def get_stage_map_names(root=None):
if root is None:
root = paths.map_dir
sms = glob_list_directory(root, '.txt', remove_extension=True)
print(root, sms)
sms = [si for si in sms if not si.endswith('.center')]
us = glob_list_directory(paths.user_points_dir, '.yaml', remove_extension=True)
if us:
sms.extend(us)
return sms
def get_stage_map_names(root=None):
if root is None:
root = paths.map_dir
sms = glob_list_directory(root, '.txt', remove_extension=True)
print(root, sms)
sms = [si for si in sms if not si.endswith('.center')]
us = glob_list_directory(paths.user_points_dir,
'.yaml',
remove_extension=True)
if us:
sms.extend(us)
return sms
def _hops_ext(self):
def hop_action(name):
def func():
return HopsAction(name=name, hop_name=name)
return func
actions = []
for f in glob_list_directory(paths.hops_dir, extension='.yaml', remove_extension=True):
actions.append(SchemaAddition(id='procedure.{}'.format(f),
factory=hop_action(f),
path='MenuBar/procedures.menu/hops.group'))
if actions:
m = SchemaAddition(id='procedures.menu',
before='window.menu',
after='tools.menu',
factory=lambda: SMenu(name='Procedures', id='procedures.menu'),
path='MenuBar')
g = SchemaAddition(id='hops.group',
factory=lambda: SGroup(name='Hops', id='hops.group'),
path='MenuBar/procedures.menu')
actions.insert(0, g)
actions.insert(0, m)
ext = TaskExtension(actions=actions)
return ext
def _scripts_ext(self):
def script_action(name):
def func():
p = os.path.join(paths.spectrometer_scripts_dir, '{}.py'.format(name))
return SpectrometerScriptAction(name=name, script_path=p)
return func
actions = []
for f in glob_list_directory(paths.spectrometer_scripts_dir, extension='.py', remove_extension=True):
actions.append(SchemaAddition(id='spectrometer_script.{}'.format(f),
factory=script_action(f),
path='MenuBar/procedures.menu/spectrometer_script.group'))
if actions:
m = SchemaAddition(id='procedures.menu',
before='window.menu',
after='tools.menu',
factory=lambda: SMenu(name='Procedures', id='procedures.menu'),
path='MenuBar')
g = SchemaAddition(id='spectrometer_script.group',
factory=lambda: SGroup(name='Spectrometer',
id='spectrometer_script.group'),
path='MenuBar/procedures.menu')
actions.insert(0, g)
actions.insert(0, m)
ext = TaskExtension(actions=actions)
return ext
def _scripts_ext(self):
def script_action(name):
def func():
p = os.path.join(paths.spectrometer_scripts_dir, '{}.py'.format(name))
return SpectrometerScriptAction(name=name, script_path=p)
return func
actions = []
for f in glob_list_directory(paths.spectrometer_scripts_dir, extension='.py', remove_extension=True):
actions.append(SchemaAddition(id='spectrometer_script.{}'.format(f),
factory=script_action(f),
path='MenuBar/procedures.menu/spectrometer_script.group'))
if actions:
m = SchemaAddition(id='procedures.menu',
before='window.menu',
after='tools.menu',
factory=lambda: SMenu(name='Procedures', id='procedures.menu'),
path='MenuBar')
g = SchemaAddition(id='spectrometer_script.group',
factory=lambda: SGroup(name='Spectrometer',
id='spectrometer_script.group'),
path='MenuBar/procedures.menu')
actions.insert(0, g)
actions.insert(0, m)
ext = TaskExtension(actions=actions)
return ext
def _hops_ext(self):
def hop_action(name):
def func():
return HopsAction(name=name, hop_name=name)
return func
actions = []
for f in glob_list_directory(paths.hops_dir, extension='.yaml', remove_extension=True):
actions.append(SchemaAddition(id='procedure.{}'.format(f),
factory=hop_action(f),
path='MenuBar/procedures.menu/hops.group'))
if actions:
m = SchemaAddition(id='procedures.menu',
before='window.menu',
after='tools.menu',
factory=lambda: SMenu(name='Procedures', id='procedures.menu'),
path='MenuBar')
g = SchemaAddition(id='hops.group',
factory=lambda: SGroup(name='Hops', id='hops.group'),
path='MenuBar/procedures.menu')
actions.insert(0, g)
actions.insert(0, m)
ext = TaskExtension(actions=actions)
return ext
def _setup_pattern_extensions(self, exts, actions=None):
if actions is None:
actions = []
lactions = []
for f in glob_list_directory(paths.pattern_dir, extension='.lp', remove_extension=True):
actions.append(SchemaAddition(id='pattern.{}'.format(f),
factory=pattern_action(f, self.application, self.name),
path='MenuBar/laser.menu/patterns.menu'))
lactions.append(SchemaAddition(id='pattern.lase.{}'.format(f),
factory=pattern_action(f, self.application, self.name, lase=True),
path='MenuBar/laser.menu/patterns.lase.menu'))
if actions:
actions.insert(0, SchemaAddition(id='patterns.menu',
factory=lambda: SMenu(name='Execute Patterns', id='patterns.menu'),
path='MenuBar/laser.menu'))
lactions.insert(0, SchemaAddition(id='patterns.lase.menu',
factory=lambda: SMenu(name='Execute and Lase Patterns',
id='patterns.lase.menu'),
path='MenuBar/laser.menu'))
exts.append(TaskExtension(actions=lactions))
exts.append(TaskExtension(actions=actions))
else:
self.warning('no patterns scripts located in "{}"'.format(paths.pattern_dir))
def _task_extensions_default(self):
ex = [TaskExtension(actions=[SchemaAddition(id='refresh_canvas',
factory=RefreshCanvasAction,
path='MenuBar/tools.menu'),
SchemaAddition(id='stopwatch',
factory=StopWatchAction,
path='MenuBar/tools.menu')])]
if self.application.get_plugin('pychron.pyscript.plugin'):
actions = []
for f in glob_list_directory(paths.procedures_dir, extension='.py', remove_extension=True):
actions.append(SchemaAddition(id='procedure.{}'.format(f),
factory=procedure_action(f, self.application),
path='MenuBar/procedures.menu/extraction_line.group'))
if actions:
actions.insert(0, SchemaAddition(id='procedures.menu',
before='window.menu',
after='tools.menu',
factory=lambda: SMenu(name='Procedures', id='procedures.menu'),
path='MenuBar'))
actions.insert(1, SchemaAddition(id='extraction_line.group',
factory=lambda: SGroup(name='ExtractionLine',
id='extraction_line.group'),
path='MenuBar/procedures.menu'))
ex.append(TaskExtension(actions=actions))
else:
self.warning('no procedure scripts located in "{}"'.format(paths.procedures_dir))
return ex
def load(self, **kw):
names = glob_list_directory(self.root, remove_extension=True, extension='.p')
if 'Default' not in names:
item = self.item_klass()
item.name = 'Default'
self.dump_item(item)
names = glob_list_directory(self.root, remove_extension=True, extension='.p')
name = 'Default'
p = os.path.join(paths.hidden_dir, add_extension('config', '.p'))
if os.path.isfile(p):
with open(p, 'rb') as rfile:
obj = pickle.load(rfile)
name = obj.get('name', 'Default')
self.names = names
self.active_name = name
self.active_item.trait_set(**kw)
def load(self, **kw):
names = glob_list_directory(self.root, remove_extension=True, extension='.p')
if 'Default' not in names:
item = self.item_klass()
item.name = 'Default'
self.dump_item(item)
names = glob_list_directory(self.root, remove_extension=True, extension='.p')
name = 'Default'
p = os.path.join(paths.hidden_dir, add_extension('config', '.p'))
if os.path.isfile(p):
with open(p, 'rb') as rfile:
obj = pickle.load(rfile)
name = obj.get('name', 'Default')
self.names = names
self.active_name = name
self.active_item.trait_set(**kw)
def load(self):
self.load_molecular_weights()
self.load_detectors()
self.magnet.load()
# load local configurations
self.spectrometer_configurations = glob_list_directory(paths.spectrometer_config_dir, remove_extension=True,
extension='.cfg')
name = get_spectrometer_config_name()
sc, _ = os.path.splitext(name)
self.spectrometer_configuration = sc
p = get_spectrometer_config_path(name)
config = self.get_configuration_writer(p)
return config
def _task_extensions_default(self):
ex = [
TaskExtension(actions=[
SchemaAddition(id='refresh_canvas',
factory=RefreshCanvasAction,
path='MenuBar/tools.menu'),
SchemaAddition(id='stopwatch',
factory=StopWatchAction,
path='MenuBar/tools.menu')
])
]
if self.application.get_plugin('pychron.pyscript.plugin'):
actions = []
for f in glob_list_directory(paths.procedures_dir,
extension='.py',
remove_extension=True):
actions.append(
SchemaAddition(
id='procedure.{}'.format(f),
factory=procedure_action(f, self.application),
path='MenuBar/procedures.menu/extraction_line.group'))
if actions:
actions.insert(
0,
SchemaAddition(id='procedures.menu',
before='window.menu',
after='tools.menu',
factory=lambda: SMenu(name='Procedures',
id='procedures.menu'),
path='MenuBar'))
actions.insert(
1,
SchemaAddition(
id='extraction_line.group',
factory=lambda: SGroup(name='ExtractionLine',
id='extraction_line.group'),
path='MenuBar/procedures.menu'))
ex.append(TaskExtension(actions=actions))
else:
self.warning('no procedure scripts located in "{}"'.format(
paths.procedures_dir))
return ex
def load(self):
self.load_molecular_weights()
self.load_detectors()
self.magnet.load()
# load local configurations
self.spectrometer_configurations = glob_list_directory(
paths.spectrometer_config_dir,
remove_extension=True,
extension='.cfg')
name = get_spectrometer_config_name()
sc, _ = os.path.splitext(name)
self.spectrometer_configuration = sc
p = get_spectrometer_config_path(name)
config = self.get_configuration_writer(p)
return config
def _setup_pattern_extensions(self, exts, actions=None):
if actions is None:
actions = []
lactions = []
for f in glob_list_directory(paths.pattern_dir,
extension='.lp',
remove_extension=True):
actions.append(
SchemaAddition(id='pattern.{}'.format(f),
factory=pattern_action(f, self.application,
self.name),
path='MenuBar/laser.menu/patterns.menu'))
lactions.append(
SchemaAddition(id='pattern.lase.{}'.format(f),
factory=pattern_action(f,
self.application,
self.name,
lase=True),
path='MenuBar/laser.menu/patterns.lase.menu'))
if actions:
actions.insert(
0,
SchemaAddition(id='patterns.menu',
factory=lambda: SMenu(name='Execute Patterns',
id='patterns.menu'),
path='MenuBar/laser.menu'))
lactions.insert(
0,
SchemaAddition(
id='patterns.lase.menu',
factory=lambda: SMenu(name='Execute and Lase Patterns',
id='patterns.lase.menu'),
path='MenuBar/laser.menu'))
exts.append(TaskExtension(actions=lactions))
exts.append(TaskExtension(actions=actions))
else:
self.warning('no patterns scripts located in "{}"'.format(
paths.pattern_dir))
def _load_available_names(self):
ps = glob_list_directory(paths.fits_dir, extension='.yaml', remove_extension=True)
self.available_names = ps
def _get_available_default_fits(self):
return glob_list_directory(paths.fits_dir, extension='.yaml', remove_extension=True)
def _get_available_hops(self):
return glob_list_directory(os.path.join(paths.measurement_dir, 'hops'),
extension='.txt', remove_extension=True)
def _load_names(self):
names = glob_list_directory(self.root, remove_extension=True, extension='.p')
self.names = names
def get_irradiation_holder_names(self):
return glob_list_directory(os.path.join(paths.meta_root,
'irradiation_holders'),
extension='.txt',
remove_extension=True)
def _load_names(self):
self.names = [
n for n in glob_list_directory(
self.persistence_root, extension='.p', remove_extension=True)
if n != 'selected'
]
def load_predefined_templates(self):
self.debug('load predefined templates')
root = PipelineTemplateRoot()
nodes = {n.__name__: n for n in self.nodes}
node_factories = {v.name: v for v in self.node_factories}
groups = []
default = [
('Fit',
(('Define Equilibration', DEFINE_EQUILIBRATION),
('Iso Evo', ISOEVO), ('Blanks', BLANKS), ('IC Factor', ICFACTOR),
('Flux', FLUX), ('Ca Correction Factors', CA_CORRECTION_FACTORS),
('K Correction Factors', K_CORRECTION_FACTORS), ('Audit',
AUDIT))),
('Edit', (('Bulk Edit', BULK_EDIT), )),
('Plot',
(('Ideogram', IDEO), ('CSV Ideogram', CSV_IDEO),
('Interpreted Age Ideogram',
INTERPRETED_AGE_IDEOGRAM), ('Hybrid Ideogram', HYBRID_IDEOGRAM),
('SubGroup Ideogram', SUBGROUP_IDEOGRAM), ('Spectrum', SPEC),
('Spectrum/Isochron', COMPOSITE), ('Series', SERIES),
('InverseIsochron', INVERSE_ISOCHRON),
('XY Scatter', XY_SCATTER), ('Regression', REGRESSION_SERIES),
('Flux Visualization', FLUX_VISUALIZATION), ('Vertical Flux',
VERTICAL_FLUX))),
('Table',
(('SubGrouped Analyses', ANALYSIS_TABLE), ('Grouped Analyses',
SIMPLE_ANALYSIS_TABLE),
('Interpreted Age', INTERPRETED_AGE_TABLE), ('Report', REPORT))),
('History', (('Ideogram', HISTORY_IDEOGRAM), ('Spectrum',
HISTORY_SPECTRUM))),
('Share', (('CSV Analyses Export', CSV_ANALYSES_EXPORT),
('CSV Raw Data Export', CSV_RAW_DATA_EXPORT))),
('Transfer', (('Mass Spec Reduced', MASSSPEC_REDUCED),
('Mass Spec Flux', MASS_SPEC_FLUX)))
]
# predefined_templates contributed to by other plugins
for name, gs in groupby_key(default + self.predefined_templates,
key=itemgetter(0)):
grp = PipelineTemplateGroup(name=name)
templates = [
PipelineTemplate(n, t, nodes, node_factories) for nn, gg in gs
for n, t in gg
]
pp = os.path.join(paths.user_pipeline_template_dir, name.lower())
# add templates from named user directory
for temp in glob_list_directory(pp,
extension='.yaml',
remove_extension=True):
path = os.path.join(pp, '{}.yaml'.format(temp))
templates.append(
PipelineTemplate(temp, path, nodes, node_factories))
grp.templates = templates
groups.append(grp)
# add user templates from user directory
grp = PipelineTemplateGroup(name='User')
user_templates = []
for temp in glob_list_directory(paths.user_pipeline_template_dir,
extension='.yaml',
remove_extension=True):
path = os.path.join(paths.user_pipeline_template_dir,
'{}.yaml'.format(temp))
user_templates.append(
PipelineTemplate(temp, path, nodes, node_factories))
grp.templates = user_templates
groups.append(grp)
# reorder groups
ngroups = []
for gi in DEFAULT_PIPELINE_ROOTS: # ('Fit', 'Plot', 'Table',...)
g = next((gii for gii in groups if gii.name == gi), None)
if g is not None:
ngroups.append(g)
# add in groups contributed to by plugins or from users template directories
for gi in groups:
if gi.name not in DEFAULT_PIPELINE_ROOTS:
ngroups.append(gi)
self.debug('loaded {} user templates'.format(len(user_templates)))
root.groups = ngroups
self.pipeline_template_root = root
def get_irradiation_holder_names(self):
return glob_list_directory(os.path.join(paths.meta_root, 'irradiation_holders'),
extension='.txt',
remove_extension=True)
def _load_names(self):
self.names = [n for n in glob_list_directory(self.persistence_root,
extension='.p',
remove_extension=True) if n != 'selected']
def get_run_blocks():
p = paths.run_block_dir
blocks = glob_list_directory(p, '.txt', remove_extension=True)
return ['RunBlock', LINE_STR] + blocks
def _load_names(self):
names = glob_list_directory(self.root, remove_extension=True, extension='.p')
self.names = names
def _load_pattern_names(self):
self.patterns = glob_list_directory(paths.pattern_dir, extension='.lp', remove_extension=True)
def load_predefined_templates(self):
self.debug('load predefined templates')
root = PipelineTemplateRoot()
nodes = {n.__name__: n for n in self.nodes}
node_factories = {v.name: v for v in self.node_factories}
groups = []
default = [('Fit', (('Define Equilibration', DEFINE_EQUILIBRATION),
('Iso Evo', ISOEVO),
('Blanks', BLANKS),
('IC Factor', ICFACTOR),
('Flux', FLUX),
('Ca Correction Factors', CA_CORRECTION_FACTORS),
('K Correction Factors', K_CORRECTION_FACTORS),
('Bulk Edit', BULK_EDIT),
('Audit', AUDIT))),
('Plot', (('Ideogram', IDEO),
('CSV Ideogram', CSV_IDEO),
('Interpreted Age Ideogram', INTERPRETED_AGE_IDEOGRAM),
('Hybrid Ideogram', HYBRID_IDEOGRAM),
('SubGroup Ideogram', SUBGROUP_IDEOGRAM),
('Spectrum', SPEC),
('Series', SERIES),
('InverseIsochron', INVERSE_ISOCHRON),
('XY Scatter', XY_SCATTER),
('Regression', REGRESSION_SERIES),
('Flux Visualization', FLUX_VISUALIZATION),
('Vertical Flux', VERTICAL_FLUX))),
('Table', (('Analysis', ANALYSIS_TABLE),
('Analysis w/Set IA', ANALYSIS_TABLE_W_IA),
('Interpreted Age', INTERPRETED_AGE_TABLE),
('Report', REPORT))),
('History', (('Ideogram', HISTORY_IDEOGRAM),
('Spectrum', HISTORY_SPECTRUM))),
('Share', (('CSV Analyses Export', CSV_ANALYSES_EXPORT),)),
('Transfer', (('Mass Spec Reduced', MASSSPEC_REDUCED),))]
# predefined_templates contributed to by other plugins
for name, gs in groupby_key(default + self.predefined_templates, key=itemgetter(0)):
grp = PipelineTemplateGroup(name=name)
templates = [PipelineTemplate(n, t, nodes, node_factories) for nn, gg in gs for n, t in gg]
pp = os.path.join(paths.user_pipeline_template_dir, name.lower())
# add templates from named user directory
for temp in glob_list_directory(pp, extension='.yaml', remove_extension=True):
path = os.path.join(pp, '{}.yaml'.format(temp))
templates.append(PipelineTemplate(temp, path, nodes, node_factories))
grp.templates = templates
groups.append(grp)
# add user templates from user directory
grp = PipelineTemplateGroup(name='User')
user_templates = []
for temp in glob_list_directory(paths.user_pipeline_template_dir, extension='.yaml', remove_extension=True):
path = os.path.join(paths.user_pipeline_template_dir, '{}.yaml'.format(temp))
user_templates.append(PipelineTemplate(temp, path, nodes, node_factories))
grp.templates = user_templates
groups.append(grp)
# reorder groups
ngroups = []
for gi in DEFAULT_PIPELINE_ROOTS: #('Fit', 'Plot', 'Table',...)
g = next((gii for gii in groups if gii.name == gi), None)
if g is not None:
ngroups.append(g)
# add in groups contributed to by plugins or from users template directories
for gi in groups:
if gi.name not in DEFAULT_PIPELINE_ROOTS:
ngroups.append(gi)
self.debug('loaded {} user templates'.format(len(user_templates)))
root.groups = ngroups
self.pipeline_template_root = root
def _load_queue_conditionals(self):
root = paths.queue_conditionals_dir
cs = glob_list_directory(root, remove_extension=True)
self.available_conditionals = [NULL_STR] + cs
def _load_available_names(self):
ps = glob_list_directory(paths.fits_dir, extension='.yaml', remove_extension=True)
self.available_names = ps
def _load_queue_conditionals(self):
root = paths.queue_conditionals_dir
cs = glob_list_directory(root, remove_extension=True)
self.available_conditionals = [NULL_STR] + cs
def _load_blocks(self):
p = paths.run_block_dir
blocks = glob_list_directory(p, '.txt', remove_extension=True)
self.blocks = blocks
