def _repopulate(self):
self._clear()
for structure_idx, structure in enumerate(self._structures):
self._grid.addWidget(QtGui.QLabel(structure.display_name), 0,
structure_idx + 1)
for param_idx, param in enumerate(self._params):
self._grid.addWidget(QtGui.QLabel(param.display_name),
param_idx + 1, 0)
for structure_idx, structure in enumerate(self._structures):
# The initial value for a parameter in a structure is the previous value set (if any),
# the default value for that structure (if any), the default value for the parent
# structure (if any), the generic parameter default (if any), and if none of the above, zero.
if structure.name in self._values and param.name in self._values[
structure.name]:
initial = self._values[structure.name][param.name]
elif structure.name in param.kwargs.get("struc_defaults", {}):
initial = param.kwargs["struc_defaults"][structure.name]
elif structure.kwargs.get("parent_struc",
"") in param.kwargs.get(
"struc_defaults", {}):
initial = param.kwargs["struc_defaults"][
structure.kwargs.get("parent_struc", "")]
else:
initial = [param.kwargs.get("default", 0.0)]
if isinstance(initial, (int, float)):
initial = [initial]
self._grid.addWidget(
NumberListOption(initial=initial,
intonly=param.kwargs.get(
"intonly", False),
load_btn=False), param_idx + 1,
structure_idx + 1)
def _refresh_gui(self):
options = dict(self.model.options)
self.gui.clear()
for struc in self.model.default_strucs:
data_opt = self.gui.add("%s map" % struc.name.upper(), DataOption(self.model._ivm, explicit=True), checked=True, enabled=struc.name in options["pvmaps"], key=struc.name)
data_opt.value = options["pvmaps"].get(struc.name, None)
for struc in options["additional"].values():
del_btn = self._struc_delete_btn(struc)
display_type = {"add" : "map", "embed" : "embedding", "act" : "mask"}.get(struc["struc_type"], "map")
data_opt = self.gui.add("%s %s" % (struc["name"], display_type), DataOption(self.model._ivm, explicit=True, rois=True), del_btn, key=struc["name"])
data_opt.value = struc.get("pvmap", None)
res_opts = options.get("resampling", {})
self.gui.add("Resampling", ChoiceOption(["Downsample", "From another data set", "Specified resolution"], ["down", "data", "res"],
default=res_opts.get("type", "res")), checked=True, enabled="type" in res_opts, key="type")
self.gui.add("Output space from", DataOption(self.ivm), key="grid")
self.gui.add("Output resample factor", NumericOption(intonly=True, minval=1, maxval=10, default=2), key="factor")
self.gui.add("Voxel sizes (mm)", NumberListOption(load_btn=False), key="voxel-sizes")
for opt in ("grid", "factor", "voxel-sizes"):
if opt in res_opts:
self.gui.option(opt).value = res_opts[opt]
self.gui.add(None, RunButton("Add user-defined structure", callback=self._add_embedding), key="add_embedding")
self._update_resamp_visibility()
def _update_params(self):
FabberWidget._update_params(self)
self.param_values_box.clear()
for param in self._fabber_params:
current_values = self._param_test_values.get(param, [1.0])
self.param_values_box.add(param, NumberListOption(initial=current_values))
self._param_test_values[param] = current_values
# Remove references to parameters which no longer exist
for param in list(self._param_test_values.keys()):
if param not in self._fabber_params:
del self._param_test_values[param]
def __init__(self, ivm):
self.model = DceDataModel(ivm)
self.gui = OptionBox()
self.gui.add(
"Model",
ChoiceOption([
"Standard Tofts model", "Extended Tofts model (ETM)",
"2 Compartment exchange model",
"Compartmental Tissue Update (CTU) model",
"Adiabatic Approximation to Tissue Homogeneity (AATH) Model"
], ["dce_tofts", "dce_ETM", "dce_2CXM", "dce_CTU", "dce_AATH"]),
key="model")
self.gui.add("Contrast agent R1 relaxivity (l/mmol s)",
NumericOption(minval=0, maxval=10, default=3.7),
key="r1")
self.gui.add("Flip angle (\N{DEGREE SIGN})",
NumericOption(minval=0, maxval=90, default=12),
key="fa")
self.gui.add("TR (ms)",
NumericOption(minval=0, maxval=10, default=4.108),
key="tr")
self.gui.add("Time between volumes (s)",
NumericOption(minval=0, maxval=30, default=12),
key="delt")
self.gui.add("AIF",
ChoiceOption([
"Population (Orton 2008)", "Population (Parker)",
"Measured DCE signal", "Measured concentration curve"
], ["orton", "parker", "signal", "conc"]),
key="aif")
self.gui.add("Number of volumes",
NumericOption(minval=0,
maxval=100,
default=20,
intonly=True),
key="nt")
self.gui.add("Bolus injection time (s)",
NumericOption(minval=0, maxval=60, default=30),
key="tinj")
self.gui.add("AIF data values",
NumberListOption([
0,
]),
key="aif-data")
self.gui.add("Arterial transit time (s)",
NumericOption(minval=0, maxval=1.0, default=0),
key="delay")
self.gui.option("model").sig_changed.connect(self._model_changed)
self.gui.option("aif").sig_changed.connect(self._aif_changed)
self._aif_changed()
self._model_changed()
self.gui.sig_changed.connect(self._update_options)
self._update_options()
def __init__(self, ivm):
self.model = DscDataModel(ivm)
self.gui = OptionBox()
self.gui.add("Time between volumes (s)",
NumericOption(minval=0, maxval=5, default=1.0),
key="delt")
self.gui.add("TE (s)",
NumericOption(minval=0, maxval=5, default=1.0),
key="te")
self.gui.add("AIF", NumberListOption(), key="aif")
self.gui.sig_changed.connect(self._update_options)
self._update_options()
def __init__(self, ivm):
self.model = AslDataModel(ivm)
self.gui = OptionBox()
self.gui.add("Bolus duration",
NumericOption(minval=0, maxval=5, default=1.8),
key="tau")
self.gui.add("Labelling",
ChoiceOption(["CASL/pCASL", "PASL"], [True, False],
default=True),
key="casl")
self.gui.add("PLDs",
NumberListOption([0.25, 0.5, 0.75, 1.0, 1.25, 1.5]),
key="plds")
self.gui.add("Time per slice (ms)",
NumericOption(minval=0,
maxval=1000,
default=0,
intonly=True),
key="slicedt")
self.gui.add("Data format",
ChoiceOption(["Differenced data", "Label/Control pairs"],
["diff", "tc"]),
key="iaf")
self.gui.add("Repeats",
NumericOption(minval=1,
maxval=100,
default=1,
intonly=True),
key="repeats")
self.gui.add("Group by",
ChoiceOption(["PLDs", "Repeats"], ["tis", "rpt"]),
key="ibf")
self.gui.add("Inversion efficiency",
NumericOption(minval=0.5, maxval=1.0, default=0.85),
key="alpha")
self.gui.add("M0",
NumericOption(minval=0, maxval=2000, default=1000),
key="m0")
self.gui.add("TR (s)",
NumericOption(minval=0, maxval=10, default=4),
key="tr")
self.gui.add("TE (ms)",
NumericOption(minval=0, maxval=1000, default=13),
key="te")
self.gui.add("Tissue/arterial partition coefficient",
NumericOption(minval=0, maxval=1, default=0.9),
key="pct")
#self.gui.add("Arterial component", BoolOption(), key="incart")
self.gui.sig_changed.connect(self._update_options)
self._update_options()
def __init__(self, ivm):
QtGui.QWidget.__init__(self)
self.ivm = ivm
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
self.optbox = OptionBox()
self.optbox.add(
"AIF source",
ChoiceOption(["Global sequence of values", "Voxelwise image"],
["global", "voxelwise"]),
key="aif_source")
self.optbox.option("aif_source").sig_changed.connect(
self._aif_source_changed)
self.optbox.add("AIF", NumberListOption(), key="aif")
self.optbox.add("AIF image", DataOption(self.ivm), key="suppdata")
self.optbox.add("AIF type",
ChoiceOption(["DSC signal", "Concentration"],
[False, True]),
key="aifconc")
vbox.addWidget(self.optbox)
vbox.addStretch()
self._aif_source_changed()
def __init__(self, ivm=None):
QtGui.QWidget.__init__(self)
self._ivm = ivm
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
self.optbox = OptionBox()
vbox.addWidget(self.optbox)
self.optbox.add("CEST data", DataOption(self._ivm), key="data")
self.optbox.add("ROI",
DataOption(self._ivm, rois=True, data=False),
key="mask")
self.optbox.add("Frequency offsets", NumberListOption(), key="freqs")
self.optbox.add("B0", ChoiceOption(B0_DEFAULTS), key="b0")
self.optbox.add("Custom B0 (T)",
NumericOption(minval=0.0,
maxval=15,
default=3.0,
decimals=3),
key="b0_custom")
# FIXME multiple B1 values
self.optbox.add("B1 (\u03bcT)",
NumericOption(minval=0.0,
maxval=2,
default=0.55,
decimals=6),
key="b1")
self.optbox.add(
"Saturation",
ChoiceOption(["Continuous Saturation", "Pulsed Saturation"],
["continuous", "pulsed"]),
key="sat")
self.optbox.add("Saturation time (s)",
NumericOption(minval=0.0,
maxval=5,
default=2,
decimals=2),
key="sat_time")
self.optbox.add("Pulse Magnitudes",
NumberListOption(),
key="pulse_mag")
self.optbox.add("Pulse Durations (s)",
NumberListOption(),
key="pulse_dur")
self.optbox.add("Pulse Repeats",
NumberListOption(),
key="pulse_repeats")
self.optbox.option("b0").sig_changed.connect(self._b0_changed)
self.optbox.option("b0_custom").sig_changed.connect(self._b0_changed)
self.optbox.option("sat").sig_changed.connect(self._sat_changed)
self.warn_box = WarningBox()
vbox.addWidget(self.warn_box)
# B1 field
#hbox = QtGui.QHBoxLayout()
#self.unsat_cb = QtGui.QCheckBox("Unsaturated")
#self.unsat_cb.stateChanged.connect(self.update_ui)
#hbox.addWidget(self.unsat_cb)
#self.unsat_combo = QtGui.QComboBox()
#self.unsat_combo.addItem("first")
#self.unsat_combo.addItem("last")
#self.unsat_combo.addItem("first and last ")
#hbox.addWidget(self.unsat_combo)
#hbox.addStretch(1)
#grid.addLayout(hbox, 2, 2)
vbox.addStretch(1)
self._sat_changed()
self._b0_changed()
def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
try:
self.FabberProcess = get_plugins("processes", "FabberProcess")[0]
except IndexError:
self.FabberProcess = None
if self.FabberProcess is None:
vbox.addWidget(
QtGui.QLabel(
"Fabber core library not found.\n\n You must install Fabber to use this widget"
))
return
title = TitleWidget(
self,
help="fabber-dsc",
subtitle="DSC modelling using the Fabber process %s" % __version__)
vbox.addWidget(title)
cite = Citation(FAB_CITE_TITLE, FAB_CITE_AUTHOR, FAB_CITE_JOURNAL)
vbox.addWidget(cite)
self.input = OptionBox("Input data")
self.input.add("DCE data",
DataOption(self.ivm, include_3d=False, include_4d=True),
key="data")
self.input.add("ROI",
DataOption(self.ivm, data=False, rois=True),
key="roi",
checked=True)
self.input.add("T1 map",
DataOption(self.ivm, include_3d=True, include_4d=False),
key="t1",
checked=True)
self.input.option("t1").sig_changed.connect(self._t1_map_changed)
vbox.addWidget(self.input)
self.acquisition = OptionBox("Acquisition")
self.acquisition.add("Contrast agent R1 relaxivity (l/mmol s)",
NumericOption(minval=0, maxval=10, default=3.7),
key="r1")
self.acquisition.add("Flip angle (\N{DEGREE SIGN})",
NumericOption(minval=0, maxval=90, default=12),
key="fa")
self.acquisition.add("TR (ms)",
NumericOption(minval=0, maxval=10, default=4.108),
key="tr")
self.acquisition.add("Time between volumes (s)",
NumericOption(minval=0, maxval=30, default=12),
key="delt")
vbox.addWidget(self.acquisition)
self.model = OptionBox("Model options")
self.model.add(
"Model",
ChoiceOption([
"Standard Tofts model", "Extended Tofts model (ETM)",
"2 Compartment exchange model",
"Compartmental Tissue Update (CTU) model",
"Adiabatic Approximation to Tissue Homogeneity (AATH) Model"
], ["dce_tofts", "dce_ETM", "dce_2CXM", "dce_CTU", "dce_AATH"]),
key="model")
self.model.add(
"AIF",
ChoiceOption([
"Population (Orton 2008)", "Population (Parker)",
"Measured DCE signal", "Measured concentration curve"
], ["orton", "parker", "signal", "conc"]),
key="aif")
self.model.add("Bolus injection time (s)",
NumericOption(minval=0, maxval=60, default=30),
key="tinj")
self.model.add("AIF data values",
NumberListOption([
0,
]),
key="aif-data")
self.model.add("T1 (s)",
NumericOption(minval=0.0, maxval=5.0, default=1.0),
key="t10")
self.model.add("Allow T1 to vary",
BoolOption(default=False),
key="infer-t10")
self.model.add("Bolus arrival time (s)",
NumericOption(minval=0, maxval=2.0, default=0),
key="delay")
self.model.add("Allow bolus arrival time to vary",
BoolOption(default=False),
key="infer-delay")
self.model.add("Infer kep rather than ve",
BoolOption(default=False),
key="infer-kep")
self.model.add("Infer flow", BoolOption(default=True), key="infer-fp")
self.model.add("Infer permeability-surface area",
BoolOption(default=False),
key="infer-ps")
self.model.add("Spatial regularization",
BoolOption(default=False),
key="spatial")
self.model.option("model").sig_changed.connect(self._model_changed)
self.model.option("aif").sig_changed.connect(self._aif_changed)
vbox.addWidget(self.model)
# Run button and progress
vbox.addWidget(RunWidget(self, title="Run modelling"))
vbox.addStretch(1)
self._aif_changed()
self._model_changed()
def __init__(self, opt, **kwargs):
OptionWidget.__init__(self, opt, **kwargs)
self.edit = NumberListOption(intonly=opt["type"] == "INT")
self.edit.sig_changed.connect(self.update_options)
self.widgets.append(self.edit)