def __init__(self, *args, **kw):
super(HeadlessLoggable, self).__init__(*args, **kw)
if self.logger_name:
name = self.logger_name
elif self.name:
name = self.name
else:
name = self.__class__.__name__
self.logger = new_logger(name)
def __init__(self, *args, **kw):
super(HeadlessLoggable, self).__init__(*args, **kw)
if self.logger_name:
name = self.logger_name
elif self.name:
name = self.name
else:
name = self.__class__.__name__
self.logger = new_logger(name)
def _add_logger(self):
'''
'''
if self.logger_name:
name = self.logger_name
elif self.name:
name = self.name
else:
name = self.__class__.__name__
self.logger = new_logger(name)
c = color_name_gen.next()
if c in ['gray', 'silver', 'greenyellow']:
c = color_name_gen.next()
self.logcolor = c
def _add_logger(self):
'''
'''
if self.logger_name:
name = self.logger_name
elif self.name:
name = self.name
else:
name = self.__class__.__name__
self.logger = new_logger(name)
c = color_name_gen.next()
if c in ['gray', 'silver', 'greenyellow']:
c = color_name_gen.next()
self.logcolor = c
def _add_logger(self):
"""
"""
if self.logger_name:
name = self.logger_name
elif self.name:
name = self.name
else:
name = self.__class__.__name__
if self.logger is None:
self.logger = new_logger(name)
__gloggers__[name] = self.logger
c = next(color_name_gen)
if c in ['gray', 'silver', 'greenyellow']:
c = next(color_name_gen)
self.logcolor = c
def _add_logger(self):
"""
"""
if self.logger_name:
name = self.logger_name
elif self.name:
name = self.name
else:
name = self.__class__.__name__
if self.logger is None:
self.logger = new_logger(name)
__gloggers__[name] = self.logger
c = color_name_gen.next()
if c in ['gray', 'silver', 'greenyellow']:
c = color_name_gen.next()
self.logcolor = c
import yaml
from pychron.core.helpers.isotope_utils import extract_mass
from pychron.core.helpers.logger_setup import new_logger
from pychron.paths import paths
from pychron.processing.analyses.analysis_view import DBAnalysisView, AnalysisView
from pychron.processing.analyses.changes import FitChange, BlankChange
from pychron.processing.arar_age import ArArAge
#from pychron.processing.analyses.summary import AnalysisSummary
#from pychron.processing.analyses.db_summary import DBAnalysisSummary
from pychron.experiment.utilities.identifier import make_runid, make_aliquot_step
from pychron.processing.isotope import Isotope, Blank, Baseline, Sniff
from pychron.core.helpers.formatting import calc_percent_error
Fit = namedtuple('Fit', 'fit filter_outliers filter_outlier_iterations filter_outlier_std_devs error_type')
logger = new_logger('Analysis')
class Analysis(ArArAge):
#analysis_summary_klass = AnalysisSummary
#analysis_summary = Instance(AnalysisSummary)
analysis_view_klass = AnalysisView
analysis_view = Instance(AnalysisView)
labnumber = Str
aliquot = Int
step = Str
aliquot_step_str = Str
is_plateau_step = False
# ============= enthought library imports =======================
from traits.api import Str, Int, Bool, Float, Property, \
Enum, on_trait_change, CStr, Long, HasTraits, Instance
from pychron.core.helpers.filetools import remove_extension
from pychron.core.helpers.logger_setup import new_logger
from pychron.core.helpers.strtools import csv_to_ints, to_csv_str
from pychron.core.utils import alphas, alpha_to_int
from pychron.experiment.automated_run.result import AutomatedRunResult, AirResult, UnknownResult, BlankResult
from pychron.experiment.utilities.identifier import get_analysis_type, make_rid, make_runid, is_special, \
convert_extract_device
from pychron.experiment.utilities.position_regex import XY_REGEX
from pychron.experiment.utilities.repository_identifier import make_references_repository_identifier
from pychron.pychron_constants import SCRIPT_KEYS, SCRIPT_NAMES, DETECTOR_IC
logger = new_logger('AutomatedRunSpec')
class AutomatedRunSpec(HasTraits):
"""
this class is used to as a simple container and factory for
an AutomatedRun. the AutomatedRun does the actual work. ie extraction and measurement
"""
run_klass = 'pychron.experiment.automated_run.automated_run.AutomatedRun'
spectrometer_manager = Instance('pychron.spectrometer.base_spectrometer_manager.BaseSpectrometerManager')
result = Instance(AutomatedRunResult, ())
state = Enum('not run', 'extraction',
'measurement', 'success',
'failed', 'truncated', 'canceled',
'invalid', 'test', 'aborted')
from pychron.core.helpers.isotope_utils import sort_isotopes
from pychron.core.helpers.logger_setup import new_logger
from pychron.envisage.view_util import open_view
from pychron.experiment.utilities.identifier import make_runid, make_aliquot_step
from pychron.graph.stacked_regression_graph import ColumnStackedRegressionGraph, StackedRegressionGraph
from pychron.processing.arar_age import ArArAge
from pychron.processing.arar_constants import ArArConstants
from pychron.processing.isotope import Isotope
from pychron.pychron_constants import PLUSMINUS, NULL_STR, AR_AR
Fit = namedtuple(
'Fit', 'fit '
'filter_outliers filter_outlier_iterations filter_outlier_std_devs '
'error_type include_baseline_error, time_zero_offset')
logger = new_logger('Analysis')
def min_max(a, b, vs):
return min(a, vs.min()), max(b, vs.max())
OX = 50
OY = 50
XOFFSET = 25
YOFFSET = 25
WINDOW_CNT = 0
class CloseHandler(Handler):
def closed(self, info, is_ok):
from numpy import hstack
# ============= local library imports ==========================
from pychron.processing.argon_calculations import (
calculate_F,
abundance_sensitivity_correction,
age_equation,
calculate_decay_factor,
)
from pychron.processing.arar_constants import ArArConstants
from pychron.processing.isotope import Isotope, Baseline
from pychron.loggable import Loggable
from pychron.core.helpers.isotope_utils import sort_isotopes
logger = new_logger("ArArAge")
# arar_constants = None
class ArArAge(Loggable):
j = Either(Variable, AffineScalarFunc)
irradiation = Str
irradiation_level = Str
irradiation_pos = Str
irradiation_time = Float
irradiation_label = Property(depends_on="irradiation, irradiation_level,irradiation_pos")
chron_segments = List
interference_corrections = Dict
production_ratios = Dict
# ============= enthought library imports =======================
from traits.api import Str, Int, Bool, Float, Property, \
Enum, on_trait_change, CStr, Long, HasTraits, Instance
from pychron.core.helpers.filetools import remove_extension
from pychron.core.helpers.logger_setup import new_logger
from pychron.core.helpers.strtools import csv_to_ints, to_csv_str
from pychron.experiment.automated_run.result import AutomatedRunResult, AirResult, UnknownResult, BlankResult
from pychron.experiment.utilities.identifier import get_analysis_type, make_rid, make_runid, is_special, \
convert_extract_device
from pychron.experiment.utilities.position_regex import XY_REGEX
from pychron.experiment.utilities.repository_identifier import make_references_repository_identifier
from pychron.pychron_constants import SCRIPT_KEYS, SCRIPT_NAMES, ALPHAS, DETECTOR_IC
logger = new_logger('AutomatedRunSpec')
class AutomatedRunSpec(HasTraits):
"""
this class is used to as a simple container and factory for
an AutomatedRun. the AutomatedRun does the actual work. ie extraction and measurement
"""
run_klass = 'pychron.experiment.automated_run.automated_run.AutomatedRun'
result = Instance(AutomatedRunResult, ())
state = Enum('not run', 'extraction',
'measurement', 'success',
'failed', 'truncated', 'canceled',
'invalid', 'test', 'aborted')
skip = Bool(False)
from ConfigParser import ConfigParser
from copy import copy
import os
#============= local library imports ==========================
from pychron.processing.argon_calculations import calculate_F, abundance_sensitivity_correction, age_equation, \
calculate_decay_factor
from pychron.processing.arar_constants import ArArConstants
from pychron.processing.isotope import Isotope, Baseline
from pychron.loggable import Loggable
from pychron.core.helpers.isotope_utils import sort_isotopes
from pychron.core.helpers.logger_setup import new_logger
from pychron.paths import paths
from pychron.pychron_constants import ARGON_KEYS
logger = new_logger('ArArAge')
# arar_constants = None
class ArArAge(Loggable):
j = Either(Variable, AffineScalarFunc)
irradiation = Str
irradiation_level = Str
irradiation_pos = Str
irradiation_time = Float
production_name = Str
irradiation_label = Property(depends_on='irradiation, irradiation_level,irradiation_pos')
chron_segments = List
chron_dosages = List
# ============= local library imports ==========================
from pychron.core.helpers.filetools import remove_extension
from pychron.core.helpers.logger_setup import new_logger
from pychron.experiment.utilities.identifier import (
get_analysis_type,
make_rid,
make_runid,
is_special,
convert_extract_device,
)
from pychron.experiment.utilities.position_regex import XY_REGEX
from pychron.pychron_constants import SCRIPT_KEYS, SCRIPT_NAMES, ALPHAS
logger = new_logger("AutomatedRunSpec")
class AutomatedRunSpec(HasTraits):
"""
this class is used to as a simple container and factory for
an AutomatedRun. the AutomatedRun does the actual work. ie extraction and measurement
"""
state = Enum(
"not run",
"extraction",
"measurement",
"success",
"failed",
"truncated",
from traits.api import HasTraits, Dict, Property, Instance, Float, Str, List, Either
from pychron.core.helpers.logger_setup import new_logger
from pychron.paths import paths
from pychron.pychron_constants import ARGON_KEYS
#============= standard library imports ========================
from uncertainties import ufloat, Variable, AffineScalarFunc
from numpy import hstack
#============= local library imports ==========================
from pychron.processing.argon_calculations import calculate_F, abundance_sensitivity_correction, age_equation, calculate_decay_factor
from pychron.processing.arar_constants import ArArConstants
from pychron.processing.isotope import Isotope, Baseline
from pychron.loggable import Loggable
from pychron.core.helpers.isotope_utils import sort_isotopes
logger=new_logger('ArArAge')
# arar_constants = None
class ArArAge(Loggable):
j = Either(Variable, AffineScalarFunc)
irradiation = Str
irradiation_level = Str
irradiation_pos = Str
irradiation_time = Float
irradiation_label = Property(depends_on='irradiation, irradiation_level,irradiation_pos')
chron_segments = List
interference_corrections = Dict
production_ratios = Dict
context = {'analysis_type': 'blank' if 'blank' in name else 'unknown'}
task.execute_script(name, root,
delay_start=1,
on_completion=lambda: manager.info(info('Finished Procedure "{}"'.format(name))),
context=context)
def procedure_action(name, application):
a = ProcedureAction(id='procedures.action.{}'.format(name),
name=name.capitalize(),
application=application,
script_path=os.path.join(paths.procedures_dir, name))
return lambda: a
logger = new_logger('ExtractionLinePlugin')
class ExtractionLinePlugin(BaseTaskPlugin):
id = 'pychron.extraction_line'
# manager = Instance(ExtractionLineManager)
def _my_task_extensions_default(self):
ex = [TaskExtension(actions=[SchemaAddition(id='refresh_canvas',
factory=RefreshCanvasAction,
path='MenuBar/tools.menu')])]
if self.application.get_plugin('pychron.pyscript.plugin'):
actions = []
for f in list_directory2(paths.procedures_dir, extension='.py', remove_extension=True):
actions.append(SchemaAddition(id='procedure.{}'.format(f),
# limitations under the License.
#===============================================================================
#============= enthought library imports =======================
from envisage.core_plugin import CorePlugin
from envisage.api import Plugin
#============= standard library imports ========================
#============= local library imports ==========================
from pyface.message_dialog import warning
from pychron.displays.gdisplays import gTraceDisplay
from pychron.envisage.tasks.tasks_plugin import myTasksPlugin
from pychron.core.helpers.logger_setup import new_logger
from pychron.logger.tasks.logger_plugin import LoggerPlugin
from pychron.initialization_parser import InitializationParser
logger = new_logger('launcher')
try:
from pychron.updater.tasks.update_plugin import UpdatePlugin
except ImportError:
logger.warning('Git is required to use UpdatePlugin')
UpdatePlugin=None
PACKAGE_DICT = dict(
ExperimentPlugin='pychron.experiment.tasks.experiment_plugin',
LoadingPlugin='pychron.loading.loading_plugin',
ExtractionLinePlugin='pychron.extraction_line.tasks.extraction_line_plugin',
VideoPlugin='pychron.image.tasks.video_plugin',
# CanvasDesignerPlugin='pychron.canvas.plugins.canvas_designer_plugin',
from traits.api import List, on_trait_change
from envisage.plugin import Plugin
#============= standard library imports ========================
import os
from git import Repo
#============= local library imports ==========================
from pychron import version
from pychron.applications.util.installer import Builder
from pychron.core.helpers.filetools import to_bool
from pychron.core.helpers.logger_setup import new_logger
from pychron.loggable import confirmation_dialog
from pychron.paths import paths, r_mkdir
from pychron.updater.tasks.update_preferences import UpdatePreferencesPane
logger = new_logger('UpdatePlugin')
def gen_commits(log):
def _gen():
lines=iter(log.split('\n'))
commit=None
while 1:
try:
if not commit:
commit=lines.next()
author=lines.next()
date=lines.next()
message=[]
while 1:
line=lines.next()
# limitations under the License.
# ===============================================================================
# ============= enthought library imports =======================
# ============= standard library imports ========================
# ============= local library imports ==========================
from traits.has_traits import MetaHasTraits
from pychron.core.helpers.logger_setup import new_logger
from pychron.core.helpers.strtools import camel_case, to_list
REGISTRY = {}
FUNC_REGISTRY = {}
logger = new_logger('DeviceFunctionRegistry')
class DeviceFunctionRegistry(object):
def __init__(self, name=None, camel_case=False, postprocess=None):
self.postprocess = postprocess
self.name = name
self.camel_case = camel_case
def __call__(self, func):
name = self.name
if name is None:
name = func.func_name
if self.camel_case:
name = camel_case(name)
# See the License for the specific language governing permissions and
# limitations under the License.
# ===============================================================================
# ============= enthought library imports =======================
# ============= standard library imports ========================
# ============= local library imports ==========================
from traits.has_traits import MetaHasTraits
from pychron.core.helpers.logger_setup import new_logger
from pychron.core.helpers.strtools import camel_case
REGISTRY = {}
FUNC_REGISTRY = {}
logger = new_logger('DeviceFunctionRegistry')
class DeviceFunctionRegistry(object):
def __init__(self, name=None, camel_case=False, postprocess=None):
self.postprocess = postprocess
self.name = name
self.camel_case = camel_case
def __call__(self, func):
name = self.name
if name is None:
name = func.func_name
if self.camel_case:
name = camel_case(name)
from traits.api import List, on_trait_change
from envisage.plugin import Plugin
#============= standard library imports ========================
import os
from git import Repo
#============= local library imports ==========================
from pychron import version
from pychron.applications.util.installer import Builder
from pychron.core.helpers.filetools import to_bool
from pychron.core.helpers.logger_setup import new_logger
from pychron.loggable import confirmation_dialog
from pychron.paths import paths, r_mkdir
from pychron.updater.tasks.update_preferences import UpdatePreferencesPane
logger = new_logger('UpdatePlugin')
def gen_commits(log):
def _gen():
lines = iter(log.split('\n'))
commit = None
while 1:
try:
if not commit:
commit = lines.next()
author = lines.next()
date = lines.next()
message = []
while 1:
