def add_hw_component(self, hw_comp, setting_controller, hidden=None):
""" Add setting entries for the given hardware component
hidden (None or set of str): name of VAs to not show
"""
hidden = HIDDEN_VAS | (hidden or set())
self.setting_controllers.append(setting_controller)
vas_comp = getVAs(hw_comp)
vas_config = get_hw_config(
hw_comp, self._hw_settings_config) # OrderedDict or dict
# Re-order the VAs of the component in the same order as in the config
vas_names = util.sorted_according_to(list(vas_comp.keys()),
list(vas_config.keys()))
for name in vas_names:
try:
if name in hidden:
continue
elif name in vas_config:
va_conf = vas_config[name]
else:
logging.debug("No config found for %s: %s", hw_comp.role,
name)
va_conf = None
va = vas_comp[name]
setting_controller.add_setting_entry(name, va, hw_comp,
va_conf)
except TypeError:
msg = "Error adding %s setting for: %s"
logging.exception(msg, hw_comp.name, name)
def addSettings(self, objWithVA, conf=None):
"""
Adds settings as one widget on a line for each VigilantAttribute (VA) in
the given object. Each setting entry created is added to .entries.
objWithVA (object): an object with VAs.
conf (None or dict of str->config): allows to override the automatic
selection of the VA widget. See odemis.gui.conf.data for documentation.
raise:
LookupError: if no VA is found on the objWithVA
"""
vas = getVAs(objWithVA)
if not vas:
raise LookupError("No VAs found!")
if not conf:
conf = {}
vas_names = util.sorted_according_to(vas.keys(), conf.keys())
for name in vas_names:
va = vas[name]
self.setting_controller.add_setting_entry(name,
va,
None,
conf=conf.get(
name, None))
def addSettings(self, objWithVA, conf=None):
"""
Adds settings as one widget on a line for each VigilantAttribute (VA) in
the given object. Each setting entry created is added to .entries.
objWithVA (object): an object with VAs.
conf (None or dict of str->config): allows to override the automatic
selection of the VA widget. See odemis.gui.conf.data for documentation.
raise:
LookupError: if no VA is found on the objWithVA
"""
vas = getVAs(objWithVA)
if not vas:
raise LookupError("No VAs found!")
if not conf:
conf = {}
vas_names = util.sorted_according_to(vas.keys(), conf.keys())
for name in vas_names:
va = vas[name]
self.setting_controller.add_setting_entry(name, va, None,
conf=conf.get(name, None))
def add_hw_component(self, hw_comp, setting_controller, hidden=None):
""" Add setting entries for the given hardware component
hidden (None or set of str): name of VAs to not show
"""
hidden = HIDDEN_VAS | (hidden or set())
self.setting_controllers.append(setting_controller)
vas_comp = getVAs(hw_comp)
vas_config = get_hw_config(hw_comp, self._hw_settings_config) # OrderedDict or dict
# Re-order the VAs of the component in the same order as in the config
vas_names = util.sorted_according_to(vas_comp.keys(), vas_config.keys())
for name in vas_names:
try:
if name in hidden:
continue
elif name in vas_config:
va_conf = vas_config[name]
else:
logging.debug("No config found for %s: %s", hw_comp.role, name)
va_conf = None
va = vas_comp[name]
setting_controller.add_setting_entry(name, va, hw_comp, va_conf)
except TypeError:
msg = "Error adding %s setting for: %s"
logging.exception(msg, hw_comp.name, name)
def _show_axes(self, sctrl, axes, sclass):
"""
Show axes in settings panel for a given stream.
sctrl (StreamController): stream controller
axes (str -> comp): list of axes to display
sclass (Stream): stream class of (settings) stream
"""
stream_configs = get_stream_settings_config()
stream_config = stream_configs.get(sclass, {})
# Add Axes (in same order as config)
axes_names = util.sorted_according_to(axes.keys(),
list(stream_config.keys()))
for axisname in axes_names:
comp = axes[axisname]
if comp is None:
logging.debug("Skipping axis %s for non existent component",
axisname)
continue
if axisname not in comp.axes:
logging.debug("Skipping non existent axis %s on component %s",
axisname, comp.name)
continue
conf = stream_config.get(axisname)
sctrl.add_axis_entry(axisname, comp, conf)
def _show_mn_axes(self, sctrl):
main_data = self.main_app.main_data
spg = self._getAffectingSpectrograph(main_data.monochromator)
axes = {"wavelength": spg,
"grating": spg,
"slit-in": spg,
"slit-monochromator": spg,
}
stream_configs = get_stream_settings_config()
stream_config = stream_configs.get(MonochromatorSettingsStream, {})
# Add Axes (in same order as config)
axes_names = util.sorted_according_to(axes.keys(), stream_config.keys())
for axisname in axes_names:
comp = axes[axisname]
if comp is None:
logging.debug("Skipping axis %s for non existent component",
axisname)
continue
if axisname not in comp.axes:
logging.debug("Skipping non existent axis %s on component %s",
axisname, comp.name)
continue
conf = stream_config.get(axisname)
sctrl.add_axis_entry(axisname, comp, conf)
def test_simple(self):
in_exp = ((([1, 2, 3], [3, 2, 1]), [3, 2, 1]),
(([1, 2, 3], [4, 2]), [2, 1, 3]),
(([], [4, 2]), []),
((["b", "a"], []), ["b", "a"]),
)
for i, eo in in_exp:
o = util.sorted_according_to(*i)
self.assertEqual(o, eo, "Failed to get correct output for %s" % (i,))
def test_simple(self):
in_exp = (
(([1, 2, 3], [3, 2, 1]), [3, 2, 1]),
(([1, 2, 3], [4, 2]), [2, 1, 3]),
(([], [4, 2]), []),
((["b", "a"], []), ["b", "a"]),
)
for i, eo in in_exp:
o = util.sorted_according_to(*i)
self.assertEqual(o, eo,
"Failed to get correct output for %s" % (i, ))
def _show_axes(self, sctrl, axes, sclass):
"""
Show axes in settings panel for a given stream.
sctrl (StreamController): stream controller
axes (str -> comp): list of axes to display
sclass (Stream): stream class of (settings) stream
"""
stream_configs = get_stream_settings_config()
stream_config = stream_configs.get(sclass, {})
# Add Axes (in same order as config)
axes_names = util.sorted_according_to(axes.keys(), stream_config.keys())
for axisname in axes_names:
comp = axes[axisname]
if comp is None:
logging.debug("Skipping axis %s for non existent component",
axisname)
continue
if axisname not in comp.axes:
logging.debug("Skipping non existent axis %s on component %s",
axisname, comp.name)
continue
conf = stream_config.get(axisname)
sctrl.add_axis_entry(axisname, comp, conf)
def __init__(self, name, data, *args, **kwargs):
"""
:param name: (string)
:param data: (model.DataArray(Shadow) of shape (YX) or list of such DataArray(Shadow)).
The metadata MD_POS, MD_AR_POLE and MD_POL_MODE should be provided
"""
if not isinstance(data, collections.Iterable):
data = [data] # from now it's just a list of DataArray
# TODO: support DAS, as a "delayed loading" by only calling .getData()
# when the projection for the particular data needs to be computed (or
# .raw needs to be accessed?)
# Ensure all the data is a DataArray, as we don't handle (yet) DAS
data = [d.getData() if isinstance(d, model.DataArrayShadow) else d for d in data]
# find positions of each acquisition
# (float, float, str or None)) -> DataArray: position on SEM + polarization -> data
self._pos = {}
sempositions = set()
polpositions = set()
for d in data:
try:
sempos_cur = d.metadata[MD_POS]
# When reading data: floating point error (slightly different keys for same ebeam pos)
# -> check if there is already a position specified, which is very close by
# (and therefore the same ebeam pos) and replace with that ebeam position
# (e.g. all polarization positions for the same ebeam positions will have exactly the same ebeam pos)
for sempos in sempositions:
if almost_equal(sempos_cur[0], sempos[0]) and almost_equal(sempos_cur[1], sempos[1]):
sempos_cur = sempos
break
self._pos[sempos_cur + (d.metadata.get(MD_POL_MODE, None),)] = img.ensure2DImage(d)
sempositions.add(sempos_cur)
if MD_POL_MODE in d.metadata:
polpositions.add(d.metadata[MD_POL_MODE])
except KeyError:
logging.info("Skipping DataArray without known position")
# SEM position VA
# SEM position displayed, (None, None) == no point selected (x, y)
self.point = model.VAEnumerated((None, None),
choices=frozenset([(None, None)] + list(sempositions)))
if self._pos:
# Pick one point, e.g., top-left
bbtl = (min(x for x, y in sempositions if x is not None),
min(y for x, y in sempositions if y is not None))
# top-left point is the closest from the bounding-box top-left
def dis_bbtl(v):
try:
return math.hypot(bbtl[0] - v[0], bbtl[1] - v[1])
except TypeError:
return float("inf") # for None, None
self.point.value = min(sempositions, key=dis_bbtl)
# check if any polarization analyzer data, (None) == no analyzer data (pol)
if polpositions:
# Check that for every position, all the polarizations are available,
# as the GUI expects all the combinations possible, and weird errors
# will happen when one is missing.
for pos in sempositions:
for pol in polpositions:
if pos + (pol,) not in self._pos:
logging.warning("Polarization data is not complete: missing %s,%s/%s",
pos[0], pos[1], pol)
# use first entry in acquisition to populate VA (acq could have 1 or 6 pol pos)
current_pol = util.sorted_according_to(polpositions, POL_POSITIONS)[0]
self.polarization = model.VAEnumerated(current_pol, choices=polpositions)
# Add a polarimetry VA containing the polarimetry image results.
# Note: Polarimetry analysis are only possible if all 6 images per ebeam pos exist.
# Also check if arpolarimetry package can be imported as might not be installed.
if polpositions >= set(POL_POSITIONS) and arpolarimetry:
self.polarimetry = model.VAEnumerated(MD_POL_S0, choices=set(POL_POSITIONS_RESULTS))
if "acq_type" not in kwargs:
kwargs["acq_type"] = model.MD_AT_AR
super(StaticARStream, self).__init__(name, list(self._pos.values()), *args, **kwargs)
