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Acquire microscope lock for state and settings IO

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This commit is contained in:
Joel Collins 2020-06-15 16:19:33 +01:00
parent 5d70d5f7fe
commit 1c1dcdbe1a
1 changed files with 60 additions and 57 deletions
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117
openflexure_microscope/microscope.py
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@ -153,39 +153,41 @@ class Microscope:
Return:
dict: Dictionary containing complete microscope state
"""
state = {"camera": self.camera.state, "stage": self.stage.state}
return state
with self.lock:
state = {"camera": self.camera.state, "stage": self.stage.state}
return state
def update_settings(self, settings: dict):
"""
Applies a settings dictionary to the microscope. Missing parameters will be left untouched.
"""
logging.debug("Microscope: Applying settings: {}".format(settings))
with self.lock:
logging.debug("Microscope: Applying settings: {}".format(settings))
# If attached to a camera
if ("camera" in settings) and self.camera:
self.camera.update_settings(settings.get("camera", {}))
# If attached to a camera
if ("camera" in settings) and self.camera:
self.camera.update_settings(settings.get("camera", {}))
# If attached to a stage
if ("stage" in settings) and self.stage:
self.stage.update_settings(settings.get("stage", {}))
# If attached to a stage
if ("stage" in settings) and self.stage:
self.stage.update_settings(settings.get("stage", {}))
# Capture manager
self.captures.update_settings(settings.get("captures", {}))
# Capture manager
self.captures.update_settings(settings.get("captures", {}))
# Microscope settings
if "id" in settings:
self.id = settings["id"]
if "name" in settings:
self.name = settings["name"]
if "fov" in settings:
self.fov = settings["fov"]
# Microscope settings
if "id" in settings:
self.id = settings["id"]
if "name" in settings:
self.name = settings["name"]
if "fov" in settings:
self.fov = settings["fov"]
# Extension settings
if "extensions" in settings:
self.extension_settings.update(settings["extensions"])
# Extension settings
if "extensions" in settings:
self.extension_settings.update(settings["extensions"])
# TODO: warn if there are settings that we silently ignore
# TODO: warn if there are settings that we silently ignore
def read_settings(self, full: bool = True):
"""
@ -197,49 +199,50 @@ class Microscope:
This is to ensure that settings for currently disconnected hardware
don't get removed from the settings file.
"""
with self.lock:
settings_current = {
"id": self.id,
"name": self.name,
"fov": self.fov,
"extensions": self.extension_settings,
}
settings_current = {
"id": self.id,
"name": self.name,
"fov": self.fov,
"extensions": self.extension_settings,
}
# If attached to a camera
if self.camera:
settings_current_camera = self.camera.read_settings()
settings_current["camera"] = settings_current_camera
# If attached to a camera
if self.camera:
settings_current_camera = self.camera.read_settings()
settings_current["camera"] = settings_current_camera
# Store an encoded copy of the PiCamera lens shading table, if it exists
if hasattr(self.camera, "read_lens_shading_table"):
# Read LST. Returns None if no LST is active
lst_arr = self.camera.read_lens_shading_table()
# Store an encoded copy of the PiCamera lens shading table, if it exists
if hasattr(self.camera, "read_lens_shading_table"):
# Read LST. Returns None if no LST is active
lst_arr = self.camera.read_lens_shading_table()
if lst_arr is not None:
b64_string, dtype, shape = serialise_array_b64(lst_arr)
if lst_arr is not None:
b64_string, dtype, shape = serialise_array_b64(lst_arr)
settings_current["camera"]["lens_shading_table"] = {
"@type": "ndarray",
"b64_string": b64_string,
"dtype": dtype,
"shape": shape,
}
settings_current["camera"]["lens_shading_table"] = {
"@type": "ndarray",
"b64_string": b64_string,
"dtype": dtype,
"shape": shape,
}
# If attached to a stage
if self.stage:
settings_current_stage = self.stage.read_settings()
settings_current["stage"] = settings_current_stage
# If attached to a stage
if self.stage:
settings_current_stage = self.stage.read_settings()
settings_current["stage"] = settings_current_stage
# Capture manager
settings_current_captures = self.captures.read_settings()
settings_current["captures"] = settings_current_captures
# Capture manager
settings_current_captures = self.captures.read_settings()
settings_current["captures"] = settings_current_captures
settings_full = self.settings_file.merge(settings_current)
settings_full = self.settings_file.merge(settings_current)
if full:
return settings_full
else:
return settings_current
if full:
return settings_full
else:
return settings_current
def save_settings(self):
"""
@ -341,7 +344,7 @@ class Microscope:
)
# Gether metadata from hardware in a greenlet
gevent.spawn(self.add_metadata_to_capture, output, metadata, annotations, tags)
gevent.get_hub().threadpool.spawn(self.add_metadata_to_capture, output, metadata, annotations, tags)
logging.info(f"Finished capture to {output.file}")