def _save(self, type_='pic', path=None):
"""
"""
if path is None:
path = get_file_path(default_directory=os.path.expanduser('~'))
# from pyface.api import FileDialog, OK
# dlg = FileDialog(action='save as', default_directory=os.path.expanduser('~'))
# if dlg.open() == OK:
# path = dlg.path
# self.status_text = 'Image Saved: %s' % path
if path is not None:
if type_ == 'pdf' or path.endswith('.pdf'):
self._render_to_pdf(filename=path)
else:
# auto add an extension to the filename if not present
# extension is necessary for PIL compression
# set default save type_ DEFAULT_IMAGE_EXT='.png'
# see http://infohost.nmt.edu/tcc/help/pubs/pil/formats.html
for ei in IMAGE_EXTENSIONS:
if path.endswith(ei):
self._render_to_pic(path)
break
else:
path = add_extension(path, DEFAULT_IMAGE_EXT)
self._render_to_pic(path)
def perform(self, event):
hc = HopConfig()
info = hc.edit_traits(kind='livemodal')
if not info.result:
return
p = os.path.join(paths.hops_dir,
add_extension(self.hop_name, ext='.yaml'))
with open(p, 'r') as rfile:
hops = yaml.load(rfile)
prog = self._open_prog(hc.ncycles, hops)
msg_queue = Queue()
app = event.task.application
self._alive = True
producer = Thread(target=self._perform,
args=(app, hc.ncycles, hops, msg_queue))
producer.setDaemon(True)
producer.start()
consumer = Thread(target=self._consumer, args=(prog, msg_queue))
consumer.setDaemon(True)
consumer.start()
def _execute_extraction(self, name, root, kind, new_thread=True,
delay_start=0,
on_completion=None,
context=None):
from pychron.pyscripts.extraction_line_pyscript import ExtractionPyScript
klass = ExtractionPyScript
if kind == 'Laser':
from pychron.pyscripts.laser_pyscript import LaserPyScript
klass = LaserPyScript
script = klass(application=self.application,
root=root,
name=add_extension(name, '.py'),
runner=self._runner)
if script.bootstrap():
if context:
script.setup_context(**context)
else:
script.set_default_context()
try:
script.test()
except Exception, e:
return
self._current_script = script
script.setup_context(extract_device='fusions_diode')
if self.use_trace:
self.active_editor.trace_delay = self.trace_delay
ret = script.execute(trace=self.use_trace, new_thread=new_thread, delay_start=delay_start,
on_completion=on_completion)
return not script.is_canceled() and ret
def get_production(self, pname, **kw):
root = os.path.join(paths.meta_dir, 'productions')
if not os.path.isdir(root):
os.mkdir(root)
p = os.path.join(root, add_extension(pname))
ip = Production(p)
return ip
def _gain_path(self, name):
root = os.path.join(paths.meta_dir, 'spectrometers')
if not os.path.isdir(root):
os.mkdir(root)
p = os.path.join(root, add_extension('{}.gain'.format(name), '.json'))
return p
def dump(self):
p = os.path.join(paths.hidden_dir, add_extension('config', '.p'))
with open(p, 'wb') as wfile:
obj = {'name': self.active_name}
pickle.dump(obj, wfile)
self.dump_item(self.active_item)
def _gain_path(self, name):
root = os.path.join(paths.meta_root, 'spectrometers')
if not os.path.isdir(root):
os.mkdir(root)
p = os.path.join(root, add_extension('{}.gain'.format(name), '.json'))
return p
def get_file_path(root, action='open'):
dlg = FileDialog(action=action,
wildcard=FileDialog.create_wildcard('YAML', '*.yaml *.yml'),
default_directory=root)
if dlg.open():
if dlg.path:
return add_extension(dlg.path, ext=('.yaml', '.yml'))
def dump(self):
p = os.path.join(paths.hidden_dir, add_extension('config', '.p'))
with open(p, 'wb') as wfile:
obj = {'name': self.active_name}
pickle.dump(obj, wfile)
self.dump_item(self.active_item)
def make_gosub(self):
selection = self.control.code.textCursor().selectedText()
dlg = FileDialog(action='save as',
default_directory=os.path.dirname(self.path))
p = None
# root = os.path.dirname(self.path)
# p = os.path.join(root, 'common', 'test_gosub.py')
if dlg.open():
p = dlg.path
if p:
p = add_extension(p, '.py')
# p='/Users/ross/Desktop/foosub.py'
with open(p, 'w') as wfile:
wfile.write('# Extracted Gosub\n')
wfile.write('# Source: from {}\n'.format(self.path))
wfile.write('# Date: {}\n'.format(datetime.now().strftime('%m-%d-%Y %H:%M')))
wfile.write('def main():\n')
for li in selection.split(u'\u2029'):
wfile.write(u' {}\n'.format(li.lstrip()))
p = remove_extension(p)
rp = os.path.relpath(p, self.path)
rp = rp.replace('/', ':')
self.control.code.replace_selection("gosub('{}')".format(rp[3:]))
def dump_item(self, item):
name = item.name
p = os.path.join(self.root, add_extension(name, '.p'))
print('dump itme')
with open(p, 'wb') as wfile:
pickle.dump(item, wfile)
print('sdfasdf')
def _render_to_pdf(self,
save=True,
canvas=None,
filename=None,
dest_box=None):
"""
"""
from chaco.pdf_graphics_context import PdfPlotGraphicsContext
if filename:
# if not filename.endswith('.pdf'):
# filename += '.pdf'
filename = add_extension(filename, ext='.pdf')
gc = PdfPlotGraphicsContext(filename=filename,
pdf_canvas=canvas,
dest_box=dest_box)
pc = self.plotcontainer
# pc.do_layout(force=True)
# pc.use_backbuffer=False
gc.render_component(pc, valign='center')
if save:
gc.save()
# pc.use_backbuffer=True
return gc
def _save_(self, type_='pic', path=None):
"""
"""
if path is None:
dlg = FileDialog(action='save as', default_directory=os.path.expanduser('~'))
if dlg.open() == OK:
path = dlg.path
self.status_text = 'Image Saved: %s' % path
if path is not None:
if type_ == 'pdf' or path.endswith('.pdf'):
self._render_to_pdf(filename=path)
else:
# auto add an extension to the filename if not present
# extension is necessary for PIL compression
# set default save type_ DEFAULT_IMAGE_EXT='.png'
# see http://infohost.nmt.edu/tcc/help/pubs/pil/formats.html
saved = False
for ei in IMAGE_EXTENSIONS:
if path.endswith(ei):
self._render_to_pic(path)
saved = True
break
if not saved:
self._render_to_pic(add_extension(path, DEFAULT_IMAGE_EXT))
def save_csv(record_id, items):
path = os.path.join(paths.data_det_ic_dir, add_extension(record_id, '.csv'))
with open(path, 'w') as wfile:
wrt = csv.writer(wfile, delimiter='\t')
wrt.writerow(['#det', 'intensity', 'err'] + DETECTOR_ORDER)
for i in items:
wrt.writerow(i.to_row())
def _get_save_path(self, path, ext='.pdf'):
if path is None:
dlg = FileDialog(action='save as', default_directory=paths.processed_dir)
if dlg.open():
if dlg.path:
path = add_extension(dlg.path, ext)
return path
def _backup_editor(self, editor):
p = editor.path
p = add_extension(p, '.txt')
if os.path.isfile(p):
# make a backup copy of the original experiment file
bp, pp = backup(p, paths.backup_experiment_dir)
self.info('{} - saving a backup copy to {}'.format(bp, pp))
def get_file_path(root, action='open'):
dlg = FileDialog(action=action,
wildcard=FileDialog.create_wildcard(
'YAML', '*.yaml *.yml'),
default_directory=root)
if dlg.open():
if dlg.path:
return add_extension(dlg.path, ext=('.yaml', '.yml'))
def load_spectrometer_parameters(self, spec_sha):
if spec_sha:
name = add_extension(spec_sha, '.json')
p = repository_path(self.repository_identifier, name)
sd = get_spec_sha(p)
self.source_parameters = sd['spectrometer']
self.gains = sd['gains']
self.deflections = sd['deflections']
def _backup_editor(self, editor):
p = editor.path
p = add_extension(p, '.txt')
if os.path.isfile(p):
# make a backup copy of the original experiment file
bp, pp = backup(p, paths.backup_experiment_dir)
self.info('{} - saving a backup copy to {}'.format(bp, pp))
def get_production(self, irrad, level, **kw):
path = os.path.join(paths.meta_root, irrad, 'productions.json')
obj = dvc_load(path)
pname = obj[level]
p = os.path.join(paths.meta_root, irrad, 'productions', add_extension(pname, ext='.json'))
ip = Production(p)
return pname, ip
def dump_item(self, item):
name = item.name
if not name:
name = 'Default'
p = os.path.join(self.root, add_extension(name, '.p'))
with open(p, 'wb') as wfile:
pickle.dump(item, wfile)
def experiment_blob(self):
path = self.experiment_queue.path
path = add_extension(path, '.txt')
if os.path.isfile(path):
with open(path, 'r') as fp:
return '{}\n{}'.format(path, fp.read())
else:
self.warning('{} is not a valid file'.format(path))
def script_path(self):
if self.name_prefix:
name = '{}{}'.format(self.name_prefix, self.name)
name = add_extension(name, '.py')
p = os.path.join(self._get_root(), name)
return p
def save_as(self):
if self._validate_sequence():
dialog = FileDialog(action='save as', default_directory=paths.hops_dir)
if dialog.open() == OK:
p = dialog.path
p = add_extension(p, '.txt')
self._save_file(p)
self.path = p
def save_csv(record_id, items):
path = os.path.join(paths.data_det_ic_dir,
add_extension(record_id, '.csv'))
with open(path, 'w') as wfile:
wrt = csv.writer(wfile, delimiter='\t')
wrt.writerow(['#det', 'intensity', 'err'] + DETECTOR_ORDER)
for i in items:
wrt.writerow(i.to_row())
def script_path(self):
if self.name_prefix:
name = '{}{}'.format(self.name_prefix, self.name)
name = add_extension(name, '.py')
p = os.path.join(self._get_root(), name)
return p
def _prepare(self, extraction_script):
extraction_script = add_extension(extraction_script)
task = self.pyscript_task
root, name = os.path.split(extraction_script)
ctx = {'analysis_type': 'blank' if 'blank' in name else 'unknown'}
ret = task.execute_script(name, root, new_thread=False, context=ctx)
self.info('Extraction script {} {}'.format(name, 'completed successfully' if ret else 'failed'))
return ret
def load_spectrometer_parameters(self, spec_sha):
if spec_sha:
name = add_extension(spec_sha, '.json')
p = repository_path(self.repository_identifier, name)
sd = get_spec_sha(p)
self.source_parameters = sd['spectrometer']
self.gains = sd['gains']
self.deflections = sd['deflections']
def save_as(self):
if self._validate_sequence():
dialog = FileDialog(action='save as',
default_directory=paths.hops_dir)
if dialog.open() == OK:
p = dialog.path
p = add_extension(p, '.txt')
self._save_file(p)
self.path = p
def get_production(self, irrad, level, **kw):
path = os.path.join(paths.meta_root, irrad, 'productions.json')
obj = dvc_load(path)
pname = obj[level]
p = os.path.join(paths.meta_root, irrad, 'productions',
add_extension(pname, ext='.json'))
ip = Production(p)
return pname, ip
def experiment_blob(self):
path = self.experiment_queue.path
path = add_extension(path, '.txt')
if os.path.isfile(path):
with open(path, 'r') as fp:
return '{}\n{}'.format(path,
fp.read())
else:
self.warning('{} is not a valid file'.format(path))
def make_irradiation_load_template(self):
path = self.save_file_dialog()
if path:
# p = '/Users/ross/Sandbox/irrad_load_template.xls'
path = add_extension(path, ".xls")
self.manager.make_irradiation_load_template(path)
self.information_dialog("Template saved to {}".format(path))
self.view_xls(path)
def export_data(self, path=None, plotid=None):
"""
"""
if path is None:
path = get_file_path()
if path is not None:
path = add_extension(path, '.csv')
self._export_data(path, plotid)
def make_irradiation_load_template(self):
path = self.save_file_dialog()
if path:
# p = '/Users/ross/Sandbox/irrad_load_template.xls'
path = add_extension(path, '.xls')
self.manager.make_irradiation_load_template(path)
self.information_dialog('Template saved to {}'.format(path))
self.view_xls(path)
def image(name):
name = add_extension(name, '.png')
for si in paths.image_search_path:
if si and os.path.isfile(os.path.join(si, name)):
break
else:
print 'no image for "{}"'.format(name)
return ImageResource(name=name, search_path=paths.image_search_path)
def get(self, name):
p = os.path.join(paths.peak_center_config_dir, add_extension(name, '.p'))
if os.path.isfile(p):
with open(p, 'rb') as rfile:
obj = pickle.load(rfile)
else:
obj = self.item_klass()
return obj
def export_data(self, path=None, plotid=None):
"""
"""
if path is None:
path = self._path_factory()
if path is not None:
path = add_extension(path, '.csv')
self._export_data(path, plotid)
def _prepare(self, extraction_script):
extraction_script = add_extension(extraction_script)
task = self.pyscript_task
root, name = os.path.split(extraction_script)
ctx = {'analysis_type': 'blank' if 'blank' in name else 'unknown'}
ret = task.execute_script(name, root, new_thread=False, context=ctx)
self.info('Extraction script {} {}'.format(
name, 'completed successfully' if ret else 'failed'))
return ret
def _stage_map_name_changed(self, new):
if new:
self.debug('setting stage map to {}'.format(new))
sm = self.stage_map_klass(file_path=os.path.join(self.root, add_extension(new, '.txt')))
self.stage_map = sm
self.tray_calibration_manager.load_calibration(stage_map=new)
self.canvas.set_map(sm)
self.canvas.request_redraw()
def add_production_to_irradiation(self, irrad, name, params, add=True, commit=False):
self.debug('adding production {} to irradiation={}'.format(name, irrad))
p = os.path.join(paths.meta_root, irrad, 'productions', add_extension(name, '.json'))
prod = Production(p, new=not os.path.isfile(p))
prod.update(params)
prod.dump()
if add:
self.add(p, commit=commit)
def export_data(self, path=None, plotid=None):
"""
"""
if path is None:
path = self._path_factory()
if path is not None:
path = add_extension(path, '.csv')
self._export_data(path, plotid)
def _get_gosub_text(self, gosub):
root = os.path.dirname(self.path)
new = gosub.replace('/', ':')
new = add_extension(new, '.py')
paths = new.split(':')
p = os.path.join(root, *paths)
if os.path.isfile(p):
with open(p, 'r') as rfile:
return rfile.read()
def _script_factory(self, script_name):
if os.path.isfile(os.path.join(paths.extraction_dir, add_extension(script_name, '.py'))):
runner = self.application.get_service('pychron.extraction_line.ipyscript_runner.IPyScriptRunner')
script = ExtractionPyScript(root=paths.extraction_dir,
name=script_name,
manager=self.extraction_line_manager,
allow_lock=True,
runner=runner)
return script
def image(name):
name = add_extension(name, '.png')
for si in paths.image_search_path:
if si and os.path.isfile(os.path.join(si, name)):
break
else:
print('no image for "{}"'.format(name))
return ImageResource(name=name, search_path=paths.image_search_path)
def export_data(self, path=None, plotid=None):
"""
"""
if path is None:
path = get_file_path()
if path is not None:
path = add_extension(path, '.csv')
self._export_data(path, plotid)
def path(self):
name = self.name
if not name or name == 'Untitled':
path, _ = unique_path2(paths.table_dir,
'Untitled',
extension='.xlsx')
else:
path = os.path.join(paths.table_dir,
add_extension(name, ext='.xlsx'))
return path
def save_sensitivities(self, sens):
ps = []
for k, v in sens.items():
root = os.path.join(paths.meta_root, 'spectrometers')
p = os.path.join(root, add_extension('{}.sens'.format(k), '.json'))
dvc_dump(v, p)
ps.append(p)
if self.add_paths(ps):
self.commit('Updated sensitivity')
def save_file_dialog(self, ext=None, **kw):
if "default_directory" not in kw:
kw["default_directory"] = self.default_directory
dialog = FileDialog(parent=self.window.control, action="save as", **kw)
if dialog.open() == OK:
path = dialog.path
if path:
if ext is None:
ext = self._default_extension
return add_extension(path, ext=ext)
def add_irradiation_holder(self, name, blob, commit=False, overwrite=False):
p = os.path.join(paths.meta_dir, 'irradiation_holders', add_extension(name))
if not os.path.isfile(p) or overwrite:
with open(p, 'w') as wfile:
holes = list(iter_geom(blob))
n = len(holes)
wfile.write('{},0.0175\n'.format(n))
for idx, (x, y, r) in holes:
wfile.write('{:0.4f},{:0.4f},{:0.4f}\n'.format(x, y, r))
self.add(p, commit=commit)
def _save_button_fired(self):
from pyface.file_dialog import FileDialog
dialog = FileDialog(action='save as',
default_directory=os.path.join(os.path.expanduser('~')))
from pyface.constant import OK
if dialog.open() == OK:
path = dialog.path
if path:
self.selected_image.save(add_extension(path, '.jpg'))
def _get_experiment(self, tokens):
if not tokens:
name = "Current Experiment"
else:
name = " ".join(tokens)
p = os.path.join(paths.experiment_dir, add_extension(name))
if not os.path.isfile(p):
raise InvalidExperiment(name)
return name, p
def save_file_dialog(self, ext=None, **kw):
if 'default_directory' not in kw:
kw['default_directory'] = self.default_directory
dialog = FileDialog(parent=self.window.control, action='save as', **kw)
if dialog.open() == OK:
path = dialog.path
if path:
if ext is None:
ext = self._default_extension
return add_extension(path, ext=ext)
def _selected_pattern_name_changed(self, new):
if not new:
return
p = add_extension(new, '.lp')
if self.save_enabled:
if self.confirmation_dialog('You have unsaved changes. Are you sure you want to continue?'):
self.load_pattern(p)
else:
self.load_pattern(p)
def get(self, name):
p = os.path.join(paths.peak_center_config_dir,
add_extension(name, '.p'))
if os.path.isfile(p):
with open(p, 'rb') as rfile:
obj = pickle.load(rfile)
else:
obj = self.item_klass()
return obj
def _get_experiment(self, tokens):
if not tokens:
name = 'Current Experiment'
else:
name = ' '.join(tokens)
p = os.path.join(paths.experiment_dir, add_extension(name))
if not os.path.isfile(p):
raise InvalidExperiment(name)
return name,p