Reimplemented serialising LST (cf663595) · Commits · OpenFlexure / openflexure-microscope-server

openflexure_microscope/camera/base.py

+0 −4

Original line number	Diff line number	Diff line
		@@ -146,10 +146,6 @@ class BaseCamera(metaclass=ABCMeta):
		"""Return the current settings as a dictionary"""
		return {"paths": self.paths}

		def save_settings(self):
		"""(Optional) Save any settings to disk that need to be stored"""
		return

		def __enter__(self):
		"""Create camera on context enter."""
		return self

openflexure_microscope/camera/pi.py

+26 −55

Original line number	Diff line number	Diff line
		@@ -47,7 +47,11 @@ from .base import BaseCamera, CaptureObject
		from .set_picamera_gain import set_analog_gain, set_digital_gain

		from openflexure_microscope.paths import settings_file_path
		from openflexure_microscope.utilities import serialise_array_b64
		from openflexure_microscope.utilities import (
		serialise_array_b64,
		ndarray_to_json,
		json_to_ndarray,
		)


		# MAIN CLASS
		@@ -154,9 +158,6 @@ class PiCameraStreamer(BaseCamera):
		"image_resolution": self.image_resolution,
		"numpy_resolution": self.numpy_resolution,
		"jpeg_quality": self.jpeg_quality,
		"picamera_lst_path": self.picamera_lst_path
		if (self.picamera_lst_path and os.path.isfile(self.picamera_lst_path))
		else None,
		"picamera": {},
		}
		)
		@@ -170,12 +171,16 @@ class PiCameraStreamer(BaseCamera):
		except AttributeError:
		logging.debug("Unable to read PiCamera attribute {}".format(key))

		return conf_dict
		# Include a serialised lens shading table
		if (
		hasattr(self.camera, "lens_shading_table")
		and getattr(self.camera, "lens_shading_table") is not None
		):
		conf_dict["picamera"]["lens_shading_table"] = ndarray_to_json(
		getattr(self.camera, "lens_shading_table")
		)

		def save_settings(self):
		"""Save lens-shading table to disk"""
		logging.info("Saving picamera_lst to {}".format(self.picamera_lst_path))
		self.save_lens_shading_table()
		return conf_dict

		def update_settings(self, config: dict):
		"""
		@@ -209,22 +214,23 @@ class PiCameraStreamer(BaseCamera):
		config["picamera"], pause_for_effect=True
		)

		# Handle lens shading if camera supports it
		if (
		hasattr(self.camera, "lens_shading_table")
		and "lens_shading_table" in config["picamera"]
		):
		try:
		self.camera.lens_shading_table = json_to_ndarray(
		config["picamera"].get("lens_shading_table")
		)
		except KeyError as e:
		logging.error(e)

		# PiCameraStreamer parameters
		for key, value in config.items(): # For each provided setting
		if (key != "picamera") and hasattr(self, key):
		setattr(self, key, value)

		# Handle lens shading if camera supports it
		if ("picamera_lst_path" in config) and hasattr(
		self.camera, "lens_shading_table"
		):
		logging.debug(
		"Applying lens_shading_table from file: {}".format(
		config["picamera_lst_path"]
		)
		)
		self.apply_lens_shading_table(config["picamera_lst_path"])

		# If stream was paused to update config, unpause
		if paused_stream:
		logging.info("Resuming stream.")
		@@ -293,41 +299,6 @@ class PiCameraStreamer(BaseCamera):
		if pause_for_effect:
		time.sleep(0.2)

		def read_lens_shading_table(self):
		"""
		Read the current lens shading table as a numpy array, if it exists. Return None otherwise.
		"""
		if hasattr(self.camera, "lens_shading_table"):
		return self.camera.lens_shading_table
		else:
		return None

		def save_lens_shading_table(self):
		"""
		Save the current lens shading table to an .npy file, if it exists.
		"""
		logging.debug(self.read_lens_shading_table())
		if self.read_lens_shading_table() is not None:
		np.save(self.picamera_lst_path, self.read_lens_shading_table())
		else:
		logging.warning("Unable to save a nonexistant lens shading table")

		def apply_lens_shading_table(self, lst_array_or_path):
		"""
		Apply a lens shading table from an .npy file, or numpy array.

		Args:
		lst_array_or_path: Numpy array, or path to .npy file, describing the lens-shading table
		"""
		if isinstance(lst_array_or_path, np.ndarray):
		self.camera.lens_shading_table = lst_array_or_path
		elif (type(lst_array_or_path) == str) and os.path.isfile(lst_array_or_path):
		self.camera.lens_shading_table = np.load(lst_array_or_path)
		else:
		logging.error(
		"Unsupported or missing data for camera lens_shading_table. Must be numpy ndarray, or .npy file path string. Skipping."
		)

		def set_zoom(self, zoom_value: float = 1.0) -> None:
		"""
		Change the camera zoom, handling re-centering and scaling.

openflexure_microscope/microscope.py

+0 −4

Original line number	Diff line number	Diff line
		@@ -205,10 +205,6 @@ class Microscope:
		# Read curent config
		current_config = self.read_settings()
		# Save config to file
		if self.camera:
		self.camera.save_settings()
		if self.stage:
		self.stage.save_settings()
		self.settings_file.save(current_config, backup=True)

		@property

openflexure_microscope/stage/base.py

+0 −4

Original line number	Diff line number	Diff line
		@@ -23,10 +23,6 @@ class BaseStage(metaclass=ABCMeta):
		"""Return the current settings as a dictionary"""
		pass

		def save_settings(self):
		"""(Optional) Save any settings to disk that need to be stored"""
		return

		@property
		@abstractmethod
		def state(self):

openflexure_microscope/utilities.py

+22 −0

Original line number	Diff line number	Diff line
		@@ -4,6 +4,7 @@ import operator
		import base64
		from uuid import UUID
		import numpy as np
		import logging
		from collections import abc
		from functools import reduce
		from contextlib import contextmanager
		@@ -21,6 +22,27 @@ def serialise_array_b64(npy_arr):
		return b64_string, dtype, shape


		def ndarray_to_json(arr: np.ndarray):
		b64_string, dtype, shape = serialise_array_b64(arr)
		return {
		"@type": "ndarray",
		"dtype": dtype,
		"shape": shape,
		"base64": b64_string
		}


		def json_to_ndarray(json_dict: dict):
		if not json_dict.get("@type") != "ndarray":
		logging.warning("No valid @type attribute found. Conversion may fail.")
		for required_param in ("dtype", "shape", "base64"):
		if not json_dict.get(required_param):
		raise KeyError(f"Missing required key {required_param}")

		return deserialise_array_b64(json_dict.get("base64"), json_dict.get("dtype"), json_dict.get("shape"))



		@contextmanager
		def set_properties(obj, **kwargs):
		"""A context manager to set, then reset, certain properties of an object.