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Merge branch 'new-semantics-testing' into 'master'

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New metadata semantics

See merge request openflexure/openflexure-microscope-server!38
This commit is contained in:
Joel Collins 2020-01-29 17:48:58 +00:00
commit ae589a7063
28 changed files with 536 additions and 861 deletions
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2
docs/source/extensions/example_extension/03_marshaling_data.py
View file

@ -14,7 +14,7 @@ from labthings.server import fields
class MicroscopeIdentifySchema(Schema):
name = fields.String() # Microscopes name
id = fields.UUID() # Microscopes unique ID
status = fields.Dict() # Status dictionary
state = fields.Dict() # Status dictionary
camera = fields.String() # Camera object (represented as a string)
stage = fields.String() # Stage object (represented as a string)

2
docs/source/extensions/example_extension/04_properties.py
View file

@ -19,7 +19,7 @@ from labthings.server import fields
class MicroscopeIdentifySchema(Schema):
name = fields.String() # Microscopes name
id = fields.UUID() # Microscopes unique ID
status = fields.Dict() # Status dictionary
state = fields.Dict() # Status dictionary
camera = fields.String() # Camera object (represented as a string)
stage = fields.String() # Stage object (represented as a string)

2
docs/source/extensions/example_extension/05_actions.py
View file

@ -24,7 +24,7 @@ import io # Used in our capture action
class MicroscopeIdentifySchema(Schema):
name = fields.String() # Microscopes name
id = fields.UUID() # Microscopes unique ID
status = fields.Dict() # Status dictionary
state = fields.Dict() # Status dictionary
camera = fields.String() # Camera object (represented as a string)
stage = fields.String() # Stage object (represented as a string)

2
docs/source/extensions/marshaling.rst
View file

@ -107,7 +107,7 @@ We start by creating a schema to describe how to serialise a :py:class:`openflex
class MicroscopeIdentifySchema(Schema):
name = fields.String() # Microscopes name
id = fields.UUID() # Microscopes unique ID
status = fields.Dict() # Status dictionary
state = fields.Dict() # Status dictionary
camera = fields.String() # Camera object (represented as a string)
stage = fields.String() # Stage object (represented as a string)

24
openflexure_microscope/api/app.py
View file

@ -19,7 +19,7 @@ from openflexure_microscope.paths import (
OPENFLEXURE_VAR_PATH,
OPENFLEXURE_EXTENSIONS_PATH,
settings_file_path,
logs_file_path
logs_file_path,
)
from labthings.server.quick import create_app
@ -92,15 +92,21 @@ labthing.add_root_link(views.CaptureList, "captures")
labthing.add_view(views.CaptureView, f"/captures/<id>")
labthing.add_view(views.CaptureDownload, f"/captures/<id>/download/<filename>")
labthing.add_view(views.CaptureTags, f"/captures/<id>/tags")
labthing.add_view(views.CaptureMetadata, f"/captures/<id>/metadata")
labthing.add_view(views.CaptureAnnotations, f"/captures/<id>/annotations")
# Attach settings and state resources
labthing.add_view(views.SettingsProperty, f"/instrument/settings")
labthing.add_root_link(views.SettingsProperty, "instrumentSettings")
labthing.add_view(views.NestedSettingsProperty, "/instrument/settings/<path:route>")
labthing.add_view(views.StateProperty, "/instrument/state")
labthing.add_view(views.NestedStateProperty, "/instrument/state/<path:route>")
labthing.add_root_link(views.StateProperty, "instrumentState")
labthing.add_view(views.ConfigurationProperty, "/instrument/configuration")
labthing.add_view(
views.NestedConfigurationProperty, "/instrument/configuration/<path:route>"
)
labthing.add_root_link(views.ConfigurationProperty, "instrumentConfiguration")
# Attach settings and status resources
labthing.add_view(views.SettingsProperty, f"/settings")
labthing.add_root_link(views.SettingsProperty, "settings")
labthing.add_view(views.NestedSettingsProperty, "/settings/<path:route>")
labthing.add_view(views.StatusProperty, "/status")
labthing.add_view(views.NestedStatusProperty, "/status/<path:route>")
labthing.add_root_link(views.StatusProperty, "status")
# Attach streams resources
labthing.add_view(views.MjpegStream, f"/streams/mjpeg")

4
openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
View file

@ -21,8 +21,8 @@ def recalibrate(microscope):
"""
scamera = microscope.camera
with scamera.lock:
assert not scamera.status["record_active"], "Can't recalibrate while recording!"
streaming = scamera.status["stream_active"]
assert not scamera.record_active, "Can't recalibrate while recording!"
streaming = scamera.stream_active
if streaming:
logging.info("Stopping stream before recalibration")
scamera.stop_stream_recording(resolution=(640, 480))

101
openflexure_microscope/api/default_extensions/scan.py
View file

@ -1,6 +1,7 @@
import itertools
import logging
import uuid
import datetime
from typing import Tuple
from functools import reduce
@ -71,12 +72,12 @@ def progress():
def capture(
microscope,
basename,
scan_id,
temporary: bool = False,
use_video_port: bool = False,
resize: Tuple[int, int] = None,
bayer: bool = False,
metadata: dict = {},
annotations: dict = {},
tags: list = [],
):
@ -94,16 +95,14 @@ def capture(
output.file, use_video_port=use_video_port, resize=resize, bayer=bayer
)
# Affix metadata
if "scan" not in tags:
tags.append("scan")
# Inject system metadata
output.put_metadata(microscope.metadata, system=True)
output.put_metadata({"instrument": microscope.metadata})
# Insert custom metadata
output.put_metadata(metadata)
# Insert custom metadata
output.put_annotations(annotations)
# Insert custom tags
output.put_tags(tags)
@ -115,7 +114,7 @@ def tile(
microscope,
basename: str = None,
temporary: bool = False,
step_size: int = [2000, 1500, 100],
stride_size: int = [2000, 1500, 100],
grid: list = [3, 3, 5],
style="raster",
autofocus_dz: int = 50,
@ -124,13 +123,13 @@ def tile(
bayer: bool = False,
fast_autofocus=False,
metadata: dict = {},
annotations: dict = {},
tags: list = [],
):
global _images_to_be_captured
global _images_captured_so_far
# Keep task progress
# TODO: Make this line not nasty
_images_to_be_captured = reduce((lambda x, y: x * y), grid)
_images_captured_so_far = 0
@ -138,28 +137,22 @@ def tile(
if not basename:
basename = generate_basename()
# Generate a stack ID
scan_id = uuid.uuid4()
# Store initial position
initial_position = microscope.stage.position
# Add scan metadata
if "time" not in metadata:
metadata["time"] = generate_basename()
metadata.update(
{
"scan_id": scan_id,
"basename": basename,
"scan_parameters": {
"step_size": step_size,
"grid": grid,
"style": style,
"autofocus_dz": autofocus_dz,
},
# Add dataset metadata
dataset_d = {
"dataset": {
"id": uuid.uuid4(),
"type": "xyzScan",
"name": basename,
"acquisitionDate": datetime.datetime.now().isoformat(),
"strideSize": stride_size,
"grid": grid,
"style": style,
"autofocusDz": autofocus_dz,
}
)
}
# Check if autofocus is enabled
autofocus_extension = find_extension("org.openflexure.autofocus")
@ -174,11 +167,11 @@ def tile(
autofocus_enabled = False
z_stack_dz = (
grid[2] * step_size[2] if grid[2] > 1 else 0
grid[2] * stride_size[2] if grid[2] > 1 else 0
) # shorthand for Z stack range
# Construct an x-y grid (worry about z later)
x_y_grid = construct_grid(initial_position, step_size[:2], grid[:2], style=style)
x_y_grid = construct_grid(initial_position, stride_size[:2], grid[:2], style=style)
# Keep the initial Z position the same as our current position
next_z = initial_position[2]
@ -209,26 +202,25 @@ def tile(
target_z=-z_stack_dz / 2.0, # Finish below the focus
initial_move_up=False, # We're already at the top of the scan
)
# TODO: save the focus data for future reference? Use it for diagnostics?
else:
logging.debug("Running autofocus")
autofocus_extension.autofocus(
range(-3 * autofocus_dz, 4 * autofocus_dz, autofocus_dz)
)
logging.debug("Finished autofocus")
time.sleep(1) # TODO: Remove
time.sleep(1)
# If we're not doing a z-stack, just capture
if grid[2] <= 1:
capture(
microscope,
basename,
scan_id,
temporary=temporary,
use_video_port=use_video_port,
resize=resize,
bayer=bayer,
metadata=metadata,
metadata=dataset_d,
annotations=annotations,
tags=tags,
)
# Update task progress
@ -240,15 +232,14 @@ def tile(
microscope=microscope,
basename=basename,
temporary=temporary,
scan_id=scan_id,
step_size=step_size[2],
step_size=stride_size[2],
steps=grid[2],
center=not fast_autofocus, # fast_autofocus does this for us!
return_to_start=not fast_autofocus,
use_video_port=use_video_port,
resize=resize,
bayer=bayer,
metadata=metadata,
metadata=dataset_d,
annotations=annotations,
tags=tags,
)
# Make sure we use our current best estimate of focus (i.e. the current position) next point
@ -259,7 +250,7 @@ def tile(
) # Fast autofocus requires us to start at the top of the range
if grid[2] > 1:
next_z -= int(
grid[2] / 2.0 * step_size[2]
grid[2] / 2.0 * stride_size[2]
) # Z stacking means we're higher up to start with
logging.debug("Returning to {}".format(initial_position))
@ -270,39 +261,25 @@ def stack(
microscope,
basename: str = None,
temporary: bool = False,
scan_id: str = None,
step_size: int = 100,
steps: int = 5,
center: bool = True,
return_to_start: bool = True,
use_video_port: bool = False,
resize: Tuple[int, int] = None,
bayer: bool = False,
metadata: dict = {},
annotations: dict = {},
tags: list = [],
):
global _images_captured_so_far
# Generate a basename if none given
if not basename:
basename = generate_basename()
# Generate a stack ID
if not scan_id:
scan_id = uuid.uuid4()
# Add scan metadata
if not "time" in metadata:
metadata["time"] = generate_basename()
# Store initial position
initial_position = microscope.stage.position
with microscope.lock:
# Move to center scan
if center:
logging.debug("Moving to starting position")
microscope.stage.move_rel([0, 0, int((-step_size * steps) / 2)])
logging.debug("Moving to starting position")
microscope.stage.move_rel([0, 0, int((-step_size * steps) / 2)])
for i in range(steps):
time.sleep(0.1)
@ -310,12 +287,12 @@ def stack(
capture(
microscope,
basename,
scan_id,
temporary=temporary,
use_video_port=use_video_port,
resize=resize,
bayer=bayer,
metadata=metadata,
annotations=annotations,
tags=tags,
)
# Update task progress
@ -337,16 +314,18 @@ def stack(
class TileScanAPI(View):
@use_args(
{
"filename": fields.String(),
"filename": fields.String(missing=None, example=None),
"temporary": fields.Boolean(missing=False),
"step_size": fields.List(fields.Integer, missing=[2000, 1500, 100]),
"grid": fields.List(fields.Integer, missing=[3, 3, 5]),
"stride_size": fields.List(
fields.Integer, missing=[2000, 1500, 100], example=[2000, 1500, 100]
),
"grid": fields.List(fields.Integer, missing=[3, 3, 3], example=[3, 3, 3]),
"style": fields.String(missing="raster"),
"autofocus_dz": fields.Integer(missing=50),
"fast_autofocus": fields.Boolean(missing=False),
"use_video_port": fields.Boolean(missing=False),
"bayer": fields.Boolean(missing=False),
"metadata": fields.Dict(missing={}),
"annotations": fields.Dict(missing={}, example={"Foo": "Bar"}),
"tags": fields.List(fields.String, missing=[]),
"resize": fields.Dict(missing=None), # TODO: Validate keys
}
@ -373,7 +352,7 @@ class TileScanAPI(View):
microscope,
basename=args.get("filename"),
temporary=args.get("temporary"),
step_size=args.get("step_size"),
stride_size=args.get("stride_size"),
grid=args.get("grid"),
style=args.get("style"),
autofocus_dz=args.get("autofocus_dz"),
@ -381,7 +360,7 @@ class TileScanAPI(View):
resize=resize,
bayer=args.get("bayer"),
fast_autofocus=args.get("fast_autofocus"),
metadata=args.get("metadata"),
annotations=args.get("annotations"),
tags=args.get("tags"),
)

14
openflexure_microscope/api/default_extensions/zip_builder.py
View file

@ -73,17 +73,15 @@ class ZipManager:
# Update task progress
update_task_progress(int((index / n_files) * 100))
session_id = uuid.uuid4()
session_key = str(session_id)
# self.session_zips[session_id] = fp
self.session_zips[session_key] = {
session_id = str(uuid.uuid4())
self.session_zips[session_id] = {
"id": session_id,
"fp": fp,
"data_size": data_size_megabytes,
"zip_size": os.path.getsize(fp.name) * 1e-6,
}
return self.session_zips[session_key]
return self.session_zips[session_id]
def zip_from_id(self, session_id):
return self.session_zips[session_id]["fp"]
@ -103,13 +101,13 @@ class ZipBuilderAPIView(View):
task = taskify(default_zip_manager.build_zip_from_capture_ids)(microscope, ids)
# Return a handle on the autofocus task
return jsonify(task.state), 201
return task.state, 201
@ThingProperty
class ZipListAPIView(View):
def get(self):
return jsonify(default_zip_manager.session_zips)
return default_zip_manager.session_zips
class ZipGetterAPIView(View):
@ -141,7 +139,7 @@ class ZipGetterAPIView(View):
del default_zip_manager.session_zips[session_id]
return jsonify({"return": session_id})
return {"return": session_id}
zip_extension_v2 = BaseExtension("org.openflexure.zipbuilder", version="2.0.0-beta.1")

29
openflexure_microscope/api/microscope.py
View file

@ -3,38 +3,9 @@ from openflexure_microscope.camera.capture import build_captures_from_exif
import logging
# Import device modules
# NB this will eventually be handled by the RC file, so you can choose what device
# class should be attached.
try:
from openflexure_microscope.camera.pi import PiCameraStreamer
except ImportError:
logging.warning("Unable to import PiCameraStreamer")
from openflexure_microscope.camera.mock import MockStreamer
from openflexure_microscope.stage.sanga import SangaStage
from openflexure_microscope.stage.mock import MockStage
default_microscope = Microscope()
# Initialise camera
logging.debug("Creating camera object...")
try:
api_camera = PiCameraStreamer()
except Exception as e:
logging.error(e)
logging.warning("No valid camera hardware found. Falling back to mock camera!")
api_camera = MockStreamer()
# Initialise stage
logging.debug("Creating stage object...")
api_stage = MockStage()
# Attach devices to microscope
logging.debug("Attaching devices to microscope...")
default_microscope.attach(api_camera, api_stage)
# Restore loaded capture array to camera object
logging.debug("Restoring captures...")
default_microscope.camera.images = build_captures_from_exif(

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

@ -1,4 +1,4 @@
from .actions import enabled_root_actions
from .captures import *
from .state import *
from .instrument import *
from .streams import *

15
openflexure_microscope/api/v2/views/actions/camera.py
View file

@ -36,7 +36,7 @@ class CaptureAPI(View):
"bayer": fields.Boolean(
missing=False, description="Store raw bayer data in file"
),
"metadata": fields.Dict(missing={}, example={"Client": "SwaggerUI"}),
"annotations": fields.Dict(missing={}, example={"Client": "SwaggerUI"}),
"tags": fields.List(fields.String, missing=[], example=["docs"]),
"resize": fields.Dict(
missing=None, example={"width": 640, "height": 480}
@ -75,11 +75,10 @@ class CaptureAPI(View):
)
# Inject system metadata
output.put_metadata(microscope.metadata, system=True)
output.put_metadata({"instrument": microscope.metadata})
# Insert custom metadata
output.put_metadata(args.get("metadata"))
output.put_annotations(args.get("annotations"))
# Insert custom tags
output.put_tags(args.get("tags"))
@ -164,8 +163,8 @@ class GPUPreviewStartAPI(View):
microscope.camera.start_preview(fullscreen=fullscreen, window=window)
# TODO: Make schema for microscope status
return jsonify(microscope.status)
# TODO: Make schema for microscope state
return jsonify(microscope.state)
@ThingAction
@ -176,5 +175,5 @@ class GPUPreviewStopAPI(View):
"""
microscope = find_component("org.openflexure.microscope")
microscope.camera.stop_preview()
# TODO: Make schema for microscope status
return jsonify(microscope.status)
# TODO: Make schema for microscope state
return jsonify(microscope.state)

8
openflexure_microscope/api/v2/views/actions/stage.py
View file

@ -52,8 +52,8 @@ class MoveStageAPI(View):
else:
logging.warning("Unable to move. No stage found.")
# TODO: Make schema for microscope status
return jsonify(microscope.status["stage"]["position"])
# TODO: Make schema for microscope state
return jsonify(microscope.state["stage"]["position"])
@ThingAction
@ -66,5 +66,5 @@ class ZeroStageAPI(View):
microscope = find_component("org.openflexure.microscope")
microscope.stage.zero_position()
# TODO: Make schema for microscope status
return jsonify(microscope.status["stage"])
# TODO: Make schema for microscope state
return jsonify(microscope.state["stage"])

26
openflexure_microscope/api/v2/views/captures.py
View file

@ -20,7 +20,7 @@ class CaptureSchema(Schema):
data_key="path", description="Path of file on microscope device"
)
exists = fields.Bool(data_key="available")
filename = fields.String()
name = fields.String()
metadata = fields.Dict()
links = fields.Dict()
@ -39,16 +39,18 @@ class CaptureSchema(Schema):
"mimetype": "application/json",
**description_from_view(CaptureTags),
},
"metadata": {
"href": url_for(CaptureMetadata.endpoint, id=data.id, _external=True),
"annotations": {
"href": url_for(
CaptureAnnotations.endpoint, id=data.id, _external=True
),
"mimetype": "application/json",
**description_from_view(CaptureMetadata),
**description_from_view(CaptureAnnotations),
},
"download": {
"href": url_for(
CaptureDownload.endpoint,
id=data.id,
filename=data.filename,
filename=data.name,
_external=True,
),
"mimetype": "image/jpeg",
@ -62,6 +64,9 @@ capture_schema = CaptureSchema()
capture_list_schema = CaptureSchema(many=True)
from pprint import pprint
@ThingProperty
@Tag("captures")
class CaptureList(View):
@ -197,10 +202,10 @@ class CaptureTags(View):
@Tag("captures")
class CaptureMetadata(View):
class CaptureAnnotations(View):
def get(self, id):
"""
Get metadata associated with a single image capture
Get annotations associated with a single image capture
"""
microscope = find_component("org.openflexure.microscope")
capture_obj = microscope.camera.image_from_id(id)
@ -208,7 +213,7 @@ class CaptureMetadata(View):
if not capture_obj:
return abort(404) # 404 Not Found
return jsonify(capture_obj.metadata)
return jsonify(capture_obj.annotations)
def put(self, id):
"""
@ -226,7 +231,6 @@ class CaptureMetadata(View):
if type(data_dict) != dict:
return abort(400)
# TODO: Allow putting system metadata maybe?
capture_obj.put_metadata(data_dict)
capture_obj.put_annotations(data_dict)
return jsonify(capture_obj.metadata)
return jsonify(capture_obj.annotations)

40
openflexure_microscope/api/v2/views/state.py → openflexure_microscope/api/v2/views/instrument.py
View file

@ -30,7 +30,7 @@ class SettingsProperty(View):
logging.debug("Updating settings from PUT request:")
logging.debug(payload.json)
microscope.apply_settings(payload.json)
microscope.update_settings(payload.json)
microscope.save_settings()
return self.get()
@ -65,24 +65,24 @@ class NestedSettingsProperty(View):
dictionary = create_from_path(keys)
set_by_path(dictionary, keys, payload.json)
microscope.apply_settings(dictionary)
microscope.update_settings(dictionary)
microscope.save_settings()
return self.get(route)
@ThingProperty
class StatusProperty(View):
class StateProperty(View):
def get(self):
"""
Show current read-only state of the microscope
"""
microscope = find_component("org.openflexure.microscope")
return jsonify(microscope.status)
return jsonify(microscope.state)
@Tag("properties")
class NestedStatusProperty(View):
class NestedStateProperty(View):
@doc_response(404, description="Status key cannot be found")
def get(self, route):
"""
@ -92,7 +92,35 @@ class NestedStatusProperty(View):
keys = route.split("/")
try:
value = get_by_path(microscope.status, keys)
value = get_by_path(microscope.state, keys)
except KeyError:
return abort(404)
return jsonify(value)
@ThingProperty
class ConfigurationProperty(View):
def get(self):
"""
Show current read-only state of the microscope
"""
microscope = find_component("org.openflexure.microscope")
return jsonify(microscope.configuration)
@Tag("properties")
class NestedConfigurationProperty(View):
@doc_response(404, description="Configuration key cannot be found")
def get(self, route):
"""
Show a nested section of the current microscope state
"""
microscope = find_component("org.openflexure.microscope")
keys = route.split("/")
try:
value = get_by_path(microscope.configuration, keys)
except KeyError:
return abort(404)

49
openflexure_microscope/camera/base.py
View file

@ -91,20 +91,6 @@ class CameraEvent(object):
class BaseCamera(metaclass=ABCMeta):
"""
Base implementation of StreamingCamera.
Attributes:
thread: Background thread reading frames from camera
camera: Camera object
lock (:py:class:`labthings.lock.StrictLock`): Strict lock controlling thread
access to stage hardware
frame (bytes): Current frame is stored here by background thread
last_access (time): Time of last client access to the camera
stream_timeout (int): Number of inactive seconds before timing out the stream
stream_timeout_enabled (bool): Enable or disable timing out the stream
status (dict): Dictionary for capture state
paths (dict): Dictionary of capture paths
images (list): List of image capture objects
videos (list): List of video capture objects
"""
def __init__(self):
@ -121,7 +107,8 @@ class BaseCamera(metaclass=ABCMeta):
self.stream_timeout = 20
self.stream_timeout_enabled = False
self.status = {"board": None}
self.stream_active = False
self.record_active = False
self.paths = {"default": BASE_CAPTURE_PATH, "temp": TEMP_CAPTURE_PATH}
@ -129,8 +116,24 @@ class BaseCamera(metaclass=ABCMeta):
self.images = []
self.videos = []
@property
@abstractmethod
def apply_settings(self, config: dict):
def configuration(self):
"""The current camera configuration."""
pass
@property
@abstractmethod
def state(self):
"""The current read-only camera state."""
pass
@property
def settings(self):
return self.read_settings()
@abstractmethod
def update_settings(self, config: dict):
"""Update settings from a config dictionary"""
with self.lock:
# Apply valid config params to camera object
@ -187,7 +190,7 @@ class BaseCamera(metaclass=ABCMeta):
self.last_access = time.time()
self.stop = False
if not self.status["stream_active"]:
if not self.stream_active:
# start background frame thread
self.thread = threading.Thread(target=self._thread)
self.thread.daemon = True
@ -207,12 +210,12 @@ class BaseCamera(metaclass=ABCMeta):
logging.debug("Stopping worker thread")
timeout_time = time.time() + timeout
if self.status["stream_active"]:
if self.stream_active:
self.stop = True
self.thread.join() # Wait for stream thread to exit
logging.debug("Waiting for stream thread to exit.")
while self.status["stream_active"]:
while self.stream_active:
if time.time() > timeout_time:
logging.debug("Timeout waiting for worker thread close.")
raise TimeoutError("Timeout waiting for worker thread close.")
@ -352,7 +355,7 @@ class BaseCamera(metaclass=ABCMeta):
self.frames_iterator = self.frames()
logging.debug("Entering worker thread.")
self.status["stream_active"] = True
self.stream_active = True
for frame in self.frames_iterator:
self.frame = frame
@ -365,9 +368,7 @@ class BaseCamera(metaclass=ABCMeta):
and ( # If using timeout
time.time() - self.last_access > self.stream_timeout
)
and not self.status[ # And timeout time
"preview_active"
] # And GPU preview is not active
and not self.preview_active # And GPU preview is not active
):
self.frames_iterator.close()
break
@ -383,4 +384,4 @@ class BaseCamera(metaclass=ABCMeta):
logging.debug("BaseCamera worker thread exiting...")
# Set stream_activate state
self.status["stream_active"] = False
self.stream_active = False

96
openflexure_microscope/camera/capture.py
View file

@ -8,6 +8,7 @@ import yaml
import json
import logging
from PIL import Image
import dateutil.parser
import atexit
from openflexure_microscope.camera import piexif
@ -93,18 +94,18 @@ def capture_from_exif(path, exif_dict):
# Build file path information
capture.split_file_path(capture.file)
# Populate capture parameters
capture.id = exif_dict["id"]
capture.timestring = exif_dict["time"]
capture.format = exif_dict["format"]
# Image metadata
image_metadata = exif_dict.pop("image")
capture.custom_metadata = (
exif_dict["custom"] if "custom" in exif_dict.keys() else {}
)
capture.system_metadata = (
exif_dict["system"] if "system" in exif_dict.keys() else {}
)
capture.tags = exif_dict["tags"]
# Populate capture parameters
capture.id = image_metadata.get("id")
capture.datetime = dateutil.parser.isoparse(image_metadata.get("acquisitionDate"))
capture.format = image_metadata.get("format")
capture.tags = image_metadata.get("tags")
capture.annotations = image_metadata.get("annotations")
# Since we popped the "image" key, we dump whatever is left in _metadata
capture._metadata = exif_dict
return capture
@ -113,16 +114,6 @@ class CaptureObject(object):
"""
StreamObject used to store and process on-disk capture data, and metadata.
Serves to simplify modifying properties of on-disk capture data.
Attributes:
timestring (str): Timestring of capture creation time
custom_metadata (dict): Dictionary of custom metadata to be included in metadata file
tags (list): List of tags. Essentially just as extra custom metadata field, but useful for quick organisation
filefolder (str): Folder in which the capture file will be stored
filename (str): Full name of the capture file
basename (str): Filename of the capture, without a file extension
format (str): Format of the capture data
"""
def __init__(self, filepath) -> None:
@ -131,17 +122,20 @@ class CaptureObject(object):
# Store a nice ID
self.id = uuid.uuid4() #: str: Unique capture ID
logging.debug("Created StreamObject {}".format(self.id))
self.timestring = datetime.datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
self.datetime = datetime.datetime.now()
# Create file name. Default to UUID
self.file = filepath
self.split_file_path(self.file)
# Dictionary for storing custom metadata
self.custom_metadata = {}
# Dictionary for adding top-level metadata (cannmot be accessed through web API)
self.system_metadata = {}
if not os.path.exists(self.filefolder):
os.makedirs(self.filefolder)
# Dictionary for adding top-level metadata (cannmot be accessed through web API)
self._metadata = {}
# Dictionary for storing custom annotations
self.annotations = {}
# List for storing tags
self.tags = []
@ -158,15 +152,11 @@ class CaptureObject(object):
Args:
filepath (str): String of the full file path, including file format extension
"""
# Split the full file path into a folder and a filename
self.filefolder, self.filename = os.path.split(filepath)
# Split the filename out from it's file extension
self.basename = os.path.splitext(self.filename)[0]
self.format = self.filename.split(".")[-1]
# Create folder and file
if not os.path.exists(self.filefolder):
os.makedirs(self.filefolder)
# Split the full file path into a folder and a name
self.filefolder, self.name = os.path.split(filepath)
# Split the name out from it's file extension
self.basename = os.path.splitext(self.name)[0]
self.format = self.name.split(".")[-1]
@property
def exists(self) -> bool:
@ -204,17 +194,24 @@ class CaptureObject(object):
# HANDLE METADATA
def put_metadata(self, data: dict, system: bool = False) -> None:
def put_annotations(self, data: dict) -> None:
"""
Merge metadata from a passed dictionary into the capture metadata, and saves.
Merge annotations from a passed dictionary into the capture metadata, and saves.
Args:
data (dict): Dictionary of metadata to be added
"""
if system:
self.system_metadata.update(data)
else:
self.custom_metadata.update(data)
self.annotations.update(data)
self.save_metadata()
def put_metadata(self, data: dict) -> None:
"""
Merge root metadata from a passed dictionary into the capture metadata, and saves.
Args:
data (dict): Dictionary of metadata to be added
"""
self._metadata.update(data)
self.save_metadata()
def save_metadata(self) -> None:
@ -244,12 +241,15 @@ class CaptureObject(object):
and any added custom metadata and tags.
"""
d = {
"id": self.id,
"time": self.timestring,
"format": self.format,
"tags": self.tags,
"custom": self.custom_metadata,
"system": self.system_metadata,
"image": {
"id": self.id,
"name": self.name,
"acquisitionDate": self.datetime.isoformat(),
"format": self.format,
"tags": self.tags,
"annotations": self.annotations,
},
**self._metadata,
}
# Add custom metadata to dictionary
@ -262,7 +262,7 @@ class CaptureObject(object):
"""
# Create basic state dictionary
d = {"path": self.file, "filename": self.filename, "metadata": self.metadata}
d = {"path": self.file, "name": self.name, "metadata": self.metadata}
# Combined availability of data
if self.exists:

22
openflexure_microscope/camera/mock.py
View file

@ -26,17 +26,13 @@ We override the logging settings in api.app by setting a level for PIL here.
pil_logger = logging.getLogger("PIL")
pil_logger.setLevel(logging.INFO)
# MAIN CLASS
class MockStreamer(BaseCamera):
class MissingCamera(BaseCamera):
def __init__(self):
# Run BaseCamera init
BaseCamera.__init__(self)
# Store state of PiCameraStreamer
self.status.update(
{"stream_active": False, "record_active": False, "board": None}
)
# Update config properties
self.image_resolution = (1312, 976)
self.stream_resolution = (640, 480)
@ -71,6 +67,16 @@ class MockStreamer(BaseCamera):
image.save(self.stream, format="JPEG")
@property
def configuration(self):
"""The current camera configuration."""
return {}
@property
def state(self):
"""The current read-only camera state."""
return {}
def initialisation(self):
"""Run any initialisation code when the frame iterator starts."""
pass
@ -101,7 +107,7 @@ class MockStreamer(BaseCamera):
return conf_dict
def apply_settings(self, config: dict):
def update_settings(self, config: dict):
"""
Write a config dictionary to the PiCameraStreamer config.
@ -117,7 +123,7 @@ class MockStreamer(BaseCamera):
with self.lock:
# Apply valid config params to camera object
if not self.status["record_active"]: # If not recording a video
if not self.record_active: # If not recording a video
for key, value in config.items(): # For each provided setting
if hasattr(self, key):

68
openflexure_microscope/camera/pi.py
View file

@ -47,6 +47,7 @@ from .base import BaseCamera, CaptureObject
from .set_picamera_gain import set_analog_gain, set_digital_gain
from openflexure_microscope.paths import settings_file_path
from openflexure_microscope.utilities import serialise_array_b64
# MAIN CLASS
@ -84,15 +85,8 @@ class PiCameraStreamer(BaseCamera):
picamera.PiCamera()
) #: :py:class:`picamera.PiCamera`: Picamera object
# Store status of PiCameraStreamer
self.status.update(
{
"stream_active": False,
"record_active": False,
"preview_active": False,
"board": f"picamera_{self.camera.revision}",
}
)
# Store state of PiCameraStreamer
self.preview_active = False
# Reset variable states
self.set_zoom(1.0)
@ -116,15 +110,22 @@ class PiCameraStreamer(BaseCamera):
"picamera_lst.npy"
) #: str: Path of .npy lens shading table file
# Update board identifier
self.status.update({})
# Create an empty stream
self.stream = io.BytesIO()
# Start streaming
self.start_worker()
@property
def configuration(self):
"""The current camera configuration."""
return {"board": self.camera.revision}
@property
def state(self):
"""The current read-only camera state."""
return {}
def initialisation(self):
"""Run any initialisation code when the frame iterator starts."""
pass
@ -156,7 +157,7 @@ class PiCameraStreamer(BaseCamera):
"picamera_lst_path": self.picamera_lst_path
if os.path.isfile(self.picamera_lst_path)
else None,
"picamera_settings": {},
"picamera": {},
}
)
@ -165,7 +166,7 @@ class PiCameraStreamer(BaseCamera):
try:
value = getattr(self.camera, key)
logging.debug("Reading PiCamera().{}: {}".format(key, value))
conf_dict["picamera_settings"][key] = value
conf_dict["picamera"][key] = value
except AttributeError:
logging.debug("Unable to read PiCamera attribute {}".format(key))
@ -176,7 +177,7 @@ class PiCameraStreamer(BaseCamera):
logging.info("Saving picamera_lst to {}".format(self.picamera_lst_path))
self.save_lens_shading_table()
def apply_settings(self, config: dict):
def update_settings(self, config: dict):
"""
Write a config dictionary to the PiCameraStreamer config.
@ -194,23 +195,23 @@ class PiCameraStreamer(BaseCamera):
with self.lock:
# Apply valid config params to Picamera object
if not self.status["record_active"]: # If not recording a video
if not self.record_active: # If not recording a video
# Pause stream while changing settings
if self.status["stream_active"]: # If stream is active
if self.stream_active: # If stream is active
logging.info("Pausing stream to update config.")
self.stop_stream_recording() # Pause stream
paused_stream = True # Remember to unpause stream when done
# PiCamera parameters
if "picamera_settings" in config: # If new settings are given
if "picamera" in config: # If new settings are given
self.apply_picamera_settings(
config["picamera_settings"], pause_for_effect=True
config["picamera"], pause_for_effect=True
)
# PiCameraStreamer parameters
for key, value in config.items(): # For each provided setting
if (key != "picamera_settings") and hasattr(self, key):
if (key != "picamera") and hasattr(self, key):
setattr(self, key, value)
# Handle lens shading if camera supports it
@ -332,13 +333,13 @@ class PiCameraStreamer(BaseCamera):
Change the camera zoom, handling re-centering and scaling.
"""
with self.lock:
self.status["zoom_value"] = float(zoom_value)
if self.status["zoom_value"] < 1:
self.status["zoom_value"] = 1
self.zoom_value = float(zoom_value)
if self.zoom_value < 1:
self.zoom_value = 1
# Richard's code for zooming !
fov = self.camera.zoom
centre = np.array([fov[0] + fov[2] / 2.0, fov[1] + fov[3] / 2.0])
size = 1.0 / self.status["zoom_value"]
size = 1.0 / self.zoom_value
# If the new zoom value would be invalid, move the centre to
# keep it within the camera's sensor (this is only relevant
# when zooming out, if the FoV is not centred on (0.5, 0.5)
@ -365,7 +366,7 @@ class PiCameraStreamer(BaseCamera):
self.camera.preview.window = window
if fullscreen:
self.camera.preview.fullscreen = fullscreen
self.status["preview_active"] = True
self.preview_active = True
except picamera.exc.PiCameraMMALError as e:
logging.error(
"Suppressed a MMALError in start_preview. Exception: {}".format(e)
@ -380,7 +381,7 @@ class PiCameraStreamer(BaseCamera):
def stop_preview(self):
"""Stop the on board GPU camera preview."""
self.camera.stop_preview()
self.status["preview_active"] = False
self.preview_active = False
def start_recording(self, output, fmt: str = "h264", quality: int = 15):
"""Start recording.
@ -398,7 +399,7 @@ class PiCameraStreamer(BaseCamera):
"""
with self.lock:
# Start recording method only if a current recording is not running
if not self.status["record_active"]:
if not self.record_active:
# Start the camera video recording on port 2
logging.info("Recording to {}".format(output))
@ -411,8 +412,8 @@ class PiCameraStreamer(BaseCamera):
quality=quality,
)
# Update status dictionary
self.status["record_active"] = True
# Update state
self.record_active = True
return output
@ -431,8 +432,8 @@ class PiCameraStreamer(BaseCamera):
self.camera.stop_recording(splitter_port=2)
logging.info("Recording stopped")
# Update status dictionary
self.status["record_active"] = False
# Update state
self.record_active = False
def stop_stream_recording(
self, splitter_port: int = 1, resolution: Tuple[int, int] = None
@ -500,7 +501,7 @@ class PiCameraStreamer(BaseCamera):
self.camera.resolution = resolution
# If the stream should be active
if self.status["stream_active"]:
if self.stream_active:
try:
# Start recording on stream port
self.camera.start_recording(
@ -551,7 +552,7 @@ class PiCameraStreamer(BaseCamera):
if isinstance(output, CaptureObject):
target = output.file
else:
target = target
target = output
with self.lock:
logging.info("Capturing to {}".format(output))
@ -680,7 +681,6 @@ class PiCameraStreamer(BaseCamera):
# Start stream recording (and set resolution)
self.start_stream_recording()
# Update status
logging.debug("STREAM ACTIVE")
# While the iterator is not closed

53
openflexure_microscope/config.py
View file

@ -1,4 +1,5 @@
import json
import flask
import os
import errno
import logging
@ -7,7 +8,12 @@ from uuid import UUID
import numpy as np
from fractions import Fraction
from .paths import CONFIG_FILE_PATH, DEFAULT_CONFIG_FILE_PATH
from .paths import (
SETTINGS_FILE_PATH,
DEFAULT_SETTINGS_FILE_PATH,
CONFIGURATION_FILE_PATH,
DEFAULT_CONFIGURATION_FILE_PATH,
)
class OpenflexureSettingsFile:
@ -19,21 +25,21 @@ class OpenflexureSettingsFile:
expand (bool): Expand paths to valid auxillary config files.
"""
def __init__(self, config_path: str = None):
global DEFAULT_CONFIG, CONFIG_FILE_PATH
def __init__(self, path: str, defaults: dict = {}):
global DEFAULT_SETTINGS
# Set arguments
self.config_path = config_path or CONFIG_FILE_PATH
self.path = path
# Initialise basic config file with defaults if it doesn't exist
initialise_file(self.config_path, populate=DEFAULT_CONFIG)
initialise_file(self.path, populate=defaults)
def load(self) -> dict:
"""
Loads settings from a file on-disk.
"""
# Unexpanded config dictionary (used at load/save time)
loaded_config = load_json_file(self.config_path)
loaded_config = load_json_file(self.path)
logging.debug("Reading settings from disk")
return loaded_config
@ -50,11 +56,11 @@ class OpenflexureSettingsFile:
save_settings = config
if backup:
if os.path.isfile(self.config_path):
shutil.copyfile(self.config_path, self.config_path + ".bk")
if os.path.isfile(self.path):
shutil.copyfile(self.path, self.path + ".bk")
logging.debug("Saving settings dictionary to disk")
save_json_file(self.config_path, save_settings)
save_json_file(self.path, save_settings)
def merge(self, config: dict) -> dict:
"""
@ -71,7 +77,7 @@ class OpenflexureSettingsFile:
return settings
class JSONEncoder(json.JSONEncoder):
class JSONEncoder(flask.json.JSONEncoder):
"""
A custom JSON encoder, with type conversions for PiCamera fractions, Numpy integers, and Numpy arrays
"""
@ -88,11 +94,14 @@ class JSONEncoder(json.JSONEncoder):
# Numpy arrays
elif isinstance(o, np.ndarray):
return o.tolist()
# UUIDs
elif isinstance(o, UUID):
return str(o)
else:
# call base class implementation which takes care of
# raising exceptions for unsupported types
try:
return json.JSONEncoder.default(self, o)
return flask.json.JSONEncoder.default(self, o)
# if it's some mystery object, just return a string representation
except TypeError:
return str(o)
@ -178,10 +187,22 @@ def initialise_file(config_path, populate: str = "{}\n"):
outfile.write(populate)
# Load the default config
with open(DEFAULT_CONFIG_FILE_PATH, "r") as default_rc:
DEFAULT_CONFIG = default_rc.read()
# Load the default settings
with open(DEFAULT_SETTINGS_FILE_PATH, "r") as default_settings:
DEFAULT_SETTINGS = default_settings.read()
#: Default user settings object
user_settings = OpenflexureSettingsFile(config_path=CONFIG_FILE_PATH)
user_settings = OpenflexureSettingsFile(
path=SETTINGS_FILE_PATH, defaults=DEFAULT_SETTINGS
)
# Load the default configuration
with open(DEFAULT_CONFIGURATION_FILE_PATH, "r") as default_configuration:
DEFAULT_CONFIGURATION = default_configuration.read()
#: Default user settings object
user_configuration = OpenflexureSettingsFile(
path=CONFIGURATION_FILE_PATH, defaults=DEFAULT_CONFIGURATION
)

220
openflexure_microscope/microscope.py
View file

@ -6,15 +6,21 @@ import logging
import pkg_resources
import uuid
from openflexure_microscope.stage.base import BaseStage
from openflexure_microscope.stage.mock import MockStage
from openflexure_microscope.camera.base import BaseCamera
from openflexure_microscope.camera.mock import MockStreamer
from openflexure_microscope.stage.mock import MissingStage
from openflexure_microscope.camera.mock import MissingCamera
from openflexure_microscope.stage.sanga import SangaStage
try:
from openflexure_microscope.camera.pi import PiCameraStreamer
except ImportError:
logging.warning("Unable to import PiCameraStreamer")
from openflexure_microscope.camera.mock import MissingCamera
from openflexure_microscope.utilities import serialise_array_b64
from openflexure_microscope.config import user_settings
from openflexure_microscope.config import user_settings, user_configuration
from labthings.core.lock import CompositeLock
from labthings.core.utilities import rupdate
class Microscope:
@ -24,20 +30,26 @@ class Microscope:
The camera and stage objects may already be initialised, and can be passed as arguments.
"""
def __init__(self):
# Initial attributes
self.id = uuid.uuid4() #: Microscope UUID
self.name = self.id #: Microscope name (modifiable)
def __init__(self, settings=user_settings, configuration=user_configuration):
self.id = uuid.uuid4()
self.name = self.id
self.fov = [0, 0] #: Microscope field-of-view in stage motor steps
self.camera = None #: Currently connected camera object
self.stage = None #: Currently connected stage object
# Store settings and configuration files
self.settings_file = settings
self.configuration_file = configuration
# Initialise with an empty composite lock
#: :py:class:`labthings.lock.CompositeLock`: Composite lock for locking both camera and stage
self.lock = CompositeLock([])
self.camera = None #: Currently connected camera object
self.stage = None #: Currently connected stage object
self.setup(self.configuration_file.load()) # Attach components
# Apply settings loaded from file
self.apply_settings(user_settings.load())
self.update_settings(self.settings_file.load())
def __enter__(self):
"""Create microscope on context enter."""
@ -56,58 +68,45 @@ class Microscope:
self.stage.close()
logging.info("Closed {}".format(self))
def attach(self, camera: BaseCamera, stage: BaseStage):
def setup(self, configuration):
"""
Retroactively attaches a camera and stage to the microscope object.
Allows the microscope to be created as a "dummy", with hardware communications
opened at a later time.
Args:
camera (:py:class:`openflexure_microscope.camera.base.BaseCamera`): camera object
stage (:py:class:`openflexure_microscope.stage.base.BaseStage`): stage object
Attach microscope components based on initially passed configuration file
"""
settings_full = self.read_settings()
### Detector
if configuration.get("camera"):
camera_type = configuration["camera"].get("type")
if camera_type in ("PiCamera", "PiCameraStreamer"):
try:
self.camera = PiCameraStreamer()
except Exception as e:
logging.error(e)
logging.warning("No compatible camera hardware found.")
logging.debug("Attaching camera...")
self.camera = (
camera
) #: :py:class:`openflexure_microscope.camera.base.BaseCamera`: Picamera object
### Stage
if configuration.get("stage"):
stage_type = configuration["stage"].get("type")
stage_port = configuration["stage"].get("port")
if stage_type in ("SangaBoard", "SangaStage"):
self.stage = SangaStage(port=stage_port)
### Fallbacks
if not self.camera:
logging.info("No camera attached.")
else:
logging.info("Attached camera {}".format(camera))
if hasattr(self.camera, "lock"): # If camera has a lock
logging.info("Attaching {} to composite lock.".format(self.camera.lock))
# Add the lock to the microscope composite lock
self.lock.locks.append(self.camera.lock)
logging.debug("Attaching stage...")
self.stage = (
stage
) #: :py:class:`openflexure_microscope.stage.base.BaseStage`: OpenFlexure stage object
self.camera = MissingCamera()
if not self.stage:
logging.info("No stage attached.")
else:
logging.info("Attached stage {}".format(stage))
self.stage = MissingStage()
if hasattr(self.stage, "lock"): # If stage object has a lock
logging.info(
"Attaching lock {} to composite lock.".format(self.stage.lock)
)
# Add the lock to the microscope composite lock
self.lock.locks.append(self.stage.lock)
logging.info("Reapplying settings to newly attached devices")
self.apply_settings(settings_full)
### Locks
if hasattr(self.camera, "lock"):
self.lock.locks.append(self.camera.lock)
if hasattr(self.stage, "lock"):
self.lock.locks.append(self.stage.lock)
def has_real_stage(self) -> bool:
"""
Check if a real (non-mock) stage is currently attached.
"""
if hasattr(self, "stage") and not isinstance(self.stage, MockStage):
if hasattr(self, "stage") and not isinstance(self.stage, MissingStage):
return True
else:
return False
@ -116,49 +115,45 @@ class Microscope:
"""
Check if a real (non-mock) camera is currently attached.
"""
if hasattr(self, "camera") and not isinstance(self.camera, MockStreamer):
if hasattr(self, "camera") and not isinstance(self.camera, MissingCamera):
return True
else:
return False
# Create unified status
# Create unified state
@property
def status(self):
"""Dictionary of the basic microscope status.
def state(self):
"""Dictionary of the basic microscope state.
Return:
dict: Dictionary containing complete microscope status
dict: Dictionary containing complete microscope state
"""
state = {
"camera": self.camera.status,
"stage": self.stage.status,
"version": pkg_resources.get_distribution("openflexure_microscope").version,
}
state = {"camera": self.camera.state, "stage": self.stage.state}
return state
def apply_settings(self, config: dict):
def update_settings(self, settings: dict):
"""
Applies a settings dictionary to the microscope. Missing parameters will be left untouched.
"""
logging.debug("Microscope: Applying config: {}".format(config))
logging.debug("Microscope: Applying settings: {}".format(settings))
# If attached to a camera
if ("camera_settings" in config) and self.camera:
self.camera.apply_settings(config["camera_settings"])
if ("camera" in settings) and self.camera:
self.camera.update_settings(settings["camera"])
# If attached to a stage
if ("stage_settings" in config) and self.stage:
self.stage.apply_settings(config["stage_settings"])
if ("stage" in settings) and self.stage:
self.stage.update_settings(settings["stage"])
# Todo: tidy up with some loopy goodness
if "id" in config:
self.id = config["id"]
if "name" in config:
self.name = config["name"]
if "fov" in config:
self.fov = config["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"]
def read_settings(self, json_safe=False):
def read_settings(self, full: bool = True):
"""
Get an updated settings dictionary.
@ -174,16 +169,34 @@ class Microscope:
# If attached to a camera
if self.camera:
settings_current_camera = self.camera.read_settings()
settings_current["camera_settings"] = settings_current_camera
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()
if lst_arr:
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,
}
# If attached to a stage
if self.stage:
settings_current_stage = self.stage.read_settings()
settings_current["stage_settings"] = settings_current_stage
settings_current["stage"] = settings_current_stage
settings_full = user_settings.merge(settings_current)
settings_full = self.settings_file.merge(settings_current)
return settings_full
if full:
return settings_full
else:
return settings_current
def save_settings(self):
"""
@ -196,7 +209,31 @@ class Microscope:
self.camera.save_settings()
if self.stage:
self.stage.save_settings()
user_settings.save(current_config, backup=True)
self.settings_file.save(current_config, backup=True)
@property
def configuration(self):
initial_configuration = self.configuration_file.load()
current_configuration = {
"application": {
"name": "openflexure_microscope",
"version": pkg_resources.get_distribution(
"openflexure_microscope"
).version,
},
"stage": {
"type": self.stage.__class__.__name__,
**self.stage.configuration,
},
"camera": {
"type": self.camera.__class__.__name__,
**self.camera.configuration,
},
}
initial_configuration.update(current_configuration)
return initial_configuration
@property
def metadata(self):
@ -204,23 +241,10 @@ class Microscope:
Microscope system metadata, to be applied to basically all captures
"""
system_metadata = {
"microscope_settings": self.read_settings(),
"microscope_state": self.status,
"microscope_id": self.id,
"microscope_name": self.name,
"id": self.id,
"settings": self.read_settings(full=False),
"state": self.state,
"configuration": self.configuration,
}
# Store an encoded copy of the PiCamera lens shading table, if it exists
if self.camera and hasattr(self.camera, "read_lens_shading_table"):
# Read LST. Returns None if no LST is active
lst_arr = self.camera.read_lens_shading_table()
b64_string, dtype, shape = serialise_array_b64(lst_arr)
system_metadata["lens_shading_table"] = {
"b64_string": b64_string,
"dtype": dtype,
"shape": shape,
}
return system_metadata

9
openflexure_microscope/microscope_configuration.default.json Normal file
View file

@ -0,0 +1,9 @@
{
"camera": {
"type": "PiCamera"
},
"stage": {
"type": "SangaStage",
"port": null
}
}

6
openflexure_microscope/microscope_settings.default.json
View file

@ -1,7 +1,3 @@
{
"fov": [
4100,
3146
],
"jpeg_quality": 75
"jpeg_quality": 100
}

11
openflexure_microscope/paths.py
View file

@ -32,8 +32,9 @@ def logs_file_path(filename: str):
HERE = os.path.abspath(os.path.dirname(__file__))
#: Path of default (first-run) microscope settings
DEFAULT_CONFIG_FILE_PATH = os.path.join(HERE, "microscope_settings.default.json")
DEFAULT_SETTINGS_FILE_PATH = os.path.join(HERE, "microscope_settings.default.json")
#: Path of default (first-run) microscope configuration
DEFAULT_CONFIGURATION_FILE_PATH = os.path.join(HERE, "microscope_configuration.default.json")
# BASE PATHS
@ -60,7 +61,9 @@ else:
# SERVER PATHS
#: Path of microscope settings directory
CONFIG_FILE_PATH = settings_file_path("microscope_settings.json")
#: Path of microscope settings file
SETTINGS_FILE_PATH = settings_file_path("microscope_settings.json")
#: Path of microscope configuration file
CONFIGURATION_FILE_PATH = settings_file_path("microscope_configuration.json")
#: Path of microscope extensions directory
OPENFLEXURE_EXTENSIONS_PATH = extensions_file_path("microscope_extensions")

16
openflexure_microscope/stage/base.py
View file

@ -14,7 +14,7 @@ class BaseStage(metaclass=ABCMeta):
self.lock = StrictLock(timeout=5)
@abstractmethod
def apply_settings(self, config: dict):
def update_settings(self, config: dict):
"""Update settings from a config dictionary"""
pass
@ -29,12 +29,14 @@ class BaseStage(metaclass=ABCMeta):
@property
@abstractmethod
def status(self):
"""The general state dictionary of the board.
Should at least contain 'position', and 'board' keys.
Note: A None/Null value for 'board' will disable stage
movement in the OpenFlexure eV client software,
"""
def state(self):
"""The general state dictionary of the board."""
pass
@property
@abstractmethod
def configuration(self):
"""The general stage configuration."""
pass
@property

22
openflexure_microscope/stage/mock.py
View file

@ -7,7 +7,7 @@ import time
import logging
class MockStage(BaseStage):
class MissingStage(BaseStage):
def __init__(self, port=None, **kwargs):
BaseStage.__init__(self)
self._position = [0, 0, 0]
@ -17,19 +17,17 @@ class MockStage(BaseStage):
self.axis_names = ["x", "y", "z"] # Assume all sangaboards are 3 axis
@property
def status(self):
"""The general status dictionary of the board."""
status = {
"position": self.position_map,
"board": None,
"firmware": None,
"version": None,
}
return status
def state(self):
"""The general state dictionary of the board."""
state = {"position": self.position_map}
return state
def apply_settings(self, config: dict):
@property
def configuration(self):
return {}
def update_settings(self, config: dict):
"""Update settings from a config dictionary"""
# Set backlash. Expects a dictionary with axis labels
if "backlash" in config:
# Construct backlash array

16
openflexure_microscope/stage/sanga.py
View file

@ -23,6 +23,7 @@ class SangaStage(BaseStage):
"""Class managing serial communications with the motors for an Openflexure stage"""
BaseStage.__init__(self)
self.port = port
self.board = Sangaboard(port, **kwargs)
self._backlash = (
@ -31,14 +32,17 @@ class SangaStage(BaseStage):
self.axis_names = ["x", "y", "z"] # Assume all sangaboards are 3 axis
@property
def status(self):
"""The general status dictionary of the board."""
status = {
"position": self.position_map,
def state(self):
"""The general state dictionary of the board."""
return {"position": self.position_map}
@property
def configuration(self):
return {
"port": self.port,
"board": self.board.board,
"firmware": self.board.firmware,
}
return status
@property
def n_axes(self):
@ -81,7 +85,7 @@ class SangaStage(BaseStage):
else:
self._backlash = np.array([int(blsh)] * self.n_axes, dtype=np.int)
def apply_settings(self, config: dict):
def update_settings(self, config: dict):
"""Update settings from a config dictionary"""
# Set backlash. Expects a dictionary with axis labels

537
poetry.lock generated
View file

@ -14,14 +14,6 @@ optional = false
python-versions = ">=3.5"
version = "3.2.0"
[package.extras]
dev = ["PyYAML (>=3.10)", "prance (>=0.11)", "marshmallow (>=2.19.2)", "pytest", "mock", "flake8 (3.7.9)", "flake8-bugbear (19.8.0)", "pre-commit (>=1.20,<2.0)", "tox"]
docs = ["marshmallow (>=2.19.2)", "pyyaml (5.2)", "sphinx (2.3.0)", "sphinx-issues (1.2.0)", "sphinx-rtd-theme (0.4.3)"]
lint = ["flake8 (3.7.9)", "flake8-bugbear (19.8.0)", "pre-commit (>=1.20,<2.0)"]
tests = ["PyYAML (>=3.10)", "prance (>=0.11)", "marshmallow (>=2.19.2)", "pytest", "mock"]
validation = ["prance (>=0.11)"]
yaml = ["PyYAML (>=3.10)"]
[[package]]
category = "dev"
description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
@ -55,12 +47,6 @@ optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
version = "19.3.0"
[package.extras]
azure-pipelines = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "pytest-azurepipelines"]
dev = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "sphinx", "pre-commit"]
docs = ["sphinx", "zope.interface"]
tests = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
[[package]]
category = "dev"
description = "Internationalization utilities"
@ -86,9 +72,6 @@ attrs = ">=17.4.0"
click = ">=6.5"
toml = ">=0.9.4"
[package.extras]
d = ["aiohttp (>=3.3.2)"]
[[package]]
category = "dev"
description = "Python package for providing Mozilla's CA Bundle."
@ -144,11 +127,6 @@ Werkzeug = ">=0.15"
click = ">=5.1"
itsdangerous = ">=0.24"
[package.extras]
dev = ["pytest", "coverage", "tox", "sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"]
docs = ["sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"]
dotenv = ["python-dotenv"]
[[package]]
category = "main"
description = "A Flask extension adding a decorator for CORS support"
@ -185,12 +163,6 @@ optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
version = "4.3.21"
[package.extras]
pipfile = ["pipreqs", "requirementslib"]
pyproject = ["toml"]
requirements = ["pipreqs", "pip-api"]
xdg_home = ["appdirs (>=1.4.0)"]
[[package]]
category = "main"
description = "Various helpers to pass data to untrusted environments and back."
@ -204,15 +176,12 @@ category = "main"
description = "A very fast and expressive template engine."
name = "jinja2"
optional = false
python-versions = "*"
version = "2.10.3"
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
version = "2.11.0"
[package.dependencies]
MarkupSafe = ">=0.23"
[package.extras]
i18n = ["Babel (>=0.8)"]
[[package]]
category = "main"
description = ""
@ -229,7 +198,7 @@ marshmallow = "^3.3.0"
webargs = "^5.5.2"
[package.source]
reference = "23732b17074486367541439a1caa2eb61b9cc22f"
reference = "cb1ef6a1f8849f4d58601a7a9617ffea12703f39"
type = "git"
url = "https://github.com/labthings/python-labthings.git"
[[package]]
@ -256,12 +225,6 @@ optional = false
python-versions = ">=3.5"
version = "3.3.0"
[package.extras]
dev = ["pytest", "pytz", "simplejson", "mypy (0.750)", "flake8 (3.7.9)", "flake8-bugbear (19.8.0)", "pre-commit (>=1.20,<2.0)", "tox"]
docs = ["sphinx (2.2.2)", "sphinx-issues (1.2.0)", "alabaster (0.7.12)", "sphinx-version-warning (1.1.2)"]
lint = ["mypy (0.750)", "flake8 (3.7.9)", "flake8-bugbear (19.8.0)", "pre-commit (>=1.20,<2.0)"]
tests = ["pytest", "pytz", "simplejson"]
[[package]]
category = "dev"
description = "McCabe checker, plugin for flake8"
@ -298,11 +261,6 @@ optional = true
python-versions = "*"
version = "1.13.1b0"
[package.extras]
array = ["numpy"]
doc = ["sphinx"]
test = ["coverage", "pytest", "mock", "pillow", "numpy"]
[package.source]
reference = "b39c2b6e42f5f7f57bb46eafcb5c9e2bbdb5d0cb"
type = "git"
@ -353,6 +311,17 @@ optional = false
python-versions = "*"
version = "3.4"
[[package]]
category = "main"
description = "Extensions to the standard Python datetime module"
name = "python-dateutil"
optional = false
python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
version = "2.8.1"
[package.dependencies]
six = ">=1.5"
[[package]]
category = "dev"
description = "World timezone definitions, modern and historical"
@ -383,10 +352,6 @@ chardet = ">=3.0.2,<3.1.0"
idna = ">=2.5,<2.9"
urllib3 = ">=1.21.1,<1.25.0 || >1.25.0,<1.25.1 || >1.25.1,<1.26"
[package.extras]
security = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)"]
socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7)", "win-inet-pton"]
[[package]]
category = "dev"
description = "a python refactoring library..."
@ -414,6 +379,14 @@ version = "1.3.0"
[package.dependencies]
numpy = ">=1.13.3"
[[package]]
category = "main"
description = "Simple, fast, extensible JSON encoder/decoder for Python"
name = "simplejson"
optional = false
python-versions = ">=2.5, !=3.0.*, !=3.1.*, !=3.2.*"
version = "3.17.0"
[[package]]
category = "main"
description = "Python 2 and 3 compatibility utilities"
@ -457,10 +430,6 @@ sphinxcontrib-jsmath = "*"
sphinxcontrib-qthelp = "*"
sphinxcontrib-serializinghtml = "*"
[package.extras]
docs = ["sphinxcontrib-websupport"]
test = ["pytest", "pytest-cov", "html5lib", "flake8 (>=3.5.0)", "flake8-import-order", "mypy (>=0.761)", "docutils-stubs"]
[[package]]
category = "dev"
description = ""
@ -469,9 +438,6 @@ optional = false
python-versions = "*"
version = "1.0.1"
[package.extras]
test = ["pytest", "flake8", "mypy"]
[[package]]
category = "dev"
description = ""
@ -480,9 +446,6 @@ optional = false
python-versions = "*"
version = "1.0.1"
[package.extras]
test = ["pytest", "flake8", "mypy"]
[[package]]
category = "dev"
description = ""
@ -491,9 +454,6 @@ optional = false
python-versions = "*"
version = "1.0.2"
[package.extras]
test = ["pytest", "flake8", "mypy", "html5lib"]
[[package]]
category = "dev"
description = "Sphinx domain for documenting HTTP APIs"
@ -514,9 +474,6 @@ optional = false
python-versions = ">=3.5"
version = "1.0.1"
[package.extras]
test = ["pytest", "flake8", "mypy"]
[[package]]
category = "dev"
description = ""
@ -525,9 +482,6 @@ optional = false
python-versions = "*"
version = "1.0.2"
[package.extras]
test = ["pytest", "flake8", "mypy"]
[[package]]
category = "dev"
description = ""
@ -536,9 +490,6 @@ optional = false
python-versions = "*"
version = "1.1.3"
[package.extras]
test = ["pytest", "flake8", "mypy"]
[[package]]
category = "dev"
description = "Python Library for Tom's Obvious, Minimal Language"
@ -564,28 +515,17 @@ optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
version = "1.25.8"
[package.extras]
brotli = ["brotlipy (>=0.6.0)"]
secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"]
socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7,<2.0)"]
[[package]]
category = "main"
description = "Declarative parsing and validation of HTTP request objects, with built-in support for popular web frameworks, including Flask, Django, Bottle, Tornado, Pyramid, webapp2, Falcon, and aiohttp."
name = "webargs"
optional = false
python-versions = "*"
version = "5.5.2"
version = "5.5.3"
[package.dependencies]
marshmallow = ">=2.15.2"
[package.extras]
dev = ["pytest", "mock", "webtest (2.0.33)", "Flask (>=0.12.2)", "Django (>=1.11.16)", "bottle (>=0.12.13)", "tornado (>=4.5.2)", "pyramid (>=1.9.1)", "webapp2 (>=3.0.0b1)", "falcon (>=1.4.0,<2.0)", "flake8 (3.7.8)", "pre-commit (>=1.17,<2.0)", "tox", "webtest-aiohttp (2.0.0)", "pytest-aiohttp (>=0.3.0)", "aiohttp (>=3.0.0)", "mypy (0.730)", "flake8-bugbear (19.8.0)"]
docs = ["Sphinx (2.2.0)", "sphinx-issues (1.2.0)", "sphinx-typlog-theme (0.7.3)", "Flask (>=0.12.2)", "Django (>=1.11.16)", "bottle (>=0.12.13)", "tornado (>=4.5.2)", "pyramid (>=1.9.1)", "webapp2 (>=3.0.0b1)", "falcon (>=1.4.0,<2.0)", "aiohttp (>=3.0.0)"]
frameworks = ["Flask (>=0.12.2)", "Django (>=1.11.16)", "bottle (>=0.12.13)", "tornado (>=4.5.2)", "pyramid (>=1.9.1)", "webapp2 (>=3.0.0b1)", "falcon (>=1.4.0,<2.0)", "aiohttp (>=3.0.0)"]
lint = ["flake8 (3.7.8)", "pre-commit (>=1.17,<2.0)", "mypy (0.730)", "flake8-bugbear (19.8.0)"]
tests = ["pytest", "mock", "webtest (2.0.33)", "Flask (>=0.12.2)", "Django (>=1.11.16)", "bottle (>=0.12.13)", "tornado (>=4.5.2)", "pyramid (>=1.9.1)", "webapp2 (>=3.0.0b1)", "falcon (>=1.4.0,<2.0)", "webtest-aiohttp (2.0.0)", "pytest-aiohttp (>=0.3.0)", "aiohttp (>=3.0.0)"]
simplejson = ">=2.1.0"
[[package]]
category = "main"
@ -593,12 +533,7 @@ description = "The comprehensive WSGI web application library."
name = "werkzeug"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
version = "0.16.0"
[package.extras]
dev = ["pytest", "coverage", "tox", "sphinx", "pallets-sphinx-themes", "sphinx-issues"]
termcolor = ["termcolor"]
watchdog = ["watchdog"]
version = "0.16.1"
[[package]]
category = "dev"
@ -612,373 +547,63 @@ version = "1.11.2"
rpi = ["picamera", "RPi.GPIO"]
[metadata]
content-hash = "cd4e5d59e9a63ae053a05c994a61a46be87a29ec6867bcd47f6ef9b39bb785d3"
content-hash = "34da76b3341563a0bebfa3e4a3fca90f34b857027e90811fed92b106ad06c2ba"
python-versions = "^3.6"
[metadata.files]
alabaster = [
{file = "alabaster-0.7.12-py2.py3-none-any.whl", hash = "sha256:446438bdcca0e05bd45ea2de1668c1d9b032e1a9154c2c259092d77031ddd359"},
{file = "alabaster-0.7.12.tar.gz", hash = "sha256:a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02"},
]
apispec = [
{file = "apispec-3.2.0-py2.py3-none-any.whl", hash = "sha256:f2ecb3a6534cfb42cf69b5c1222d2c0e695aab5ec3d7edde31b7354670948f05"},
{file = "apispec-3.2.0.tar.gz", hash = "sha256:c1625ae910f699c9adb21928693a3245b9faab6843f1b1c94ab2d505549cd78a"},
]
appdirs = [
{file = "appdirs-1.4.3-py2.py3-none-any.whl", hash = "sha256:d8b24664561d0d34ddfaec54636d502d7cea6e29c3eaf68f3df6180863e2166e"},
{file = "appdirs-1.4.3.tar.gz", hash = "sha256:9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92"},
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astroid = [
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pyparsing = ["4c830582a84fb022400b85429791bc551f1f4871c33f23e44f353119e92f969f", "c342dccb5250c08d45fd6f8b4a559613ca603b57498511740e65cd11a2e7dcec"]
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python-dateutil = ["73ebfe9dbf22e832286dafa60473e4cd239f8592f699aa5adaf10050e6e1823c", "75bb3f31ea686f1197762692a9ee6a7550b59fc6ca3a1f4b5d7e32fb98e2da2a"]
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rope = ["6b728fdc3e98a83446c27a91fc5d56808a004f8beab7a31ab1d7224cecc7d969", "c5c5a6a87f7b1a2095fb311135e2a3d1f194f5ecb96900fdd0a9100881f48aaf", "f0dcf719b63200d492b85535ebe5ea9b29e0d0b8aebeb87fe03fc1a65924fdaf"]
"rpi.gpio" = ["a4210ad63bfe844e43995286de0d3950dfacfa0f3799bb9392770ac54a7d2e47"]
scipy = ["03b1e0775edbe6a4c64effb05fff2ce1429b76d29d754aa5ee2d848b60033351", "09d008237baabf52a5d4f5a6fcf9b3c03408f3f61a69c404472a16861a73917e", "10325f0ffac2400b1ec09537b7e403419dcd25d9fee602a44e8a32119af9079e", "1db9f964ed9c52dc5bd6127f0dd90ac89791daa690a5665cc01eae185912e1ba", "409846be9d6bdcbd78b9e5afe2f64b2da5a923dd7c1cd0615ce589489533fdbb", "4907040f62b91c2e170359c3d36c000af783f0fa1516a83d6c1517cde0af5340", "6c0543f2fdd38dee631fb023c0f31c284a532d205590b393d72009c14847f5b1", "826b9f5fbb7f908a13aa1efd4b7321e36992f5868d5d8311c7b40cf9b11ca0e7", "a7695a378c2ce402405ea37b12c7a338a8755e081869bd6b95858893ceb617ae", "a84c31e8409b420c3ca57fd30c7589378d6fdc8d155d866a7f8e6e80dec6fd06", "adadeeae5500de0da2b9e8dd478520d0a9945b577b2198f2462555e68f58e7ef", "b283a76a83fe463c9587a2c88003f800e08c3929dfbeba833b78260f9c209785", "c19a7389ab3cd712058a8c3c9ffd8d27a57f3d84b9c91a931f542682bb3d269d", "c3bb4bd2aca82fb498247deeac12265921fe231502a6bc6edea3ee7fe6c40a7a", "c5ea60ece0c0c1c849025bfc541b60a6751b491b6f11dd9ef37ab5b8c9041921", "db61a640ca20f237317d27bc658c1fc54c7581ff7f6502d112922dc285bdabee"]
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six = ["236bdbdce46e6e6a3d61a337c0f8b763ca1e8717c03b369e87a7ec7ce1319c0a", "8f3cd2e254d8f793e7f3d6d9df77b92252b52637291d0f0da013c76ea2724b6c"]
snowballstemmer = ["209f257d7533fdb3cb73bdbd24f436239ca3b2fa67d56f6ff88e86be08cc5ef0", "df3bac3df4c2c01363f3dd2cfa78cce2840a79b9f1c2d2de9ce8d31683992f52"]
sphinx = ["298537cb3234578b2d954ff18c5608468229e116a9757af3b831c2b2b4819159", "e6e766b74f85f37a5f3e0773a1e1be8db3fcb799deb58ca6d18b70b0b44542a5"]
sphinxcontrib-applehelp = ["edaa0ab2b2bc74403149cb0209d6775c96de797dfd5b5e2a71981309efab3897", "fb8dee85af95e5c30c91f10e7eb3c8967308518e0f7488a2828ef7bc191d0d5d"]
sphinxcontrib-devhelp = ["6c64b077937330a9128a4da74586e8c2130262f014689b4b89e2d08ee7294a34", "9512ecb00a2b0821a146736b39f7aeb90759834b07e81e8cc23a9c70bacb9981"]
sphinxcontrib-htmlhelp = ["4670f99f8951bd78cd4ad2ab962f798f5618b17675c35c5ac3b2132a14ea8422", "d4fd39a65a625c9df86d7fa8a2d9f3cd8299a3a4b15db63b50aac9e161d8eff7"]
sphinxcontrib-httpdomain = ["1fb5375007d70bf180cdd1c79e741082be7aa2d37ba99efe561e1c2e3f38191e", "ac40b4fba58c76b073b03931c7b8ead611066a6aebccafb34dc19694f4eb6335"]
sphinxcontrib-jsmath = ["2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178", "a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"]
sphinxcontrib-qthelp = ["513049b93031beb1f57d4daea74068a4feb77aa5630f856fcff2e50de14e9a20", "79465ce11ae5694ff165becda529a600c754f4bc459778778c7017374d4d406f"]
sphinxcontrib-serializinghtml = ["c0efb33f8052c04fd7a26c0a07f1678e8512e0faec19f4aa8f2473a8b81d5227", "db6615af393650bf1151a6cd39120c29abaf93cc60db8c48eb2dddbfdc3a9768"]
toml = ["229f81c57791a41d65e399fc06bf0848bab550a9dfd5ed66df18ce5f05e73d5c", "235682dd292d5899d361a811df37e04a8828a5b1da3115886b73cf81ebc9100e", "f1db651f9657708513243e61e6cc67d101a39bad662eaa9b5546f789338e07a3"]
typed-ast = ["0666aa36131496aed8f7be0410ff974562ab7eeac11ef351def9ea6fa28f6355", "0c2c07682d61a629b68433afb159376e24e5b2fd4641d35424e462169c0a7919", "249862707802d40f7f29f6e1aad8d84b5aa9e44552d2cc17384b209f091276aa", "24995c843eb0ad11a4527b026b4dde3da70e1f2d8806c99b7b4a7cf491612652", "269151951236b0f9a6f04015a9004084a5ab0d5f19b57de779f908621e7d8b75", "4083861b0aa07990b619bd7ddc365eb7fa4b817e99cf5f8d9cf21a42780f6e01", "498b0f36cc7054c1fead3d7fc59d2150f4d5c6c56ba7fb150c013fbc683a8d2d", "4e3e5da80ccbebfff202a67bf900d081906c358ccc3d5e3c8aea42fdfdfd51c1", "6daac9731f172c2a22ade6ed0c00197ee7cc1221aa84cfdf9c31defeb059a907", "715ff2f2df46121071622063fc7543d9b1fd19ebfc4f5c8895af64a77a8c852c", "73d785a950fc82dd2a25897d525d003f6378d1cb23ab305578394694202a58c3", "8c8aaad94455178e3187ab22c8b01a3837f8ee50e09cf31f1ba129eb293ec30b", "8ce678dbaf790dbdb3eba24056d5364fb45944f33553dd5869b7580cdbb83614", "aaee9905aee35ba5905cfb3c62f3e83b3bec7b39413f0a7f19be4e547ea01ebb", "bcd3b13b56ea479b3650b82cabd6b5343a625b0ced5429e4ccad28a8973f301b", "c9e348e02e4d2b4a8b2eedb48210430658df6951fa484e59de33ff773fbd4b41", "d205b1b46085271b4e15f670058ce182bd1199e56b317bf2ec004b6a44f911f6", "d43943ef777f9a1c42bf4e552ba23ac77a6351de620aa9acf64ad54933ad4d34", "d5d33e9e7af3b34a40dc05f498939f0ebf187f07c385fd58d591c533ad8562fe", "fc0fea399acb12edbf8a628ba8d2312f583bdbdb3335635db062fa98cf71fca4", "fe460b922ec15dd205595c9b5b99e2f056fd98ae8f9f56b888e7a17dc2b757e7"]
urllib3 = ["2f3db8b19923a873b3e5256dc9c2dedfa883e33d87c690d9c7913e1f40673cdc", "87716c2d2a7121198ebcb7ce7cccf6ce5e9ba539041cfbaeecfb641dc0bf6acc"]
webargs = ["4f04918864c7602886335d8099f9b8960ee698b6b914f022736ed50be6b71235", "871642a2e0c62f21d5b78f357750ac7a87e6bc734c972f633aa5fb6204fbf29a", "fc81c9f9d391acfbce406a319217319fd8b2fd862f7fdb5319ad06944f36ed25"]
werkzeug = ["1e0dedc2acb1f46827daa2e399c1485c8fa17c0d8e70b6b875b4e7f54bf408d2", "b353856d37dec59d6511359f97f6a4b2468442e454bd1c98298ddce53cac1f04"]
wrapt = ["565a021fd19419476b9362b05eeaa094178de64f8361e44468f9e9d7843901e1"]

1
pyproject.toml
View file

@ -35,6 +35,7 @@ picamera = { git = "https://github.com/rwb27/picamera.git", branch = "lens-shadi
pyserial = "^3.4" # Used for sangaboard (basic_serial_instrument) until we move to sangaboard pip library
labthings = { git = "https://github.com/labthings/python-labthings.git", branch = "master"} # TODO: Pin to a fixed version before 2.0.0 stable
python-dateutil = "^2.8"
[tool.poetry.extras]
rpi = ["picamera", "RPi.GPIO"]