Capture list now persists through server restart (4e985fe8) · Commits · OpenFlexure / openflexure-microscope-server

openflexure_microscope/api/static/main_v1.js

+4 −4

Original line number	Diff line number	Diff line
		@@ -143,7 +143,7 @@ function getStagePositions() {
		}

		// Capture methods
		function newCapture(filename, keep_on_disk, use_video_port, bayer, resizeWidth=null, resizeHeight=null) {
		function newCapture(filename, temporary, use_video_port, bayer, resizeWidth=null, resizeHeight=null) {
		// Make a position request
		function newCaptureCallback(response, status) {
		if (status != 200) {
		@@ -155,7 +155,7 @@ function newCapture(filename, keep_on_disk, use_video_port, bayer, resizeWidth=n

		payload = {
		"filename": filename,
		"keep_on_disk": keep_on_disk,
		"temporary": temporary,
		"use_video_port": use_video_port,
		"bayer": bayer
		}
		@@ -173,7 +173,7 @@ function newCapture(filename, keep_on_disk, use_video_port, bayer, resizeWidth=n

		function newCaptureFromInput() {
		captureFilenameInput = document.getElementById('captureFilenameInput');
		captureKeepOnDiskCheck = document.getElementById('captureKeepOnDiskCheck');
		captureTemporaryCheck = document.getElementById('captureTemporaryCheck');
		captureFullResolutionCheck = document.getElementById('captureFullResolutionCheck');
		captureBayerCheck = document.getElementById('captureBayerCheck')

		@@ -200,7 +200,7 @@ function newCaptureFromInput() {

		newCapture(
		filename,
		captureKeepOnDiskCheck.checked,
		captureTemporaryCheck.checked,
		!(captureFullResolutionCheck.checked),
		captureBayerCheck.checked,
		resizeWidth,

openflexure_microscope/api/templates/index_v1.html

+1 −1

Original line number	Diff line number	Diff line
		@@ -91,7 +91,7 @@
		<h2>Capture</h2>
		Filename: <br>
		<input type="text" id="captureFilenameInput" placeholder="Leave blank for default"><br>
		Store on Pi: <input type="checkbox" id="captureKeepOnDiskCheck"><br>
		Temporary: <input type="checkbox" id="captureTemporaryCheck"><br>
		Full resolution: <input type="checkbox" id="captureFullResolutionCheck"><br>
		Keep raw data: <input type="checkbox" id="captureBayerCheck"><br>
		Resize capture: <input type="checkbox" id="captureResizeCheck" onclick="newCaptureResizeToggle(this);"><br>

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

+5 −5

Original line number	Diff line number	Diff line
		@@ -68,7 +68,7 @@ class ListAPI(MicroscopeView):

		{
		"filename": "myfirstcapture",
		"keep_on_disk": true,
		"temporary": false,
		"use_video_port": true,
		"bayer": true,
		"size": {
		@@ -80,7 +80,7 @@ class ListAPI(MicroscopeView):
		:>header Accept: application/json

		:<json string filename: filename of stored capture
		:<json boolean keep_on_disk: keep the capture file on microscope after closing
		:<json boolean temporary: delete the capture file on microscope after closing
		:<json boolean use_video_port: capture still image from the video port
		:<json boolean bayer: keep raw capture data in the image file
		:<json json size: - x (int): x-axis resize
		@@ -89,7 +89,7 @@ class ListAPI(MicroscopeView):
		:>json boolean available: availability of capture data
		:>json string filename: filename of capture
		:>json string id: unique id of the capture object
		:>json boolean keep_on_disk: keep the capture file on microscope after closing
		:>json boolean temporary: delete the capture file on microscope after closing
		:>json boolean locked: file locked for modifications (mostly used for video recording)
		:>json string path: path on pi storage to the capture file, if available
		:>json boolean stream: capture stored in-memory as a BytesIO stream
		@@ -102,7 +102,7 @@ class ListAPI(MicroscopeView):
		payload = JsonPayload(request)

		filename = payload.param('filename')
		keep_on_disk = payload.param('keep_on_disk', default=True, convert=bool)
		temporary = payload.param('temporary', default=True, convert=bool)
		use_video_port = payload.param('use_video_port', default=False, convert=bool)
		bayer = payload.param('bayer', default=True, convert=bool)

		@@ -115,7 +115,7 @@ class ListAPI(MicroscopeView):

		output = self.microscope.camera.new_image(
		write_to_file=True,
		keep_on_disk=keep_on_disk,
		temporary=temporary,
		filename=filename)

		self.microscope.camera.capture(

openflexure_microscope/camera/base.py

+74 −19

Original line number	Diff line number	Diff line
		@@ -5,6 +5,7 @@ import os
		import threading
		from PIL import Image
		import datetime
		import yaml
		import logging

		try:
		@@ -15,7 +16,8 @@ except ImportError:
		except ImportError:
		from _thread import get_ident

		from .capture import CaptureObject, BASE_CAPTURE_PATH
		from .capture import CaptureObject, capture_from_dict, BASE_CAPTURE_PATH
		from openflexure_microscope.config import USER_CONFIG_DIR


		def last_entry(object_list: list):
		@@ -110,6 +112,14 @@ class BaseCamera(object):
		self.images = [] #: list: List of image capture objects
		self.videos = [] #: list: List of video recording objects

		# Capture data files
		self.images_db = os.path.join(USER_CONFIG_DIR, "images_db.yaml")
		self.videos_db = os.path.join(USER_CONFIG_DIR, "videos_db.yaml")

		# Load captures from persistent db
		self.images = self.load_capture_db(self.images_db)
		self.videos = self.load_capture_db(self.videos_db)

		def __enter__(self):
		"""Create camera on context enter."""
		return self
		@@ -208,19 +218,51 @@ class BaseCamera(object):
		"""Return a video StreamObject with a matching ID."""
		return entry_by_id(id, self.videos)

		# CREATING NEW CAPTURES
		# MANAGE CAPTURE DATABASE

		def new_stream_object(
		self,
		stream_object,
		target_list: list,
		shunt_others: bool=True):
		"""Add a new capture to a list of captures, and shunt all others."""
		if shunt_others: # If shunting all older captures
		for obj in target_list: # For each older capture
		obj.shunt() # Shunt capture from memory to storage
		target_list.append(stream_object)
		return stream_object
		def save_capture_db(self, capture_list, db_path):
		capture_state = [capture.state for capture in capture_list]

		with open(db_path, 'w') as outfile:
		yaml.safe_dump(capture_state, outfile)

		def validate_captures(self, capture_list):
		# Purge captures with missing data files
		valid_captures = []
		for capture in capture_list:
		if capture.file_exists:
		valid_captures.append(capture)
		else:
		if os.path.isfile(capture.metadata_file):
		logging.warning("Capture data missing. Deleting metadata file {}.".format(capture.metadata_file))
		os.remove(capture.metadata_file)

		# Validate and repair captures
		for capture in valid_captures:
		# If the captures metadata file is missing
		if not os.path.isfile(capture.metadata_file):
		# Recreate the metadata file
		capture.save_metadata()

		return valid_captures

		def load_capture_db(self, db_path):
		if os.path.isfile(db_path):
		# Load list of capture dictionary representations from db_path
		with open(db_path, 'r') as infile:
		capture_dict_list = yaml.load(infile)

		# Create capture object list, and validate captures
		capture_list = self.validate_captures(
		[capture_from_dict(capture_dict) for capture_dict in capture_dict_list]
		)

		return capture_list

		else:
		return []

		# CREATING NEW CAPTURES

		def shunt_captures(self, target_list: list):
		for obj in target_list: # For each older capture
		@@ -229,7 +271,7 @@ class BaseCamera(object):
		def new_image(
		self,
		write_to_file: bool=False,
		keep_on_disk: bool=True,
		temporary: bool=True,
		filename: str=None,
		fmt: str='jpeg',
		shunt_others: bool=True):
		@@ -239,31 +281,37 @@ class BaseCamera(object):

		Args:
		write_to_file (bool): Should the StreamObject write to a file, or an in-memory byte stream.
		keep_on_disk (bool): Should the data be kept on disk after session ends. Creating the capture with a content manager sets this to false.
		keep_on_disk (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.
		fmt (str): Format of the capture.
		"""

		# Generate file name
		if not filename:
		filename = self.generate_basename(self.images)
		logging.debug(filename)

		# Create capture object
		output = CaptureObject(
		write_to_file=write_to_file,
		keep_on_disk=keep_on_disk,
		temporary=temporary,
		filename=filename,
		folder=self.paths['image'],
		fmt=fmt)

		# Update capture list
		self.shunt_captures(self.images)
		self.images.append(output)

		# Update capture database
		self.save_capture_db(self.images, self.images_db)

		return output

		def new_video(
		self,
		write_to_file: bool=True,
		keep_on_disk: bool=True,
		temporary: bool=False,
		filename: str=None,
		fmt: str='h264',
		shunt_others: bool=True):
		@@ -273,28 +321,35 @@ class BaseCamera(object):

		Args:
		write_to_file (bool): Should the StreamObject write to a file, or an in-memory byte stream.
		keep_on_disk (bool): Should the data be kept on disk after session ends. Creating the capture with a content manager sets this to false.
		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.
		fmt (str): Format of the capture.
		"""

		# Generate file name
		if not filename:
		filename = self.generate_basename(self.videos)
		logging.debug(filename)

		# Create capture object
		output = CaptureObject(
		write_to_file=write_to_file,
		keep_on_disk=keep_on_disk,
		temporary=temporary,
		filename=filename,
		folder=self.paths['video'],
		fmt=fmt)

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

		# Update capture database
		self.save_capture_db(self.videos, self.videos_db)

		return output

		# INTELLIGENTLY GENERATE FILENAMES

		def generate_basename(self, obj_list: list) -> str:
		initial_basename = generate_basename()
		basename = initial_basename

openflexure_microscope/camera/capture.py

+40 −21

Original line number	Diff line number	Diff line
		@@ -24,6 +24,24 @@ def clear_tmp():
		os.remove(f)
		logging.debug("Removed {}".format(f))

		def capture_from_dict(capture_dict):
		capture = CaptureObject(create_metadata_file=False) # Create a placeholder capture

		# Populate capture parameters
		capture.temporary = capture_dict['temporary']
		capture.id = capture_dict['metadata']['id']
		capture.timestring = capture_dict['metadata']['time']
		capture.format = capture_dict['metadata']['format']

		if 'custom' in capture_dict['metadata']:
		capture._metadata = capture_dict['metadata']['custom']

		capture.file = capture_dict['metadata']['path']
		capture.split_file_path(capture.file)

		return capture


		class CaptureObject(object):
		"""
		StreamObject used to store and process capture data, and metadata.
		@@ -33,10 +51,11 @@ class CaptureObject(object):
		def __init__(
		self,
		write_to_file: bool=False,
		keep_on_disk: bool=True,
		temporary: bool=False,
		filename: str='',
		folder: str='',
		fmt: str='') -> None:
		fmt: str='',
		create_metadata_file: bool=True) -> None:
		"""Create a new StreamObject, to manage capture data."""

		# Store a nice ID
		@@ -48,7 +67,7 @@ class CaptureObject(object):
		self.format = fmt

		# Keep on disk after close by default
		self.keep_on_disk = keep_on_disk
		self.temporary = temporary

		# Explicitally state if capture should be written to a file, not a bytestream
		self.write_to_file = write_to_file
		@@ -56,15 +75,18 @@ class CaptureObject(object):
		# Create file name. Default to UUID
		if not filename:
		filename = self.id

		self.filename = "{}.{}".format(filename, fmt)

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

		# Dictionary for storing custom metadata
		self._metadata = {}

		# Initialise the capture stream
		self.initialise_capture()
		self.initialise_capture(create_metadata_file=create_metadata_file)

		# Log if created by context manager
		self.context_manager = False
		@@ -78,7 +100,7 @@ class CaptureObject(object):
		def __enter__(self):
		"""Create StreamObject in context, to auto-clean disk data."""
		logging.debug("Entering context for {}. Stored files will be cleaned up automatically regardless of location.".format(self.id))
		self.keep_on_disk = False # Flag file to be removed on close.
		self.temporary = True # Flag file to be removed on close.
		self.context_manager = True # Used in metadata

		logging.info("Rebuilding as a temporary capture...")
		@@ -91,7 +113,7 @@ class CaptureObject(object):
		logging.info("Cleaning up {}".format(self.id))
		self.close()

		def initialise_capture(self):
		def initialise_capture(self, create_metadata_file=True):
		self.build_file_path(self.filename, self.folder)

		# Byte bytestream properties
		@@ -106,6 +128,7 @@ class CaptureObject(object):
		self.stream = self.file

		# Save initial metadata file
		if create_metadata_file:
		self.save_metadata()

		def build_file_path(
		@@ -128,7 +151,7 @@ class CaptureObject(object):
		raise Exception("Captures cannot be stored in a lower-level directory than {}.".format(BASE_CAPTURE_PATH))

		# Move to tmp directory if not being kept
		if not self.keep_on_disk:
		if self.temporary:
		self.file_notmp = self.file # Store originally defined folder
		self.filefolder = TEMP_CAPTURE_PATH
		self.file = os.path.join(self.filefolder, self.filename)
		@@ -201,11 +224,12 @@ class CaptureObject(object):
		'id': self.id,
		'filename': self.filename,
		'path': self.file,
		'time': self.timestring
		'time': self.timestring,
		'format': self.format
		}

		# Add custom metadata to dictionary
		d.update(self._metadata)
		d['custom'] = self._metadata

		return d

		@@ -224,7 +248,7 @@ class CaptureObject(object):
		# Create basic state dictionary
		d = {
		'locked': self.locked,
		'keep_on_disk': self.keep_on_disk,
		'temporary': self.temporary,
		}

		# Add metadata to state
		@@ -243,10 +267,6 @@ class CaptureObject(object):
		else:
		d['available'] = False

		# Check if file was manually deleted
		if self.keep_on_disk and not self.file_exists:
		d['metadata']['path'] = "{} (Deleted)".format(d['metadata']['path'])

		return d

		@property
		@@ -281,11 +301,10 @@ class CaptureObject(object):
		# If no thumbnail exists, try and make one
		if not self.thumb_bytes:
		logging.info("Building thumbnail")
		self.thumb_bytes = io.BytesIO()
		if self.format.upper() in pil_formats:
		im = Image.open(self.data)
		im.thumbnail(thumbnail_size)

		self.thumb_bytes = io.BytesIO()
		im.save(self.thumb_bytes, self.format)
		self.thumb_bytes.seek(0)
		else:
		@@ -307,9 +326,9 @@ class CaptureObject(object):

		def save_file(self) -> bool:
		"""Write the StreamObjects bytestream to a file."""
		if not self.keep_on_disk: # If capture is currently temporary
		if self.temporary: # If capture is currently temporary
		self.load_file() # Load data from tmp file into bytestream, if tmp file exists
		self.keep_on_disk = True # Flag as kept on disk
		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))
		@@ -367,7 +386,7 @@ class CaptureObject(object):
		"""Both clear the bytestream, and delete any associated on-disk data."""
		logging.info("Closing {}".format(self.id))
		self.delete_stream()
		if not self.keep_on_disk:
		if self.temporary:
		self.delete()

		atexit.register(clear_tmp)
		No newline at end of file