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Static type analysis

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This commit is contained in:
Joel Collins 2020-11-30 13:36:45 +00:00
parent 3aebb8bead
commit 7866ec0f47
63 changed files with 1825 additions and 2722 deletions
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80
openflexure_microscope/microscope.py
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@ -4,13 +4,16 @@ Defines a microscope object, binding a camera and stage with basic functionality
"""
import logging
import uuid
from typing import Tuple
from typing import Dict, List, Optional, Tuple, Union
import pkg_resources
from expiringdict import ExpiringDict
from openflexure_microscope.camera.base import BaseCamera
from openflexure_microscope.camera.mock import MissingCamera
from openflexure_microscope.captures import THUMBNAIL_SIZE, CaptureManager
from openflexure_microscope.config import OpenflexureSettingsFile
from openflexure_microscope.stage.base import BaseStage
from openflexure_microscope.stage.mock import MissingStage
from openflexure_microscope.stage.sanga import SangaDeltaStage, SangaStage
@ -19,7 +22,7 @@ try:
except Exception as e: # pylint: disable=W0703
logging.error(e)
logging.warning("Unable to import PiCameraStreamer")
from labthings import CompositeLock
from labthings import CompositeLock, StrictLock
from openflexure_microscope.config import user_configuration, user_settings
@ -32,23 +35,23 @@ class Microscope:
"""
def __init__(self, settings=user_settings, configuration=user_configuration):
self.id = f"openflexure:microscope:{uuid.uuid4()}"
self.name = self.id
self.id: str = f"openflexure:microscope:{uuid.uuid4()}"
self.name: str = self.id
self.captures = CaptureManager()
self.captures: CaptureManager = CaptureManager()
# Store settings and configuration files
self.settings_file = settings
self.configuration_file = configuration
self.settings_file: OpenflexureSettingsFile = settings
self.configuration_file: OpenflexureSettingsFile = configuration
self.extension_settings = {}
self.extension_settings: dict = {}
# Initialise with an empty composite lock
#: :py:class:`labthings.CompositeLock`: Composite lock for locking both camera and stage
self.lock = CompositeLock([])
self.lock: Union[CompositeLock, StrictLock] = CompositeLock([])
self.camera = None #: Currently connected camera object
self.stage = None #: Currently connected stage object
self.camera: BaseCamera = None #: Currently connected camera object
self.stage: BaseStage = None #: Currently connected stage object
self.setup(self.configuration_file.load()) # Attach components
@ -59,8 +62,12 @@ class Microscope:
# Sometimes, like when doing large scans, we don't need to read the hardware
# state for every single capture. We can get the data once at the start,
# cache it, and reuse that to save on IO. Cached data is stored here.
self.configuration_cache = ExpiringDict(max_len=100, max_age_seconds=3600)
self.metadata_cache = ExpiringDict(max_len=100, max_age_seconds=3600)
self.configuration_cache: Union[dict, ExpiringDict] = ExpiringDict(
max_len=100, max_age_seconds=3600
)
self.metadata_cache: Union[dict, ExpiringDict] = ExpiringDict(
max_len=100, max_age_seconds=3600
)
def __enter__(self):
"""Create microscope on context enter."""
@ -86,7 +93,7 @@ class Microscope:
self.captures.close()
logging.info("Closed %s", (self))
def setup(self, configuration):
def setup(self, configuration: dict):
"""
Attach microscope components based on initially passed configuration file
"""
@ -119,12 +126,13 @@ class Microscope:
if hasattr(self.stage, "lock"):
self.lock.locks.append(self.stage.lock)
def set_stage(self, configuration=None, stage_type=None):
def set_stage(
self, configuration: Optional[dict] = None, stage_type: Optional[str] = None
):
"""
Set or change the stage geometry
"""
if not configuration:
configuration = self.configuration
configuration = configuration or self.configuration
if stage_type:
if stage_type == configuration["stage"].get("type"):
@ -135,7 +143,7 @@ class Microscope:
### Close any existing stages
if self.stage:
stage_port = self.stage.port
stage_port = getattr(self.stage, "port")
self.stage.close()
logging.info("Setting stage")
@ -151,7 +159,7 @@ class Microscope:
except Exception as e: # pylint: disable=W0703
logging.error(e)
logging.warning("No compatible Sangaboard hardware found.")
elif stage_type in ("SangaDeltaStage"):
elif stage_type in ("SangaDeltaStage",):
try:
logging.info("Trying SangaDeltaStage")
self.stage = SangaDeltaStage(port=stage_port)
@ -173,7 +181,7 @@ class Microscope:
else:
return False
def has_real_camera(self):
def has_real_camera(self) -> bool:
"""
Check if a real (non-mock) camera is currently attached.
"""
@ -184,7 +192,7 @@ class Microscope:
# Create unified state
@property
def state(self):
def state(self) -> dict:
"""Dictionary of the basic microscope state.
Return:
@ -224,7 +232,7 @@ class Microscope:
for key in settings.keys():
logging.warning("Key %s is unused and was ignored", key)
def read_settings(self, full: bool = True):
def read_settings(self, full: bool = True) -> dict:
"""
Get an updated settings dictionary.
@ -270,7 +278,7 @@ class Microscope:
# Save config to file
self.settings_file.save(current_config, backup=True)
def force_get_configuration(self):
def force_get_configuration(self) -> dict:
initial_configuration = self.configuration_file.load()
current_configuration = {
@ -293,7 +301,7 @@ class Microscope:
initial_configuration.update(current_configuration)
return initial_configuration
def get_configuration(self, cache_key=None):
def get_configuration(self, cache_key: Optional[str] = None) -> dict:
if cache_key:
cached_config = self.configuration_cache.get(cache_key, None)
if cached_config:
@ -308,7 +316,7 @@ class Microscope:
def configuration(self):
return self.get_configuration()
def force_get_metadata(self):
def force_get_metadata(self) -> dict:
"""
Read cachable bits of microscope metadata.
Currently ID, settings, and configuration can be cached
@ -321,7 +329,7 @@ class Microscope:
return system_metadata
def get_metadata(self, cache_key=None):
def get_metadata(self, cache_key: Optional[str] = None):
"""
Read microscope metadata, with partial caching
"""
@ -345,22 +353,23 @@ class Microscope:
return metadata
@property
def metadata(self):
def metadata(self) -> dict:
return self.get_metadata()
def capture(
self,
filename: str = None,
filename: Optional[str] = None,
folder: str = "",
temporary: bool = False,
use_video_port: bool = False,
resize: Tuple[int, int] = None,
bayer: bool = True,
fmt: str = "jpeg",
annotations: dict = None,
tags: list = None,
metadata: dict = None,
cache_key: str = None,
annotations: Optional[Dict[str, str]] = None,
tags: Optional[List[str]] = None,
dataset: Optional[Dict[str, str]] = None,
metadata: Optional[dict] = None,
cache_key: Optional[str] = None,
):
logging.debug("Microscope capturing to %s", filename)
if not annotations:
@ -381,9 +390,6 @@ class Microscope:
)
# Capture to output object
extras = {}
if fmt == "jpeg":
extras["thumbnail"] = (*THUMBNAIL_SIZE, 85)
logging.info("Starting microscope capture %s", output.file)
self.camera.capture(
output,
@ -391,10 +397,10 @@ class Microscope:
resize=resize,
bayer=bayer,
fmt=fmt,
**extras,
thumbnail=(*THUMBNAIL_SIZE, 85),
)
output.put_and_save(tags, annotations, full_metadata)
output.put_and_save(tags, annotations, dataset, full_metadata)
logging.debug("Finished capture to %s", output.file)
return output