Static type analysis
This commit is contained in:
Joel Collins
parent
3aebb8bead
commit
7866ec0f47
63 changed files with 1825 additions and 2722 deletions
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@ -6,12 +6,13 @@ import logging
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import os
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import uuid
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from collections import OrderedDict
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from typing import Callable, Dict, List, Optional
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import dateutil.parser
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import piexif
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from piexif import InvalidImageDataError
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from PIL import Image
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from openflexure_microscope.captures import piexif
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from openflexure_microscope.captures.piexif import InvalidImageDataError
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from openflexure_microscope.json import JSONEncoder
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EXIF_FORMATS = ["JPG", "JPEG", "TIF", "TIFF"]
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@ -39,7 +40,7 @@ def build_captures_from_exif(capture_path):
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logging.debug("Reloading capture %s...", (f))
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capture = capture_from_path(f)
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if capture:
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captures[capture.id] = capture
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captures[str(capture.id)] = capture
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logging.info("%s capture files successfully reloaded", (len(captures)))
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@ -68,33 +69,42 @@ class CaptureObject(object):
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Serves to simplify modifying properties of on-disk capture data.
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"""
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def __init__(self, filepath) -> None:
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def __init__(self, filepath: str) -> None:
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"""Create a new StreamObject, to manage capture data."""
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# Stream for buffering capture data
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self.stream = io.BytesIO()
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self.stream: io.BytesIO = io.BytesIO()
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# Store a nice ID
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self.id = uuid.uuid4() #: str: Unique capture ID
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self.id: uuid.UUID = uuid.uuid4() #: str: Unique capture ID
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logging.debug("Created CaptureObject %s", (self.id))
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self.time = datetime.datetime.now()
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self.time: datetime.datetime = datetime.datetime.now()
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# Create file name. Default to UUID
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self.format = None
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self.file = filepath
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self.file: str = filepath
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# Placeholders for split file info
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self.format: str = ""
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self.basename: str = ""
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self.filefolder: str = ""
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self.name: str = ""
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# Replace placeholders with actual split file info
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self.split_file_path(self.file)
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if not os.path.exists(self.filefolder):
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os.makedirs(self.filefolder)
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# Dataset information
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self._dataset = None
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self.dataset: Dict[str, str] = {}
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# Dictionary for storing custom annotations
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# Can be modified via the web API
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self.annotations = {}
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self.annotations: Dict[str, str] = {}
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# List for storing tags
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# Can be modified via the web API
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self.tags = []
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self.tags: List[str] = []
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# On-delete callback
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self.on_delete: Optional[Callable] = None
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def write(self, s):
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logging.debug("Writing to %s", self)
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@ -112,7 +122,7 @@ class CaptureObject(object):
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def open(self, mode):
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return open(self.file, mode)
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def split_file_path(self, filepath):
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def split_file_path(self, filepath: str):
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"""
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Take a full file path, and split it into separated class properties.
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@ -125,10 +135,10 @@ class CaptureObject(object):
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self.basename = os.path.splitext(self.name)[0]
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self.format = self.name.split(".")[-1]
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def _read_exif(self):
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def _read_exif(self) -> dict:
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return piexif.load(self.file)
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def _decode_usercomment(self, exif_dict: dict):
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def _decode_usercomment(self, exif_dict: dict) -> dict:
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if "Exif" not in exif_dict:
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raise InvalidImageDataError
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if piexif.ExifIFD.UserComment not in exif_dict["Exif"]:
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@ -150,15 +160,17 @@ class CaptureObject(object):
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)
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def sync_basic_metadata(self):
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exif_dict = self._read_exif()
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exif_dict: dict = self._read_exif()
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metadata_dict = self._decode_usercomment(exif_dict) or {}
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image_metadata = metadata_dict.get("image")
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metadata_dict: dict = self._decode_usercomment(exif_dict) or {}
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self.dataset = metadata_dict.get("dataset")
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image_metadata: Optional[dict] = metadata_dict.get("image")
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if not image_metadata:
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raise InvalidImageDataError("No capture metadata found")
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self.id = image_metadata.get("id")
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self.id = uuid.UUID(image_metadata.get("id"))
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self.format = image_metadata.get("format")
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self.time = dateutil.parser.isoparse(
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image_metadata.get("time") or image_metadata.get("acquisitionDate")
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@ -166,24 +178,11 @@ class CaptureObject(object):
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self.tags = image_metadata.get("tags")
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self.annotations = image_metadata.get("annotations")
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dataset = metadata_dict.get("dataset")
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if dataset:
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self._dataset = {
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"id": dataset.get("id"),
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"name": dataset.get("name"),
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"type": dataset.get("type"),
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}
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def read_full_metadata(self):
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def read_full_metadata(self) -> dict:
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logging.info("Reading full capture metadata from %s...", self.file)
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exif_dict = self._read_exif()
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return self._decode_usercomment(exif_dict)
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@property
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def dataset(self):
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"""Read-only dataset property"""
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return self._dataset
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@property
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def exists(self) -> bool:
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"""Check if capture data file exists on disk."""
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@ -193,7 +192,7 @@ class CaptureObject(object):
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return False
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# HANDLE TAGS
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def put_tags(self, tags: list):
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def put_tags(self, tags: List[str]):
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"""
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Add a new tag to the ``tags`` list attribute.
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@ -218,7 +217,7 @@ class CaptureObject(object):
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# HANDLE ANNOTATIONS
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def put_annotations(self, data: dict) -> None:
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def put_annotations(self, data: Dict[str, str]):
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"""
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Merge annotations from a passed dictionary into the capture metadata, and saves.
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@ -227,7 +226,7 @@ class CaptureObject(object):
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"""
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self.put_and_save(annotations=data)
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def delete_annotation(self, key: str) -> None:
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def delete_annotation(self, key: str):
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# Update in-memory annotations list
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if key in self.annotations:
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del self.annotations[key]
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@ -237,7 +236,7 @@ class CaptureObject(object):
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# HANDLE METADATA
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def put_metadata(self, data: dict) -> None:
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def put_metadata(self, data: dict):
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"""
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Merge root metadata from a passed dictionary into the capture metadata, and saves.
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@ -246,10 +245,19 @@ class CaptureObject(object):
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"""
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self.put_and_save(metadata=data)
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# HANDLE DATASET
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def put_dataset(self, data: dict):
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self.put_and_save(dataset=data)
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# BULK OPERATIONS
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def put_and_save(
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self, tags: list = None, annotations: dict = None, metadata: dict = None
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self,
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tags: Optional[List[str]] = None,
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annotations: Optional[Dict[str, str]] = None,
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dataset: Optional[Dict[str, str]] = None,
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metadata: Optional[dict] = None,
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):
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"""
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Batch-write tags, metadata, and annotations in a single disk operation
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@ -258,6 +266,8 @@ class CaptureObject(object):
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tags = []
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if not annotations:
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annotations = {}
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if not dataset:
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dataset = {}
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if not metadata:
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metadata = {}
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@ -269,6 +279,9 @@ class CaptureObject(object):
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# Update in-memory annotations dictionary
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self.annotations.update(annotations)
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# Update in-memory dataset dictionary
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self.dataset.update(dataset)
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# Write new data to file EXIF, if supported
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if self.format.upper() in EXIF_FORMATS and self.exists:
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logging.info("Writing Exif data to %s", self.file)
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@ -281,6 +294,8 @@ class CaptureObject(object):
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metadata_dict.get("image", {})["tags"] = self.tags
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# Add new annotations to exif dictionary
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metadata_dict.get("image", {})["annotations"] = self.annotations
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# Set new dataset info in exif dictionary
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metadata_dict["dataset"] = self.dataset
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# Add new custom metadata to exif dictionary
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metadata_dict.update(metadata)
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@ -310,7 +325,7 @@ class CaptureObject(object):
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return self.read_full_metadata()
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@property
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def data(self) -> io.BytesIO:
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def data(self) -> Optional[io.BytesIO]:
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"""
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Return a BytesIO object of the capture data.
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"""
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@ -321,16 +336,17 @@ class CaptureObject(object):
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d = io.BytesIO(f.read()) # Load bytes from file
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d.seek(0) # Rewind loaded bytestream
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# Create a copy of the bytestream bytes
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data = io.BytesIO(d.getbuffer())
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return io.BytesIO(d.getbuffer())
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else:
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data = None
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return data # Read and return bytes data
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return None
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@property
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def binary(self) -> bytes:
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def binary(self) -> Optional[bytes]:
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"""Return a byte string of the capture data."""
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return self.data.getvalue()
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if self.data:
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return self.data.getvalue()
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else:
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return None
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@property
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def thumbnail(self) -> io.BytesIO:
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@ -354,7 +370,7 @@ class CaptureObject(object):
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# FILE MANAGEMENT
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def save(self) -> None:
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def save(self):
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"""Write stream to file, and save/update metadata file"""
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# If a stream OR file exists, save the metadata file
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if self.exists:
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@ -367,6 +383,9 @@ class CaptureObject(object):
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logging.info("Deleting file %s", (self.file))
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os.remove(self.file)
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if self.on_delete:
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self.on_delete(self, self.id)
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return True
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else:
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return False
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