Commit b69c9034 authored by Joel Collins's avatar Joel Collins
Browse files

Removed full capture metadata from top-level resource list

parent 982154ce

openflexure_microscope/api/v2/views/captures.py

+19 −10
Original line number Diff line number Diff line
@@ -17,9 +17,9 @@ class InstrumentSchema(Schema): 
    state = fields.Dict()





class CaptureMetadataImageSchema(Schema):

class ImageSchema(Schema):

    id = fields.UUID()

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

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

    format = fields.String()

    name = fields.String()

    tags = fields.List(fields.String())
@@ -30,19 +30,20 @@ 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())

    image = fields.Nested(ImageSchema())

    instrument = fields.Nested(InstrumentSchema())





class CaptureSchema(Schema):

    id = fields.String()

class CaptureSchema(ImageSchema):

    """

    Schema containing only basic attributes required

    for interacting with a capture. Additional attributes

    are returned by using FullCaptureSchema 

    """

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

    file = fields.String(

        data_key="path", description="Path of file on microscope device"

    )

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

    name = fields.String()

    metadata = fields.Nested(CaptureMetadataSchema())



    links = fields.Dict()



    @pre_dump
@@ -91,6 +92,14 @@ class CaptureSchema(Schema): 


        return data



class FullCaptureSchema(CaptureSchema):

    """

    Capture schema including metadata. We exclude this by default

    since it can become huge due to complex settings including

    lens shading tables and CSM matrices.

    """

    metadata = fields.Nested(CaptureMetadataSchema())





class CaptureList(PropertyView):

    tags = ["captures"]
@@ -108,7 +117,7 @@ class CaptureList(PropertyView): 
class CaptureView(View):

    tags = ["captures"]



    @marshal_with(CaptureSchema())

    @marshal_with(FullCaptureSchema())

    def get(self, id_):

        """

        Description of a single image capture

openflexure_microscope/captures/capture.py

+38 −5
Original line number Diff line number Diff line
@@ -120,7 +120,8 @@ class CaptureObject(object): 
        # Store a nice ID

        self.id = uuid.uuid4()  #: str: Unique capture ID

        logging.debug("Created CaptureObject {}".format(self.id))

        self.datetime = datetime.datetime.now()

        

        self.time = datetime.datetime.now()



        # Create file name. Default to UUID

        self.format = None
@@ -130,12 +131,15 @@ class CaptureObject(object): 
        if not os.path.exists(self.filefolder):

            os.makedirs(self.filefolder)



        # Dictionary for adding top-level metadata (cannmot be accessed through web API)

        # Dictionary for adding top-level metadata

        # This can ONLY be modified by the server application

        # Top level metadata cannot be modified via the web API

        self._metadata = {}



        # Dictionary for storing custom annotations

        # Can be modified via the web API

        self.annotations = {}

        # List for storing tags

        # Can be modified via the web API

        self.tags = []



    def write(self, s):
@@ -173,6 +177,22 @@ class CaptureObject(object): 
        else:

            return False





    @property

    def dataset(self) -> str:

        """

        If capture is part of a dataset, return basic dataset info.

        Otherwise return None

        """

        dataset = self.metadata.get("dataset")

        if not dataset:

            return None

        return {

            "id": dataset.get("id"),

            "name": dataset.get("name"),

            "type": dataset.get("type")

        }



    # HANDLE TAGS

    def put_tags(self, tags: list):

        """
@@ -199,7 +219,7 @@ class CaptureObject(object): 


        self.save_metadata()



    # HANDLE METADATA

    # HANDLE ANNOTATIONS



    def put_annotations(self, data: dict) -> None:

        """
@@ -211,6 +231,13 @@ class CaptureObject(object): 
        self.annotations.update(data)

        self.save_metadata()



    def delete_annotation(self, key: str) -> None:

        if key in self.annotations:

            del self.annotations[key]

        self.save_metadata()



    # HANDLE METADATA



    def put_metadata(self, data: dict) -> None:

        """

        Merge root metadata from a passed dictionary into the capture metadata, and saves.
@@ -230,6 +257,8 @@ class CaptureObject(object): 
        """

        self._metadata = data



    # BULK OPERATIONS



    def put_and_save(

        self, tags: list = None, annotations: dict = None, metadata: dict = None

    ):
@@ -273,6 +302,8 @@ class CaptureObject(object): 
            piexif.insert(exif_bytes, self.file)

            logging.info("Finished saving metadata to %s", self.file)



    # PROPERTIES



    @property

    def metadata(self) -> dict:

        """
@@ -283,7 +314,7 @@ class CaptureObject(object): 
            "image": {

                "id": self.id,

                "name": self.name,

                "acquisitionDate": self.datetime.isoformat(),

                "time": self.time.isoformat(),

                "format": self.format,

                "tags": self.tags,

                "annotations": self.annotations,
@@ -354,6 +385,8 @@ class CaptureObject(object): 
        piexif.insert(exif_bytes, self.file)

        return io.BytesIO(thumbnail)



    # FILE MANAGEMENT



    def save(self) -> None:

        """Write stream to file, and save/update metadata file"""

        # If a stream OR file exists, save the metadata file