Blackened tests and docs (d9cb0056) · Commits · OpenFlexure / openflexure-microscope-server

docs/source/conf.py

+53 −38

Original line number	Diff line number	Diff line
		@@ -17,32 +17,34 @@ import sys

		# Load module from relative imports

		module_path = os.path.abspath('../..')
		module_path = os.path.abspath("../..")
		sys.path.insert(0, module_path)

		# Handle mock imports for non-platform-agnostic modules

		from unittest.mock import MagicMock


		class Mock(MagicMock):
		@classmethod
		def __getattr__(cls, name):
		return MagicMock()

		mock_imports = ['picamera', 'picamera.array', 'picamera.mmalobj']

		mock_imports = ["picamera", "picamera.array", "picamera.mmalobj"]

		sys.modules.update((mod_name, Mock()) for mod_name in mock_imports)

		# -- Project information -----------------------------------------------------

		project = 'OpenFlexure Microscope Software'
		copyright = '2018, Bath Open Instrumentation Group'
		author = 'Bath Open Instrumentation Group'
		project = "OpenFlexure Microscope Software"
		copyright = "2018, Bath Open Instrumentation Group"
		author = "Bath Open Instrumentation Group"

		# The short X.Y version
		version = ''
		version = ""
		# The full version, including alpha/beta/rc tags
		release = ''
		release = ""


		# -- General configuration ---------------------------------------------------
		@@ -55,32 +57,32 @@ release = ''
		# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
		# ones.
		extensions = [
		'sphinx.ext.autodoc',
		'sphinx.ext.napoleon',
		'sphinx.ext.intersphinx',
		'sphinx.ext.todo',
		'sphinx.ext.viewcode',
		'sphinx.ext.githubpages',
		'sphinx.ext.ifconfig',
		'sphinxcontrib.httpdomain',
		'sphinxcontrib.autohttp.flask',
		'sphinxcontrib.autohttp.flaskqref'
		"sphinx.ext.autodoc",
		"sphinx.ext.napoleon",
		"sphinx.ext.intersphinx",
		"sphinx.ext.todo",
		"sphinx.ext.viewcode",
		"sphinx.ext.githubpages",
		"sphinx.ext.ifconfig",
		"sphinxcontrib.httpdomain",
		"sphinxcontrib.autohttp.flask",
		"sphinxcontrib.autohttp.flaskqref",
		]

		# Override ordering
		autodoc_member_order = 'bysource'
		autodoc_member_order = "bysource"

		# Add any paths that contain templates here, relative to this directory.
		templates_path = ['_templates']
		templates_path = ["_templates"]

		# The suffix(es) of source filenames.
		# You can specify multiple suffix as a list of string:
		#
		# source_suffix = ['.rst', '.md']
		source_suffix = '.rst'
		source_suffix = ".rst"

		# The master toctree document.
		master_doc = 'index'
		master_doc = "index"

		# The language for content autogenerated by Sphinx. Refer to documentation
		# for a list of supported languages.
		@@ -114,7 +116,7 @@ html_theme = "sphinx_rtd_theme"
		# Add any paths that contain custom static files (such as style sheets) here,
		# relative to this directory. They are copied after the builtin static files,
		# so a file named "default.css" will overwrite the builtin "default.css".
		html_static_path = ['_static']
		html_static_path = ["_static"]

		# Custom sidebar templates, must be a dictionary that maps document names
		# to template names.
		@@ -130,7 +132,7 @@ html_static_path = ['_static']
		# -- Options for HTMLHelp output ---------------------------------------------

		# Output file base name for HTML help builder.
		htmlhelp_basename = 'OpenFlexureMicroscopeSoftwaredoc'
		htmlhelp_basename = "OpenFlexureMicroscopeSoftwaredoc"


		# -- Options for LaTeX output ------------------------------------------------
		@@ -139,15 +141,12 @@ latex_elements = {
		# The paper size ('letterpaper' or 'a4paper').
		#
		# 'papersize': 'letterpaper',

		# The font size ('10pt', '11pt' or '12pt').
		#
		# 'pointsize': '10pt',

		# Additional stuff for the LaTeX preamble.
		#
		# 'preamble': '',

		# Latex figure (float) alignment
		#
		# 'figure_align': 'htbp',
		@@ -157,8 +156,13 @@ latex_elements = {
		# (source start file, target name, title,
		# author, documentclass [howto, manual, or own class]).
		latex_documents = [
		(master_doc, 'OpenFlexureMicroscopeSoftware.tex', 'OpenFlexure Microscope Software Documentation',
		'Bath Open Instrumentation Group', 'manual'),
		(
		master_doc,
		"OpenFlexureMicroscopeSoftware.tex",
		"OpenFlexure Microscope Software Documentation",
		"Bath Open Instrumentation Group",
		"manual",
		)
		]


		@@ -167,8 +171,13 @@ latex_documents = [
		# One entry per manual page. List of tuples
		# (source start file, name, description, authors, manual section).
		man_pages = [
		(master_doc, 'openflexuremicroscopesoftware', 'OpenFlexure Microscope Software Documentation',
		[author], 1)
		(
		master_doc,
		"openflexuremicroscopesoftware",
		"OpenFlexure Microscope Software Documentation",
		[author],
		1,
		)
		]


		@@ -178,9 +187,15 @@ man_pages = [
		# (source start file, target name, title, author,
		# dir menu entry, description, category)
		texinfo_documents = [
		(master_doc, 'OpenFlexureMicroscopeSoftware', 'OpenFlexure Microscope Software Documentation',
		author, 'OpenFlexureMicroscopeSoftware', 'One line description of project.',
		'Miscellaneous'),
		(
		master_doc,
		"OpenFlexureMicroscopeSoftware",
		"OpenFlexure Microscope Software Documentation",
		author,
		"OpenFlexureMicroscopeSoftware",
		"One line description of project.",
		"Miscellaneous",
		)
		]


		@@ -199,7 +214,7 @@ epub_title = project
		# epub_uid = ''

		# A list of files that should not be packed into the epub file.
		epub_exclude_files = ['search.html']
		epub_exclude_files = ["search.html"]


		# -- Extension configuration -------------------------------------------------
		@@ -208,8 +223,8 @@ epub_exclude_files = ['search.html']

		# Example configuration for intersphinx: refer to the Python standard library.
		intersphinx_mapping = {
		'openflexure_stage': ('https://openflexure-stage.readthedocs.io/en/latest/', None),
		'picamera': ('https://picamera.readthedocs.io/en/release-1.13/', None)
		"openflexure_stage": ("https://openflexure-stage.readthedocs.io/en/latest/", None),
		"picamera": ("https://picamera.readthedocs.io/en/release-1.13/", None),
		}

		# -- Options for todo extension ----------------------------------------------

docs/source/plugins/example/plugin.py

+27 −26

Original line number	Diff line number	Diff line
		@@ -13,6 +13,7 @@ FORM_PATH = os.path.join(HERE, "forms.json")

		### MICROSCOPE PLUGIN ###


		class MyPluginClass(MicroscopePlugin):
		"""
		A set of default plugins
		@@ -20,13 +21,13 @@ class MyPluginClass(MicroscopePlugin):

		global FORM_PATH

		with open(FORM_PATH, 'r') as sc:
		with open(FORM_PATH, "r") as sc:
		api_form = json.load(sc)

		api_views = {
		'/identify': IdentifyAPI,
		'/hello': HelloWorldAPI,
		'/timelapse': TimelapseAPI,
		"/identify": IdentifyAPI,
		"/hello": HelloWorldAPI,
		"/timelapse": TimelapseAPI,
		}

		def identify(self):
		@@ -34,8 +35,9 @@ class MyPluginClass(MicroscopePlugin):
		Demonstrate access to Microscope.camera, and Microscope.stage
		"""

		response = "My parent camera is {}, and my parent stage is {}.".format(self.microscope.camera,
		self.microscope.stage)
		response = "My parent camera is {}, and my parent stage is {}.".format(
		self.microscope.camera, self.microscope.stage
		)
		return response

		def hello_world(self):
		@@ -58,13 +60,11 @@ class MyPluginClass(MicroscopePlugin):

		# Create a data stream to capture to
		capture_data = self.microscope.camera.new_image(
		write_to_file=True,
		temporary=False)
		write_to_file=True, temporary=False
		)

		# Capture a still image from the Pi camera, into the data stream
		self.microscope.camera.capture(
		capture_data,
		use_video_port=True)
		self.microscope.camera.capture(capture_data, use_video_port=True)

		# Append the capture data to our list
		capture_array.append(capture_data)
		@@ -75,10 +75,12 @@ class MyPluginClass(MicroscopePlugin):

		### API VIEWS ###


		class IdentifyAPI(MicroscopeViewPlugin):
		"""
		A simple example API plugin, attached through the main microscope plugin.
		"""

		def get(self):
		"""
		Method to call when an HTTP GET request is made.
		@@ -99,13 +101,11 @@ class HelloWorldAPI(MicroscopeViewPlugin):
		"""

		# If the microscope does not already contain our plugin_string attribute
		if not hasattr(self.microscope, 'plugin_string'):
		if not hasattr(self.microscope, "plugin_string"):
		# Make a string, using the MicroscopeViewPlugin.plugin shortcut
		self.microscope.plugin_string = self.plugin.hello_world()

		json_response = jsonify({
		'plugin_string': self.microscope.plugin_string
		})
		json_response = jsonify({"plugin_string": self.microscope.plugin_string})

		return Response(json_response)

		@@ -118,18 +118,17 @@ class HelloWorldAPI(MicroscopeViewPlugin):
		payload = JsonResponse(request)

		# Extract a value from the JSON key 'plugin_string', and convert to a string. If no value is given, default to empty.
		new_plugin_string = payload.param('plugin_string', default='', convert=str)
		new_plugin_string = payload.param("plugin_string", default="", convert=str)

		if new_plugin_string: # If not None or empty
		# Set microscope attribute to the specified string
		self.microscope.plugin_string = new_plugin_string

		json_response = jsonify({
		'plugin_string': self.microscope.plugin_string
		})
		json_response = jsonify({"plugin_string": self.microscope.plugin_string})

		return Response(json_response)


		class TimelapseAPI(MicroscopeViewPlugin):
		def post(self):

		@@ -137,10 +136,12 @@ class TimelapseAPI(MicroscopeViewPlugin):
		payload = JsonResponse(request)

		# Extract the "n_images" parameter if it was passed. Otherwise, default to 10.
		n_images = payload.param('n_images', default=10, convert=int)
		n_images = payload.param("n_images", default=10, convert=int)

		# Attach the long-running method as a microscope task
		self.timelapse_task = self.microscope.task.start(self.plugin.timelapse, n_images)
		self.timelapse_task = self.microscope.task.start(
		self.plugin.timelapse, n_images
		)

		# Return the state of the task (will show ID, start time, and status before the task has finished)
		return jsonify(self.timelapse_task.state), 202

tests/api_client.py

+29 −33

Original line number	Diff line number	Diff line
		@@ -30,63 +30,61 @@ class APIconnection:
		return r.json()

		def set_overlay(self, message="", size=50):
		json = {
		"text": message,
		"size": size
		}
		return self.post('/camera/overlay', json=json)
		json = {"text": message, "size": size}
		return self.post("/camera/overlay", json=json)

		def get_overlay(self):
		return self.get('/camera/overlay')
		return self.get("/camera/overlay")

		def get_config(self):
		return self.get('/config')
		return self.get("/config")

		def set_config(self, config_dict):
		return self.post('/config', json=config_dict)
		return self.post("/config", json=config_dict)

		def get_state(self):
		return self.get('/state')
		return self.get("/state")

		def start_preview(self):
		return self.post('/camera/preview/start')
		return self.post("/camera/preview/start")

		def stop_preview(self):
		return self.post('/camera/preview/stop')
		return self.post("/camera/preview/stop")

		def move_by(self, x=0, y=0, z=0):
		json = {
		"x": x,
		"y": y,
		"z": z
		}
		return self.post('/stage/position', json=json)
		json = {"x": x, "y": y, "z": z}
		return self.post("/stage/position", json=json)

		def new_capture(self, use_video_port=True, keep_on_disk=False, resize=None):
		json = {
		"keep_on_disk": keep_on_disk,
		"use_video_port": use_video_port
		}
		json = {"keep_on_disk": keep_on_disk, "use_video_port": use_video_port}

		if resize:
		json['size'] = {'width': resize[0], 'height': resize[1]}
		json["size"] = {"width": resize[0], "height": resize[1]}

		return self.post('/camera/capture', json=json)
		return self.post("/camera/capture", json=json)

		def get_capture(self, capture_id):
		uri_route = '/camera/capture/{}/download'.format(capture_id)
		uri_route = "/camera/capture/{}/download".format(capture_id)
		r = self.get(uri_route, json=False)
		img = Image.open(BytesIO(r.content))
		array = np.asarray(img, dtype=np.int32)
		return array

		def del_capture(self, capture_id):
		uri_route = '/camera/capture/{}'.format(capture_id)
		uri_route = "/camera/capture/{}".format(capture_id)
		return self.delete(uri_route)

		def capture(self, use_video_port=True, keep_on_disk=False, delete_after_use=True, resize=None):
		p = self.new_capture(use_video_port=use_video_port, keep_on_disk=keep_on_disk, resize=resize)
		capture_id = p['metadata']['id']
		def capture(
		self,
		use_video_port=True,
		keep_on_disk=False,
		delete_after_use=True,
		resize=None,
		):
		p = self.new_capture(
		use_video_port=use_video_port, keep_on_disk=keep_on_disk, resize=resize
		)
		capture_id = p["metadata"]["id"]
		img_array = self.get_capture(capture_id)

		if delete_after_use:
		@@ -95,10 +93,8 @@ class APIconnection:
		return img_array

		def set_zoom(self, zoom_value=1.0):
		json = {
		"zoom_value": zoom_value,
		}
		return self.post('/camera/zoom', json=json)
		json = {"zoom_value": zoom_value}
		return self.post("/camera/zoom", json=json)

		def get_zoom(self):
		return self.get('/camera/zoom')
		return self.get("/camera/zoom")

tests/test_api.py

+25 −32

Original line number	Diff line number	Diff line
		@@ -6,27 +6,23 @@ import unittest

		import logging
		import sys

		logging.basicConfig(stream=sys.stderr, level=logging.INFO)


		class TestCapture(unittest.TestCase):

		def test_capture_config(self):
		connection = APIconnection(host="localhost", port=5000, api_ver="v1")
		config = connection.get_config()

		expected_keys = [
		'image_resolution',
		'stream_resolution',
		'numpy_resolution',
		]
		expected_keys = ["image_resolution", "stream_resolution", "numpy_resolution"]

		for key in expected_keys:
		self.assertTrue(key in config)

		def test_capture_videoport(self):
		connection = APIconnection(host="localhost", port=5000, api_ver="v1")
		resolution = connection.get_config()['stream_resolution']
		resolution = connection.get_config()["stream_resolution"]

		for resize in [None, (640, 480)]:

		@@ -37,13 +33,14 @@ class TestCapture(unittest.TestCase):
		use_video_port=True,
		keep_on_disk=False,
		delete_after_use=True,
		resize=resize)
		resize=resize,
		)

		self.assertTrue(capture_array.shape == (resolution[1], resolution[0], 3))

		def test_capture_full(self):
		connection = APIconnection(host="localhost", port=5000, api_ver="v1")
		resolution = connection.get_config()['image_resolution']
		resolution = connection.get_config()["image_resolution"]

		for resize in [None, (640, 480)]:

		@@ -54,20 +51,18 @@ class TestCapture(unittest.TestCase):
		use_video_port=False,
		keep_on_disk=False,
		delete_after_use=True,
		resize=resize)
		resize=resize,
		)

		self.assertTrue(capture_array.shape == (resolution[1], resolution[0], 3))


		class TestStage(unittest.TestCase):

		def test_stage_config(self):
		connection = APIconnection(host="localhost", port=5000, api_ver="v1")
		config = connection.get_config()

		expected_keys = [
		'backlash',
		]
		expected_keys = ["backlash"]

		for key in expected_keys:
		self.assertTrue(key in config)
		@@ -76,14 +71,12 @@ class TestStage(unittest.TestCase):
		connection = APIconnection(host="localhost", port=5000, api_ver="v1")
		state = connection.get_state()

		self.assertTrue('stage' in state)
		self.assertTrue("stage" in state)

		expected_keys = [
		'position',
		]
		expected_keys = ["position"]

		for key in expected_keys:
		self.assertTrue(key in state['stage'])
		self.assertTrue(key in state["stage"])

		def test_stage_movement(self):
		connection = APIconnection(host="localhost", port=5000, api_ver="v1")
		@@ -91,16 +84,16 @@ class TestStage(unittest.TestCase):
		move_distance = 500
		for axis in range(3):
		for direction in [1, -1]:
		pos_i_dict = connection.get_state()['stage']['position']
		pos_i = [pos_i_dict['x'], pos_i_dict['y'], pos_i_dict['z']]
		pos_i_dict = connection.get_state()["stage"]["position"]
		pos_i = [pos_i_dict["x"], pos_i_dict["y"], pos_i_dict["z"]]

		move = [0, 0, 0]
		move[axis] = move_distance * direction

		connection.move_by(*move)

		pos_f_dict = connection.get_state()['stage']['position']
		pos_f = [pos_f_dict['x'], pos_f_dict['y'], pos_f_dict['z']]
		pos_f_dict = connection.get_state()["stage"]["position"]
		pos_f = [pos_f_dict["x"], pos_f_dict["y"], pos_f_dict["z"]]

		diff = np.subtract(pos_f, pos_i)
		logging.debug("{} > {}".format(pos_i, pos_f))
		@@ -108,7 +101,7 @@ class TestStage(unittest.TestCase):
		self.assertTrue(np.array_equal(diff, move))


		if __name__ == '__main__':
		if __name__ == "__main__":

		suites = [
		unittest.TestLoader().loadTestsFromTestCase(TestCapture),

tests/test_camera.py

+11 −31

Original line number	Diff line number	Diff line
		@@ -12,11 +12,11 @@ import unittest

		import logging
		import sys

		logging.basicConfig(stream=sys.stderr, level=logging.DEBUG)


		class TestCaptureMethods(unittest.TestCase):

		def test_still_capture(self):
		"""Tests capturing still images to a BytesIO stream."""
		global camera
		@@ -30,11 +30,7 @@ class TestCaptureMethods(unittest.TestCase):
		# Capture to a context (auto-deletes files when done)
		with camera.new_image(write_to_file=False) as output:

		camera.capture(
		output,
		use_video_port=use_video_port,
		resize=resize
		)
		camera.capture(output, use_video_port=use_video_port, resize=resize)

		# Ensure file deletion fails and returns False
		self.assertFalse(output.delete_file())
		@@ -43,14 +39,8 @@ class TestCaptureMethods(unittest.TestCase):

		# BEFORE DELETE: Ensure StreamObject 'stream' has
		# a valid BytesIO object and byte string
		self.assertTrue(isinstance(
		output.data,
		io.IOBase
		))
		self.assertTrue(isinstance(
		output.binary,
		(bytes, bytearray)
		))
		self.assertTrue(isinstance(output.data, io.IOBase))
		self.assertTrue(isinstance(output.binary, (bytes, bytearray)))

		# Save capture to file
		output.save_file()
		@@ -65,10 +55,7 @@ class TestCaptureMethods(unittest.TestCase):
		# AFTER DELETE: Ensure StreamObject 'stream' has
		# a valid BytesIO object and byte string
		self.assertTrue(isinstance(output.data, io.IOBase))
		self.assertTrue(isinstance(
		output.binary,
		(bytes, bytearray)
		))
		self.assertTrue(isinstance(output.binary, (bytes, bytearray)))

		# Create a PIL image from stream
		image = Image.open(output.data)
		@@ -102,7 +89,8 @@ class TestCaptureMethods(unittest.TestCase):
		output = camera.capture(
		camera.new_image(write_to_file=True),
		use_video_port=use_video_port,
		resize=resize)
		resize=resize,
		)

		# Check file got saved
		self.assertTrue(os.path.isfile(output.file))
		@@ -122,7 +110,6 @@ class TestCaptureMethods(unittest.TestCase):


		class TestUnencodedMethods(unittest.TestCase):

		def test_yuv_array(self):
		"""Tests capturing unencoded YUV data to a Numpy array."""
		global camera
		@@ -136,9 +123,7 @@ class TestUnencodedMethods(unittest.TestCase):
		camera.wait_for_camera()

		# Capture RGB array
		yuv = camera.yuv(
		use_video_port=use_video_port,
		resize=resize)
		yuv = camera.yuv(use_video_port=use_video_port, resize=resize)

		# Ensure capture output is a valid numpy array
		self.assertTrue(isinstance(yuv, np.ndarray))
		@@ -168,9 +153,7 @@ class TestUnencodedMethods(unittest.TestCase):
		camera.wait_for_camera()

		# Capture RGB array
		rgb = camera.array(
		use_video_port=use_video_port,
		resize=resize)
		rgb = camera.array(use_video_port=use_video_port, resize=resize)

		# Ensure capture output is a valid numpy array
		self.assertTrue(isinstance(rgb, np.ndarray))
		@@ -189,7 +172,6 @@ class TestUnencodedMethods(unittest.TestCase):


		class TestRecordMethods(unittest.TestCase):

		def test_video_record(self):
		"""Tests recording videos to BytesIO stream, and to file on disk."""
		global camera
		@@ -201,9 +183,7 @@ class TestRecordMethods(unittest.TestCase):
		# Wait for camera
		camera.wait_for_camera()

		with camera.new_video(
		write_to_file=write_to_file
		) as output:
		with camera.new_video(write_to_file=write_to_file) as output:

		# Start recording
		camera.start_recording(output)
		@@ -278,7 +258,7 @@ class TestThreadStarting(unittest.TestCase):
		self.assertIsInstance(camera.stream, io.IOBase)


		if __name__ == '__main__':
		if __name__ == "__main__":
		with PiCameraStreamer() as camera:

		suites = [