def test():
filename = osp.join(osp.dirname(__file__), "mr-brain.dcm")
image = make.image(filename=filename, title="DICOM img", colormap='gray')
win = ImageDialog(edit=False, toolbar=True, wintitle="DICOM I/O test",
options=dict(show_contrast=True))
plot = win.get_plot()
plot.add_item(image)
plot.select_item(image)
contrast = win.get_contrast_panel()
contrast.histogram.eliminate_outliers(54.)
win.resize(600, 700)
return win
def test():
filename = osp.join(osp.dirname(__file__), "mr-brain.dcm")
image = make.image(filename=filename, title="DICOM img", colormap='gray')
win = ImageDialog(edit=False,
toolbar=True,
wintitle="DICOM I/O test",
options=dict(show_contrast=True))
plot = win.get_plot()
plot.add_item(image)
plot.select_item(image)
contrast = win.get_contrast_panel()
contrast.histogram.eliminate_outliers(54.)
win.resize(600, 700)
return win
class Gui(object):
def __init__(self, xlabel=None, ylabel=None, winTitle=None):
"""
Boilerplate code for guiqwt image window. Includes qt application,
x-,y-crosssection, itemlistpanel, contrast adjustment.
Returns
--------
win : guiqwt.plot.ImageDialog
_app : PyQt4.QtGui.QApplication
"""
self._app = qapplication()
self.win = ImageDialog(edit=False,
toolbar=True,
wintitle=winTitle,
options=dict(xlabel=xlabel,
ylabel=ylabel,
yreverse=False,
lock_aspect_ratio=False))
self.itemlist_panel = self.win.get_itemlist_panel()
self.itemlist_panel.show()
action = QAction(get_icon('busy.png'), "Reload", self.itemlist_panel)
action.triggered.connect(self.reload_measurement)
self.itemlist_panel.children()[-2].addAction(action)
self.win.plot_widget.plot.SIG_ITEM_REMOVED.connect(
self.remove_measurement)
action = QAction(get_icon('save_all.png'), "Save all",
self.itemlist_panel)
action.triggered.connect(self.save_measurements)
self.itemlist_panel.children()[-3].addAction(action)
def fun(shape):
shape.symbol.pen().setWidth(2)
shape.symbol.setColor(QColor(255, 0, 0))
self.win.add_tool(PointTool, handle_final_shape_cb=fun)
self.win.get_xcs_panel().show()
self.win.get_ycs_panel().show()
self.win.get_contrast_panel().show()
action = QAction(get_icon('fileopen.png'), "Open measurement",
self.itemlist_panel)
action.triggered.connect(self.load_measurement)
self.win.get_toolbar().addAction(action)
self.win.get_toolbar().addAction("Load VNA measurement",
self.load_VNAMeasurement)
self.win.get_toolbar().addAction(
"Load VNA measurement ...",
self.load_VNAMeasurement_select_channels)
self.win.get_toolbar().addAction(
"Load VNA fields measurement ",
self.load_VNASeparateFieldsMeasurement)
self.win.get_toolbar().addAction("Get points", self.get_points)
if peakit:
self.win.get_toolbar().addAction("Fitting tool ...",
self.launchFittingTool)
self.fitting_controller = MeasurementController()
else:
self.fitting_controller = None
self.operations_widget = OperationsWidget()
bbfmr_operations = list(
filter(None,
[("bbFMR.processing.%s" % s) if "__" not in s else None
for s in dir(bp)]))
self.operations_widget.populate_available_operations(bbfmr_operations)
self.itemlist_panel.layout().addWidget(self.operations_widget)
self.itemlist_panel.listwidget.selectionModel(
).selectionChanged.connect(self.refresh_operations)
self.operations_widget.operations_changed.connect(
self.replot_measurement)
self.plot_items = self.win.plot_widget.plot.items
self.measurements = []
def _get_current_plot_item(self):
selection = self.itemlist_panel.listwidget.selectedIndexes()
if len(selection) > 0:
list_idx = selection[0].row()
plot_item_idx = len(self.plot_items) - 1 - list_idx
return self.plot_items[plot_item_idx], plot_item_idx
else:
return None, None
def get_points(self):
points = []
for item in self.itemlist_panel.listwidget.items:
if isinstance(item, PointShape):
print(item.get_pos())
points.append(item.get_pos())
fileName = QFileDialog.getSaveFileName(caption='Save file',
filter="dat (*.dat *.)")
if fileName:
print(fileName)
np.savetxt(fileName, points, delimiter='\t')
return points
def refresh_operations(self):
plot_item, _ = self._get_current_plot_item()
if plot_item is not None:
self.operations_widget.set_operations(
plot_item.measurement.operations)
def add_measurement(self, m, **kwargs):
self.measurements.append(m)
if "title" not in m.metadata or not m.metadata["title"]:
m.metadata["title"] = m.metadata["fname"]
_, image = self.imshow(m.X[:, 0],
m.Y[0, :],
m.Z.T,
title=m.metadata["title"],
**kwargs)
image.measurement = m
def remove_measurement(self, item):
self.measurements.remove(item.measurement)
def reload_measurement(self):
"""
Trigger reloading of the currently selected measurement
"""
plot_item, plot_item_idx = self._get_current_plot_item()
if plot_item is None:
return False
plot_item.measurement.reload()
self.replot_measurement()
def replot_measurement(self):
"""
Recreate theimage for the currently selected image. Taking into account
any changed operations. Called when operations_widget.operations_changed
is emitted
"""
plot_item, plot_item_idx = self._get_current_plot_item()
if plot_item is None:
return False
m = plot_item.measurement
m.operations = self.operations_widget.get_operations()
m.process()
# recreate the image (this handles sorting of data and other bla)
from guiqwt.builder import make
image = make.xyimage(m.X[:, 0],
m.Y[0, :],
m.Z.T,
interpolation="nearest",
title=m.metadata["title"])
# update image to the new data values
plot_item.set_data(image.data)
plot_item.set_xy(image.x, image.y)
plot_item.plot().replot()
#self.win.get_plot().replot()
def imshow(self, x, y, data, title=None, cmap="RdYlGn"):
"""
Create 2D xyimage for guiqwt image dialog
Returns
--------
plot : guiqwt.image.ImagePlot
Plot widget in guiqwt ImageDialog
image : guiqwt.image.XYImageItem
Newly created image object
"""
from guiqwt.builder import make
image = make.xyimage(
x,
y,
data,
interpolation="nearest",
title=title,
)
plot = self.win.get_plot()
plot.add_item(image)
plot.do_autoscale()
plot.replot()
image.set_color_map(cmap)
image.measurement = None
return plot, image
def pcolorshow(self, aX, aY, aData, title=None):
"""
Create 2D xyimage for guiqwt image dialog
Returns
--------
plot : ?
Plot widget in guiqwt ImageDialog
image : ?
new image object
"""
from guiqwt.builder import make
image = make.pcolor(
aX,
aY,
aData,
interpolation="nearest",
title=title,
)
plot = self.win.get_plot()
plot.add_item(image)
plot.do_autoscale()
plot.replot()
return plot, image
def save_measurements(self):
"""
Save measurements object descriptions to .measurement.json file(s)
"""
folder = QFileDialog.getExistingDirectory(caption="Save measurements")
for m in self.measurements:
fname = os.path.basename(m.metadata["fname"]) + ".measurement.json"
m.save(os.path.join(folder, fname))
def load_measurement(self):
"""
Load measurements according to .measurement.json file(s)
"""
fnames = QFileDialog.getOpenFileNames(
caption="Open Tdms file(s)",
filter=
u"Measurements Object Descriptions (*.measurement.json);;All files (*.*)"
)
for fname in fnames:
with open(fname, "r") as f:
m = jsonpickle.loads(f.read())
self.add_measurement(m, cmap="RdYlGn")
return fnames
def load_VNAMeasurement(self):
"""
Load a VNA measurement from a TDMS file. Apply certain standard
operations and plot data.
"""
fnames = QFileDialog.getOpenFileNames(
caption="Open Tdms file(s)",
filter=u"TDMS (*.tdms);;All files (*.*)")
for fname in fnames:
m = VNAMeasurement(fname)
m.add_operation(bp.derivative_divide, modulation_amp=4)
m.add_operation(bp.mag)
self.add_measurement(m, cmap="RdYlGn")
return fnames
def load_VNAMeasurement_select_channels(self):
"""
Load a VNA measurement from a TDMS file. Apply certain standard
operations and plot data. Allow to select used channels.
"""
fnames = QFileDialog.getOpenFileNames(
caption="Open Tdms file(s)",
filter=u"TDMS (*.tdms);;All files (*.*)")
for fname in fnames:
tdms_file = TdmsFile(fname)
channel_labels = [
"Field channel", "Frequency channel", "Re(signal) channel",
"Im(signal) channel"
]
paths, accepted = TdmsChannelSelectDialog.get_group_channels(
tdms_file=tdms_file, channel_labels=channel_labels)
m = VNAMeasurement(fname=fname,
tdms_file=tdms_file,
group=paths[2][0],
field_channel=paths[0][1],
freq_channel=paths[1][1],
signal_channel=paths[2][1],
imag_channel=paths[3][1])
m.add_operation(bp.derivative_divide, modulation_amp=4)
m.add_operation(bp.mag)
self.add_measurement(m, cmap="RdYlGn")
return fnames
def launchFittingTool(self):
"""
...
"""
plot_item, _ = self._get_current_plot_item()
if plot_item is not None:
measurement = plot_item.measurement
else:
measurement = None
self.fitting_controller.measurement = measurement
self.fitting_controller.show_view()
def load_VNASeparateFieldsMeasurement(self):
"""
Load a VNA measurement from a TDMS file with two magnetic field channels
(field_before, field_after). Apply certain standard operations and
plot data. Allow to select used channels.
"""
fnames = QFileDialog.getOpenFileNames(
caption="Open Tdms file(s)",
filter=u"TDMS (*.tdms);;All files (*.*)")
for fname in fnames:
tdms_file = TdmsFile(fname)
channel_labels = [
"Field_before", "Field_after", "Frequency", "Re(signal)",
"Im(signal)"
]
paths, accepted = TdmsChannelSelectDialog.get_group_channels(
tdms_file=tdms_file, channel_labels=channel_labels)
m = VNASeparateFieldsMeasurement(fname=fname,
tdms_file=tdms_file,
path_field_before=paths[0],
path_field_after=paths[1],
path_frequency=paths[2],
path_real_signal=paths[3],
path_imag_signal=paths[4])
m.add_operation(bp.derivative_divide, modulation_amp=4)
m.add_operation(bp.mag)
self.add_measurement(m, cmap="RdYlGn")
return fnames
def run(self):
self.win.show()
self.win.exec()