Temp capture folder now handled by camera (7cf54240) · Commits · OpenFlexure / openflexure-microscope-server

openflexure_microscope/camera/base.py

+8 −10

Original line number	Diff line number	Diff line
		@@ -14,7 +14,7 @@ except ImportError:
		except ImportError:
		from _thread import get_ident

		from .capture import CaptureObject, capture_from_dict, BASE_CAPTURE_PATH
		from .capture import CaptureObject, capture_from_dict, BASE_CAPTURE_PATH, TEMP_CAPTURE_PATH
		from openflexure_microscope.config import USER_CONFIG_DIR
		from openflexure_microscope.utilities import entry_by_id
		from openflexure_microscope.lock import StrictLock
		@@ -111,6 +111,8 @@ class BaseCamera(object):
		self.paths = {
		'image': BASE_CAPTURE_PATH,
		'video': BASE_CAPTURE_PATH,
		'image_tmp': TEMP_CAPTURE_PATH,
		'video_tpm': TEMP_CAPTURE_PATH
		} #: dict: Dictionary of capture paths

		# Capture data
		@@ -284,7 +286,7 @@ class BaseCamera(object):
		write_to_file: bool = False,
		temporary: bool = True,
		filename: str = None,
		folder: str = None,
		folder: str = "",
		fmt: str = 'jpeg'):

		"""
		@@ -303,10 +305,8 @@ class BaseCamera(object):
		logging.debug(filename)

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

		# Create capture object
		output = CaptureObject(
		@@ -349,10 +349,8 @@ class BaseCamera(object):
		logging.debug(filename)

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

		# Create capture object
		output = CaptureObject(

openflexure_microscope/camera/capture.py

+11 −27

Original line number	Diff line number	Diff line
		@@ -81,8 +81,8 @@ def capture_from_dict(capture_dict):

		# Get inherent capture information from database
		capture.file = capture_dict['path']
		capture.split_file_path(capture.file)
		capture.temporary = capture_dict['temporary']
		capture.split_file_path(capture.file)

		if capture.format.upper() in EXIF_FORMATS:
		md_exif = pull_usercomment_dict(capture.file)
		@@ -137,9 +137,7 @@ class CaptureObject(object):
		filename = self.id
		self.filename = "{}.{}".format(filename, fmt)

		# Create folder path. Default to BASE_CAPTURE_PATH
		if not folder:
		folder = BASE_CAPTURE_PATH
		# Create folder path
		self.folder = folder

		# Dictionary for storing custom metadata
		@@ -185,7 +183,7 @@ class CaptureObject(object):
		file on disk.

		"""
		self.build_file_path(self.filename, self.folder)
		self.build_file_path()

		# Byte bytestream properties
		self.bytestream = io.BytesIO() # Byte bytestream that data will be written to
		@@ -201,31 +199,23 @@ class CaptureObject(object):
		# Save initial metadata file
		self.save_metadata()

		def build_file_path(
		self,
		filename: str,
		folder: str):
		def build_file_path(self):
		"""
		Construct a full file path, based on filename, folder, and file format.
		Defaults to UUID.

		Args:
		filename (str): Filename of capture
		folder (str): Directory on disk to store capture file
		"""
		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.

		if self.temporary:
		# Store original file path
		self.file_notmp = os.path.join(folder, filename)
		# Move user-specified folder to TEMP
		self.folder = os.path.join(TEMP_CAPTURE_PATH, self.folder)

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

		@@ -448,13 +438,6 @@ class CaptureObject(object):

		def save_file(self) -> bool:
		"""Write the StreamObjects bytestream to a file."""
		if self.temporary: # If capture is currently temporary
		self.load_file() # Load data from tmp file into bytestream, if tmp file exists
		self.temporary = False # Flag as kept on disk
		self.file = self.file_notmp # Reset file path to non-temporary path
		self.split_file_path(self.file) # Set split properties based on new path
		logging.info("Moved temporary file out to {}".format(self.file))

		if self.stream_exists: # If there's a bytestream to save
		with open(self.file, 'ab') as f: # Load file as bytes
		logging.debug("Writing bytestream to file {}".format(self.file))
		@@ -504,6 +487,7 @@ class CaptureObject(object):
		"""Both clear the bytestream, and delete any associated on-disk data."""
		logging.info("Closing {}".format(self.id))
		self.delete_stream()
		# Delete the file from disk if temporary
		if self.temporary:
		self.delete()

openflexure_microscope/plugins/default/scan/plugin.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -62,14 +62,14 @@ class ScanPlugin(MicroscopePlugin):

		# Construct a tile filename
		filename = "{}_{}_{}_{}".format(basename, *self.microscope.stage.position)
		foldername = "SCAN_{}".format(basename)
		folder = "SCAN_{}".format(basename)

		# Create output object
		output = self.microscope.camera.new_image(
		write_to_file=True,
		temporary=temporary,
		filename=filename,
		folder=foldername)
		folder=folder)

		# Capture
		self.microscope.camera.capture(