Simplified creation of new capture objects (ea44bbef) · Commits · OpenFlexure / openflexure-microscope-server

openflexure_microscope/camera/base.py

+10 −6

Original line number	Diff line number	Diff line
		@@ -316,18 +316,20 @@ class BaseCamera(object):
		if not filename:
		filename = generate_numbered_basename(self.images)
		logging.debug(filename)
		filename = "{}.{}".format(filename, fmt)

		# Generate folder
		base_folder = self.paths['image_tmp'] if temporary else self.paths['image']
		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,
		filename=filename,
		folder=folder,
		fmt=fmt)
		filepath=filepath)

		# Update capture list
		self.shunt_captures(self.images)
		@@ -360,18 +362,20 @@ class BaseCamera(object):
		if not filename:
		filename = generate_numbered_basename(self.videos)
		logging.debug(filename)
		filename = "{}.{}".format(filename, fmt)

		# Generate folder
		base_folder = self.paths['video_tmp'] if temporary else self.paths['video']
		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,
		filename=filename,
		folder=folder,
		fmt=fmt)
		filepath=filepath)

		# Update capture list
		self.shunt_captures(self.videos)

openflexure_microscope/camera/capture.py

+27 −79

Original line number	Diff line number	Diff line
		@@ -18,7 +18,7 @@ THUMBNAIL_SIZE = (200, 150)
		BASE_CAPTURE_PATH = os.path.join(os.path.expanduser('~'), 'micrographs') #: str: Base path to store all captures
		TEMP_CAPTURE_PATH = os.path.join(BASE_CAPTURE_PATH, 'tmp') #: str: Base path to store all temporary captures (automatically emptied)


		# TODO: Move these methods to a camera utilities module?
		def clear_tmp():
		"""
		Removes all files in the ``TEMP_CAPTURE_PATH`` directory
		@@ -75,11 +75,9 @@ def capture_from_dict(capture_dict):
		"""
		global EXIF_FORMATS

		capture = CaptureObject() # Create a placeholder capture

		# Get inherent capture information from database
		capture.file = capture_dict['path']
		capture.temporary = capture_dict['temporary']
		capture = CaptureObject(
		filepath=capture_dict['path']
		) # Create a placeholder capture
		capture.split_file_path(capture.file)

		if capture.format.upper() in EXIF_FORMATS:
		@@ -111,9 +109,7 @@ class CaptureObject(object):
		self,
		write_to_file: bool = False,
		temporary: bool = False,
		filename: str = '',
		folder: str = '',
		fmt: str = '') -> None:
		filepath: str = '') -> None:
		"""Create a new StreamObject, to manage capture data."""

		# Store a nice ID
		@@ -121,22 +117,15 @@ class CaptureObject(object):
		logging.info("Created StreamObject {}".format(self.id))
		self.timestring = datetime.datetime.now().strftime("%Y-%m-%d_%H-%M-%S") #: str: Timestring of capture creation time

		# Store file format
		self.format = fmt #: str: Capture data format (e.g. jpeg, h264)

		# Keep on disk after close by default
		self.temporary = temporary #: bool: Mark the capture as temporary, to be deleted as the server closes, or as resources are required

		# Explicitally state if capture should be written to a file, not a bytestream
		self.write_to_file = write_to_file #: bool: Write capture data to disk immediately, rather than to memory initially (useful for video recordings)

		# Create file name. Default to UUID
		if not filename:
		filename = self.id
		self.filename = "{}.{}".format(filename, fmt)

		# Create folder path
		self.folder = folder
		if not filepath:
		self.file = self.build_file_path()
		else:
		self.file = filepath
		self.split_file_path(self.file)

		# Dictionary for storing custom metadata
		self._metadata = {} #: dict: Dictionary of custom metadata to be included in metadata file
		@@ -144,15 +133,18 @@ class CaptureObject(object):
		# List for storing tags
		self.tags = [] #: list: List of tags. Essentially just as extra custom metadata field, but useful for quick organisation

		# Initialise the capture stream
		self.initialise_capture()
		# Byte bytestream properties
		self.bytestream = io.BytesIO() # Byte bytestream that data will be written to

		# Set default write target
		if not write_to_file:
		self.stream = self.bytestream
		else:
		self.stream = self.file

		# Log if created by context manager
		self.context_manager = False

		# Object lock
		self.locked = False

		# Thumbnail (populated only for PIL captures)
		self.thumb_bytes = None

		@@ -165,7 +157,7 @@ class CaptureObject(object):
		self.context_manager = True # Used in metadata

		logging.info("Rebuilding as a temporary capture...")
		self.initialise_capture()
		self.build_file_path()

		return self

		@@ -174,52 +166,13 @@ class CaptureObject(object):
		logging.info("Cleaning up {}".format(self.id))
		self.close()

		def initialise_capture(self):
		"""
		Initialise the capture object. Creates a file name and builds a file path,
		creates an in-memory byte stream for capture data, and creates a metadata
		file on disk.

		"""
		self.build_file_path()

		# Byte bytestream properties
		self.bytestream = io.BytesIO() # Byte bytestream that data will be written to

		# Set default write target
		if not self.write_to_file:
		logging.debug("Target for {} set to 'bytestream'".format(self.id))
		self.stream = self.bytestream
		else:
		logging.debug("Target for {} set to 'file'".format(self.id))
		self.stream = self.file

		# Save initial metadata file
		self.save_metadata()

		def build_file_path(self):
		"""
		Construct a full file path, based on filename, folder, and file format.
		Defaults to UUID.
		"""
		global TEMP_CAPTURE_PATH
		# TODO: Combine this and split_file_path, and tidy. Let the device (camera) handle folders. This should be more basic.
		# TODO: Even let the base camera manage moving captures to temp folder
		# This module will clear out the temp folder, but won't MOVE anything there.
		# In Base cameras new_image method, the full folder is constructed. Temp folder should be inserted there.

		self.file = os.path.join(self.folder, self.filename) # Full file name by joining given folder to given name

		self.split_file_path(self.file) # Split file path into folder, filename, and basename

		# Check directory is a subdirectory of BASE_CAPTURE_PATH
		# TODO: Do we need this?
		if not os.path.commonprefix([self.file, BASE_CAPTURE_PATH]) == BASE_CAPTURE_PATH:
		raise Exception("Captures cannot be stored in a lower-level directory than {}.".format(BASE_CAPTURE_PATH))

		# Create folder and file
		if not os.path.exists(self.filefolder):
		os.makedirs(self.filefolder)
		return os.path.join(self.folder, self.filename) # Full file name by joining given folder to given name

		def split_file_path(self, filepath):
		"""
		@@ -230,17 +183,11 @@ class CaptureObject(object):
		"""
		self.filefolder, self.filename = os.path.split(filepath) # Split the full file path into a folder and a filename
		self.basename = os.path.splitext(self.filename)[0] # Split the filename out from it's file extension

		if not self.format:
		self.format = self.filename.split('.')[-1]

		def lock(self):
		"""Set locked flag to True."""
		self.locked = True

		def unlock(self):
		"""Set locked flag to False."""
		self.locked = False
		# Create folder and file
		if not os.path.exists(self.filefolder):
		os.makedirs(self.filefolder)

		@property
		def stream_exists(self, auto_rewind=True) -> bool:
		@@ -325,7 +272,7 @@ class CaptureObject(object):
		Create basic metadata dictionary from basic capture data,
		and any added custom metadata and tags.
		"""
		d = {'id': self.id, 'filename': self.filename, 'path': self.file, 'time': self.timestring,
		d = {'id': self.id, 'filename': self.filename, 'time': self.timestring,
		'format': self.format, 'tags': self.tags, 'custom': self._metadata}

		# Add custom metadata to dictionary
		@@ -354,7 +301,7 @@ class CaptureObject(object):
		"""

		# Create basic state dictionary
		d = {'path': self.file, 'locked': self.locked, 'temporary': self.temporary, 'metadata': self.metadata}
		d = {'path': self.file, 'temporary': self.temporary, 'metadata': self.metadata}

		# Check bytestream
		if self.stream_exists:
		@@ -382,6 +329,7 @@ class CaptureObject(object):

		if self.stream_exists: # If data bytestream contains data
		# Create a copy of the bytestream bytes
		logging.debug("STREAM EXISTS")
		data = io.BytesIO(self.bytestream.getbuffer())

		else: # If data bytestream is empty