diff --git a/docs/source/capture.rst b/docs/source/capture.rst index 21c3dd27..a2d0846f 100644 --- a/docs/source/capture.rst +++ b/docs/source/capture.rst @@ -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: \ No newline at end of file diff --git a/docs/source/extensions/actions.rst b/docs/source/extensions/actions.rst index e68a614a..5463ccfd 100644 --- a/docs/source/extensions/actions.rst +++ b/docs/source/extensions/actions.rst @@ -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 ---------------- diff --git a/docs/source/extensions/example_extension/02_adding_views.py b/docs/source/extensions/example_extension/02_adding_views.py index ce815d55..8e313e30 100644 --- a/docs/source/extensions/example_extension/02_adding_views.py +++ b/docs/source/extensions/example_extension/02_adding_views.py @@ -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") diff --git a/docs/source/extensions/example_extension/03_marshaling_data.py b/docs/source/extensions/example_extension/03_marshaling_data.py index d3179c10..4015b9fc 100644 --- a/docs/source/extensions/example_extension/03_marshaling_data.py +++ b/docs/source/extensions/example_extension/03_marshaling_data.py @@ -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 diff --git a/docs/source/extensions/example_extension/04_properties.py b/docs/source/extensions/example_extension/04_properties.py index 68d06933..5e1614d3 100644 --- a/docs/source/extensions/example_extension/04_properties.py +++ b/docs/source/extensions/example_extension/04_properties.py @@ -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 diff --git a/docs/source/extensions/example_extension/05_actions.py b/docs/source/extensions/example_extension/05_actions.py index e67711d4..bba3fd03 100644 --- a/docs/source/extensions/example_extension/05_actions.py +++ b/docs/source/extensions/example_extension/05_actions.py @@ -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. diff --git a/docs/source/extensions/example_extension/06_tasks_locks.py b/docs/source/extensions/example_extension/06_tasks_locks.py index 0d2e435d..e38d9b60 100644 --- a/docs/source/extensions/example_extension/06_tasks_locks.py +++ b/docs/source/extensions/example_extension/06_tasks_locks.py @@ -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") diff --git a/docs/source/extensions/example_extension/07_ev_gui.py b/docs/source/extensions/example_extension/07_ev_gui.py index 0726020f..8203f802 100644 --- a/docs/source/extensions/example_extension/07_ev_gui.py +++ b/docs/source/extensions/example_extension/07_ev_gui.py @@ -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") diff --git a/docs/source/extensions/marshaling.rst b/docs/source/extensions/marshaling.rst index 1f09162a..9ee8f384 100644 --- a/docs/source/extensions/marshaling.rst +++ b/docs/source/extensions/marshaling.rst @@ -14,7 +14,7 @@ The OpenFlexure Microscope Server makes use of the `Marshmallow library `_, 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 `_, 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 diff --git a/docs/source/extensions/properties.rst b/docs/source/extensions/properties.rst index cb23761e..3a86e2d5 100644 --- a/docs/source/extensions/properties.rst +++ b/docs/source/extensions/properties.rst @@ -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 diff --git a/docs/source/extensions/views.rst b/docs/source/extensions/views.rst index ea35ddd2..a27ec4b2 100644 --- a/docs/source/extensions/views.rst +++ b/docs/source/extensions/views.rst @@ -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 `_ 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 `_ 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``. diff --git a/docs/source/microscope.rst b/docs/source/microscope.rst index 60933839..55a96cdb 100644 --- a/docs/source/microscope.rst +++ b/docs/source/microscope.rst @@ -7,5 +7,5 @@ The main microscope class handles microscope settings, passing these between the :maxdepth: 2 :caption: Contents: -.. automodule:: openflexure_microscope - :members: \ No newline at end of file +.. automodule:: openflexure_microscope.microscope + :members: \ No newline at end of file diff --git a/openflexure_microscope/api/default_extensions/autofocus.py b/openflexure_microscope/api/default_extensions/autofocus.py index d61f72df..aa3b47f8 100644 --- a/openflexure_microscope/api/default_extensions/autofocus.py +++ b/openflexure_microscope/api/default_extensions/autofocus.py @@ -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...") diff --git a/openflexure_microscope/api/default_extensions/autostorage.py b/openflexure_microscope/api/default_extensions/autostorage.py index da282827..5f0640c0 100644 --- a/openflexure_microscope/api/default_extensions/autostorage.py +++ b/openflexure_microscope/api/default_extensions/autostorage.py @@ -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 diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py index 5a6f4b21..45a3e213 100644 --- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py +++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py @@ -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 diff --git a/openflexure_microscope/api/default_extensions/scan.py b/openflexure_microscope/api/default_extensions/scan.py index b7eb0b94..eace367e 100644 --- a/openflexure_microscope/api/default_extensions/scan.py +++ b/openflexure_microscope/api/default_extensions/scan.py @@ -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") diff --git a/openflexure_microscope/api/default_extensions/zip_builder.py b/openflexure_microscope/api/default_extensions/zip_builder.py index e168e42f..d012741c 100644 --- a/openflexure_microscope/api/default_extensions/zip_builder.py +++ b/openflexure_microscope/api/default_extensions/zip_builder.py @@ -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() diff --git a/openflexure_microscope/api/dev_extensions/tools.py b/openflexure_microscope/api/dev_extensions/tools.py index 564dcd6d..3d0077b3 100644 --- a/openflexure_microscope/api/dev_extensions/tools.py +++ b/openflexure_microscope/api/dev_extensions/tools.py @@ -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}...") diff --git a/openflexure_microscope/api/static/README.md b/openflexure_microscope/api/static/README.md index 1e8fbe26..4e5d9005 100644 --- a/openflexure_microscope/api/static/README.md +++ b/openflexure_microscope/api/static/README.md @@ -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 + } } ``` \ No newline at end of file diff --git a/openflexure_microscope/api/static/package-lock.json b/openflexure_microscope/api/static/package-lock.json index fd6ff999..88511dc4 100644 --- a/openflexure_microscope/api/static/package-lock.json +++ b/openflexure_microscope/api/static/package-lock.json @@ -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", diff --git a/openflexure_microscope/api/static/package.json b/openflexure_microscope/api/static/package.json index bcdca6a0..055d4b50 100644 --- a/openflexure_microscope/api/static/package.json +++ b/openflexure_microscope/api/static/package.json @@ -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", diff --git a/openflexure_microscope/api/static/src/App.vue b/openflexure_microscope/api/static/src/App.vue index 0fc0f38c..9e1a31c1 100644 --- a/openflexure_microscope/api/static/src/App.vue +++ b/openflexure_microscope/api/static/src/App.vue @@ -7,6 +7,26 @@
+ + -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); } } }; diff --git a/openflexure_microscope/api/static/src/assets/less/theme.less b/openflexure_microscope/api/static/src/assets/less/theme.less index 17d014a2..7ab97249 100644 --- a/openflexure_microscope/api/static/src/assets/less/theme.less +++ b/openflexure_microscope/api/static/src/assets/less/theme.less @@ -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; diff --git a/openflexure_microscope/api/static/src/components/appContent.vue b/openflexure_microscope/api/static/src/components/appContent.vue index 319ddc35..24439529 100644 --- a/openflexure_microscope/api/static/src/components/appContent.vue +++ b/openflexure_microscope/api/static/src/components/appContent.vue @@ -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.$refs["calibrationModal"].show(); }, diff --git a/openflexure_microscope/api/static/src/components/controlComponents/paneNavigate.vue b/openflexure_microscope/api/static/src/components/controlComponents/paneNavigate.vue index f5040ff5..fbaa567c 100644 --- a/openflexure_microscope/api/static/src/components/controlComponents/paneNavigate.vue +++ b/openflexure_microscope/api/static/src/components/controlComponents/paneNavigate.vue @@ -111,6 +111,8 @@ :submit-url="fastAutofocusUri" :submit-data="{ dz: 2000 }" :submit-label="'Fast'" + :button-primary="false" + :submit-on-event="'globalFastAutofocusEvent'" @taskStarted="isAutofocusing = 1" @finished="isAutofocusing = 0" > @@ -122,6 +124,7 @@ :submit-url="normalAutofocusUri" :submit-data="{ dz: [-60, -30, 0, 30, 60] }" :submit-label="'Medium'" + :button-primary="false" @taskStarted="isAutofocusing = 2" @finished="isAutofocusing = 0" > @@ -133,6 +136,7 @@ :submit-url="normalAutofocusUri" :submit-data="{ dz: [-20, -10, 0, 10, 20] }" :submit-label="'Fine'" + :button-primary="false" @taskStarted="isAutofocusing = 3" @finished="isAutofocusing = 0" > @@ -201,6 +205,7 @@ export default { this.$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.$off("globalMoveStepEvent"); }, methods: { diff --git a/openflexure_microscope/api/static/src/components/genericComponents/tabIcon.vue b/openflexure_microscope/api/static/src/components/genericComponents/tabIcon.vue index 15dfd38f..e352f334 100644 --- a/openflexure_microscope/api/static/src/components/genericComponents/tabIcon.vue +++ b/openflexure_microscope/api/static/src/components/genericComponents/tabIcon.vue @@ -93,13 +93,9 @@ export default { @import "../../assets/less/theme.less"; .tabicon-active { - color: @global-primary-background !important; -} - -.hook-inverse() { - .tabicon-active { - color: @inverse-primary-muted-color !important; - } + color: #fff !important; + background-color: @global-primary-background !important; + box-shadow: @small-shadow; } .tabtitle { diff --git a/openflexure_microscope/api/static/src/components/genericComponents/taskSubmitter.vue b/openflexure_microscope/api/static/src/components/genericComponents/taskSubmitter.vue index 845bad9e..da5e695d 100644 --- a/openflexure_microscope/api/static/src/components/genericComponents/taskSubmitter.vue +++ b/openflexure_microscope/api/static/src/components/genericComponents/taskSubmitter.vue @@ -78,7 +78,12 @@ export default { buttonPrimary: { type: Boolean, required: false, - default: false + default: true + }, + submitOnEvent: { + type: String, + required: false, + default: null } }, @@ -101,7 +106,20 @@ export default { created() {}, - beforeDestroy() {}, + mounted() { + // A global signal listener to perform a move action + if (this.submitOnEvent) { + this.$root.$on(this.submitOnEvent, () => { + this.bootstrapTask(); + }); + } + }, + + beforeDestroy() { + if (this.submitOnEvent) { + this.$root.$off(this.submitOnEvent); + } + }, methods: { bootstrapTask: function() { diff --git a/openflexure_microscope/api/static/src/components/tabContentComponents/aboutContent.vue b/openflexure_microscope/api/static/src/components/tabContentComponents/aboutContent.vue index 5133f558..3f5ebd6e 100644 --- a/openflexure_microscope/api/static/src/components/tabContentComponents/aboutContent.vue +++ b/openflexure_microscope/api/static/src/components/tabContentComponents/aboutContent.vue @@ -9,7 +9,7 @@ Report an issue diff --git a/openflexure_microscope/api/static/src/components/viewComponents/settingsDisplay.vue b/openflexure_microscope/api/static/src/components/viewComponents/settingsDisplay.vue index 303c5cf2..9d3266dd 100644 --- a/openflexure_microscope/api/static/src/components/viewComponents/settingsDisplay.vue +++ b/openflexure_microscope/api/static/src/components/viewComponents/settingsDisplay.vue @@ -153,11 +153,11 @@ export default { }; - diff --git a/openflexure_microscope/api/static/src/main.js b/openflexure_microscope/api/static/src/main.js index 567298e6..b53b43a4 100644 --- a/openflexure_microscope/api/static/src/main.js +++ b/openflexure_microscope/api/static/src/main.js @@ -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 { diff --git a/openflexure_microscope/api/v2/views/actions/__init__.py b/openflexure_microscope/api/v2/views/actions/__init__.py index e06454c5..56a3a4c4 100644 --- a/openflexure_microscope/api/v2/views/actions/__init__.py +++ b/openflexure_microscope/api/v2/views/actions/__init__.py @@ -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): """ diff --git a/openflexure_microscope/api/v2/views/actions/camera.py b/openflexure_microscope/api/v2/views/actions/camera.py index 59872992..176112cc 100644 --- a/openflexure_microscope/api/v2/views/actions/camera.py +++ b/openflexure_microscope/api/v2/views/actions/camera.py @@ -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. diff --git a/openflexure_microscope/api/v2/views/actions/stage.py b/openflexure_microscope/api/v2/views/actions/stage.py index 0b9d1372..b21202e1 100644 --- a/openflexure_microscope/api/v2/views/actions/stage.py +++ b/openflexure_microscope/api/v2/views/actions/stage.py @@ -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 diff --git a/openflexure_microscope/api/v2/views/actions/system.py b/openflexure_microscope/api/v2/views/actions/system.py index d8756891..8677478d 100644 --- a/openflexure_microscope/api/v2/views/actions/system.py +++ b/openflexure_microscope/api/v2/views/actions/system.py @@ -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} diff --git a/openflexure_microscope/api/v2/views/captures.py b/openflexure_microscope/api/v2/views/captures.py index b4b00e04..09f3ae4f 100644 --- a/openflexure_microscope/api/v2/views/captures.py +++ b/openflexure_microscope/api/v2/views/captures.py @@ -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 diff --git a/openflexure_microscope/api/v2/views/instrument.py b/openflexure_microscope/api/v2/views/instrument.py index 3a51633e..e7198373 100644 --- a/openflexure_microscope/api/v2/views/instrument.py +++ b/openflexure_microscope/api/v2/views/instrument.py @@ -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 diff --git a/openflexure_microscope/api/v2/views/streams.py b/openflexure_microscope/api/v2/views/streams.py index f8b8cbe7..02eddc2e 100644 --- a/openflexure_microscope/api/v2/views/streams.py +++ b/openflexure_microscope/api/v2/views/streams.py @@ -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 diff --git a/openflexure_microscope/camera/base.py b/openflexure_microscope/camera/base.py index 9d2c197d..637fc34c 100644 --- a/openflexure_microscope/camera/base.py +++ b/openflexure_microscope/camera/base.py @@ -35,6 +35,7 @@ class BaseCamera(metaclass=ABCMeta): self.stream_active = False self.record_active = False + self.preview_active = False @property @abstractmethod diff --git a/openflexure_microscope/camera/piexif/_remove.py b/openflexure_microscope/camera/piexif/_remove.py index c55fa101..10940b96 100644 --- a/openflexure_microscope/camera/piexif/_remove.py +++ b/openflexure_microscope/camera/piexif/_remove.py @@ -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): diff --git a/openflexure_microscope/microscope.py b/openflexure_microscope/microscope.py index 1c55ac39..1a0abd8a 100644 --- a/openflexure_microscope/microscope.py +++ b/openflexure_microscope/microscope.py @@ -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() diff --git a/poetry.lock b/poetry.lock index 18605b9c..b5cf53cb 100644 --- a/poetry.lock +++ b/poetry.lock @@ -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"}, diff --git a/pyproject.toml b/pyproject.toml index a97d67f8..425902de 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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"