import uuid import io import os import glob import datetime import copy import yaml import logging from PIL import Image import atexit pil_formats = ['JPG', 'JPEG', 'PNG', 'TIF', 'TIFF'] thumbnail_size = (60, 60) BASE_CAPTURE_PATH = os.path.join(os.path.expanduser('~'), 'micrographs') TEMP_CAPTURE_PATH = os.path.join(BASE_CAPTURE_PATH, 'tmp') def clear_tmp(): global TEMP_CAPTURE_PATH logging.info("Clearing {}...".format(TEMP_CAPTURE_PATH)) files = glob.glob('{}/*'.format(TEMP_CAPTURE_PATH)) for f in files: 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. Note: Captures cannot be stored in a lower-level directory than BASE_CAPTURE_PATH. """ def __init__( self, write_to_file: bool=False, temporary: bool=False, filename: str='', folder: str='', fmt: str='', create_metadata_file: bool=True) -> None: """Create a new StreamObject, to manage capture data.""" # Store a nice ID self.id = uuid.uuid4().hex logging.info("Created StreamObject {}".format(self.id)) self.timestring = datetime.datetime.now().strftime("%Y-%m-%d_%H-%M-%S") # Store file format self.format = fmt # Keep on disk after close by default self.temporary = temporary # Explicitally state if capture should be written to a file, not a bytestream self.write_to_file = write_to_file # 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 = {} # List for storing tags self.tags = [] # Initialise the capture stream self.initialise_capture(create_metadata_file=create_metadata_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 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.temporary = True # Flag file to be removed on close. self.context_manager = True # Used in metadata logging.info("Rebuilding as a temporary capture...") self.initialise_capture() return self def __exit__(self, *args): """Exit StreamObject, and auto-clean disk data.""" logging.info("Cleaning up {}".format(self.id)) self.close() def initialise_capture(self, create_metadata_file=True): self.build_file_path(self.filename, self.folder) # 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 if create_metadata_file: self.save_metadata() def build_file_path( self, filename: str, folder: str): """ Construct a full file path, based on filename, folder, and file format. Defaults to UUID. """ global TEMP_CAPTURE_PATH self.file = os.path.join(folder, 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 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)) # Move to tmp directory if not being kept 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) # Create folder and file if not os.path.exists(self.filefolder): os.makedirs(self.filefolder) logging.debug(self.file) logging.debug(self.filename) logging.debug(self.basename) logging.debug(self.filefolder) def split_file_path(self, filepath): """Takes a full file path, and splits it into separated class properties.""" 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 self.metadataname = "{}.yaml".format(self.basename) def lock(self): """Set locked flag to True.""" self.locked = True def unlock(self): """Set locked flag to False.""" self.locked = False @property def stream_exists(self, auto_rewind=True) -> bool: """Check if BytesIO bytestream is empty.""" if auto_rewind: self.bytestream.seek(0) # Rewind the data bytes for reading if self.bytestream.getvalue(): # If data bytestream contains data self.bytestream.seek(0) # Rewind the data bytes for reading return True else: self.bytestream.seek(0) # Rewind the data bytes for reading return False @property def file_exists(self) -> bool: """Check if corresponding file exists.""" if os.path.isfile(self.file): return True else: return False # HANDLE TAGS def put_tag(self, tag: str): if not tag in self.tags: self.tags.append(tag) def delete_tag(self, tag: str): if tag in self.tags: self.tags = [new_tag for new_tag in self.tags if new_tag != tag] # HANDLE METADATA @property def metadata_file(self) -> str: return "{}.yaml".format(os.path.splitext(self.file)[0]) def put_metadata(self, data: dict) -> None: self._metadata.update(data) self.save_metadata() def save_metadata(self) -> None: logging.debug("Writing metadata to file {}".format(self.metadata_file)) with open(self.metadata_file, 'w') as outfile: yaml.dump(self.metadata, outfile, default_flow_style=False) def delete_metadata(self) -> None: if os.path.isfile(self.metadata_file): logging.info("Deleting file {}".format(self.metadata_file)) os.remove(self.metadata_file) @property def metadata(self) -> dict: # Create basic metadata dictionary d = { 'id': self.id, 'filename': self.filename, 'path': self.file, 'time': self.timestring, 'format': self.format, 'tags': self.tags } # Add custom metadata to dictionary d['custom'] = self._metadata return d @property def yaml(self) -> str: return yaml.dump(self.metadata, default_flow_style=False) @property def exists(self) -> bool: return self.stream_exists or self.file_exists @property def state(self) -> dict: """Return dictionary of StreamObject properties.""" # Create basic state dictionary d = { 'locked': self.locked, 'temporary': self.temporary, } # Add metadata to state d['metadata'] = self.metadata d['metadata_path'] = self.metadata_file # Check bytestream if self.stream_exists: d['bytestream'] = True else: d['bytestream'] = False # Combined availability of data if self.exists: d['available'] = True else: d['available'] = False return d @property def data(self) -> io.BytesIO: """Return a byte string of the capture data.""" self.bytestream.seek(0) # Rewind the data bytes for reading if self.stream_exists: # If data bytestream contains data # Create a copy of the bytestream bytes data = io.BytesIO(self.bytestream.getbuffer()) else: # If data bytestream is empty if self.file_exists: # If data file exists logging.info("Opening from file {}".format(self.file)) with open(self.file, 'rb') as f: d = io.BytesIO(f.read()) # Load bytes from file d.seek(0) # Rewind loaded bytestream # Create a copy of the bytestream bytes data = io.BytesIO(d.getbuffer()) else: data = None return data # Read and return bytes data @property def binary(self) -> bytes: """Return a byte string of the capture data.""" return self.data.getvalue() @property def thumbnail(self) -> io.BytesIO: # 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) im.save(self.thumb_bytes, self.format) self.thumb_bytes.seek(0) else: self.thumb_bytes.seek(0) # Copy the buffer, to avoid closing the file data = io.BytesIO(self.thumb_bytes.getbuffer()) return data def load_file(self) -> bool: """Load data stored on disk to the in-memory bytestream.""" if self.file_exists: # If data file exists with open(self.file, 'rb') as f: self.bytestream = io.BytesIO(f.read()) # Load bytes from file self.bytestream.seek(0) # Rewind data bytes again return True else: return False 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)) f.seek(0, 0) # Seek to the start of the file f.write(self.binary) # Write data bytes to file return True else: return False def save(self) -> None: """Write stream to file, and save/update metadata file""" # Try to save the file (only succeeds if an unsaved stream exists) self.save_file() # If a stream OR file exists, save the metadata file if self.exists: self.save_metadata() def delete_stream(self): """Clear the BytesIO bytestream of the StreamObject.""" self.bytestream = io.BytesIO() def delete_file(self) -> bool: """If the StreamObject has been saved, delete the file.""" if os.path.isfile(self.metadata_file): logging.info("Deleting file {}".format(self.metadata_file)) os.remove(self.metadata_file) if os.path.isfile(self.file): logging.info("Deleting file {}".format(self.file)) os.remove(self.file) return True else: return False def delete(self): """Entirely delete all capture data.""" logging.info("Deleting {}".format(self.id)) self.delete_stream() self.delete_file() self.delete_metadata() def shunt(self): """Demote the StreamObject from being stored in memory.""" if not self.file_exists: # If file doesn't already exist self.save() # Save bytestream to disk, if it exists self.delete_stream() # Delete the bytestream from memory def close(self): """Both clear the bytestream, and delete any associated on-disk data.""" logging.info("Closing {}".format(self.id)) self.delete_stream() if self.temporary: self.delete() atexit.register(clear_tmp)