def interface(self):
grid = Tool.interface(self)
grid.addWidget(QtGui.QLabel("Source data: "), 1, 0)
self.ov_combo = OverlayCombo(self.ivm)
grid.addWidget(self.ov_combo)
grid.addWidget(QtGui.QLabel("Click to select points: "), 2, 0)
self.pickmode_combo = QtGui.QComboBox()
self.pickmode_combo.addItem("Inside the ROI")
self.pickmode_combo.addItem("Outside the ROI")
self.pickmode_combo.currentIndexChanged.connect(self._pick_mode_changed)
grid.addWidget(self.pickmode_combo, 2, 1)
grid.addWidget(QtGui.QLabel("Segmentation mode: "), 3, 0)
self.segmode_combo = QtGui.QComboBox()
self.segmode_combo.addItem("Slice")
self.segmode_combo.addItem("3D")
self.segmode_combo.currentIndexChanged.connect(self._seg_mode_changed)
grid.addWidget(self.segmode_combo, 3, 1)
self.beta = NumericOption("Diffusion difficulty", grid, 4, 0, intonly=True, maxval=20000, default=10000, step=1000)
btn = QtGui.QPushButton("Segment")
btn.clicked.connect(self._segment)
grid.addWidget(btn, 5, 0)
btn = QtGui.QPushButton("Clear points")
btn.clicked.connect(self._init)
grid.addWidget(btn, 5, 1)
return grid
def __init__(self, ivm, parent=None, **kwargs):
LogSource.__init__(self)
QtGui.QWidget.__init__(self, parent)
self.ivm = ivm
self.data = None
self.default_md = kwargs.get("default_metadata", DEFAULT_METADATA)
self.md = dict(self.default_md)
self.aslimage = None
self.valid = True
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
grid = QtGui.QGridLayout()
grid.addWidget(QtGui.QLabel("ASL data"), 0, 0)
self.data_combo = OverlayCombo(self.ivm)
self.data_combo.currentIndexChanged.connect(self._data_changed)
grid.addWidget(self.data_combo, 0, 1)
view_classes = [
LabelType, RepeatsChoice, NumPhases, NumEncodings, BlockFormat,
DataStructure, SignalView, Labelling, Readout, SliceTime,
Multiband, Times, BolusDurations, VariableRepeats
]
self.views = []
for idx, view_class in enumerate(view_classes):
if view_class in kwargs.get("ignore_views", ()):
continue
view = view_class(grid, ypos=idx + 2)
view.ivm = self.ivm
view.sig_md_changed.connect(self._metadata_changed)
self.views.append(view)
#grid.addWidget(QtGui.QLabel("Data order preview"), 5, 0)
# Code below is for specific multiple phases
#self.phases_lbl = QtGui.QLabel("Phases (\N{DEGREE SIGN})")
#grid.addWidget(self.phases_lbl, 3, 0)
#self.phases_lbl.setVisible(False)
#self.phases = NumberList([float(x)*360/8 for x in range(8)])
#grid.addWidget(self.phases, 3, 1)
#self.phases.setVisible(False)
grid.setColumnStretch(0, 0)
grid.setColumnStretch(1, 1)
grid.setColumnStretch(2, 0)
grid.setRowStretch(len(view_classes) + 2, 1)
self.grid = grid
vbox.addLayout(grid)
self.warn_label = WarningBox()
vbox.addWidget(self.warn_label)
self._update_ui()
self._data_changed()
class ChooseDataDialog(QtGui.QDialog):
def __init__(self, parent, ivm, used=[]):
super(ChooseDataDialog, self).__init__(parent)
self.setWindowTitle("Add VFA data set")
vbox = QtGui.QVBoxLayout()
grid = QtGui.QGridLayout()
grid.addWidget(QtGui.QLabel("Data set"), 0, 0)
self.data_combo = OverlayCombo(ivm, static_only=True)
# Default to first data which hasn't been used
data = [
i for i in range(self.data_combo.count())
if self.data_combo.itemText(i) not in used
]
if len(data) > 0: self.data_combo.setCurrentIndex(data[0])
self.data_combo.currentIndexChanged.connect(self._guess_fa)
grid.addWidget(self.data_combo, 0, 1)
grid.addWidget(QtGui.QLabel("Flip angle (\N{DEGREE SIGN})"), 1, 0)
self.fa_edit = QtGui.QLineEdit()
self.fa_edit.textChanged.connect(self._validate)
grid.addWidget(self.fa_edit, 1, 1)
vbox.addLayout(grid)
self.buttonBox = QtGui.QDialogButtonBox(
QtGui.QDialogButtonBox.Ok | QtGui.QDialogButtonBox.Cancel)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
self.buttonBox.button(QtGui.QDialogButtonBox.Ok).setEnabled(False)
vbox.addWidget(self.buttonBox)
self.setLayout(vbox)
self._guess_fa()
self._validate()
def _guess_fa(self):
name = self.data_combo.currentText()
m = re.search(r".*?(\d+).*$", name)
if m is not None:
guess = m.group(1)
else:
guess = ""
self.fa_edit.setText(guess)
def _validate(self):
valid = True
try:
fa = float(self.fa_edit.text())
self.fa_edit.setStyleSheet("")
except:
self.fa_edit.setStyleSheet("QLineEdit {background-color: red}")
valid = False
self.buttonBox.button(QtGui.QDialogButtonBox.Ok).setEnabled(valid)
def __init__(self, ivl, view):
QtGui.QGroupBox.__init__(self)
self.ivl = ivl
self.ivm = ivl.ivm
self.view = view
grid = QtGui.QGridLayout()
grid.setVerticalSpacing(2)
grid.setContentsMargins(5, 5, 5, 5)
self.setLayout(grid)
grid.addWidget(QtGui.QLabel("Overlay"), 0, 0)
self.overlay_combo = OverlayCombo(self.ivm,
none_option=True,
set_first=False)
grid.addWidget(self.overlay_combo, 0, 1)
grid.addWidget(QtGui.QLabel("View"), 1, 0)
self.ov_view_combo = QtGui.QComboBox()
self.ov_view_combo.addItem("All")
self.ov_view_combo.addItem("Only in ROI")
self.ov_view_combo.addItem("None")
grid.addWidget(self.ov_view_combo, 1, 1)
grid.addWidget(QtGui.QLabel("Color map"), 2, 0)
hbox = QtGui.QHBoxLayout()
self.ov_cmap_combo = QtGui.QComboBox()
self.ov_cmap_combo.addItem("jet")
self.ov_cmap_combo.addItem("hot")
self.ov_cmap_combo.addItem("gist_heat")
self.ov_cmap_combo.addItem("flame")
self.ov_cmap_combo.addItem("bipolar")
self.ov_cmap_combo.addItem("spectrum")
hbox.addWidget(self.ov_cmap_combo)
self.ov_levels_btn = QtGui.QPushButton()
self.ov_levels_btn.setIcon(QtGui.QIcon(get_icon("levels.png")))
self.ov_levels_btn.setFixedSize(16, 16)
self.ov_levels_btn.setToolTip("Adjust colour map levels")
self.ov_levels_btn.clicked.connect(self._show_ov_levels)
self.ov_levels_btn.setEnabled(False)
hbox.addWidget(self.ov_levels_btn)
grid.addLayout(hbox, 2, 1)
grid.addWidget(QtGui.QLabel("Alpha"), 3, 0)
self.ov_alpha_sld = QtGui.QSlider(QtCore.Qt.Horizontal, self)
self.ov_alpha_sld.setFocusPolicy(QtCore.Qt.NoFocus)
self.ov_alpha_sld.setRange(0, 255)
self.ov_alpha_sld.setValue(255)
grid.addWidget(self.ov_alpha_sld, 3, 1)
grid.setRowStretch(4, 1)
self.overlay_combo.currentIndexChanged.connect(self._combo_changed)
self.ov_view_combo.currentIndexChanged.connect(self._view_changed)
self.ov_cmap_combo.currentIndexChanged.connect(self._cmap_changed)
self.ov_alpha_sld.valueChanged.connect(self._alpha_changed)
self.view.sig_view_changed.connect(self._update)
def __init__(self, **kwargs):
super(MeanValuesWidget, self).__init__(
name="Mean in ROI",
icon="meanvals",
desc="Replace data with its mean value within each ROI region",
group="ROIs",
**kwargs)
layout = QtGui.QVBoxLayout()
title = TitleWidget(self,
"Generate Mean Values Data",
help="mean_values")
layout.addWidget(title)
desc = QtGui.QLabel(
"This widget will convert the current data set into a "
"new data set in which each ROI region contains the mean "
"value for that region.\n\nThis is generally only useful for "
"multi-level ROIs such as clusters or supervoxels")
desc.setWordWrap(True)
layout.addWidget(desc)
hbox = QtGui.QHBoxLayout()
gbox = QtGui.QGroupBox()
gbox.setTitle("Options")
grid = QtGui.QGridLayout()
gbox.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 regions"), 1, 0)
self.roi = RoiCombo(self.ivm)
grid.addWidget(self.roi, 1, 1)
grid.addWidget(QtGui.QLabel("Output name"), 2, 0)
self.output_name = QtGui.QLineEdit()
grid.addWidget(self.output_name, 2, 1)
btn = QtGui.QPushButton('Generate', self)
btn.clicked.connect(self._generate)
grid.addWidget(btn, 2, 0)
hbox.addWidget(gbox)
hbox.addStretch(1)
layout.addLayout(hbox)
layout.addStretch(1)
self.setLayout(layout)
def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
title = TitleWidget(self,
title="Data Smoothing",
subtitle="Smooth data using a Gaussian kernel",
help="smoothing")
vbox.addWidget(title)
hbox = QtGui.QHBoxLayout()
gbox = QtGui.QGroupBox()
gbox.setTitle("Options")
grid = QtGui.QGridLayout()
gbox.setLayout(grid)
grid.addWidget(QtGui.QLabel("Data to smooth"), 0, 0)
self.data_combo = OverlayCombo(self.ivm)
self.data_combo.currentIndexChanged.connect(self.data_changed)
grid.addWidget(self.data_combo, 0, 1)
self.sigma = NumericOption("Sigma (mm)",
grid,
xpos=0,
ypos=1,
minval=0,
step=0.1,
default=1.0)
grid.addWidget(QtGui.QLabel("Output name"), 2, 0)
self.output_name = QtGui.QLineEdit()
grid.addWidget(self.output_name, 2, 1)
hbox.addWidget(gbox)
hbox.addStretch(1)
vbox.addLayout(hbox)
hbox = QtGui.QHBoxLayout()
self.run_btn = QtGui.QPushButton("Run")
self.run_btn.clicked.connect(self.run)
hbox.addWidget(self.run_btn)
hbox.addStretch(1)
vbox.addLayout(hbox)
vbox.addStretch(1)
self.data_changed()
class ImageOptionWidget(OptionWidget):
"""
OptionWidget subclass which allows image options to be chosen
from the current list of overlays
"""
def __init__(self, opt, **kwargs):
OptionWidget.__init__(self, opt, **kwargs)
self.combo = OverlayCombo(self.ivm, static_only=True)
self.widgets.append(self.combo)
def get_value(self):
return self.combo.currentText()
def set_value(self, value):
idx = self.combo.findText(value)
self.combo.setCurrentIndex(idx)
def add(self, grid, row):
OptionWidget.add(self, grid, row)
grid.addWidget(self.combo, row, 1)
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 _get_widgets(self, idx):
prior_idx = self._get_prior_idx(self.params[idx])
ptype = self.rundata.get("PSP_byname%i_type" % prior_idx, "N")
image = self.rundata.get("PSP_byname%i_image" % prior_idx, "")
mean = self.rundata.get("PSP_byname%i_mean" % prior_idx, "")
prec = self.rundata.get("PSP_byname%i_prec" % prior_idx, "")
trans = self.rundata.get("PSP_byname%i_transform" % prior_idx, "")
type_combo = QtGui.QComboBox()
type_combo.addItem("Normal", "N")
type_combo.addItem("Image Prior", "I")
type_combo.addItem("Spatial prior, type M", "M")
type_combo.addItem("Spatial prior , type P", "P")
type_combo.addItem("Spatial prior, type m", "m")
type_combo.addItem("Spatial prior , type p", "p")
type_combo.addItem("ARD prior", "A")
type_combo.setSizeAdjustPolicy(QtGui.QComboBox.AdjustToContents)
type_combo.setCurrentIndex(type_combo.findData(ptype))
type_combo.currentIndexChanged.connect(self._changed)
image_combo = OverlayCombo(self.ivm, static_only=True)
image_combo.setSizeAdjustPolicy(QtGui.QComboBox.AdjustToContents)
if image != "":
image_combo.setCurrentIndex(image_combo.findText(image))
image_combo.currentIndexChanged.connect(self._changed)
mean_cb = QtGui.QCheckBox()
mean_cb.setChecked(ptype != "I" and mean != "")
mean_cb.stateChanged.connect(self._changed)
mean_edit = QtGui.QLineEdit(mean)
mean_edit.editingFinished.connect(self._changed)
prec_cb = QtGui.QCheckBox()
prec_cb.setChecked(prec != "")
prec_cb.stateChanged.connect(self._changed)
prec_edit = QtGui.QLineEdit(prec)
prec_edit.editingFinished.connect(self._changed)
trans_combo = QtGui.QComboBox()
trans_combo.addItem("Default transformation", "")
trans_combo.addItem("No transformation", "I")
trans_combo.addItem("Log transformation", "L")
trans_combo.addItem("Soft-plus transformation", "S")
trans_combo.addItem("Fractional transformation", "F")
trans_combo.setSizeAdjustPolicy(QtGui.QComboBox.AdjustToContents)
trans_combo.setCurrentIndex(trans_combo.findData(trans))
trans_combo.currentIndexChanged.connect(self._changed)
return (type_combo, QtGui.QLabel("Image: "), image_combo, mean_cb,
QtGui.QLabel("Custom mean: "), mean_edit, prec_cb,
QtGui.QLabel("Custom precision: "), prec_edit, trans_combo)
def __init__(self, parent, ivm, used=[]):
super(ChooseDataDialog, self).__init__(parent)
self.setWindowTitle("Add VFA data set")
vbox = QtGui.QVBoxLayout()
grid = QtGui.QGridLayout()
grid.addWidget(QtGui.QLabel("Data set"), 0, 0)
self.data_combo = OverlayCombo(ivm, static_only=True)
# Default to first data which hasn't been used
data = [
i for i in range(self.data_combo.count())
if self.data_combo.itemText(i) not in used
]
if len(data) > 0: self.data_combo.setCurrentIndex(data[0])
self.data_combo.currentIndexChanged.connect(self._guess_fa)
grid.addWidget(self.data_combo, 0, 1)
grid.addWidget(QtGui.QLabel("Flip angle (\N{DEGREE SIGN})"), 1, 0)
self.fa_edit = QtGui.QLineEdit()
self.fa_edit.textChanged.connect(self._validate)
grid.addWidget(self.fa_edit, 1, 1)
vbox.addLayout(grid)
self.buttonBox = QtGui.QDialogButtonBox(
QtGui.QDialogButtonBox.Ok | QtGui.QDialogButtonBox.Cancel)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
self.buttonBox.button(QtGui.QDialogButtonBox.Ok).setEnabled(False)
vbox.addWidget(self.buttonBox)
self.setLayout(vbox)
self._guess_fa()
self._validate()
class ClusteringWidget(QpWidget):
"""
Widget for doing K-means clustering on 3D or 4D data
"""
def __init__(self, **kwargs):
super(ClusteringWidget,
self).__init__(name="KMeans Clustering",
icon="clustering",
desc="Generate clusters from 3D or 4D data",
group="Clustering",
position=2,
**kwargs)
self.curves = {}
def init_ui(self):
self.process = KMeansProcess(self.ivm)
layout = QtGui.QVBoxLayout()
self.setLayout(layout)
title = TitleWidget(self, help="cluster")
layout.addWidget(title)
DESC = """
<i>Performs clustering of 3D or 4D data using the K-means algorithm.
PCA reduction is used on 4D data to extract representative curves
"""
desc = QtGui.QLabel(DESC)
desc.setWordWrap(True)
layout.addWidget(desc)
gbox = QtGui.QGroupBox()
gbox.setTitle('Clustering options')
grid = QtGui.QGridLayout()
gbox.setLayout(grid)
# Data to cluster
grid.addWidget(QtGui.QLabel("Data"), 0, 0)
self.data_combo = OverlayCombo(self.ivm)
self.data_combo.currentIndexChanged.connect(self._data_changed)
grid.addWidget(self.data_combo, 0, 1)
grid.addWidget(QtGui.QLabel("ROI"), 1, 0)
self.roi_combo = RoiCombo(self.ivm, none_option=True)
grid.addWidget(self.roi_combo, 1, 1)
# Number of clusters inside the ROI
self.n_clusters = NumericOption("Number of clusters",
grid,
xpos=2,
ypos=0,
minval=2,
maxval=20,
default=4,
intonly=True)
self.n_clusters.spin.setToolTip("")
# Number of PCA modes
self.n_pca = NumericOption("Number of PCA modes",
grid,
xpos=2,
ypos=1,
minval=1,
maxval=10,
default=3,
intonly=True)
self.n_pca.spin.setToolTip("")
# Output ROI name
grid.addWidget(QtGui.QLabel("Output name"), 2, 0)
self.output_name = QtGui.QLineEdit("clusters")
grid.addWidget(self.output_name, 2, 1)
layout.addWidget(gbox)
# Run clustering button
hbox = QtGui.QHBoxLayout()
self.run_btn = QtGui.QPushButton('Run', self)
self.run_btn.clicked.connect(self.run_clustering)
hbox.addWidget(self.run_btn)
hbox.addStretch(1)
layout.addLayout(hbox)
# Plot window, showing representative curves for 4D data
self.show_curves_btn = QtGui.QPushButton('Show representative curves',
self)
self.show_curves_btn.clicked.connect(self._show_curves)
layout.addWidget(self.show_curves_btn)
self.plotwin = pg.GraphicsLayoutWidget()
self.plotwin.setBackground(background=None)
self.plot = self.plotwin.addPlot(title="Cluster representative curves")
self.plot.setLabel('left', "Signal Enhancement")
self.plotwin.setVisible(False)
layout.addWidget(self.plotwin)
# Statistics
self.show_count_btn = QtGui.QPushButton('Show voxel counts', self)
self.show_count_btn.clicked.connect(self._show_counts)
layout.addWidget(self.show_count_btn)
self.stats_gbox = QtGui.QGroupBox()
self.stats_gbox.setTitle('Voxel count')
self.count_table = QtGui.QStandardItemModel()
self.count_view = QtGui.QTableView()
self.count_view.resizeColumnsToContents()
self.count_view.setModel(self.count_table)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.count_view)
self.stats_gbox.setLayout(hbox)
self.stats_gbox.setVisible(False)
layout.addWidget(self.stats_gbox)
# Merge regions
self.show_merge_btn = QtGui.QPushButton('Show merge options', self)
self.show_merge_btn.clicked.connect(self._show_merge)
layout.addWidget(self.show_merge_btn)
self.merge_gbox = QtGui.QGroupBox()
self.merge_gbox.setTitle('Merge regions')
vbox = QtGui.QVBoxLayout()
self.merge_gbox.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
self.merge_btn = QtGui.QPushButton('Merge', self)
self.merge_btn.clicked.connect(self._run_merge)
hbox.addWidget(self.merge_btn)
hbox.addWidget(QtGui.QLabel('Merge region '))
self.merge_region1 = QtGui.QLineEdit('1', self)
hbox.addWidget(self.merge_region1)
hbox.addWidget(QtGui.QLabel(' with '))
self.merge_region2 = QtGui.QLineEdit('2', self)
hbox.addWidget(self.merge_region2)
vbox.addLayout(hbox)
hbox = QtGui.QHBoxLayout()
self.auto_merge_btn = QtGui.QPushButton('AutoMerge', self)
self.auto_merge_btn.clicked.connect(self._run_automerge)
hbox.addWidget(self.auto_merge_btn)
hbox.addStretch(1)
vbox.addLayout(hbox)
self.merge_gbox.setVisible(False)
layout.addWidget(self.merge_gbox)
layout.addStretch(1)
def activate(self):
self.ivl.sig_focus_changed.connect(self._focus_changed)
self.ivm.sig_current_roi.connect(self._current_roi_changed)
self.ivm.sig_main_data.connect(self._main_data_changed)
self._data_changed()
def deactivate(self):
self.ivl.sig_focus_changed.disconnect(self._focus_changed)
self.ivm.sig_current_roi.disconnect(self._current_roi_changed)
self.ivm.sig_main_data.disconnect(self._main_data_changed)
def _current_roi_changed(self, roi):
if roi is not None and roi.name != self.output_name.text():
self.roi_combo.setCurrentIndex(self.roi_combo.findText(roi.name))
def _main_data_changed(self, data):
if data is not None:
idx = self.data_combo.findText(data.name)
else:
idx = 0
self.data_combo.setCurrentIndex(idx)
def _data_changed(self):
data = self.ivm.data.get(self.data_combo.currentText(), None)
if data is not None:
is4d = data.nvols > 1
self.debug("Number of vols: %i, 4d=%s", data.nvols, is4d)
self.n_pca.label.setVisible(is4d)
self.n_pca.spin.setVisible(is4d)
self.show_curves_btn.setVisible(is4d)
self.plotwin.setVisible(is4d and self.plotwin.isVisible())
self.auto_merge_btn.setEnabled(is4d)
self.run_btn.setEnabled(data is not None)
def _focus_changed(self):
self._update_voxel_count()
def _show_curves(self):
if self.plotwin.isVisible():
self.plotwin.setVisible(False)
self.show_curves_btn.setText("Show representative curves")
else:
self.plotwin.setVisible(True)
self.show_curves_btn.setText("Hide representative curves")
def _show_counts(self):
if self.stats_gbox.isVisible():
self.stats_gbox.setVisible(False)
self.show_count_btn.setText("Show voxel counts")
else:
self.stats_gbox.setVisible(True)
self.show_count_btn.setText("Hide voxel counts")
def _show_merge(self):
if self.merge_gbox.isVisible():
self.merge_gbox.setVisible(False)
self.show_merge_btn.setText("Show merge_options")
else:
self.merge_gbox.setVisible(True)
self.show_merge_btn.setText("Hide merge options")
def batch_options(self):
options = {
"data": self.data_combo.currentText(),
"roi": self.roi_combo.currentText(),
"n-clusters": self.n_clusters.spin.value(),
"output-name": self.output_name.text(),
"invert-roi": False,
}
if options["roi"] == "<none>":
del options["roi"]
if self.n_pca.label.isVisible():
# 4D PCA options
options["n-pca"] = self.n_pca.spin.value()
options["reduction"] = "pca"
options["norm-data"] = True
return "KMeans", options
def run_clustering(self):
"""
Run kmeans clustering using normalised PCA modes
"""
options = self.batch_options()[1]
self.process.run(options)
self._update_voxel_count()
if self.n_pca.label.isVisible():
self.update_plot()
def _update_voxel_count(self):
self.count_table.clear()
self.count_table.setVerticalHeaderItem(
0, QtGui.QStandardItem("Voxel count"))
roi = self.ivm.rois.get(self.output_name.text(), None)
if roi is not None:
col_idx = 0
for region, name in roi.regions.items():
self.count_table.setHorizontalHeaderItem(
col_idx, QtGui.QStandardItem(name))
# Volume count
voxel_count = np.sum(roi.raw() == region)
self.count_table.setItem(
0, col_idx,
QtGui.QStandardItem(str(np.around(voxel_count))))
col_idx += 1
def update_plot(self):
"""
Plot the cluster curves
:return:
"""
# Clear graph
self.plot.clear()
self.plot.setLabel('bottom', "Volume", "")
if self.plot.legend is not None:
# Work around pyqtgraph legend bug - the legend is recreated multiple times!
# https://stackoverflow.com/questions/42792858/pyqtgraph-delete-persisting-legend-in-pyqt4-gui
self.plot.legend.scene().removeItem(self.plot.legend)
data = self.ivm.data.get(self.data_combo.currentText(), None)
roi = self.ivm.rois.get(self.output_name.text(), None)
if roi is not None and data is not None and data.nvols > 1:
# Generate mean curve for each cluster
self._generate_cluster_means(roi, data)
self.plot.addLegend()
# Plotting using single or multiple plots
for region, name in roi.regions.items():
if np.sum(self.curves[region]) == 0:
continue
pencol = get_pencol(roi, region)
curve = self.plot.plot(pen=pencol, width=8.0, name=name)
xx = np.arange(len(self.curves[region]))
curve.setData(xx, self.curves[region])
def _run_merge(self):
m1 = int(self.merge_region1.text())
m2 = int(self.merge_region2.text())
self._merge(m1, m2)
def _run_automerge(self):
# Use PCA features or true curves?
# Mean features from each cluster
# Distance matrix between features
if len(self.curves) < 2: return
curvemat = np.zeros((len(self.curves), self.ivm.main.nvols))
row_region = {}
idx = 0
for region, curve in self.curves.items():
row_region[idx] = region
curvemat[idx, :] = curve
idx += 1
distmat = pairwise.euclidean_distances(curvemat)
distmat[distmat == 0] = np.inf
loc1 = np.where(distmat == distmat.min())[0]
self._merge(row_region[loc1[0]], row_region[loc1[1]])
def _generate_cluster_means(self, roi, data):
"""
Generate the mean curves for each cluster
Returns:
"""
self.curves = {}
for region in roi.regions:
roi_data = data.mask(roi, region=region, output_flat=True)
mean = np.median(roi_data, axis=0)
self.curves[region] = mean
def _merge(self, m1, m2):
roi = self.ivm.rois.get(self.output_name.text(), None)
if roi is not None:
roi_data = roi.raw()
roi_data[roi_data == m1] = m2
# signal the change
self.ivm.add(NumpyData(roi_data,
grid=roi.grid,
name=self.output_name.text(),
roi=True),
make_current=True)
# replot
self.update_plot()
self._update_voxel_count()
class SmoothingWidget(QpWidget):
"""
Gaussian smoothing widget
"""
def __init__(self, **kwargs):
super(SmoothingWidget, self).__init__(name="Smoothing",
icon="smooth.png",
desc="Gaussian smoothing",
group="Processing",
**kwargs)
def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
title = TitleWidget(self,
title="Data Smoothing",
subtitle="Smooth data using a Gaussian kernel",
help="smoothing")
vbox.addWidget(title)
hbox = QtGui.QHBoxLayout()
gbox = QtGui.QGroupBox()
gbox.setTitle("Options")
grid = QtGui.QGridLayout()
gbox.setLayout(grid)
grid.addWidget(QtGui.QLabel("Data to smooth"), 0, 0)
self.data_combo = OverlayCombo(self.ivm)
self.data_combo.currentIndexChanged.connect(self.data_changed)
grid.addWidget(self.data_combo, 0, 1)
self.sigma = NumericOption("Sigma (mm)",
grid,
xpos=0,
ypos=1,
minval=0,
step=0.1,
default=1.0)
grid.addWidget(QtGui.QLabel("Output name"), 2, 0)
self.output_name = QtGui.QLineEdit()
grid.addWidget(self.output_name, 2, 1)
hbox.addWidget(gbox)
hbox.addStretch(1)
vbox.addLayout(hbox)
hbox = QtGui.QHBoxLayout()
self.run_btn = QtGui.QPushButton("Run")
self.run_btn.clicked.connect(self.run)
hbox.addWidget(self.run_btn)
hbox.addStretch(1)
vbox.addLayout(hbox)
vbox.addStretch(1)
self.data_changed()
def data_changed(self):
self.output_name.setText("%s_smoothed" % self.data_combo.currentText())
self.run_btn.setEnabled(self.data_combo.currentText() in self.ivm.data)
def batch_options(self):
return "Smooth", {
"data": self.data_combo.currentText(),
"sigma": self.sigma.spin.value(),
"output-name": self.output_name.text()
}
def run(self):
process = SmoothingProcess(self.ivm)
process.run(self.batch_options()[1])
def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
title = TitleWidget(self, batch_btn=False, help="compare")
vbox.addWidget(title)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(QtGui.QLabel("Compare "))
self.d1_combo = OverlayCombo(self.ivm)
self.d1_combo.currentIndexChanged.connect(self._update_data)
hbox.addWidget(self.d1_combo)
hbox.addWidget(QtGui.QLabel(" with "))
self.d2_combo = OverlayCombo(self.ivm)
self.d2_combo.currentIndexChanged.connect(self._update_data)
hbox.addWidget(self.d2_combo)
hbox.addStretch(1)
vbox.addLayout(hbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(QtGui.QLabel("Within ROI "))
self.roi_combo = OverlayCombo(self.ivm,
rois=True,
data=False,
none_option=True)
self.roi_combo.currentIndexChanged.connect(self._update_data)
hbox.addWidget(self.roi_combo)
hbox.addStretch(1)
vbox.addLayout(hbox)
hbox = QtGui.QHBoxLayout()
gbox = QtGui.QGroupBox("Options")
grid = QtGui.QGridLayout()
gbox.setLayout(grid)
self.id_cb = QtGui.QCheckBox("Include identity line")
grid.addWidget(self.id_cb, 0, 0)
self.sample_cb = QtGui.QCheckBox("Sample values")
self.sample_cb.setChecked(True)
self.sample_cb.stateChanged.connect(self._update_data)
self.sample_cb.stateChanged.connect(self._update_gui)
grid.addWidget(self.sample_cb, 1, 0)
self.sample_spin = QtGui.QSpinBox()
self.sample_spin.setMinimum(10)
self.sample_spin.setMaximum(10000000)
self.sample_spin.setSingleStep(100)
self.sample_spin.setValue(1000)
self.sample_spin.valueChanged.connect(self._update_data)
grid.addWidget(self.sample_spin, 1, 1)
self.warn_label = QtGui.QLabel(
"WARNING: plotting all values may take a long time")
self.warn_label.setStyleSheet("QLabel { color : red; }")
self.warn_label.setVisible(False)
grid.addWidget(self.warn_label, 2, 0)
self.plot_mode = ChoiceOption("Plot mode",
grid,
3,
choices=["Scatter", "Heat map"])
self.plot_mode.combo.currentIndexChanged.connect(
self._plot_mode_changed)
self.bins = NumericOption("Bins",
grid,
3,
xpos=2,
minval=20,
default=50,
intonly=True)
self.bins.label.setVisible(False)
self.bins.spin.setVisible(False)
self.run_btn = QtGui.QPushButton("Update")
self.run_btn.clicked.connect(self._run)
grid.addWidget(self.run_btn, 4, 0)
hbox.addWidget(gbox)
hbox.addStretch(1)
vbox.addLayout(hbox)
hbox = QtGui.QHBoxLayout()
win = pg.GraphicsLayoutWidget()
win.setBackground(background=None)
self.plot = win.addPlot(enableAutoRange=True)
self.plot.clear() # Unsure why this is necessary
hbox.addWidget(win)
self.hist = pg.HistogramLUTWidget()
self.hist.setVisible(False)
self.hist.setBackground(None)
self.hist.gradient.loadPreset("thermal")
hbox.addWidget(self.hist)
vbox.addLayout(hbox)
self._update_gui()
self._update_data()
class CompareDataWidget(QpWidget):
"""
Compare two data sets
"""
def __init__(self, **kwargs):
QpWidget.__init__(self,
name="Compare Data",
icon="compare.png",
desc="Compare two data sets",
group="Visualisation",
**kwargs)
def init_ui(self):
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
title = TitleWidget(self, batch_btn=False, help="compare")
vbox.addWidget(title)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(QtGui.QLabel("Compare "))
self.d1_combo = OverlayCombo(self.ivm)
self.d1_combo.currentIndexChanged.connect(self._update_data)
hbox.addWidget(self.d1_combo)
hbox.addWidget(QtGui.QLabel(" with "))
self.d2_combo = OverlayCombo(self.ivm)
self.d2_combo.currentIndexChanged.connect(self._update_data)
hbox.addWidget(self.d2_combo)
hbox.addStretch(1)
vbox.addLayout(hbox)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(QtGui.QLabel("Within ROI "))
self.roi_combo = OverlayCombo(self.ivm,
rois=True,
data=False,
none_option=True)
self.roi_combo.currentIndexChanged.connect(self._update_data)
hbox.addWidget(self.roi_combo)
hbox.addStretch(1)
vbox.addLayout(hbox)
hbox = QtGui.QHBoxLayout()
gbox = QtGui.QGroupBox("Options")
grid = QtGui.QGridLayout()
gbox.setLayout(grid)
self.id_cb = QtGui.QCheckBox("Include identity line")
grid.addWidget(self.id_cb, 0, 0)
self.sample_cb = QtGui.QCheckBox("Sample values")
self.sample_cb.setChecked(True)
self.sample_cb.stateChanged.connect(self._update_data)
self.sample_cb.stateChanged.connect(self._update_gui)
grid.addWidget(self.sample_cb, 1, 0)
self.sample_spin = QtGui.QSpinBox()
self.sample_spin.setMinimum(10)
self.sample_spin.setMaximum(10000000)
self.sample_spin.setSingleStep(100)
self.sample_spin.setValue(1000)
self.sample_spin.valueChanged.connect(self._update_data)
grid.addWidget(self.sample_spin, 1, 1)
self.warn_label = QtGui.QLabel(
"WARNING: plotting all values may take a long time")
self.warn_label.setStyleSheet("QLabel { color : red; }")
self.warn_label.setVisible(False)
grid.addWidget(self.warn_label, 2, 0)
self.plot_mode = ChoiceOption("Plot mode",
grid,
3,
choices=["Scatter", "Heat map"])
self.plot_mode.combo.currentIndexChanged.connect(
self._plot_mode_changed)
self.bins = NumericOption("Bins",
grid,
3,
xpos=2,
minval=20,
default=50,
intonly=True)
self.bins.label.setVisible(False)
self.bins.spin.setVisible(False)
self.run_btn = QtGui.QPushButton("Update")
self.run_btn.clicked.connect(self._run)
grid.addWidget(self.run_btn, 4, 0)
hbox.addWidget(gbox)
hbox.addStretch(1)
vbox.addLayout(hbox)
hbox = QtGui.QHBoxLayout()
win = pg.GraphicsLayoutWidget()
win.setBackground(background=None)
self.plot = win.addPlot(enableAutoRange=True)
self.plot.clear() # Unsure why this is necessary
hbox.addWidget(win)
self.hist = pg.HistogramLUTWidget()
self.hist.setVisible(False)
self.hist.setBackground(None)
self.hist.gradient.loadPreset("thermal")
hbox.addWidget(self.hist)
vbox.addLayout(hbox)
self._update_gui()
self._update_data()
def _plot_mode_changed(self, idx):
self.bins.label.setVisible(idx == 1)
self.bins.spin.setVisible(idx == 1)
self.sample_cb.setChecked(idx == 0)
self._update_gui()
self._update_data()
def _update_gui(self):
self.sample_spin.setEnabled(self.sample_cb.isChecked())
def _update_data(self):
name1 = self.d1_combo.currentText()
name2 = self.d2_combo.currentText()
roi_name = self.roi_combo.currentText()
qpd1 = self.ivm.data.get(name1, None)
qpd2 = self.ivm.data.get(name2, None)
roi = self.ivm.rois.get(roi_name, None)
if qpd1 is not None and qpd2 is not None:
current_vol = self.ivl.focus()[3]
d1 = qpd1.volume(current_vol)
d2 = qpd2.resample(qpd1.grid).volume(current_vol)
if roi is not None:
roi_data = roi.resample(qpd1.grid).raw()
d1 = d1[roi_data > 0]
d2 = d2[roi_data > 0]
else:
d1 = d1.reshape(-1)
d2 = d2.reshape(-1)
if self.sample_cb.isChecked():
n_samples = self.sample_spin.value()
idx = np.random.choice(np.arange(len(d1)), n_samples)
d1 = np.take(d1, idx)
d2 = np.take(d2, idx)
self.warn_label.setVisible(False)
else:
# Warn about plotting all data in scatter mode
self.warn_label.setVisible(
self.plot_mode.combo.currentIndex() == 0)
self.d1 = d1
self.d2 = d2
self.run_btn.setEnabled(True)
else:
self.run_btn.setEnabled(False)
def _run(self):
self.plot.clear()
self.plot.setLabel('bottom', self.d1_combo.currentText())
self.plot.setLabel('left', self.d2_combo.currentText())
if self.plot_mode.combo.currentIndex() == 0:
self.plot.setAspectLocked(False)
self.hist.setVisible(False)
self.plot.plot(self.d1,
self.d2,
pen=None,
symbolBrush=(200, 200, 200),
symbolPen='k',
symbolSize=5.0)
else:
heatmap, xedges, yedges = np.histogram2d(self.d1,
self.d2,
bins=self.bins.value())
rect = QtCore.QRectF(xedges[0], yedges[0], xedges[-1] - xedges[0],
yedges[-1] - yedges[0])
img = pg.ImageItem(heatmap)
img.setRect(rect)
#self.plot.setAspectLocked(True)
self.hist.setVisible(True)
self.hist.setImageItem(img)
self.plot.addItem(img)
if self.id_cb.isChecked():
real_min = max(self.d1.min(), self.d2.min())
real_max = min(self.d1.max(), self.d2.max())
pen = pg.mkPen((255, 255, 255), style=QtCore.Qt.DashLine)
self.plot.plot([real_min, real_max], [real_min, real_max],
pen=pen,
width=2.0)
class FabberT1Widget(QpWidget):
"""
T1 from VFA images, using the Fabber process
"""
def __init__(self, **kwargs):
QpWidget.__init__(
self,
name="Fabber T1",
icon="t10_fabber",
group="T1",
desc="T1 mapping from VFA images using Bayesian inference",
**kwargs)
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()
def update_ui(self):
multivol = self.multivol_choice.combo.currentIndex() == 0
self.multivol_label.setVisible(multivol)
self.multivol_combo.setVisible(multivol)
self.multivol_fas_label.setVisible(multivol)
self.multivol_fas.setVisible(multivol)
self.singlevol_label.setVisible(not multivol)
self.singlevol_table.setVisible(not multivol)
self.singlevol_add.setVisible(not multivol)
self.singlevol_clear.setVisible(not multivol)
def add_vol(self):
used = [
self.singlevol_table.item(i, 0).text()
for i in range(self.singlevol_table.rowCount())
]
dlg = ChooseDataDialog(self, self.ivm, used)
if dlg.exec_():
nrows = self.singlevol_table.rowCount()
self.singlevol_table.setRowCount(nrows + 1)
self.singlevol_table.setItem(
nrows, 0, QtGui.QTableWidgetItem(dlg.data_combo.currentText()))
self.singlevol_table.setItem(
nrows, 1, QtGui.QTableWidgetItem(dlg.fa_edit.text()))
def clear_vols(self):
self.singlevol_table.setRowCount(0)
def get_process(self):
return self.FabberProcess(self.ivm)
def batch_options(self):
return "Fabber", self.get_rundata()
def get_rundata(self):
rundata = {}
rundata["model-group"] = "t1"
rundata["save-mean"] = ""
rundata["save-model-fit"] = ""
rundata["noise"] = "white"
rundata["max-iterations"] = "20"
rundata["model"] = "vfa"
rundata["tr"] = self.tr.spin.value() / 1000
multivol = self.multivol_choice.combo.currentIndex() == 0
if multivol and self.multivol_combo.currentText() in self.ivm.data:
rundata["data"] = self.multivol_combo.currentText()
fas = self.multivol_fas.values()
nvols = self.ivm.data[self.multivol_combo.currentText()].nvols
if nvols != len(fas):
raise QpException(
"Number of flip angles must match the number of volumes in the selected data (%i)"
% nvols)
for idx, fa in enumerate(fas):
rundata["fa%i" % (idx + 1)] = fa
else:
rundata["data"] = []
for r in range(self.singlevol_table.rowCount()):
rundata["data"].append(self.singlevol_table.item(r, 0).text())
rundata["fa%i" % (r + 1)] = float(
self.singlevol_table.item(r, 1).text())
return rundata
class PerfSlicWidget(QpWidget):
"""
Generates supervoxels using SLIC method
"""
def __init__(self, **kwargs):
super(PerfSlicWidget, self).__init__(name="Super Voxels", icon="sv",
desc="Generate supervoxel clusters",
group="Clustering", **kwargs)
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 _data_changed(self, _):
name = self.ovl.currentText()
if name:
ovl = self.ivm.data[name]
self.n_comp.label.setVisible(ovl.nvols > 1)
self.n_comp.spin.setVisible(ovl.nvols > 1)
def batch_options(self):
options = {
"data" : self.ovl.currentText(),
"roi" : self.roi.currentText(),
"n-components" : self.n_comp.spin.value(),
"compactness" : self.compactness.spin.value(),
"sigma" : self.sigma.spin.value(),
"n-supervoxels" : self.n_supervoxels.spin.value(),
"output-name" : self.output_name.text()
}
return "Supervoxels", options
def _generate(self):
process = SupervoxelsProcess(self.ivm, sync=True)
process.run(self.batch_options()[1])
def init_ui(self):
self.process = KMeansProcess(self.ivm)
layout = QtGui.QVBoxLayout()
self.setLayout(layout)
title = TitleWidget(self, help="cluster")
layout.addWidget(title)
DESC = """
<i>Performs clustering of 3D or 4D data using the K-means algorithm.
PCA reduction is used on 4D data to extract representative curves
"""
desc = QtGui.QLabel(DESC)
desc.setWordWrap(True)
layout.addWidget(desc)
gbox = QtGui.QGroupBox()
gbox.setTitle('Clustering options')
grid = QtGui.QGridLayout()
gbox.setLayout(grid)
# Data to cluster
grid.addWidget(QtGui.QLabel("Data"), 0, 0)
self.data_combo = OverlayCombo(self.ivm)
self.data_combo.currentIndexChanged.connect(self._data_changed)
grid.addWidget(self.data_combo, 0, 1)
grid.addWidget(QtGui.QLabel("ROI"), 1, 0)
self.roi_combo = RoiCombo(self.ivm, none_option=True)
grid.addWidget(self.roi_combo, 1, 1)
# Number of clusters inside the ROI
self.n_clusters = NumericOption("Number of clusters",
grid,
xpos=2,
ypos=0,
minval=2,
maxval=20,
default=4,
intonly=True)
self.n_clusters.spin.setToolTip("")
# Number of PCA modes
self.n_pca = NumericOption("Number of PCA modes",
grid,
xpos=2,
ypos=1,
minval=1,
maxval=10,
default=3,
intonly=True)
self.n_pca.spin.setToolTip("")
# Output ROI name
grid.addWidget(QtGui.QLabel("Output name"), 2, 0)
self.output_name = QtGui.QLineEdit("clusters")
grid.addWidget(self.output_name, 2, 1)
layout.addWidget(gbox)
# Run clustering button
hbox = QtGui.QHBoxLayout()
self.run_btn = QtGui.QPushButton('Run', self)
self.run_btn.clicked.connect(self.run_clustering)
hbox.addWidget(self.run_btn)
hbox.addStretch(1)
layout.addLayout(hbox)
# Plot window, showing representative curves for 4D data
self.show_curves_btn = QtGui.QPushButton('Show representative curves',
self)
self.show_curves_btn.clicked.connect(self._show_curves)
layout.addWidget(self.show_curves_btn)
self.plotwin = pg.GraphicsLayoutWidget()
self.plotwin.setBackground(background=None)
self.plot = self.plotwin.addPlot(title="Cluster representative curves")
self.plot.setLabel('left', "Signal Enhancement")
self.plotwin.setVisible(False)
layout.addWidget(self.plotwin)
# Statistics
self.show_count_btn = QtGui.QPushButton('Show voxel counts', self)
self.show_count_btn.clicked.connect(self._show_counts)
layout.addWidget(self.show_count_btn)
self.stats_gbox = QtGui.QGroupBox()
self.stats_gbox.setTitle('Voxel count')
self.count_table = QtGui.QStandardItemModel()
self.count_view = QtGui.QTableView()
self.count_view.resizeColumnsToContents()
self.count_view.setModel(self.count_table)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.count_view)
self.stats_gbox.setLayout(hbox)
self.stats_gbox.setVisible(False)
layout.addWidget(self.stats_gbox)
# Merge regions
self.show_merge_btn = QtGui.QPushButton('Show merge options', self)
self.show_merge_btn.clicked.connect(self._show_merge)
layout.addWidget(self.show_merge_btn)
self.merge_gbox = QtGui.QGroupBox()
self.merge_gbox.setTitle('Merge regions')
vbox = QtGui.QVBoxLayout()
self.merge_gbox.setLayout(vbox)
hbox = QtGui.QHBoxLayout()
self.merge_btn = QtGui.QPushButton('Merge', self)
self.merge_btn.clicked.connect(self._run_merge)
hbox.addWidget(self.merge_btn)
hbox.addWidget(QtGui.QLabel('Merge region '))
self.merge_region1 = QtGui.QLineEdit('1', self)
hbox.addWidget(self.merge_region1)
hbox.addWidget(QtGui.QLabel(' with '))
self.merge_region2 = QtGui.QLineEdit('2', self)
hbox.addWidget(self.merge_region2)
vbox.addLayout(hbox)
hbox = QtGui.QHBoxLayout()
self.auto_merge_btn = QtGui.QPushButton('AutoMerge', self)
self.auto_merge_btn.clicked.connect(self._run_automerge)
hbox.addWidget(self.auto_merge_btn)
hbox.addStretch(1)
vbox.addLayout(hbox)
self.merge_gbox.setVisible(False)
layout.addWidget(self.merge_gbox)
layout.addStretch(1)
class AslImageWidget(QtGui.QWidget, LogSource):
"""
QWidget which allows an ASL data set to be described
This is intended to be embedded into a QpWidget which supports processing of ASL data
"""
# Signal emitted when the data or metadata is changed
sig_changed = QtCore.Signal()
def __init__(self, ivm, parent=None, **kwargs):
LogSource.__init__(self)
QtGui.QWidget.__init__(self, parent)
self.ivm = ivm
self.data = None
self.default_md = kwargs.get("default_metadata", DEFAULT_METADATA)
self.md = dict(self.default_md)
self.aslimage = None
self.valid = True
vbox = QtGui.QVBoxLayout()
self.setLayout(vbox)
grid = QtGui.QGridLayout()
grid.addWidget(QtGui.QLabel("ASL data"), 0, 0)
self.data_combo = OverlayCombo(self.ivm)
self.data_combo.currentIndexChanged.connect(self._data_changed)
grid.addWidget(self.data_combo, 0, 1)
view_classes = [
LabelType, RepeatsChoice, NumPhases, NumEncodings, BlockFormat,
DataStructure, SignalView, Labelling, Readout, SliceTime,
Multiband, Times, BolusDurations, VariableRepeats
]
self.views = []
for idx, view_class in enumerate(view_classes):
if view_class in kwargs.get("ignore_views", ()):
continue
view = view_class(grid, ypos=idx + 2)
view.ivm = self.ivm
view.sig_md_changed.connect(self._metadata_changed)
self.views.append(view)
#grid.addWidget(QtGui.QLabel("Data order preview"), 5, 0)
# Code below is for specific multiple phases
#self.phases_lbl = QtGui.QLabel("Phases (\N{DEGREE SIGN})")
#grid.addWidget(self.phases_lbl, 3, 0)
#self.phases_lbl.setVisible(False)
#self.phases = NumberList([float(x)*360/8 for x in range(8)])
#grid.addWidget(self.phases, 3, 1)
#self.phases.setVisible(False)
grid.setColumnStretch(0, 0)
grid.setColumnStretch(1, 1)
grid.setColumnStretch(2, 0)
grid.setRowStretch(len(view_classes) + 2, 1)
self.grid = grid
vbox.addLayout(grid)
self.warn_label = WarningBox()
vbox.addWidget(self.warn_label)
self._update_ui()
self._data_changed()
def set_data_name(self, name):
""" Set the name of the data item being displayed """
if name not in self.ivm.data:
raise QpException("Data not found: %s" % name)
else:
idx = self.data_combo.findText(name)
self.data_combo.setCurrentIndex(idx)
def _data_changed(self):
"""
New data selected - load any previously defined metadata, and validate it
"""
self.data = self.ivm.data.get(self.data_combo.currentText(), None)
for idx in range(self.grid.count()):
if idx > 1:
w = self.grid.itemAt(idx).widget()
if w is not None:
w.setEnabled(self.data is not None)
if self.data is not None:
self.md = self.data.metadata.get("AslData", None)
if self.md is None:
self.md = dict(self.default_md)
if self.data.nvols % 2 == 0:
# Even number of volumes - guess TC pairs
# FIXME don't need block format for single TI
self.md["iaf"] = "tc"
self.md["ibf"] = "tis"
for view in self.views:
view.set_data(self.data, self.md)
self._validate_metadata()
self.sig_changed.emit()
def _metadata_changed(self, sender):
"""
Called when a view has changed the metadata
"""
self.debug("Metadata changed %s", sender)
if self.data is not None:
self.debug("Current metadata: %s", self.md)
self.debug("New metadata: %s", sender.md)
self.md = sender.md
self._validate_metadata()
self._save_metadata()
self.sig_changed.emit()
def _save_metadata(self):
"""
Set the metadata on the dataset
"""
if self.data is not None:
current_md = self.data.metadata.get("AslData", {})
self.debug("Save: Current metadata: %s", current_md)
if self.md != current_md:
self.debug("Different!")
self.data.metadata["AslData"] = dict(self.md)
self.debug("Saved: %s ", self.md)
self._update_ui()
def _update_ui(self, ignore=()):
"""
Update user interface from the current metadata
"""
try:
for view in self.views:
if view not in ignore:
view.set_data(self.data, self.md)
finally:
self.updating_ui = False
def _validate_metadata(self):
"""
Validate data against specified TIs, etc
"""
try:
if self.md and self.data is not None:
self.debug("Validating metadata: %s", str(self.md))
self.aslimage, _ = qpdata_to_aslimage(self.data,
metadata=self.md)
self.warn_label.clear()
self.valid = True
except ValueError as e:
self.debug("Failed: %s", str(e))
self.aslimage = None
self.warn_label.warn(str(e))
self.valid = False
def get_options(self):
""" Get batch options """
options = {}
if self.data is not None:
options["data"] = self.data.name
options.update(self.md)
return options
class WalkerTool(Tool):
"""
Tool which uses the random walker method to select a region
FIXME this does not work properly in slice mode at the moment because the zaxis/pos
given by the picker does not necessarily correspond to the data axes.
"""
def __init__(self):
Tool.__init__(self, "Walker", "Automatic segmentation using the random walk algorithm")
self.segmode = 0
self.pickmode = 0
def interface(self):
grid = Tool.interface(self)
grid.addWidget(QtGui.QLabel("Source data: "), 1, 0)
self.ov_combo = OverlayCombo(self.ivm)
grid.addWidget(self.ov_combo)
grid.addWidget(QtGui.QLabel("Click to select points: "), 2, 0)
self.pickmode_combo = QtGui.QComboBox()
self.pickmode_combo.addItem("Inside the ROI")
self.pickmode_combo.addItem("Outside the ROI")
self.pickmode_combo.currentIndexChanged.connect(self._pick_mode_changed)
grid.addWidget(self.pickmode_combo, 2, 1)
grid.addWidget(QtGui.QLabel("Segmentation mode: "), 3, 0)
self.segmode_combo = QtGui.QComboBox()
self.segmode_combo.addItem("Slice")
self.segmode_combo.addItem("3D")
self.segmode_combo.currentIndexChanged.connect(self._seg_mode_changed)
grid.addWidget(self.segmode_combo, 3, 1)
self.beta = NumericOption("Diffusion difficulty", grid, 4, 0, intonly=True, maxval=20000, default=10000, step=1000)
btn = QtGui.QPushButton("Segment")
btn.clicked.connect(self._segment)
grid.addWidget(btn, 5, 0)
btn = QtGui.QPushButton("Clear points")
btn.clicked.connect(self._init)
grid.addWidget(btn, 5, 1)
return grid
def _pick_mode_changed(self, idx=None):
self.pickmode = idx
if self.pickmode == 0:
self.ivl.picker.col = (255, 0, 0)
else:
self.ivl.picker.col = (255, 255, 255)
def _seg_mode_changed(self, idx=None):
self.segmode = idx
self._init()
def _init(self):
if self.segmode == 1:
self.ivl.set_picker(PickMode.MULTIPLE)
else:
self.ivl.set_picker(PickMode.SLICE_MULTIPLE)
self.labels = np.zeros(self.builder.grid.shape, dtype=np.int)
self._pick_mode_changed(self.pickmode)
def selected(self):
self.pickmode = 0
self.segmode = 0
self.ivl.sig_selection_changed.connect(self._points_changed)
self._init()
def deselected(self):
self.ivl.sig_selection_changed.disconnect(self._points_changed)
Tool.deselected(self)
def _points_changed(self):
for col, points in self.ivl.picker.selection(grid=self.builder.grid).items():
if col == ((255, 0, 0)):
label = 1
else:
label = 2
for pos in points:
pos = [int(p+0.5) for p in pos]
# Clamp points to within range of ROI
for dim in range(3):
pos[dim] = min(max(pos[dim], 0), self.labels.shape[dim]-1)
self.labels[pos[0], pos[1], pos[2]] = label
def _segment(self):
data = self.ivm.data[self.ov_combo.currentText()].resample(self.builder.grid)
labels = self.labels
kwargs = {}
# Use voxel size correctly
spacing = [data.grid.spacing[0] / data.grid.spacing[0],
data.grid.spacing[0] / data.grid.spacing[1],
data.grid.spacing[0] / data.grid.spacing[2]]
arr = data.raw()
if arr.ndim > 3:
# Reduce 4D data to PCA modes
pca = PcaFeatReduce(n_components=5)
arr = pca.get_training_features(arr, feature_volume=True)
kwargs["multichannel"] = True
else:
# Normalize data
arr = (arr / (np.max(arr)-np.min(arr))) + np.min(arr)
kwargs["multichannel"] = False
if self.segmode == 0:
# Segment using 2D slice only
zaxis = self.ivl.picker.zaxis
zpos = int(self.ivl.picker.zpos + 0.5)
#print(zaxis, zpos)
sl = [slice(None)] * 3
sl[zaxis] = zpos
arr = arr[sl]
labels = self.labels[sl]
del spacing[zaxis]
#print(labels)
#print(np.count_nonzero(labels))
#print(np.count_nonzero(arr))
seg = skimage.segmentation.random_walker(arr, labels, beta=self.beta.spin.value(),
mode='cg_mg', spacing=spacing, **kwargs)
if self.segmode == 0:
# Create 3D volume using 2D slice
seg_3d = np.zeros(self.builder.grid.shape, dtype=np.int)
seg_3d[sl] = seg
seg = seg_3d
# Label 2 is used for 'outside region'
seg[seg == 2] = 0
self.builder.modify(vol=seg, mode=self.builder.ADD)
self._init()
class MeanValuesWidget(QpWidget):
"""
Convert a data + multi-level ROI into mean values data set
"""
def __init__(self, **kwargs):
super(MeanValuesWidget, self).__init__(
name="Mean in ROI",
icon="meanvals",
desc="Replace data with its mean value within each ROI region",
group="ROIs",
**kwargs)
layout = QtGui.QVBoxLayout()
title = TitleWidget(self,
"Generate Mean Values Data",
help="mean_values")
layout.addWidget(title)
desc = QtGui.QLabel(
"This widget will convert the current data set into a "
"new data set in which each ROI region contains the mean "
"value for that region.\n\nThis is generally only useful for "
"multi-level ROIs such as clusters or supervoxels")
desc.setWordWrap(True)
layout.addWidget(desc)
hbox = QtGui.QHBoxLayout()
gbox = QtGui.QGroupBox()
gbox.setTitle("Options")
grid = QtGui.QGridLayout()
gbox.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 regions"), 1, 0)
self.roi = RoiCombo(self.ivm)
grid.addWidget(self.roi, 1, 1)
grid.addWidget(QtGui.QLabel("Output name"), 2, 0)
self.output_name = QtGui.QLineEdit()
grid.addWidget(self.output_name, 2, 1)
btn = QtGui.QPushButton('Generate', self)
btn.clicked.connect(self._generate)
grid.addWidget(btn, 2, 0)
hbox.addWidget(gbox)
hbox.addStretch(1)
layout.addLayout(hbox)
layout.addStretch(1)
self.setLayout(layout)
def _data_changed(self):
name = self.ovl.currentText()
if name:
self.output_name.setText(name + "_means")
def batch_options(self):
options = {
"roi": self.roi.currentText(),
"data": self.ovl.currentText(),
"output-name": self.output_name.text()
}
return "MeanValues", options
def _generate(self):
options = self.batch_options()[1]
if not options["data"]:
QtGui.QMessageBox.warning(
self, "No data selected",
"Load data to generate mean values from",
QtGui.QMessageBox.Close)
return
if not options["roi"]:
QtGui.QMessageBox.warning(self, "No ROI selected",
"Load an ROI for mean value regions",
QtGui.QMessageBox.Close)
return
process = MeanValuesProcess(self.ivm)
process.run(options)
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()
def __init__(self, opt, **kwargs):
OptionWidget.__init__(self, opt, **kwargs)
self.combo = OverlayCombo(self.ivm, static_only=True)
self.widgets.append(self.combo)
class OverlayViewWidget(QtGui.QGroupBox):
""" Change view options for ROI """
def __init__(self, ivl, view):
QtGui.QGroupBox.__init__(self)
self.ivl = ivl
self.ivm = ivl.ivm
self.view = view
grid = QtGui.QGridLayout()
grid.setVerticalSpacing(2)
grid.setContentsMargins(5, 5, 5, 5)
self.setLayout(grid)
grid.addWidget(QtGui.QLabel("Overlay"), 0, 0)
self.overlay_combo = OverlayCombo(self.ivm,
none_option=True,
set_first=False)
grid.addWidget(self.overlay_combo, 0, 1)
grid.addWidget(QtGui.QLabel("View"), 1, 0)
self.ov_view_combo = QtGui.QComboBox()
self.ov_view_combo.addItem("All")
self.ov_view_combo.addItem("Only in ROI")
self.ov_view_combo.addItem("None")
grid.addWidget(self.ov_view_combo, 1, 1)
grid.addWidget(QtGui.QLabel("Color map"), 2, 0)
hbox = QtGui.QHBoxLayout()
self.ov_cmap_combo = QtGui.QComboBox()
self.ov_cmap_combo.addItem("jet")
self.ov_cmap_combo.addItem("hot")
self.ov_cmap_combo.addItem("gist_heat")
self.ov_cmap_combo.addItem("flame")
self.ov_cmap_combo.addItem("bipolar")
self.ov_cmap_combo.addItem("spectrum")
hbox.addWidget(self.ov_cmap_combo)
self.ov_levels_btn = QtGui.QPushButton()
self.ov_levels_btn.setIcon(QtGui.QIcon(get_icon("levels.png")))
self.ov_levels_btn.setFixedSize(16, 16)
self.ov_levels_btn.setToolTip("Adjust colour map levels")
self.ov_levels_btn.clicked.connect(self._show_ov_levels)
self.ov_levels_btn.setEnabled(False)
hbox.addWidget(self.ov_levels_btn)
grid.addLayout(hbox, 2, 1)
grid.addWidget(QtGui.QLabel("Alpha"), 3, 0)
self.ov_alpha_sld = QtGui.QSlider(QtCore.Qt.Horizontal, self)
self.ov_alpha_sld.setFocusPolicy(QtCore.Qt.NoFocus)
self.ov_alpha_sld.setRange(0, 255)
self.ov_alpha_sld.setValue(255)
grid.addWidget(self.ov_alpha_sld, 3, 1)
grid.setRowStretch(4, 1)
self.overlay_combo.currentIndexChanged.connect(self._combo_changed)
self.ov_view_combo.currentIndexChanged.connect(self._view_changed)
self.ov_cmap_combo.currentIndexChanged.connect(self._cmap_changed)
self.ov_alpha_sld.valueChanged.connect(self._alpha_changed)
self.view.sig_view_changed.connect(self._update)
def _update(self, view):
widgets = [
self.ov_view_combo, self.ov_cmap_combo, self.ov_alpha_sld,
self.overlay_combo
]
try:
for widget in widgets:
widget.blockSignals(True)
if not view.get("visible"):
self.ov_view_combo.setCurrentIndex(2)
elif view.get("roi_only"):
self.ov_view_combo.setCurrentIndex(1)
else:
self.ov_view_combo.setCurrentIndex(0)
# 'Custom' only appears as a flag to indicate the user has messed with the
# LUT using the histogram widget. Otherwise is is hidden
cmap = view.get("cmap")
if cmap == "custom":
idx = self.ov_cmap_combo.findText("custom")
if idx >= 0:
self.ov_cmap_combo.setCurrentIndex(idx)
else:
self.ov_cmap_combo.addItem("custom")
idx = self.ov_cmap_combo.findText("custom")
self.ov_cmap_combo.setCurrentIndex(idx)
else:
idx = self.ov_cmap_combo.findText("custom")
if idx >= 0:
self.ov_cmap_combo.removeItem(idx)
idx = self.ov_cmap_combo.findText(view.get("cmap"))
self.ov_cmap_combo.setCurrentIndex(idx)
self.ov_alpha_sld.setValue(view.get("alpha"))
self.ov_levels_btn.setEnabled(view.data is not None)
if view.data is not None:
idx = self.overlay_combo.findText(view.data.name)
self.overlay_combo.setCurrentIndex(idx)
else:
self.overlay_combo.setCurrentIndex(-1)
except:
import traceback
traceback.print_exc()
finally:
for widget in widgets:
widget.blockSignals(False)
def _combo_changed(self, idx):
if idx > 0:
data_name = self.overlay_combo.itemText(idx)
self.ivm.set_current_data(data_name)
else:
self.ivl.ivm.set_current_data(None)
def _cmap_changed(self, idx):
cmap = self.ov_cmap_combo.itemText(idx)
self.view.set("cmap", cmap)
def _view_changed(self, idx):
""" Viewing style (all or within ROI only) changed """
self.view.set("visible", idx in (0, 1))
self.view.set("roi_only", (idx == 1))
def _alpha_changed(self, alpha):
""" Set the data transparency """
self.view.set("alpha", alpha)
def _show_ov_levels(self):
dlg = LevelsDialog(self, self.ivl, self.ivm, self.view)
dlg.exec_()