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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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42
openflexure_microscope/api/v2/views/actions/camera.py
View file

@ -1,5 +1,6 @@
import io
import logging
from typing import Dict, Optional, Tuple
from flask import send_file
from labthings import Schema, fields, find_component
@ -42,12 +43,14 @@ class CaptureAPI(ActionView):
"""
microscope = find_component("org.openflexure.microscope")
resize = args.get("resize", None)
if resize:
resize = (
int(resize["width"]),
int(resize["height"]),
resize_dict: Optional[Dict[str, int]] = args.get("resize", None)
if resize_dict:
resize: Optional[Tuple[int, int]] = (
int(resize_dict["width"]),
int(resize_dict["height"]),
) # Convert dict to tuple
else:
resize = None
# Explicitally acquire lock (prevents empty files being created if lock is unavailable)
with microscope.camera.lock:
@ -76,12 +79,14 @@ class RAMCaptureAPI(ActionView):
"""
microscope = find_component("org.openflexure.microscope")
resize = args.get("resize", None)
if resize:
resize = (
int(resize["width"]),
int(resize["height"]),
resize_dict: Optional[Dict[str, int]] = args.get("resize", None)
if resize_dict:
resize: Optional[Tuple[int, int]] = (
int(resize_dict["width"]),
int(resize_dict["height"]),
) # Convert dict to tuple
else:
resize = None
# Open a BytesIO stream to be destroyed once request has returned
with microscope.camera.lock, io.BytesIO() as stream:
@ -113,15 +118,18 @@ class GPUPreviewStartAPI(ActionView):
"""
microscope = find_component("org.openflexure.microscope")
window = args.get("window")
logging.debug(window)
# Get window argument from request
window_arg = args.get("window")
logging.debug(window_arg)
if len(window) != 4:
fullscreen = True
window = None
else:
# Default to no window
fullscreen: bool = True
window: Optional[Tuple[int, int, int, int]] = None
# If request argument is well formed, use that
if len(window_arg) == 4:
fullscreen = False
window = [int(w) for w in window]
window = (int(w) for w in window_arg)
microscope.camera.start_preview(fullscreen=fullscreen, window=window)
return microscope.state

7
openflexure_microscope/api/v2/views/actions/stage.py
View file

@ -1,4 +1,5 @@
import logging
from typing import List, Tuple
from labthings import fields, find_component
from labthings.views import ActionView
@ -24,11 +25,11 @@ class MoveStageAPI(ActionView):
# Handle absolute positioning (calculate a relative move from current position and target)
if (args.get("absolute")) and (microscope.stage): # Only if stage exists
target_position = axes_to_array(args, ["x", "y", "z"])
target_position: List[int] = axes_to_array(args, ["x", "y", "z"])
logging.debug("TARGET: %s", (target_position))
position = [
position: Tuple[int, int, int] = (
target_position[i] - microscope.stage.position[i] for i in range(3)
]
)
logging.debug("DELTA: %s", (position))
else:

2
openflexure_microscope/api/v2/views/actions/system.py
View file

@ -4,7 +4,7 @@ import subprocess
from labthings.views import ActionView
def is_raspberrypi():
def is_raspberrypi() -> bool:
"""
Checks if Raspberry Pi.
"""

11
openflexure_microscope/api/v2/views/camera.py
View file

@ -34,17 +34,18 @@ class LSTImageProperty(PropertyView):
logging.warning("PiCamera.lens_shading_table returned as None")
return ("", 204)
else:
# Get the LST Numpy array from the camera's memoryview
lst = np.asarray(microscope.camera.camera.lens_shading_table)
# R next to G1
# Create array of R next to G1
top = np.concatenate(lst[:2], axis=1)
# G2 next to B
# Create array of G2 next to B
bottom = np.concatenate(lst[2:], axis=1)
# Combined into a 2x2 grid of greyscale images
# Create combined array of 2x2 grid of greyscale images
all_channels = np.concatenate((top, bottom), axis=0)
# Create a PNG
img_bytes = BytesIO()
img_bytes: BytesIO = BytesIO()
Image.fromarray(np.uint8(all_channels), "L").save(img_bytes, "PNG")
img_bytes.seek(0)
# Return the image
fname = f"lst-{datetime.date.today().isoformat()}.png"
fname: str = f"lst-{datetime.date.today().isoformat()}.png"
return send_file(img_bytes, as_attachment=True, attachment_filename=fname)

41
openflexure_microscope/api/v2/views/captures.py
View file

@ -1,3 +1,7 @@
from io import BytesIO
from typing import List, Optional, Union
from uuid import UUID
from flask import abort, redirect, request, send_file, url_for
from labthings import Schema, fields, find_component
from labthings.marshalling import marshal_with, use_args
@ -6,6 +10,7 @@ from labthings.views import PropertyView, View
from marshmallow import pre_dump
from openflexure_microscope.api.utilities import get_bool
from openflexure_microscope.captures import CaptureObject
# SCHEMAS
@ -61,10 +66,10 @@ class CaptureSchema(ImageSchema):
links = fields.Dict()
@pre_dump
def generate_links(self, data, **_):
def generate_links(self, data: Union[dict, CaptureObject], **_):
if isinstance(data, dict):
capture_id = data.get("id")
capture_name = data.get("name")
capture_id: Optional[Union[str, UUID]] = data.get("id")
capture_name: Optional[str] = data.get("name")
else:
capture_id = data.id
capture_name = data.name
@ -102,7 +107,7 @@ class CaptureSchema(ImageSchema):
if isinstance(data, dict):
data["links"] = links
else:
data.links = links
setattr(data, "links", links)
return data
@ -129,7 +134,7 @@ class CaptureList(PropertyView):
List all image captures
"""
microscope = find_component("org.openflexure.microscope")
image_list = microscope.captures.images.values()
image_list: List[CaptureObject] = microscope.captures.images.values()
return image_list
@ -142,7 +147,7 @@ class CaptureView(View):
Description of a single image capture
"""
microscope = find_component("org.openflexure.microscope")
capture_obj = microscope.captures.images.get(id_)
capture_obj: Optional[CaptureObject] = microscope.captures.images.get(id_)
if not capture_obj:
return abort(404) # 404 Not Found
@ -154,7 +159,7 @@ class CaptureView(View):
Delete a single image capture
"""
microscope = find_component("org.openflexure.microscope")
capture_obj = microscope.captures.images.get(id_)
capture_obj: Optional[CaptureObject] = microscope.captures.images.get(id_)
if not capture_obj:
return abort(404) # 404 Not Found
@ -171,17 +176,17 @@ class CaptureDownload(View):
tags = ["captures"]
responses = {200: {"content_type": "image/jpeg"}}
def get(self, id_, filename):
def get(self, id_, filename: Optional[str]):
"""
Image data for a single image capture
"""
microscope = find_component("org.openflexure.microscope")
capture_obj = microscope.captures.images.get(id_)
capture_obj: Optional[CaptureObject] = microscope.captures.images.get(id_)
if not capture_obj:
return abort(404) # 404 Not Found
thumbnail = get_bool(request.args.get("thumbnail"))
thumbnail: bool = get_bool(request.args.get("thumbnail", ""))
# If no filename is specified, redirect to the capture's currently set filename
if not filename:
@ -189,7 +194,7 @@ class CaptureDownload(View):
url_for(
"DownloadAPI",
id=id_,
filename=capture_obj.filename,
filename=capture_obj.name,
thumbnail=thumbnail,
),
code=307,
@ -197,10 +202,14 @@ class CaptureDownload(View):
# Download the image data using the requested filename
if thumbnail:
img = capture_obj.thumbnail
img: Optional[BytesIO] = capture_obj.thumbnail
else:
img = capture_obj.data
# If we can't get any data, return 404
if not img:
return abort(404) # 404 Not Found
return send_file(img, mimetype="image/jpeg")
@ -212,7 +221,7 @@ class CaptureTags(View):
Get tags associated with a single image capture
"""
microscope = find_component("org.openflexure.microscope")
capture_obj = microscope.captures.images.get(id_)
capture_obj: Optional[CaptureObject] = microscope.captures.images.get(id_)
if not capture_obj:
return abort(404) # 404 Not Found
@ -225,7 +234,7 @@ class CaptureTags(View):
Add tags to a single image capture
"""
microscope = find_component("org.openflexure.microscope")
capture_obj = microscope.captures.images.get(id_)
capture_obj: Optional[CaptureObject] = microscope.captures.images.get(id_)
if not capture_obj:
return abort(404) # 404 Not Found
@ -240,7 +249,7 @@ class CaptureTags(View):
Delete tags from a single image capture
"""
microscope = find_component("org.openflexure.microscope")
capture_obj = microscope.captures.images.get(id_)
capture_obj: Optional[CaptureObject] = microscope.captures.images.get(id_)
if not capture_obj:
return abort(404) # 404 Not Found
@ -259,7 +268,7 @@ class CaptureAnnotations(View):
Get annotations associated with a single image capture
"""
microscope = find_component("org.openflexure.microscope")
capture_obj = microscope.captures.images.get(id_)
capture_obj: Optional[CaptureObject] = microscope.captures.images.get(id_)
if not capture_obj:
return abort(404) # 404 Not Found

21
openflexure_microscope/api/v2/views/instrument.py
View file

@ -1,4 +1,5 @@
import logging
from typing import Any, List
from flask import abort
from labthings import fields, find_component
@ -35,29 +36,29 @@ class NestedSettingsProperty(View):
tags = ["properties"]
responses = {404: {"description": "Settings key cannot be found"}}
def get(self, route):
def get(self, route: str):
"""
Show a nested section of the current microscope settings
"""
microscope = find_component("org.openflexure.microscope")
keys = route.split("/")
keys: List[str] = route.split("/")
try:
value = get_by_path(microscope.read_settings(), keys)
value: Any = get_by_path(microscope.read_settings(), keys)
except KeyError:
return abort(404)
return value
@use_args(fields.Dict())
def put(self, args, route):
def put(self, args: Any, route: str):
"""
Update a nested section of the current microscope settings
"""
microscope = find_component("org.openflexure.microscope")
keys = route.split("/")
keys: List[str] = route.split("/")
dictionary = create_from_path(keys)
dictionary: dict = create_from_path(keys)
set_by_path(dictionary, keys, args)
microscope.update_settings(dictionary)
@ -84,10 +85,10 @@ class NestedStateProperty(View):
Show a nested section of the current microscope state
"""
microscope = find_component("org.openflexure.microscope")
keys = route.split("/")
keys: List[str] = route.split("/")
try:
value = get_by_path(microscope.state, keys)
value: Any = get_by_path(microscope.state, keys)
except KeyError:
return abort(404)
@ -112,10 +113,10 @@ class NestedConfigurationProperty(View):
Show a nested section of the current microscope state
"""
microscope = find_component("org.openflexure.microscope")
keys = route.split("/")
keys: List[str] = route.split("/")
try:
value = get_by_path(microscope.configuration, keys)
value: Any = get_by_path(microscope.configuration, keys)
except KeyError:
return abort(404)

2
openflexure_microscope/api/v2/views/streams.py
View file

@ -7,7 +7,7 @@ def gen(camera):
"""Video streaming generator function."""
while True:
# the obtained frame is a jpeg
frame = camera.stream.getframe()
frame: bytes = camera.stream.getframe()
yield (b"--frame\r\n" b"Content-Type: image/jpeg\r\n\r\n" + frame + b"\r\n")