Commit 309b3481 authored by Joel Collins's avatar Joel Collins
Browse files

Store encoded LST in microscope system metadata

parent abff27fd

openflexure_microscope/api/v2/blueprints/actions/camera.py

+1 −7
Original line number Diff line number Diff line
@@ -87,13 +87,7 @@ class CaptureAPI(MicroscopeView): 
            )



            # Inject system metadata

            system_metadata = {

                "microscope_settings": self.microscope.read_settings(),

                "microscope_state": self.microscope.state,

                "microscope_id": self.microscope.id,

                "microscope_name": self.microscope.name,

            }

            output.system_metadata.update(system_metadata)

            output.system_metadata.update(self.microscope.metadata)



            # Insert custom metadata

            output.put_metadata(metadata)

openflexure_microscope/microscope.py

+29 −0
Original line number Diff line number Diff line
@@ -10,7 +10,9 @@ from openflexure_microscope.stage.base import BaseStage 
from openflexure_microscope.stage.mock import MockStage

from openflexure_microscope.camera.base import BaseCamera

from openflexure_microscope.camera.mock import MockStreamer

from openflexure_microscope.camera.pi import PiCameraStreamer



from openflexure_microscope.utilities import serialise_array_b64

from openflexure_microscope.plugins import PluginLoader

from openflexure_microscope.task import TaskOrchestrator

from openflexure_microscope.common.lock import CompositeLock
@@ -270,3 +272,30 @@ class Microscope: 
            Please use apply_settings method instead."

        )

        self.apply_settings(config)



    @property

    def metadata(self):

        """

        Microscope system metadata, to be applied to basically all captures

        """

        system_metadata = {

            "microscope_settings": self.read_settings(),

            "microscope_state": self.state,

            "microscope_id": self.id,

            "microscope_name": self.name,

        }



        # Store an encoded copy of the PiCamera lens shading table, if it exists

        if self.camera and isinstance(self.camera, PiCameraStreamer):

            # Read LST. Returns None if no LST is active

            lst_arr = self.camera.read_lens_shading_table()



            b64_string, dtype, shape = serialise_array_b64(lst_arr)

            

            system_metadata["lens_shading_table"] = {

                "b64_string": b64_string,

                "dtype": dtype,

                "shape": shape

            }

        

        return system_metadata
 
 No newline at end of file

openflexure_microscope/plugins/default/scan/plugin.py

+1 −7
Original line number Diff line number Diff line
@@ -100,13 +100,7 @@ class ScanPlugin(MicroscopePlugin): 
            tags.append("scan")



        # Inject system metadata

        system_metadata = {

            "microscope_settings": self.microscope.read_settings(),

            "microscope_state": self.microscope.state,

            "microscope_id": self.microscope.id,

            "microscope_name": self.microscope.name,

        }

        output.system_metadata.update(system_metadata)

        output.system_metadata.update(self.microscope.metadata)



        # Insert custom metadata

        output.put_metadata(metadata)

openflexure_microscope/utilities.py

+12 −0
Original line number Diff line number Diff line 
import re

import copy

import operator

import base64

import numpy as np

from collections import abc

from functools import reduce

from contextlib import contextmanager





def deserialise_array_b64(b64_string, dtype, shape):

    flat_arr = np.fromstring(base64.b64decode(b64_string), dtype)

    return flat_arr.reshape(shape)



def serialise_array_b64(npy_arr):

    b64_string = base64.b64encode(npy_arr).decode('ascii')

    dtype = str(npy_arr.dtype)

    shape = npy_arr.shape

    return b64_string, dtype, shape



def get_by_path(root, items):

    """Access a nested object in root by item sequence."""

    return reduce(operator.getitem, items, root)