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jtc42 2019-11-15 16:52:57 +00:00
parent 0907d013cd
commit 76af0891e9
14 changed files with 95 additions and 63 deletions
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10
openflexure_microscope/api/v1/blueprints/camera/capture.py
View file

@ -132,11 +132,11 @@ class ListAPI(MicroscopeView):
# Inject system metadata # Inject system metadata
system_metadata = { system_metadata = {
"microscope_settings": self.microscope.read_settings(), "microscope_settings": self.microscope.read_settings(),
"microscope_state": self.microscope.state, "microscope_state": self.microscope.state,
"microscope_id": self.microscope.id, "microscope_id": self.microscope.id,
"microscope_name": self.microscope.name, "microscope_name": self.microscope.name,
} }
output.system_metadata.update(system_metadata) output.system_metadata.update(system_metadata)
# Insert custom metadata # Insert custom metadata

16
openflexure_microscope/api/v2/blueprints/actions/__init__.py
View file

@ -8,38 +8,38 @@ _actions = {
"rule": "/camera/capture/", "rule": "/camera/capture/",
"view_class": camera.CaptureAPI, "view_class": camera.CaptureAPI,
"description": "Take a single still capture", "description": "Take a single still capture",
"conditions": True "conditions": True,
}, },
"preview_start": { "preview_start": {
"rule": "/camera/preview/start", "rule": "/camera/preview/start",
"view_class": camera.GPUPreviewStartAPI, "view_class": camera.GPUPreviewStartAPI,
"description": "Start the on-board GPU preview", "description": "Start the on-board GPU preview",
"conditions": True "conditions": True,
}, },
"preview_stop": { "preview_stop": {
"rule": "/camera/preview/stop", "rule": "/camera/preview/stop",
"view_class": camera.GPUPreviewStopAPI, "view_class": camera.GPUPreviewStopAPI,
"description": "Stop the on-board GPU preview", "description": "Stop the on-board GPU preview",
"conditions": True "conditions": True,
}, },
"move": { "move": {
"rule": "/stage/move/", "rule": "/stage/move/",
"view_class": stage.MoveStageAPI, "view_class": stage.MoveStageAPI,
"description": "Move the microscope stage", "description": "Move the microscope stage",
"conditions": True "conditions": True,
}, },
"shutdown": { "shutdown": {
"rule": "/system/shutdown/", "rule": "/system/shutdown/",
"view_class": system.ShutdownAPI, "view_class": system.ShutdownAPI,
"description": "Shutdown the device", "description": "Shutdown the device",
"conditions": (platform == "linux") "conditions": (platform == "linux"),
}, },
"reboot": { "reboot": {
"rule": "/system/reboot/", "rule": "/system/reboot/",
"view_class": system.RebootAPI, "view_class": system.RebootAPI,
"description": "Reboot the device", "description": "Reboot the device",
"conditions": (platform == "linux") "conditions": (platform == "linux"),
} },
} }
@ -57,7 +57,7 @@ def actions_representation():
"links": {"self": url_for(f".{name}")}, "links": {"self": url_for(f".{name}")},
"description": action["description"], "description": action["description"],
"rule": action["rule"], "rule": action["rule"],
"view_class": str(action["view_class"]) "view_class": str(action["view_class"]),
} }
actions[name] = d actions[name] = d

10
openflexure_microscope/api/v2/blueprints/actions/camera.py
View file

@ -84,11 +84,11 @@ class CaptureAPI(MicroscopeView):
# Inject system metadata # Inject system metadata
system_metadata = { system_metadata = {
"microscope_settings": self.microscope.read_settings(), "microscope_settings": self.microscope.read_settings(),
"microscope_state": self.microscope.state, "microscope_state": self.microscope.state,
"microscope_id": self.microscope.id, "microscope_id": self.microscope.id,
"microscope_name": self.microscope.name, "microscope_name": self.microscope.name,
} }
output.system_metadata.update(system_metadata) output.system_metadata.update(system_metadata)
# Insert custom metadata # Insert custom metadata

4
openflexure_microscope/api/v2/blueprints/actions/system.py
View file

@ -11,7 +11,7 @@ class ShutdownAPI(MicroscopeView):
.. :quickref: Actions; Shutdown .. :quickref: Actions; Shutdown
""" """
subprocess.Popen(['shutdown', '-h', 'now']) subprocess.Popen(["shutdown", "-h", "now"])
return "{}", 201 return "{}", 201
@ -24,6 +24,6 @@ class RebootAPI(MicroscopeView):
.. :quickref: Actions; Shutdown .. :quickref: Actions; Shutdown
""" """
subprocess.Popen(['sudo', 'shutdown', '-r', 'now']) subprocess.Popen(["sudo", "shutdown", "-r", "now"])
return "{}", 201 return "{}", 201

23
openflexure_microscope/api/v2/blueprints/captures.py
View file

@ -20,14 +20,22 @@ def captures_representation(capture_list: list, include_unavailable: bool = Fals
if include_unavailable: if include_unavailable:
captures = {image.id: image.state for image in capture_list} captures = {image.id: image.state for image in capture_list}
else: else:
captures = {image.id: image.state for image in capture_list if image.state["available"]} captures = {
image.id: image.state for image in capture_list if image.state["available"]
}
for capture_key, capture_repr in captures.items(): for capture_key, capture_repr in captures.items():
# Add API routes to returned representations # Add API routes to returned representations
extra_state = { extra_state = {
"links": { "links": {
"self": "{}".format(url_for(".capture", capture_id=capture_key)), "self": "{}".format(url_for(".capture", capture_id=capture_key)),
"download": "{}".format(url_for(".capture_download", capture_id=capture_key, filename=capture_repr["filename"])), "download": "{}".format(
url_for(
".capture_download",
capture_id=capture_key,
filename=capture_repr["filename"],
)
),
"tags": "{}".format(url_for(".capture_tags", capture_id=capture_key)), "tags": "{}".format(url_for(".capture_tags", capture_id=capture_key)),
} }
} }
@ -131,7 +139,9 @@ class CaptureAPI(MicroscopeView):
""" """
try: try:
representation = captures_representation(self.microscope.camera.images)[capture_id] representation = captures_representation(self.microscope.camera.images)[
capture_id
]
except KeyError: except KeyError:
return abort(404) # 404 Not Found return abort(404) # 404 Not Found
@ -379,9 +389,7 @@ def construct_blueprint(microscope_obj):
# Capture routes # Capture routes
blueprint.add_url_rule( blueprint.add_url_rule(
"/<capture_id>/download/<filename>", "/<capture_id>/download/<filename>",
view_func=DownloadAPI.as_view( view_func=DownloadAPI.as_view("capture_download", microscope=microscope_obj),
"capture_download", microscope=microscope_obj
),
) )
blueprint.add_url_rule( blueprint.add_url_rule(
@ -397,7 +405,6 @@ def construct_blueprint(microscope_obj):
) )
blueprint.add_url_rule( blueprint.add_url_rule(
"/", "/", view_func=ListAPI.as_view("capture_list", microscope=microscope_obj)
view_func=ListAPI.as_view("capture_list", microscope=microscope_obj),
) )
return blueprint return blueprint

5
openflexure_microscope/api/v2/blueprints/plugins.py
View file

@ -25,7 +25,7 @@ def plugins_representation(plugin_loader_object: PluginLoader):
"name": plugin["name"], "name": plugin["name"],
"plugin": str(plugin["plugin"]), "plugin": str(plugin["plugin"]),
"routes": plugin["routes"], "routes": plugin["routes"],
"form": plugin["form"] "form": plugin["form"],
} }
plugins.append(d) plugins.append(d)
@ -55,8 +55,7 @@ def construct_blueprint(microscope_obj):
# Create a base route to return plugin API forms, if any exist # Create a base route to return plugin API forms, if any exist
blueprint.add_url_rule( blueprint.add_url_rule(
"/", "/", view_func=PluginFormAPI.as_view("plugins", microscope=microscope_obj)
view_func=PluginFormAPI.as_view("plugins", microscope=microscope_obj),
) )
all_routes = [] all_routes = []

4
openflexure_microscope/api/v2/blueprints/tasks.py
View file

@ -16,9 +16,7 @@ def tasks_representation():
for task_key, task_repr in tasks_dict.items(): for task_key, task_repr in tasks_dict.items():
# Add API routes to returned representations # Add API routes to returned representations
extra_state = { extra_state = {
"links": { "links": {"self": "{}".format(url_for(".task", task_id=task_key))}
"self": "{}".format(url_for(".task", task_id=task_key)),
}
} }
tasks_dict[task_key].update(extra_state) tasks_dict[task_key].update(extra_state)

5
openflexure_microscope/camera/capture.py
View file

@ -35,7 +35,9 @@ def pull_usercomment_dict(filepath):
return json.loads(exif_dict["Exif"][37510].decode()) return json.loads(exif_dict["Exif"][37510].decode())
except json.decoder.JSONDecodeError: except json.decoder.JSONDecodeError:
# TODO: Remove YAML support in a later version # TODO: Remove YAML support in a later version
logging.warning(f"Capture {filepath} has metadata stored in YAML format. This is now deprecated in favour of JSON.") logging.warning(
f"Capture {filepath} has metadata stored in YAML format. This is now deprecated in favour of JSON."
)
return yaml.load(exif_dict["Exif"][37510].decode()) return yaml.load(exif_dict["Exif"][37510].decode())
else: else:
return None return None
@ -227,7 +229,6 @@ class CaptureObject(object):
# Insert exif into file # Insert exif into file
piexif.insert(exif_bytes, self.file) piexif.insert(exif_bytes, self.file)
@property @property
def metadata(self) -> dict: def metadata(self) -> dict:
""" """

34
openflexure_microscope/camera/pi.py
View file

@ -68,7 +68,7 @@ class PiCameraStreamer(BaseCamera):
"sharpness", "sharpness",
"annotate_text", "annotate_text",
"annotate_text_size", "annotate_text_size",
"zoom" "zoom",
] ]
def __init__(self): def __init__(self):
@ -93,13 +93,23 @@ class PiCameraStreamer(BaseCamera):
self.set_zoom(1.0) self.set_zoom(1.0)
# Set default settings # Set default settings
self.image_resolution = tuple(self.camera.MAX_RESOLUTION) #: tuple: Resolution for image captures self.image_resolution = tuple(
self.stream_resolution = (832, 624) #: tuple: Resolution for stream and video captures self.camera.MAX_RESOLUTION
self.numpy_resolution = (1312, 976) #: tuple: Resolution for numpy array captures ) #: tuple: Resolution for image captures
self.stream_resolution = (
832,
624,
) #: tuple: Resolution for stream and video captures
self.numpy_resolution = (
1312,
976,
) #: tuple: Resolution for numpy array captures
self.jpeg_quality = 75 #: int: JPEG quality self.jpeg_quality = 75 #: int: JPEG quality
# Set default lens shading table path # Set default lens shading table path
self.picamera_lst_path = settings_file_path("picamera_lst.npy") #: str: Path of .npy lens shading table file self.picamera_lst_path = settings_file_path(
"picamera_lst.npy"
) #: str: Path of .npy lens shading table file
# Update board identifier # Update board identifier
self.status.update({}) self.status.update({})
@ -138,7 +148,9 @@ class PiCameraStreamer(BaseCamera):
"image_resolution": self.image_resolution, "image_resolution": self.image_resolution,
"numpy_resolution": self.numpy_resolution, "numpy_resolution": self.numpy_resolution,
"jpeg_quality": self.jpeg_quality, "jpeg_quality": self.jpeg_quality,
"picamera_lst_path": self.picamera_lst_path if os.path.isfile(self.picamera_lst_path) else None, "picamera_lst_path": self.picamera_lst_path
if os.path.isfile(self.picamera_lst_path)
else None,
"picamera_settings": {}, "picamera_settings": {},
} }
) )
@ -273,7 +285,7 @@ class PiCameraStreamer(BaseCamera):
""" """
Read the current lens shading table as a numpy array, if it exists. Return None otherwise. Read the current lens shading table as a numpy array, if it exists. Return None otherwise.
""" """
if hasattr(self.camera, 'lens_shading_table'): if hasattr(self.camera, "lens_shading_table"):
return self.camera.lens_shading_table return self.camera.lens_shading_table
else: else:
return None return None
@ -297,13 +309,17 @@ class PiCameraStreamer(BaseCamera):
elif (type(lst_array_or_path) == str) and os.path.isfile(lst_array_or_path): elif (type(lst_array_or_path) == str) and os.path.isfile(lst_array_or_path):
self.camera.lens_shading_table = np.load(lst_array_or_path) self.camera.lens_shading_table = np.load(lst_array_or_path)
else: else:
logging.error("Unsupported or missing data for camera lens_shading_table. Must be numpy ndarray, or .npy file path string. Skipping.") logging.error(
"Unsupported or missing data for camera lens_shading_table. Must be numpy ndarray, or .npy file path string. Skipping."
)
def set_zoom(self, zoom_value: float = 1.0) -> None: def set_zoom(self, zoom_value: float = 1.0) -> None:
""" """
Change the camera zoom, handling re-centering and scaling. Change the camera zoom, handling re-centering and scaling.
""" """
logging.warning("set_zoom is deprecated. Please use the 'zoom' property in picamera_settings.") logging.warning(
"set_zoom is deprecated. Please use the 'zoom' property in picamera_settings."
)
with self.lock: with self.lock:
self.status["zoom_value"] = float(zoom_value) self.status["zoom_value"] = float(zoom_value)
if self.status["zoom_value"] < 1: if self.status["zoom_value"] < 1:

3
openflexure_microscope/config.py
View file

@ -21,6 +21,7 @@ class JSONEncoder(json.JSONEncoder):
""" """
A custom JSON encoder, with type conversions for PiCamera fractions, Numpy integers, and Numpy arrays A custom JSON encoder, with type conversions for PiCamera fractions, Numpy integers, and Numpy arrays
""" """
def default(self, o, markers=None): def default(self, o, markers=None):
# PiCamera fractions # PiCamera fractions
if isinstance(o, Fraction): if isinstance(o, Fraction):
@ -39,6 +40,7 @@ class JSONEncoder(json.JSONEncoder):
# MAIN CONFIG CLASS # MAIN CONFIG CLASS
class OpenflexureSettingsFile: class OpenflexureSettingsFile:
""" """
An object to handle expansion, conversion, and saving of the microscope configuration. An object to handle expansion, conversion, and saving of the microscope configuration.
@ -164,6 +166,7 @@ class OpenflexureSettingsFile:
# HANDLE BASIC LOADING AND SAVING OF SETTINGS FILES # HANDLE BASIC LOADING AND SAVING OF SETTINGS FILES
def load_json_file(config_path) -> dict: def load_json_file(config_path) -> dict:
""" """
Open a .json config file Open a .json config file

4
openflexure_microscope/microscope.py
View file

@ -160,7 +160,9 @@ class Microscope:
and :py:attr:`openflexure_microscope.camera.base.BaseCamera.status` and :py:attr:`openflexure_microscope.camera.base.BaseCamera.status`
""" """
# DEPRECATED # DEPRECATED
logging.warning("Microscope.state is deprecated. Use Microscope.status instead. State will be removed in a future version.") logging.warning(
"Microscope.state is deprecated. Use Microscope.status instead. State will be removed in a future version."
)
state = { state = {
"camera": self.camera.status, "camera": self.camera.status,
"stage": self.stage.status, "stage": self.stage.status,

4
openflexure_microscope/plugins/default/autofocus/api.py
View file

@ -32,7 +32,7 @@ class AutofocusAPI(MicroscopeViewPlugin):
return jsonify(task.state), 202 return jsonify(task.state), 202
else: else:
abort(503, 'No stage connected. Unable to autofocus.') abort(503, "No stage connected. Unable to autofocus.")
class FastAutofocusAPI(MicroscopeViewPlugin): class FastAutofocusAPI(MicroscopeViewPlugin):
@ -53,4 +53,4 @@ class FastAutofocusAPI(MicroscopeViewPlugin):
return jsonify(task.state), 202 return jsonify(task.state), 202
else: else:
abort(503, 'No stage connected. Unable to autofocus.') abort(503, "No stage connected. Unable to autofocus.")

16
openflexure_microscope/plugins/default/scan/plugin.py
View file

@ -147,14 +147,16 @@ class ScanPlugin(MicroscopePlugin):
if "time" not in metadata: if "time" not in metadata:
metadata["time"] = generate_basename() metadata["time"] = generate_basename()
metadata.update({ metadata.update(
"scan_parameters": { {
"step_size": step_size, "scan_parameters": {
"grid": grid, "step_size": step_size,
"style": style, "grid": grid,
"autofocus_dz": autofocus_dz "style": style,
"autofocus_dz": autofocus_dz,
}
} }
}) )
# Check if autofocus is enabled # Check if autofocus is enabled
if ( if (

20
openflexure_microscope/plugins/loader.py
View file

@ -154,7 +154,9 @@ class PluginLoader(object):
@property @property
def state(self): def state(self):
# DEPRECATED # DEPRECATED
logging.warning("PluginMount.state is deprecated. Use PluginMount.active instead. State will be removed in a future version.") logging.warning(
"PluginMount.state is deprecated. Use PluginMount.active instead. State will be removed in a future version."
)
return [m["python_name"] for m in self._plugins] return [m["python_name"] for m in self._plugins]
@property @property
@ -195,13 +197,15 @@ class PluginLoader(object):
setattr(self, pythonsafe_plugin_name, plugin_object) setattr(self, pythonsafe_plugin_name, plugin_object)
# Store the plugin object, and it's properties # Store the plugin object, and it's properties
self._plugins.append({ self._plugins.append(
"name": plugin_name, {
"python_name": pythonsafe_plugin_name, "name": plugin_name,
"plugin": plugin_object, "python_name": pythonsafe_plugin_name,
"routes": [], "plugin": plugin_object,
"form": None "routes": [],
}) "form": None,
}
)
# Grant plugin access to the hardware # Grant plugin access to the hardware
plugin_object.microscope = self.parent plugin_object.microscope = self.parent