def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
try:
proc = get_plugins("processes", "FabberProcess")[0]
except:
proc = None
if proc 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="Bayesian modelling for DSC-MRI %s" %
__version__)
vbox.addWidget(title)
cite = Citation(FAB_CITE_TITLE, FAB_CITE_AUTHOR, FAB_CITE_JOURNAL)
vbox.addWidget(cite)
tabs = QtGui.QTabWidget()
vbox.addWidget(tabs)
self.dsc_widget = DscOptionsWidget(self.ivm)
tabs.addTab(self.dsc_widget, "DSC Options")
self.aif_widget = AifWidget(self.ivm)
tabs.addTab(self.aif_widget, "AIF")
vbox.addWidget(tabs)
vbox.addWidget(RunWidget(self, save_option=True))
vbox.addStretch(1)
def __init__(self, ivm, parent, acq_options):
OptionsWidget.__init__(self, ivm, parent)
self.acq_options = acq_options
vbox = QtWidgets.QVBoxLayout()
self.setLayout(vbox)
self._optbox = OptionBox()
self._optbox.add("<b>Model options</b>")
self._optbox.add("Delay minimum (s)",
NumericOption(minval=-100, maxval=100, default=0),
key="delay-min")
self._optbox.add("Delay maximum (s)",
NumericOption(minval=-100, maxval=100, default=0),
key="delay-max")
self._optbox.add("Delay step (s)",
NumericOption(minval=-5, maxval=5, default=1),
key="delay-step")
self._optbox.add("<b>Output options</b>")
self._optbox.add("Output data name suffix",
TextOption(),
checked=True,
key="output-suffix")
vbox.addWidget(self._optbox)
vbox.addWidget(RunWidget(self, save_option=True))
vbox.addStretch(1)
def __init__(self, ivm, parent, acq_options):
OptionsWidget.__init__(self, ivm, parent)
self.acq_options = acq_options
vbox = QtWidgets.QVBoxLayout()
self.setLayout(vbox)
cite = Citation(FAB_CITE_TITLE, FAB_CITE_AUTHOR, FAB_CITE_JOURNAL)
vbox.addWidget(cite)
self._optbox = OptionBox()
self._optbox.add("<b>Model options</b>")
self._optbox.add("Infer constant signal offset",
BoolOption(default=True),
key="infer-sig0")
self._optbox.add("Infer delay",
BoolOption(default=True),
key="infer-delay")
#self._optbox.add("<b>Model fitting options</b>")
#self._optbox.add("Spatial regularization", BoolOption(default=True), key="spatial")
self._optbox.add("<b>Output options</b>")
self._optbox.add("Output data name suffix",
TextOption(),
checked=True,
key="output-suffix")
vbox.addWidget(self._optbox)
vbox.addWidget(RunWidget(self, save_option=True))
vbox.addStretch(1)
def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
title = TitleWidget(
self,
title="PCA reduction",
subtitle="Principal Component Analysis for 4D data")
vbox.addWidget(title)
self._options = OptionBox("Options")
self._options.add("Data",
DataOption(self.ivm, include_3d=False),
key="data")
self._options.add("ROI",
DataOption(self.ivm, data=False, rois=True),
key="roi")
self._options.add("Number of components",
NumericOption(minval=1, intonly=True, default=4),
key="n-components")
self._options.add("Output name",
OutputNameOption(
src_data=self._options.option("data"),
suffix="_pca"),
key="output-name")
self._options.option("data").sig_changed.connect(self._data_changed)
vbox.addWidget(self._options)
self._run = RunWidget(self)
self._run.sig_postrun.connect(self._postrun)
vbox.addWidget(self._run)
self.plot = Plot(qpo=None, parent=self, title="PCA modes")
self.variance_model = QtGui.QStandardItemModel()
variance_table = QtGui.QTableView()
variance_table.verticalHeader().hide()
variance_table.setModel(self.variance_model)
tabs = QtGui.QTabWidget()
tabs.addTab(self.plot, "PCA modes")
tabs.addTab(variance_table, "Explained variance")
tabs.setCurrentWidget(self.plot)
vbox.addWidget(tabs)
vbox.addStretch(1)
self._data_changed()
def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
title = TitleWidget(
self,
help="asl",
subtitle="Data processing for Arterial Spin Labelling MRI")
vbox.addWidget(title)
cite = Citation(FAB_CITE_TITLE, FAB_CITE_AUTHOR, FAB_CITE_JOURNAL)
vbox.addWidget(cite)
self.tabs = QtGui.QTabWidget()
vbox.addWidget(self.tabs)
self.asldata = AslImageWidget(self.ivm, parent=self)
self.asldata.sig_changed.connect(self._data_changed)
self.tabs.addTab(self.asldata, "ASL data")
self.preproc = PreprocOptions(self.ivm)
self.preproc.sig_enable_tab.connect(self._enable_tab)
self.tabs.addTab(self.preproc, "Corrections")
# Only add these if appropriate
self._optional_tabs = {
"veasl": VeaslOptions(self.ivm, self.asldata),
"enable": EnableOptions(self.ivm),
"deblur": DeblurOptions(),
}
self.structural = StructuralData(self.ivm)
self.tabs.addTab(self.structural, "Structural data")
self.calibration = CalibrationOptions(self.ivm)
self.tabs.addTab(self.calibration, "Calibration")
self.analysis = AnalysisOptions(self.ivm)
self.analysis.optbox.option("wp").sig_changed.connect(self._wp_changed)
self.tabs.addTab(self.analysis, "Analysis")
self.output = OutputOptions()
self.tabs.addTab(self.output, "Output")
runbox = RunWidget(self, title="Run processing", save_option=True)
runbox.sig_postrun.connect(self._postrun)
vbox.addWidget(runbox)
vbox.addStretch(1)
fsldir_qwidgets = get_plugins("qwidgets", "FslDirWidget")
if len(fsldir_qwidgets) > 0:
fsldir = fsldir_qwidgets[0]()
vbox.addWidget(fsldir)
def init_ui(self):
layout = QtGui.QVBoxLayout()
self.setLayout(layout)
title = TitleWidget(self, title="Registration and Motion Correction", help="reg")
layout.addWidget(title)
if not self.reg_methods:
layout.addWidget(QtGui.QLabel("No registration methods found"))
layout.addStretch(1)
return
self.options = OptionBox("General Options")
self.options.add("Mode", ChoiceOption(["Registration", "Motion Correction"], ["reg", "moco"]), key="mode")
self.options.add("Method", ChoiceOption([method.display_name for method in self.reg_methods], self.reg_methods), key="method")
self.options.add("Registration data", DataOption(self.ivm), key="reg")
self.options.add("Reference data", DataOption(self.ivm), key="ref")
self.options.add("Reference volume", ChoiceOption(["Middle volume", "Mean volume", "Specified volume"], ["median", "mean", "idx"]), key="ref-vol")
self.options.add("Reference volume index", NumericOption(intonly=True), key="ref-idx")
self.options.add("Output space", ChoiceOption(["Reference", "Registration", "Transformed"], ["ref", "reg", "trans"]), key="output-space")
self.options.add("Output name", OutputNameOption(src_data=self.options.option("reg"), suffix="_reg"), key="output-name", checked=True)
self.options.add("Also apply transform to", DataOption(self.ivm, multi=True), key="add-reg")
self.options.add("Save transformation", TextOption(), key="save-transform", checked=True, default=False)
self.options.option("mode").sig_changed.connect(self._update_option_visibility)
self.options.option("method").sig_changed.connect(self._method_changed)
self.options.option("ref").sig_changed.connect(self._update_option_visibility)
self.options.option("ref-vol").sig_changed.connect(self._update_option_visibility)
self.options.option("reg").sig_changed.connect(self._update_option_visibility)
layout.addWidget(self.options)
# Create the options boxes for reg methods - only one visible at a time!
self.opt_boxes = {}
for method in self.reg_methods:
hbox = QtGui.QHBoxLayout()
opt_box = QtGui.QGroupBox()
opt_box.setTitle(method.display_name)
vbox = QtGui.QVBoxLayout()
opt_box.setLayout(vbox)
vbox.addWidget(method.interface())
hbox.addWidget(opt_box)
opt_box.setVisible(False)
layout.addLayout(hbox)
self.opt_boxes[method.name] = opt_box
layout.addWidget(RunWidget(self))
layout.addStretch(1)
self._method_changed()
def init_ui(self):
main_vbox = QtGui.QVBoxLayout()
self.setLayout(main_vbox)
title = TitleWidget(
self,
help="generic/datasim",
subtitle=
"Simulates data for various imaging sequences, from known parameter inputs %s"
% __version__)
main_vbox.addWidget(title)
self.tabs = QtGui.QTabWidget()
main_vbox.addWidget(self.tabs)
self.struc_model = ModelOptions(self.ivm,
parent=self,
model_type="Structural",
abbrev="struc",
model_classes=get_struc_models())
self.struc_model.sig_changed.connect(self._update_params)
self.data_model = ModelOptions(self.ivm,
parent=self,
model_type="Data",
abbrev="data",
model_classes=get_data_models())
self.data_model.sig_changed.connect(self._update_params)
self.params = ParamsOptions(self.ivm, parent=self)
self.noise = NoiseOptions(self.ivm, parent=self)
self.motion = MotionOptions(self.ivm, parent=self)
self.output = OutputOptions(self.ivm, parent=self)
self.tabs.addTab(self.struc_model, "Structure model")
self.tabs.addTab(self.data_model, "Data model")
self.tabs.addTab(self.params, "Parameter values")
self.tabs.addTab(self.noise, "Noise")
self.tabs.addTab(self.motion, "Motion")
self.tabs.addTab(self.output, "Output")
main_vbox.addStretch(1)
main_vbox.addWidget(RunWidget(self))
self._update_params()
class PcaWidget(QpWidget):
"""
PCA widget
"""
def __init__(self, **kwargs):
super(PcaWidget, self).__init__(name="PCA",
icon="pca",
desc="PCA reduction",
group="Processing",
**kwargs)
def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
title = TitleWidget(
self,
title="PCA reduction",
subtitle="Principal Component Analysis for 4D data")
vbox.addWidget(title)
self._options = OptionBox("Options")
self._options.add("Data",
DataOption(self.ivm, include_3d=False),
key="data")
self._options.add("ROI",
DataOption(self.ivm, data=False, rois=True),
key="roi")
self._options.add("Number of components",
NumericOption(minval=1, intonly=True, default=4),
key="n-components")
self._options.add("Output name",
OutputNameOption(
src_data=self._options.option("data"),
suffix="_pca"),
key="output-name")
self._options.option("data").sig_changed.connect(self._data_changed)
vbox.addWidget(self._options)
self._run = RunWidget(self)
self._run.sig_postrun.connect(self._postrun)
vbox.addWidget(self._run)
self.plot = Plot(qpo=None, parent=self, title="PCA modes")
self.variance_model = QtGui.QStandardItemModel()
variance_table = QtGui.QTableView()
variance_table.verticalHeader().hide()
variance_table.setModel(self.variance_model)
tabs = QtGui.QTabWidget()
tabs.addTab(self.plot, "PCA modes")
tabs.addTab(variance_table, "Explained variance")
tabs.setCurrentWidget(self.plot)
vbox.addWidget(tabs)
vbox.addStretch(1)
self._data_changed()
def processes(self):
return {"PCA": self._options.values()}
def _data_changed(self):
self._run.setEnabled(
self._options.option("data").value in self.ivm.data)
def _postrun(self):
self._update_plot()
self._update_table()
def _update_plot(self):
self.plot.clear()
extra = self.ivm.extras.get(
self._options.option("output-name").value + "_modes", None)
if extra is not None:
arr = np.array(extra.arr)
for idx in range(arr.shape[1] - 1):
self.plot.add_line(arr[:, idx], name="Mode %i" % idx)
self.plot.add_line(arr[:, -1],
name="Mean",
line_col=(255, 0, 0),
line_width=3.0)
def _update_table(self):
self.variance_model.clear()
extra = self.ivm.extras.get(
self._options.option("output-name").value + "_variance", None)
if extra is not None:
self.debug(str(extra))
for idx, header in enumerate(extra.col_headers):
self.variance_model.setHorizontalHeaderItem(
idx, QtGui.QStandardItem(header))
for idx, variance in enumerate(extra.arr):
self.variance_model.setItem(
idx, 0, QtGui.QStandardItem(str(variance[0])))
self.variance_model.setItem(
idx, 1, QtGui.QStandardItem(sf(variance[1])))
self.variance_model.setItem(
idx, 2, QtGui.QStandardItem(sf(variance[2])))
def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
title = TitleWidget(self, help="pk", batch_btn=True, opts_btn=False)
vbox.addWidget(title)
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")
self.input.add("T1 map",
DataOption(self.ivm, include_3d=True, include_4d=False),
key="t1")
vbox.addWidget(self.input)
self.options = OptionBox("Options")
self.options.add("Contrast agent R1 relaxivity (l/mmol s)",
NumericOption(minval=0, maxval=10, default=3.7),
key="r1")
self.options.add("Contrast agent R2 relaxivity (l/mmol s)",
NumericOption(minval=0, maxval=10, default=4.8),
key="r2")
self.options.add("Flip angle (\N{DEGREE SIGN})",
NumericOption(minval=0, maxval=90, default=12),
key="fa")
self.options.add("TR (ms)",
NumericOption(minval=0, maxval=10, default=4.108),
key="tr")
self.options.add("TE (ms)",
NumericOption(minval=0, maxval=10, default=1.832),
key="te")
self.options.add("Time between volumes (s)",
NumericOption(minval=0, maxval=30, default=12),
key="dt")
self.options.add("Estimated injection time (s)",
NumericOption(minval=0, maxval=60, default=30),
key="tinj")
self.options.add("Ktrans/kep percentile threshold",
NumericOption(minval=0, maxval=100, default=100),
key="ve-thresh")
self.options.add("Dose (mM/kg) - preclinical only",
NumericOption(minval=0, maxval=5, default=0.6),
key="dose",
visible=False)
models = [
"Clinical: Toft / OrtonAIF (3rd) with offset",
"Clinical: Toft / OrtonAIF (3rd) no offset",
"Preclinical: Toft / BiexpAIF (Heilmann)",
"Preclinical: Ext Toft / BiexpAIF (Heilmann)",
]
self.options.add("Pharmacokinetic model choice",
ChoiceOption(models, [1, 2, 3, 4]),
key="model")
self.options.option("model").sig_changed.connect(self._aif_changed)
vbox.addWidget(self.options)
# Run button and progress
vbox.addWidget(RunWidget(self, title="Run modelling"))
vbox.addStretch(1)
self._aif_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()