def __init__(self, project=None):
""" Initializes the AppModel with the given Project. """
super(AppModel, self).__init__()
self.needs_plot_update = Signal()
self.current_project = project
if project: project.parent = self
def __init__(self, *args, **kwargs):
"""
Constructor takes any of its properties as a keyword argument.
It also support two UUID list keyword arguments:
- phase_uuids: a list of UUID's for the phases in the mixture
- specimen_uuids: a list of UUID's for the specimens in the mixture
These should be *instead* of the phases and specimens keywords.
In addition to the above, the constructor still supports the
following deprecated keywords, mapping to a current keyword:
- phase_indeces: a list of project indices for the phases in the mixture
- specimen_indeces: a list of project indices for the specimens in the mixture
Any other arguments or keywords are passed to the base class.
"""
my_kwargs = self.pop_kwargs(
kwargs, "data_name", "phase_uuids", "phase_indeces",
"specimen_uuids", "specimen_indeces", "data_phases", "data_scales",
"data_bgshifts", "data_fractions", "refine_method",
"data_refine_method", "fractions", "bgshifts", "scales", "phases",
*[
names[0]
for names in type(self).Meta.get_local_storable_properties()
])
super(Mixture, self).__init__(*args, **kwargs)
kwargs = my_kwargs
with self.data_changed.hold():
self._data_object = MixtureData()
self.needs_reset = Signal()
self.needs_update = HoldableSignal()
self.name = self.get_kwarg(kwargs, "New Mixture", "name",
"data_name")
self.auto_run = self.get_kwarg(kwargs, False, "auto_run")
self.auto_bg = self.get_kwarg(kwargs, True, "auto_bg")
# 2D matrix, rows match specimens, columns match mixture 'phases'; contains the actual phase objects
phase_uuids = self.get_kwarg(kwargs, None, "phase_uuids")
phase_indeces = self.get_kwarg(kwargs, None, "phase_indeces")
if phase_uuids is not None:
self.phase_matrix = np.array([[
type(type(self)).object_pool.get_object(uuid)
if uuid else None for uuid in row
] for row in phase_uuids],
dtype=np.object_)
elif phase_indeces and self.parent is not None:
warn(
"The use of object indices is deprecated since version 0.4. Please switch to using object UUIDs.",
DeprecationWarning)
self.phase_matrix = np.array([[
self.parent.phases.get_user_data_from_index(index)
if index != -1 else None for index in row
] for row in phase_indeces],
dtype=np.object_)
else:
self.phase_matrix = np.empty(shape=(0, 0), dtype=np.object_)
# list with actual specimens, indexes match with rows in phase_matrix
specimen_uuids = self.get_kwarg(kwargs, None, "specimen_uuids")
specimen_indeces = self.get_kwarg(kwargs, None, "specimen_indeces")
if specimen_uuids:
self.specimens = [
type(type(self)).object_pool.get_object(uuid)
if uuid else None for uuid in specimen_uuids
]
elif specimen_indeces and self.parent is not None:
warn(
"The use of object indices is deprecated since version 0.4. Please switch to using object UUIDs.",
DeprecationWarning)
self.specimens = [
self.parent.specimens.get_user_data_from_index(index)
if index != -1 else None for index in specimen_indeces
]
else:
self.specimens = list()
# list with mixture phase names, indexes match with cols in phase_matrix
self.phases = self.get_kwarg(kwargs, list(), "phases",
"data_phases")
# list with scale values, indexes match with rows in phase_matrix (= specimens)
self.scales = np.asarray(
self.get_kwarg(kwargs, [1.0] * len(self.specimens), "scales",
"data_scales"))
# list with specimen background shift values, indexes match with rows in phase_matrix (=specimens)
self.bgshifts = np.asarray(
self.get_kwarg(kwargs, [0.0] * len(self.specimens), "bgshifts",
"data_bgshifts"))
# list with phase fractions, indexes match with cols in phase_matrix (=phases)
self.fractions = np.asarray(
self.get_kwarg(kwargs, [0.0] * len(self.phases), "fractions",
"data_fractions"))
# sanity check:
n, m = self.phase_matrix.shape if self.phase_matrix.ndim == 2 else (
0, 0)
if len(self.scales) != n or len(self.specimens) != n or len(
self.bgshifts) != n:
raise IndexError, "Shape mismatch: scales (%d), background shifts (%d) or specimens (%d) list lengths do not match with row count (%d) of phase matrix" % (
len(self.scales), len(self.specimens), len(
self.bgshifts), n)
if len(self.phases) != m or len(self.fractions) != m:
raise IndexError, "Shape mismatch: fractions or phases lists do not match with column count of phase matrix"
self._observe_specimens()
self._observe_phases()
self.optimizer = Optimizer(parent=self)
self.refinement = Refinement(
refine_method_index=self.get_kwarg(kwargs, 0,
"refine_method_index",
"refine_method",
"data_refine_method"),
refine_options=self.get_kwarg(kwargs, dict(),
"refine_options"),
parent=self)
self.update()
self.observe_model(self)
pass # end hold data_changed
def __init__(self, parent=None, *args, **kwargs):
super(ChildModel, self).__init__(*args, **kwargs)
self.removed = Signal()
self.added = Signal()
self.parent = parent
def __init__(self, marker_peaks=[], *args, **kwargs):
super(MineralScorer, self).__init__(*args, **kwargs)
self._matches = []
self.matches_changed = Signal()
self.marker_peaks = marker_peaks # position, intensity
