def init_ui(self, run_box=True):
self.vbox = QtGui.QVBoxLayout()
self.setLayout(self.vbox)
title = TitleWidget(self,
help="fsl",
subtitle="%s %s" % (self.description, __version__))
self.vbox.addWidget(title)
cite = Citation(*CITATIONS.get(self.prog, CITATIONS["fsl"]))
self.vbox.addWidget(cite)
self.options = OptionBox("%s options" % self.prog.upper())
self.vbox.addWidget(self.options)
if run_box:
self.run_box = RunBox(self.get_process, self.get_options)
self.vbox.addWidget(self.run_box)
self.vbox.addStretch(1)
fsldir = FslDirWidget()
self.vbox.addWidget(fsldir)
fsldir.sig_changed.connect(self._fsldir_changed)
self._fsldir_changed(fsldir.fsldir)
def interface(self, generic_options=None):
if generic_options is None:
generic_options = {}
if self.options_widget is None:
self.options_widget = QtGui.QWidget()
vbox = QtGui.QVBoxLayout()
self.options_widget.setLayout(vbox)
cite = Citation(CITE_TITLE, CITE_AUTHOR, CITE_JOURNAL)
vbox.addWidget(cite)
self.optbox = OptionBox()
self.optbox.add("Mask for registration data",
DataOption(self.ivm, rois=True, data=False),
key="inmask",
checked=True)
self.optbox.add("Mask for reference data",
DataOption(self.ivm, rois=True, data=False),
key="refmask",
checked=True)
self.optbox.add("Spline order",
ChoiceOption([2, 3]),
key="splineorder",
checked=True)
self.optbox.add("Use pre-defined configuration",
ChoiceOption(
["T1_2_MNI152_2mm", "FA_2_FMRIB58_1mm"]),
key="config",
checked=True)
vbox.addWidget(self.optbox)
return self.options_widget
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)
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)
try:
self.fabber_process = get_plugins("processes", "FabberProcess")[0]
except:
self.fabber_process = None
if self.fabber_process 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="cest",
subtitle=
"Bayesian Modelling for Chemical Exchange Saturation Transfer MRI %s"
% __version__)
vbox.addWidget(title)
cite = Citation(CEST_CITE_TITLE, CEST_CITE_AUTHOR, CEST_CITE_JOURNAL)
vbox.addWidget(cite)
self.tabs = QtGui.QTabWidget()
self.seqtab = SequenceOptions(self.ivm)
self.tabs.addTab(self.seqtab, "Sequence")
self.pooltab = PoolOptions(self.ivm)
self.tabs.addTab(self.pooltab, "Pools")
self.analysistab = AnalysisOptions(self.ivm)
self.tabs.addTab(self.analysistab, "Analysis")
self.pooltab.sig_pools_changed.connect(self.analysistab.set_pools)
self.seqtab.sig_b0_changed.connect(self.pooltab.set_b0)
vbox.addWidget(self.tabs)
run_tabs = QtGui.QTabWidget()
run_box = RunBox(self._get_process_model,
self._options,
title="Run model-based analysis",
save_option=True)
run_tabs.addTab(run_box, "Model based analysis")
run_box = RunBox(self._get_process_lda,
self._options_lda,
title="Run Lorentzian Difference analysis",
save_option=True)
run_tabs.addTab(run_box, "Lorentzian Difference analysis")
vbox.addWidget(run_tabs)
vbox.addStretch(1)
self.analysistab.set_pools(self.pooltab.pools)
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__(self, ivm=None):
QtGui.QWidget.__init__(self)
self.ivm = ivm
self.vbox = QtGui.QVBoxLayout()
self.setLayout(self.vbox)
if hasattr(self, "CITE"):
self.vbox.addWidget(Citation(*self.CITE))
self.optbox = OptionBox()
self.vbox.addWidget(self.optbox)
self._init_ui()
self.vbox.addStretch(1)
def init_ui(self):
self.vbox = QtGui.QVBoxLayout()
self.setLayout(self.vbox)
title = TitleWidget(self, subtitle="Plugin %s" % __version__, help="fabber")
self.vbox.addWidget(title)
cite = Citation(FAB_CITE_TITLE, FAB_CITE_AUTHOR, FAB_CITE_JOURNAL)
self.vbox.addWidget(cite)
self.options = OptionBox("Options")
self.options.sig_changed.connect(self._options_changed)
self.vbox.addWidget(self.options)
self.warn_box = WarningBox("")
self.warn_box.setVisible(False)
self.vbox.addWidget(self.warn_box)
def interface(self, generic_options=None):
"""
:return: QWidget containing registration options
"""
if generic_options is None:
generic_options = {}
if self.options_widget is None:
self.options_widget = QtGui.QWidget()
vbox = QtGui.QVBoxLayout()
self.options_widget.setLayout(vbox)
cite = Citation(CITE_TITLE, CITE_AUTHOR, CITE_JOURNAL)
vbox.addWidget(cite)
self.optbox = OptionBox()
self.optbox.add("Cost Model",
ChoiceOption(self.cost_models,
self.cost_model_options,
default="normcorr"),
key="cost")
#self.optbox.add("Number of search stages", ChoiceOption([1, 2, 3, 4]), key="nstages")
#self.optbox.option("stages").value = 2
#self.optbox.add("Final stage interpolation", ChoiceOption(["None", "Sinc", "Spline", "Nearest neighbour"], ["", "sinc_final", "spline_final", "nn_final"]), key="final")
#self.optbox.add("Field of view (mm)", NumericOption(minval1, maxval=100, default=20), key="fov")
self.optbox.add("Number of bins",
NumericOption(intonly=True,
minval=1,
maxval=1000,
default=256),
key="bins")
self.optbox.add("Degrees of freedom",
ChoiceOption([6, 9, 12]),
key="dof")
#self.optbox.add("Scaling", NumericOption(minval=0.1, maxval=10, default=6), key="scaling")
#self.optbox.add("Smoothing in cost function", NumericOption(minval=0.1, maxval=10, default=1), key="smoothing")
#self.optbox.add("Scaling factor for rotation\noptimization tolerances", NumericOption(minval=0.1, maxval=10, default=1), key="rotscale")
#self.optbox.add("Search on gradient images", BoolOption, key="grad")
vbox.addWidget(self.optbox)
return self.options_widget
def init_ui(self):
layout = QtGui.QVBoxLayout()
self.setLayout(layout)
title = TitleWidget(self, "Supervoxel Generation", help="sv")
layout.addWidget(title)
cite = Citation(CITE_TITLE, CITE_AUTHOR, CITE_JOURNAL)
layout.addWidget(cite)
hbox = QtGui.QHBoxLayout()
optbox = QtGui.QGroupBox()
optbox.setTitle("Options")
grid = QtGui.QGridLayout()
optbox.setLayout(grid)
grid.addWidget(QtGui.QLabel("Data"), 0, 0)
self.ovl = OverlayCombo(self.ivm)
self.ovl.currentIndexChanged.connect(self._data_changed)
grid.addWidget(self.ovl, 0, 1)
grid.addWidget(QtGui.QLabel("ROI"), 1, 0)
self.roi = RoiCombo(self.ivm)
grid.addWidget(self.roi, 1, 1)
self.n_comp = NumericOption("Number of components", grid, 2, minval=1, maxval=3, default=3, intonly=True)
self.compactness = NumericOption("Compactness", grid, 3, minval=0.01, maxval=1, step=0.05, default=0.1, intonly=False)
self.sigma = NumericOption("Smoothing", grid, 4, minval=0, maxval=5, step=0.1, default=1, intonly=False)
self.n_supervoxels = NumericOption("Number of supervoxels", grid, 5, minval=2, maxval=1000, default=20, intonly=True)
grid.addWidget(QtGui.QLabel("Output name"), 6, 0)
self.output_name = QtGui.QLineEdit("supervoxels")
grid.addWidget(self.output_name, 6, 1)
self.gen_btn = QtGui.QPushButton('Generate', self)
self.gen_btn.clicked.connect(self._generate)
grid.addWidget(self.gen_btn, 7, 0)
hbox.addWidget(optbox)
hbox.addStretch(1)
layout.addLayout(hbox)
layout.addStretch(1)
def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
vbox.addWidget(TitleWidget(self))
vbox.addWidget(Citation(*CITATIONS["fsl"]))
self.data_list = FslDataListWidget(self)
vbox.addWidget(self.data_list)
self.data_list.sig_selected.connect(self._data_selected)
hbox = QtGui.QHBoxLayout()
self._load_btn = QtGui.QPushButton("Load")
self._load_btn.clicked.connect(self._load)
hbox.addWidget(self._load_btn)
hbox.addWidget(QtGui.QLabel("Dataset name: "))
self._load_name = QtGui.QLineEdit()
hbox.addWidget(self._load_name)
vbox.addLayout(hbox)
fsldir = FslDirWidget()
vbox.addWidget(fsldir)
def init_ui(self):
vbox = QtGui.QVBoxLayout()
vbox.setSpacing(1)
self.setLayout(vbox)
vbox.addWidget(TitleWidget(self))
vbox.addWidget(Citation(*CITATIONS["fsl"]))
self.atlas_list = AtlasListWidget(self, self._registry)
vbox.addWidget(self.atlas_list)
self.atlas_desc = AtlasDescription(self, self._registry)
vbox.addWidget(self.atlas_desc)
self.atlas_list.sig_selected.connect(self.atlas_desc.set_atlas)
fsldir = FslDirWidget()
vbox.addWidget(fsldir)
# This needs to be done after creating the FslDirWidget because otherwise we may not
# have picked up a previously saved FSLDIR setting and the atlas list will be empty
self._registry.rescanAtlases()
self.atlas_list.init_list()
def __init__(self, ivm=None):
QtGui.QWidget.__init__(self)
self._ivm = ivm
self._poolvals_edited = False
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
self.optbox = OptionBox()
vbox.addWidget(self.optbox)
self.optbox.add("<b>Output options</b>")
self.optbox.add("CEST R*",
BoolOption(default=True),
key="save-model-extras")
self.optbox.add("Parameter maps",
BoolOption(default=False),
key="save-mean")
#self.optbox.add("Parameter variance", BoolOption(default=False), key="var")
self.optbox.add("Model fit",
BoolOption(default=False),
key="save-model-fit")
self.optbox.add("Prefix for output",
TextOption(),
checked=True,
key="output-prefix")
self.optbox.add(" ")
self.optbox.add("<b>Analysis options</b>")
self.optbox.add("Spatial Regularization", BoolOption(), key="spatial")
self.optbox.add("Allow uncertainty in T1/T2 values",
BoolOption(),
key="t12prior")
self.optbox.add("Prior T1 map",
DataOption(self._ivm),
key="t1img",
checked=True)
self.optbox.add("Prior T2 map",
DataOption(self._ivm),
key="t2img",
checked=True)
self.optbox.add("Tissue PV map (GM+WM)",
DataOption(self._ivm),
key="pvimg",
checked=True)
self.optbox.option("t12prior").sig_changed.connect(self._update_ui)
self.optbox.add("Use steady state solution for MT bias reduction",
BoolOption(default=False),
key="new-ss")
self.optbox.option("new-ss").sig_changed.connect(self._update_ui)
self.optbox.add("TR (s)",
NumericOption(default=3.0,
minval=0,
maxval=5,
digits=3,
step=0.1),
key="tr")
self.optbox.add("Excitation flip angle (\N{DEGREE SIGN})",
NumericOption(default=12.0,
minval=0,
maxval=25,
digits=3,
step=1.0),
key="fa")
self.optbox.add(
"MT pool Line shape",
ChoiceOption(
["None", "Gaussian", "Lorentzian", "Super Lorentzian"],
["none", "gaussian", "lorentzian", "superlorentzian"]),
key="lineshape")
self.alexmt_cite = Citation(ALEXMT_CITE_TITLE, ALEXMT_CITE_AUTHOR,
ALEXMT_CITE_JOURNAL)
vbox.addWidget(self.alexmt_cite)
vbox.addStretch(1)
self._update_ui()
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_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
try:
self.FabberProcess = get_plugins("processes", "FabberProcess")[0]
except:
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-t1",
subtitle="T1 mapping from VFA images using the Fabber process %s" %
__version__)
vbox.addWidget(title)
cite = Citation(FAB_CITE_TITLE, FAB_CITE_AUTHOR, FAB_CITE_JOURNAL)
vbox.addWidget(cite)
grid = QtGui.QGridLayout()
self.multivol_choice = ChoiceOption(
"VFA data in",
grid,
ypos=0,
choices=["Single data set", "Multiple data sets"])
self.multivol_choice.combo.currentIndexChanged.connect(self.update_ui)
self.multivol_label = QtGui.QLabel("VFA data set")
grid.addWidget(self.multivol_label, 1, 0)
self.multivol_combo = OverlayCombo(self.ivm)
grid.addWidget(self.multivol_combo, 1, 1)
self.multivol_fas_label = QtGui.QLabel("FAs (\N{DEGREE SIGN})")
grid.addWidget(self.multivol_fas_label, 2, 0)
self.multivol_fas = NumberList(initial=[
1,
])
grid.addWidget(self.multivol_fas, 2, 1, 1, 2)
self.singlevol_label = QtGui.QLabel("VFA data sets")
grid.addWidget(self.singlevol_label, 3, 0)
grid.setAlignment(self.singlevol_label, QtCore.Qt.AlignTop)
self.singlevol_table = QtGui.QTableWidget()
self.singlevol_table.setColumnCount(2)
self.singlevol_table.setHorizontalHeaderLabels(
["Data set", "Flip angle"])
self.singlevol_table.setEditTriggers(
QtGui.QAbstractItemView.NoEditTriggers)
grid.addWidget(self.singlevol_table, 3, 1)
hbox = QtGui.QHBoxLayout()
self.singlevol_add = QtGui.QPushButton("Add")
self.singlevol_add.clicked.connect(self.add_vol)
hbox.addWidget(self.singlevol_add)
self.singlevol_clear = QtGui.QPushButton("Clear")
self.singlevol_clear.clicked.connect(self.clear_vols)
hbox.addWidget(self.singlevol_clear)
grid.addLayout(hbox, 4, 1)
self.tr = NumericOption("TR (ms)",
grid,
ypos=5,
default=4.108,
minval=0,
step=0.1,
decimals=3)
grid.setColumnStretch(3, 1)
vbox.addLayout(grid)
self.run = RunBox(self.get_process, self.get_rundata)
vbox.addWidget(self.run)
vbox.addStretch(1)
self.update_ui()