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Removed default JSON files and submoduled JSON encoder class

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This commit is contained in:
Joel Collins 2020-11-12 12:02:09 +00:00
parent 8c180ca285
commit 4a9d1c5e3c
8 changed files with 65 additions and 88 deletions
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2
openflexure_microscope/api/app.py
View file

@ -30,7 +30,7 @@ from labthings.extensions import find_extensions
from openflexure_microscope.api.microscope import default_microscope as api_microscope
from openflexure_microscope.api.utilities import init_default_extensions, list_routes
from openflexure_microscope.api.v2 import views
from openflexure_microscope.config import JSONEncoder
from openflexure_microscope.json import JSONEncoder
from openflexure_microscope.paths import (
OPENFLEXURE_EXTENSIONS_PATH,
OPENFLEXURE_VAR_PATH,

2
openflexure_microscope/captures/capture.py
View file

@ -12,7 +12,7 @@ import dateutil.parser
from openflexure_microscope.camera import piexif
from openflexure_microscope.camera.piexif._exceptions import InvalidImageDataError
from openflexure_microscope.config import JSONEncoder
from openflexure_microscope.json import JSONEncoder
EXIF_FORMATS = ["JPG", "JPEG", "TIF", "TIFF"]
THUMBNAIL_SIZE = (200, 150)

65
openflexure_microscope/config.py
View file

@ -3,18 +3,9 @@ import json
import logging
import os
import shutil
from fractions import Fraction
from uuid import UUID
import numpy as np
from labthings.json import LabThingsJSONEncoder
from .paths import (
CONFIGURATION_FILE_PATH,
DEFAULT_CONFIGURATION_FILE_PATH,
DEFAULT_SETTINGS_FILE_PATH,
SETTINGS_FILE_PATH,
)
from .json import JSONEncoder
from .paths import CONFIGURATION_FILE_PATH, SETTINGS_FILE_PATH
class OpenflexureSettingsFile:
@ -33,7 +24,12 @@ class OpenflexureSettingsFile:
self.path = path
# Initialise basic config file with defaults if it doesn't exist
initialise_file(self.path, populate=defaults)
initialise_file(
self.path,
# Populate with default dictionary, or empty JSON if empty
populate=json.dumps(defaults, cls=JSONEncoder, indent=2, sort_keys=True)
or "{}\n",
)
def load(self) -> dict:
"""
@ -78,32 +74,6 @@ class OpenflexureSettingsFile:
return settings
class JSONEncoder(LabThingsJSONEncoder):
"""
A custom JSON encoder, with type conversions for PiCamera fractions, Numpy integers, and Numpy arrays
"""
def default(self, o):
if isinstance(o, UUID):
return str(o)
# PiCamera fractions
elif isinstance(o, Fraction):
return float(o)
# Numpy integers
elif isinstance(o, np.integer):
return int(o)
# Numpy arrays
elif isinstance(o, np.ndarray):
return o.tolist()
# UUIDs
elif isinstance(o, UUID):
return str(o)
else:
# call base class implementation which takes care of
# raising exceptions for unsupported types
return LabThingsJSONEncoder.default(self, o)
# HANDLE BASIC LOADING AND SAVING OF SETTINGS FILES
@ -184,21 +154,14 @@ def initialise_file(config_path, populate: str = "{}\n"):
outfile.write(populate)
# Load the default settings
with open(DEFAULT_SETTINGS_FILE_PATH, "r") as default_settings:
DEFAULT_SETTINGS = default_settings.read()
#: Default user settings object
user_settings = OpenflexureSettingsFile(
path=SETTINGS_FILE_PATH, defaults=DEFAULT_SETTINGS
)
# Load the default configuration
with open(DEFAULT_CONFIGURATION_FILE_PATH, "r") as default_configuration:
DEFAULT_CONFIGURATION = default_configuration.read()
user_settings = OpenflexureSettingsFile(path=SETTINGS_FILE_PATH)
#: Default user settings object
user_configuration = OpenflexureSettingsFile(
path=CONFIGURATION_FILE_PATH, defaults=DEFAULT_CONFIGURATION
path=CONFIGURATION_FILE_PATH,
defaults={
"camera": {"type": "PiCamera"},
"stage": {"type": "SangaStage", "port": None},
},
)

31
openflexure_microscope/json.py Normal file
View file

@ -0,0 +1,31 @@
from fractions import Fraction
from uuid import UUID
import numpy as np
from labthings.json import LabThingsJSONEncoder
class JSONEncoder(LabThingsJSONEncoder):
"""
A custom JSON encoder, with type conversions for PiCamera fractions, Numpy integers, and Numpy arrays
"""
def default(self, o):
if isinstance(o, UUID):
return str(o)
# PiCamera fractions
elif isinstance(o, Fraction):
return float(o)
# Numpy integers
elif isinstance(o, np.integer):
return int(o)
# Numpy arrays
elif isinstance(o, np.ndarray):
return o.tolist()
# UUIDs
elif isinstance(o, UUID):
return str(o)
else:
# call base class implementation which takes care of
# raising exceptions for unsupported types
return LabThingsJSONEncoder.default(self, o)

9
openflexure_microscope/microscope_configuration.default.json
View file

@ -1,9 +0,0 @@
{
"camera": {
"type": "PiCamera"
},
"stage": {
"type": "SangaStage",
"port": null
}
}

7
openflexure_microscope/microscope_settings.default.json
View file

@ -1,7 +0,0 @@
{
"fov": [
4100,
3146
],
"jpeg_quality": 100
}

12
openflexure_microscope/paths.py
View file

@ -38,18 +38,6 @@ def logs_file_path(filename: str):
os.makedirs(logs_dir)
return os.path.join(logs_dir, filename)
# HANDLE DEFAULTS FILES STORED IN THIS APPLICATION
HERE = os.path.abspath(os.path.dirname(__file__))
#: Path of default (first-run) microscope settings
DEFAULT_SETTINGS_FILE_PATH = os.path.join(HERE, "microscope_settings.default.json")
#: Path of default (first-run) microscope configuration
DEFAULT_CONFIGURATION_FILE_PATH = os.path.join(
HERE, "microscope_configuration.default.json"
)
# BASE PATHS
if os.name == "nt":

25
openflexure_microscope/rescue/check_settings.py
View file

@ -1,5 +1,6 @@
import json
import logging
from .error_sources import ErrorSource
ERROR_SOURCES = []
@ -8,27 +9,35 @@ def trace_config_exceptions():
error_sources = []
from openflexure_microscope.paths import (
DEFAULT_CONFIGURATION_FILE_PATH,
CONFIGURATION_FILE_PATH,
SETTINGS_FILE_PATH,
)
try:
default_config = json.load(DEFAULT_CONFIGURATION_FILE_PATH)
default_config = json.load(CONFIGURATION_FILE_PATH)
if not default_config:
error_sources.append("default_config_empty")
error_sources.append(ErrorSource(
"Configuration file is missing or empty. This may occur if the server has never been started."
))
except Exception as e: # pylint: disable=W0703
logging.error("Error parsing config:")
logging.error(e)
error_sources.append("default_config_error")
error_sources.append(ErrorSource(
f"Configuration file is malformed. You can reset to the default configuration by deleting {CONFIGURATION_FILE_PATH}."
))
try:
default_settings = json.load(SETTINGS_FILE_PATH)
if not default_settings:
error_sources.append("default_settings_empty")
error_sources.append(ErrorSource(
"Settings file is missing or empty. This may occur if the server has never been started."
))
except Exception as e: # pylint: disable=W0703
logging.error("Error parsing settings:")
logging.error(e)
error_sources.append("default_settings_error")
error_sources.append(ErrorSource(
f"Settings file is malformed. You can reset to the default settings by deleting {SETTINGS_FILE_PATH}."
))
return error_sources
@ -39,7 +48,9 @@ def main():
try:
from openflexure_microscope import config as _
except Exception as e: # pylint: disable=W0703
error_sources.append("config_settings_import_error")
error_sources.append(ErrorSource(
"Error importing configuration submodule. This could be an error in our code."
))
logging.error("Error importing config:")
logging.error(e)
error_sources.extend(trace_config_exceptions())