Usually >1, if we calibrated at low res
csm = np.array(csm_matrix) / scale # Decrease the CSM if pixels are smaller]
return csm
def generate_config(
folder_path: str,
positions: list,
names: list,
camera_to_sample_matrix,
csm_calibration_width,
img_width,
logger,
):
positions = np.array(positions)
mean_loc = np.mean(positions, axis=0)
# TODO: positions from recent scans need to be 2x bigger - change to CSM res?
# TODO: fully test this with whether it works in Fiji as expected
camera_to_sample_matrix = scale_csm(
camera_to_sample_matrix, csm_calibration_width, img_width
)
with open(os.path.join(folder_path, "TileConfiguration.txt"), "w") as fp:
fp.write(
"# Define the number of dimensions we are working on\ndim = 2\n\n# Define the image coordinates\n"
)
for i in range(len(names)):
loc = np.dot(
(positions[i] - mean_loc), np.linalg.inv(camera_to_sample_matrix)
)
fp.write(f"{names[i]}; ; {loc[1], loc[0]} \n")
class NotEnoughFreeSpaceError(IOError):
pass
@ -190,81 +153,26 @@ ZipBlob = blob_type("application/zip")
class SmartScanThing(Thing):
def __init__(self, path_to_openflexure_stitch: str):
self._script = path_to_openflexure_stitch
self._preview_stitch_popen = None
self._preview_stitch_popen_lock = threading.Lock()
self._correlate_popen = None
self._correlate_popen_lock = threading.Lock()
self._scan_lock = threading.Lock()
@property
def scans_folder_path(self) -> str:
"""This folder will hold all the scans we do."""
# TODO: This should be determined using sensible configuration.
# If the working directory is `/var/openflexure` this will result
# in scans being saved at `/var/openflexure/scans/`
return "scans"
_latest_scan_name = None
@thing_property
def latest_scan_name(self) -> Optional[str]:
"""The name of the last scan to be started."""
return self._latest_scan_name
def scan_folder_path(self, scan_name: Optional[str] = None):
"""The path to the scan folder with a given name"""
if not scan_name:
if not self.latest_scan_name:
raise IOError("There is no latest scan to return")
scan_name = self.latest_scan_name
return os.path.join(self.scans_folder_path, scan_name)
def new_scan_folder(self, scan_name: str = "scan") -> str:
"""Create a new empty folder, into which we can save scan images
The folder will be named `{scan_name}_000001/` where the number is
zero-padded to be 6 digits long (to allow correct sorting if the
scans are ordered alphanumerically).
Note that if you have discontinuous numbering (e.g. you've got scans
numbered 1 through 10, but you deleted scan 5), then the gaps will
get filled in - so there's no guarantee, for now, that the numbers
will correspond to order of creation. This may change in the future.
"""
if not os.path.exists(self.scans_folder_path):
os.makedirs(self.scans_folder_path)
if not scan_name:
scan_name = "scan"
for j in range(9999):
folder_path = os.path.join(self.scans_folder_path, f"{scan_name}_{j:04}")
if not os.path.exists(folder_path):
os.makedirs(folder_path)
self._latest_scan_name = os.path.basename(folder_path)
return folder_path
raise FileExistsError("Could not create a new scan folder: all names in use!")
def move_to_next_point(
self,
stage: StageDep,
logger: InvocationLogger,
path: list[list[int]],
focused_path: list[list[int]],
) -> list[int]:
"""Remove the first point from the path, and move there.
This will move to the next XY position in `path`, taking the `z` value
either from the current z value of the stage, or from `focused_path`.
Returns the point we have moved to.
"""
loc = [path[0][0], path[0][1]]
path.remove(path[0])
if len(focused_path) > 1:
z_index = closest(loc, focused_path)
z = int(focused_path[z_index][2])
else:
z = stage.position["z"]
logger.info(f"Moving to {loc}")
stage.move_absolute(x=int(loc[0]), y=int(loc[1]), z=z - self.autofocus_dz / 2)
return loc + [z]
# Variables set by the scan
self._latest_scan_name = None
self._cancel = None
self._logger = None
self._autofocus = None
self._stage = None
self._cam = None
self._metadata_getter = None
self._csm = None
self._background_detect = None
self._ongoing_scan_name = None
self._starting_position = None
self._scan_images_taken = None
@thing_action
def sample_scan(
@ -284,72 +192,199 @@ class SmartScanThing(Thing):
The stage will move in a pattern that grows outwards from the starting point,
stopping once it is surrounded by "background" (as detected by the
background_detect Thing).
Input:
* `overlap` is the fraction by which images should overlap, i.e.
`0.3` means we will move by 70% of the field of view each time.
"""
self._check_background_is_set(background_detect)
locked = self._scan_lock.acquire(timeout=0.1)
if not locked:
raise RuntimeError("Trying to run scan while scan is already running!")
# Set private variables for this scan
self._cancel = cancel
self._logger = logger
self._autofocus = autofocus
self._stage = stage
self._cam = cam
self._metadata_getter = metadata_getter
self._csm = csm
self._background_detect = background_detect
self._scan_images_taken = 0
try:
self._ongoing_scan_name = self._get_uniuqe_scan_name_and_dir(scan_name)
overlap = self.overlap
# record starting position so we can return there
self._starting_position = self._stage.position
self._run_scan(scan_name, overlap)
except:
self._return_to_starting_position()
self._perform_final_stitch(overlap)
finally:
# However the scan finnishes unset all variables and release lock
self._cancel = None
self._logger = None
self._autofocus = None
self._stage = None
self._cam = None
self._metadata_getter = None
self._csm = None
self._background_detect = None
self._ongoing_scan_name = None
self._scan_images_taken = None
self._scan_lock.release()
def _check_background_is_set(self, background_detect):
"""Before starting a scand check that we've got a background set
Raise error if it is not set but backroung detect is being used.
"""
if self.skip_background:
d = background_detect.background_distributions
if not d:
raise RuntimeError(
"Background is not set: you need to calibrate background detection."
)
else:
self._logger.warning(
"This scan will run in a spiral from the starting point "
f"until you cancel it, or until it has moved by {self.max_range} steps "
"in every direction. Make sure you watch it run to stop it leaving "
"the area of interest, or (worse) leading the microscope's range "
"of motion."
)
@property
def base_scan_dir(self) -> str:
"""This folder will hold all the scans we do."""
# TODO: This should be determined using sensible configuration.
# If the working directory is `/var/openflexure` this will result
# in scans being saved at `/var/openflexure/scans/`
return "scans"
@thing_property
def latest_scan_name(self) -> Optional[str]:
"""The name of the last scan to be started."""
return self._latest_scan_name
def dir_for_scan_name(self, scan_name: Optional[str] = None):
"""The path to the scan folder with a given name"""
if not scan_name:
if not self.latest_scan_name:
raise IOError("There is no latest scan to return")
scan_name = self.latest_scan_name
return os.path.join(self.base_scan_dir, scan_name)
@property
def _ongoing_scan_folder(self):
if not self._ongoing_scan_name:
return None
return self.dir_for_scan_name(self._ongoing_scan_name)
def _get_uniuqe_scan_name_and_dir(self, scan_name: str = "scan") -> str:
"""Get a unique name for this scan and create a directory for it
The scan will be named `{scan_name}_000001` where the number is
zero-padded to be 6 digits long (to allow correct sorting if the
scans are ordered alphanumerically).
Note that if you have discontinuous numbering (e.g. you've got scans
numbered 1 through 10, but you deleted scan 5), then the gaps will
get filled in - so there's no guarantee, for now, that the numbers
will correspond to order of creation. This may change in the future.
Creates a new empty folder, into which scans are saved
Returns the scan name.
The directory can be accessed by self.dir_for_scan_name(unique_scan_name)
"""
if not os.path.exists(self.base_scan_dir):
os.makedirs(self.base_scan_dir)
for j in range(9999):
trial_unique_scan_name = f"{scan_name}_{j:04}"
trial_dir = self.dir_for_scan_name(trial_unique_scan_name)
if not os.path.exists(trial_dir):
os.makedirs(trial_dir)
# If we made the directory this is the scan name
# Save it as the most latest scan (this persists as a
# property after the scan finishes)
self._latest_scan_name = trial_unique_scan_name
# Return the scan name
return trial_unique_scan_name
raise FileExistsError("Could not create a new scan folder: all names in use!")
def move_to_next_point(
self,
path: list[list[int]],
focused_path: list[list[int]],
) -> list[int]:
"""Remove the first point from the path, and move there.
This will move to the next XY position in `path`, taking the `z` value
either from the current z value of the stage, or from `focused_path`.
Returns the point we have moved to.
"""
loc = [path[0][0], path[0][1]]
path.remove(path[0])
if len(focused_path) > 1:
z_index = closest(loc, focused_path)
z = int(focused_path[z_index][2])
else:
z = self._stage.position["z"]
self._logger.info(f"Moving to {loc}")
self._stage.move_absolute(
x=int(loc[0]), y=int(loc[1]), z=z - self.autofocus_dz / 2
)
return loc + [z]
def _run_scan(self, scan_name, overlap):
# Define these variables so we can use them in the finally: block
# (after testing they are not None)
scan_sucessful = True
scan_folder = None
images_folder = None
starting_position = None
capture_thread = None
self._scan_lock.acquire(timeout=0.1)
try:
images_folder = os.path.join(self._ongoing_scan_folder, "images")
os.mkdir(images_folder)
raw_images_folder = os.path.join(images_folder, "raw")
os.mkdir(raw_images_folder)
self._logger.info(f"Saving images to {images_folder}")
max_dist = self.max_range
if self.autofocus_dz == 0:
logger.info("Running scan without autofocus")
self._logger.info("Running scan without autofocus")
elif self.autofocus_dz <= 200:
logger.warning(
self._logger.warning(
f"Your dz range is {self.autofocus_dz} steps, which is too short to attempt to focus. Running without autofocus"
)
# Before anything else, check that we've got a background set
# It's annoying to have to wait to find out!
if self.skip_background:
d = background_detect.background_distributions
if not d:
raise RuntimeError(
"Background is not set: you need to calibrate background detection."
)
else:
logger.warning(
"This scan will run in a spiral from the starting point "
f"until you cancel it, or until it has moved by {max_dist} steps "
"in every direction. Make sure you watch it run to stop it leaving "
"the area of interest, or (worse) leading the microscope's range "
"of motion."
)
names = []
positions = []
# Record the starting position so we can move back there afterwards
starting_position = stage.position
r = cam.grab_jpeg()
r = self._cam.grab_jpeg()
arr = np.array(Image.open(r.open()))
if csm.image_resolution is None:
if self._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(
if list(arr.shape[:2]) != [int(i) for i in self._csm.image_resolution]:
self._logger.error(
f"Images are, by default, {arr.shape[:2]}, but the CSM was "
f"calibrated at {csm.image_resolution}."
f"calibrated at {self._csm.image_resolution}."
)
# Here, we calculate the x and y step size based on the desired overlap
# TODO: Consider using CSM calibration size instead
# TODO: generalise to have 2D displacements for x and y (as the
# camera and stage may not be aligned).
CSM = csm.image_to_stage_displacement_matrix
overlap = self.overlap
CSM = self._csm.image_to_stage_displacement_matrix
dx = int(
np.abs(np.dot(np.array([0, arr.shape[1] * (1 - overlap)]), CSM)[0])
@ -358,24 +393,17 @@ class SmartScanThing(Thing):
np.abs(np.dot(np.array([arr.shape[0] * (1 - overlap), 0]), CSM)[1])
)
logger.info(
self._logger.info(
f"Based on an overlap of {overlap}, we will make steps of {dx}, {dy}"
)
# construct a 2D scan path
path = [[stage.position["x"], stage.position["y"]]]
path = [[self._stage.position["x"], self._stage.position["y"]]]
focused_path = [] # This holds a list of all points where focus succeeded
true_path = [] # This holds a list of all points visited
i = 0
start_time = time.strftime("%H_%M_%S-%d_%m_%Y")
scan_folder = self.new_scan_folder(scan_name)
images_folder = os.path.join(scan_folder, "images")
os.mkdir(images_folder)
raw_images_folder = os.path.join(images_folder, "raw")
os.mkdir(raw_images_folder)
logger.info(f"Saving images to {images_folder}")
start_time = time.strftime("%H_%M_%S-%d_%m_%Y")
data = {
"scan_name": scan_name,
@ -392,39 +420,41 @@ class SmartScanThing(Thing):
) as f:
json.dump(data, f, ensure_ascii=False, indent=4)
if self._scan_images_taken != 0:
raise RuntimeError(
"_scan_images_taken fhould be zero before starting scanning"
)
# At the start of the loop, we simultaneously capture an image and move to the next scan point.
# We skip capturing on the first run, because we've not focused yet - and also we skip capturing if
# it looks like background.
while len(path) > 0:
loc = self.move_to_next_point(
stage, logger, path=path, focused_path=focused_path
)
loc = self.move_to_next_point(path=path, focused_path=focused_path)
if not self.preview_stitch_running():
self.preview_stitch_start(images_folder)
if self.stitch_automatically:
if not self.correlate_running():
self.correlate_start(images_folder, overlap=overlap)
ensure_free_disk_space(scan_folder)
ensure_free_disk_space(self._ongoing_scan_folder)
# Check if the image is background
if self.skip_background:
image_is_sample = background_detect.image_is_sample()
image_is_sample = self._background_detect.image_is_sample()
else:
image_is_sample = True
# if more than 92% of the image is background, treat it as background and continue
if not image_is_sample:
logger.info(
f"Skipping {stage.position} as it is {round(background_detect.background_fraction(), 0)}% background."
self._logger.info(
f"Skipping {self._stage.position} as it is {round(self._background_detect.background_fraction(), 0)}% background."
)
else:
# if not, it's sample. run an autofocus and use the updated height
new_pos = [
[stage.position["x"] - dx, stage.position["y"]],
[stage.position["x"] + dx, stage.position["y"]],
[stage.position["x"], stage.position["y"] - dy],
[stage.position["x"], stage.position["y"] + dy],
[self._stage.position["x"] - dx, self._stage.position["y"]],
[self._stage.position["x"] + dx, self._stage.position["y"]],
[self._stage.position["x"], self._stage.position["y"] - dy],
[self._stage.position["x"], self._stage.position["y"] + dy],
]
for pos in new_pos:
if (
@ -436,15 +466,15 @@ class SmartScanThing(Thing):
attempts = 0
if self.autofocus_dz > 200:
while True:
jpeg_zs, jpeg_sizes = autofocus.looping_autofocus(
jpeg_zs, jpeg_sizes = self._autofocus.looping_autofocus(
dz=self.autofocus_dz, start="base"
)
current_height = stage.position["z"]
current_height = self._stage.position["z"]
time.sleep(0.2)
autofocus_success = autofocus.verify_focus_sharpness(
autofocus_success = self._autofocus.verify_focus_sharpness(
sweep_sizes=jpeg_sizes, camera=CamDep, threshold=0.92
)
logger.info(
self._logger.info(
f"We just tested the focus! Result was {autofocus_success}"
)
@ -471,17 +501,19 @@ class SmartScanThing(Thing):
# if the autofocus worked, add the current position to the list of successful locations
if result == "accept":
loc = list(stage.position.values())
loc = list(self._stage.position.values())
focused_path.append(loc)
break
if attempts >= 3:
logger.warning("Could not autofocus after 3 attempts.")
self._logger.warning(
"Could not autofocus after 3 attempts."
)
break
# if the autofocus was rejected, we return to the height of the closest successful autofocus. not perfect, but better than wandering out of focus
logger.info(
self._logger.info(
"The focus has shifted further than we expect: retrying."
)
stage.move_absolute(z=int(loc[2]))
self._stage.move_absolute(z=int(loc[2]))
attempts += 1
# Acquire the image in a thread, and continue once it's acquired (i.e. leave saving in the background)
@ -496,9 +528,12 @@ class SmartScanThing(Thing):
time.sleep(0.2)
if thread_was_alive:
wait_time = time.time() - wait_start
logger.info(
self._logger.info(
f"Waited {wait_time:.1f}s for the previous capture to finish saving."
)
# increment capure counter as thread has completed
self._scan_images_taken += 1
acquired = Event()
name = f"image_{loc[0]}_{loc[1]}.jpg"
jpeg_path = os.path.join(images_folder, name)
@ -511,9 +546,6 @@ class SmartScanThing(Thing):
kwargs={
"acquired": acquired,
"jpeg_path": jpeg_path,
"cam": cam,
"logger": logger,
"metadata_getter": metadata_getter,
},
)
capture_thread.start()
@ -530,7 +562,9 @@ class SmartScanThing(Thing):
if distance_to_site(i, true_path[0][:2]) < max_dist:
temp_path.append(i)
else:
logger.info(f"Rejected moving to {i} as it is out of range")
self._logger.info(
f"Rejected moving to {i} as it is out of range"
)
path = temp_path.copy()
path = sorted(
path,
@ -540,24 +574,23 @@ class SmartScanThing(Thing):
),
)
self.create_zip_of_scan(
logger=logger,
scan_name=scan_folder.split("scans/")[1],
scan_name=self._ongoing_scan_name,
download_zip=False,
)
except InvocationCancelledError:
scan_sucessful = False
logger.error("Stopping scan because it was cancelled.")
self._logger.info("Stopping scan because it was cancelled.")
except NotEnoughFreeSpaceError as e:
scan_sucessful = False
logger.error(
self._logger.error(
f"Stopping scan to avoid filling up the disk: {e}",
exc_info=e,
)
raise e
except Exception as e:
scan_sucessful = False
logger.error(
self._logger.error(
f"The scan stopped because of an error: {e} "
"Attempting to stitch and archive the images acquired so far.",
exc_info=e,
@ -573,42 +606,52 @@ class SmartScanThing(Thing):
# ignore any excppetions, but if it appeared to be succesfull
# we will log an error.
if scan_sucessful:
logger.error(
self._logger.error(
"The appears to have been successful however the final capture raised"
f"the following error: {e}."
"Attempting to stitch and archive images.",
exc_info=e,
)
try:
logger.info("Returning to starting position.")
if starting_position is not None:
stage.move_absolute(**starting_position, block_cancellation=True)
finally:
self._scan_lock.release()
self.create_zip_of_scan(
logger=logger,
scan_name=scan_folder.split("scans/")[1],
download_zip=False,
# This is what happens if the scan completes sucessfully or the
# user cancels it.
self._return_to_starting_position()
self._perform_final_stitch(overlap)
def _return_to_starting_position(self):
self._logger.info("Returning to starting position.")
if self._starting_position is not None:
self._stage.move_absolute(
**self._starting_position, block_cancellation=True
)
logger.info("Waiting for background processes to finish...")
self.preview_stitch_wait()
self.correlate_wait()
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.error(f"Stitching failed: {e}", exc_info=e)
def _perform_final_stitch(self, overlap):
"""Perform final stitch of the data"""
if self._scan_images_taken <= 3:
self._logger.info("Not performing a stitch as 3 or fewer images taken")
return
self.create_zip_of_scan(
scan_name=self._ongoing_scan_name,
download_zip=False,
)
self._logger.info("Waiting for background processes to finish...")
self.preview_stitch_wait()
self.correlate_wait()
try:
if self._ongoing_scan_folder and self.stitch_automatically:
self._logger.info("Stitching final image (may take some time)...")
self.stitch_scan(
os.path.basename(self._ongoing_scan_folder), overlap=overlap
)
except SubprocessError as e:
self._logger.error(f"Stitching failed: {e}", exc_info=e)
def capture_and_save(
self,
acquired: Event,
jpeg_path: str,
cam: CamDep,
metadata_getter: GetThingStates,
logger: InvocationLogger,
) -> None:
"""Capture an image and save it to disk
@ -616,23 +659,18 @@ class SmartScanThing(Thing):
that the stage may be moved while it's saved.
"""
capture_start = time.time()
image, metadata = self.capture_image(cam, metadata_getter, logger)
image, metadata = self.capture_image()
acquired.set()
acquisition_time = time.time()
self.save_capture(jpeg_path, image, metadata, logger)
self.save_capture(jpeg_path, image, metadata)
save_time = time.time()
acquisition_duration = round(acquisition_time - capture_start, 1)
saving_duration = round(save_time - acquisition_time, 1)
logger.debug(
self._logger.debug(
f"Acquired {jpeg_path} in {acquisition_duration}s then {saving_duration}s saving to disk"
)
def capture_image(
self,
cam: CamDep,
metadata_getter: GetThingStates,
logger: InvocationLogger,
) -> tuple[np.ndarray, dict]:
def capture_image(self) -> tuple[np.ndarray, dict]:
"""Capture an image in memory and return it with metadata
This will set the event `acquired` once the image has been acquired, so
that the stage may be moved while it's saved.
@ -640,8 +678,8 @@ class SmartScanThing(Thing):
returns tuple with numpy array of image data, and dict of metadata
"""
try:
metadata = metadata_getter()
image = cam.capture_array()[..., :3]
metadata = self._metadata_getter()
image = self._cam.capture_array()[..., :3]
except Exception as e:
raise CaptureError(
"An error occurred while capturing: {}".format(e), exc_info=e
@ -653,7 +691,6 @@ class SmartScanThing(Thing):
jpeg_path: str,
image: np.ndarray,
metadata: dict,
logger: InvocationLogger,
) -> None:
"""Saving the captured image and metadata to disk
logger warning (via InvocationLogger) is raised if metadata is failed to be added
@ -670,7 +707,7 @@ class SmartScanThing(Thing):
).encode("utf-8")
piexif.insert(piexif.dump(exif_dict), jpeg_path)
except:
logger.warning(f"Failed to add metadata to {jpeg_path}")
self._logger.warning(f"Failed to add metadata to {jpeg_path}")
except Exception as e:
raise IOError(
f"An error occurred while saving {jpeg_path}: {e}",
@ -745,10 +782,10 @@ class SmartScanThing(Thing):
in the `images` folder.
"""
scans: list[ScanInfo] = []
if not os.path.isdir(self.scans_folder_path):
if not os.path.isdir(self.base_scan_dir):
return scans
for f in os.listdir(self.scans_folder_path):
path = os.path.join(self.scans_folder_path, f)
for f in os.listdir(self.base_scan_dir):
path = os.path.join(self.base_scan_dir, f)
if os.path.isdir(path):
images_folder = os.path.join(path, "images")
if os.path.isdir(images_folder):
@ -788,7 +825,7 @@ class SmartScanThing(Thing):
raise HTTPException(
403, f"You may only download files named {DOWNLOADABLE_SCAN_FILES}"
)
path = os.path.join(self.scans_folder_path, scan_name, file)
path = os.path.join(self.base_scan_dir, scan_name, file)
if not os.path.isfile(path):
raise HTTPException(404, "File not found")
return FileResponse(path)
@ -806,7 +843,7 @@ class SmartScanThing(Thing):
This endpoint allows scans to be deleted from disk.
"""
path = os.path.join(self.scans_folder_path, scan_name)
path = os.path.join(self.base_scan_dir, scan_name)
if not os.path.isdir(path):
print(f"can't find {path}")
raise HTTPException(404, "Scan not found")
@ -827,7 +864,7 @@ class SmartScanThing(Thing):
self.delete_scan(scan.name)
def images_folder(self, scan_name: Optional[str] = None) -> str:
scan_folder = self.scan_folder_path(scan_name=scan_name)
scan_folder = self.dir_for_scan_name(scan_name=scan_name)
return os.path.join(scan_folder, "images")
@property
@ -867,8 +904,6 @@ class SmartScanThing(Thing):
raise HTTPException(404, "File not found")
return FileResponse(path)
_preview_stitch_popen = None
def preview_stitch_start(self, images_folder: str) -> None:
"""Start stitching a preview of the scan in a subprocess"""
if self.preview_stitch_running():
@ -892,8 +927,6 @@ class SmartScanThing(Thing):
with self._preview_stitch_popen_lock:
self._preview_stitch_popen.wait()
_correlate_popen = None
def correlate_start(self, images_folder: str, overlap: float = 0.1) -> None:
"""Start stitching a preview of the scan in a subprocess"""
if self.correlate_running():
@ -926,20 +959,21 @@ class SmartScanThing(Thing):
def run_subprocess(
self,
logger: InvocationLogger,
cmd: list[str],
) -> CompletedProcess:
"""Run a subprocess and log any output"""
logger.info(f"Running command in subprocess: `{' '.join(cmd)}`")
self._logger.info(f"Running command in subprocess: `{' '.join(cmd)}`")
p = Popen(cmd, stdout=PIPE, stderr=STDOUT, bufsize=1, universal_newlines=True)
os.set_blocking(p.stdout.fileno(), False)
logger.info(time.strftime("%Y-%m-%d %H:%M:%S", time.localtime(time.time())))
self._logger.info(
time.strftime("%Y-%m-%d %H:%M:%S", time.localtime(time.time()))
)
while p.poll() is None:
try:
output = p.stdout.readline()
if output != "" and output is not None:
logger.info(output)
self._logger.info(output)
except:
pass
@ -947,17 +981,16 @@ class SmartScanThing(Thing):
try:
output = p.stdout.readline()
if output != "" and output is not None:
logger.info(output)
self._logger.info(output)
except:
pass
logger.info("Stitching complete")
self._logger.info("Stitching complete")
return p
@thing_action
def stitch_scan(
self,
logger: InvocationLogger,
scan_name: Optional[str] = None,
overlap: float = 0.0,
) -> None:
@ -973,12 +1006,11 @@ class SmartScanThing(Thing):
try:
with open(os.path.join(images_folder, "scan_inputs.json")) as data_file:
data_loaded = json.load(data_file)
logger.info(data_loaded)
self._logger.info(data_loaded)
overlap = data_loaded["overlap"]
except:
overlap = 0.1
self.run_subprocess(
logger,
[
self._script,
"--stitching_mode",
@ -993,27 +1025,19 @@ class SmartScanThing(Thing):
@thing_action
def create_zip_of_scan(
self,
logger: InvocationLogger,
scan_name: Optional[str] = None,
scan_name: str,
download_zip=True,
) -> 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}."
)
scan_folder = self.dir_for_scan_name(scan_name=scan_name)
if not os.path.isdir(images_folder):
raise FileNotFoundError(
f"Tried to make a zip archive of {images_folder} but it does not exist."
)
zip_fname = f"{os.path.join(scan_folder, 'images')}.zip"
zip_fname = os.path.join(scan_folder, "images.zip")
# Create an empty zip file - we don't want to autofill it with files,
# as some of them should only be added at the end (as we can't overwrite)
@ -1026,9 +1050,9 @@ class SmartScanThing(Thing):
current_zip = self.get_files_in_zip(zip_fname)
# get a list of files in the folder we're zipping
folder_path = self.scan_folder_path(scan_name)
files = glob.glob(folder_path + "/**/*", recursive=True)
files = [i.split(f"{folder_path}/")[1] for i in files]
files = glob.glob(scan_folder + "/**/*", recursive=True)
files = [os.path.relpath(file, scan_folder) for file in files]
# This is a list of file names that are updated as the scan goes,
# and should only be zipped at the end of the scan - otherwise they'll
@ -1055,10 +1079,9 @@ class SmartScanThing(Thing):
elif ".zip" in file or "raw" in file:
pass
else:
logger.info(f"appending {file} to zip")
zip.write(os.path.join(folder_path, file), arcname=file)
self._logger.info(f"appending {file} to zip")
zip.write(os.path.join(scan_folder, file), arcname=file)
images_folder = os.path.join(folder_path, "images")
# Promote key files to the top level of the zip only at the end of the scan (when downloading)
# and finally zip some of the final files
# TODO: if you download multiple times, you get duplicate files - is this a problem?
@ -1067,13 +1090,13 @@ class SmartScanThing(Thing):
for fname in ["stitched_from_stage.jpg", stitch_name, tiff_name]:
fpath = os.path.join(images_folder, fname)
if os.path.exists(fpath):
logger.info(f"copying {fpath} to upper level")
self._logger.info(f"copying {fpath} to upper level")
zip.write(fpath, arcname=fname)
for file in files:
if any(banned_name in file for banned_name in files_to_delay):
logger.info(f"we are finally adding {file} into zip")
zip.write(os.path.join(folder_path, file), arcname=file)
logger.info("about to download zip")
self._logger.info(f"we are finally adding {file} into zip")
zip.write(os.path.join(scan_folder, file), arcname=file)
self._logger.info("about to download zip")
return ZipBlob.from_file(zip_fname)
@thing_action

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

@ -37,7 +37,7 @@ class Stitcher(Thing):
def images_folder(
self, smart_scan: SmartScanDep, scan_name: Optional[str] = None
) -> str:
scan_folder = smart_scan.scan_folder_path(scan_name=scan_name)
scan_folder = smart_scan.dir_for_scan_name(scan_name=scan_name)
return os.path.join(scan_folder, "images")
@staticmethod