Handle captures as an OrderedDict. Fixes file deletion (60c6ae72) · Commits · OpenFlexure / openflexure-microscope-server

openflexure_microscope/api/default_extensions/zip_builder.py

+1 −2

Original line number	Diff line number	Diff line
		@@ -81,8 +81,7 @@ class ZipManager:

		# Get array of captures from IDs
		capture_list = [
		microscope.camera.image_from_id(capture_id)
		for capture_id in capture_id_list
		microscope.camera.images.get(capture_id) for capture_id in capture_id_list
		]
		# Remove Nones from list (missing/invalid captures)
		capture_list = [capture for capture in capture_list if capture]

openflexure_microscope/api/v2/views/captures.py

+14 −9

Original line number	Diff line number	Diff line
		@@ -20,6 +20,7 @@ class InstrumentSchema(Schema):
		settings = fields.Dict()
		state = fields.Dict()


		class CaptureMetadataImageSchema(Schema):
		id = fields.UUID()
		acquisitionDate = fields.String(format="date")
		@@ -36,6 +37,7 @@ class CaptureMetadataSchema(Schema):
		image = fields.Nested(CaptureMetadataImageSchema())
		instrument = fields.Nested(InstrumentSchema())


		class CaptureSchema(Schema):
		id = fields.String()
		file = fields.String(
		@@ -98,7 +100,7 @@ class CaptureList(View):
		List all image captures
		"""
		microscope = find_component("org.openflexure.microscope")
		image_list = microscope.camera.images
		image_list = microscope.camera.images.values()
		return image_list


		@@ -110,7 +112,7 @@ class CaptureView(View):
		Description of a single image capture
		"""
		microscope = find_component("org.openflexure.microscope")
		capture_obj = microscope.camera.image_from_id(id)
		capture_obj = microscope.camera.images.get(id)

		if not capture_obj:
		return abort(404) # 404 Not Found
		@@ -122,12 +124,15 @@ class CaptureView(View):
		Delete a single image capture
		"""
		microscope = find_component("org.openflexure.microscope")
		capture_obj = microscope.camera.image_from_id(id)
		capture_obj = microscope.camera.images.get(id)

		if not capture_obj:
		return abort(404) # 404 Not Found

		# Delete the capture file
		capture_obj.delete()
		# Delete from capture list
		del microscope.camera.images[id]

		return "", 204

		@@ -140,7 +145,7 @@ class CaptureDownload(View):
		Image data for a single image capture
		"""
		microscope = find_component("org.openflexure.microscope")
		capture_obj = microscope.camera.image_from_id(id)
		capture_obj = microscope.camera.images.get(id)

		if not capture_obj:
		return abort(404) # 404 Not Found
		@@ -175,7 +180,7 @@ class CaptureTags(View):
		Get tags associated with a single image capture
		"""
		microscope = find_component("org.openflexure.microscope")
		capture_obj = microscope.camera.image_from_id(id)
		capture_obj = microscope.camera.images.get(id)

		if not capture_obj:
		return abort(404) # 404 Not Found
		@@ -187,7 +192,7 @@ class CaptureTags(View):
		Add tags to a single image capture
		"""
		microscope = find_component("org.openflexure.microscope")
		capture_obj = microscope.camera.image_from_id(id)
		capture_obj = microscope.camera.images.get(id)

		if not capture_obj:
		return abort(404) # 404 Not Found
		@@ -207,7 +212,7 @@ class CaptureTags(View):
		Delete tags from a single image capture
		"""
		microscope = find_component("org.openflexure.microscope")
		capture_obj = microscope.camera.image_from_id(id)
		capture_obj = microscope.camera.images.get(id)

		if not capture_obj:
		return abort(404) # 404 Not Found
		@@ -230,7 +235,7 @@ class CaptureAnnotations(View):
		Get annotations associated with a single image capture
		"""
		microscope = find_component("org.openflexure.microscope")
		capture_obj = microscope.camera.image_from_id(id)
		capture_obj = microscope.camera.images.get(id)

		if not capture_obj:
		return abort(404) # 404 Not Found
		@@ -242,7 +247,7 @@ class CaptureAnnotations(View):
		Update metadata for a single image capture
		"""
		microscope = find_component("org.openflexure.microscope")
		capture_obj = microscope.camera.image_from_id(id)
		capture_obj = microscope.camera.images.get(id)

		if not capture_obj:
		return abort(404) # 404 Not Found

openflexure_microscope/camera/base.py

+15 −11

Original line number	Diff line number	Diff line
		@@ -7,6 +7,7 @@ import datetime
		import logging

		from abc import ABCMeta, abstractmethod
		from collections import OrderedDict

		from .capture import CaptureObject, build_captures_from_exif
		from openflexure_microscope.utilities import entry_by_uuid
		@@ -113,8 +114,8 @@ class BaseCamera(metaclass=ABCMeta):
		self.paths = {"default": BASE_CAPTURE_PATH, "temp": TEMP_CAPTURE_PATH}

		# Capture data
		self.images = []
		self.videos = []
		self.images = OrderedDict()
		self.videos = OrderedDict()

		@property
		@abstractmethod
		@@ -158,7 +159,7 @@ class BaseCamera(metaclass=ABCMeta):
		"""Close the BaseCamera and all attached StreamObjects."""
		logging.info("Closing {}".format(self))
		# Close all StreamObjects
		for capture_list in [self.images, self.videos]:
		for capture_list in [self.images.values(), self.videos.values()]:
		for stream_object in capture_list:
		stream_object.close()
		# Empty temp directory
		@@ -244,20 +245,22 @@ class BaseCamera(metaclass=ABCMeta):
		@property
		def image(self):
		"""Return the latest captured image."""
		return last_entry(self.images)
		return last_entry(self.images.values())

		@property
		def video(self):
		"""Return the latest recorded video."""
		return last_entry(self.videos)
		return last_entry(self.videos.values())

		def image_from_id(self, image_id):
		"""Return an image StreamObject with a matching ID."""
		return entry_by_uuid(image_id, self.images)
		logging.warning("image_from_id is deprecated. Access captures as a dictionary.")
		return entry_by_uuid(image_id, self.images.values())

		def video_from_id(self, video_id):
		"""Return a video StreamObject with a matching ID."""
		return entry_by_uuid(video_id, self.videos)
		logging.warning("video_from_id is deprecated. Access captures as a dictionary.")
		return entry_by_uuid(video_id, self.videos.values())

		# CREATING NEW CAPTURES

		@@ -282,7 +285,7 @@ class BaseCamera(metaclass=ABCMeta):

		# Generate file name
		if not filename:
		filename = generate_numbered_basename(self.images)
		filename = generate_numbered_basename(self.images.values())
		logging.debug(filename)
		filename = "{}.{}".format(filename, fmt)

		@@ -300,7 +303,7 @@ class BaseCamera(metaclass=ABCMeta):
		output.put_tags(["temporary"])

		# Update capture list
		self.images.append(output)
		self.images[output.id] = output

		return output

		@@ -322,10 +325,11 @@ class BaseCamera(metaclass=ABCMeta):
		folder (str): Name of the folder in which to store the capture.
		fmt (str): Format of the capture.
		"""
		# TODO: Remove the redundancy here

		# Generate file name
		if not filename:
		filename = generate_numbered_basename(self.videos)
		filename = generate_numbered_basename(self.videos.values())
		logging.debug(filename)
		filename = "{}.{}".format(filename, fmt)

		@@ -343,7 +347,7 @@ class BaseCamera(metaclass=ABCMeta):
		output.put_tags(["temporary"])

		# Update capture list
		self.videos.append(output)
		self.videos[output.id] = output

		return output

openflexure_microscope/camera/capture.py

+4 −2

Original line number	Diff line number	Diff line
		@@ -10,6 +10,8 @@ from PIL import Image
		import dateutil.parser
		import atexit

		from collections import OrderedDict

		from openflexure_microscope.camera import piexif
		from openflexure_microscope.camera.piexif._exceptions import InvalidImageDataError
		from openflexure_microscope.config import JSONEncoder
		@@ -58,7 +60,7 @@ def build_captures_from_exif(capture_path):

		logging.debug("Reloading captures from {}...".format(capture_path))
		files = make_file_list(capture_path, EXIF_FORMATS)
		captures = []
		captures = OrderedDict()

		for f in files:
		logging.debug("Reloading capture {}...".format(f))
		@@ -66,7 +68,7 @@ def build_captures_from_exif(capture_path):
		if exif:
		capture = capture_from_exif(f, exif)
		if capture:
		captures.append(capture)
		captures[capture.id] = capture
		else:
		logging.error("Invalid data at {}. Skipping.".format(f))