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Sorted remaining content_type issues and blackened

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This commit is contained in:
Richard 2021-07-19 20:09:09 +01:00
parent 38fbe530d2
commit b7c9d3b73b
13 changed files with 114 additions and 92 deletions
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81
openflexure_microscope/api/default_extensions/autofocus.py
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@ -24,6 +24,7 @@ class JPEGSharpnessMonitor:
"""Monitor JPEG frame size in a background thread
This class starts a background thread """
def __init__(self, microscope: Microscope):
self.microscope: Microscope = microscope
self.camera: BaseCamera = microscope.camera
@ -164,6 +165,7 @@ def find_microscope() -> Microscope:
return microscope
def find_microscope_with_real_stage() -> Microscope:
"""Find the microscope and ensure it has a real stage.
@ -199,6 +201,7 @@ def extension_action(args=None):
responsible for collating and adding the views in its `__init__` method.
"""
supplied_args = args
def decorator(func):
class_docstring = f"""Manage actions for {func.__name__}.
@ -206,6 +209,7 @@ def extension_action(args=None):
each time {func.__name__} has been run in response to a `GET` request,
and will start a new `Action` in response to a `POST` request.
"""
class ActionViewWrapper(ActionView):
__doc__ = class_docstring
args = supplied_args
@ -222,9 +226,9 @@ def extension_action(args=None):
# aren't guaranteed to have the same leading whitespace, we just make sure
# both docstrings are stripped of leading indent, using `inspect.cleandoc()`
ActionViewWrapper.post.description = (
get_docstring(func, remove_newlines=False) +
"\n\n" +
inspect.cleandoc(
get_docstring(func, remove_newlines=False)
+ "\n\n"
+ inspect.cleandoc(
"""
This `POST` request starts an Action, i.e. the hardware will do something
that may continue after the HTTP request has been responded to. The
@ -242,11 +246,13 @@ def extension_action(args=None):
ActionViewWrapper.post.summary = get_summary(func)
ActionViewWrapper.post.__doc__ = ActionViewWrapper.post.description
ActionViewWrapper.__name__ = func.__name__
ActionViewWrapper.get.summary = f"List running and completed `{func.__name__}` actions."
ActionViewWrapper.get.summary = (
f"List running and completed `{func.__name__}` actions."
)
ActionViewWrapper.get.description = (
ActionViewWrapper.get.summary +
"\n\n" +
inspect.cleandoc(
ActionViewWrapper.get.summary
+ "\n\n"
+ inspect.cleandoc(
f"""
This `GET` request will return a list of `Action` objects corresponding
to the `{func.__name__}` action. It will include all the times it has
@ -258,8 +264,8 @@ def extension_action(args=None):
func.flask_view = ActionViewWrapper
return func
return decorator
return decorator
### Autofocus extension
@ -291,7 +297,9 @@ class AutofocusExtension(BaseExtension):
self.add_view(obj.flask_view, f"/{name}", name)
def measure_sharpness(
self, microscope: Optional[Microscope] = None, metric_fn: Callable = sharpness_sum_lap2
self,
microscope: Optional[Microscope] = None,
metric_fn: Callable = sharpness_sum_lap2,
) -> float:
"""Measure the sharpness from the MJPEG stream
@ -309,13 +317,13 @@ class AutofocusExtension(BaseExtension):
raise RuntimeError(f"Object {microscope.camera} has no method `array`")
@extension_action(
args = {
args={
"dz": fields.List(
fields.Int(),
fields.Int(),
description="An ascending list of relative z positions",
example = [int(x) for x in np.linspace(-300, 300, 7)],
example=[int(x) for x in np.linspace(-300, 300, 7)],
)
},
}
)
def autofocus(
self,
@ -360,16 +368,20 @@ class AutofocusExtension(BaseExtension):
return positions, sharpnesses
def move_and_find_focus(self, microscope: Optional[Microscope] = None, dz: int = 0) -> int:
def move_and_find_focus(
self, microscope: Optional[Microscope] = None, dz: int = 0
) -> int:
"""Make a relative Z move and return the peak sharpness position"""
if not microscope:
microscope = find_microscope_with_real_stage()
with monitor_sharpness(microscope) as m:
m.focus_rel(dz)
return m.sharpest_z_on_move(0)
@extension_action(
args={"dz": fields.Int(required=True, description="The relative Z move to make")},
args={
"dz": fields.Int(required=True, description="The relative Z move to make")
}
)
def move_and_measure(
self, microscope: Optional[Microscope] = None, dz: int = 0
@ -390,11 +402,11 @@ class AutofocusExtension(BaseExtension):
@extension_action(
args={
"dz": fields.Int(
missing=2000,
example=2000,
description="Total Z range to search over (in stage steps)"
missing=2000,
example=2000,
description="Total Z range to search over (in stage steps)",
)
},
}
)
def fast_autofocus(
self, microscope: Optional[Microscope] = None, dz: int = 2000
@ -484,27 +496,27 @@ class AutofocusExtension(BaseExtension):
return m.data_dict()
@extension_action(
args = {
args={
"dz": fields.Int(
missing = 2000,
example = 2000,
description = "Total Z range to search over (in stage steps)"
missing=2000,
example=2000,
description="Total Z range to search over (in stage steps)",
),
"target_z": fields.Int(
missing = 0,
example = -100,
description = "Target finishing position, relative to the focus."
missing=0,
example=-100,
description="Target finishing position, relative to the focus.",
),
"initial_move_up": fields.Bool(
missing = True,
description = "Set to Flase to disable the initial move upwards"
missing=True,
description="Set to Flase to disable the initial move upwards",
),
"backlash": fields.Int(
missing=25,
missing=25,
minimum=0,
description="Distance to undershoot, before correction move."
description="Distance to undershoot, before correction move.",
),
},
}
)
def fast_up_down_up_autofocus(
self,
@ -563,7 +575,7 @@ class AutofocusExtension(BaseExtension):
"""
if not microscope:
microscope = find_microscope_with_real_stage()
if not mini_backlash: # I renamed the argument,
if not mini_backlash: # I renamed the argument,
mini_backlash = backlash or 25
with microscope.lock(timeout=1), microscope.camera.lock, microscope.stage.lock:
with monitor_sharpness(microscope) as m:
@ -617,5 +629,6 @@ class AutofocusExtension(BaseExtension):
class MeasureSharpnessAPI(View):
__doc__ = AutofocusExtension.measure_sharpness.__doc__
def post(self):
return {"sharpness": self.extension.measure_sharpness()}
return {"sharpness": self.extension.measure_sharpness()}