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Jsonify lens-shading as lists

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This commit is contained in:
Joel Collins 2019-09-15 14:05:33 +01:00
parent 756f18d853
commit 354524de64
1 changed files with 30 additions and 51 deletions
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81
openflexure_microscope/config.py
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@ -4,8 +4,10 @@ import errno
import logging
import shutil
import copy
import numpy as np
from fractions import Fraction
from collections import abc
from .utilities import recursively_apply
"""
Attributes:
@ -18,7 +20,7 @@ Attributes:
# HANDLE THE DEFAULT CONFIGURATION FILE
HERE = os.path.abspath(os.path.dirname(__file__))
DEFAULT_CONFIG_PATH = os.path.join(HERE, 'microscope_settings.default.yaml')
DEFAULT_CONFIG_PATH = os.path.join(HERE, "microscope_settings.default.yaml")
USER_CONFIG_DIR = os.path.join(os.path.expanduser("~"), ".openflexure")
USER_CONFIG_FILE = os.path.join(USER_CONFIG_DIR, "microscope_settings.yaml")
@ -26,7 +28,7 @@ USER_CONFIG_FILE = os.path.join(USER_CONFIG_DIR, "microscope_settings.yaml")
USER_CONFIG_FILE_OLD = os.path.join(USER_CONFIG_DIR, "microscoperc.yaml")
# Load the default config
with open(DEFAULT_CONFIG_PATH, 'r') as default_rc:
with open(DEFAULT_CONFIG_PATH, "r") as default_rc:
DEFAULT_CONFIG = default_rc.read()
# HANDLE CUSTOM YAML PARSING
@ -36,76 +38,51 @@ def construct_yaml_bool(self, node):
YAML otherwise caused grief for picamera properties where 'off' is a valid string value.
"""
override_bool_values = {
'yes': True,
'no': False,
'true': True,
'false': False,
'on': 'on',
'off': 'off',
"yes": True,
"no": False,
"true": True,
"false": False,
"on": "on",
"off": "off",
}
value = self.construct_scalar(node)
return override_bool_values[value.lower()]
yaml.Loader.add_constructor(u'tag:yaml.org,2002:bool', construct_yaml_bool)
yaml.Loader.add_constructor(u"tag:yaml.org,2002:bool", construct_yaml_bool)
# HANDLE CONVERTING ARBITRARY CONFIG TO JSON-SAFE JSON
def convert_type_to_json_safe(v):
"""Make an individual attribute JSON-safe"""
if isinstance(v, Fraction):
return float(v)
elif isinstance(v, np.ndarray):
return v.tolist()
else:
return v
def recursively_apply(data, func):
"""
Recursively apply a function to a dictionary, list, array, or tuple
Args:
data: Input iterable data
func: Function to apply to all non-iterable values
"""
# If the object is a dictionary
if isinstance(data, abc.Mapping):
return {key: recursively_apply(val, func) for key, val in data.items()}
# If the object is iterable but NOT a dictionary or a string
elif (isinstance(data, abc.Iterable) and
not isinstance(data, abc.Mapping) and
not isinstance(data, str)):
return [recursively_apply(x, func) for x in data]
# if the object is neither a map nor iterable
else:
return func(data)
def settings_to_json(data: dict, clean_keys=True):
def settings_to_json(data: dict):
"""
Make a copy of an input dictionary that's safe for JSON return
Args:
data: Input dictionary
clean_keys: Modify any keys unsuitable for JSON return
"""
# Do not overwrite original data dictionary
d = copy.deepcopy(data)
# If we're cleaning up unsuitable keys
if clean_keys:
# Convert lens_shading_table to a bool
if 'picamera_settings' in d['camera_settings'] and 'lens_shading_table' in d['camera_settings']['picamera_settings']:
logging.debug("Bool-ifying lens_shading_table")
if d['camera_settings']['picamera_settings']['lens_shading_table'] is not None:
d['camera_settings']['picamera_settings']['lens_shading_table'] = True
return recursively_apply(d, convert_type_to_json_safe)
# HANDLE BASIC LOADING AND SAVING OF YAML FILES
def load_yaml_file(config_path) -> dict:
"""
Open a .yaml config file
@ -138,7 +115,7 @@ def save_yaml_file(config_path: str, config_dict: dict, safe: bool = False):
logging.info("Saving {}...".format(config_path))
logging.debug(config_dict)
with open(config_path, 'w') as outfile:
with open(config_path, "w") as outfile:
if not safe:
yaml.dump(config_dict, outfile)
else:
@ -173,7 +150,7 @@ def initialise_file(config_path, populate: str = ""):
create_file(config_path)
logging.info("Populating {}...".format(config_path))
with open(config_path, 'w') as outfile:
with open(config_path, "w") as outfile:
outfile.write(populate)
@ -186,12 +163,13 @@ class OpenflexureSettingsFile:
config_path (str): Path to the config YAML file (None falls back to default location)
expand (bool): Expand paths to valid auxillary config files.
"""
def __init__(self, config_path: str = None, expand: bool = True):
global DEFAULT_CONFIG, USER_CONFIG_FILE
self.expandable_keys = {
'camera_settings': None,
'stage_settings': None
"camera_settings": None,
"stage_settings": None,
} #: Dictionary of keys that can be passed as a file path string and expanded automatically
# Set arguments
@ -226,10 +204,10 @@ class OpenflexureSettingsFile:
save_config = self.contract_config(config)
else:
save_config = config
if backup:
if os.path.isfile(self.config_path):
shutil.copyfile(self.config_path, self.config_path+".bk")
shutil.copyfile(self.config_path, self.config_path + ".bk")
logging.debug("Saving settings dictionary to disk")
save_yaml_file(self.config_path, save_config)
@ -255,8 +233,7 @@ class OpenflexureSettingsFile:
# For each value in the raw loaded config
for key, value in config_dict.items():
# If it's a valid expandable parameter
if (key in self.expandable_keys and
type(value) is str):
if key in self.expandable_keys and type(value) is str:
logging.debug("Expanding {}".format(value))
@ -282,9 +259,11 @@ class OpenflexureSettingsFile:
# For each value in the expanded config
for key, value in config_dict.items():
# If it's a valid expandable parameter
if (key in self.expandable_keys and
self.expandable_keys[key] is not None and
type(value) is dict):
if (
key in self.expandable_keys
and self.expandable_keys[key] is not None
and type(value) is dict
):
logging.debug("Saving to {}".format(self.expandable_keys[key]))
# Create the file if it doesn't exist