def test_config(example_subarray):
calibrator = CameraCalibrator(subarray=example_subarray)
# test defaults
assert len(calibrator.image_extractors) == 1
assert isinstance(calibrator.image_extractors["NeighborPeakWindowSum"],
NeighborPeakWindowSum)
assert isinstance(calibrator.data_volume_reducer, NullDataVolumeReducer)
# test we can configure different extractors with different options
# per telescope.
config = Config({
"CameraCalibrator": {
"image_extractor_type": [
("type", "*", "GlobalPeakWindowSum"),
("id", 1, "LocalPeakWindowSum"),
],
"LocalPeakWindowSum": {
"window_width": 15
},
"GlobalPeakWindowSum": {
"window_width": [("type", "*", 10), ("id", 2, 8)]
},
"data_volume_reducer_type":
"TailCutsDataVolumeReducer",
"TailCutsDataVolumeReducer": {
"TailcutsImageCleaner": {
"picture_threshold_pe": 20.0
}
},
}
})
calibrator = CameraCalibrator(example_subarray, config=config)
assert "GlobalPeakWindowSum" in calibrator.image_extractors
assert "LocalPeakWindowSum" in calibrator.image_extractors
assert isinstance(calibrator.image_extractors["LocalPeakWindowSum"],
LocalPeakWindowSum)
assert isinstance(calibrator.image_extractors["GlobalPeakWindowSum"],
GlobalPeakWindowSum)
extractor_1 = calibrator.image_extractors[
calibrator.image_extractor_type.tel[1]]
assert isinstance(extractor_1, LocalPeakWindowSum)
assert extractor_1.window_width.tel[1] == 15
extractor_2 = calibrator.image_extractors[
calibrator.image_extractor_type.tel[2]]
assert isinstance(extractor_2, GlobalPeakWindowSum)
assert extractor_2.window_width.tel[2] == 8
extractor_3 = calibrator.image_extractors[
calibrator.image_extractor_type.tel[3]]
assert isinstance(extractor_3, GlobalPeakWindowSum)
assert extractor_3.window_width.tel[3] == 10
assert isinstance(calibrator.data_volume_reducer,
TailCutsDataVolumeReducer)
assert calibrator.data_volume_reducer.cleaner.picture_threshold_pe.tel[
None] == 20
def test_config(example_subarray):
calibrator = CameraCalibrator(subarray=example_subarray)
# test defaults
assert isinstance(calibrator.image_extractor, NeighborPeakWindowSum)
assert isinstance(calibrator.data_volume_reducer, NullDataVolumeReducer)
config = Config({
"CameraCalibrator": {
"image_extractor_type": "LocalPeakWindowSum",
"LocalPeakWindowSum": {
"window_width": 15
},
"data_volume_reducer_type": "TailCutsDataVolumeReducer",
"TailCutsDataVolumeReducer": {
"TailcutsImageCleaner": {
"picture_threshold_pe": 20.0
}
},
}
})
calibrator = CameraCalibrator(example_subarray, config=config)
assert isinstance(calibrator.image_extractor, LocalPeakWindowSum)
assert calibrator.image_extractor.window_width.tel[None] == 15
assert isinstance(calibrator.data_volume_reducer,
TailCutsDataVolumeReducer)
assert calibrator.data_volume_reducer.cleaner.picture_threshold_pe.tel[
None] == 20
def __init__(self, **kwargs):
try:
cfg = PyFileConfigLoader(os.path.expanduser(
self.config_file)).load_config()
except ConfigFileNotFound:
cfg = Config()
super().__init__(config=cfg, **kwargs)
def test_config():
window_shift = 3
window_width = 9
config = Config({
"LocalPeakWindowSum": {
"window_shift": window_shift,
"window_width": window_width,
}
})
calibrator = CameraCalibrator(
image_extractor=LocalPeakWindowSum(config=config), config=config)
assert calibrator.image_extractor.window_shift.tel[None] == window_shift
assert calibrator.image_extractor.window_width.tel[None] == window_width
def test_config():
window_shift = 3
window_width = 9
config = Config({"LocalPeakWindowSum": {
"window_shift": window_shift,
"window_width": window_width,
}})
calibrator = CameraCalibrator(
extractor_name='LocalPeakWindowSum',
config=config
)
assert calibrator.dl1.extractor.window_shift == window_shift
assert calibrator.dl1.extractor.window_width == window_width
def _init_all_preferences(self):
# Get preferences from the config file
# ---------------------------------------------------------------------
if not self.config:
self.config = Config()
configfiles = []
if self.config_file_name:
config_file = self.config_dir / self.config_file_name
configfiles.append(config_file)
lis = self.config_dir.iterdir()
for fil in lis:
if fil.suffix == ".json":
jsonname = self.config_dir / fil
if self.reset_config or fil == "PlotPreferences.json":
# remove the user json file to reset to defaults
jsonname.unlink()
else:
configfiles.append(jsonname)
for cfgname in configfiles:
self.load_config_file(cfgname)
if cfgname not in self._loaded_config_files:
self._loaded_config_files.append(cfgname)
# Eventually write the default config file
# --------------------------------------
self._make_default_config_file()
self.datadir = (
DataDir()
) # config=self.config) -- passing args deprecated in traitlets 4.2
self.preferences = GeneralPreferences(config=self.config, parent=self)
self.plot_preferences = PlotPreferences(config=self.config,
parent=self)
def test_config(example_subarray):
window_shift = 3
window_width = 9
config = Config(
{
"LocalPeakWindowSum": {
"window_shift": window_shift,
"window_width": window_width,
}
}
)
calibrator = CameraCalibrator(
subarray=example_subarray,
image_extractor=LocalPeakWindowSum(subarray=example_subarray, config=config),
config=config,
)
assert calibrator.image_extractor.window_shift.tel[None] == window_shift
assert calibrator.image_extractor.window_width.tel[None] == window_width
class SpectroChemPy(Application):
"""
This class SpectroChemPy is the main class, containing most of the setup,
configuration and more.
"""
icon = Unicode('scpy.png')
"Icon for the application"
running = Bool(False)
"Running status of the |scpy| application"
name = Unicode('SpectroChemPy')
"Running name of the application"
description = Unicode(
'SpectroChemPy is a framework for processing, analysing and modelling Spectroscopic data for '
'Chemistry with Python.')
"Short description of the |scpy| application"
long_description = Unicode()
"Long description of the |scpy| application"
@default('long_description')
def _get_long_description(self):
desc = """
Welcome to <strong>SpectroChemPy</strong> Application<br><br>
<p><strong>SpectroChemPy</strong> is a framework for processing, analysing and modelling
<strong>Spectro</>scopic data for <strong>Chem</strong>istry with <strong>Py</strong>thon.
It is a cross platform software, running on Linux, Windows or OS X.</p><br><br>
<strong>Version:</strong> {version}<br>
<strong>Authors:</strong> {authors}<br>
<strong>License:</strong> {license}<br>
<div class='warning'> SpectroChemPy is still experimental and under active development. Its current design and
functionalities are subject to major changes, reorganizations, bugs and crashes!!!. Please report any issues
to the <a url='https://redmine.spectrochempy.fr/projects/spectrochempy/issues'>Issue Tracker<a>
</div><br><br>
When using <strong>SpectroChemPy</strong> for your own work, you are kindly requested to cite it this way:
<pre>Arnaud Travert & Christian Fernandez, SpectroChemPy, a framework for processing, analysing and modelling of
Spectroscopic data for Chemistry with Python https://www.spectrochempy.fr, (version {version})
Laboratoire Catalyse and Spectrochemistry, ENSICAEN/University of Caen/CNRS, 2021
</pre></p>""".format(version=__release__,
authors=__author__,
license=__license__)
return desc
# ------------------------------------------------------------------------------------------------------------------
# Configuration parameters
# ------------------------------------------------------------------------------------------------------------------
# Config file setting
# ------------------------------------------------------------------------------------------------------------------
_loaded_config_files = List()
reset_config = Bool(
False,
help='Should we restore a default configuration ?').tag(config=True)
"""Flag: True if one wants to reset settings to the original config defaults"""
config_file_name = Unicode(None,
help="Configuration file name").tag(config=True)
"""Configuration file name"""
@default('config_file_name')
def _get_config_file_name_default(self):
return str(self.name).lower() + '_cfg'
config_dir = Instance(
Path, help="Set the configuration directory location").tag(config=True)
"""Configuration directory"""
@default('config_dir')
def _get_config_dir_default(self):
return self.get_config_dir()
config_manager = Instance(BaseJSONConfigManager)
@default('config_manager')
def _get_default_config_manager(self):
return BaseJSONConfigManager(config_dir=str(self.config_dir))
log_format = Unicode(
"%(highlevel)s %(message)s",
help="The Logging format template",
).tag(config=True)
debug = Bool(True,
help='Set DEBUG mode, with full outputs').tag(config=True)
"""Flag to set debugging mode"""
info = Bool(False, help='Set INFO mode, with msg outputs').tag(config=True)
"""Flag to set info mode"""
quiet = Bool(False,
help='Set Quiet mode, with minimal outputs').tag(config=True)
"""Flag to set in fully quite mode (even no warnings)"""
nodisplay = Bool(
False,
help='Set NO DISPLAY mode, i.e., no graphics outputs').tag(config=True)
"""Flag to set in NO DISPLAY mode """
# last_project = Unicode('', help='Last used project').tag(config=True, type='project')
# """Last used project"""
#
# @observe('last_project')
# def _last_project_changed(self, change):
# if change.name in self.traits(config=True):
# self.config_manager.update(self.config_file_name, {self.__class__.__name__: {change.name: change.new, }})
show_config = Bool(help="Dump configuration to stdout at startup").tag(
config=True)
@observe('show_config')
def _show_config_changed(self, change):
if change.new:
self._save_start = self.start
self.start = self.start_show_config
show_config_json = Bool(help="Dump configuration to stdout (as JSON)").tag(
config=True)
@observe('show_config_json')
def _show_config_json_changed(self, change):
self.show_config = change.new
test = Bool(False, help='test flag').tag(config=True)
"""Flag to set the application in testing mode"""
port = Integer(7000, help='Dash server port').tag(config=True)
"""Dash server port"""
# Command line interface
# ------------------------------------------------------------------------------------------------------------------
aliases = dict(
test='SpectroChemPy.test',
project='SpectroChemPy.last_project',
f='SpectroChemPy.startup_filename',
port='SpectroChemPy.port',
)
flags = dict(
debug=({
'SpectroChemPy': {
'log_level': DEBUG
}
}, "Set log_level to DEBUG - most verbose mode"),
info=({
'SpectroChemPy': {
'log_level': INFO
}
}, "Set log_level to INFO - verbose mode"),
quiet=({
'SpectroChemPy': {
'log_level': ERROR
}
}, "Set log_level to ERROR - no verbosity at all"),
nodisplay=({
'SpectroChemPy': {
'nodisplay': True
}
}, "Set NO DISPLAY mode to true - no graphics at all"),
reset_config=({
'SpectroChemPy': {
'reset_config': True
}
}, "Reset config to default"),
show_config=({
'SpectroChemPy': {
'show_config': True,
}
}, "Show the application's configuration (human-readable "
"format)"),
show_config_json=({
'SpectroChemPy': {
'show_config_json': True,
}
}, "Show the application's configuration (json "
"format)"),
)
classes = List([
GeneralPreferences,
PlotPreferences,
DataDir,
])
# ------------------------------------------------------------------------------------------------------------------
# Initialisation of the application
# ------------------------------------------------------------------------------------------------------------------
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.logs = self.log # we change the noame in order to avoid latter conflict with numpy.log
self.initialize()
def initialize(self, argv=None):
"""
Initialisation function for the API applications
Parameters
----------
argv : List, [optional].
List of configuration parameters.
"""
# parse the argv
# --------------------------------------------------------------------
# if we are running this under ipython and jupyter notebooks
# deactivate potential command line arguments
# (such that those from jupyter which cause problems here)
IN_IPYTHON = False
if InteractiveShell.initialized():
IN_IPYTHON = True
if not IN_IPYTHON:
# remove argument not known by spectrochempy
if 'make.py' in sys.argv[0] or 'pytest' in sys.argv[
0]: # building docs
options = []
for item in sys.argv[:]:
for k in list(self.flags.keys()):
if item.startswith("--" +
k) or k in ['--help', '--help-all']:
options.append(item)
continue
for k in list(self.aliases.keys()):
if item.startswith("-" + k) or k in [
'h',
]:
options.append(item)
self.parse_command_line(options)
else:
self.parse_command_line(sys.argv)
# Get preferences from the config file and init everything
# ---------------------------------------------------------------------
self._init_all_preferences()
# we catch warnings and error for a ligther display to the end-user.
# except if we are in debugging mode
# warning handler
# --------------------------------------------------------------------
def send_warnings_to_log(message, category):
self.logs.warning(f'{category.__name__} - {message}')
return
warnings.showwarning = send_warnings_to_log
# exception handler
# --------------------------------------------------------------------
if IN_IPYTHON:
ip = get_ipython()
def _custom_exc(shell, etype, evalue, tb, tb_offset=None):
if self.log_level == logging.DEBUG:
shell.showtraceback((etype, evalue, tb),
tb_offset=tb_offset)
else:
self.logs.error(f"{etype.__name__}: {evalue}")
ip.set_custom_exc((Exception, ), _custom_exc)
# load our custom magic extensions
# --------------------------------------------------------------------
if ip is not None:
ip.register_magics(SpectroChemPyMagics)
def _init_all_preferences(self):
# Get preferences from the config file
# ---------------------------------------------------------------------
if not self.config:
self.config = Config()
configfiles = []
if self.config_file_name:
config_file = self.config_dir / self.config_file_name
configfiles.append(config_file)
lis = self.config_dir.iterdir()
for f in lis:
if f.suffix == '.json':
jsonname = self.config_dir / f
if self.reset_config or f == 'PlotPreferences.json':
# remove the user json file to reset to defaults
jsonname.unlink()
else:
configfiles.append(jsonname)
for cfgname in configfiles:
self.load_config_file(cfgname)
if cfgname not in self._loaded_config_files:
self._loaded_config_files.append(cfgname)
# Eventually write the default config file
# --------------------------------------
self._make_default_config_file()
self.datadir = DataDir(config=self.config)
self.preferences = GeneralPreferences(config=self.config, parent=self)
self.plot_preferences = PlotPreferences(config=self.config,
parent=self)
# ..................................................................................................................
def get_config_dir(self):
"""
Determines the SpectroChemPy configuration directory name and
creates the directory if it doesn't exist.
This directory is typically ``$HOME/.spectrochempy/config``,
but if the
SCP_CONFIG_HOME environment variable is set and the
``$SCP_CONFIG_HOME`` directory exists, it will be that
directory.
If neither exists, the former will be created.
Returns
-------
config_dir : str
The absolute path to the configuration directory.
"""
# first look for SCP_CONFIG_HOME
scp = environ.get('SCP_CONFIG_HOME')
if scp is not None and Path(scp).exists():
return Path(scp)
config = _find_or_create_spectrochempy_dir() / 'config'
if not config.exists():
config.mkdir(exist_ok=True)
return config
def start_show_config(self, **kwargs):
"""start function used when show_config is True"""
config = self.config.copy()
# exclude show_config flags from displayed config
for cls in self.__class__.mro():
if cls.__name__ in config:
cls_config = config[cls.__name__]
cls_config.pop('show_config', None)
cls_config.pop('show_config_json', None)
if self.show_config_json:
json.dump(config,
sys.stdout,
indent=1,
sort_keys=True,
default=repr)
# add trailing newlines
sys.stdout.write('\n')
print()
return self._start()
if self._loaded_config_files:
print("Loaded config files:")
for f in self._loaded_config_files:
print(' ' + f)
print()
for classname in sorted(config):
class_config = config[classname]
if not class_config:
continue
print(classname)
pformat_kwargs = dict(indent=4)
if sys.version_info >= (3, 4):
# use compact pretty-print on Pythons that support it
pformat_kwargs['compact'] = True
for traitname in sorted(class_config):
value = class_config[traitname]
print(' .{} = {}'.format(
traitname,
pprint.pformat(value, **pformat_kwargs),
))
print()
# now run the actual start function
return self._start()
def reset_preferences(self):
"""
Reset all preferences to default
"""
self.reset_config = True
self._init_all_preferences()
self.reset_config = False
# ------------------------------------------------------------------------------------------------------------------
# start the application
# ------------------------------------------------------------------------------------------------------------------
def start(self):
"""
Start the |scpy| API
All configuration must have been done before calling this function
"""
# print(f'{sys.argv}')
return self._start()
# ------------------------------------------------------------------------------------------------------------------
# Private methods
# ------------------------------------------------------------------------------------------------------------------
def _start(self):
if self.running:
# API already started. Nothing done!
return
if self.preferences.show_info_on_loading:
info_string = "SpectroChemPy's API - v.{}\n" \
"© Copyright {}".format(__version__, __copyright__)
ip = get_ipython()
if ip is not None and "TerminalInteractiveShell" not in str(ip):
display_info_string(message=info_string.strip())
else:
if "/bin/scpy" not in sys.argv[
0]: # deactivate for console scripts
print(info_string.strip())
# force update of rcParams
for rckey in mpl.rcParams.keys():
key = rckey.replace('_', '__').replace('.',
'_').replace('-', '___')
try:
mpl.rcParams[rckey] = getattr(self.plot_preferences, key)
except ValueError:
mpl.rcParams[rckey] = getattr(self.plot_preferences,
key).replace('\'', '')
except AttributeError:
# print(f'{e} -> you may want to add it to PlotPreferences.py')
pass
self.plot_preferences.set_latex_font(self.plot_preferences.font_family)
self.running = True
# display needs for update
# time.sleep(1)
fi = Path.home() / ".scpy_update"
if fi.exists():
try:
msg = fi.read_text()
self.logs.warning(msg)
except Exception:
pass
return True
# ..................................................................................................................
def _make_default_config_file(self):
"""auto generate default config file."""
fname = self.config_dir / self.config_file_name
fname = fname.with_suffix('.py')
if not fname.exists() or self.reset_config:
s = self.generate_config_file()
self.logs.info("Generating default config file: %r" % fname)
with open(fname, 'w') as f:
f.write(s)
# ------------------------------------------------------------------------------------------------------------------
# Events from Application
# ------------------------------------------------------------------------------------------------------------------
@observe('log_level')
def _log_level_changed(self, change):
self.log_format = '%(message)s'
if change.new == DEBUG:
self.log_format = '[%(filename)s-%(funcName)s %(levelname)s] %(' \
'message)s'
self.logs._cache = {}
self.logs.level = self.log_level
for handler in self.logs.handlers:
handler.level = self.log_level
self.logs.info("changed default log_level to {}".format(
logging.getLevelName(change.new)))
def _config_default(self):
# load application config by default
if JupyterHub.initialized():
return JupyterHub.instance().config
else:
return Config()
class SpectroChemPy(Application):
"""
This class SpectroChemPy is the main class, containing most of the setup,
configuration and more.
"""
icon = Unicode("scpy.png")
"Icon for the application"
running = Bool(False)
"Running status of the |scpy| application"
name = Unicode("SpectroChemPy")
"Running name of the application"
description = Unicode(
"SpectroChemPy is a framework for processing, analysing and modelling Spectroscopic data for "
"Chemistry with Python.")
"Short description of the |scpy| application"
long_description = Unicode()
"Long description of the |scpy| application"
@default("long_description")
def _get_long_description(self):
desc = f"""
<p><strong>SpectroChemPy</strong> is a framework for processing, analysing and modelling
<strong>Spectro</>scopic data for <strong>Chem</strong>istry with <strong>Py</strong>thon.
It is a cross platform software, running on Linux, Windows or OS X.</p><br><br>
<strong>Version:</strong> {__release__}<br>
<strong>Authors:</strong> {__author__}<br>
<strong>License:</strong> {__license__}<br>
<div class='warning'> SpectroChemPy is still experimental and under active development. Its current design and
functionalities are subject to major changes, reorganizations, bugs and crashes!!!. Please report any issues
to the <a url='https://github.com/spectrochempy/spectrochempy/issues'>Issue Tracker<a>
</div><br><br>
When using <strong>SpectroChemPy</strong> for your own work,
you are kindly requested to cite it this way: <pre>{__cite__}</pre></p>.
"""
return desc
# ------------------------------------------------------------------------
# Configuration parameters
# ------------------------------------------------------------------------
# Config file setting
# ------------------------------------------------------------------------
_loaded_config_files = List()
reset_config = Bool(
False,
help="Should we restore a default configuration ?").tag(config=True)
"""Flag: True if one wants to reset settings to the original config defaults."""
config_file_name = Unicode(None,
help="Configuration file name").tag(config=True)
"""Configuration file name."""
@default("config_file_name")
def _get_config_file_name_default(self):
return str(self.name).lower() + "_cfg"
config_dir = Instance(
Path, help="Set the configuration directory location").tag(config=True)
"""Configuration directory."""
@default("config_dir")
def _get_config_dir_default(self):
return self.get_config_dir()
config_manager = Instance(BaseJSONConfigManager)
@default("config_manager")
def _get_default_config_manager(self):
return BaseJSONConfigManager(config_dir=str(self.config_dir))
log_format = Unicode(
"%(highlevel)s %(message)s",
help="The Logging format template",
).tag(config=True)
debug = Bool(True,
help="Set DEBUG mode, with full outputs").tag(config=True)
"""Flag to set debugging mode."""
info = Bool(False, help="Set INFO mode, with msg outputs").tag(config=True)
"""Flag to set info mode."""
quiet = Bool(False,
help="Set Quiet mode, with minimal outputs").tag(config=True)
"""Flag to set in fully quite mode (even no warnings)."""
nodisplay = Bool(
False,
help="Set NO DISPLAY mode, i.e., no graphics outputs").tag(config=True)
"""Flag to set in NO DISPLAY mode."""
# last_project = Unicode('', help='Last used project').tag(config=True, type='project')
# """Last used project"""
#
# @observe('last_project')
# def _last_project_changed(self, change):
# if change.name in self.traits(config=True):
# self.config_manager.update(self.config_file_name, {self.__class__.__name__: {change.name: change.new, }})
show_config = Bool(help="Dump configuration to stdout at startup").tag(
config=True)
@observe("show_config")
def _show_config_changed(self, change):
if change.new:
self._save_start = self.start
self.start = self.start_show_config
show_config_json = Bool(help="Dump configuration to stdout (as JSON)").tag(
config=True)
@observe("show_config_json")
def _show_config_json_changed(self, change):
self.show_config = change.new
test = Bool(False, help="test flag").tag(config=True)
"""Flag to set the application in testing mode."""
port = Integer(7000, help="Dash server port").tag(config=True)
"""Dash server port."""
# Command line interface
# ------------------------------------------------------------------------
aliases = dict(
test="SpectroChemPy.test",
project="SpectroChemPy.last_project",
f="SpectroChemPy.startup_filename",
port="SpectroChemPy.port",
)
flags = dict(
debug=(
{
"SpectroChemPy": {
"log_level": DEBUG
}
},
"Set log_level to DEBUG - most verbose mode.",
),
info=(
{
"SpectroChemPy": {
"log_level": INFO
}
},
"Set log_level to INFO - verbose mode.",
),
quiet=(
{
"SpectroChemPy": {
"log_level": ERROR
}
},
"Set log_level to ERROR - no verbosity at all.",
),
nodisplay=(
{
"SpectroChemPy": {
"nodisplay": True
}
},
"Set NO DISPLAY mode to true - no graphics at all",
),
reset_config=(
{
"SpectroChemPy": {
"reset_config": True
}
},
"Reset config to default",
),
show_config=(
{
"SpectroChemPy": {
"show_config": True,
}
},
"Show the application's configuration (human-readable format).",
),
show_config_json=(
{
"SpectroChemPy": {
"show_config_json": True,
}
},
"Show the application's configuration (json format).",
),
)
classes = List([
GeneralPreferences,
PlotPreferences,
DataDir,
])
# ------------------------------------------------------------------------
# Initialisation of the application
# ------------------------------------------------------------------------
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.logs = (
self.log
) # we change the no name in order to avoid latter conflict with numpy.log
self.logs.setLevel(0) # reset to NOTSET
# Set a log filehandler
logdir = self.get_config_dir().parent / "logs"
logdir.mkdir(exist_ok=True)
rh = RotatingFileHandler(str(logdir / "spectrochempy.log"),
maxBytes=32 * 1024,
backupCount=5)
rh.setLevel(INFO)
rh.setFormatter(logging.Formatter("%(message)s"))
self.logs.addHandler(rh)
self.log.info("started")
self.initialize()
def initialize(self, argv=None):
"""
Initialisation function for the API applications.
Parameters
----------
argv : List, [optional].
List of configuration parameters.
"""
# parse the argv
# --------------------------------------------------------------------
# if we are running this under ipython and jupyter notebooks
# deactivate potential command line arguments
# (such that those from jupyter which cause problems here)
in_python = False
if InteractiveShell.initialized():
in_python = True
if not in_python:
# remove argument not known by spectrochempy
if ("make.py" in sys.argv[0] or "pytest" in sys.argv[0]
or "validate_docstrings" in sys.argv[0]): # building docs
options = []
for item in sys.argv[:]:
for k in list(self.flags.keys()):
if item.startswith("--" +
k) or k in ["--help", "--help-all"]:
options.append(item)
continue
for k in list(self.aliases.keys()):
if item.startswith("-" + k) or k in [
"h",
]:
options.append(item)
self.parse_command_line(options)
else: # pragma: no cover
self.parse_command_line(sys.argv)
# Get preferences from the config file and init everything
# ---------------------------------------------------------------------
self._init_all_preferences()
# we catch warnings and error for a lighter display to the end-user.
# except if we are in debugging mode
# warning handler
# --------------------------------------------------------------------
def send_warnings_to_log(message, category):
self.logs.warning(f"{category.__name__} - {message}")
warnings.showwarning = send_warnings_to_log
# exception handler
# --------------------------------------------------------------------
if in_python: # pragma: no cover
ipy = get_ipython()
def _custom_exc(shell, etype, evalue, tb, tb_offset=None):
if self.log_level == logging.DEBUG:
shell.showtraceback((etype, evalue, tb),
tb_offset=tb_offset)
else:
self.logs.error(f"{etype.__name__}: {evalue}")
ipy.set_custom_exc((Exception, ), _custom_exc)
# load our custom magic extensions
# --------------------------------------------------------------------
if ipy is not None:
ipy.register_magics(SpectroChemPyMagics)
def _init_all_preferences(self):
# Get preferences from the config file
# ---------------------------------------------------------------------
if not self.config:
self.config = Config()
configfiles = []
if self.config_file_name:
config_file = self.config_dir / self.config_file_name
configfiles.append(config_file)
lis = self.config_dir.iterdir()
for fil in lis:
if fil.suffix == ".json":
jsonname = self.config_dir / fil
if self.reset_config or fil == "PlotPreferences.json":
# remove the user json file to reset to defaults
jsonname.unlink()
else:
configfiles.append(jsonname)
for cfgname in configfiles:
self.load_config_file(cfgname)
if cfgname not in self._loaded_config_files:
self._loaded_config_files.append(cfgname)
# Eventually write the default config file
# --------------------------------------
self._make_default_config_file()
self.datadir = (
DataDir()
) # config=self.config) -- passing args deprecated in traitlets 4.2
self.preferences = GeneralPreferences(config=self.config, parent=self)
self.plot_preferences = PlotPreferences(config=self.config,
parent=self)
# ..........................................................................
@staticmethod
def get_config_dir():
"""
Determines the SpectroChemPy configuration directory name and
creates the directory if it doesn't exist.
This directory is typically ``$HOME/.spectrochempy/config``,
but if the
SCP_CONFIG_HOME environment variable is set and the
``$SCP_CONFIG_HOME`` directory exists, it will be that
directory.
If neither exists, the former will be created.
Returns
-------
config_dir : str
The absolute path to the configuration directory.
"""
# first look for SCP_CONFIG_HOME
scp = environ.get("SCP_CONFIG_HOME")
if scp is not None and Path(scp).exists():
return Path(scp)
config = _find_or_create_spectrochempy_dir() / "config"
if not config.exists():
config.mkdir(exist_ok=True)
return config
def start_show_config(self):
"""
Start function used when show_config is True.
"""
config = self.config.copy()
# exclude show_config flags from displayed config
for cls in self.__class__.mro():
if cls.__name__ in config:
cls_config = config[cls.__name__]
cls_config.pop("show_config", None)
cls_config.pop("show_config_json", None)
if self.show_config_json:
json.dump(config,
sys.stdout,
indent=1,
sort_keys=True,
default=repr)
# add trailing newlines
sys.stdout.write("\n")
return self._start()
if self._loaded_config_files:
print("Loaded config files:")
for fil in self._loaded_config_files:
print(f" {fil}")
for classname in sorted(config):
class_config = config[classname]
if not class_config:
continue
print(classname)
pformat_kwargs = dict(indent=4)
if sys.version_info >= (3, 4):
# use compact pretty-print on Pythons that support it
pformat_kwargs["compact"] = True
for traitname in sorted(class_config):
value = class_config[traitname]
print(
f" {traitname} = {pprint.pformat(value, **pformat_kwargs)}"
)
# now run the actual start function
return self._start()
def reset_preferences(self):
"""
Reset all preferences to default.
"""
self.reset_config = True
self._init_all_preferences()
self.reset_config = False
# ------------------------------------------------------------------------
# start the application
# ------------------------------------------------------------------------
def start(self):
"""
Start the |scpy| API.
All configuration must have been done before calling this function.
"""
# print(f'{sys.argv}')
return self._start()
# ------------------------------------------------------------------------
# Private methods
# ------------------------------------------------------------------------
def _start(self):
if self.running:
# API already started. Nothing done!
return True
if self.preferences.show_info_on_loading:
info_string = (
f"SpectroChemPy's API - v.{__version__}\n© Copyright {__copyright__}"
)
ipy = get_ipython()
if ipy is not None and "TerminalInteractiveShell" not in str(ipy):
display_info_string(message=info_string.strip())
else:
if "/bin/scpy" not in sys.argv[
0]: # deactivate for console scripts
print(info_string.strip())
# force update of rcParams
for rckey in mpl.rcParams.keys():
key = rckey.replace("_", "__").replace(".",
"_").replace("-", "___")
try:
mpl.rcParams[rckey] = getattr(self.plot_preferences, key)
except ValueError:
mpl.rcParams[rckey] = getattr(self.plot_preferences,
key).replace("'", "")
except AttributeError:
# print(f'{e} -> you may want to add it to PlotPreferences.py')
pass
self.plot_preferences.set_latex_font(self.plot_preferences.font_family)
self.running = True
# display needs for update
msg = _display_needs_update_message()
if msg:
self.log.warning(msg)
self.logs.info("\n\nAPI loaded - application is ready")
return True
# ..........................................................................
def _make_default_config_file(self):
"""auto generate default config file."""
fname = self.config_dir / self.config_file_name
fname = fname.with_suffix(".py")
if not fname.exists() or self.reset_config:
sfil = self.generate_config_file()
self.logs.info(f"Generating default config file: {fname}")
with open(fname, "w") as fil:
fil.write(sfil)
# ------------------------------------------------------------------------
# Events from Application
# ------------------------------------------------------------------------
@observe("log_level")
def _log_level_changed(self, change):
# log file
if change.new == DEBUG:
self.logs.handlers[0].setLevel(INFO) # no debug in the stdout
self.logs.handlers[1].setLevel(DEBUG)
else:
self.logs.handlers[0].setLevel(change.new)
self.logs.handlers[1].setLevel(change.new)
# root
self.logs.setLevel(DEBUG) # reset to DEBUG
self.logs.info(
f"changed default log_level to {logging.getLevelName(change.new)}")