def test_reproduceTypedValue_good(self):
"""
check various inputs and compare to expected output
for values that should work
"""
lva = model.ListVA([12, -3])
# example value / input str / expected output
tc = [(3, "-1561", -1561),
(-9.3, "0.123", 0.123),
(False, "true", True),
({"a": 12.5, "b": 3.}, "c:6,d:1.3", {"c": 6., "d":1.3}),
((-5, 0, 6), " 9, -8", (9, -8)), # we don't force to be the same size
((1.2, 0.0), "0, -8, -15e-3, 6.", (0.0, -8.0, -15e-3, 6.0)),
([1.2, 0.0], "0.1", [0.1]),
(("cou", "bafd"), "aa,bb", ("aa", "bb")),
# more complicated but nice to support for the user
((1200, 256), "256 x 256 px", (256, 256)),
((1.2, 256), " 21 x 0.2 m", (21, 0.2)),
([-5, 0, 6], "9,, -8", [9, -8]),
((1.2, 0.0), "", tuple()),
(lva.value, "-1, 63, 12", [-1, 63, 12]), #NotifyingList becomes a list
((-5, 0, 6), "9.3, -8", (9, 3, -8)), # maybe this shouldn't work?
# Note: we don't support SI prefixes
(("cou",), "aa, c a", ("aa", " c a")), # TODO: need to see if spaces should be kept or trimmed
]
for ex_val, str_val, expo in tc:
out = reproduceTypedValue(ex_val, str_val)
self.assertEqual(out, expo,
"Testing with %s / '%s' -> %s" % (ex_val, str_val, out))
def main(args):
"""
Handles the command line arguments
args is the list of arguments passed
return (int): value to return to the OS as program exit code
"""
# arguments handling
parser = argparse.ArgumentParser(description=
"SEM fluorescence bleaching map")
parser.add_argument("--dt", "-d", dest="dt", type=float, required=True,
help="ebeam (bleaching) dwell time in s (for each sub-pixel)")
parser.add_argument("--pxs", "-p", dest="pxs", type=float, required=True,
help="distance between 2 spots in nm")
parser.add_argument("--subpx", "-s", dest="subpx", type=int, default=1,
help="number of sub-pixels scanned by the ebeam for "
"each pixel acquired by the CCD. Must be a the "
"square of an integer.")
parser.add_argument("--roi", dest="roi", required=True,
help="e-beam ROI positions (ltrb, relative to the SEM "
"field of view)")
parser.add_argument("--output", "-o", dest="filename", required=True,
help="name of the file output")
options = parser.parse_args(args[1:])
roi = driver.reproduceTypedValue([1.0], options.roi)
if not all(0 <= r <= 1 for r in roi):
raise ValueError("roi values must be between 0 and 1")
a = Acquirer(options.dt, roi, options.pxs * 1e-9, options.subpx)
a.acquire(options.filename)
def main(args):
"""
Handles the command line arguments
args is the list of arguments passed
return (int): value to return to the OS as program exit code
"""
# arguments handling
parser = argparse.ArgumentParser(description=
"AR spectral acquisition")
parser.add_argument("-x", dest="X", type=int, required=True,
help="shape of AR image on the X axis")
parser.add_argument("-y", dest="Y", type=int, required=True,
help="shape of AR image on the Y axis")
parser.add_argument("--spot", dest="spot", required=True,
help="e-beam spot position")
parser.add_argument("--drift", "-d", dest="drift", type=float, default=None,
help="time between 2 drift corrections")
parser.add_argument("--anchor", dest="anchor", default=None,
help="e-beam spot position")
parser.add_argument("--output", "-o", dest="filename", required=True,
help="name of the file output")
options = parser.parse_args(args[1:])
shape = (options.X, options.Y)
if shape[0] <= 0 or shape[1] <= 0:
raise ValueError("X/Y must be > 0")
spot = driver.reproduceTypedValue([1.0], options.spot)
if not (0 <= spot[0] <= 1 and 0 <= spot[1] <= 1):
raise ValueError("spot must be between 0 and 1")
if options.anchor is None or options.drift is None:
anchor = None
else:
anchor = driver.reproduceTypedValue([1.0], options.anchor)
a = Acquirer()
a.acquire_arcube(shape, spot, dperiod=options.drift, anchor=anchor,
filename=options.filename)
def main(args):
"""
Handles the command line arguments
args is the list of arguments passed
return (int): value to return to the OS as program exit code
"""
# arguments handling
parser = argparse.ArgumentParser(description=
"AR spectral acquisition")
parser.add_argument("-x", dest="X", type=int, required=True,
help="shape of AR image on the X axis")
parser.add_argument("-y", dest="Y", type=int, required=True,
help="shape of AR image on the Y axis")
parser.add_argument("--spot", dest="spot", required=True,
help="e-beam spot position")
parser.add_argument("--drift", "-d", dest="drift", type=float, default=None,
help="time between 2 drift corrections")
parser.add_argument("--anchor", dest="anchor", default=None,
help="e-beam spot position")
parser.add_argument("--output", "-o", dest="filename", required=True,
help="name of the file output")
options = parser.parse_args(args[1:])
shape = (options.X, options.Y)
if shape[0] <= 0 or shape[1] <= 0:
raise ValueError("X/Y must be > 0")
spot = driver.reproduceTypedValue([1.0], options.spot)
if not (0 <= spot[0] <= 1 and 0 <= spot[1] <= 1):
raise ValueError("spot must be between 0 and 1")
if options.anchor is None or options.drift is None:
anchor = None
else:
anchor = driver.reproduceTypedValue([1.0], options.anchor)
a = Acquirer()
a.acquire_arcube(shape, spot, dperiod=options.drift, anchor=anchor,
filename=options.filename)
def test_reproduceTypedValue_bad(self):
"""
check various inputs and compare to expected output
for values that should raise an exception
"""
# example value / input str
tc = [(3, "-"),
(-9, "0.123"),
(False, "56"),
({"a": 12.5, "b": 3.}, "6,1.3"),
(9.3, "0, 123"),
]
for ex_val, str_val in tc:
with self.assertRaises((ValueError, TypeError)):
out = reproduceTypedValue(ex_val, str_val)
def main(args):
"""
Handles the command line arguments
args is the list of arguments passed
return (int): value to return to the OS as program exit code
"""
# arguments handling
parser = argparse.ArgumentParser(description=
"SEM fluorescence bleaching map")
parser.add_argument("--dt", "-d", dest="dt", type=float, required=True,
help="ebeam (bleaching) dwell time in s (for each sub-pixel)")
parser.add_argument("--pxs", "-p", dest="pxs", type=float, required=True,
help="distance between 2 spots in nm")
parser.add_argument("--subpx", "-s", dest="subpx", type=int, default=1,
help="number of sub-pixels scanned by the ebeam for "
"each pixel acquired by the CCD. Must be a the "
"square of an integer.")
parser.add_argument("--roi", dest="roi", required=True,
help="e-beam ROI positions (ltrb, relative to the SEM "
"field of view)")
parser.add_argument("--lpower", "-lp", dest="lpower", type=float, default=0.02,
help="excitation light power on the first fluorescence pixel. "
"Choose the value between 0.004 and 0.4 (in W). "
"Power will be gradually scaled up to the maximum (0.4 W) "
"on the last pixel to compensate photobleaching effect "
"in the signal drop.")
parser.add_argument("--output", "-o", dest="filename", required=True,
help="name of the file output")
options = parser.parse_args(args[1:])
roi = driver.reproduceTypedValue([1.0], options.roi)
if not all(0 <= r <= 1 for r in roi):
raise ValueError("roi values must be between 0 and 1")
a = Acquirer(options.dt, roi, options.pxs * 1e-9, options.subpx, options.lpower)
a.acquire(options.filename)
def main(args):
"""
Handles the command line arguments
args is the list of arguments passed
return (int): value to return to the OS as program exit code
"""
# arguments handling
parser = argparse.ArgumentParser(description=
"SEM fluorescence bleaching map")
parser.add_argument("--dt", "-d", dest="dt", type=float, required=True,
help="ebeam (bleaching) dwell time in s (for each sub-pixel)")
parser.add_argument("--pxs", "-p", dest="pxs", type=float, required=True,
help="distance between 2 spots in nm")
parser.add_argument("--subpx", "-s", dest="subpx", type=int, default=1,
help="number of sub-pixels scanned by the ebeam for "
"each pixel acquired by the CCD. Must be a the "
"square of an integer.")
parser.add_argument("--roi", dest="roi", required=True,
help="e-beam ROI positions (ltrb, relative to the SEM "
"field of view)")
parser.add_argument("--lpower", "-lp", dest="lpower", type=float, default=0.02,
help="excitation light power on the first fluorescence pixel. "
"Choose the value between 0.004 and 0.4 (in W). "
"Power will be gradually scaled up to the maximum (0.4 W) "
"on the last pixel to compensate photobleaching effect "
"in the signal drop.")
parser.add_argument("--output", "-o", dest="filename", required=True,
help="name of the file output")
options = parser.parse_args(args[1:])
roi = driver.reproduceTypedValue([1.0], options.roi)
if not all(0 <= r <= 1 for r in roi):
raise ValueError("roi values must be between 0 and 1")
a = Acquirer(options.dt, roi, options.pxs * 1e-9, options.subpx, options.lpower)
a.acquire(options.filename)