def main():
'''
entry point
'''
from pychron.envisage.pychron_run import launch
from pychron.core.helpers.logger_setup import logging_setup
from pychron.paths import build_directories, paths
# import application
# from pychron.applications.pyexperiment import PyExperiment as app
from pychron.applications.pyview import PyView as app
# build directories
build_directories(paths)
# from pychron.core.helpers.paths import hidden_dir
# path = os.path.join(hidden_dir, 'version_info')
# a = VersionInfoDisplay(local_path=path,
# src_path=os.path.join(SRC_DIR,
# 'version_info.txt'))
# a.check()
logging_setup('pychron', level='DEBUG')
#===============================================================================
# test flag
# set if you want to execute tests after startup
# explicitly set the flag here once. mode is a readonly property
#===============================================================================
from pychron.globals import globalv
globalv._test = False
globalv.debug = DEBUG
launch(app)
os._exit(0)
def main():
'''
entry point
'''
# from pychron.envisage.pychron_run import launch
from pychron.core.helpers.logger_setup import logging_setup
from pychron.paths import build_directories, paths
# build directories
build_directories(paths)
#
# from pychron.core.helpers.paths import hidden_dir
# path = os.path.join(hidden_dir, 'version_info')
# a = VersionInfoDisplay(local_path=path,
# src_path=os.path.join(SRC_DIR,
# 'version_info.txt'))
# a.check()
logging_setup('pychron', level='DEBUG')
# ===============================================================================
# test flag
# set if you want to execute tests after startup
# explicitly set the flag here once. mode is a readonly property
# ===============================================================================
# from pychron.globals import globalv
# globalv._test = False
# launch()
# os._exit(0)
from pychron.image.video_server import VideoServer
s = VideoServer()
s.configure_traits()
def run():
import argparse
import os
paths.build(os.getenv('PYCHRON_ROOT'))
logging_setup('furnace_firmware', use_archiver=False)
parser = argparse.ArgumentParser(description='Run NMGRL Furnace Firmware')
# parser.add_argument('--host',
# type=str,
# default='127.0.0.1',
# help='host')
parser.add_argument('--port',
type=int,
default=4567,
help='TCP port to listen')
# parser.add_argument('--debug',
# action='store_true',
# default=False,
# help='run in debug mode')
fm = Firmware()
fm.bootstrap(**vars(parser.parse_args()))
def main():
from pychron.paths import paths
paths.build('_dev')
from pychron.core.helpers.logger_setup import logging_setup
from pychron.experiment.automated_run.spec import AutomatedRunSpec
logging_setup('dvcdb')
from pychron.dvc.dvc_database import DVCDatabase
from itertools import groupby
db = DVCDatabase(kind='mysql', host='localhost', username='******', name='pychronmeta', password='******')
db.connect()
identifiers = ['63290', '63291']
runs = [AutomatedRunSpec(identifier='63290', repository_identifier='Cather_McIntoshd')]
cr = ConflictResolver()
experiments = {}
cr.available_ids = db.get_repository_identifiers()
eas = db.get_associated_repositories(identifiers)
for idn, exps in groupby(eas, key=lambda x: x[1]):
experiments[idn] = [e[0] for e in exps]
conflicts = []
for ai in runs:
identifier = ai.identifier
es = experiments[identifier]
if ai.repository_identifier not in es:
conflicts.append((ai, es))
if conflicts:
cr.add_conflicts('Foo', conflicts)
if cr.conflicts:
info = cr.edit_traits(kind='livemodal')
if info.result:
cr.apply()
def setup():
"""
entry point
"""
from pychron.core.helpers.logger_setup import logging_setup
from pychron.paths import build_directories, paths
# import application
# from pychron.applications.pydiode import PyDiode as app
from pychron.applications.pyexperiment import PyExperiment as app
# build directories
build_directories(paths)
#
# from pychron.core.helpers.paths import hidden_dir
# path = os.path.join(hidden_dir, 'version_info')
# a = VersionInfoDisplay(local_path=path,
# src_path=os.path.join(SRC_DIR,
# 'version_info.txt'))
# a.check()
logging_setup('pychron', level='DEBUG')
# #===============================================================================
# # test flag
# # set if you want to execute tests after startup
# # explicitly set the flag here once. mode is a readonly property
# #===============================================================================
# from pychron.globals import globalv
# globalv._test = False
# globalv.debug = DEBUG
return app
def main():
'''
entry point
'''
from pychron.envisage.pychron_run import launch
from pychron.core.helpers.logger_setup import logging_setup
from pychron.paths import build_directories, paths
# import application
# from pychron.applications.pyexperiment import PyExperiment as app
from pychron.applications.pyview import PyView as app
# build directories
build_directories(paths)
# from pychron.core.helpers.paths import hidden_dir
# path = os.path.join(hidden_dir, 'version_info')
# a = VersionInfoDisplay(local_path=path,
# src_path=os.path.join(SRC_DIR,
# 'version_info.txt'))
# a.check()
logging_setup('pychron', level='DEBUG')
#===============================================================================
# test flag
# set if you want to execute tests after startup
# explicitly set the flag here once. mode is a readonly property
#===============================================================================
from pychron.globals import globalv
globalv._test = False
globalv.debug = DEBUG
launch(app)
os._exit(0)
def initialize_version(appname, debug):
root = os.path.dirname(__file__)
if not debug:
add_eggs(root)
else:
build_sys_path()
# from pychron.environment.util import get_environment
# env = get_environment(appname)
from pychron.envisage.user_login import get_user
args = get_user()
if args is None:
return False
else:
user, env = args
if not env:
return False
set_application_home(appname, env)
from pychron.paths import paths
logger.debug('using Pychron environment: {}'.format(env))
paths.build(env)
from configparser import ConfigParser, NoSectionError
cp = ConfigParser()
pref_path = os.path.join(ETSConfig.application_home, 'preferences.ini')
cp.read(pref_path)
try:
cp.set('pychron.general', 'environment', env)
except NoSectionError:
cp.add_section('pychron.general')
cp.set('pychron.general', 'environment', env)
root = os.path.dirname(pref_path)
if not os.path.isdir(root):
os.mkdir(root)
with open(pref_path, 'w') as wfile:
cp.write(wfile)
# build globals
build_globals(user, debug)
from pychron.core.helpers.logger_setup import logging_setup
from pychron.paths import build_directories
# build directories
build_directories()
paths.write_defaults()
# setup logging. set a basename for log files and logging level
logging_setup('pychron', level='DEBUG')
from pychron.core.helpers.exception_helper import set_exception_handler
set_exception_handler()
return env
def main():
'''
entry point
'''
# from pychron.envisage.pychron_run import launch
from pychron.core.helpers.logger_setup import logging_setup
from pychron.paths import build_directories, paths
# build directories
build_directories(paths)
#
# from pychron.core.helpers.paths import hidden_dir
# path = os.path.join(hidden_dir, 'version_info')
# a = VersionInfoDisplay(local_path=path,
# src_path=os.path.join(SRC_DIR,
# 'version_info.txt'))
# a.check()
logging_setup('pychron', level='DEBUG')
# ===============================================================================
# test flag
# set if you want to execute tests after startup
# explicitly set the flag here once. mode is a readonly property
# ===============================================================================
# from pychron.globals import globalv
# globalv._test = False
# launch()
# os._exit(0)
from pychron.image.video_server import VideoServer
s = VideoServer()
s.configure_traits()
def suite():
# set env. variables
os.environ['MassSpecDBVersion'] = '16'
from pychron.paths import paths
paths.build('_dev')
if use_logger:
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('unittests')
from pychron.canvas.canvas2D.tests.calibration_item import CalibrationObjectTestCase
from pychron.stage.tests.stage_map import StageMapTestCase, \
TransformTestCase
from pychron.entry.tests.sample_loader import SampleLoaderTestCase
from pychron.core.helpers.tests.floatfmt import FloatfmtTestCase
from pychron.processing.tests.analysis_modifier import AnalysisModifierTestCase
from pychron.experiment.tests.backup import BackupTestCase
from pychron.core.xml.tests.xml_parser import XMLParserTestCase
from pychron.entry.tests.analysis_loader import XLSAnalysisLoaderTestCase
from pychron.entry.tests.irradiation_loader import XLSIrradiationLoaderParseTestCase, \
XLSIrradiationLoaderLoadTestCase
from pychron.entry.tests.massspec_irrad_export import MassSpecIrradExportTestCase
from pychron.core.regression.tests.regression import OLSRegressionTest, MeanRegressionTest, \
FilterOLSRegressionTest, OLSRegressionTest2
from pychron.experiment.tests.frequency_test import FrequencyTestCase, FrequencyTemplateTestCase
from pychron.experiment.tests.position_regex_test import XYTestCase
from pychron.experiment.tests.renumber_aliquot_test import RenumberAliquotTestCase
from pychron.external_pipette.tests.external_pipette import ExternalPipetteTestCase
from pychron.processing.tests.plateau import PlateauTestCase
from pychron.processing.tests.ratio import RatioTestCase
from pychron.pyscripts.tests.extraction_script import WaitForTestCase
from pychron.pyscripts.tests.measurement_pyscript import InterpolationTestCase, DocstrContextTestCase
from pychron.experiment.tests.conditionals import ConditionalsTestCase, ParseConditionalsTestCase
from pychron.experiment.tests.identifier import IdentifierTestCase
from pychron.experiment.tests.comment_template import CommentTemplaterTestCase
loader = unittest.TestLoader()
suite = unittest.TestSuite()
tests = (CalibrationObjectTestCase, StageMapTestCase, TransformTestCase,
SampleLoaderTestCase, AnalysisModifierTestCase, BackupTestCase,
MassSpecIrradExportTestCase, XMLParserTestCase,
XLSIrradiationLoaderLoadTestCase,
XLSIrradiationLoaderParseTestCase, XLSAnalysisLoaderTestCase,
RatioTestCase, InterpolationTestCase, DocstrContextTestCase,
OLSRegressionTest, OLSRegressionTest2, MeanRegressionTest,
FilterOLSRegressionTest, PlateauTestCase, ExternalPipetteTestCase,
WaitForTestCase, XYTestCase, FrequencyTestCase,
FrequencyTemplateTestCase, RenumberAliquotTestCase,
ConditionalsTestCase, ParseConditionalsTestCase,
IdentifierTestCase, CommentTemplaterTestCase, FloatfmtTestCase)
for t in tests:
suite.addTest(loader.loadTestsFromTestCase(t))
return suite
def main():
paths.build('_dev')
global log
if not log:
logging_setup('heapy')
log = True
return run()
def main():
paths.build('_dev')
global log
if not log:
logging_setup('heapy')
log = True
return run()
def initialize_version(appname, debug):
root = os.path.dirname(__file__)
if not debug:
add_eggs(root)
else:
build_sys_path()
# can now use pychron.
from pychron.paths import paths
# paths.bundle_root = root
# if '-' in setup_ver:
# setup_ver = setup_ver.split('-')[0]
from pychron.envisage.user_login import get_user
user = get_user()
if not user:
logger.info('user login failed')
os._exit(0)
if appname.startswith('py'):
appname = appname[2:]
pref_path = os.path.join(paths.base, '.enthought',
'pychron.{}.application.{}'.format(appname, user),
'preferences.ini')
from ConfigParser import ConfigParser
cp = ConfigParser()
cp.read(pref_path)
try:
proot = cp.get('pychron.general', 'root_dir')
except BaseException:
proot = '/Users/ross/Pychron'
paths.build(proot)
# build globals
build_globals(debug)
from pychron.core.helpers.logger_setup import logging_setup
from pychron.paths import build_directories
# build directories
build_directories()
# setup logging. set a basename for log files and logging level
logging_setup('pychron', level='DEBUG')
return user
def main():
"""
entry point
"""
from pychron.envisage.pychron_run import launch
from pychron.core.helpers.logger_setup import logging_setup
from pychron.paths import build_directories, paths
# build directories
build_directories(paths)
# from pychron.core.helpers.paths import hidden_dir
# path = os.path.join(hidden_dir, 'version_info')
# a = VersionInfoDisplay(local_path=path,
# src_path=os.path.join(SRC_DIR,
# 'version_info.txt'))
# a.check()
logging_setup('pychron', level='DEBUG')
from pychron.applications.pyexperiment import PyExperiment as app
launch(app)
def main():
"""
entry point
"""
from pychron.envisage.pychron_run import launch
from pychron.core.helpers.logger_setup import logging_setup
from pychron.paths import build_directories, paths
# build directories
build_directories(paths)
# from pychron.core.helpers.paths import hidden_dir
# path = os.path.join(hidden_dir, 'version_info')
# a = VersionInfoDisplay(local_path=path,
# src_path=os.path.join(SRC_DIR,
# 'version_info.txt'))
# a.check()
logging_setup('pychron', level='DEBUG')
from pychron.applications.pyexperiment import PyExperiment as app
launch(app)
def main():
from pychron.paths import paths
paths.build('_dev')
from pychron.core.helpers.logger_setup import logging_setup
from pychron.experiment.automated_run.spec import AutomatedRunSpec
logging_setup('dvcdb')
from pychron.dvc.dvc_database import DVCDatabase
from itertools import groupby
db = DVCDatabase(kind='mysql',
host='localhost',
username='******',
name='pychronmeta',
password='******')
db.connect()
identifiers = ['63290', '63291']
runs = [
AutomatedRunSpec(identifier='63290',
repository_identifier='Cather_McIntoshd')
]
cr = ConflictResolver()
experiments = {}
with db.session_ctx():
cr.available_ids = db.get_repository_identifiers()
eas = db.get_associated_repositories(identifiers)
for idn, exps in groupby(eas, key=lambda x: x[1]):
experiments[idn] = [e[0] for e in exps]
conflicts = []
for ai in runs:
identifier = ai.identifier
es = experiments[identifier]
if ai.repository_identifier not in es:
conflicts.append((ai, es))
if conflicts:
cr.add_conflicts('Foo', conflicts)
if cr.conflicts:
info = cr.edit_traits(kind='livemodal')
if info.result:
cr.apply()
def main():
"""
entry point
"""
from pychron.envisage.pychron_run import launch
from pychron.core.helpers.logger_setup import logging_setup
from pychron.paths import build_directories, paths
# import application
from pychron.applications.pyexperiment import PyExperiment as app
# from pychron.applications.pyvalve import PyValve as app
# build directories
build_directories(paths)
# from pychron.core.helpers.paths import hidden_dir
# path = os.path.join(hidden_dir, 'version_info')
# a = VersionInfoDisplay(local_path=path,
# src_path=os.path.join(SRC_DIR,
# 'version_info.txt'))
# a.check()
logging_setup('pychron', level='DEBUG')
# #===============================================================================
# # test flag
# # set if you want to execute tests after startup
# # explicitly set the flag here once. mode is a readonly property
# #===============================================================================
# from pychron.globals import globalv
# globalv._test = False
# globalv.debug = DEBUG
# from guppy import hpy
# app.hp = hp = hpy()
try:
launch(app)
except RuntimeError:
pass
def main():
"""
entry point
"""
from pychron.envisage.pychron_run import launch
from pychron.core.helpers.logger_setup import logging_setup
from pychron.paths import build_directories, paths
# import application
from pychron.applications.pyexperiment import PyExperiment as app
# from pychron.applications.pyvalve import PyValve as app
# build directories
build_directories(paths)
# from pychron.core.helpers.paths import hidden_dir
# path = os.path.join(hidden_dir, 'version_info')
# a = VersionInfoDisplay(local_path=path,
# src_path=os.path.join(SRC_DIR,
# 'version_info.txt'))
# a.check()
logging_setup('pychron', level='DEBUG')
# #===============================================================================
# # test flag
# # set if you want to execute tests after startup
# # explicitly set the flag here once. mode is a readonly property
# #===============================================================================
# from pychron.globals import globalv
# globalv._test = False
# globalv.debug = DEBUG
# from guppy import hpy
# app.hp = hp = hpy()
try:
launch(app)
except RuntimeError:
pass
# v = View()
# for a in self._get_axes():
#
# a.load_parameters_from_device()
# v = super(AerotechMotionControllerManager, self).traits_view()
# return v
def _motion_controller_default(self):
a = AerotechMotionController(name='unidex')
return a
def initialize(self, *args, **kw):
self.motion_controller.bootstrap()
return True
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('amc')
globalv.show_infos = False
globalv.show_warnings = False
paths.build('_experiment')
amc = AerotechMotionControllerManager()
amc.bootstrap()
amc.configure_traits()
# ============= EOF ====================================
return b
#============= views ===================================
def traits_view(self):
v = View(
Item('control', show_label=False, style='custom'),
# VGroup(
# Item('laser_amps', format_str = '%0.2f', style = 'readonly'),
# Item('laser_temperature', format_str = '%0.2f', style = 'readonly'),
# Item('laser_power', format_str = '%0.2f', style = 'readonly'),
# Item('laser_voltage', format_str = '%0.2f', style = 'readonly'),
# ),
# handler = self.handler_klass,
width=500,
height=500,
resizable=True
)
return v
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('vue_metrix')
v = VueMetrixManager()
v.control.bootstrap()
v.configure_traits()
#============= EOF ====================================
# See the License for the specific language governing permissions and
# limitations under the License.
# ===============================================================================
from __future__ import absolute_import
from __future__ import print_function
import yaml
from mako.template import Template
from traitsui.handler import Controller
from pychron.core.ui import set_qt
set_qt()
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('dcreator')
# ============= enthought library imports =======================
from traits.api import HasTraits, Str
from traitsui.api import View, Item
# ============= standard library imports ========================
# ============= local library imports ==========================
class DeviceModel(HasTraits):
name = Str
def make_from_file(self):
tmp = self.get_template()
p = '/Users/ross/Sandbox/device_creator.yaml'
from pychron.globals import globalv
from pychron.core.ui import set_toolkit
set_toolkit('qt4')
from pychron.paths import paths
paths.build('_unittest')
#build_directories(paths)
from pychron.core.helpers.logger_setup import logging_setup
from pychron.lasers.laser_managers.fusions_diode_manager import FusionsDiodeManager
logging_setup('arar')
import unittest
globalv.ignore_connection_warnings=True
class Diode(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.manager = FusionsDiodeManager()
cls.manager.temperature_controller.bootstrap()
def test_pid_bins_first(self):
temp=300
pd=self.manager._get_pid_bin(temp)
self.assertEqual(pd, [0.0,0.0,0.0])
def test_pid_bins(self):
from pychron.core.ui import set_toolkit
set_toolkit('qt4')
from pychron.paths import paths
paths.build('_unittest')
#build_directories(paths)
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('packager')
from test.database import isotope_manager_factory
from pychron.processing.vcs_data.packager import Packager
import unittest
class ArArAgeCase(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.isotope_man = isotope_manager_factory(name='pychrondata_minnabluff')
cls.isotope_man.db.connect()
man = cls.isotope_man
db = man.db
with db.session_ctx():
ans, tc = db.get_sample_analyses(['AF-72', ], ['Minna Bluff'])
cls.analyses=man.make_analyses(ans)
TEST_PARSE_XLS = False
DEBUGGING = False
# automatically disable debugging if running on a travis ci linux box.
import sys
if sys.platform != 'darwin':
DEBUGGING = False
DBNAME = 'loader.db'
if DEBUGGING:
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('irrad_loader')
def get_data_dir():
op = 'pychron/entry/tests/data'
return mget_data_dir(op)
# if not os.path.isdir(op):
# op = os.path.join('.', 'data')
# return op
def db_factory():
path = os.path.join(get_data_dir(), DBNAME)
db = dvc_db_factory(path)
# from pychron.database.adapters.isotope_adapter import IsotopeAdapter
# from pychron.database.orms.isotope.util import Base
# v = View(Item('records', show_label=False,
# editor=TabularEditor(adapter=SensitivityAdapter(),
# operations=['edit'],
# editable=True,
# )
# ),
#
# HGroup(Item('add_button', show_label=False),
# Item('save_button', show_label=False)),
# resizable=True,
# width=500,
# height=200,
# title='Sensitivity Table'
# )
# return v
class SensitivitySelector(SensitivityEntry):
pass
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
paths.build('_experiment')
logging_setup('runid')
m = SensitivityEntry()
m.configure_traits()
# ============= EOF =============================================
# operations=[]
# ),
# width=0.3,
# ),
Item('image_container', style='custom',
width=0.7,
show_label=False)
),
# Item('container', show_label=False,
# width=0.7,
# editor=ComponentEditor())),
resizable=True,
height=800,
width=900
)
return v
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('image_viewer')
im = ImageBrowser(cache_dir='/Users/ross/Sandbox/cache')
im.load_remote_directory('')
# im.load_from_remote_source('raster2.png')
# im.load_remote_directory()
# im.names = 'snapshot001.jpg,snapshot002.jpg,snapshot003.jpg,snapshot004.jpg'.split(',')
# im.load_from_remote_source('foo')
# im.load_image_from_file('/Users/ross/Sandbox/diodefailsnapshot.jpg')
im.configure_traits()
#============= EOF =============================================
return py
def _title_default(self):
return 'Diode Manager'
def _control_module_manager_default(self):
v = VueMetrixManager() # control = self.control_module)
return v
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
from pychron.initializer import Initializer
logging_setup('fusions diode')
f = FusionsDiodeManager()
f.use_video = True
f.record_brightness = True
ini = Initializer()
a = dict(manager=f, name='FusionsDiode')
ini.add_initialization(a)
ini.run()
# f.bootstrap()
f.configure_traits()
#======================= EOF ============================
# def get_laser_amps(self):
# '''
# '''
Item('tru_tune_band', label='Band'),
Item('tru_tune_gain',
label='Gain',
tooltip='1:Most overshot, 6:Least overshoot'),
enabled_when='enable_tru_tune'),
show_border=True,
label='TRU-TUNE+'),
title='Autotune Configuration',
kind='livemodal')
return v
def control_view(self):
return View(self.get_control_group())
def configure_view(self):
return View(self.get_configure_group())
def _get_autotune_label(self):
return 'On' if self.autotuning else 'Off'
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('watlowezzone')
w = WatlowEZZone(name='temperature_controller',
configuration_dir_name='diode')
w.bootstrap()
w.configure_traits(view='configure_view')
# ============================== EOF ==========================
# klass = VideoStageManager
# else:
# klass = StageManager
#
# args['parent'] = self
# sm = klass(**args)
# return sm
# def _power_calibration_manager_default(self):
# return PowerCalibrationManager(
# parent=self,
# db=self.get_power_calibration_database(),
# application=self.application
# )
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('calib')
lm = LaserManager(name='FusionsDiode')
lm.set_laser_power(10)
# from pychron.lasers.power.power_calibration_manager import PowerCalibrationManager, PowerCalibrationObject
#
# pc=PowerCalibrationObject()
# pc.coefficients=[0.84,-13.76]
#
# pm=PowerCalibrationManager(parent=lm)
# pm._dump_calibration(pc)
# lm.set_laser_power(10)
#============= EOF ====================================
from pychron.core.ui import set_toolkit
set_toolkit('qt4')
from pychron.processing.autoupdate_parser import AutoupdateParser
from test.database import isotope_manager_factory
ISOTOPE_MANAGER = isotope_manager_factory(name='pychrondata_minnabluff')
ISOTOPE_MANAGER.connect()
SKIP_BLANKS = False, 'skip blanks'
SKIP_SIGNALS = False, 'skip signals'
SKIP_FITS = False, 'skip fits'
logging_setup('arar_diff')
class MassSpecPychronIsotopeTestCase(object):
def setUp(self):
pass
def get_expected_value(self, k):
p = self.parser
s = p.samples[self.sample_id]
an = s.analyses[self.analysis_id]
ev = getattr(an, k)
sev = str(ev)
if '.' in sev:
loc.test_image = self.test_image
dx, dy = loc.find(im, frame, dim * self.pxpermm)
# print dx, dy
def setup_image(self):
frame = self.new_image_frame()
im = self.new_image(frame)
self.view_image(im)
return im
def test1():
from pychron.image.video import Video
from pychron.globals import globalv
globalv.video_test = True
globalv.video_test_path = '/Users/ross/Sandbox/pos_err/snapshot007.jpg'
# globalv.video_test_path = '/Users/ross/Sandbox/pos_err/pos_err_53002.jpg'
globalv.video_test_path = '/Users/ross/Sandbox/pos_err/pos_err_221_0-005.jpg'
# globalv.video_test_path = '/Users/ross/Sandbox/pos_err/diodefailsnapshot.jpg'
video = Video()
video.open()
mv = MachineVisionManager(video=video)
mv.configure_traits()
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('mv')
test()
#============= EOF =============================================
r_mkdir(ldir)
paths.log_dir = ldir
paths.root = root
if __name__ == '__main__':
root = os.path.dirname(__file__)
from helpers import add_eggs
add_eggs(root)
build_directories()
from pychron.core.helpers.logger_setup import logging_setup
from pychron.managers.remote_hardware_server_manager import RemoteHardwareServerManager
logging_setup('server')
s = RemoteHardwareServerManager() # handler_klass=AppHandler)
s.load()
s.configure_traits()
os._exit(0)
# launch()
# ============= EOF ====================================
#
# def read_configuration():
# '''
# read the server initialization file in the initialization dir.
#
# ex
# [General]
# servers= server_names
# p = '/Users/ross/Sandbox/pos_err/pos_err_200_0-002.jpg'
p = '/Users/ross/Sandbox/poserror/pos_err_221_0-007.jpg'
p = '/Users/ross/Sandbox/poserror/snapshot009.jpg'
# p = '/Users/argonlab3/Pychron_co2/data/snapshots/pos_err_220_0--001.jpg'
globalv.video_test_path = p
globalv.video_test = True
def _test1_button_fired(self):
self._set_test_image()
self._test1()
if __name__ == '__main__':
logging_setup('mv', use_archiver=False, use_file=False)
t = TestAutocenter()
t.configure_traits(view=View(UItem('test1_button')))
# ============= EOF =============================================
# class TestMVManager(MachineVisionManager):
# step = Button
# test_image = Instance(MVImage, ())
#
# def _step_fired(self):
# self.step_signal.set()
#
# def traits_view(self):
# return View(Item('test'),
# Item('step'),
# Item('image', show_label=False,
# editor=ImageEditor())
# ),
# x=0.05,
# y=0.1,
# #386365
# width=1000,
# height=700,
# resizable=True,
# title=self.title
# )
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('video')
vm = VideoManager()
# p = '/Users/fargo2/Desktop/laser_tray_50.tiff'
# vm.process_image(p, crop=(0, 0, 250, 250))
vm.start()
vm.configure_traits() # view='image_view')
# ================== EOF ========================
# def process_image_dir(self, root):
# '''
# @type root: C{str}
# @param root:
from pychron.core.helpers.iterfuncs import partition
from pychron.core.ui import set_qt
set_qt()
# ============= enthought library imports =======================
# ============= standard library imports ========================
# ============= local library imports ==========================
from pychron.paths import paths
from pychron.geo.shape_file_writer import ShapeFileWriter
from pychron.core.helpers.logger_setup import logging_setup
from pychron.geo.processor import GeoProcessor
paths.build('_dev')
logging_setup('geo')
SamplePoint = namedtuple('SamplePoint', 'x,y,sample,material,labnumber')
src = pyproj.Proj(init='EPSG:4326')
dest = pyproj.Proj(init='EPSG:3031') #,proj='utm', zone='58')
# ellps='WGS84')
def proj_pt(lat, long):
x, y = pyproj.transform(src, dest, long, lat)
return x, y
def get_processor(database='pychrondata_dev'):
geo = GeoProcessor(bind=False, connect=False)
geo.db.trait_set(username='******', host='localhost',
default_directory=paths.irradiation_tray_maps_dir)
if dlg.open() == OK:
if dlg.path:
# verify this is a valid irradiation map file
if parse_irradiation_tray_map(dlg.path) is not None:
db = self.db
with db.session_ctx():
load_irradiation_map(db,
dlg.path,
os.path.basename(dlg.path),
overwrite_geometry=True)
if __name__ == '__main__':
paths.build('_dev')
logging_setup('le')
from pychron.dvc.dvc_database import DVCDatabase
dbt = DVCDatabase(kind='sqlite',
path='/Users/ross/Programming/test3.sqlite')
dbt.connect()
# from pychron.dvc.meta_repo import MetaRepo
mr = MetaRepo()
mr.open_repo(paths.meta_root)
class Demo(HasTraits):
test = Button
traits_view = View('test')
def _test_fired(self):
# print dx, dy
def setup_image(self):
frame = self.new_image_frame()
im = self.new_image(frame)
self.view_image(im)
return im
def test1():
from pychron.image.video import Video
from pychron.globals import globalv
globalv.video_test = True
globalv.video_test_path = '/Users/ross/Sandbox/pos_err/snapshot007.jpg'
# globalv.video_test_path = '/Users/ross/Sandbox/pos_err/pos_err_53002.jpg'
globalv.video_test_path = '/Users/ross/Sandbox/pos_err/pos_err_221_0-005.jpg'
# globalv.video_test_path = '/Users/ross/Sandbox/pos_err/diodefailsnapshot.jpg'
video = Video()
video.open()
mv = MachineVisionManager(video=video)
mv.configure_traits()
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('mv')
test()
#============= EOF =============================================
self._set(0)
def _set(self, v):
self.handle.ask('Set {} {}'.format(self.name, v))
class RemotePyScriptRunner(PyScriptRunner):
handle = None
def __init__(self, host, port, kind, *args, **kw):
super(RemotePyScriptRunner, self).__init__(*args, **kw)
self.handle = EthernetCommunicator()
self.handle.host = host
self.handle.port = port
self.handle.kind = kind
# self.handle.open()
def _get_resource(self, name):
r = RemoteResource()
r.name = name
r.handle = self.handle
return r
def connect(self):
return self.handle.open()
if __name__ == '__main__':
logging_setup('py_runner')
p = PyScriptRunner()
p.configure_traits()
#============= EOF ====================================
import os
import shutil
import sys
from pychron.core.test_helpers import isotope_db_factory, get_data_dir as mget_data_dir, massspec_db_factory
from pychron.experiment.utilities.identifier import make_runid
from pychron.processing.analysis_modifier import AnalysisModifier
__author__ = 'ross'
import unittest
if sys.platform == 'darwin':
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('amod')
def get_data_dir():
op = 'pychron/processing/tests/data'
return mget_data_dir(op)
def pychron_source_factory():
src = os.path.join(get_data_dir(), 'opychrondata.db')
dest = os.path.join(get_data_dir(), 'pychrondata.db')
# duplicate the original database
shutil.copyfile(src, dest)
db = isotope_db_factory(dest, remove=False)
# Item('image', show_label=False,
# editor=ImageEditor())
# ),
# x=0.05,
# y=0.1,
# #386365
# width=1000,
# height=700,
# resizable=True,
# title=self.title
# )
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('video')
vm = VideoManager()
# p = '/Users/fargo2/Desktop/laser_tray_50.tiff'
# vm.process_image(p, crop=(0, 0, 250, 250))
vm.start()
vm.configure_traits() # view='image_view')
#================== EOF ========================
# def process_image_dir(self, root):
# '''
# @type root: C{str}
# @param root:
# '''
# A = 60
# ===============================================================================
# _temp_position = None
# def _get_temp_position(self):
# return self._temp_position
#
# def _set_temp_position(self, v):
# self._temp_position = v
#
# temp_position = property(fget=_get_temp_position,
# fset=_set_temp_position)
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('stage_manager')
name = 'diode'
s = StageManager(
name='{}stage'.format(name),
configuration_dir_name=name,
# parent = DummyParent(),
window_width=945,
window_height=545
)
# from pychron.initializer import Initializer
#
# i = Initializer()
# i.add_initialization(dict(name = 'stage_manager',
# manager = s
# ))
def traits_view(self):
grp = HGroup()
for controller in self.get_controller_names():
grp.content.append(
Item(controller, show_label=False, style='custom'))
v = View(grp)
return v
def get_controller_names(self):
return ['pumpcontroller{}'.format(i + 1) for i in range(4)]
def get_controllers(self):
return [getattr(self, name) for name in self.get_controller_names()]
def load_controllers(self):
for controller in self.get_controller_names():
p = PumpController(name=controller,
configuration_dir_name='pumping')
p.bootstrap()
setattr(self, controller, p)
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
logging_setup(name='pumpman')
c = PumpManager()
c.load_controllers()
c.configure_traits()
# ===============================================================================
# deleters
# ===============================================================================
@delete_one
def delete_analysis(self, rid):
return AnalysesTable, 'RID'
# ===============================================================================
# private
# ===============================================================================
def _get_fittype(self, value):
return self._retrieve_item(FittypeTable, value, key='Label', )
def _add_analysis_position(self, analysis, pi, po):
a = AnalysisPositionTable(Hole=pi, PositionOrder=po)
analysis.positions.append(a)
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('ia')
ia = MassSpecDatabaseAdapter()
ia.connect()
# ia.selector_factory()
# dbs = ia.selector
# dbs.load_recent()
# dbs.configure_traits()
# ==================EOF======================================================
# '''
# v = View()
# for a in self._get_axes():
#
# a.load_parameters_from_device()
# v = super(AerotechMotionControllerManager, self).traits_view()
# return v
def _motion_controller_default(self):
a = AerotechMotionController(name='unidex')
return a
def initialize(self, *args, **kw):
self.motion_controller.bootstrap()
return True
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('amc')
globalv.show_infos = False
globalv.show_warnings = False
paths.build('_experiment')
amc = AerotechMotionControllerManager()
amc.bootstrap()
amc.configure_traits()
# ============= EOF ====================================
import time
from uncertainties import ufloat
from pychron.core.ui import set_toolkit
set_toolkit('qt4')
from pychron.paths import paths, build_directories
paths.build('_unittest')
build_directories(paths)
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('peak_hop')
from threading import Thread
from pychron.experiment.utilities.mass_spec_database_importer import MassSpecDatabaseImporter
from pychron.processing.arar_age import ArArAge
from pychron.spectrometer.ion_optics.ion_optics_manager import IonOpticsManager
from pychron.spectrometer.thermo.manager.argus import ArgusSpectrometerManager
from pychron.experiment.automated_run.automated_run import AutomatedRun
from pychron.experiment.automated_run.spec import AutomatedRunSpec
import unittest
#HOPS = [('Ar40:H1:10, Ar39:AX, Ar36:CDD', 5, 1),
# #('Ar40:L2, Ar39:CDD', 5, 1)
# #('Ar38:CDD', 5, 1)
# ('Ar37:CDD', 5, 1)
# p = '/Users/ross/Sandbox/pos_err/pos_err_200_0-002.jpg'
p = '/Users/ross/Sandbox/poserror/pos_err_221_0-007.jpg'
p = '/Users/ross/Sandbox/poserror/snapshot009.jpg'
p = '/Users/ross/Sandbox/graintest/image0269.png'
# p = '/Users/argonlab3/Pychron_co2/data/snapshots/pos_err_220_0--001.jpg'
globalv.video_test_path = p
globalv.video_test = True
def _test1_button_fired(self):
self._set_test_image()
self._test1()
if __name__ == '__main__':
logging_setup('mv', use_archiver=False, use_file=False)
t = TestAutocenter()
t.init()
t.configure_traits(
view=View(UItem('test1_button'),
UItem('object.display_image.source_frame',
width=254,
height=254,
editor=ImageEditor(
refresh='object.display_image.refresh_needed')),
width=500,
height=300))
# ============= EOF =============================================
# class TestMVManager(MachineVisionManager):
f, s = '<h', 2
m = 2 ** nbits - 1
def vfunc(v):
nd = int(math.log10(m))
return round(v / float(m) * self.max_voltage, nd)
return [vfunc(struct.unpack(f, resp[i:i + s])[0])
for i in range(0, nbytes, s)]
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('adc')
from pychron.paths import paths
paths.build('_dev')
a = ProXRADC(name='ProXRADC')
#a = MultiBankADCExpansion(name='proxr_adc')
a.bootstrap()
#print 'read bank', a.read_bank()
a.read_bank(nbits=12)
a.read_bank(1, nbits=12)
a.read_bank(2, nbits=12)
#print a._communicator.handle
#a.read_device_info()
#print 'read channel 0',a.read_channel(0, nbits=8)
TEST_PARSE_XLS = False
DEBUGGING = False
# automatically disable debugging if running on a travis ci linux box.
import sys
if sys.platform != 'darwin':
DEBUGGING = False
DBNAME = 'loader.db'
if DEBUGGING:
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('irrad_loader')
def get_data_dir():
op = 'pychron/entry/tests/data'
return mget_data_dir(op)
# if not os.path.isdir(op):
# op = os.path.join('.', 'data')
# return op
def db_factory():
path = os.path.join(get_data_dir(), DBNAME)
db = isotope_db_factory(path)
# from pychron.database.adapters.isotope_adapter import IsotopeAdapter
# from pychron.database.orms.isotope.util import Base
return state
def _load_tests(self):
p = os.path.join(paths.root_dir, 'qa_env', 'config.yaml')
if os.path.isfile(p):
with open(p, 'r') as rfile:
return yaml.load(rfile)
else:
self.warning_dialog('No tests. Config file at "{}" required'.format(p))
def _do_test(self, state, test):
self.info('doing test {}'.format(test))
qatest = self._get_test(test)
def _get_test(self, test):
mod = __import__('pychron.qa.test', fromlist=[test])
return getattr(mod, test)()
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
from pychron.paths import paths
paths.build('_dev')
logging_setup('qa')
qar = QARunner()
qar.run()
# ============= EOF =============================================
# n = len(s)
# if n % 2 != 0:
# sn = s[:n / 2 * 2]
# else:
# sn = s
# s = ''.join(self.states)
self.info('states = {}'.format(s))
return s
# v = ValveManager()
# p = os.path.join(paths.extraction_line_dir, 'valves.xml')
# v._load_valves_from_file(p)
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('foo')
f = Foo()
for i in range(10):
r = f.get_states()
time.sleep(2)
# print r, len(r)
#==================== EOF ==================================
# def _get_system_address(self, name):
# return next((h for k, h in self.systems.iteritems() if k == name), None)
#
# def _load_system_dict(self):
# # config = self.configparser_factory()
#
# from pychron.core.helpers.parsers.initialization_parser import InitializationParser
# # ip = InitializationParser(os.path.join(setup_dir, 'initialization.xml'))
configuration_dir_name=self.configuration_dir_name)
return py
def _title_default(self):
return 'Diode Manager'
def _control_module_manager_default(self):
v = VueMetrixManager() # control = self.control_module)
return v
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
from pychron.initializer import Initializer
logging_setup('fusions diode')
f = FusionsDiodeManager()
f.use_video = True
f.record_brightness = True
ini = Initializer()
a = dict(manager=f, name='FusionsDiode')
ini.add_initialization(a)
ini.run()
# f.bootstrap()
f.configure_traits()
#======================= EOF ============================
# def get_laser_amps(self):
# '''
# '''
r_mkdir(ldir)
paths.log_dir = ldir
paths.root = root
if __name__ == '__main__':
root = os.path.dirname(__file__)
from .helpers import add_eggs
add_eggs(root)
build_directories()
from pychron.core.helpers.logger_setup import logging_setup
from pychron.managers.remote_hardware_server_manager import RemoteHardwareServerManager
logging_setup('server')
s = RemoteHardwareServerManager() # handler_klass=AppHandler)
s.load()
s.configure_traits()
os._exit(0)
# launch()
# ============= EOF ====================================
#
# def read_configuration():
# '''
# read the server initialization file in the initialization dir.
#
# ex
# [General]
# servers= server_names
if __name__ == '__main__':
class PermutatorView(HasTraits):
test = Button
def _test_fired(self):
# self.permutator.fits_permutation()
self.permutator.ic_permutation()
def traits_view(self):
v = View('test')
return v
p = Permutator()
p.path = './tests/data/config.yaml'
logging_setup('perm')
from pychron.database.isotope_database_manager import IsotopeDatabaseManager
class Record(object):
analysis_type = 'unknown'
def __init__(self, u):
self.uuid = u
man = IsotopeDatabaseManager(bind=False, connect=False)
db = man.db
db.trait_set(kind='mysql',
host='localhost',
name='pychrondata_dev',
username='******',
def _load_tests(self):
p = os.path.join(paths.root_dir, 'qa_env', 'config.yaml')
if os.path.isfile(p):
with open(p, 'r') as rfile:
return yaml.load(rfile)
else:
self.warning_dialog(
'No tests. Config file at "{}" required'.format(p))
def _do_test(self, state, test):
self.info('doing test {}'.format(test))
qatest = self._get_test(test)
def _get_test(self, test):
mod = __import__('pychron.qa.test', fromlist=[test])
return getattr(mod, test)()
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
from pychron.paths import paths
paths.build('_dev')
logging_setup('qa')
qar = QARunner()
qar.run()
# ============= EOF =============================================
#
# return args
# def _update_parameter_list(self, names, s, l):
# '''
#
# '''
# resp = self._send_query(s, l)
# if resp is not None:
# args = self._parse_parameter_answers(resp, s, l)
# # kw = dict()
# for n, a in zip(names, args):
# v = int(a, 16)
# if isinstance(n, tuple):
# v = n[1](v)
# n = n[0]
# self.trait_set(n=v)
# kw[n] = v
# self.trait_set(**kw)
if __name__ == '__main__':
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('atl')
a = ATLLaserControlUnit(name='ATLLaserControlUnit',
configuration_dir_name='fusions_uv')
a.bootstrap()
a.laser_off()
# ============= EOF ====================================
# limitations under the License.
# ===============================================================================
from pychron.hardware.core.data_helper import make_bitarray
'''
National Control Devices
http://www.controlanything.com/
The Complete ProXR Command Set:
http://www.controlanything.com/Relay/Device/A0010
http://assets.controlanything.com/manuals/ProXR.pdf
'''
from pychron.paths import paths
from pychron.core.helpers.logger_setup import logging_setup
logging_setup('prox')
paths.build('_prox')
# ============= enthought library imports =======================
# ============= standard library imports ========================
# ============= local library imports ==========================
from pychron.hardware.ncd import ON_MAP, OFF_MAP, STATE_MAP
from pychron.hardware.ncd.ncd_device import NCDDevice
class ProXR(NCDDevice):
'''
implement the actuator interface
open_channel
close_channel
get_channel_state