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Merge branch 'sangaboard-v4' into 'master'

Browse source 
Support latest sangaboard firmware

See merge request openflexure/openflexure-microscope-server!154
This commit is contained in:
Richard Bowman 2023-04-12 07:23:15 +00:00
commit ac45423739
38 changed files with 1572 additions and 967 deletions
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111
.gitlab-ci.yml
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@ -6,8 +6,12 @@ stages:
- deploy
# Re-usable block to install (and cache) Poetry and openflexure-microscope-server
.python-install-template: &python-install
.python:
image: balenalib/raspberry-pi:buster
retry: 1
before_script:
- apt-get update
- apt-get install apt-utils curl wget python3 python3-pip python3-venv raspi-gpio libgfortran3 libatlas3-base libffi-dev vim git-lfs libtiff5 libpango-1.0-0 libavcodec58 libgdk-pixbuf2.0-0 libjasper1 libswscale5 libpangocairo-1.0-0 libilmbase23 libatk1.0-0 libgtk-3-0 libwebp6 libcairo2 libavutil56 libcairo-gobject2 libopenexr23 libavformat58 libxslt1.1
- python3 -m venv .venv # NB this does not overwrite an existing cached venv
- source .venv/bin/activate
- pip install pipenv # Should be cached after first run
@ -17,9 +21,14 @@ stages:
paths:
- .cache/pip
- .venv
only:
- branches
- merge_requests
- tags
- web
# Re-usable block to install (and cache) openflexure-microscope-server static app
.node-install-template: &node-install
.javascript:
image: node:15
before_script:
- cd webapp
- npm install
@ -27,93 +36,54 @@ stages:
key: "${CI_COMMIT_REF_SLUG}"
paths:
- webapp/node_modules
only:
- branches
- merge_requests
- tags
- web
# Python static analysis with PyLint
pylint:
stage: analysis
image: python:3.7
retry: 1
<<: *python-install
extends: .python
script:
- poe pylint
only:
- branches
- merge_requests
- tags
- web
# Python type checking with Mypy
mypy:
stage: analysis
image: python:3.7
retry: 1
<<: *python-install
extends: .python
script:
- poe mypy
artifacts:
reports:
cobertura: openflexure_microscope/cobertura.xml
only:
- branches
- merge_requests
- tags
- web
coverage_report:
coverage_format: cobertura
path: openflexure_microscope/cobertura.xml
# Python style analysis with Black
black:
stage: analysis
image: python:3.7
retry: 1
allow_failure: true
<<: *python-install
extends: .python
script:
# Run static build script
- poe black_check
only:
- branches
- merge_requests
- tags
- web
# Python unit tests with PyTest
pytest:
stage: testing
image: python:3.7
retry: 1
<<: *python-install
extends: .python
script:
- poe test
only:
- branches
- merge_requests
- tags
- web
artifacts:
when: always
reports:
junit: pytest_report.xml
# Generate and validate OpenAPI description
openapi:
stage: testing
image: python:3.7
retry: 1
<<: *python-install
extends: .python
script:
- mkdir -p docs/build/
- ofm-generate-openapi -o docs/build/swagger.yaml --validate
@ -123,53 +93,28 @@ openapi:
expire_in: 1 week
paths:
- "./docs/build/swagger.yaml"
only:
- branches
- merge_requests
- tags
- web
# JavaScript linting with ESLint (via Vue CLI)
eslint:
stage: analysis
image: node:15
<<: *node-install
extends: .javascript
script:
# Build JS application for production
- npm run lint
only:
- branches
- merge_requests
- tags
- web
# Build JS app
build:
stage: build
image: node:15
<<: *node-install
extends: .javascript
script:
# Build JS application for production
- npm run build
artifacts:
name: "dist"
expire_in: 1 week
paths:
- "openflexure_microscope/api/static/dist/"
only:
- master
- merge_requests
- tags
- web
# Package application into distribution tarball
package:
stage: package

6
CHANGELOG.md
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@ -1,3 +1,9 @@
# [v2.11.0](https://gitlab.com/openflexure/openflexure-microscope-server/compare/v2.10.1...v2.11.0) (2022-08-08)
## New features
* Background detection can now be used in scans, if you have the background-detect extension. ([!153](https://gitlab.com/openflexure/openflexure-microscope-server/-/merge_requests/153))
* Support for Sangaboard firmware v1, via updated `sangaboard` dependency ([!154](https://gitlab.com/openflexure/openflexure-microscope-server/-/merge_requests/154))
* Fixed links in the OpenAPI documentation describing actions etc. ([!155](https://gitlab.com/openflexure/openflexure-microscope-server/-/merge_requests/154))
# [v2.10.1](https://gitlab.com/openflexure/openflexure-microscope-server/compare/v2.10.0...v2.10.1) (2022-01-17)
## Bug fixes
* Fixed a typo in the serialisation of numpy arrays (#243) ([!148](https://gitlab.com/openflexure/openflexure-microscope-server/-/merge_requests/148))

5
Pipfile
View file

@ -1,8 +1,3 @@
[[source]]
url = "https://pypi.python.org/simple"
verify_ssl = true
name = "pypi"
[[source]]
url = "https://www.piwheels.org/simple"
verify_ssl = true

2007
Pipfile.lock generated
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File diff suppressed because it is too large Load diff

9
README.md
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@ -69,7 +69,7 @@ To set up a development version of the software (most likely using emulated came
* Create a virtual environment and activate it:
* `python -m venv .venv`
* `source .venv/bin/activate` (on Linux) or `.venv/Scripts/activate` (on Windows)
* `pip install pipenv`
* `pip install --upgrade pip wheel pipenv`
* `pipenv install --dev` (This will install development dependencies. If you don't need these, `pipenv install` will get you just the dependencies needed to run the server, which takes about half the time.)
* Finally, run the server:
* You can use `ofm serve` or `ofm restart` on the Raspberry Pi to manage the server.
@ -146,6 +146,10 @@ As of `2.10.0b0` we have switched to using `pipenv` for managing dependencies, a
* `pyproject.toml` is retained, but *no longer includes package metadata or dependencies* and does not have a `[tool.poetry]` table. It does define the build system as per PEP517, which is `setuptools`, and it also contains settings for `black`, `poe` and `isort`.
* `Pipfile` is very minimal, and only declares dependencies on the current module, i.e. the dependencies declared in `setup.py`. It also specifies the Python version. This allows us to single-source dependency information from `setup.py` but use the dependency resolution/locking functionality of `pipenv`
* `Pipfile.lock` locks the dependency versions in the same way as `poetry.lock` used to, i.e. it specifies exact versions of everything, derived from the looser specifications in `setup.py`.
* Dependency resolution is a pain, in part because compiling packages like scipy and numpy from source on a Pi is slow and unreliable. To avoid this, we usually lock the dependencies on a Raspberry Pi, using:
`PIP_ONLY_BINARY="numpy, scipy, matplotlib" pipenv lock --dev`
This forces the use of wheels only, and thus restricts us to things that built OK on Piwheels. The resulting Pipfile.lock should then work nicely on other Raspberry Pis.
* **The Pipfile we use is now Raspberry Pi-specific** so if you attempt to use it on other platforms it will probably fail. This is because we've removed `pypi` to avoid hash conflicts. The CI now runs on a Raspberry Pi image, so that the tests use a similar environment to our deployment. Currently, changing the `[source]` entry back to PyPi will allow you to re-lock the dependencies on other platforms. In the future we may need to maintain two Pipfiles and two Pipfile.lock files.
## Creating releases
@ -166,3 +170,6 @@ As of `2.10.0b0` we have switched to using `pipenv` for managing dependencies, a
The Microscope module, and Flask app, both support plugins for extending lower-level functionality not well suited to web API calls. The current documentation can be found [here](https://openflexure-microscope-software.readthedocs.io/en/latest/plugins.html).
If you want to add functions to the microscope software, this is probably the best mechanism to use if it works for you.
```

2
docs/source/extensions/actions.rst
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@ -18,7 +18,7 @@ Like properties, we use a special view class to identify a view as an action: ``
Take an image capture and return it without saving
"""
# Expect a "use_video_port" boolean, which defaults to True if none is given
args = {"use_video_port": fields.Boolean(missing=True)}
args = {"use_video_port": fields.Boolean(load_default=True)}
# Our success response (200) returns an image (image/jpeg mimetype)
responses = {

2
docs/source/extensions/example_extension/02_adding_views.py
View file

@ -46,7 +46,7 @@ class ExampleIdentifyView(View):
class ExampleRenameView(View):
# Expect a request parameter called "name", which is a string.
# Passed to the argument "args".
args = fields.String(required=True, example="My Example Microscope")
args = fields.String(required=True, metadata={"example": "My Example Microscope"})
def post(self, args):
# Look for our new name in the request body

6
docs/source/extensions/example_extension/03_marshaling_data.py
View file

@ -49,7 +49,11 @@ class ExampleRenameView(View):
# Format our returned object using MicroscopeIdentifySchema
schema = MicroscopeIdentifySchema()
# Expect a request parameter called "name", which is a string. Pass to argument "args".
args = {"name": fields.String(required=True, example="My Example Microscope")}
args = {
"name": fields.String(
required=True, metadata={"example": "My Example Microscope"}
)
}
def post(self, args):
# Look for our "name" parameter in the request arguments

6
docs/source/extensions/example_extension/04_properties.py
View file

@ -53,7 +53,11 @@ class ExampleIdentifyView(PropertyView):
# We can use a single schema as the input and output will be formatted identically
# Eg. We always expect a "name" string argument, and always return a "name" string attribute
class ExampleRenameView(PropertyView):
schema = {"name": fields.String(required=True, example="My Example Microscope")}
schema = {
"name": fields.String(
required=True, metadata={"example": "My Example Microscope"}
)
}
def get(self):
"""

8
docs/source/extensions/example_extension/05_actions.py
View file

@ -56,7 +56,11 @@ class ExampleIdentifyView(PropertyView):
# We can use a single schema as the input and output will be formatted identically
# Eg. We always expect a "name" string argument, and always return a "name" string attribute
class ExampleRenameView(PropertyView):
schema = {"name": fields.String(required=True, example="My Example Microscope")}
schema = {
"name": fields.String(
required=True, metadata={"example": "My Example Microscope"}
)
}
def get(self):
"""
@ -91,7 +95,7 @@ class QuickCaptureAPI(ActionView):
"""
# Expect a "use_video_port" boolean, which defaults to True if none is given
args = {"use_video_port": fields.Boolean(missing=True)}
args = {"use_video_port": fields.Boolean(load_default=True)}
# Our success response (200) returns an image (image/jpeg mimetype)
responses = {200: {"content": {"image/jpeg": {}}}}

5
docs/source/extensions/example_extension/06_tasks_locks.py
View file

@ -66,10 +66,11 @@ class TimelapseAPIView(ActionView):
args = {
"n_images": fields.Integer(
required=True, example=5, description="Number of images"
required=True, metadata={"example": 5, "description": "Number of images"}
),
"t_between": fields.Number(
missing=1, example=1, description="Time (seconds) between images"
load_default=1,
metadata={"example": 1, "description": "Time (seconds) between images"},
),
}

5
docs/source/extensions/example_extension/07_ev_gui.py
View file

@ -99,10 +99,11 @@ class TimelapseAPIView(ActionView):
args = {
"n_images": fields.Integer(
required=True, example=5, description="Number of images"
required=True, metadata={"example": 5, "description": "Number of images"}
),
"t_between": fields.Number(
missing=1, example=1, description="Time (seconds) between images"
load_default=1,
metadata={"example": 1, "description": "Time (seconds) between images"},
),
}

10
docs/source/extensions/marshaling.rst
View file

@ -23,7 +23,7 @@ A **field** describes the data type of a single parameter, as well as any other
.. code-block:: python
fields.String(required=False, missing="Default value", example="Example value")
fields.String(required=False, load_default="Default value", metadata={"example: "Example value"})
A **schema** is a collection of keys and fields describing how an object should be serialized/deserialized. Schemas can be created in several ways, either by creating a ``Schema`` class, or by passing a dictionary of key-field pairs. Both methods will be discussed in the following examples.
@ -43,7 +43,7 @@ For example, if you are creating an API route, in which you expect parameters ``
class UserSchema(Schema):
name = fields.String(required=True)
age = fields.Integer(required=True)
job = fields.String(required=False, missing="Unknown")
job = fields.String(required=False, load_default="Unknown")
To inform your POST method to expect these arguments, use the ``args`` class attribute:
@ -63,7 +63,7 @@ Alternatively, if your schema is only used in a single location, it may be simpl
args = {
"name": fields.String(required=True),
"age": fields.Integer(required=True),
"job": fields.String(required=False, missing="Unknown")
"job": fields.String(required=False, load_default="Unknown")
}
def post(self, args):
@ -88,7 +88,7 @@ This JSON data is the parsed, converted into a Python dictionary, and passed as
args = {
"name": fields.String(required=True),
"age": fields.Integer(required=True),
"job": fields.String(required=False, missing="Unknown")
"job": fields.String(required=False, load_default="Unknown")
}
def post(self, args):
@ -146,7 +146,7 @@ Our ``rename`` view class may now look like:
# Format our returned object using MicroscopeIdentifySchema
schema = MicroscopeIdentifySchema()
# Expect a request parameter called "name", which is a string. Pass to argument "args".
args = {"name": fields.String(required=True, example="My Example Microscope")}
args = {"name": fields.String(required=True, metadata={"example": "My Example Microscope"})}
def post(self, args):
# Look for our "name" parameter in the request arguments

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

@ -78,7 +78,7 @@ We will implement the ``schema`` attribute in our ``ExampleRenameView`` view fro
# We can use a single schema as the input and output will be formatted identically
# Eg. We always expect a "name" string argument, and always return a "name" string attribute
class ExampleRenameView(PropertyView):
schema = {"name": fields.String(required=True, example="My Example Microscope")}
schema = {"name": fields.String(required=True, metadata={"example": "My Example Microscope"})}
def get(self):
"""

4
openflexure_microscope/api/app.py
View file

@ -261,10 +261,10 @@ def generate_openapi():
if fname.endswith(".json"):
import json
with open(fname, "w") as fd:
with open(fname, "w", encoding="utf-8") as fd:
json.dump(labthing.spec.to_dict(), fd)
else:
with open(fname, "w") as fd:
with open(fname, "w", encoding="utf-8") as fd:
fd.write(labthing.spec.to_yaml())

68
openflexure_microscope/api/default_extensions/autofocus.py
View file

@ -245,7 +245,9 @@ def extension_action(args=None):
# Run the action
return func(self.extension, **arguments)
def get(self, *args, **kwargs): # pylint: disable=useless-super-delegation
def get(
self, *args, **kwargs
): # pylint: disable=useless-super-delegation,arguments-differ
# Explicitly wrap the `get` method to allow us to add a docstring
return super().get(*args, **kwargs)
@ -347,8 +349,10 @@ class AutofocusExtension(BaseExtension):
args={
"dz": fields.List(
fields.Int(),
description="An ascending list of relative z positions",
example=[int(x) for x in np.linspace(-300, 300, 7)],
metadata={
"description": "An ascending list of relative z positions",
"example": [int(x) for x in np.linspace(-300, 300, 7)],
},
)
}
)
@ -408,7 +412,9 @@ class AutofocusExtension(BaseExtension):
@extension_action(
args={
"dz": fields.Int(required=True, description="The relative Z move to make")
"dz": fields.Int(
required=True, metadata={"description": "The relative Z move to make"}
)
}
)
def move_and_measure(
@ -430,9 +436,11 @@ class AutofocusExtension(BaseExtension):
@extension_action(
args={
"dz": fields.Int(
missing=2000,
example=2000,
description="Total Z range to search over (in stage steps)",
load_default=2000,
metadata={
"description": "Total Z range to search over (in stage steps)",
"example": 2000,
},
)
}
)
@ -526,14 +534,18 @@ class AutofocusExtension(BaseExtension):
@extension_action(
args={
"dz": fields.Int(
missing=500,
example=500,
description="Total Z range to move down, then up (in stage steps)",
load_default=500,
metadata={
"description": "Total Z range to move down, then up (in stage steps)",
"example": 500,
},
),
"delay": fields.Int(
missing=5,
example=5,
description="How long to measure sharpness for after the move",
load_default=5,
metadata={
"description": "How long to measure sharpness for after the move, in seconds",
"example": 5,
},
),
}
)
@ -554,23 +566,31 @@ class AutofocusExtension(BaseExtension):
@extension_action(
args={
"dz": fields.Int(
missing=2000,
example=2000,
description="Total Z range to search over (in stage steps)",
load_default=2000,
metadata={
"description": "Total Z range to search over (in stage steps)",
"example": 2000,
},
),
"target_z": fields.Int(
missing=0,
example=-100,
description="Target finishing position, relative to the focus.",
load_default=0,
metadata={
"description": "Target finishing position, relative to the focus.",
"example": -100,
},
),
"initial_move_up": fields.Bool(
missing=True,
description="Set to Flase to disable the initial move upwards",
load_default=True,
metadata={
"description": "Set to False to disable the initial move upwards"
},
),
"backlash": fields.Int(
missing=25,
minimum=0,
description="Distance to undershoot, before correction move.",
load_default=25,
metadata={
"description": "Distance to undershoot, before correction move.",
"minimum": 0,
},
),
}
)

2
openflexure_microscope/api/default_extensions/autostorage.py
View file

@ -242,7 +242,7 @@ class GetLocationsView(PropertyView):
class PreferredLocationView(PropertyView):
schema = fields.String(required=True, example="Default")
schema = fields.String(required=True, metadata={"example": "Default"})
def get(self):
self.extension.check_location()

50
openflexure_microscope/api/default_extensions/camera_stage_mapping.py
View file

@ -200,7 +200,7 @@ class CSMExtension(BaseExtension):
"linear_calibration_y": cal_y,
}
with open(CSM_DATAFILE_PATH, "w") as f:
with open(CSM_DATAFILE_PATH, "w", encoding="utf-8") as f:
json.dump(data, f, cls=JSONEncoder)
return data
@ -279,7 +279,11 @@ class CSMExtension(BaseExtension):
class Calibrate1DView(ActionView):
args = {"direction": fields.List(fields.Float(), required=True, example=[1, 0, 0])}
args = {
"direction": fields.List(
fields.Float(), required=True, metadata={"example": [1, 0, 0]}
)
}
def post(self, args):
"""Calibrate one axis of the microscope stage against the camera."""
@ -298,10 +302,18 @@ class CalibrateXYView(ActionView):
class MoveInImageCoordinatesView(ActionView):
args = {
"x": fields.Float(
description="The number of pixels to move in X", required=True, example=100
metadata={
"description": "The number of pixels to move in X",
"example": 100,
},
required=True,
),
"y": fields.Float(
description="The number of pixels to move in Y", required=True, example=100
metadata={
"description": "The number of pixels to move in Y",
"example": 100,
},
required=True,
),
}
@ -316,10 +328,18 @@ class MoveInImageCoordinatesView(ActionView):
class ClosedLoopMoveInImageCoordinatesView(ActionView):
args = {
"x": fields.Float(
description="The number of pixels to move in X", required=True, example=100
metadata={
"description": "The number of pixels to move in X",
"example": 100,
},
required=True,
),
"y": fields.Float(
description="The number of pixels to move in Y", required=True, example=100
metadata={
"description": "The number of pixels to move in Y",
"example": 100,
},
required=True,
),
}
@ -336,15 +356,25 @@ class ClosedLoopMoveInImageCoordinatesView(ActionView):
class TestClosedLoopSpiralScanView(ActionView):
args = {
"x_step": fields.Float(
description="The number of pixels to move in X", required=True, example=100
metadata={
"description": "The number of pixels to move in X",
"example": 100,
},
required=True,
),
"y_step": fields.Float(
description="The number of pixels to move in Y", required=True, example=100
metadata={
"description": "The number of pixels to move in Y",
"example": 100,
},
required=True,
),
"N": fields.Int(
description="The number of rings in the spiral scan",
metadata={
"description": "The number of rings in the spiral scan",
"example": 100,
},
required=True,
example=3,
),
}

80
openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
View file

@ -169,39 +169,50 @@ class DeleteLSTView(ActionView):
microscope.save_settings()
percentile_field = fields.Float(
load_default=99.9,
metadata={
"example": 99.9,
"description": (
"A float between 0 and 100 setting the centile to use "
"to measure the white point of the image. A value "
"of 99.9 allows 0.1% of the pixels to be erroneously "
"bright - this helps stability in low light."
),
},
)
class AutoExposureFromRawView(ActionView):
args = {
"target_white_level": fields.Int(
missing=700,
example=700,
description=(
"The pixel value (10-bit format) that we aim for when adjusting shutter/gain."
),
load_default=700,
metadata={
"example": 700,
"description": (
"The pixel value (10-bit format) that we aim for when adjusting shutter/gain."
),
},
),
"max_iterations": fields.Int(
missing=20,
description=(
"The number of adjustments to the camera's settings to make before giving up."
),
load_default=20,
metadata={
"description": (
"The number of adjustments to the camera's settings to make before giving up."
)
},
),
"tolerance": fields.Float(
missing=0.05,
example=0.05,
description=(
"We stop adjusting when we get within this fraction of the target "
"value. It is a number between 0 and 1, usually 0.01--0.1."
),
),
"percentile": fields.Float(
missing=99.9,
example=99.9,
description=(
"A float between 0 and 100 setting the centile to use "
"to measure the white point of the image. A value "
"of 99.9 allows 0.1% of the pixels to be erroneously "
"bright - this helps stability in low light."
),
load_default=0.05,
metadata={
"example": 0.05,
"description": (
"We stop adjusting when we get within this fraction of the target "
"value. It is a number between 0 and 1, usually 0.01--0.1."
),
},
),
"percentile": percentile_field,
}
def post(self, args):
@ -210,18 +221,7 @@ class AutoExposureFromRawView(ActionView):
class AutoWhiteBalanceFromRawView(ActionView):
args = {
"percentile": fields.Float(
missing=99.9,
example=99.9,
description=(
"A float between 0 and 100 setting the centile to use "
"to measure the white point of the image. A value "
"of 99.9 allows 0.1% of the pixels to be erroneously "
"bright - this helps stability in low light."
),
)
}
args = {"percentile": percentile_field}
def post(self, args):
with find_picamera() as (picamera, _, _):
@ -231,8 +231,10 @@ class AutoWhiteBalanceFromRawView(ActionView):
class GetRawChannelPercentilesView(ActionView):
args = {
"percentile": fields.Float(
example=99.9,
description="A float between 0 and 100 setting the centile to calculate",
metadata={
"description": "A float between 0 and 100 setting the centile to calculate",
"example": 99.9,
}
)
}
schema = fields.List(fields.Integer)

20
openflexure_microscope/api/default_extensions/scan.py
View file

@ -578,19 +578,23 @@ class ScanExtension(BaseExtension):
class TileScanArgs(FullCaptureArgs):
namemode = fields.String(missing="coordinates", example="coordinates")
namemode = fields.String(
load_default="coordinates", metadata={"example": "coordinates"}
)
grid = fields.List(
fields.Integer(validate=marshmallow.validate.Range(min=1)),
missing=[3, 3, 3],
example=[3, 3, 3],
load_default=[3, 3, 3],
metadata={"example": [3, 3, 3]},
)
style = fields.String(missing="raster")
autofocus_dz = fields.Integer(missing=50)
fast_autofocus = fields.Boolean(missing=False)
style = fields.String(load_default="raster")
autofocus_dz = fields.Integer(load_default=50)
fast_autofocus = fields.Boolean(load_default=False)
stride_size = fields.List(
fields.Integer, missing=[2000, 1500, 100], example=[2000, 1500, 100]
fields.Integer,
load_default=[2000, 1500, 100],
metadata={"example": [2000, 1500, 100]},
)
detect_empty_fields_and_skip_autofocus = fields.Boolean(missing=False)
detect_empty_fields_and_skip_autofocus = fields.Boolean(load_default=False)
class TileScanAPI(ActionView):

6
openflexure_microscope/api/dev_extensions/tools.py
View file

@ -24,7 +24,11 @@ class RaiseException(ActionView):
class SleepFor(ActionView):
schema = {"TimeAsleep": fields.Float()}
args = {"time": fields.Float(description="Time to sleep, in seconds", example=0.5)}
args = {
"time": fields.Float(
metadata={"description": "Time to sleep, in seconds", "example": 0.5}
)
}
def post(self, args):
sleep_time: int = args.get("time", 0)

8
openflexure_microscope/api/openapi.py
View file

@ -8,8 +8,8 @@ API_TAGS = [
"embedded in the JSON action description."
),
"externalDocs": {
"url": "https://iot.mozilla.org/wot/#action-resource",
"description": "Mozilla's description of Web of Things 'Action' resources.",
"url": "https://www.w3.org/TR/wot-thing-description/#actionaffordance",
"description": "W3C's description of Web of Things 'Action' resources.",
},
},
{
@ -19,8 +19,8 @@ API_TAGS = [
"state of the microscope."
),
"externalDocs": {
"url": "https://iot.mozilla.org/wot/#property-resource",
"description": "Mozilla's description of Web of Things 'Property' resources.",
"url": "https://www.w3.org/TR/wot-thing-description/#propertyaffordance",
"description": "W3C's description of Web of Things 'Property' resources.",
},
},
{"name": "captures", "description": ""},

2
openflexure_microscope/api/utilities/__init__.py
View file

@ -81,7 +81,7 @@ def init_default_extensions(extension_dir: str):
create_file(default_ext_path)
logging.info("Populating %s...", (default_ext_path))
with open(default_ext_path, "w") as outfile:
with open(default_ext_path, "w", encoding="utf-8") as outfile:
outfile.write(_DEFAULT_EXTENSION_INIT)

27
openflexure_microscope/api/v2/views/actions/camera.py
View file

@ -10,23 +10,28 @@ from openflexure_microscope.api.v2.views.captures import CaptureSchema
class CaptureResizeSchema(Schema):
width = fields.Integer(example=640, required=True)
height = fields.Integer(example=480, required=True)
width = fields.Integer(metadata={"example": 640}, required=True)
height = fields.Integer(metadata={"example": 480}, required=True)
class BasicCaptureArgs(Schema):
use_video_port = fields.Boolean(missing=False)
use_video_port = fields.Boolean(load_default=False)
bayer = fields.Boolean(
missing=False, description="Include raw bayer data in capture"
load_default=False,
metadata={"description": "Include raw bayer data in capture"},
)
resize = fields.Nested(CaptureResizeSchema(), required=False)
class FullCaptureArgs(BasicCaptureArgs):
filename = fields.String(example="MyFileName")
temporary = fields.Boolean(missing=False, description="Delete capture on shutdown")
annotations = fields.Dict(missing={}, example={"Client": "SwaggerUI"})
tags = fields.List(fields.String, missing=[], example=["docs"])
filename = fields.String(metadata={"example": "MyFileName"})
temporary = fields.Boolean(
load_default=False, metadata={"description": "Delete capture on shutdown"}
)
annotations = fields.Dict(
load_default={}, metadata={"example": {"Client": "SwaggerUI"}}
)
tags = fields.List(fields.String, load_default=[], metadata={"example": ["docs"]})
class CaptureAPI(ActionView):
@ -113,7 +118,11 @@ class GPUPreviewStartAPI(ActionView):
in the format ``[x, y, width, height]``.
"""
args = {"window": fields.List(fields.Integer, missing=[], example=[0, 0, 640, 480])}
args = {
"window": fields.List(
fields.Integer, load_default=[], metadata={"example": [0, 0, 640, 480]}
)
}
def post(self, args):
"""

9
openflexure_microscope/api/v2/views/actions/stage.py
View file

@ -7,11 +7,12 @@ from labthings.views import ActionView
class MoveStageAPI(ActionView):
args = {
"absolute": fields.Boolean(
missing=False, example=False, description="Move to an absolute position"
load_default=False,
metadata={"description": "Move to an absolute position", "example": False},
),
"x": fields.Int(missing=None, example=100, allow_none=False),
"y": fields.Int(missing=None, example=100, allow_none=False),
"z": fields.Int(missing=None, example=20, allow_none=False),
"x": fields.Int(load_default=None, metadata={"example": 100}, allow_none=True),
"y": fields.Int(load_default=None, metadata={"example": 100}, allow_none=True),
"z": fields.Int(load_default=None, metadata={"example": 20}, allow_none=True),
}
def post(self, args):

4
openflexure_microscope/api/v2/views/captures.py
View file

@ -24,7 +24,7 @@ class InstrumentSchema(Schema):
class ImageSchema(Schema):
id = fields.UUID()
time = fields.String(format="date")
time = fields.String(metadata={"format": "date"})
format = fields.String()
name = fields.String()
tags = fields.List(fields.String())
@ -59,7 +59,7 @@ class CaptureSchema(ImageSchema):
# without the server having to do a tonne of file IO
dataset = fields.Nested(BasicDatasetSchema())
file = fields.String(
data_key="path", description="Path of file on microscope device"
data_key="path", metadata={"description": "Path of file on microscope device"}
)
# No need to make a schema for links as we only ever
# create the dictionary right here in `generate_links`

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

@ -7,10 +7,12 @@ class StageTypeProperty(PropertyView):
"""The type of the stage"""
schema = fields.String(
missing=None,
example="SangaStage",
load_default="SangaStage",
validate=validate.OneOf(["SangaStage", "SangaDeltaStage"]),
description="The translation stage geometry",
metadata={
"description": "The translation stage geometry",
"example": "SangaStage",
},
allow_none=False,
)

2
openflexure_microscope/camera/base.py
View file

@ -54,7 +54,7 @@ class FrameStream(io.BytesIO):
t: Optional[Type[BaseException]],
value: Optional[BaseException],
traceback: Optional[TracebackType],
) -> Optional[bool]:
) -> None:
self.stop_tracking()
return super().__exit__(t, value, traceback)

10
openflexure_microscope/camera/pi.py
View file

@ -30,7 +30,7 @@ import logging
import time
# Type hinting
from typing import BinaryIO, Tuple, Union
from typing import BinaryIO, Optional, Tuple, Union
import numpy as np
@ -307,7 +307,9 @@ class PiCameraStreamer(BaseCamera):
self.picamera.zoom = new_fov
def start_preview(
self, fullscreen: bool = True, window: Tuple[int, int, int, int] = None
self,
fullscreen: bool = True,
window: Optional[Tuple[int, int, int, int]] = None,
):
"""Start the on board GPU camera preview."""
with self.lock(timeout=1):
@ -462,9 +464,9 @@ class PiCameraStreamer(BaseCamera):
output: Union[str, BinaryIO],
fmt: str = "jpeg",
use_video_port: bool = False,
resize: Tuple[int, int] = None,
resize: Optional[Tuple[int, int]] = None,
bayer: bool = True,
thumbnail: Tuple[int, int, int] = None,
thumbnail: Optional[Tuple[int, int, int]] = None,
):
"""
Capture a still image to a StreamObject.

3
openflexure_microscope/captures/capture.py
View file

@ -120,7 +120,8 @@ class CaptureObject(object):
logging.debug("Finished writing to disk %s", self.file)
def open(self, mode):
return open(self.file, mode)
# We don't specify an encoding because this will be a binary file.
return open(self.file, mode) # pylint: disable=unspecified-encoding
def split_file_path(self, filepath: str):
"""

9
openflexure_microscope/config.py
View file

@ -3,6 +3,7 @@ import json
import logging
import os
import shutil
from typing import Optional
from .json import JSONEncoder
from .paths import CONFIGURATION_FILE_PATH, SETTINGS_FILE_PATH
@ -17,7 +18,7 @@ class OpenflexureSettingsFile:
expand (bool): Expand paths to valid auxillary config files.
"""
def __init__(self, path: str, defaults: dict = None):
def __init__(self, path: str, defaults: Optional[dict] = None):
defaults = defaults or {}
# Set arguments
@ -88,7 +89,7 @@ def load_json_file(config_path) -> dict:
logging.info("Loading %s...", config_path)
with open(config_path) as config_file:
with open(config_path, encoding="utf-8") as config_file:
try:
config_data = json.load(config_file)
except json.decoder.JSONDecodeError as e:
@ -112,7 +113,7 @@ def save_json_file(config_path: str, config_dict: dict):
logging.info("Saving %s...", config_path)
logging.debug(config_dict)
with open(config_path, "w") as outfile:
with open(config_path, "w", encoding="utf-8") as outfile:
json.dump(config_dict, outfile, cls=JSONEncoder, indent=2, sort_keys=True)
@ -150,7 +151,7 @@ def initialise_file(config_path, populate: str = "{}\n"):
create_file(config_path)
logging.info("Populating %s...", (config_path))
with open(config_path, "w") as outfile:
with open(config_path, "w", encoding="utf-8") as outfile:
outfile.write(populate)

2
openflexure_microscope/microscope.py
View file

@ -370,7 +370,7 @@ class Microscope:
folder: str = "",
temporary: bool = False,
use_video_port: bool = False,
resize: Tuple[int, int] = None,
resize: Optional[Tuple[int, int]] = None,
bayer: bool = True,
fmt: str = "jpeg",
annotations: Optional[Dict[str, str]] = None,

4
openflexure_microscope/rescue/check_picamera.py
View file

@ -26,11 +26,11 @@ def main():
try:
import picamerax
except Exception as e: # pylint: disable=W0703
except Exception as _e: # pylint: disable=W0703
error_sources.append(PICAMERA_IMPORT_ERROR)
else:
try:
_ = picamerax.PiCamera()
_cam = picamerax.PiCamera()
except picamerax.PiCameraError as e:
msg = e.args[0]
if msg in PICAMERA_ERROR_MAP:

2
openflexure_microscope/rescue/check_sangaboard.py
View file

@ -20,7 +20,7 @@ def main():
# Try connecting on the specified port
try:
stage = Sangaboard(stage_port)
except FileNotFoundError as e:
except FileNotFoundError as _:
if stage_port:
error_sources.append(
ErrorSource(

4
scripts/zenodo/upload_to_zenodo.py
View file

@ -31,7 +31,7 @@ def script_directory(path):
def get_meta():
with open(script_directory("metadata.yaml")) as f:
with open(script_directory("metadata.yaml"), encoding="utf-8") as f:
metadata = f.read()
return yaml.safe_load(metadata)
@ -51,7 +51,7 @@ def main():
zenodo.upload_file(deposit["id"], path)
link = deposit["links"]["latest_draft_html"]
with open("zenodo-link.html", "w") as f:
with open("zenodo-link.html", "w", encoding="utf-8") as f:
f.write(f'<a href="{link}">{link}</a>')

25
setup.py
View file

@ -22,7 +22,7 @@ with open(path.join(here, "README.md"), encoding="utf-8") as f:
setup(
name="openflexure-microscope-server",
version="2.10.1",
version="2.11.0",
description="Python module, and Flask-based web API, to run the OpenFlexure Microscope.",
long_description=long_description,
long_description_content_type="text/markdown",
@ -51,8 +51,9 @@ setup(
"scipy ~= 1.6.1",
"python-dateutil ~= 2.8",
"psutil ~= 5.6.7", # Autostorage extension
"markupsafe ~= 2.0.0", # 2.1.x breaks jinja2
"opencv-python-headless ~= 4.5.1",
"sangaboard ~= 0.2",
"sangaboard ~= 0.3.3",
"expiringdict ~= 1.2.1",
"camera-stage-mapping == 0.1.4",
"picamerax ~= 20.9.1",
@ -60,7 +61,7 @@ setup(
"pytest-cov ~= 2.10.1",
"piexif ~= 1.1.3",
"labthings ~= 1.3.0",
"typing-extensions ~= 3.7.4", # Needed for some type-hints in Python < 3.8 (e.g. Literal)
"typing-extensions ~= 4.3.0", # Needed for some type-hints in Python < 3.8 (e.g. Literal)
"RPi.GPIO ~= 0.7.0; platform_machine == 'armv7l'",
],
# "dev" specifies extra packages used for development (linting, testing, etc.)
@ -71,19 +72,15 @@ setup(
"sphinx < 4.0", # Currently httpdomain isn't ready for 4.0
"sphinxcontrib-openapi ~= 0.7",
"sphinx_rtd_theme ~=0.5.2",
"rope ~= 0.14.0",
"pylint ~= 2.8.0", # 2.9.2 crashes and I've not yet figured out why.
"pytest ~= 6.1.2",
"mypy ~= 0.790",
"pylint ~= 2.14.0", # 2.9.2 crashes and I've not yet figured out why.
"pytest ~= 7.1.2",
"mypy ~= 0.971",
"types-python-dateutil",
"types-setuptools",
"poethepoet ~= 0.10.0",
"freezegun ~= 1.0.0",
"lxml ~= 4.6",
"black == 18.9b0", # Because black is in prerelease, giving a flexible version
# specifier causes all manner of problems. A fixed version
# avoids issues with prereleases (which are normally not
# allowed by pipenv) but can be a bit of a pain sometimes!
"poethepoet ~= 0.16.0",
"freezegun ~= 1.2.1",
"lxml ~= 4.9",
"black == 18.9b0",
]
},
dependency_links=[],

2
tests/test_app.py
View file

@ -28,7 +28,7 @@ def test_thing_description_valid():
# TODO: it would be nice to put this into LabThings
# First load the schema from file and check it validates
schema_fname = os.path.join(os.path.dirname(__file__), "w3c_td_schema.json")
schema = json.load(open(schema_fname, "r"))
schema = json.load(open(schema_fname, "r"), encoding="utf-8")
jsonschema.Draft7Validator.check_schema(schema)
# Build a TD dictionary

4
tests/w3c_td_schema.json
View file

@ -66,10 +66,10 @@
"thing-context": {
"oneOf": [{
"type": "array",
"items": [{
"prefixItems": [{
"$ref": "#/definitions/thing-context-w3c-uri"
}],
"additionalItems": {
"items": {
"anyOf": [{
"$ref": "#/definitions/anyUri"
},