def __init__(self, parent=None, width=5, height=4, dpi=100):
super(QWidget, self).__init__(parent)
self.setLayout(QVBoxLayout())
self.header_layout = QHBoxLayout()
self.layout().addLayout(self.header_layout)
self.header_layout.addWidget(QLabel("Selection group"))
self.group_combobox = QComboBox(self)
self.header_layout.addWidget(self.group_combobox)
self.tw_checkbox = QCheckBox(self)
self.tw_checkbox.setText("Tera-Wasserburg?")
self.header_layout.addWidget(self.tw_checkbox)
axes_button = QToolButton(self)
axes_button.setText("Setup axes")
axes_button.clicked.connect(self.setup_axes)
self.header_layout.addWidget(axes_button)
spacer = QWidget(self)
spacer.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Minimum)
self.header_layout.addWidget(spacer)
save_button = QToolButton(self)
save_button.setText("Save")
save_button.clicked.connect(self.save_figure)
self.header_layout.addWidget(save_button)
self.plot = QLabel("Select a group above...")
self.layout().addWidget(self.plot)
self.group_combobox.addItems(data.selectionGroupNames())
self.group_combobox.currentTextChanged.connect(self.update_plot)
self.tw_checkbox.toggled.connect(self.update_plot)
self.setWindowTitle("U-Pb contour")
def calculate():
d = QDialog()
d.setWindowTitle('Channel Calculator')
hl = QHBoxLayout()
name_le = QLineEdit(d)
hl.addWidget(name_le)
hl.addWidget(QLabel('='))
channel_names = [
re.sub('\W|^(?=\d)', '_', channel_name)
for channel_name in data.timeSeriesNames()
]
eqn_le = AutoCompleteEdit(channel_names, parent=d)
hl.addWidget(eqn_le)
type_cb = QComboBox(d)
channel_types = {
'Input': data.Input,
'Intermediate': data.Intermediate,
'Output': data.Output
}
for tname, tv in channel_types.items():
type_cb.addItem(tname, tv)
hl.addWidget(type_cb)
bb = QDialogButtonBox(QDialogButtonBox.Cancel | QDialogButtonBox.Ok,
Qt.Horizontal, d)
bb.accepted.connect(d.accept)
bb.rejected.connect(d.reject)
hl.addWidget(bb)
d.setLayout(hl)
if d.exec() == QDialog.Accepted:
for channel_name in data.timeSeriesNames():
exec('%s = data.timeSeries("%s").data()' %
(re.sub('\W|^(?=\d)', '_', channel_name), channel_name))
new_data = eval('%s' % eqn_le.text)
new_type = type_cb.currentData
new_channel = data.createTimeSeries(name_le.text, new_type, None,
new_data)
new_channel.setProperty('Created by', 'Channel Calculator')
data.dataChanged.emit()
def __init__(self, parent = None):
super(QWidget, self).__init__(parent)
self.setLayout(QVBoxLayout())
header_layout = QHBoxLayout()
header_layout.addWidget(QLabel("Selection group:"))
self.group_combobox = QComboBox()
self.group_combobox.addItems(data.selectionGroupNames())
self.group_combobox.currentTextChanged.connect(self.update_dendrogram)
header_layout.addWidget(self.group_combobox)
self.layout().addLayout(header_layout)
self.plot = QLabel("Select a group above...")
self.layout().addWidget(self.plot)
self.resize(600, 800)
self.setWindowTitle("Dendrogram Example")
self.show()
def __init__(self, parent=None, width=5, height=4, dpi=100):
super(QWidget, self).__init__(parent)
self.setLayout(QVBoxLayout())
self.header_layout = QHBoxLayout()
self.layout().addLayout(self.header_layout)
self.header_layout.addWidget(QLabel("Selection group"))
self.group_combobox = QComboBox(self)
self.header_layout.addWidget(self.group_combobox)
self.header_layout.addWidget(QLabel("Channel"))
self.channel_combobox = QComboBox(self)
self.header_layout.addWidget(self.channel_combobox)
axes_button = QToolButton(self)
axes_button.setText("Setup axes")
axes_button.clicked.connect(self.setup_axes)
self.header_layout.addWidget(axes_button)
spacer = QWidget(self)
spacer.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Minimum)
self.header_layout.addWidget(spacer)
save_button = QToolButton(self)
save_button.setText("Save")
save_button.clicked.connect(self.save_figure)
self.header_layout.addWidget(save_button)
self.plot = QLabel("Select a group above...")
self.layout().addWidget(self.plot)
self.group_combobox.addItems(data.selectionGroupNames())
self.group_combobox.currentTextChanged.connect(
lambda: self.update_plot())
self.channel_combobox.addItems(data.timeSeriesNames())
self.channel_combobox.currentTextChanged.connect(
lambda: self.update_plot())
self.setWindowTitle("Density Plot")
class DensityWidget(QWidget):
xrange_plot = None
yrange_plot = None
def __init__(self, parent=None, width=5, height=4, dpi=100):
super(QWidget, self).__init__(parent)
self.setLayout(QVBoxLayout())
self.header_layout = QHBoxLayout()
self.layout().addLayout(self.header_layout)
self.header_layout.addWidget(QLabel("Selection group"))
self.group_combobox = QComboBox(self)
self.header_layout.addWidget(self.group_combobox)
self.header_layout.addWidget(QLabel("Channel"))
self.channel_combobox = QComboBox(self)
self.header_layout.addWidget(self.channel_combobox)
axes_button = QToolButton(self)
axes_button.setText("Setup axes")
axes_button.clicked.connect(self.setup_axes)
self.header_layout.addWidget(axes_button)
spacer = QWidget(self)
spacer.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Minimum)
self.header_layout.addWidget(spacer)
save_button = QToolButton(self)
save_button.setText("Save")
save_button.clicked.connect(self.save_figure)
self.header_layout.addWidget(save_button)
self.plot = QLabel("Select a group above...")
self.layout().addWidget(self.plot)
self.group_combobox.addItems(data.selectionGroupNames())
self.group_combobox.currentTextChanged.connect(
lambda: self.update_plot())
self.channel_combobox.addItems(data.timeSeriesNames())
self.channel_combobox.currentTextChanged.connect(
lambda: self.update_plot())
self.setWindowTitle("Density Plot")
def update_plot(self, xrange=None, yrange=None):
self.layout().removeWidget(self.plot)
self.plot.deleteLater()
group_name = self.group_combobox.currentText
channel_name = self.channel_combobox.currentText
print("density: update_plot %s %s" % (group_name, channel_name))
group = data.selectionGroup(group_name)
channel = data.timeSeries(channel_name)
x = np.empty(group.count) * np.nan
err = np.empty(group.count) * np.nan
for i, s in enumerate(group.selections()):
r = data.result(s, channel)
x[i] = r.value()
err[i] = r.uncertaintyAs2SE()
self.fig = plt.figure()
self.fig.set_size_inches(8, 8)
self.fig.set_dpi(120)
ax = self.fig.add_subplot(111)
kde = stats.gaussian_kde(x, bw_method=kde_bandwidth)
ax.plot(x, np.zeros(x.shape), 'b|', ms=5)
x_eval = np.linspace(0.8 * x.min(), 1.2 * x.max(), num=2000)
ax.plot(x_eval, kde(x_eval), 'k-', label='kde')
if xrange is None:
self.xrange_plot = ax.get_xlim()
else:
print('xrange=%s' % (xrange))
ax.set_xlim(xrange)
if yrange is None:
self.yrange_plot = ax.get_ylim()
else:
print('yrange=%s' % (yrange))
ax.set_ylim(yrange)
ax.set_xlabel(channel.name)
self.fig.canvas.draw()
self.plot = FigureCanvas(self.fig)
self.plot.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.layout().addWidget(self.plot)
def save_figure(self):
fname = QFileDialog.getSaveFileName(
self, "Save figure", QDir.homePath(),
"Images (*.png, *.jpg, *.tif, *.pdf, *.svg")
print("Trying to save to file %s" % (fname))
if fname:
self.fig.savefig(fname)
def setup_axes(self):
d = QDialog(self)
l = QVBoxLayout()
fl = QFormLayout()
d.setLayout(l)
params = {
'X plot range': (self.xrange_plot, QLineEdit(), QLineEdit()),
'Y plot range': (self.yrange_plot, QLineEdit(), QLineEdit())
}
for key in params:
ll = QHBoxLayout()
params[key][1].setText(params[key][0][0])
params[key][2].setText(params[key][0][1])
ll.addWidget(params[key][1])
ll.addWidget(params[key][2])
fl.addRow(key, ll)
l.addLayout(fl)
ok_button = QPushButton('Ok')
cancel_button = QPushButton('Cancel')
button_layout = QHBoxLayout()
button_layout.addWidget(cancel_button)
button_layout.addWidget(ok_button)
l.addLayout(button_layout)
ok_button.clicked.connect(lambda: d.accept())
cancel_button.clicked.connect(lambda: d.reject())
if (d.exec() == QDialog.Accepted):
self.xrange_plot = (float(params['X plot range'][1].text),
float(params['X plot range'][2].text))
self.yrange_plot = (float(params['Y plot range'][1].text),
float(params['Y plot range'][2].text))
self.update_plot(xrange=self.xrange_plot, yrange=self.yrange_plot)
class DendrogramWidget(QWidget):
channel_type = data.Input
image_widget = None
group_combobox = None
def __init__(self, parent = None):
super(QWidget, self).__init__(parent)
self.setLayout(QVBoxLayout())
header_layout = QHBoxLayout()
header_layout.addWidget(QLabel("Selection group:"))
self.group_combobox = QComboBox()
self.group_combobox.addItems(data.selectionGroupNames())
self.group_combobox.currentTextChanged.connect(self.update_dendrogram)
header_layout.addWidget(self.group_combobox)
self.layout().addLayout(header_layout)
self.plot = QLabel("Select a group above...")
self.layout().addWidget(self.plot)
self.resize(600, 800)
self.setWindowTitle("Dendrogram Example")
self.show()
def update_dendrogram(self):
self.layout().removeWidget(self.plot)
self.plot.deleteLater()
group_name = self.group_combobox.currentText
print("dendrogram: update_dendrogram %s"%(group_name))
plt.clf()
fig = plt.gcf()
fig.set_size_inches(8, 8)
fig.set_dpi(120)
X = np.array([])
labels = []
for channel in data.timeSeriesList(self.channel_type):
if channel.name == "TotalBeam":
continue
labels += [channel.name]
d = np.array([])
for s in data.selectionGroup(group_name).selections():
selection_data = channel.dataForSelection(s)
d = np.insert(d, 0, selection_data)
try:
d = d/np.max(d)
except:
labels.pop()
print('Error processing channel %s'%(channel.name))
continue
if len(X) == 0:
X = d
else:
X = np.column_stack((X, d))
try:
linked = linkage(np.transpose(X), 'ward')
dendrogram(linked, labels=labels)
except RuntimeError as r:
print(r)
self.plot = QLabel('There was a problem processing the selected group.')
self.layout().addWidget(self.plot)
return
fig.canvas.draw()
self.plot = FigureCanvas(fig)
self.plot.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.layout().addWidget(self.plot)
class UPbContourWidget(QWidget):
xrange_mask = (0, 30)
yrange_mask = (0, 3)
zrange_mask = (5000, math.inf)
xrange_plot = (0, 30)
yrange_plot = (0, 3)
marker_sep = 100 * 10**6
def __init__(self, parent=None, width=5, height=4, dpi=100):
super(QWidget, self).__init__(parent)
self.setLayout(QVBoxLayout())
self.header_layout = QHBoxLayout()
self.layout().addLayout(self.header_layout)
self.header_layout.addWidget(QLabel("Selection group"))
self.group_combobox = QComboBox(self)
self.header_layout.addWidget(self.group_combobox)
self.tw_checkbox = QCheckBox(self)
self.tw_checkbox.setText("Tera-Wasserburg?")
self.header_layout.addWidget(self.tw_checkbox)
axes_button = QToolButton(self)
axes_button.setText("Setup axes")
axes_button.clicked.connect(self.setup_axes)
self.header_layout.addWidget(axes_button)
spacer = QWidget(self)
spacer.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Minimum)
self.header_layout.addWidget(spacer)
save_button = QToolButton(self)
save_button.setText("Save")
save_button.clicked.connect(self.save_figure)
self.header_layout.addWidget(save_button)
self.plot = QLabel("Select a group above...")
self.layout().addWidget(self.plot)
self.group_combobox.addItems(data.selectionGroupNames())
self.group_combobox.currentTextChanged.connect(self.update_plot)
self.tw_checkbox.toggled.connect(self.update_plot)
self.setWindowTitle("U-Pb contour")
def update_plot(self):
self.layout().removeWidget(self.plot)
self.plot.deleteLater()
TW = self.tw_checkbox.checked
group_name = self.group_combobox.currentText
print("UPb_contour: update_plot %s %s" % (group_name, TW))
channel_data = {}
channel_names = ()
if TW:
channel_names = ('Final U238/Pb206', 'Final Pb207/Pb206',
'Zr96_CPS')
else:
channel_names = ('Final Pb207/U235', 'Final Pb206/U238',
'Zr96_CPS')
for channel_name in channel_names:
channel = data.timeSeries(channel_name)
channel_data[channel_name] = np.array([])
for s in data.selectionGroup(group_name).selections():
selection_data = channel.dataForSelection(s)
channel_data[channel_name] = np.insert(
channel_data[channel_name], 0, selection_data)
masks = [self.xrange_mask, self.yrange_mask, self.zrange_mask]
for i, mask in enumerate(masks):
if mask is None:
masks[i] = (-math.inf, math.inf)
df = pd.DataFrame({
'x': channel_data[channel_names[0]],
'y': channel_data[channel_names[1]],
'z': channel_data[channel_names[2]]
})
df = df.loc[(df['x'] > masks[0][0]) & (df['x'] < masks[0][1]) &
(df['y'] > masks[1][0]) & (df['y'] < masks[1][1]) &
(df['z'] > masks[2][0]) & (df['z'] < masks[2][1])]
# Calculate concordia and markers
t = np.array(range(1, 4001 * 10**6, 1 * 10**6))
tmarkers = np.array(range(100 * 10**6, 4001 * 10**6, self.marker_sep))
Xcon, Ycon = np.array([]), np.array([])
Xmarkers, Ymarkers = np.array([]), np.array([])
if TW:
(Xcon, Ycon) = (1 / (np.exp(l238U * t) - 1), (1 / U85r) *
(np.exp(l235U * t) - 1) / (np.exp(l238U * t) - 1))
(Xmarkers,
Ymarkers) = (1 / (np.exp(l238U * tmarkers) - 1),
(1 / U85r) * (np.exp(l235U * tmarkers) - 1) /
(np.exp(l238U * tmarkers) - 1))
else:
(Xcon, Ycon) = (np.exp(l235U * t) - 1, np.exp(l238U * t) - 1)
(Xmarkers, Ymarkers) = (np.exp(l235U * tmarkers) - 1,
np.exp(l238U * tmarkers) - 1)
# Do joint plot
sb.set_style('ticks')
self.jointgrid = sb.jointplot(df['x'],
df['y'],
kind="kde",
height=8,
space=0,
n_levels=50,
shade_lowest=False,
xlim=self.xrange_plot,
ylim=self.yrange_plot)
self.jointgrid.ax_joint.plot(Xcon, Ycon, zorder=1)
self.jointgrid.ax_joint.scatter(Xmarkers, Ymarkers, s=50, zorder=2)
if TW:
self.jointgrid.set_axis_labels(
r'${^{238}\rm{U}}/{^{206}\rm{Pb}}$',
r'${^{207}\rm{Pb}}/{^{206}\rm{Pb}}$',
fontsize=24)
else:
self.jointgrid.set_axis_labels(r'${^{207}\rm{Pb}}/{^{235}\rm{U}}$',
r'${^{206}\rm{Pb}}/{^{238}\rm{U}}$',
fontsize=24)
x_scale = 9 * 0.78 / (self.xrange_plot[1] - self.xrange_plot[0])
y_scale = 7 * 0.80 / (self.yrange_plot[1] - self.yrange_plot[0])
for i, a in enumerate(tmarkers):
if (a == 0 or i < 2):
continue
rotation = np.degrees(
np.arctan2((Ymarkers[i] - Ymarkers[i - 1]) * y_scale,
(Xmarkers[i] - Xmarkers[i - 1]) * x_scale))
offset = (0, 0)
self.jointgrid.ax_joint.annotate("%i" % (a / 1e6) + " Ma",
xy=(Xmarkers[i], Ymarkers[i]),
xytext=offset,
textcoords='offset points',
rotation=rotation - 90,
ha='right',
va='center',
rotation_mode='anchor',
fontsize=14)
self.plot = FigureCanvas(self.jointgrid.fig)
self.plot.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.layout().addWidget(self.plot)
def save_figure(self):
fname = QFileDialog.getSaveFileName(
self, "Save figure", QDir.homePath(),
"Images (*.png, *.jpg, *.tif, *.pdf, *.svg")
print("Trying to save to file %s" % (fname))
if fname:
self.jointgrid.savefig(fname)
def setup_axes(self):
d = QDialog(self)
l = QVBoxLayout()
fl = QFormLayout()
d.setLayout(l)
params = {
'X mask range': (self.xrange_mask, QLineEdit(), QLineEdit()),
'Y mask range': (self.yrange_mask, QLineEdit(), QLineEdit()),
'Z mask range': (self.zrange_mask, QLineEdit(), QLineEdit()),
'X plot range': (self.xrange_plot, QLineEdit(), QLineEdit()),
'Y plot range': (self.yrange_plot, QLineEdit(), QLineEdit())
}
for key in params:
ll = QHBoxLayout()
params[key][1].setText(params[key][0][0])
params[key][2].setText(params[key][0][1])
ll.addWidget(params[key][1])
ll.addWidget(params[key][2])
fl.addRow(key, ll)
l.addLayout(fl)
ok_button = QPushButton('Ok')
cancel_button = QPushButton('Cancel')
button_layout = QHBoxLayout()
button_layout.addWidget(cancel_button)
button_layout.addWidget(ok_button)
l.addLayout(button_layout)
ok_button.clicked.connect(lambda: d.accept())
cancel_button.clicked.connect(lambda: d.reject())
if (d.exec() == QDialog.Accepted):
self.xrange_mask = (float(params['X mask range'][1].text),
float(params['X mask range'][2].text))
self.yrange_mask = (float(params['Y mask range'][1].text),
float(params['Y mask range'][2].text))
self.zrange_mask = (float(params['Z mask range'][1].text),
float(params['Z mask range'][2].text))
self.xrange_plot = (float(params['X plot range'][1].text),
float(params['X plot range'][2].text))
self.yrange_plot = (float(params['Y plot range'][1].text),
float(params['Y plot range'][2].text))
self.update_plot()