Commit f2588a50 authored by jtc42's avatar jtc42
Browse files

Add more complete Capture object schemas

parent 2d6ead5f

openflexure_microscope/api/v2/views/captures.py

+23 −1
Original line number Diff line number Diff line
@@ -14,6 +14,28 @@ from labthings.server.find import find_component 
from marshmallow import pre_dump





class InstrumentSchema(Schema):

    id = fields.UUID()

    configuration = fields.Dict()

    settings = fields.Dict()

    state = fields.Dict()



class CaptureMetadataImageSchema(Schema):

    id = fields.UUID()

    acquisitionDate = fields.String(format="date")

    format = fields.String()

    name = fields.String()

    tags = fields.List(fields.String())

    annotations = fields.Dict()





class CaptureMetadataSchema(Schema):

    experimenter = fields.Dict()  # TODO: Make schema

    experimenterGroup = fields.Dict()  # TODO: Make schema

    dataset = fields.Dict()  # TODO: Make schema

    image = fields.Nested(CaptureMetadataImageSchema())

    instrument = fields.Nested(InstrumentSchema())



class CaptureSchema(Schema):

    id = fields.String()

    file = fields.String(
@@ -21,7 +43,7 @@ class CaptureSchema(Schema): 
    )

    exists = fields.Bool(data_key="available")

    name = fields.String()

    metadata = fields.Dict()

    metadata = fields.Nested(CaptureMetadataSchema())



    links = fields.Dict()

openflexure_microscope/camera/capture.py

+9 −7
Original line number Diff line number Diff line
@@ -4,7 +4,6 @@ import os 
import shutil

import glob

import datetime

import yaml

import json

import logging

from PIL import Image
@@ -35,11 +34,9 @@ def pull_usercomment_dict(filepath): 
        try:

            return json.loads(exif_dict["Exif"][37510].decode())

        except json.decoder.JSONDecodeError:

            # TODO: Remove YAML support in a later version

            logging.warning(

                f"Capture {filepath} has metadata stored in YAML format. This is now deprecated in favour of JSON."

            logging.error(

                f"Capture {filepath} has old, corrupt, or missing OpenFlexure metadata. Unable to reload to server."

            )

            return yaml.load(exif_dict["Exif"][37510].decode())

    else:

        return None
@@ -68,6 +65,7 @@ def build_captures_from_exif(capture_path): 
        exif = pull_usercomment_dict(f)

        if exif:

            capture = capture_from_exif(f, exif)

            if capture:

                captures.append(capture)

        else:

            logging.error("Invalid data at {}. Skipping.".format(f))
@@ -95,7 +93,11 @@ def capture_from_exif(path, exif_dict): 
    capture.split_file_path(capture.file)



    # Image metadata

    try:

        image_metadata = exif_dict.pop("image")

    except KeyError as e:

        logging.error(f"Unable to obtain OpenFlexure metadata from file {path}")

        return None



    # Populate capture parameters

    capture.id = image_metadata.get("id")