rahix/openflexure-microscope-server
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Merge branch 'labthings-070' into 'master'

Browse source 
Convert to LabThings 0.7 style

See merge request openflexure/openflexure-microscope-server!67
This commit is contained in:
Joel Collins 2020-07-06 10:44:38 +00:00
commit 369af1649e
42 changed files with 541 additions and 459 deletions
Download patch file Download diff file Expand all files Collapse all files

4
docs/source/capture.rst
View file

@ -1,11 +1,11 @@
Capture Object
=======================================================
By default, all image and video capture data are stored to instances of :py:class:`openflexure_microscope.camera.capture.CaptureObject`. This class mostly wraps up complexity associated with moving data between disk and memory.
By default, all image and video capture data are stored to instances of :py:class:`openflexure_microscope.captures.CaptureObject`. This class mostly wraps up complexity associated with moving data between disk and memory.
The class also includes some convenience features such as handling metadata tags and file names, and generating image thumbnails. Additionally, the class handles storing capture metadata to Exif tags in supported formats.
Below are details of available methods and attributes.
.. automodule:: openflexure_microscope.camera.capture
.. automodule:: openflexure_microscope.captures.capture
:members:

11
docs/source/extensions/actions.rst
View file

@ -17,11 +17,14 @@ 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
@use_args({"use_video_port": fields.Boolean(missing=True)})
args = {"use_video_port": fields.Boolean(missing=True)}
# Our success response (200) returns an image (image/jpeg mimetype)
@doc_response(200, mimetype="image/jpeg")
responses = {
200: {"content_type": "image/jpeg"}
}
def post(self, args):
"""
Take a non-persistant image capture.
@ -41,7 +44,7 @@ Like properties, we use a special view class to identify a view as an action: ``
# Return our image data using Flasks send_file function
return send_file(io.BytesIO(stream.read()), mimetype="image/jpeg")
In this example, we are also making use of the ``@doc_response`` decorator, to document that our successful response (HTTP code 200) will return data with a mimetype ``image/jpeg``, as well as ``@use_args`` to accept optional parameters with POST requests.
In this example, we are also making use of the ``responses`` attribute, to document that our successful response (HTTP code 200) will return data with a mimetype ``image/jpeg``, as well as ``args`` to accept optional parameters with POST requests.
Complete example
----------------

11
docs/source/extensions/example_extension/02_adding_views.py
View file

@ -2,7 +2,6 @@ from labthings.server.extensions import BaseExtension
from labthings.server.find import find_component
from labthings.server.view import View
from labthings.server.decorators import use_body
from labthings.server import fields
## Extension methods
@ -44,11 +43,13 @@ class ExampleIdentifyView(View):
class ExampleRenameView(View):
# Expect a request parameter called "name", which is a string. Pass to argument "args".
@use_body(fields.String(required=True, example="My Example Microscope"))
def post(self, body):
# Expect a request parameter called "name", which is a string.
# Passed to the argument "args".
args = fields.String(required=True, example="My Example Microscope")
def post(self, args):
# Look for our new name in the request body
new_name = body
new_name = args
# Find our microscope component
microscope = find_component("org.openflexure.microscope")

14
docs/source/extensions/example_extension/03_marshaling_data.py
View file

@ -2,7 +2,6 @@ from labthings.server.extensions import BaseExtension
from labthings.server.find import find_component
from labthings.server.view import View
from labthings.server.decorators import use_args, marshal_with
from labthings.server.schema import Schema
from labthings.server import fields
@ -30,24 +29,25 @@ def rename(microscope, new_name):
## Extension views
class ExampleIdentifyView(View):
# Format our returned object using MicroscopeIdentifySchema
@marshal_with(MicroscopeIdentifySchema())
schema = MicroscopeIdentifySchema()
def get(self):
# Find our microscope component
microscope = find_component("org.openflexure.microscope")
# Return our microscope object,
# let @marshal_with handle formatting the output
# let schema handle formatting the output
return microscope
class ExampleRenameView(View):
# Format our returned object using MicroscopeIdentifySchema
@marshal_with(MicroscopeIdentifySchema())
schema = MicroscopeIdentifySchema()
# Expect a request parameter called "name", which is a string. Pass to argument "args".
@use_args({"name": fields.String(required=True, example="My Example Microscope")})
args = {"name": fields.String(required=True, example="My Example Microscope")}
def post(self, args):
# Look for our "name" parameter in the request arguments
new_name = args.get("name")
@ -59,7 +59,7 @@ class ExampleRenameView(View):
rename(microscope, new_name)
# Return our microscope object,
# let @marshal_with handle formatting the output
# let schema handle formatting the output
return microscope

20
docs/source/extensions/example_extension/04_properties.py
View file

@ -2,12 +2,6 @@ from labthings.server.extensions import BaseExtension
from labthings.server.find import find_component
from labthings.server.view import View, PropertyView
from labthings.server.decorators import (
use_args,
marshal_with,
ThingProperty,
PropertySchema,
)
from labthings.server.schema import Schema
from labthings.server import fields
@ -38,7 +32,8 @@ def rename(microscope, new_name):
# Since we only have a GET method here, it'll register as a read-only property
class ExampleIdentifyView(PropertyView):
# Format our returned object using MicroscopeIdentifySchema
@marshal_with(MicroscopeIdentifySchema())
schema = MicroscopeIdentifySchema()
def get(self):
"""
Show identifying information about the current microscope object
@ -47,14 +42,15 @@ class ExampleIdentifyView(PropertyView):
microscope = find_component("org.openflexure.microscope")
# Return our microscope object,
# let @marshal_with handle formatting the output
# let schema handle formatting the output
return microscope
# We can use a single schema for all methods if the input and output will be formatted identically
# Eg. Here, we will always expect a "name" string argument, and always return a "name" string attribute
@PropertySchema({"name": fields.String(required=True, example="My Example Microscope")})
# 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")}
def get(self):
"""
Show the current microscope name
@ -78,7 +74,7 @@ class ExampleRenameView(PropertyView):
rename(microscope, new_name)
# Return our microscope object,
# let @marshal_with handle formatting the output
# let schema handle formatting the output
return microscope

32
docs/source/extensions/example_extension/05_actions.py
View file

@ -2,14 +2,6 @@ from labthings.server.extensions import BaseExtension
from labthings.server.find import find_component
from labthings.server.view import View, ActionView, PropertyView
from labthings.server.decorators import (
use_args,
marshal_with,
ThingProperty,
PropertySchema,
ThingAction,
doc_response,
)
from labthings.server.schema import Schema
from labthings.server import fields
@ -43,7 +35,8 @@ def rename(microscope, new_name):
# Since we only have a GET method here, it'll register as a read-only property
class ExampleIdentifyView(PropertyView):
# Format our returned object using MicroscopeIdentifySchema
@marshal_with(MicroscopeIdentifySchema())
schema = MicroscopeIdentifySchema()
def get(self):
"""
Show identifying information about the current microscope object
@ -52,14 +45,16 @@ class ExampleIdentifyView(PropertyView):
microscope = find_component("org.openflexure.microscope")
# Return our microscope object,
# let @marshal_with handle formatting the output
# let schema handle formatting the output
return microscope
# We can use a single schema for all methods if the input and output will be formatted identically
# Eg. Here, we will always expect a "name" string argument, and always return a "name" string attribute
@PropertySchema({"name": fields.String(required=True, example="My Example Microscope")})
# 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")}
def get(self):
"""
Show the current microscope name
@ -83,7 +78,7 @@ class ExampleRenameView(PropertyView):
rename(microscope, new_name)
# Return our microscope object,
# let @marshal_with handle formatting the output
# let schema handle formatting the output
return microscope
@ -91,11 +86,14 @@ class QuickCaptureAPI(ActionView):
"""
Take an image capture and return it without saving
"""
# Expect a "use_video_port" boolean, which defaults to True if none is given
@use_args({"use_video_port": fields.Boolean(missing=True)})
args = {"use_video_port": fields.Boolean(missing=True)}
# Our success response (200) returns an image (image/jpeg mimetype)
@doc_response(200, mimetype="image/jpeg")
responses = {
200: {"content_type": "image/jpeg"}
}
def post(self, args):
"""
Take a non-persistant image capture.

31
docs/source/extensions/example_extension/06_tasks_locks.py
View file

@ -2,14 +2,6 @@ from labthings.server.extensions import BaseExtension
from labthings.server.find import find_component
from labthings.server.view import View, ActionView
from labthings.server.decorators import (
use_args,
marshal_with,
ThingProperty,
PropertySchema,
ThingAction,
doc_response,
)
from labthings.server.schema import Schema
from labthings.server import fields
@ -18,10 +10,10 @@ import io # Used in our capture action
import time # Used in our timelapse function
# Used in our timelapse function
from openflexure_microscope.camera.base import generate_basename
from openflexure_microscope.captures.capture_manager import generate_basename
# Used to run our timelapse in a background thread
from labthings.core.tasks import taskify, update_task_progress
from labthings.core.tasks import update_task_progress
## Extension methods
@ -70,16 +62,15 @@ class TimelapseAPI(ActionView):
"""
Take a series of images in a timelapse
"""
@use_args(
{
"n_images": fields.Integer(
required=True, example=5, description="Number of images"
),
"t_between": fields.Number(
missing=1, example=1, description="Time (seconds) between images"
),
}
)
args = {
"n_images": fields.Integer(
required=True, example=5, description="Number of images"
),
"t_between": fields.Number(
missing=1, example=1, description="Time (seconds) between images"
),
}
def post(self, args):
# Find our microscope component
microscope = find_component("org.openflexure.microscope")

31
docs/source/extensions/example_extension/07_ev_gui.py
View file

@ -2,14 +2,6 @@ from labthings.server.extensions import BaseExtension
from labthings.server.find import find_component
from labthings.server.view import View, ActionView
from labthings.server.decorators import (
use_args,
marshal_with,
ThingProperty,
PropertySchema,
ThingAction,
doc_response,
)
from labthings.server.schema import Schema
from labthings.server import fields
@ -18,10 +10,10 @@ import io # Used in our capture action
import time # Used in our timelapse function
# Used in our timelapse function
from openflexure_microscope.camera.base import generate_basename
from openflexure_microscope.captures.capture_manager import generate_basename
# Used to run our timelapse in a background thread
from labthings.core.tasks import taskify, update_task_progress
from labthings.core.tasks import update_task_progress
# Used to convert our GUI dictionary into a complete eV extension GUI
from openflexure_microscope.api.utilities.gui import build_gui
@ -72,16 +64,15 @@ class TimelapseAPI(ActionView):
"""
Take a series of images in a timelapse, running as a background task
"""
@use_args(
{
"n_images": fields.Integer(
required=True, example=5, description="Number of images"
),
"t_between": fields.Number(
missing=1, example=1, description="Time (seconds) between images"
),
}
)
args = {
"n_images": fields.Integer(
required=True, example=5, description="Number of images"
),
"t_between": fields.Number(
missing=1, example=1, description="Time (seconds) between images"
),
}
def post(self, args):
# Find our microscope component
microscope = find_component("org.openflexure.microscope")

62
docs/source/extensions/marshaling.rst
View file

@ -14,7 +14,7 @@ The OpenFlexure Microscope Server makes use of the `Marshmallow library <https:/
- **Deserialize** input data to app-level objects.
- **Serialize** app-level objects to primitive Python types. The serialized objects can then be rendered to standard formats such as JSON for use in an HTTP API.
When developing extensions, you are encouraged to make use of the ``@marshal_with`` and ``@use_args`` decorators, along with schemas, to handle serialisation of your API responses, and parsing of request parameters respectively.
When developing extensions, you are encouraged to make use of your View ``schema`` and ``args`` class attributes to handle serialisation of your API responses, and parsing of request parameters respectively.
Schemas and fields
++++++++++++++++++
@ -31,7 +31,7 @@ A **schema** is a collection of keys and fields describing how an object should
Argument parsing
++++++++++++++++
In the previous section we saw how to use fields and ``@use_body`` to get simple arguments from requests, in which a single parameter is required. By making use of Marshmallow schemas, and the `Webargs library <https://github.com/marshmallow-code/webargs>`_, we can allow for more complex requests containing many parameters of different types. The parsed request parameters are then passed to the view function as a positional argument (as before), in the form of a dictionary.
In the previous section we saw how to use fields and ``args`` to get simple arguments from requests, in which a single parameter is required. By making use of Marshmallow schemas, and the `Webargs library <https://github.com/marshmallow-code/webargs>`_, we can allow for more complex requests containing many parameters of different types. The parsed request parameters are then passed to the view function as a positional argument (as before), in the form of a dictionary.
For example, if you are creating an API route, in which you expect parameters ``name``, ``age``, and optionally, ``job``, your schema class may look like:
@ -45,25 +45,29 @@ For example, if you are creating an API route, in which you expect parameters ``
age = fields.Integer(required=True)
job = fields.String(required=False, missing="Unknown")
To inform your POST method to expect these arguments, use the ``@use_args`` decorator:
To inform your POST method to expect these arguments, use the ``args`` class attribute:
.. code-block:: python
@use_args(UserSchema())
def post(self, args):
class MyView(View):
args = UserSchema()
def post(self, args):
..
Alternatively, if your schema is only used in a single location, it may be simpler to create a dictionary schema only where it is used, for example:
.. code-block:: python
@use_args({
"name": fields.String(required=True),
"age": fields.Integer(required=True),
"job": fields.String(required=False, missing="Unknown")
})
def post(self, args):
...
class MyView(View):
args = {
"name": fields.String(required=True),
"age": fields.Integer(required=True),
"job": fields.String(required=False, missing="Unknown")
}
def post(self, args):
...
A compatible request body, in JSON format, may look like:
@ -80,15 +84,17 @@ This JSON data is the parsed, converted into a Python dictionary, and passed as
.. code-block:: python
@use_args({
"name": fields.String(required=True),
"age": fields.Integer(required=True),
"job": fields.String(required=False, missing="Unknown")
})
def post(self, args):
name = args.get("name") # Returns "John Doe", type str
age = args.get("age") # Returns 45, type int
job = args.get("job") # Returns "Python developer", type str
class MyView(View):
args = {
"name": fields.String(required=True),
"age": fields.Integer(required=True),
"job": fields.String(required=False, missing="Unknown")
}
def post(self, args):
name = args.get("name") # Returns "John Doe", type str
age = args.get("age") # Returns 45, type int
job = args.get("job") # Returns "Python developer", type str
Object serialization
@ -118,16 +124,17 @@ We use this new schema in our ``identify`` view like so:
class ExampleIdentifyView(View):
# Format our returned object using MicroscopeIdentifySchema
@marshal_with(MicroscopeIdentifySchema())
schema = MicroscopeIdentifySchema()
def get(self):
# Find our microscope component
microscope = find_component("org.openflexure.microscope")
# Return our microscope object,
# let @marshal_with handle formatting the output
# let schema handle formatting the output
return microscope
Note that our ``get`` method now returns the :py:class:`openflexure_microscope.Microscope` object itself. No formatting is done by the function, it is entirely handled by ``@marshal_with(MicroscopeIdentifySchema())``. Additionally, since we defined our schema as a class, it can be re-used elsewhere.
Note that our ``get`` method now returns the :py:class:`openflexure_microscope.Microscope` object itself. No formatting is done by the function, it is entirely handled by the view class, and its `schema` attribute. Additionally, since we defined our schema as a class, it can be re-used elsewhere.
For our ``rename`` view, we will use a simpler schema for our input arguments, defined by a dictionary (since we are only expecting a single parameter in, and it will likely not be re-used elsewhere). Our response, however, will use our ``MicroscopeIdentifySchema`` class. This means that the *response* of our ``identify`` and ``rename`` views will be identically formatted.
@ -137,9 +144,10 @@ Our ``rename`` view class may now look like:
class ExampleRenameView(View):
# Format our returned object using MicroscopeIdentifySchema
@marshal_with(MicroscopeIdentifySchema())
schema = MicroscopeIdentifySchema()
# Expect a request parameter called "name", which is a string. Pass to argument "args".
@use_args({"name": fields.String(required=True, example="My Example Microscope")})
args = {"name": fields.String(required=True, example="My Example Microscope")}
def post(self, args):
# Look for our "name" parameter in the request arguments
new_name = args.get("name")
@ -151,7 +159,7 @@ Our ``rename`` view class may now look like:
rename(microscope, new_name)
# Return our microscope object,
# let @marshal_with handle formatting the output
# let schema handle formatting the output
return microscope

21
docs/source/extensions/properties.rst
View file

@ -21,7 +21,8 @@ In order to register a view as a Thing property, we use the ``PropertyView`` cla
# Since we only have a GET method here, it'll register as a read-only property
class ExampleIdentifyView(PropertyView):
# Format our returned object using MicroscopeIdentifySchema
@marshal_with(MicroscopeIdentifySchema())
schema = MicroscopeIdentifySchema()
def get(self):
"""
Show identifying information about the current microscope object
@ -30,12 +31,9 @@ In order to register a view as a Thing property, we use the ``PropertyView`` cla
microscope = find_component("org.openflexure.microscope")
# Return our microscope object,
# let @marshal_with handle formatting the output
# let schemah handle formatting the output
return microscope
This decorator serves only to add documentation: The view will be tagged with ``property`` in Swagger documentation, and will appear as a property in the microscopes Thing Description.
However, the additional ``@PropertySchema`` decorator allows for simplified argument parsing and object marshaling.
Property schema
---------------
@ -71,16 +69,17 @@ This request would update the property, such that a GET request would *now* retu
"job": "Landscape gardener"
}
The ``@PropertySchema`` decorator can be applied to your view *class*, and essentially acts as shorthand for applying ``@marshal_with`` to all methods, and ``@use_args`` to all POST and PUT methods (or ``@use_body`` if only a single field is given).
In Property Views the ``schema`` class attribute acts as the schema for both marshalling responses *and* parsing arguments. This is because property requests and responses should be identically formatted.
We will implement the ``@PropertySchema`` decorator in our ``ExampleRenameView`` view from our previous example:
We will implement the ``schema`` attribute in our ``ExampleRenameView`` view from our previous example:
.. code-block:: python
# We can use a single schema for all methods if the input and output will be formatted identically
# Eg. Here, we will always expect a "name" string argument, and always return a "name" string attribute
@PropertySchema({"name": fields.String(required=True, example="My Example Microscope")})
# 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")}
def get(self):
"""
Show the current microscope name
@ -104,7 +103,7 @@ We will implement the ``@PropertySchema`` decorator in our ``ExampleRenameView``
rename(microscope, new_name)
# Return our microscope object,
# let @marshal_with handle formatting the output
# let schema handle formatting the output
return microscope
Complete example

8
docs/source/extensions/views.rst
View file

@ -18,17 +18,17 @@ In this case, our extension will have two new API views at `/identify` and `/ren
Request arguments
+++++++++++++++++
For POST and PUT requests, data usually needs to be provided to the view in order to perform its function. In this example, our ``rename`` view requires a new microscope name to be passed. We make use of the ``@use_body`` decorator to provide this functionality.
For POST and PUT requests, data usually needs to be provided to the view in order to perform its function. In this example, our ``rename`` view requires a new microscope name to be passed. We make use of the ``args`` class attribute to provide this functionality.
``@use_body`` defines the type of data expected in the request body. In this example, we use ``String`` type data. The arguments of ``fields.String`` allow us to provide additional information, such as the parameter being required, and example values to appear in API documentation.
``args`` defines the type of data expected in the request body. In this example, we use ``String`` type data. The arguments of ``fields.String`` allow us to provide additional information, such as the parameter being required, and example values to appear in API documentation.
Adding additional fields, and the meaning of the field types, will be discussed further in the next section.
When a POST request is made to our API view, the ``@use_body`` converts the body of the request into a ``String``, and passes it as a positional argument to our ``post`` function.
When a POST request is made to our API view, the server converts the body of the request into a ``String``, and passes it as a positional argument to our ``post`` function.
Swagger documentation
+++++++++++++++++++++
At this point, it is useful to introduce the automatically generated Swagger documentation. From any web browser, go to ``http://microscope.local/api/v2/swagger-ui`` (or replace ``microscope.local`` with your microscope's IP address if ``microscope.local`` doesn't work for your system).
This page uses `SwaggerUI <https://swagger.io/tools/swagger-ui/>`_ to provide visual, interactive API documentation. Find your extensions URL in the documentation under the ``extensions`` group. Basic documentation about the parameters required for your POST method should be visible, as well as an interactive example filled out with the example request given in ``@use_body``.
This page uses `SwaggerUI <https://swagger.io/tools/swagger-ui/>`_ to provide visual, interactive API documentation. Find your extensions URL in the documentation under the ``extensions`` group. Basic documentation about the parameters required for your POST method should be visible, as well as an interactive example filled out with the example request given in the view ``schema``.

4
docs/source/microscope.rst
View file

@ -7,5 +7,5 @@ The main microscope class handles microscope settings, passing these between the
:maxdepth: 2
:caption: Contents:
.. automodule:: openflexure_microscope
:members:
.. automodule:: openflexure_microscope.microscope
:members:

22
openflexure_microscope/api/default_extensions/autofocus.py
View file

@ -1,7 +1,7 @@
from labthings.server.find import find_component
from labthings.server.extensions import BaseExtension
from labthings.server.view import View, ActionView, PropertyView
from labthings.server.decorators import ThingAction, ThingProperty
from labthings.server import fields
from openflexure_microscope.devel import JsonResponse, request, abort
from openflexure_microscope.utilities import set_properties
@ -336,7 +336,9 @@ class AutofocusAPI(ActionView):
"""
Run a standard autofocus
"""
def post(self):
args = {"dz": fields.List(fields.Int())}
def post(self, args):
payload = JsonResponse(request)
microscope = find_component("org.openflexure.microscope")
@ -344,7 +346,7 @@ class AutofocusAPI(ActionView):
abort(503, "No microscope connected. Unable to autofocus.")
# Figure out the range of z values to use
dz = payload.param("dz", default=np.linspace(-300, 300, 7), convert=np.array)
dz = np.array(args.get("dz", np.linspace(-300, 300, 7)))
if microscope.has_real_stage():
logging.debug("Running autofocus...")
@ -360,18 +362,20 @@ class FastAutofocusAPI(ActionView):
"""
Run a fast autofocus
"""
def post(self):
payload = JsonResponse(request)
args = {
"dz": fields.Int(missing=2000),
"backlash": fields.Int(missing=25, minimum=0)
}
def post(self, args):
microscope = find_component("org.openflexure.microscope")
if not microscope:
abort(503, "No microscope connected. Unable to autofocus.")
# Figure out the parameters to use
dz = payload.param("dz", default=2000, convert=int)
backlash = payload.param("backlash", default=25, convert=int)
if backlash < 0:
backlash = 0
dz = args.get("dz")
backlash = args.get("backlash")
if microscope.has_real_stage():
logging.debug("Running autofocus...")

7
openflexure_microscope/api/default_extensions/autostorage.py
View file

@ -1,6 +1,5 @@
from labthings.server.extensions import BaseExtension
from labthings.server.view import View, PropertyView
from labthings.server.decorators import ThingProperty, PropertySchema, use_args
from labthings.server import fields
from labthings.server.find import find_component
@ -198,8 +197,9 @@ class GetLocationsView(PropertyView):
return autostorage_extension_v2.get_locations()
@PropertySchema(fields.String(required=True, example="Default"))
class PreferredLocationView(PropertyView):
schema = fields.String(required=True, example="Default")
def get(self):
global autostorage_extension_v2
@ -219,7 +219,8 @@ class PreferredLocationView(PropertyView):
class PreferredLocationGUIView(View):
@use_args({"new_path_title": fields.String(required=True)})
args = {"new_path_title": fields.String(required=True)}
def post(self, args):
global autostorage_extension_v2

1
openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
View file

@ -1,7 +1,6 @@
from labthings.server.view import View, ActionView
from labthings.server.find import find_component
from labthings.server.extensions import BaseExtension
from labthings.server.decorators import ThingAction
from flask import abort

38
openflexure_microscope/api/default_extensions/scan.py
View file

@ -8,7 +8,6 @@ from functools import reduce
from openflexure_microscope.captures.capture_manager import generate_basename
from labthings.server.find import find_component, find_extension
from labthings.server.extensions import BaseExtension
from labthings.server.decorators import use_args
from labthings.server import fields
from openflexure_microscope.devel import abort, update_task_progress
@ -92,7 +91,7 @@ class ScanExtension(BaseExtension):
def __init__(self):
self._images_to_be_captured: int = 1
self._images_captured_so_far: int = 0
return BaseExtension.__init__(self, "org.openflexure.scan", version="2.0.0")
BaseExtension.__init__(self, "org.openflexure.scan", version="2.0.0")
def progress(self):
progress = (self._images_captured_so_far / self._images_to_be_captured) * 100
@ -290,24 +289,23 @@ class ScanExtension(BaseExtension):
scan_extension_v2 = ScanExtension()
class TileScanAPI(ActionView):
@use_args(
{
"filename": fields.String(missing=None, example=None),
"temporary": fields.Boolean(missing=False),
"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),
"annotations": fields.Dict(missing={}, example={"Foo": "Bar"}),
"tags": fields.List(fields.String, missing=[]),
"resize": fields.Dict(missing=None), # TODO: Validate keys
}
)
args = {
"filename": fields.String(missing=None, example=None),
"temporary": fields.Boolean(missing=False),
"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),
"annotations": fields.Dict(missing={}, example={"Foo": "Bar"}),
"tags": fields.List(fields.String, missing=[]),
"resize": fields.Dict(missing=None), # TODO: Validate keys
}
def post(self, args):
microscope = find_component("org.openflexure.microscope")

12
openflexure_microscope/api/default_extensions/zip_builder.py
View file

@ -14,16 +14,10 @@ import logging
from labthings.server.find import find_component
from labthings.server.view import View, ActionView, PropertyView
from labthings.server.schema import Schema
from labthings.server.schema import Schema, pre_dump
from labthings.server import fields
from labthings.server.extensions import BaseExtension
from labthings.server.utilities import description_from_view
from labthings.server.decorators import (
ThingAction,
ThingProperty,
marshal_with,
pre_dump,
)
class ZipObjectSchema(Schema):
@ -140,7 +134,6 @@ default_zip_manager = ZipManager()
class ZipBuilderAPIView(ActionView):
def post(self):
ids = list(JsonResponse(request).json)
microscope = find_component("org.openflexure.microscope")
@ -151,7 +144,8 @@ class ZipBuilderAPIView(ActionView):
class ZipListAPIView(PropertyView):
@marshal_with(ZipObjectSchema(many=True))
schema = ZipObjectSchema(many=True)
def get(self):
return default_zip_manager.session_zips.values()

10
openflexure_microscope/api/dev_extensions/tools.py
View file

@ -2,7 +2,6 @@ from labthings.server.extensions import BaseExtension
from labthings.server.view import ActionView
from labthings.server import fields
from labthings.server.decorators import use_args, marshal_with
import logging
import time
@ -12,12 +11,9 @@ class RaiseException(ActionView):
raise Exception("The developer raised an exception")
class SleepFor(ActionView):
@marshal_with({
"TimeAsleep": fields.Float()
})
@use_args({
"time": fields.Float(description="Time to sleep, in seconds", example=0.5)
})
schema = {"TimeAsleep": fields.Float()}
args = {"time": fields.Float(description="Time to sleep, in seconds", example=0.5)}
def post(self, args):
sleep_time = args.get("time")
logging.info(f"Going to sleep for {sleep_time}...")

20
openflexure_microscope/api/static/README.md
View file

@ -10,21 +10,11 @@ To prevent the editor from interfering with ESLint, add to your project `setting
{
"editor.tabSize": 2,
"cSpell.enabled": false,
"eslint.validate": [{
"language": "vue",
"autoFix": true
},
{
"language": "javascript",
"autoFix": true
},
{
"language": "javascriptreact",
"autoFix": true
}
],
"eslint.autoFixOnSave": true,
"eslint.validate": ["vue","javascript", "javascriptreact"],
"editor.formatOnSave": false,
"vetur.validation.template": false
"vetur.validation.template": false,
"editor.codeActionsOnSave": {
"source.fixAll.eslint": true
}
}
```

49
openflexure_microscope/api/static/package-lock.json generated
View file

@ -6918,7 +6918,8 @@
"ansi-regex": {
"version": "2.1.1",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"aproba": {
"version": "1.2.0",
@ -6939,12 +6940,14 @@
"balanced-match": {
"version": "1.0.0",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"brace-expansion": {
"version": "1.1.11",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"balanced-match": "^1.0.0",
"concat-map": "0.0.1"
@ -6959,17 +6962,20 @@
"code-point-at": {
"version": "1.1.0",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"concat-map": {
"version": "0.0.1",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"console-control-strings": {
"version": "1.1.0",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"core-util-is": {
"version": "1.0.2",
@ -7086,7 +7092,8 @@
"inherits": {
"version": "2.0.4",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"ini": {
"version": "1.3.5",
@ -7098,6 +7105,7 @@
"version": "1.0.0",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"number-is-nan": "^1.0.0"
}
@ -7112,6 +7120,7 @@
"version": "3.0.4",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"brace-expansion": "^1.1.7"
}
@ -7119,12 +7128,14 @@
"minimist": {
"version": "0.0.8",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"minipass": {
"version": "2.9.0",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"safe-buffer": "^5.1.2",
"yallist": "^3.0.0"
@ -7143,6 +7154,7 @@
"version": "0.5.1",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"minimist": "0.0.8"
}
@ -7232,7 +7244,8 @@
"number-is-nan": {
"version": "1.0.1",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"object-assign": {
"version": "4.1.1",
@ -7244,6 +7257,7 @@
"version": "1.4.0",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"wrappy": "1"
}
@ -7329,7 +7343,8 @@
"safe-buffer": {
"version": "5.1.2",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"safer-buffer": {
"version": "2.1.2",
@ -7365,6 +7380,7 @@
"version": "1.0.2",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"code-point-at": "^1.0.0",
"is-fullwidth-code-point": "^1.0.0",
@ -7384,6 +7400,7 @@
"version": "3.0.1",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"ansi-regex": "^2.0.0"
}
@ -7427,12 +7444,14 @@
"wrappy": {
"version": "1.0.2",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"yallist": {
"version": "3.1.1",
"bundled": true,
"dev": true
"dev": true,
"optional": true
}
}
},
@ -9191,6 +9210,11 @@
"minimist": "^1.2.5"
}
},
"mousetrap": {
"version": "1.6.5",
"resolved": "https://registry.npmjs.org/mousetrap/-/mousetrap-1.6.5.tgz",
"integrity": "sha512-QNo4kEepaIBwiT8CDhP98umTetp+JNfQYBWvC1pc6/OAibuXtRcxZ58Qz8skvEHYvURne/7R8T5VoOI7rDsEUA=="
},
"move-concurrently": {
"version": "1.0.1",
"resolved": "https://registry.npmjs.org/move-concurrently/-/move-concurrently-1.0.1.tgz",
@ -9904,7 +9928,8 @@
"version": "2.2.2",
"resolved": "https://registry.npmjs.org/picomatch/-/picomatch-2.2.2.tgz",
"integrity": "sha512-q0M/9eZHzmr0AulXyPwNfZjtwZ/RBZlbN3K3CErVrk50T2ASYI7Bye0EvekFY3IP1Nt2DHu0re+V2ZHIpMkuWg==",
"dev": true
"dev": true,
"optional": true
},
"pify": {
"version": "4.0.1",

3
openflexure_microscope/api/static/package.json
View file

@ -13,7 +13,8 @@
"serve": "vue-cli-service serve --mode development"
},
"dependencies": {
"material-design-icons": "^3.0.1"
"material-design-icons": "^3.0.1",
"mousetrap": "^1.6.5"
},
"devDependencies": {
"@vue/cli-plugin-babel": "^3.12.1",

232
openflexure_microscope/api/static/src/App.vue
View file

@ -7,6 +7,26 @@
<loadingContent v-if="!$store.getters.ready" />
<div v-if="$store.getters.ready" id="tour-header"></div>
<appContent v-if="$store.getters.ready" />
<!-- Runtime modals -->
<div
id="modal-center"
ref="keyboardManualModal"
class="uk-flex-top"
uk-modal
>
<div class="uk-modal-dialog uk-modal-body uk-margin-auto-vertical">
<button class="uk-modal-close-default" type="button" uk-close></button>
<div
v-for="shortcut in keyboardManual"
:key="shortcut.shortcut"
class="uk-margin-small"
uk-grid
>
<div class="uk-width-small">{{ shortcut.shortcut }}</div>
<div class="uk-width-expand">{{ shortcut.description }}</div>
</div>
</div>
</div>
<v-tour
v-show="$store.getters.ready"
name="guidedTour"
@ -23,20 +43,26 @@ import appContent from "./components/appContent.vue";
import loadingContent from "./components/loadingContent.vue";
import axios from "axios";
var Mousetrap = require("mousetrap");
// Key Codes
const keyCodes = {
pgup: 33,
pgdn: 34,
left: 37,
up: 38,
right: 39,
down: 40,
enter: 13,
esc: 27,
shift: 16,
alt: 18,
t: 84
Mousetrap.prototype.stopCallback = function(e, element, combo) {
// if the element has the class "mousetrap" then no need to stop
if ((" " + element.className + " ").indexOf(" mousetrap ") > -1) {
return false;
}
// if we're in a lightbox, stop mousetrap
if (element.classList.contains("lightbox-link")) {
return true;
}
// stop for input, select, and textarea
return (
element.tagName == "INPUT" ||
element.tagName == "SELECT" ||
element.tagName == "TEXTAREA" ||
(element.contentEditable && element.contentEditable == "true")
);
};
// Export main app
@ -51,7 +77,8 @@ export default {
data: function() {
return {
appAvailable: false,
keysDown: {},
arrowKeysDown: {},
keyboardManual: [],
systemDark: undefined,
themeObserver: undefined,
tourCallbacks: {
@ -166,9 +193,7 @@ export default {
created: function() {
window.addEventListener("beforeunload", this.handleExit);
// Key events
window.addEventListener("keydown", this.keyDownMonitor);
window.addEventListener("keyup", this.keyUpMonitor);
// Scrollwheel listener
window.addEventListener("wheel", this.wheelMonitor);
// Watch for origin changes
this.unwatchOriginFunction = this.$store.watch(
@ -180,6 +205,82 @@ export default {
console.log(uriV2);
}
);
// Keyboard shortcuts
// TODO: Shortcut guide
Mousetrap.bind("?", () => {
console.log(this.keyboardManual);
this.toggleModalElement(this.$refs["keyboardManualModal"]); // Calls the mixin
});
// Arrow keys
Mousetrap.bind(
["up", "down", "left", "right"],
event => {
this.arrowKeysDown[event.keyCode] = true; //Add key to array
this.navigateKeyHandler();
},
"keydown"
);
Mousetrap.bind(
["up", "down", "left", "right"],
event => {
delete this.arrowKeysDown[event.keyCode]; //Remove key from array
},
"keyup"
);
this.keyboardManual.push({
shortcut: "←↑→↓",
description: "Move the microscope stage"
});
// Focus keys
Mousetrap.bind("pageup", () => {
this.$root.$emit("globalMoveStepEvent", 0, 0, 1);
});
Mousetrap.bind("pagedown", () => {
this.$root.$emit("globalMoveStepEvent", 0, 0, -1);
});
this.keyboardManual.push({
shortcut: "pgup / pgdn",
description: "Move the microscope focus"
});
// Capture
Mousetrap.bind("c", () => {
this.$root.$emit("globalCaptureEvent");
});
this.keyboardManual.push({
shortcut: "c",
description: "Take a capture"
});
// Autofocus
Mousetrap.bind("a", () => {
this.$root.$emit("globalFastAutofocusEvent");
});
this.keyboardManual.push({
shortcut: "a",
description: "Fast autofocus"
});
// Increment/decrement tab
Mousetrap.bind("shift+down", () => {
this.$root.$emit("globalIncrementTab");
});
Mousetrap.bind("shift+up", () => {
this.$root.$emit("globalDecrementTab");
});
this.keyboardManual.push({
shortcut: "shift+↑ / shift+↓",
description: "Switch tab"
});
// Re-run tour
Mousetrap.bind("alt+t", () => {
this.$tours["guidedTour"].start();
});
},
beforeDestroy: function() {
@ -187,12 +288,13 @@ export default {
if (this.themeObserver) {
this.themeObserver.disconnect();
}
// Remove key listeners
window.removeEventListener("keydown", this.keyDownMonitor);
window.removeEventListener("keyup", this.keyUpMonitor);
// Remove scrollwheel listener
window.removeEventListener("wheel", this.wheelMonitor);
// Remove origin watcher
this.unwatchOriginFunction();
// Remove key listeners
console.log("Resetting Mousetrap");
Mousetrap.reset();
},
methods: {
@ -231,84 +333,26 @@ export default {
}
},
// Handle global key press events to be associated with navigation
keyDownMonitor: function(event) {
this.keysDown[event.keyCode] = true; //Add key to array
// Convert keyCode dict into a list of key codes
var keyCodeList = Object.keys(keyCodes).map(function(key) {
return keyCodes[key];
});
if (
// If not inside an element we want to ignore
!(event.target instanceof HTMLInputElement) &&
!event.target.classList.contains("lightbox-link") &&
// If it's a recognised key
keyCodeList.includes(event.keyCode)
) {
this.navigateKeyHandler(keyCodes);
this.captureKeyHandler(keyCodes);
this.letterKeyHandler(keyCodes);
navigateKeyHandler: function() {
// Calculate movement array
var x_rel = 0;
var y_rel = 0;
var z_rel = 0;
if (37 in this.arrowKeysDown) {
x_rel = x_rel + 1;
}
},
keyUpMonitor: function(event) {
delete this.keysDown[event.keyCode]; //Remove key from array
},
navigateKeyHandler: function(keyCodes) {
const moveKeys = [
keyCodes.left,
keyCodes.right,
keyCodes.up,
keyCodes.down,
keyCodes.pgup,
keyCodes.pgdn
];
if (
moveKeys.some(r => Object.keys(this.keysDown).includes(r.toString()))
) {
// Calculate movement array
var x_rel = 0;
var y_rel = 0;
var z_rel = 0;
if (keyCodes.left in this.keysDown) {
x_rel = x_rel + 1;
}
if (keyCodes.right in this.keysDown) {
x_rel = x_rel - 1;
}
if (keyCodes.up in this.keysDown) {
y_rel = y_rel + 1;
}
if (keyCodes.down in this.keysDown) {
y_rel = y_rel - 1;
}
if (keyCodes.pgup in this.keysDown) {
z_rel = z_rel - 1;
}
if (keyCodes.pgdn in this.keysDown) {
z_rel = z_rel + 1;
}
// Make a position request
// Emit a signal to move, acted on by panelNavigate.vue
this.$root.$emit("globalMoveStepEvent", x_rel, y_rel, z_rel);
if (39 in this.arrowKeysDown) {
x_rel = x_rel - 1;
}
},
captureKeyHandler: function(keyCodes) {
if (keyCodes.shift in this.keysDown && keyCodes.enter in this.keysDown) {
console.log("Capturing");
this.$root.$emit("globalCaptureEvent");
if (38 in this.arrowKeysDown) {
y_rel = y_rel + 1;
}
},
letterKeyHandler: function(keyCodes) {
if (keyCodes.alt in this.keysDown && keyCodes.t in this.keysDown) {
this.$tours["guidedTour"].start();
if (40 in this.arrowKeysDown) {
y_rel = y_rel - 1;
}
// Make a position request
// Emit a signal to move, acted on by panelNavigate.vue
this.$root.$emit("globalMoveStepEvent", x_rel, y_rel, z_rel);
}
}
};

24
openflexure_microscope/api/static/src/assets/less/theme.less
View file

@ -59,6 +59,12 @@
text-rendering: optimizeLegibility;
}
//
// Decorations
//
@small-shadow: 0 1px 3px rgba(0, 0, 0, 0.12), 0 1px 2px rgba(0, 0, 0, 0.24);
@big-shadow: 0 14px 25px rgba(0, 0, 0, 0.16);
//
// Container
//
@ -148,6 +154,7 @@
// Paper
//
@paper-border-radius: 4px;
@button-border-radius: 3px;
/* ========================================================================
@ -187,9 +194,8 @@
.uk-card {
border-radius: @paper-border-radius;
border: 1px solid rgba(180, 180, 180, 0.25);
box-shadow: none;
-webkit-box-shabox-shadow: none;
//border: 1px solid rgba(180, 180, 180, 0.25);
box-shadow: @small-shadow;
}
.uk-card-media-top img {
@ -228,7 +234,7 @@
*/
.uk-modal-dialog {
border-radius: @paper-border-radius;
box-shadow: 0 14px 25px rgba(0, 0, 0, 0.16);
box-shadow: @big-shadow;
transition: 0.3s ease !important;
}
@ -245,7 +251,7 @@
*/
.uk-notification-message {
border-radius: @paper-border-radius;
box-shadow: 0 14px 25px rgba(0, 0, 0, 0.16);
box-shadow: @big-shadow;
}
.uk-notification-message-danger {
@ -287,7 +293,7 @@ a:hover {
* Buttons
*/
.uk-button {
border-radius: 2px;
border-radius: @button-border-radius;
padding: 0 8px;
}
@ -296,6 +302,12 @@ a:hover {
border-color: @global-border;
}
.uk-button-primary {
background-color: rgba(180, 180, 180, 0.10);
border-color: @global-primary-background;
color: @button-text-color;
}
.uk-button-danger {
background-color: transparent;
color: #f0506e;

28
openflexure_microscope/api/static/src/components/appContent.vue
View file

@ -218,6 +218,18 @@ export default {
}
}
return pluginGuis;
},
tabOrder: function() {
// TODO: There must be a better way to do this, somehow reading the order of the HTML elements?
var ind = ["view", "gallery", "navigate", "capture", "settings"];
for (const plugin of this.pluginsGuiList) {
ind.push(plugin.id);
}
ind.push("about");
return ind;
},
currentTabIndex: function() {
return this.tabOrder.indexOf(this.currentTab);
}
},
@ -246,6 +258,14 @@ export default {
this.$root.$on("globalSwitchTab", tabID => {
this.currentTab = tabID;
});
// A global signal listener to increment tab
this.$root.$on("globalIncrementTab", () => {
this.incrementTabBy(1);
});
// A global signal listener to decrement tab
this.$root.$on("globalDecrementTab", () => {
this.incrementTabBy(-1);
});
},
beforeDestroy() {
@ -274,6 +294,14 @@ export default {
this.currentTab = tab;
}
},
incrementTabBy: function(n) {
const newIndex =
(((this.currentTabIndex + n) % this.tabOrder.length) +
this.tabOrder.length) %
this.tabOrder.length;
const newId = this.tabOrder[newIndex];
this.currentTab = newId;
},
startModals: function() {
this.$refs["calibrationModal"].show();
},

7
openflexure_microscope/api/static/src/components/controlComponents/paneNavigate.vue
View file

@ -111,6 +111,8 @@
:submit-url="fastAutofocusUri"
:submit-data="{ dz: 2000 }"
:submit-label="'Fast'"
:button-primary="false"
:submit-on-event="'globalFastAutofocusEvent'"
@taskStarted="isAutofocusing = 1"
@finished="isAutofocusing = 0"
></taskSubmitter>
@ -122,6 +124,7 @@
:submit-url="normalAutofocusUri"
:submit-data="{ dz: [-60, -30, 0, 30, 60] }"
:submit-label="'Medium'"
:button-primary="false"
@taskStarted="isAutofocusing = 2"
@finished="isAutofocusing = 0"
></taskSubmitter>
@ -133,6 +136,7 @@
:submit-url="normalAutofocusUri"
:submit-data="{ dz: [-20, -10, 0, 10, 20] }"
:submit-label="'Fine'"
:button-primary="false"
@taskStarted="isAutofocusing = 3"
@finished="isAutofocusing = 0"
></taskSubmitter>
@ -201,6 +205,7 @@ export default {
this.$root.$on("globalMoveInImageCoordinatesEvent", (x, y, absolute) => {
this.moveInImageCoordinatesRequest(x, y, absolute);
});
// A global signal listener to perform a move in multiples of a step size
this.$root.$on("globalMoveStepEvent", (x_steps, y_steps, z_steps) => {
this.moveRequest(
x_steps * this.stepXy,
@ -219,6 +224,8 @@ export default {
beforeDestroy() {
// Remove global signal listener to perform a move action
this.$root.$off("globalMoveEvent");
this.$root.$off("globalMoveInImageCoordinatesEvent");
this.$root.$off("globalMoveStepEvent");
},
methods: {

10
openflexure_microscope/api/static/src/components/genericComponents/tabIcon.vue
View file

@ -93,13 +93,9 @@ export default {
@import "../../assets/less/theme.less";
.tabicon-active {
color: @global-primary-background !important;
}
.hook-inverse() {
.tabicon-active {
color: @inverse-primary-muted-color !important;
}
color: #fff !important;
background-color: @global-primary-background !important;
box-shadow: @small-shadow;
}
.tabtitle {

22
openflexure_microscope/api/static/src/components/genericComponents/taskSubmitter.vue
View file

@ -78,7 +78,12 @@ export default {
buttonPrimary: {
type: Boolean,
required: false,
default: false
default: true
},
submitOnEvent: {
type: String,
required: false,
default: null
}
},
@ -101,7 +106,20 @@ export default {
created() {},
beforeDestroy() {},
mounted() {
// A global signal listener to perform a move action
if (this.submitOnEvent) {
this.$root.$on(this.submitOnEvent, () => {
this.bootstrapTask();
});
}
},
beforeDestroy() {
if (this.submitOnEvent) {
this.$root.$off(this.submitOnEvent);
}
},
methods: {
bootstrapTask: function() {

2
openflexure_microscope/api/static/src/components/tabContentComponents/aboutContent.vue
View file

@ -9,7 +9,7 @@
<a
class="uk-link"
target="_blank"
href="https://gitlab.com/openflexure/openflexure-microscope-jsclient/-/issues"
href="https://gitlab.com/openflexure/openflexure-microscope-server/-/issues"
>Report an issue</a
>
</div>

13
openflexure_microscope/api/static/src/components/viewComponents/settingsDisplay.vue
View file

@ -153,11 +153,11 @@ export default {
};
</script>
<style lang="less">
<style lang="less" scoped>
// Custom UIkit CSS modifications
@import "../../assets/less/theme.less";
.settings-pane {
border-width: 0 1px 0 0;
border-style: solid;
border-color: rgba(180, 180, 180, 0.25);
}
.settings-nav {
@ -170,4 +170,9 @@ export default {
border-style: solid;
border-color: rgba(180, 180, 180, 0.25);
}
.settings-nav li > a {
padding-left: 6px !important;
border-radius: @button-border-radius;
}
</style>

4
openflexure_microscope/api/static/src/main.js
View file

@ -129,6 +129,10 @@ Vue.mixin({
UIkit.modal(element).hide();
},
toggleModalElement: function(element) {
UIkit.modal(element).toggle();
},
getLocalStorageObj: function(keyName) {
if (localStorage.getItem(keyName)) {
try {

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

@ -7,7 +7,6 @@ from . import camera, stage, system
from labthings.server.view import View
from labthings.server.find import current_labthing
from labthings.server.utilities import description_from_view
from labthings.server.decorators import Tag
_actions = {
"capture": {
@ -58,7 +57,6 @@ def enabled_root_actions():
return {k: v for k, v in _actions.items() if v["conditions"]}
# @Tag("actions")
class ActionsView(View):
def get(self):
"""

76
openflexure_microscope/api/v2/views/actions/camera.py
View file

@ -1,19 +1,11 @@
from openflexure_microscope.api.utilities import get_bool, JsonResponse
from labthings.server.view import View, ActionView
from labthings.server.find import find_component
from labthings.server.decorators import (
use_args,
marshal_with,
doc,
tag,
ThingAction,
doc_response,
)
from labthings.server import fields
from openflexure_microscope.utilities import filter_dict
from openflexure_microscope.api.v2.views.captures import capture_schema
from openflexure_microscope.api.v2.views.captures import CaptureSchema
import logging
import io
@ -25,24 +17,23 @@ class CaptureAPI(ActionView):
Create a new image capture.
"""
@use_args(
{
"filename": fields.String(example="MyFileName"),
"temporary": fields.Boolean(
missing=False, description="Delete capture on shutdown"
),
"use_video_port": fields.Boolean(missing=False),
"bayer": fields.Boolean(
missing=False, description="Store raw bayer data in file"
),
"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}
), # TODO: Validate keys
}
)
@marshal_with(capture_schema)
args = {
"filename": fields.String(example="MyFileName"),
"temporary": fields.Boolean(
missing=False, description="Delete capture on shutdown"
),
"use_video_port": fields.Boolean(missing=False),
"bayer": fields.Boolean(
missing=False, description="Store raw bayer data in file"
),
"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}
), # TODO: Validate keys
}
schema = CaptureSchema()
def post(self, args):
"""
Create a new capture
@ -78,18 +69,22 @@ class RAMCaptureAPI(ActionView):
Take a non-persistant image capture.
"""
@use_args(
{
"use_video_port": fields.Boolean(missing=True),
"bayer": fields.Boolean(
missing=False, description="Return with raw bayer data"
),
"resize": fields.Dict(
missing=None, example={"width": 640, "height": 480}
), # TODO: Validate keys
args = {
"use_video_port": fields.Boolean(missing=True),
"bayer": fields.Boolean(
missing=False, description="Return with raw bayer data"
),
"resize": fields.Dict(
missing=None, example={"width": 640, "height": 480}
), # TODO: Validate keys
}
responses = {
200: {
"content_type": "image/jpeg"
}
)
@doc_response(200, mimetype="image/jpeg")
}
def post(self, args):
"""
Take a non-persistant image capture.
@ -128,9 +123,8 @@ class GPUPreviewStartAPI(ActionView):
in the format ``[x, y, width, height]``.
"""
@use_args(
{"window": fields.List(fields.Integer, missing=[], example=[0, 0, 640, 480])}
)
args = {"window": fields.List(fields.Integer, missing=[], example=[0, 0, 640, 480])}
def post(self, args):
"""
Start the onboard GPU preview.

20
openflexure_microscope/api/v2/views/actions/stage.py
View file

@ -1,7 +1,6 @@
from openflexure_microscope.api.utilities import JsonResponse
from labthings.server.view import View, ActionView
from labthings.server.find import find_component
from labthings.server.decorators import use_args, marshal_with, doc, ThingAction
from labthings.server import fields
from openflexure_microscope.utilities import axes_to_array, filter_dict
@ -12,16 +11,15 @@ import logging
class MoveStageAPI(ActionView):
@use_args(
{
"absolute": fields.Boolean(
default=False, example=False, description="Move to an absolute position"
),
"x": fields.Int(default=0, example=100),
"y": fields.Int(default=0, example=100),
"z": fields.Int(default=0, example=20),
}
)
args = {
"absolute": fields.Boolean(
missing=False, example=False, description="Move to an absolute position"
),
"x": fields.Int(missing=0, example=100),
"y": fields.Int(missing=0, example=100),
"z": fields.Int(missing=0, example=20),
}
def post(self, args):
"""
Move the microscope stage in x, y, z

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

@ -3,8 +3,6 @@ import subprocess
import os
from sys import platform
from labthings.server.decorators import ThingAction, doc_response
def is_raspberrypi(raise_on_errors=False):
"""
@ -19,7 +17,6 @@ class ShutdownAPI(ActionView):
Attempt to shutdown the device
"""
@doc_response(201)
def post(self):
"""
Attempt to shutdown the device
@ -31,7 +28,7 @@ class ShutdownAPI(ActionView):
)
out, err = p.communicate()
return {"out": out, "err": err}, 201
return {"out": out, "err": err}
class RebootAPI(ActionView):
@ -39,7 +36,6 @@ class RebootAPI(ActionView):
Attempt to reboot the device
"""
@doc_response(201)
def post(self):
"""
Attempt to reboot the device
@ -51,4 +47,4 @@ class RebootAPI(ActionView):
)
out, err = p.communicate()
return {"out": out, "err": err}, 201
return {"out": out, "err": err}

33
openflexure_microscope/api/v2/views/captures.py
View file

@ -7,7 +7,6 @@ from labthings.server.schema import Schema
from labthings.server import fields
from labthings.server.view import View, PropertyView
from labthings.server.utilities import description_from_view
from labthings.server.decorators import marshal_with, doc_response, Tag, ThingProperty
from labthings.server.find import find_component
@ -84,16 +83,10 @@ class CaptureSchema(Schema):
return data
capture_schema = CaptureSchema()
capture_list_schema = CaptureSchema(many=True)
from pprint import pprint
@Tag("captures")
class CaptureList(PropertyView):
@marshal_with(CaptureSchema(many=True))
tags = ["captures"]
schema = CaptureSchema(many=True)
def get(self):
"""
List all image captures
@ -103,9 +96,10 @@ class CaptureList(PropertyView):
return image_list
@Tag("captures")
class CaptureView(View):
@marshal_with(CaptureSchema())
tags = ["captures"]
schema = CaptureSchema()
def get(self, id):
"""
Description of a single image capture
@ -136,9 +130,14 @@ class CaptureView(View):
return "", 204
@Tag("captures")
class CaptureDownload(View):
@doc_response(200, mimetype="image/jpeg")
tags = ["captures"]
responses = {
200: {
"content_type": "image/jpeg"
}
}
def get(self, id, filename):
"""
Image data for a single image capture
@ -172,8 +171,9 @@ class CaptureDownload(View):
return send_file(img, mimetype="image/jpeg")
@Tag("captures")
class CaptureTags(View):
tags = ["captures"]
def get(self, id):
"""
Get tags associated with a single image capture
@ -227,8 +227,9 @@ class CaptureTags(View):
return capture_obj.tags
@Tag("captures")
class CaptureAnnotations(View):
tags = ["captures"]
def get(self, id):
"""
Get annotations associated with a single image capture

24
openflexure_microscope/api/v2/views/instrument.py
View file

@ -5,8 +5,6 @@ from labthings.core.utilities import get_by_path, set_by_path, create_from_path
from labthings.server.find import find_component
from labthings.server.view import View, PropertyView
from labthings.server.decorators import ThingProperty, Tag, doc_response
from flask import request, abort
import logging
@ -35,9 +33,12 @@ class SettingsProperty(PropertyView):
return self.get()
@Tag("properties")
class NestedSettingsProperty(View):
@doc_response(404, description="Settings key cannot be found")
tags = ["properties"]
responses = {
404: {"description": "Settings key cannot be found"}
}
def get(self, route):
"""
Show a nested section of the current microscope settings
@ -52,7 +53,6 @@ class NestedSettingsProperty(View):
return value
@doc_response(404, description="Settings key cannot be found")
def put(self, route):
"""
Update a nested section of the current microscope settings
@ -79,9 +79,12 @@ class StateProperty(PropertyView):
return microscope.state
@Tag("properties")
class NestedStateProperty(View):
@doc_response(404, description="Status key cannot be found")
tags = ["properties"]
responses = {
404: {"description": "Status key cannot be found"}
}
def get(self, route):
"""
Show a nested section of the current microscope state
@ -106,9 +109,12 @@ class ConfigurationProperty(PropertyView):
return microscope.configuration
@Tag("properties")
class NestedConfigurationProperty(View):
@doc_response(404, description="Configuration key cannot be found")
tags = ["properties"]
responses = {
404: {"description": "Status key cannot be found"}
}
def get(self, route):
"""
Show a nested section of the current microscope state

18
openflexure_microscope/api/v2/views/streams.py
View file

@ -4,17 +4,19 @@ from labthings.core.utilities import get_by_path, set_by_path, create_from_path
from labthings.server.find import find_component
from labthings.server.view import View, PropertyView
from labthings.server.decorators import doc_response, ThingProperty
from flask import Response
from labthings.server.responses import Response
class MjpegStream(PropertyView):
"""
Real-time MJPEG stream from the microscope camera
"""
responses = {
200: {
"content_type": "multipart/x-mixed-replace"
}
}
@doc_response(200, mimetype="multipart/x-mixed-replace")
def get(self):
"""
MJPEG stream from the microscope camera.
@ -42,7 +44,13 @@ class SnapshotStream(PropertyView):
Single JPEG snapshot from the camera stream
"""
@doc_response(200, description="Snapshot taken", mimetype="image/jpeg")
responses = {
200: {
"content_type": "image/jpeg",
"description": "Snapshot taken"
}
}
def get(self):
"""
Single snapshot from the camera stream

1
openflexure_microscope/camera/base.py
View file

@ -35,6 +35,7 @@ class BaseCamera(metaclass=ABCMeta):
self.stream_active = False
self.record_active = False
self.preview_active = False
@property
@abstractmethod

4
openflexure_microscope/camera/piexif/_remove.py
View file

@ -40,8 +40,8 @@ def remove(src, new_file=None):
new_data = _webp.remove(src_data)
except ValueError:
new_data = src_data
except e:
print(e.args)
except Exception as e:
print(e)
raise ValueError("Error occurred.")
if isinstance(new_file, io.BytesIO):

15
openflexure_microscope/microscope.py
View file

@ -215,21 +215,6 @@ class Microscope:
settings_current_camera = self.camera.read_settings()
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 is not None:
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()

44
poetry.lock generated
View file

@ -104,17 +104,6 @@ numpy = ">=1.17,<2.0"
all = ["opencv-python-headless (>=4.1,<5.0)", "scipy (>=1.4,<2.0)"]
correlation = ["opencv-python-headless (>=4.1,<5.0)", "scipy (>=1.4,<2.0)"]
[[package]]
category = "main"
description = "Pure Python CBOR (de)serializer with extensive tag support"
name = "cbor2"
optional = false
python-versions = "*"
version = "5.1.0"
[package.extras]
test = ["pytest", "pytest-cov"]
[[package]]
category = "dev"
description = "Python package for providing Mozilla's CA Bundle."
@ -322,23 +311,26 @@ i18n = ["Babel (>=0.8)"]
[[package]]
category = "main"
description = "Python implementation of LabThings, based on the Flask microframework"
description = ""
name = "labthings"
optional = false
python-versions = ">=3.6,<4.0"
version = "0.6.7"
python-versions = "^3.6"
version = "0.7.0"
[package.dependencies]
Flask = ">=1.1.1,<2.0.0"
apispec = ">=3.2.0,<4.0.0"
cbor2 = ">=5.1.0,<6.0.0"
flask-cors = ">=3.0.8,<4.0.0"
Flask = "^1.1.1"
apispec = "^3.2.0"
flask-cors = "^3.0.8"
gevent = ">=1.4,<21.0"
gevent-websocket = ">=0.10.1,<0.11.0"
marshmallow = ">=3.4.0,<4.0.0"
webargs = ">=6.0.0,<7.0.0"
gevent-websocket = "^0.10.1"
marshmallow = "^3.4.0"
webargs = "^6.0.0"
zeroconf = ">=0.24.5,<0.28.0"
[package.source]
reference = "b718258fe219fbdca7f82d3987c0680f7157e738"
type = "git"
url = "https://github.com/labthings/python-labthings.git"
[[package]]
category = "dev"
description = "A fast and thorough lazy object proxy."
@ -841,7 +833,7 @@ testing = ["coverage (>=5.0.3)", "zope.event", "zope.testing"]
rpi = ["RPi.GPIO"]
[metadata]
content-hash = "94e35da71817800c617a54e54dc937df62953fa95caa2e2e05f69b1163582c4c"
content-hash = "fff0dba8c9a8ffe0a496148d68bedf1e12802e6700ab3e5f82788e10891eb774"
python-versions = "^3.6"
[metadata.files]
@ -877,9 +869,6 @@ camera-stage-mapping = [
{file = "camera-stage-mapping-0.1.2.tar.gz", hash = "sha256:0d1a6f93b3a60054bc8057359464adbb40488b4daeb93c672b90e4fe525e7b69"},
{file = "camera_stage_mapping-0.1.2-py3-none-any.whl", hash = "sha256:3f3da3e95792e811e6808173c368be67ebb00e6f7d7e37d68cb36fa765d13da9"},
]
cbor2 = [
{file = "cbor2-5.1.0.tar.gz", hash = "sha256:43ce11e8c2fe4971d386d1a60cf83bfa0a4a667b97668ba76acbf5e6398821aa"},
]
certifi = [
{file = "certifi-2020.6.20-py2.py3-none-any.whl", hash = "sha256:8fc0819f1f30ba15bdb34cceffb9ef04d99f420f68eb75d901e9560b8749fc41"},
{file = "certifi-2020.6.20.tar.gz", hash = "sha256:5930595817496dd21bb8dc35dad090f1c2cd0adfaf21204bf6732ca5d8ee34d3"},
@ -1021,10 +1010,7 @@ jinja2 = [
{file = "Jinja2-2.11.2-py2.py3-none-any.whl", hash = "sha256:f0a4641d3cf955324a89c04f3d94663aa4d638abe8f733ecd3582848e1c37035"},
{file = "Jinja2-2.11.2.tar.gz", hash = "sha256:89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0"},
]
labthings = [
{file = "labthings-0.6.7-py3-none-any.whl", hash = "sha256:c39d3de301cc2c0b21e44bee49c84bdc912be84ace0168de7c16dc4966b4397b"},
{file = "labthings-0.6.7.tar.gz", hash = "sha256:5c70fde942436a21764f0ba7e5a77c0f080e51270dc8b4c69917b5b23e253c7b"},
]
labthings = []
lazy-object-proxy = [
{file = "lazy-object-proxy-1.4.3.tar.gz", hash = "sha256:f3900e8a5de27447acbf900b4750b0ddfd7ec1ea7fbaf11dfa911141bc522af0"},
{file = "lazy_object_proxy-1.4.3-cp27-cp27m-macosx_10_13_x86_64.whl", hash = "sha256:a2238e9d1bb71a56cd710611a1614d1194dc10a175c1e08d75e1a7bcc250d442"},

2
pyproject.toml
View file

@ -42,7 +42,7 @@ opencv-python-headless = [
{version = "4.1.0.25", python = "~3.7"}, # PiWheels build for RPi running Py37
{version = "4.2.0.34", python = "^3.8"} # Latest for Py38 systems
]
labthings = "0.6.7"
labthings = {git = "https://github.com/labthings/python-labthings.git", rev = "100-restructure"}
pynpm = "^0.1.2"
sangaboard = "^0.2"
expiringdict = "^1.2.1"