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Reimplemented serialising LST

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This commit is contained in:
Joel Collins 2020-02-06 13:35:05 +00:00
parent ccd5e9b891
commit cf66359559
5 changed files with 48 additions and 67 deletions
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4
openflexure_microscope/camera/base.py
View file

@ -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

81
openflexure_microscope/camera/pi.py
View file

@ -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.

4
openflexure_microscope/microscope.py
View file

@ -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

4
openflexure_microscope/stage/base.py
View file

@ -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):

22
openflexure_microscope/utilities.py
View file

@ -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.