New comments on scanning
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jaknapper
parent
ee190ec66b
commit
d2ab448732
1 changed files with 76 additions and 41 deletions
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@ -92,7 +92,7 @@ def ensure_free_disk_space(path: str, min_space: int = 500000000) -> None:
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class ScanInfo(BaseModel):
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""" "Summary information about a scan folder"""
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"""Summary information about a scan folder"""
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name: str
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created: datetime
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@ -179,7 +179,7 @@ class SmartScanThing(Thing):
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The stage will move in a pattern that grows outwards from the starting point,
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stopping once it is surrounded by "background" (as detected by the
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background_detect Thing).
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background_detect Thing) or reaches the "max_range" measured in steps.
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"""
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got_lock = self._scan_lock.acquire(timeout=0.1)
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@ -204,7 +204,7 @@ class SmartScanThing(Thing):
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self._check_background_and_csm_set()
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self._ongoing_scan_name = self._get_unique_scan_name_and_dir(scan_name)
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self.create_zip_of_scan(
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logger=self._scan_logger, scan_name=self._ongoing_scan_name
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scan_name=self._ongoing_scan_name
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)
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self._autofocus.looping_autofocus(dz=self.autofocus_dz, start="centre")
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# record starting position so we can return there
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@ -220,7 +220,7 @@ class SmartScanThing(Thing):
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# Error must be raised so UI gives correct output
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raise e
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finally:
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# However the scan finishes unset all variables and release lock
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# However the scan finishes, unset all variables and release lock
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self._cancel = None
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self._scan_logger = None
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self._autofocus = None
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@ -261,11 +261,11 @@ class SmartScanThing(Thing):
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@_scan_running
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def _check_background_and_csm_set(self):
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"""Before starting a scan check that background and camera-stage-mapping are set
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"""Before starting a scan, check that background and camera-stage-mapping are set
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Raise error if:
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- background is to be skipped but is not set
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- camera stage mapping is not set
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- camera stage mapping is not set
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Raise warning if not using background detect that scan will go on until max steps reached
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"""
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@ -314,7 +314,7 @@ class SmartScanThing(Thing):
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@property
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@_scan_running
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def _ongoing_scan_dir(self):
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"""For the ongoing scan this returns the scan directory"""
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"""For the ongoing scan, this returns the scan directory"""
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if not self._ongoing_scan_name:
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raise RuntimeError("Cannot get ongoing scan name while no scan is running")
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return self.dir_for_scan(self._ongoing_scan_name)
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@ -322,7 +322,7 @@ class SmartScanThing(Thing):
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@property
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@_scan_running
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def _ongoing_scan_images_dir(self):
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"""For the ongoing scan this returns the image directory"""
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"""For the ongoing scan, this returns the image directory"""
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if not self._ongoing_scan_name:
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raise RuntimeError("Cannot get ongoing scan name while no scan is running")
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return self.images_dir_for_scan(self._ongoing_scan_name)
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@ -378,10 +378,10 @@ class SmartScanThing(Thing):
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def _move_to_next_point(
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self, next_point: tuple[int, int], z_estimate: Optional[int] = None
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) -> tuple[int, int, int]:
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"""Move to the next position (half an autofocus move below estimated z)
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Moves the stage to the next poistion. If no z_estimate is given then
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the current stage position is used.
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"""Moves the stage to the next poistion. If no z_estimate is given then
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the current stage position is used. Must move to the estimated focused position
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(although moving below would be marginally faster) because background detect is
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most reliable at the focused position.
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Returns the (x,y,z) with the chosen z_estimate
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"""
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@ -431,7 +431,7 @@ class SmartScanThing(Thing):
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dy_vec = np.dot(np.array([dy_img, 0]), csm_disp_matrix)
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# Assume no rotation or skew and take only the aligned axis of vector.
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# Cooerce to positive integer
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# Coerce to positive integer
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dx = int(np.abs(dx_vec[0]))
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dy = int(np.abs(dy_vec[1]))
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@ -475,6 +475,10 @@ class SmartScanThing(Thing):
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@_scan_running
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def _save_scan_inputs_json(self):
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"""
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Save scan inputs as a JSON file in the scan folder, to allow
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the user to review the settings used in the scan
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"""
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# This should be a method of the scan_data dataclass
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data = {
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@ -496,17 +500,27 @@ class SmartScanThing(Thing):
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@_scan_running
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def _manage_stitching_threads(self):
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"""
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Manage the stitching threads starting them if the are needed
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and not running.
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Manage the stitching threads, starting them if needed and not already running.
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"""
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# Assume 4 images means at least one offset in x and y, making the stitching
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# well constrained.
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if self._scan_images_taken > 3:
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if not self._preview_stitch_running():
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self._preview_stitch_start(overlap=self._scan_data["overlap"])
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@_scan_running
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def _run_scan(self):
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# Uset to check if finally was reached via exeption (except
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# cancel by user.
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"""
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Prepare and run the main scan, handling the threads performing
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stitching. Uses the result (or exception) from the scanning to
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determine whether the scan should be stitched and the microscope
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should return to the starting x,y,z position
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"""
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# Used to check if finally was reached via exeption (except
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# cancel by user)
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scan_successful = True
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try:
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@ -539,12 +553,12 @@ class SmartScanThing(Thing):
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raise e
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finally:
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if self._capture_thread:
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# If the capture thread had an error we capture it here
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# If the capture thread had an error, we capture it here
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try:
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self._capture_thread.join()
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except Exception as e:
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# If the scan has already ended due to an exception we will
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# ignore any exceptions, but if it appeared to be successful
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# If the scan has already ended due to an exception, we will
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# ignore any exceptions. If it appeared to be successful,
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# we will log the error.
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if scan_successful:
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self._scan_logger.error(
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@ -561,6 +575,15 @@ class SmartScanThing(Thing):
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@_scan_running
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def _main_scan_loop(self):
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"""
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The loop to run through during a scan, until no more scan x,y positions
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are remaining.
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"""
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# The initial plan for the scan should be a single x,y position. All future
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# moves will be planned around this point. In future, route planner could
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# have multiple starting positions, each of which will be visited before the
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# scan can end.
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planner_settings = {
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"dx": self._scan_data["dx"],
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"dy": self._scan_data["dy"],
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@ -571,9 +594,11 @@ class SmartScanThing(Thing):
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planner_settings=planner_settings,
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)
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# At the start of the loop, we simultaneously capture an image and move to the next scan point.
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# We skip capturing on the first run, because we've not focused yet - and also we skip capturing if
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# it looks like background.
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# The loop tests if the scan should continue, moves to the next position,
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# decides whether to capture an image, autofocuses if necessary,
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# captures an image if necessary, updates the scan path and future path,
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# and updates the zip file with new images.
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while not route_planner.scan_complete:
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ensure_free_disk_space(self._ongoing_scan_dir)
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self._manage_stitching_threads()
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@ -587,7 +612,7 @@ class SmartScanThing(Thing):
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)
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capture_image = True
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# If skipping background, take an image to check if it is background
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# If skipping background, take an image to check if current field of view is background
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if self._scan_data["skip_background"]:
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capture_image = self._background_detect.image_is_sample()
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@ -666,6 +691,7 @@ class SmartScanThing(Thing):
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@_scan_running
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def _return_to_starting_position(self):
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"""Return to the initial scan position, if set"""
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self._scan_logger.info("Returning to starting position.")
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if self._starting_position is not None:
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self._stage.move_absolute(
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@ -674,7 +700,7 @@ class SmartScanThing(Thing):
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@_scan_running
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def _perform_final_stitch(self):
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"""Perform final stitch of the data"""
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"""Update the scan zip and perform final stitch of the data"""
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if self._scan_images_taken <= 3:
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self._scan_logger.info("Not performing a stitch as 3 or fewer images taken")
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@ -724,7 +750,7 @@ class SmartScanThing(Thing):
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@thing_property
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def max_range(self) -> int:
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"""The maximum distance from the centre of the scan before we break"""
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"""The maximum distance from the centre of the scan before we break in steps"""
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return self.thing_settings.get("max_range", 45000)
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@max_range.setter
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@ -754,7 +780,7 @@ class SmartScanThing(Thing):
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@thing_property
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def autofocus_dz(self) -> int:
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"""The z distance to perform an autofocus"""
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"""The z distance to perform an autofocus in steps"""
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return self.thing_settings.get("autofocus_dz", 1000)
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@autofocus_dz.setter
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@ -763,7 +789,7 @@ class SmartScanThing(Thing):
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@thing_property
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def overlap(self) -> float:
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"""The z distance to perform an autofocus"""
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"""The fraction (0-1) that adjacent images should overlap in x or y"""
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return self.thing_settings.get("overlap", 0.45)
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@overlap.setter
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@ -772,7 +798,7 @@ class SmartScanThing(Thing):
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@thing_property
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def stitch_automatically(self) -> bool:
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"""Should we attempt to stitch scans as we go?"""
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"""Whether to run a final stitch at the end of the scan (assuming scan success)"""
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return self.thing_settings.get("stitch_automatically", True)
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@stitch_automatically.setter
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@ -785,9 +811,9 @@ class SmartScanThing(Thing):
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Each scan has a name (which can be used to access it), along with
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its modified and created times (according to the filesystem) and
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the number of items in the `images` folder. Note that the number
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of images reported may be confused if non-image files are present
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in the `images` folder.
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the number of items in the `images` folder. Note that image count
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uses a regular expression, and changes to the naming scheme will
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break it.
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"""
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scans: list[ScanInfo] = []
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if not os.path.isdir(self.base_scan_dir):
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@ -803,6 +829,11 @@ class SmartScanThing(Thing):
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else:
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number_of_images = 0
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modified = max(os.stat(root).st_mtime for root, _, _ in os.walk(path))
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# If number of images is 0, should the scan be appended or ignored?
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# When deleting images, empty scans should be deleted. When displaying
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# scans in the GUI or choosing a new scan name, should be ignored
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# A function to delete empty scan folders from the disk achieves all of this
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scans.append(
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ScanInfo(
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name=f,
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@ -867,7 +898,7 @@ class SmartScanThing(Thing):
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def delete_all_scans(self) -> None:
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"""Delete all the scans on the microscope
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**This will irreversibly remove all smart scan data from the
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**This will irreversibly remove all scanned data from the
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microscope!**
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Use with extreme caution.
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"""
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@ -960,6 +991,9 @@ class SmartScanThing(Thing):
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@_scan_running
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def _preview_stitch_wait(self):
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"""
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Wait for an ongoing preview stitch to return
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"""
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if self._preview_stitch_running():
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with self._preview_stitch_popen_lock:
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self._preview_stitch_popen.wait()
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@ -1038,7 +1072,7 @@ class SmartScanThing(Thing):
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overlap = data_loaded["overlap"]
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except (json.decoder.JSONDecodeError, FileNotFoundError, TypeError):
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# As there is no schema or pydantic model this should handle
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# The file not being there, it not being json in the file,
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# the file not being there, it not being json in the file,
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# or the imported data not being indexable
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logger.warning(
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f"Couldn't read scan data, is {json_fname} missing or corrupt? "
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@ -1067,7 +1101,6 @@ class SmartScanThing(Thing):
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@thing_action
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def create_zip_of_scan(
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self,
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logger: InvocationLogger,
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scan_name: str,
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) -> None:
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"""Generate an empty zip file for the current scan"""
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@ -1081,9 +1114,7 @@ class SmartScanThing(Thing):
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zip_fname = os.path.join(scan_folder, "images.zip")
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# Create an empty zip file - we don't want to autofill it with files,
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# as some of them should only be added at the end, as we can't overwrite
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# them once they change
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# Create an empty zip file
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if not os.path.isfile(zip_fname):
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with zipfile.ZipFile(zip_fname, mode="w"):
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pass
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@ -1112,6 +1143,10 @@ class SmartScanThing(Thing):
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# This is a list of file names that are updated as the scan goes,
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# and should only be zipped at the end of the scan - otherwise they'll
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# be appended on every loop as we can't overwrite files in the zip
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# More elegant ways would be to only zip the images matching the global regex,
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# which will all be images, then append other files at the end.
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# Alternatively, use "output_dir" in stitching to separate stitching image files
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files_to_delay = [
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"TileConfiguration",
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"tiling_cache",
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@ -1132,9 +1167,9 @@ class SmartScanThing(Thing):
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else:
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scan_zip.write(os.path.join(scan_folder, file), arcname=file)
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# Finally zip the updating files we skipped previously
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# Finally, zip the files skipped previously
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# TODO: if you download multiple times, you get duplicate files - is this a problem?
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# TODO: check if they're already in
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# TODO: check if they're already in based on file name and size
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if final_version:
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with zipfile.ZipFile(zip_fname, mode="a") as scan_zip:
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for file in files:
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@ -1146,7 +1181,7 @@ class SmartScanThing(Thing):
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self,
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scan_name: str,
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):
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"""Update the zip to include the files we leave to the end, then return the
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"""Update the zip to include the files left to the end, then return the
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zip file as a Blob"""
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self.update_zip(
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scan_name=scan_name,
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