def remove(self, name):
with open(self.path, 'w') as fp:
for line in fileiter(self.path, strip=True):
if line == name:
continue
else:
fp.write('{}\n'.format(line))
def remove(self, name):
with open(self.path, 'w') as wfile:
for line in fileiter(self.path, strip=True):
if line == name:
continue
else:
wfile.write('{}\n'.format(line))
def setUp(self):
p = '../data/hop.txt'
with open(p, 'r') as rfile:
# lines=filetolist(fp)
# lines = fileiter(fp)
hops = [eval(li) for li in fileiter(rfile)]
# hops = [eval(line) for line in fp if line.strip() and not line.strip().startswith('#')]
self.gen = parse_hops(hops)
def add(self, name):
with open(self.path, 'r') as fp:
exists = next((line for line in fileiter(fp, strip=True)
if line == name), None)
if not exists:
with open(self.path, 'a') as fp:
fp.write('{}\n'.format(name))
def setUp(self):
p = '../data/hop.txt'
with open(p, 'r') as rfile:
# lines=filetolist(fp)
# lines = fileiter(fp)
hops = [eval(li) for li in fileiter(rfile)]
# hops = [eval(line) for line in fp if line.strip() and not line.strip().startswith('#')]
self.gen = parse_hops(hops)
def add(self, name):
with open(self.path, 'r') as rfile:
exists = next(
(line for line in fileiter(rfile, strip=True) if line == name),
None)
if not exists:
with open(self.path, 'a') as wfile:
wfile.write('{}\n'.format(name))
def _open_file(self, p):
if not os.path.isfile(p):
self.debug('{} does not exist'.format(p))
return
if not p.endswith('.py'):
self.debug('{} is not a valid pyscript file'.format(p))
return
self._path = p
valve_re = re.compile(r'''(?P<action>(open|close)+)\((name *= *)*['"]{1}(?P<name>[\w\d])+['"]{1}\,*[\w\s]*\)''')
sleep_re = re.compile(r'''(?P<action>(sleep\())+((?P<value>(\d+.*\d*)))\)''')
info_re = re.compile(r'''(info\()+['"]{1}(?P<value>[\w\s\d'"]*)['"]{1}\)''')
actions = []
with open(p, 'r') as rfile:
_docstring_started = False
has__docstring = False
ds = []
for li in fileiter(rfile):
if not has__docstring and (li.startswith('"""') or li.startswith("'''")):
if _docstring_started:
has__docstring = True
_docstring_started = False
else:
_docstring_started = True
continue
if _docstring_started:
ds.append(li)
continue
sli = li.strip()
m = valve_re.match(sli)
if m:
action = m.group('action')
name = m.group('name')
actions.append(ValveAction(name=action, value=name))
continue
m = sleep_re.match(sli)
if m:
actions.append(SleepAction(value=float(m.group('value'))))
continue
m = info_re.match(sli)
if m:
actions.append(InfoAction(value=m.group('value')))
continue
if li.startswith('def main'):
continue
actions.append(BaseAction(value=sli))
self._docstring = '\n'.join(ds)
self.actions = actions
def load_hops(self, p, *args, **kw):
"""
load the hops definition from a file
:param p: path. absolute or relative to this scripts root
:return: hops
:rtype: list of tuples
"""
if not os.path.isfile(p):
p = os.path.join(self.root, p)
if os.path.isfile(p):
with open(p, 'r') as rfile:
head, ext = os.path.splitext(p)
if ext in ('.yaml', '.yml'):
hops = yaml.load(rfile)
elif ext in ('.txt', ):
def hop_factory(l):
pairs, counts, settle = eval(l)
# isos, dets = zip(*(p.split(':') for p in pairs.split(',')))
# items = (p.split(':') for p in pairs.split(','))
items = []
for p in pairs.split(','):
args = p.split(':')
defl = args[2] if len(args) == 3 else None
items.append((args[0], args[1], defl))
# n = len(isos)
cc = [{
'isotope': i,
'detector': d,
'active': True,
'deflection': de,
'is_baseline': False,
'protect': False
} for i, d, de in items]
h = {
'counts': counts,
'settle': settle,
'cup_configuration': cc,
'positioning': {
'detector': cc[0]['detector'],
'isotope': cc[0]['isotope']
}
}
return h
hops = [hop_factory(li) for li in fileiter(rfile)]
return hops
else:
self.warning_dialog('No such file {}'.format(p))
def _load(self, p):
with open(p, 'r') as fp:
hops = [eval(l) for l in fileiter(fp)]
self.hop_sequence = hs = HopSequence()
for i, (hopstr, cnt, settle) in enumerate(hops):
h = Hop(name=str(i + 1),
counts=cnt, settle=settle, detectors=self.detectors)
h.parse_hopstr(hopstr)
hs.hops.append(h)
hs.label_hops()
self.selected = hs.hops[0]
with open(p, 'r') as fp:
self.text = fp.read()
def update_gitignore(self, *args):
p = os.path.join(self.path, '.gitignore')
# mode = 'a' if os.path.isfile(p) else 'w'
args = list(args)
if os.path.isfile(p):
with open(p, 'r') as rfile:
for line in fileiter(rfile, strip=True):
for i, ai in enumerate(args):
if line == ai:
args.pop(i)
if args:
with open(p, 'a') as wfile:
for ai in args:
wfile.write('{}\n'.format(ai))
self._add_to_repo(p, msg='updated .gitignore')
def update_gitignore(self, *args):
p = os.path.join(self.path, '.gitignore')
# mode = 'a' if os.path.isfile(p) else 'w'
args = list(args)
if os.path.isfile(p):
with open(p, 'r') as rfile:
for line in fileiter(rfile, strip=True):
for i, ai in enumerate(args):
if line == ai:
args.pop(i)
if args:
with open(p, 'a') as wfile:
for ai in args:
wfile.write('{}\n'.format(ai))
self._add_to_repo(p, msg='updated .gitignore')
def _load(self, p):
self.hop_sequence = hs = HopSequence()
if p.endswith('.txt'):
self.use_yaml = False
with open(p, 'r') as rfile:
hops = [eval(l) for l in fileiter(rfile)]
for i, (hopstr, cnt, settle) in enumerate(hops):
h = Hop(name=str(i + 1),
counts=cnt,
settle=settle,
detectors=self.detectors)
h.parse_hopstr(hopstr)
hs.hops.append(h)
hs.label_hops()
self.selected = hs.hops[0]
with open(p, 'r') as rfile:
self.text = rfile.read()
else:
self.use_yaml = True
with open(p, 'r') as rfile:
self.text = rfile.read()
rfile.seek(0)
try:
for i, hop in enumerate(yaml.load(rfile)):
h = Hop(name=str(i + 1),
counts=hop.get('counts', 0),
settle=hop.get('settle', 0),
detectors=self.detectors)
for p in hop.get('cup_configurations'):
pos = Position(detector=p.get('detector', ''),
isotope=p.get('isotope', ''),
active=p.get('active', True),
is_baseline=p.get(
'is_baseline', False),
protect=p.get('protect', False),
deflection=p.get('deflection', ''))
h.positions.append(pos)
hs.hops.append(h)
hs.label_hops()
return True
except yaml.YAMLError:
pass
def _load(self, p):
with open(p, 'r') as rfile:
hops = [eval(l) for l in fileiter(rfile)]
self.hop_sequence = hs = HopSequence()
for i, (hopstr, cnt, settle) in enumerate(hops):
h = Hop(name=str(i + 1),
counts=cnt,
settle=settle,
detectors=self.detectors)
h.parse_hopstr(hopstr)
hs.hops.append(h)
hs.label_hops()
self.selected = hs.hops[0]
with open(p, 'r') as rfile:
self.text = rfile.read()
def load_hops(self, p, *args, **kw):
"""
load the hops definition from a file
:param p: path. absolute or relative to this scripts root
:return: hops
:rtype: list of tuples
"""
if not os.path.isfile(p):
p = os.path.join(self.root, p)
if os.path.isfile(p):
with open(p, 'r') as rfile:
hops = [eval(li) for li in fileiter(rfile)]
return hops
else:
self.warning_dialog('No such file {}'.format(p))
def activated(self):
p = os.path.join(paths.spectrometer_scans_dir, 'scan-005.txt')
g = self.graph
with open(p, 'r') as rfile:
fi = fileiter(rfile, strip=True)
fi.next().split(',')
plot = g.new_plot(padding=[60, 5, 5, 50])
g.set_y_title('Intensity (fA)')
data = [line.split(',') for line in fi]
data = array(data, dtype=float).T
xs = data[0]
for ys in data[1:]:
g.new_series(x=xs, y=ys)
plot.value_scale = 'log'
def _load(self, p):
self.hop_sequence = hs = HopSequence()
if p.endswith('.txt'):
self.use_yaml = False
with open(p, 'r') as rfile:
hops = [eval(l) for l in fileiter(rfile)]
for i, (hopstr, cnt, settle) in enumerate(hops):
h = Hop(name=str(i + 1),
counts=cnt, settle=settle, detectors=self.detectors)
h.parse_hopstr(hopstr)
hs.hops.append(h)
hs.label_hops()
self.selected = hs.hops[0]
with open(p, 'r') as rfile:
self.text = rfile.read()
else:
self.use_yaml = True
with open(p, 'r') as rfile:
self.text = rfile.read()
rfile.seek(0)
try:
for i, hop in enumerate(yaml.load(rfile)):
h = Hop(name=str(i + 1),
counts=hop.get('counts', 0),
settle=hop.get('settle', 0),
detectors=self.detectors)
for p in hop.get('cup_configurations'):
pos = Position(detector=p.get('detector', ''),
isotope=p.get('isotope', ''),
active=p.get('active', True),
is_baseline=p.get('is_baseline', False),
protect=p.get('protect', False),
deflection=p.get('deflection', ''))
h.positions.append(pos)
hs.hops.append(h)
hs.label_hops()
return True
except yaml.YAMLError:
pass
def load_hops(self, p, *args, **kw):
"""
load the hops definition from a file
:param p: path. absolute or relative to this scripts root
:return: hops
:rtype: list of tuples
"""
if not os.path.isfile(p):
p = os.path.join(self.root, p)
if os.path.isfile(p):
with open(p, 'r') as rfile:
head, ext = os.path.splitext(p)
if ext in ('.yaml', '.yml'):
hops = yaml.load(rfile)
elif ext in ('.txt',):
def hop_factory(l):
pairs, counts, settle = eval(l)
# isos, dets = zip(*(p.split(':') for p in pairs.split(',')))
# items = (p.split(':') for p in pairs.split(','))
items = []
for p in pairs.split(','):
args = p.split(':')
defl = args[2] if len(args) == 3 else None
items.append((args[0], args[1], defl))
# n = len(isos)
cc = [{'isotope': i, 'detector': d, 'active': True,
'deflection': de, 'is_baseline': False, 'protect': False} for i, d, de in items]
h = {'counts': counts, 'settle': settle,
'cup_configuration': cc,
'positioning': {'detector': cc[0]['detector'], 'isotope': cc[0]['isotope']}}
return h
hops = [hop_factory(li) for li in fileiter(rfile)]
return hops
else:
self.warning_dialog('No such file {}'.format(p))
def names(self):
with open(self.path, 'r') as fp:
return list(fileiter(fp, strip=True))
def names(self):
with open(self.path, 'r') as rfile:
return list(fileiter(rfile, strip=True))
def names(self):
with open(self.path, 'r') as rfile:
return list(fileiter(rfile, strip=True))