Restructured text fixes so that pydoctor would return without an error
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Julian Stirling
parent
58b056988a
commit
a84a916719
31 changed files with 269 additions and 256 deletions
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@ -33,10 +33,10 @@ class StackParams:
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:param stack_dz: The number of motor steps between images
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:param images_to_save: The number of images to save to disk
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:param min_images_to_test: The minimum number of images in the stack before, the
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stack is evaluated for focus. As more images are captured evaluation of the focus
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is always evaluated with the same number of images. i.e. if min_images_to_test=9,
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then 9 images are captured, if the stack is not well focused, a 10th image is
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captured and images 2 to 10 are evaluated for focus
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stack is evaluated for focus. As more images are captured evaluation of the
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focus is always evaluated with the same number of images. i.e. if
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``min_images_to_test=9``, then 9 images are captured, if the stack is not well
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focused, a 10th image is captured and images 2 to 10 are evaluated for focus
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:param autofocus_dz: The number of steps in a full autofocus (when required)
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:param images_dir: The directory to save images to disk
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:param save_resolution: The resolution to save the captures to disk with
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@ -101,7 +101,8 @@ class StackParams:
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Note that this is the range of the minimum number of images captured,
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which is also the range of the images stored in memory that can be
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saved."""
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saved.
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"""
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return self.stack_dz * (self.min_images_to_test - 1)
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@property
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@ -109,7 +110,6 @@ class StackParams:
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"""
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The distance to deliberately undershoot the estimated optimal starting point
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"""
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# Starting too low by "steps_undershoot" makes smart stacking faster.
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# Starting a stack too high requires it to move to the start,
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# autofocus and then re-stack. Starting slightly too low only
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@ -157,7 +157,7 @@ def _get_capture_by_id(captures: list[CaptureInfo], buffer_id: int) -> CaptureIn
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:returns: the CaptureInfo object of the capture with matching id
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:raises: ValueError if buffer_id does not match the buffer_id of any captures
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:raises ValueError: if buffer_id does not match the buffer_id of any captures
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"""
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return captures[_get_capture_index_by_id(captures, buffer_id)]
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@ -171,7 +171,7 @@ def _get_capture_index_by_id(captures: list[CaptureInfo], buffer_id: int) -> int
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:returns: the list index of the capture with matching id
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:raises: ValueError if buffer_id does not match the buffer_id of any captures
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:raises ValueError: if buffer_id does not match the buffer_id of any captures
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"""
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ids = [capture.buffer_id for capture in captures]
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if buffer_id not in ids:
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@ -290,7 +290,8 @@ class AutofocusThing(lt.Thing):
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Actions here involve moving a stage in z, and using the camera to either
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capture images (generally, z-stacking) and measuring the sharpness of the
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field of view to assess focus (autofocus and testing the success of a z-stack)"""
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field of view to assess focus (autofocus and testing the success of a z-stack)
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"""
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@lt.thing_action
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def fast_autofocus(
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@ -336,9 +337,9 @@ class AutofocusThing(lt.Thing):
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for the moves. This can be used to calibrate autofocus.
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Each move is relative to the last one, i.e. we will finish at
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`sum(dz)` relative to the starting position.
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``sum(dz)`` relative to the starting position.
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If `wait` is specified, we will wait for that many seconds
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If ``wait`` is specified, we will wait for that many seconds
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between moves.
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"""
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with sharpness_monitor.run():
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@ -358,9 +359,9 @@ class AutofocusThing(lt.Thing):
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):
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"""Repeatedly autofocus the stage until it looks focused.
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This action will run the `fast_autofocus` action until it settles on a point
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This action will run the ``fast_autofocus`` action until it settles on a point
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in the middle 3/5 of its range. Such logic can be helpful if the microscope
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is close to focus, but not quite within `dz/2`. It will attempt to autofocus
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is close to focus, but not quite within ``dz/2``. It will attempt to autofocus
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up to 10 times.
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"""
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repeat = True
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@ -444,17 +445,18 @@ class AutofocusThing(lt.Thing):
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:param cam: Camera Dependency supplied by LabThings dependency injection
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:param stage: Stage Dependency supplied by LabThings dependency injection
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:param sharpness_monitor: Sharpness Monitor Dependency (for focus detection)
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supplied by LabThings dependency injection
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supplied by LabThings dependency injection
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:param images_dir: the folder to save all images
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:param autofocus_dz: the range to autofocus over if a stack fails
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:param save_resolution: The resolution the images should be saved at, the
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images will be resampled if this doesn't match the camera's capture resolution
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images will be resampled if this doesn't match the camera's capture
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resolution
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:returns: A tuple containing:
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- A boolean, True if stack was successfully
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- The z position of the sharpest image
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"""
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* A boolean, True if stack was successfully
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* The z position of the sharpest image
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"""
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# Set the variables to prevent changes from the GUI or other windows
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stack_parameters = StackParams(
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stack_dz=self.stack_dz,
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@ -511,11 +513,12 @@ class AutofocusThing(lt.Thing):
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"""Return to the initial height of the current stack, and run
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a looping autofocus.
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Arguments:
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initial_z_pos: The initial z positions of previous captures
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autofocus_dz: the range in steps to autofocus
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variables stage and sharpness_monitor are Thing dependencies passed through from
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the calling action
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:param initial_z_pos: The initial z positions of previous captures
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:param autofocus_dz: the range in steps to autofocus
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``stage`` and ``sharpness_monitor`` are Thing dependencies passed through
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from the calling action
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"""
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stage.move_absolute(z=initial_z_pos)
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self.looping_autofocus(
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@ -534,14 +537,13 @@ class AutofocusThing(lt.Thing):
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"""Save the required captures to disk. Will save the sharpest image,
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and any images either side of focus.
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Arguments:
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sharpest_id: the buffer id index of the sharpest image
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captures: a list of captures, including file name, image data and metadata
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stack_parameters: a StackParams object holding stack parameters
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variables logger and capture are Thing dependencies passed through from the
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calling action
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"""
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:param sharpest_id: the buffer id index of the sharpest image
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:param captures: a list of captures, including file name, image data and
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metadata
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:param stack_parameters: a StackParams object holding stack parameters
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:param cam: is a Thing dependency passed through from the calling action
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"""
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sharpest_index = _get_capture_index_by_id(captures, sharpest_id)
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slice_to_save = stack_parameters.slice_to_save(sharpest_index)
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@ -569,9 +571,10 @@ class AutofocusThing(lt.Thing):
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:param stage: Stage Dependency to be passed through from the calling action
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:returns: A tuple of
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- the stack result (True for successful stack, False for failed stack),
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- a list of CaptureInfo objects,
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- the buffer_id of the shapest image (or None if the stack failed)
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* the stack result (True for successful stack, False for failed stack),
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* a list of CaptureInfo objects,
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* the buffer_id of the shapest image (or None if the stack failed)
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"""
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# Move down by the height of the z stack, plus an overshoot
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# Better to start too low and take too many images than too high and need to refocus
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@ -628,11 +631,11 @@ class AutofocusThing(lt.Thing):
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:param cam: Camera Dependency to be passed through from the calling action
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:param stage: Stage Dependency to be passed through from the calling action
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:buffer_max: The maximum number of images to tell the camera to keep in memory
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for saving once the stack is complete
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:param buffer_max: The maximum number of images to tell the camera to keep in memory
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for saving once the stack is complete
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:return: A CaptureInfo object containing the capture information including its
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camera buffer_id needed for saving.
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:returns: A CaptureInfo object containing the capture information including its
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camera buffer_id needed for saving.
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"""
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stage_location = stage.position
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buffer_id = cam.capture_to_memory(buffer_max=buffer_max)
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@ -649,14 +652,19 @@ class AutofocusThing(lt.Thing):
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stack is centrally enough in the stack
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:param captures: a list of the capture objects to for testing if the
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sharpeness has converged in the centre
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sharpness has converged in the centre
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:return: A tuple with two values:
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- result - which is one of three literal values:
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'success' if the sharpest image is towards the centre
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'continue' if the sharpest image is in the final two images of the list
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'restart' if the sharpest image is in the first two images of the list
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- capture_id - the buffer id of the sharpest image
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:returns: A tuple with two values:
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* result - which is one of three literal values:
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* ``success`` if the sharpest image is towards the centre
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* ``continue`` if the sharpest image is in the final two images of the
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list
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* ``restart`` if the sharpest image is in the first two images of the
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list
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* capture_id - the buffer id of the sharpest image
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"""
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sharpest_index = np.argmax([capture.sharpness for capture in captures])
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# The buffer id of the sharpest image
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