Microscope capture objects now just handle on-disk data (dc794d4d) · Commits · OpenFlexure / openflexure-microscope-server

docs/source/plugins/example/plugin.py

+4 −4

Original line number	Diff line number	Diff line
		@@ -59,15 +59,15 @@ class MyPluginClass(MicroscopePlugin):
		for _ in range(n_images):

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

		# Append the capture data to our list
		capture_array.append(capture_data)
		capture_array.append(output)

		# Wait for 1 minute
		time.sleep(60)

docs/source/plugins/hardware.rst

+3 −4

Original line number	Diff line number	Diff line
		@@ -103,17 +103,16 @@ For example, a timelapse plugin may look like:
		for _ in range(n_images):

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

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

		# Append the capture data to our list
		capture_array.append(capture_data)
		capture_array.append(output)

		# Wait for 1 minute
		time.sleep(60)

openflexure_microscope/api/app.py

+27 −44

Original line number	Diff line number	Diff line
		@@ -43,7 +43,7 @@ DEFAULT_LOGFILE = os.path.join(USER_CONFIG_DIR, "openflexure_microscope.log")
		if (__name__ == "__main__") or (not is_gunicorn):
		# If imported, but not by gunicorn
		print("Letting sys handle logs")
		logging.basicConfig(stream=sys.stderr, level=logging.DEBUG)
		logging.basicConfig(level=logging.DEBUG)
		else:
		# Direct standard Python logging to file and console
		root = logging.getLogger()
		@@ -66,37 +66,6 @@ else:
		# Create a dummy microscope object, with no hardware attachments
		api_microscope = Microscope()

		# Rebuild the capture list
		# TODO: Offload to a thread?
		stored_image_list = build_captures_from_exif()


		# Generate API URI based on version from filename
		def uri(suffix, api_version, base=None):
		if not base:
		base = "/api/{}".format(api_version)
		return_uri = base + suffix
		logging.debug("Created app route: {}".format(return_uri))
		return return_uri


		# Create flask app
		app = Flask(__name__)
		app.url_map.strict_slashes = False

		CORS(app, resources=r"/api/*")

		# Make errors more API friendly
		handler = JSONExceptionHandler(app)


		# After app starts, but before first request, attach hardware to global microscope
		@app.before_first_request
		def attach_microscope():
		# Create the microscope object globally (common to all spawned server threads)
		global api_microscope, stored_image_list
		logging.debug("First request made. Populating microscope with hardware...")

		# Initialise camera
		logging.debug("Creating camera object...")
		try:
		@@ -121,15 +90,29 @@ def attach_microscope():

		# Restore loaded capture array to camera object
		logging.debug("Restoring captures...")
		if stored_image_list:
		api_microscope.camera.images = stored_image_list
		api_microscope.camera.images = build_captures_from_exif(api_microscope.camera.paths["default"])

		logging.debug("Microscope successfully attached!")

		# Generate API URI based on version from filename
		def uri(suffix, api_version, base=None):
		if not base:
		base = "/api/{}".format(api_version)
		return_uri = base + suffix
		logging.debug("Created app route: {}".format(return_uri))
		return return_uri

		# WEBAPP ROUTES

		# API ROUTES
		# Create flask app
		app = Flask(__name__)
		app.url_map.strict_slashes = False

		CORS(app, resources=r"/api/*")

		# Make errors more API friendly
		handler = JSONExceptionHandler(app)

		# WEBAPP ROUTES

		# Base routes
		base_blueprint = blueprints.base.construct_blueprint(api_microscope)

openflexure_microscope/api/v1/blueprints/camera/capture.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -123,11 +123,11 @@ class ListAPI(MicroscopeView):
		# Explicitally acquire lock (prevents empty files being created if lock is unavailable)
		with self.microscope.camera.lock:
		output = self.microscope.camera.new_image(
		write_to_file=True, temporary=temporary, filename=filename
		temporary=temporary, filename=filename
		)

		self.microscope.camera.capture(
		output, use_video_port=use_video_port, resize=resize, bayer=bayer
		output.file, use_video_port=use_video_port, resize=resize, bayer=bayer
		)

		metadata.update(

openflexure_microscope/camera/base.py

+28 −19

Original line number	Diff line number	Diff line
		# -- coding: utf-8 --
		import time
		import os
		import shutil
		import threading
		import datetime
		import logging

		from abc import ABCMeta, abstractmethod

		from .capture import CaptureObject, BASE_CAPTURE_PATH, TEMP_CAPTURE_PATH
		from .capture import CaptureObject
		from openflexure_microscope.utilities import entry_by_id
		from openflexure_microscope.lock import StrictLock


		BASE_CAPTURE_PATH = os.path.join(os.path.expanduser("~"), "micrographs")
		TEMP_CAPTURE_PATH = os.path.join(BASE_CAPTURE_PATH, "tmp")


		def last_entry(object_list: list):
		"""Return the last entry of a list, if the list contains items."""
		if object_list: # If any images have been captured
		@@ -121,11 +126,11 @@ class BaseCamera(metaclass=ABCMeta):
		self.stream_timeout_enabled = False

		self.state = {}

		# TODO: Load/save these to config
		self.paths = {
		"image": BASE_CAPTURE_PATH,
		"video": BASE_CAPTURE_PATH,
		"image_tmp": TEMP_CAPTURE_PATH,
		"video_tpm": TEMP_CAPTURE_PATH,
		"default": BASE_CAPTURE_PATH,
		"temp": TEMP_CAPTURE_PATH
		}

		# Capture data
		@@ -157,10 +162,22 @@ class BaseCamera(metaclass=ABCMeta):
		for capture_list in [self.images, self.videos]:
		for stream_object in capture_list:
		stream_object.close()
		# Empty temp directory
		self.clear_tmp()
		# Stop worker thread
		self.stop_worker()
		logging.info("Closed {}".format(self))

		def clear_tmp(self):
		"""
		Removes all files in the temporary capture directories
		"""

		if os.path.isdir(self.paths["temp"]):
		logging.info("Clearing {}...".format(self.paths["temp"]))
		shutil.rmtree(self.paths["temp"])
		logging.debug("Cleared {}.".format(self.paths["temp"]))

		# START AND STOP WORKER THREAD

		def start_worker(self, timeout: int = 5) -> bool:
		@@ -244,7 +261,6 @@ class BaseCamera(metaclass=ABCMeta):

		def new_image(
		self,
		write_to_file: bool = True,
		temporary: bool = True,
		filename: str = None,
		folder: str = "",
		@@ -252,10 +268,9 @@ class BaseCamera(metaclass=ABCMeta):
		):

		"""
		Create a new image capture object. Adds to the image list, and shunt all others.
		Create a new image capture object.

		Args:
		write_to_file (bool): Should the StreamObject write to a file, or an in-memory byte stream.
		temporary (bool): Should the data be deleted after session ends.
		Creating the capture with a content manager sets this to true.
		filename (str): Name of the stored file. Defaults to timestamp.
		@@ -270,16 +285,14 @@ class BaseCamera(metaclass=ABCMeta):
		filename = "{}.{}".format(filename, fmt)

		# Generate folder
		base_folder = self.paths["image_tmp"] if temporary else self.paths["image"]
		base_folder = self.paths["temp"] if temporary else self.paths["default"]
		folder = os.path.join(base_folder, folder)

		# Generate file path
		filepath = os.path.join(folder, filename)

		# Create capture object
		output = CaptureObject(
		write_to_file=write_to_file, temporary=temporary, filepath=filepath
		)
		output = CaptureObject(filepath=filepath)

		# Update capture list
		shunt_captures(self.images)
		@@ -289,7 +302,6 @@ class BaseCamera(metaclass=ABCMeta):

		def new_video(
		self,
		write_to_file: bool = True,
		temporary: bool = False,
		filename: str = None,
		folder: str = "",
		@@ -297,10 +309,9 @@ class BaseCamera(metaclass=ABCMeta):
		):

		"""
		Create a new video capture object. Adds to the image list, and shunt all others.
		Create a new video capture object.

		Args:
		write_to_file (bool): Should the StreamObject write to a file, or an in-memory byte stream.
		temporary (bool): Should the data be deleted after session ends.
		Creating the capture with a content manager sets this to true.
		filename (str): Name of the stored file. Defaults to timestamp.
		@@ -315,16 +326,14 @@ class BaseCamera(metaclass=ABCMeta):
		filename = "{}.{}".format(filename, fmt)

		# Generate folder
		base_folder = self.paths["video_tmp"] if temporary else self.paths["video"]
		base_folder = self.paths["temp"] if temporary else self.paths["default"]
		folder = os.path.join(base_folder, folder)

		# Generate file path
		filepath = os.path.join(folder, filename)

		# Create capture object
		output = CaptureObject(
		write_to_file=write_to_file, temporary=temporary, filepath=filepath
		)
		output = CaptureObject(filepath=filepath)

		# Update capture list
		shunt_captures(self.videos)