def _create_plot_component():
# Create some x-y data series to plot
x = linspace(-2.0, 10.0, 40)
pd = ArrayPlotData(index = x, y0=jn(0,x))
# Create some line plots of some of the data
plot1 = Plot(pd, title="render_style = hold", padding=50, border_visible=True,
overlay_border = True)
plot1.legend.visible = True
lineplot = plot1.plot(("index", "y0"), name="j_0", color="red", render_style="hold")
# Attach some tools to the plot
attach_tools(plot1)
# Create a second scatter plot of one of the datasets, linking its
# range to the first plot
plot2 = Plot(pd, range2d=plot1.range2d, title="render_style = connectedhold",
padding=50, border_visible=True, overlay_border=True)
plot2.plot(('index', 'y0'), color="blue", render_style="connectedhold")
attach_tools(plot2)
# Create a container and add our plots
container = HPlotContainer()
container.add(plot1)
container.add(plot2)
return container
def _create_plot_component():
# Create some x-y data series to plot
x = linspace(-2.0, 10.0, 100)
pd = ArrayPlotData(index = x)
for i in range(5):
pd.set_data("y" + str(i), jn(i,x))
# Create some line plots of some of the data
plot1 = Plot(pd, title="Line Plot", padding=50, border_visible=True)
plot1.legend.visible = True
plot1.plot(("index", "y0", "y1", "y2"), name="j_n, n<3", color="red")
plot1.plot(("index", "y3"), name="j_3", color="blue")
# Attach some tools to the plot
plot1.tools.append(PanTool(plot1))
zoom = ZoomTool(component=plot1, tool_mode="box", always_on=False)
plot1.overlays.append(zoom)
# Create a second scatter plot of one of the datasets, linking its
# range to the first plot
plot2 = Plot(pd, range2d=plot1.range2d, title="Scatter plot", padding=50,
border_visible=True)
plot2.plot(('index', 'y3'), type="scatter", color="blue", marker="circle")
# Create a container and add our plots
container = HPlotContainer()
container.add(plot1)
container.add(plot2)
return container
def _create_plot_component():
numpoints = 100
low = -5
high = 15.0
x = arange(low, high, (high - low) / numpoints)
container = HPlotContainer(resizable="hv", bgcolor="lightgray", fill_padding=True, padding=10)
# container = VPlotContainer(resizable = "hv", bgcolor="lightgray",
# fill_padding=True, padding = 10)
# Plot some bessel functions
value_range = None
for i in range(10):
y = jn(i, x)
plot = create_line_plot((x, y), color=tuple(COLOR_PALETTE[i]), width=2.0, orientation="v")
# orientation="h")
plot.origin_axis_visible = True
plot.origin = "top left"
plot.padding_left = 10
plot.padding_right = 10
plot.border_visible = True
plot.bgcolor = "white"
if value_range is None:
value_range = plot.value_mapper.range
else:
plot.value_range = value_range
value_range.add(plot.value)
if i % 2 == 1:
plot.line_style = "dash"
container.add(plot)
container.padding_top = 50
container.overlays.append(PlotLabel("More Bessels", component=container, font="swiss 16", overlay_position="top"))
return container
def draw( self ):
"""Draw data."""
if len(self.fitResults) == 0:
return
#if not hasattr( self, 'subplot1' ):
# self.subplot1 = self.figure.add_subplot( 211 )
# self.subplot2 = self.figure.add_subplot( 212 )
a, ed = numpy.histogram(self.fitResults['tIndex'], self.Size[0]/2)
#self.subplot1.cla()
#self.subplot1.plot(ed[:-1], a, color='b' )
#self.subplot1.set_xticks([0, ed.max()])
#self.subplot1.set_yticks([0, a.max()])
#self.subplot2.cla()
#self.subplot2.plot(ed[:-1], numpy.cumsum(a), color='g' )
#self.subplot2.set_xticks([0, ed.max()])
#self.subplot2.set_yticks([0, a.sum()])
plot1 = create_line_plot(ed[:,-1], a, color = 'blue', bgcolor="white",
add_grid=True, add_axis=True)
plot2 = create_line_plot(ed[:,-1], numpy.cumsum(a), color = 'green', bgcolor="white",
add_grid=True, add_axis=True)
container = HPlotContainer(spacing=20, padding=50, bgcolor="lightgray")
container.add(plot1)
container.add(plot2)
return container
def _create_plot_component(obj):
# Setup the spectrum plot
frequencies = linspace(0.0, float(SAMPLING_RATE)/2, num=NUM_SAMPLES/2)
obj.spectrum_data = ArrayPlotData(frequency=frequencies)
empty_amplitude = zeros(NUM_SAMPLES/2)
obj.spectrum_data.set_data('amplitude', empty_amplitude)
obj.spectrum_plot = Plot(obj.spectrum_data)
spec_renderer = obj.spectrum_plot.plot(("frequency", "amplitude"), name="Spectrum",
color="red")[0]
obj.spectrum_plot.padding = 50
obj.spectrum_plot.title = "Spectrum"
spec_range = obj.spectrum_plot.plots.values()[0][0].value_mapper.range
spec_range.low = 0.0
spec_range.high = 5.0
obj.spectrum_plot.index_axis.title = 'Frequency (hz)'
obj.spectrum_plot.value_axis.title = 'Amplitude'
# Time Series plot
times = linspace(0.0, float(NUM_SAMPLES)/SAMPLING_RATE, num=NUM_SAMPLES)
obj.time_data = ArrayPlotData(time=times)
empty_amplitude = zeros(NUM_SAMPLES)
obj.time_data.set_data('amplitude', empty_amplitude)
obj.time_plot = Plot(obj.time_data)
obj.time_plot.plot(("time", "amplitude"), name="Time", color="blue")
obj.time_plot.padding = 50
obj.time_plot.title = "Time"
obj.time_plot.index_axis.title = 'Time (seconds)'
obj.time_plot.value_axis.title = 'Amplitude'
time_range = obj.time_plot.plots.values()[0][0].value_mapper.range
time_range.low = -0.2
time_range.high = 0.2
# Spectrogram plot
values = [zeros(NUM_SAMPLES/2) for i in xrange(SPECTROGRAM_LENGTH)]
p = WaterfallRenderer(index = spec_renderer.index, values = values,
index_mapper = LinearMapper(range = obj.spectrum_plot.index_mapper.range),
value_mapper = LinearMapper(range = DataRange1D(low=0, high=SPECTROGRAM_LENGTH)),
y2_mapper = LinearMapper(low_pos=0, high_pos=8,
range=DataRange1D(low=0, high=15)),
)
spectrogram_plot = p
obj.spectrogram_plot = p
dummy = Plot()
dummy.padding = 50
dummy.index_axis.mapper.range = p.index_mapper.range
dummy.index_axis.title = "Frequency (hz)"
dummy.add(p)
container = HPlotContainer()
container.add(obj.spectrum_plot)
container.add(obj.time_plot)
c2 = VPlotContainer()
c2.add(dummy)
c2.add(container)
return c2
def get_plot(self):
pixel_sizes = self.data_source.voxel_sizes
shape = self.data.shape
m = min(pixel_sizes)
s = [int(d*sz/m) for d, sz in zip(shape, pixel_sizes)]
if 1: # else physical aspect ratio is enabled
ss = max(s)/4
s = [max(s,ss) for s in s]
plot_sizes = dict (xy = (s[2], s[1]), xz = (s[2], s[0]), zy = (s[0],s[1]), zz=(s[0],s[0]))
plots = GridContainer(shape=(2,2), spacing=(3, 3), padding = 50, aspect_ratio=1)
pxy = Plot(self.plotdata, padding=1, fixed_preferred_size = plot_sizes['xy'],
x_axis=PlotAxis (orientation='top'),
)
pxz = Plot(self.plotdata, padding=1, fixed_preferred_size = plot_sizes['xz'],
)
pzy = Plot(self.plotdata, padding=1, fixed_preferred_size = plot_sizes['zy'],
#orientation = 'v', # cannot use 'v' because of img_plot assumes row-major ordering
x_axis=PlotAxis(orientation='top'),
y_axis=PlotAxis(orientation='right'),
)
pzz = Plot(self.plotdata, padding=1, fixed_preferred_size = plot_sizes['zz'])
plots.add(pxy, pzy, pxz, pzz)
self.plots = dict(xy = pxy.img_plot('xy', colormap=bone)[0],
xz = pxz.img_plot('xz', colormap=bone)[0],
zy = pzy.img_plot('zy', colormap=bone)[0],
zz = pzz.img_plot('zz')[0],
xyp = pxy.plot(('z_x', 'z_y'), type='scatter', color='orange', marker='circle', marker_size=3,
selection_marker_size = 3, selection_marker='circle')[0],
xzp = pxz.plot(('y_x', 'y_z'), type='scatter', color='orange', marker='circle', marker_size=3,
selection_marker_size = 3, selection_marker='circle')[0],
zyp = pzy.plot(('x_z', 'x_y'), type='scatter', color='orange', marker='circle', marker_size=3,
selection_marker_size = 3, selection_marker='circle')[0],
)
for p in ['xy', 'xz', 'zy']:
self.plots[p].overlays.append(ZoomTool(self.plots[p]))
self.plots[p].tools.append(PanTool(self.plots[p], drag_button='right'))
imgtool = ImageInspectorTool(self.plots[p])
self.plots[p].tools.append(imgtool)
overlay = ImageInspectorOverlay(component=self.plots[p],
bgcolor = 'white',
image_inspector=imgtool)
self.plots['zz'].overlays.append(overlay)
self.plots[p+'p'].tools.append (ScatterInspector(self.plots[p+'p'], selection_mode = 'toggle'))
self.plots['xyp'].index.on_trait_change (self._xyp_metadata_handler, 'metadata_changed')
self.plots['xzp'].index.on_trait_change (self._xzp_metadata_handler, 'metadata_changed')
self.plots['zyp'].index.on_trait_change (self._zyp_metadata_handler, 'metadata_changed')
plot = HPlotContainer()
# todo: add colormaps
plot.add(plots)
return plot
def _createWindow(self):
container = HPlotContainer(resizable = "hv", bgcolor="lightgray",
#container = Container(resizable = "hv", bgcolor="lightgray",
fill_padding=True, padding = 10)
container.add(self._createConfigurationPane())
container.add(self._createResultsPane())
#container.add(self._create_plot_component())
return container
def __init__(self, **kwargs):
super(VariableMeshPannerView, self).__init__(**kwargs)
# Create the plot
self.add_trait("field", DelegatesTo("vm_plot"))
plot = self.vm_plot.plot
img_plot = self.vm_plot.img_plot
if self.use_tools:
plot.tools.append(PanTool(img_plot))
zoom = ZoomTool(component=img_plot,
tool_mode="box",
always_on=False)
plot.overlays.append(zoom)
imgtool = ImageInspectorTool(img_plot)
img_plot.tools.append(imgtool)
overlay = ImageInspectorOverlay(component=img_plot,
image_inspector=imgtool,
bgcolor="white",
border_visible=True)
img_plot.overlays.append(overlay)
image_value_range = DataRange1D(self.vm_plot.fid)
cbar_index_mapper = LinearMapper(range=image_value_range)
self.colorbar = ColorBar(index_mapper=cbar_index_mapper,
plot=img_plot,
padding_right=40,
resizable='v',
width=30)
self.colorbar.tools.append(
PanTool(self.colorbar, constrain_direction="y", constrain=True))
zoom_overlay = ZoomTool(self.colorbar,
axis="index",
tool_mode="range",
always_on=True,
drag_button="right")
self.colorbar.overlays.append(zoom_overlay)
# create a range selection for the colorbar
range_selection = RangeSelection(component=self.colorbar)
self.colorbar.tools.append(range_selection)
self.colorbar.overlays.append(
RangeSelectionOverlay(component=self.colorbar,
border_color="white",
alpha=0.8,
fill_color="lightgray"))
# we also want to the range selection to inform the cmap plot of
# the selection, so set that up as well
range_selection.listeners.append(img_plot)
self.full_container = HPlotContainer(padding=30)
self.container = OverlayPlotContainer(padding=0)
self.full_container.add(self.colorbar)
self.full_container.add(self.container)
self.container.add(self.vm_plot.plot)
def _create_plot_component():
# Create some x-y data series to plot
plot_area = OverlayPlotContainer(border_visible=True)
container = HPlotContainer(padding=50, bgcolor="transparent")
#container.spacing = 15
x = linspace(-2.0, 10.0, 100)
for i in range(5):
color = tuple(COLOR_PALETTE[i])
y = jn(i, x)
renderer = create_line_plot((x, y), color=color)
plot_area.add(renderer)
#plot_area.padding_left = 20
axis = PlotAxis(orientation="left", resizable="v",
mapper = renderer.y_mapper,
axis_line_color=color,
tick_color=color,
tick_label_color=color,
title_color=color,
bgcolor="transparent",
title = "jn_%d" % i,
border_visible = True,)
axis.bounds = [60,0]
axis.padding_left = 10
axis.padding_right = 10
container.add(axis)
if i == 4:
# Use the last plot's X mapper to create an X axis and a
# vertical grid
x_axis = PlotAxis(orientation="bottom", component=renderer,
mapper=renderer.x_mapper)
renderer.overlays.append(x_axis)
grid = PlotGrid(mapper=renderer.x_mapper, orientation="vertical",
line_color="lightgray", line_style="dot")
renderer.underlays.append(grid)
# Add the plot_area to the horizontal container
container.add(plot_area)
# Attach some tools to the plot
broadcaster = BroadcasterTool()
for plot in plot_area.components:
broadcaster.tools.append(PanTool(plot))
# Attach the broadcaster to one of the plots. The choice of which
# plot doesn't really matter, as long as one of them has a reference
# to the tool and will hand events to it.
plot.tools.append(broadcaster)
return container
def _create_plot_component():
# Create some x-y data series to plot
x = linspace(-2.0, 10.0, 100)
pd = ArrayPlotData(index = x)
for i in range(5):
pd.set_data("y" + str(i), jn(i,x))
# Create some line plots of some of the data
plot = Plot(pd, title="Line Plot", padding=50, border_visible=True)
plot.legend.visible = True
plot.plot(("index", "y0", "y1", "y2"), name="j_n, n<3", color="auto")
plot.plot(("index", "y3"), name="j_3", color="auto")
plot.x_grid.line_color = "black"
plot.y_grid.line_color = "black"
xmin, xmax = 1.0, 6.0
ymin, ymax = 0.2, 0.80001
plot.x_grid.set(data_min = xmin, data_max = xmax,
transverse_bounds = (ymin, ymax),
transverse_mapper = plot.y_mapper)
plot.y_grid.set(data_min = ymin, data_max = ymax,
transverse_bounds = (xmin, xmax),
transverse_mapper = plot.x_mapper)
# Attach some tools to the plot
plot.tools.append(PanTool(plot))
zoom = ZoomTool(component=plot, tool_mode="box", always_on=False)
plot.overlays.append(zoom)
# A second plot whose vertical grid lines are clipped to the jn(3) function
def my_bounds_func(ticks):
""" Returns y_low and y_high for each grid tick in the array **ticks** """
tmp = array([zeros(len(ticks)),jn(3, ticks)]).T
return tmp
func_plot = Plot(pd, padding=50, border_visible=True)
func_plot.plot(("index", "y3"), color="red")
func_plot.x_grid.set(transverse_bounds = my_bounds_func,
transverse_mapper = func_plot.y_mapper,
line_color="black")
func_plot.tools.append(PanTool(func_plot))
container = HPlotContainer()
container.add(plot)
container.add(func_plot)
return container
def __init__(self):
x, y = np.ogrid[-2*np.pi:2*np.pi:256j, -2*np.pi:2*np.pi:256j]
self.img_data = np.sin(x)*y
#self.img_mask = np.zeros((len(x), len(y[0]), 4), dtype=np.uint8)
#self.img_mask[:, :, 3] = 255
self.img_index = np.array(list((np.broadcast(y, x))))
plotdata = ArrayPlotData(img_data=self.img_data, mask_data=self.img_data)
plot1 = Plot(plotdata, padding=10)
img_plot = plot1.img_plot("img_data",
xbounds=(np.min(x), np.max(x)),
ybounds=(np.min(y), np.max(y)))[0]
self.lasso = LassoSelection(img_plot)
img_plot.tools.append(self.lasso)
self.ll = LassoOverlay(img_plot, lasso_selection=self.lasso)
img_plot.overlays.append(self.ll)
self.lasso.on_trait_change(self._selection_changed, 'selection_completed')
plot2 = Plot(plotdata, padding=10)
plot2.img_plot("mask_data")
self.plot = HPlotContainer(plot1, plot2)
self.plot1 = plot1
self.plot2 = plot2
self.plotdata = plotdata
def __init__(self, **traits):
super(LassoDemoPlot, self).__init__(**traits)
x = np.random.random(N)
y = np.random.random(N)
x2 = np.array([])
y2 = np.array([])
data = ArrayPlotData(x=x, y=y, x2=x2, y2=y2)
plot1 = Plot(data, padding=10)
scatter_plot1 = plot1.plot(("x", "y"),
type="scatter",
marker="circle",
color="blue")[0]
self.lasso = LassoSelection(scatter_plot1,
incremental_select=True,
selection_datasource=scatter_plot1.index)
self.lasso.on_trait_change(self._selection_changed,
'selection_changed')
scatter_plot1.tools.append(self.lasso)
scatter_plot1.overlays.append(
LassoOverlay(scatter_plot1, lasso_selection=self.lasso))
plot2 = Plot(data, padding=10)
plot2.index_range = plot1.index_range
plot2.value_range = plot1.value_range
plot2.plot(("x2", "y2"), type="scatter", marker="circle", color="red")
self.plot = HPlotContainer(plot1, plot2)
self.plot2 = plot2
self.data = data
def __init__(self, **traits):
super(ContainerExample, self).__init__(**traits)
x = np.linspace(-14, 14, 100)
y = np.sin(x) * x**3 / 1000
data = ArrayPlotData(x=x, y=y)
p1 = Plot(data, padding=30)
p1.plot(("x", "y"), type="scatter", color="blue")
p1.plot(("x", "y"), type="line", color="blue")
p2 = Plot(data, padding=30)
p2.plot(("x", "y"), type="line", color="blue")
p2.set(bounds=[200, 100],
position=[70, 150],
bgcolor=(0.9, 0.9, 0.9),
unified_draw=True,
resizable="")
p3 = Plot(data, padding=30)
p3.plot(("x", "y"), type="line", color="blue", line_width=2.0)
p4 = Plot(data, padding=30)
p4.plot(("x", "y"), type="scatter", color="red", marker="circle")
c1 = OverlayPlotContainer(p1, p2)
c1.fixed_preferred_size = p3.get_preferred_size()
c2 = HPlotContainer(c1, p3)
c3 = VPlotContainer(p4, c2)
self.plot = c3
def _image_plot_container(self):
plot = self.render_image()
# Create a container to position the plot and the colorbar side-by-side
self.container = OverlayPlotContainer()
self.container.add(plot)
self.img_container = HPlotContainer(use_backbuffer=False)
self.img_container.add(self.container)
self.img_container.bgcolor = "white"
if self.numpeaks_img > 0:
scatplot = self.render_scatplot()
self.container.add(scatplot)
colorbar = self.draw_colorbar()
self.img_container.add(colorbar)
return self.img_container
def test_valign(self):
container = HPlotContainer(bounds=[300,200], valign="center")
comp1 = StaticPlotComponent([200,100])
container.add(comp1)
container.do_layout()
self.failUnlessEqual(comp1.position, [0,50])
container.valign="top"
container.do_layout(force=True)
self.failUnlessEqual(comp1.position, [0,100])
return
def _create_plot_component(obj):
# Setup the spectrum plot
frequencies = linspace(0.0, MAX_FREQ, num=MAX_FREQN)
obj.spectrum_data = ArrayPlotData(frequency=frequencies)
empty_amplitude = zeros(MAX_FREQN)
obj.spectrum_data.set_data("amplitude", empty_amplitude)
obj.spectrum_plot = Plot(obj.spectrum_data)
obj.spectrum_plot.plot(("frequency", "amplitude"), name="Spectrum", color="red")
obj.spectrum_plot.padding = 50
obj.spectrum_plot.title = "Spectrum"
spec_range = obj.spectrum_plot.plots.values()[0][0].value_mapper.range
spec_range.low = 0.0
spec_range.high = 150.0 # spectrum amplitude maximum
obj.spectrum_plot.index_axis.title = "Frequency (hz)"
obj.spectrum_plot.value_axis.title = "Amplitude"
# Time Series plot
times = linspace(0.0, float(TIME_NUM_SAMPLES) / SAMPLING_RATE, num=TIME_NUM_SAMPLES)
obj.time_data = ArrayPlotData(time=times)
empty_amplitude = zeros(TIME_NUM_SAMPLES)
obj.time_data.set_data("amplitude", empty_amplitude)
obj.time_data.set_data("amplitude_1", empty_amplitude)
obj.time_plot = Plot(obj.time_data)
obj.time_plot.plot(("time", "amplitude"), name="Time", color="blue", alpha=0.5)
obj.time_plot.plot(("time", "amplitude_1"), name="Time", color="red", alpha=0.5)
obj.time_plot.padding = 50
obj.time_plot.title = "Time"
obj.time_plot.index_axis.title = "Time (seconds)"
obj.time_plot.value_axis.title = "Amplitude"
time_range = obj.time_plot.plots.values()[0][0].value_mapper.range
time_range.low = -1
time_range.high = 1
# Spectrogram plot
spectrogram_data = zeros((MAX_FREQN, SPECTROGRAM_LENGTH))
obj.spectrogram_plotdata = ArrayPlotData()
obj.spectrogram_plotdata.set_data("imagedata", spectrogram_data)
spectrogram_plot = Plot(obj.spectrogram_plotdata)
max_time = float(SPECTROGRAM_LENGTH * NUM_SAMPLES) / SAMPLING_RATE
# max_freq = float(SAMPLING_RATE / 2)
max_freq = float(MAX_FREQ)
spectrogram_plot.img_plot(
"imagedata", name="Spectrogram", xbounds=(0, max_time), ybounds=(0, max_freq), colormap=jet
)
range_obj = spectrogram_plot.plots["Spectrogram"][0].value_mapper.range
range_obj.high = 2 # brightness of specgram
range_obj.low = 0.0
range_obj.edit_traits()
spectrogram_plot.title = "Spectrogram"
obj.spectrogram_plot = spectrogram_plot
container = HPlotContainer()
container.add(obj.spectrum_plot)
container.add(obj.time_plot)
container.add(spectrogram_plot)
return container
def activate_template(self):
""" Converts all contained 'TDerived' objects to real objects using the
template traits of the object. This method must be overridden in
subclasses.
Returns
-------
None
"""
plots = [
p for p in [self.scatter_plot_1.plot, self.scatter_plot_2.plot]
if p is not None
]
if len(plots) == 2:
self.plot = HPlotContainer(spacing=self.spacing)
self.plot.add(*plots)
elif len(plots) == 1:
self.plot = plots[0]
def _create_plot_component(obj):
# Setup the spectrum plot
frequencies = linspace(0.0, float(SAMPLING_RATE)/2, num=NUM_SAMPLES/2)
obj.spectrum_data = ArrayPlotData(frequency=frequencies)
empty_amplitude = zeros(NUM_SAMPLES/2)
obj.spectrum_data.set_data('amplitude', empty_amplitude)
obj.spectrum_plot = Plot(obj.spectrum_data)
obj.spectrum_plot.plot(("frequency", "amplitude"), name="Spectrum",
color="red")
obj.spectrum_plot.padding = 50
obj.spectrum_plot.title = "Spectrum"
spec_range = obj.spectrum_plot.plots.values()[0][0].value_mapper.range
spec_range.low = 0.0
spec_range.high = 5.0
obj.spectrum_plot.index_axis.title = 'Frequency (hz)'
obj.spectrum_plot.value_axis.title = 'Amplitude'
# Time Series plot
times = linspace(0.0, float(NUM_SAMPLES)/SAMPLING_RATE, num=NUM_SAMPLES)
obj.time_data = ArrayPlotData(time=times)
empty_amplitude = zeros(NUM_SAMPLES)
obj.time_data.set_data('amplitude', empty_amplitude)
obj.time_plot = Plot(obj.time_data)
obj.time_plot.plot(("time", "amplitude"), name="Time", color="blue")
obj.time_plot.padding = 50
obj.time_plot.title = "Time"
obj.time_plot.index_axis.title = 'Time (seconds)'
obj.time_plot.value_axis.title = 'Amplitude'
time_range = obj.time_plot.plots.values()[0][0].value_mapper.range
time_range.low = -0.2
time_range.high = 0.2
# Spectrogram plot
spectrogram_data = zeros(( NUM_SAMPLES/2, SPECTROGRAM_LENGTH))
obj.spectrogram_plotdata = ArrayPlotData()
obj.spectrogram_plotdata.set_data('imagedata', spectrogram_data)
spectrogram_plot = Plot(obj.spectrogram_plotdata)
max_time = float(SPECTROGRAM_LENGTH * NUM_SAMPLES) / SAMPLING_RATE
max_freq = float(SAMPLING_RATE / 2)
spectrogram_plot.img_plot('imagedata',
name='Spectrogram',
xbounds=(0, max_time),
ybounds=(0, max_freq),
colormap=jet,
)
range_obj = spectrogram_plot.plots['Spectrogram'][0].value_mapper.range
range_obj.high = 5
range_obj.low = 0.0
spectrogram_plot.title = 'Spectrogram'
obj.spectrogram_plot = spectrogram_plot
container = HPlotContainer()
container.add(obj.spectrum_plot)
container.add(obj.time_plot)
container.add(spectrogram_plot)
return container
def __init__(self):
# Create the data and the PlotData object
x = linspace(-14, 14, 100)
y = sin(x) * x**3
plotdata = ArrayPlotData(x = x, y = y)
# Create the scatter plot
scatter = Plot(plotdata)
scatter.plot(("x", "y"), type="scatter", color="blue")
# Create the line plot
line = Plot(plotdata)
line.plot(("x", "y"), type="line", color="blue")
# Create a horizontal container and put the two plots inside it
container = HPlotContainer(scatter, line)
container.spacing = 0
scatter.padding_right = 0
line.padding_left = 0
line.y_axis.orientation = "right"
self.plot = container
def _create_plot_component():
# Create the index
numpoints = 100
low = -5
high = 15.0
x = arange(low, high, (high-low)/numpoints)
plotdata = ArrayPlotData(x=x, y1=jn(0,x), y2=jn(1,x))
# Create the left plot
left_plot = Plot(plotdata)
left_plot.x_axis.title = "X"
left_plot.y_axis.title = "j0(x)"
renderer = left_plot.plot(("x", "y1"), type="line", color="blue",
width=2.0)[0]
renderer.overlays.append(LineInspector(renderer, axis='value',
write_metadata=True,
is_listener=True))
renderer.overlays.append(LineInspector(renderer, axis="index",
write_metadata=True,
is_listener=True))
left_plot.overlays.append(ZoomTool(left_plot, tool_mode="range"))
left_plot.tools.append(PanTool(left_plot))
# Create the right plot
right_plot = Plot(plotdata)
right_plot.index_range = left_plot.index_range
right_plot.orientation = "v"
right_plot.x_axis.title = "j1(x)"
right_plot.y_axis.title = "X"
renderer2 = right_plot.plot(("x","y2"), type="line", color="red", width=2.0)[0]
renderer2.index = renderer.index
renderer2.overlays.append(LineInspector(renderer2, write_metadata=True, is_listener=True))
renderer2.overlays.append(LineInspector(renderer2, axis="value", is_listener=True))
right_plot.overlays.append(ZoomTool(right_plot, tool_mode="range"))
right_plot.tools.append(PanTool(right_plot))
container = HPlotContainer(background="lightgray")
container.add(left_plot)
container.add(right_plot)
return container
def __init__(self):
super(ContainerExample, self).__init__()
x = linspace(-14, 14, 100)
y = sin(x) * x**3
plotdata = ArrayPlotData(x=x, y=y)
scatter = Plot(plotdata)
scatter.plot(("x", "y"), type="scatter", color="blue")
line = Plot(plotdata)
line.plot(("x", "y"), type="line", color="blue")
container = HPlotContainer(scatter, line)
self.plot = container
def _create_window(self):
# Create some x-y data series to plot
x = linspace(-2.0, 10.0, 100)
pd = ArrayPlotData(index = x)
for i in range(5):
pd.set_data("y" + str(i), jn(i,x))
# Create some line plots of some of the data
plot1 = Plot(pd, title="Line Plot", padding=50, border_visible=True,
overlay_border=True)
plot1.legend.visible = True
plot1.plot(("index", "y0", "y1", "y2"), name="j_n, n<3", color="red")
plot1.plot(("index", "y3"), name="j_3", color="blue")
# Create a container and add our plots
container = HPlotContainer()
container.add(plot1)
# Return a window containing our plots
return Window(self, -1, component=container)
def _create_plot_component():
# Create the index
numpoints = 100
low = -5
high = 15.0
x = arange(low, high, (high - low) / numpoints)
plotdata = ArrayPlotData(x=x, y1=jn(0, x), y2=jn(1, x))
# Create the left plot
left_plot = Plot(plotdata)
left_plot.x_axis.title = 'X'
left_plot.y_axis.title = 'j0(x)'
renderer = left_plot.plot(('x', 'y1'), type='line', color='blue',
width=2.0)[0]
renderer.overlays.append(LineInspector(renderer, axis='value',
write_metadata=True, is_listener=True))
renderer.overlays.append(LineInspector(renderer, axis='index',
write_metadata=True, is_listener=True))
left_plot.overlays.append(ZoomTool(left_plot, tool_mode='range'))
left_plot.tools.append(PanTool(left_plot))
# Create the right plot
right_plot = Plot(plotdata)
right_plot.index_range = left_plot.index_range
right_plot.orientation = 'v'
right_plot.x_axis.title = 'j1(x)'
right_plot.y_axis.title = 'X'
renderer2 = right_plot.plot(('x', 'y2'), type='line', color='red',
width=2.0)[0]
renderer2.index = renderer.index
renderer2.overlays.append(LineInspector(renderer2,
write_metadata=True, is_listener=True))
renderer2.overlays.append(LineInspector(renderer2, axis='value',
is_listener=True))
right_plot.overlays.append(ZoomTool(right_plot, tool_mode='range'))
right_plot.tools.append(PanTool(right_plot))
container = HPlotContainer(background='lightgray')
container.add(left_plot)
container.add(right_plot)
right_plot = Plot(plotdata)
right_plot.index_range = left_plot.index_range
right_plot.orientation = 'v'
right_plot.x_axis.title = 'j1(x)'
right_plot.y_axis.title = 'X'
renderer2 = right_plot.plot(('x', 'y2'), type='line', color='red',
width=2.0)[0]
renderer2.index = renderer.index
renderer2.overlays.append(LineInspector(renderer2,
write_metadata=True, is_listener=True))
renderer2.overlays.append(LineInspector(renderer2, axis='value',
is_listener=True))
right_plot.overlays.append(ZoomTool(right_plot, tool_mode='range'))
right_plot.tools.append(PanTool(right_plot))
container.add(right_plot)
return container
def _create_window(self, title, xtitle, x, ytitle, y, z):
'''
- Left-drag pans the plot.
- Mousewheel up and down zooms the plot in and out.
- Pressing "z" brings up the Zoom Box, and you can click-drag a rectangular
region to zoom. If you use a sequence of zoom boxes, pressing alt-left-arrow
and alt-right-arrow moves you forwards and backwards through the "zoom
history".
'''
self._plotname = title
# Create window
self.data = ArrayPlotData()
self.plot = Plot(self.data)
self.update_plot(x, y, z)
self.plot.title = title
self.plot.x_axis.title = xtitle
self.plot.y_axis.title = ytitle
cmap_renderer = self.plot.plots[self._plotname][0]
# Create colorbar
self._create_colorbar()
self._colorbar.plot = cmap_renderer
self._colorbar.padding_top = self.plot.padding_top
self._colorbar.padding_bottom = self.plot.padding_bottom
# Add some tools
self.plot.tools.append(PanTool(self.plot, constrain_key="shift"))
self.plot.overlays.append(ZoomTool(component=self.plot, tool_mode="box", always_on=False))
# selection = ColormappedSelectionOverlay(cmap_renderer, fade_alpha=0.35, selection_type="mask")
# cmap_renderer.overlays.append(selection)
# Create a container to position the plot and the colorbar side-by-side
container = HPlotContainer(use_backbuffer = True)
container.add(self.plot)
container.add(self._colorbar)
self.container = container
# Return a window containing our plot container
return Window(self, -1, component=container)
def _create_plot_component():
# Create some data
numpts = 1000
x = sort(random(numpts))
y = random(numpts)
color = exp(-(x**2 + y**2))
# Create a plot data obect and give it this data
pd = ArrayPlotData()
pd.set_data("index", x)
pd.set_data("value", y)
pd.set_data("color", color)
# Create the plot
plot = Plot(pd)
plot.plot(("index", "value", "color"),
type="cmap_scatter",
name="my_plot",
color_mapper=jet,
marker = "square",
fill_alpha = 0.5,
marker_size = 6,
outline_color = "black",
border_visible = True,
bgcolor = "white")
# Tweak some of the plot properties
plot.title = "Colormapped Scatter Plot"
plot.padding = 50
plot.x_grid.visible = False
plot.y_grid.visible = False
plot.x_axis.font = "modern 16"
plot.y_axis.font = "modern 16"
# Right now, some of the tools are a little invasive, and we need the
# actual ColomappedScatterPlot object to give to them
cmap_renderer = plot.plots["my_plot"][0]
# Attach some tools to the plot
plot.tools.append(PanTool(plot, constrain_key="shift"))
zoom = ZoomTool(component=plot, tool_mode="box", always_on=False)
plot.overlays.append(zoom)
selection = ColormappedSelectionOverlay(cmap_renderer, fade_alpha=0.35,
selection_type="mask")
cmap_renderer.overlays.append(selection)
# Create the colorbar, handing in the appropriate range and colormap
colorbar = create_colorbar(plot.color_mapper)
colorbar.plot = cmap_renderer
colorbar.padding_top = plot.padding_top
colorbar.padding_bottom = plot.padding_bottom
# Create a container to position the plot and the colorbar side-by-side
container = HPlotContainer(use_backbuffer = True)
container.add(plot)
container.add(colorbar)
container.bgcolor = "lightgray"
return container
def _ScanPlotContainer_default(self):
ScanImage = self.ScanImage
ScanImage.x_mapper.domain_limits = (self.x_range[0],self.x_range[1])
ScanImage.y_mapper.domain_limits = (self.y_range[0],self.y_range[1])
ScanImage.overlays.append(self.zoom_tool)
ScanImage.overlays.append(self.cursor)
colormap = ScanImage.color_mapper
colorbar = ColorBar(index_mapper=LinearMapper(range=colormap.range),
color_mapper=colormap,
plot=self.ScanPlot,
orientation='v',
resizable='v',
width=20,
height=400,
padding=50)
container = HPlotContainer()
container.add(self.ScanPlot)
container.add(colorbar)
return container
def __init__(self, **kwargs):
super(VariableMeshPannerView, self).__init__(**kwargs)
# Create the plot
self.add_trait("field", DelegatesTo("vm_plot"))
plot = self.vm_plot.plot
img_plot = self.vm_plot.img_plot
if self.use_tools:
plot.tools.append(PanTool(img_plot))
zoom = ZoomTool(component=img_plot, tool_mode="box", always_on=False)
plot.overlays.append(zoom)
imgtool = ImageInspectorTool(img_plot)
img_plot.tools.append(imgtool)
overlay = ImageInspectorOverlay(component=img_plot, image_inspector=imgtool,
bgcolor="white", border_visible=True)
img_plot.overlays.append(overlay)
image_value_range = DataRange1D(self.vm_plot.fid)
cbar_index_mapper = LinearMapper(range=image_value_range)
self.colorbar = ColorBar(index_mapper=cbar_index_mapper,
plot=img_plot,
padding_right=40,
resizable='v',
width=30)
self.colorbar.tools.append(
PanTool(self.colorbar, constrain_direction="y", constrain=True))
zoom_overlay = ZoomTool(self.colorbar, axis="index", tool_mode="range",
always_on=True, drag_button="right")
self.colorbar.overlays.append(zoom_overlay)
# create a range selection for the colorbar
range_selection = RangeSelection(component=self.colorbar)
self.colorbar.tools.append(range_selection)
self.colorbar.overlays.append(
RangeSelectionOverlay(component=self.colorbar,
border_color="white",
alpha=0.8, fill_color="lightgray"))
# we also want to the range selection to inform the cmap plot of
# the selection, so set that up as well
range_selection.listeners.append(img_plot)
self.full_container = HPlotContainer(padding=30)
self.container = OverlayPlotContainer(padding=0)
self.full_container.add(self.colorbar)
self.full_container.add(self.container)
self.container.add(self.vm_plot.plot)
def __init__(self):
super(IMUGloveDisplay, self).__init__()
x = linspace(-14, 14, 100)
y = sin(x) * x**3
plotdata = ArrayPlotData(x=x, y=y)
scatter = Plot(plotdata)
scatter.plot(("x", "y"), type="scatter", color="blue")
line = Plot(plotdata)
line.plot(("x", "y"), type="line", color="blue")
container = HPlotContainer(scatter, line)
#scatter.title = "sin(x) * x^3"
#line.title = 'line plot'
self.plot = container
self.InitGlove()
def _image_plot_container(self):
plot = self.render_image()
# Create a container to position the plot and the colorbar side-by-side
self.container=OverlayPlotContainer()
self.container.add(plot)
self.img_container = HPlotContainer(use_backbuffer = False)
self.img_container.add(self.container)
self.img_container.bgcolor = "white"
if self.numpeaks_img>0:
scatplot = self.render_scatplot()
self.container.add(scatplot)
colorbar = self.draw_colorbar()
self.img_container.add(colorbar)
return self.img_container
def activate_template ( self ):
""" Converts all contained 'TDerived' objects to real objects using the
template traits of the object. This method must be overridden in
subclasses.
Returns
-------
None
"""
plots = [ p for p in [ self.scatter_plot_1.plot,
self.scatter_plot_2.plot ] if p is not None ]
if len( plots ) == 2:
self.plot = HPlotContainer( spacing = self.spacing )
self.plot.add( *plots )
elif len( plots ) == 1:
self.plot = plots[0]
def _create_window(self, **kw):
self._colormap = default_colormaps.jet
self.data = ArrayPlotData()
self.plot = Plot(self.data)
x = linspace(-10, 10, 101)
y = linspace(-10, 10, 101)
z = zeros((101,101))
self.set_data(x, y, z, **kw)
# self.set_data(x,y,z)
self._create_colorbar()
self.container = HPlotContainer(use_backbuffer=True)
self.container.add(self.plot)
self.container.add(self._colorbar)
return Window(self, -1, component=self.container)
def test_stack_nonresize(self):
# Assuming resizable='' for all plot containers and components
container = HPlotContainer(bounds=[300,100])
comp1 = StaticPlotComponent([100,70])
comp2 = StaticPlotComponent([90,80])
comp3 = StaticPlotComponent([80,90])
container.add(comp1, comp2, comp3)
container.do_layout()
self.assert_tuple(container.get_preferred_size(), (270,90))
self.assert_tuple(container.bounds, (300,100))
self.assert_tuple(comp1.position, (0,0))
self.assert_tuple(comp2.position, (100,0))
self.assert_tuple(comp3.position, (190,0))
return
def test_stack_one_resize(self):
"Checks stacking with 1 resizable component thrown in"
container = HPlotContainer(bounds=[300,100])
comp1 = StaticPlotComponent([100,70])
comp2 = StaticPlotComponent([90,80])
comp3 = StaticPlotComponent([80,90], resizable='hv')
comp4 = StaticPlotComponent([40,50])
container.add(comp1, comp2, comp3, comp4)
container.do_layout()
self.assert_tuple(container.get_preferred_size(), (230,80))
self.assert_tuple(container.bounds, (300,100))
self.assert_tuple(comp1.position, (0,0))
self.assert_tuple(comp2.position, (100,0))
self.assert_tuple(comp3.position, (190,0))
self.assert_tuple(comp4.position, (260,0))
return
def _object_index_changed(self):
"""Handle object index slider changing."""
try:
self.current_object = self.current_image[self.object_index - 1]
# Display
sil = self.current_object.image
self._update_img_plot('sil_plot', sil, 'Extracted mask')
# .T to get major axis horizontal
rotated = self.current_object.aligned_version.image.T
self._update_img_plot('rotated_plot', rotated, 'Aligned mask')
self.image_plots = HPlotContainer(self.sil_plot,
self.rotated_plot,
valign="top",
bgcolor="transparent")
self._update_spline_plot()
except IndexError:
self.current_object = None
def __init__(self):
#读入图像
img = cv.imread("lena_full.jpg")
img2 = cv.Mat()
cv.cvtColor(img, img2, cv.CV_BGR2GRAY)
img = cv.Mat()
cv.resize(img2, img, cv.Size(N, N))
self.fimg = fft.fft2(img[:]) # 图像的频域信号
mag_img = np.log10(np.abs(self.fimg))
# 创建计算用图像
filtered_img = np.zeros((N, N), dtype=np.float)
self.mask = np.zeros((N, N), dtype=np.float)
self.mask_img = cv.asMat(self.mask) # 在self.mask上绘制多边形用的图像
# 创建数据源
self.data = ArrayPlotData(mag_img=fft.fftshift(mag_img),
filtered_img=filtered_img,
mask_img=self.mask)
# 创建三个图像绘制框以及容器
meg_plot, img = self.make_image_plot("mag_img")
mask_plot, _ = self.make_image_plot("mask_img")
filtered_plot, _ = self.make_image_plot("filtered_img")
self.plot = HPlotContainer(meg_plot, mask_plot, filtered_plot)
# 创建套索工具
lasso_selection = LassoSelection(component=img)
lasso_overlay = LassoOverlay(lasso_selection=lasso_selection,
component=img,
selection_alpha=0.3)
img.tools.append(lasso_selection)
img.overlays.append(lasso_overlay)
self.lasso_selection = lasso_selection
# 监听套索工具的事件、开启时钟事件
lasso_selection.on_trait_change(self.lasso_updated,
"disjoint_selections")
self.timer = Timer(50, self.on_timer)
def _container_default(self):
#image_container = OverlayPlotContainer(padding=20,
# use_backbuffer=True,
# unified_draw=True)
#image_container.add(self.plot)
container = HPlotContainer(padding=40,
fill_padding=True,
bgcolor="white",
use_backbuffer=False)
inner_cont = VPlotContainer(padding=0, use_backbuffer=True)
# container = HPlotContainer(bgcolor = "white", use_backbuffer=False)
# inner_cont = VPlotContainer(use_backbuffer=True)
inner_cont.add(self.h_plot)
inner_cont.add(self.plot)
container.add(inner_cont)
container.add(self.v_plot)
return container
def _create_window(self, title, xtitle, x, ytitle, y, z):
'''
- Left-drag pans the plot.
- Mousewheel up and down zooms the plot in and out.
- Pressing "z" brings up the Zoom Box, and you can click-drag a rectangular
region to zoom. If you use a sequence of zoom boxes, pressing alt-left-arrow
and alt-right-arrow moves you forwards and backwards through the "zoom
history".
'''
self._plotname = title
# Create window
self.data = ArrayPlotData()
self.plot = Plot(self.data)
self.update_plot(x, y, z)
self.plot.title = title
self.plot.x_axis.title = xtitle
self.plot.y_axis.title = ytitle
cmap_renderer = self.plot.plots[self._plotname][0]
# Create colorbar
self._create_colorbar()
self._colorbar.plot = cmap_renderer
self._colorbar.padding_top = self.plot.padding_top
self._colorbar.padding_bottom = self.plot.padding_bottom
# Add some tools
self.plot.tools.append(PanTool(self.plot, constrain_key="shift"))
self.plot.overlays.append(
ZoomTool(component=self.plot, tool_mode="box", always_on=False))
# selection = ColormappedSelectionOverlay(cmap_renderer, fade_alpha=0.35, selection_type="mask")
# cmap_renderer.overlays.append(selection)
# Create a container to position the plot and the colorbar side-by-side
container = HPlotContainer(use_backbuffer=True)
container.add(self.plot)
container.add(self._colorbar)
self.container = container
# Return a window containing our plot container
return Window(self, -1, component=container)
def create_plot_component(self):
color_range_max_value = 10
# gripper right cos field
x_axis = numpy.array(
range(self.arch._gripper_right_cos_field.
get_output_dimension_sizes()[0]))
self._gripper_right_cos_field_plotdata = ArrayPlotData(
x=x_axis, y=self.arch._gripper_right_cos_field.get_activation())
self._gripper_right_cos_field_plot = Plot(
self._gripper_right_cos_field_plotdata)
self._gripper_right_cos_field_plot.title = 'gripper right cos'
self._gripper_right_cos_field_plot.plot(("x", "y"),
name='gripper_right_cos',
type="line",
color="blue")
range_self = self._gripper_right_cos_field_plot.plots[
'gripper_right_cos'][0].value_mapper.range
range_self.high = color_range_max_value
range_self.low = -color_range_max_value
# gripper left cos field
x_axis = numpy.array(
range(
self.arch._gripper_left_cos_field.get_output_dimension_sizes()
[0]))
self._gripper_left_cos_field_plotdata = ArrayPlotData(
x=x_axis, y=self.arch._gripper_left_cos_field.get_activation())
self._gripper_left_cos_field_plot = Plot(
self._gripper_left_cos_field_plotdata)
self._gripper_left_cos_field_plot.title = 'gripper left cos'
self._gripper_left_cos_field_plot.plot(("x", "y"),
name='gripper_left_cos',
type="line",
color="blue")
range_self = self._gripper_left_cos_field_plot.plots[
'gripper_left_cos'][0].value_mapper.range
range_self.high = color_range_max_value
range_self.low = -color_range_max_value
# find red color intention field
x_axis = numpy.array(
range(self.arch._find_color.get_intention_field().
get_output_dimension_sizes()[0]))
self._find_color_intention_field_plotdata = ArrayPlotData(
x=x_axis,
y=self.arch._find_color.get_intention_field().get_activation())
self._find_color_intention_field_plot = Plot(
self._find_color_intention_field_plotdata)
self._find_color_intention_field_plot.title = 'find color int'
self._find_color_intention_field_plot.plot(("x", "y"),
name='find_color_int',
type="line",
color="blue")
range_self = self._find_color_intention_field_plot.plots[
'find_color_int'][0].value_mapper.range
range_self.high = color_range_max_value
range_self.low = -color_range_max_value
# find green color intention field
x_axis = numpy.array(
range(self.arch._find_color_ee.get_intention_field().
get_output_dimension_sizes()[0]))
self._find_color_ee_intention_field_plotdata = ArrayPlotData(
x=x_axis,
y=self.arch._find_color_ee.get_intention_field().get_activation())
self._find_color_ee_intention_field_plot = Plot(
self._find_color_ee_intention_field_plotdata)
self._find_color_ee_intention_field_plot.title = 'find color ee int'
self._find_color_ee_intention_field_plot.plot(("x", "y"),
name='find_color_ee_int',
type="line",
color="blue")
range_self = self._find_color_ee_intention_field_plot.plots[
'find_color_ee_int'][0].value_mapper.range
range_self.high = color_range_max_value
range_self.low = -color_range_max_value
# camera
self._camera_field_plotdata = ArrayPlotData()
self._camera_field_plotdata.set_data(
'imagedata',
self.arch._camera_field.get_activation().max(2).transpose())
self._camera_field_plot = Plot(self._camera_field_plotdata)
self._camera_field_plot.title = 'camera'
self._camera_field_plot.img_plot(
'imagedata',
name='camera_field',
xbounds=(0, self.arch._camera_field_sizes[0] - 1),
ybounds=(0, self.arch._camera_field_sizes[1] - 1),
colormap=jet,
)
range_self = self._camera_field_plot.plots['camera_field'][
0].value_mapper.range
range_self.high = color_range_max_value
range_self.low = -color_range_max_value
# color space red
self._color_space_field_plotdata = ArrayPlotData()
self._color_space_field_plotdata.set_data(
'imagedata',
self.arch._color_space_field.get_activation().max(1).transpose())
self._color_space_field_plot = Plot(self._color_space_field_plotdata)
self._color_space_field_plot.title = 'color space'
self._color_space_field_plot.img_plot(
'imagedata',
name='color_space_field',
xbounds=(0, self.arch._color_space_field_sizes[0] - 1),
ybounds=(0, self.arch._color_space_field_sizes[2] - 1),
colormap=jet,
)
range_self = self._color_space_field_plot.plots['color_space_field'][
0].value_mapper.range
range_self.high = color_range_max_value
range_self.low = -color_range_max_value
# color space green
self._color_space_ee_field_plotdata = ArrayPlotData()
self._color_space_ee_field_plotdata.set_data(
'imagedata',
self.arch._color_space_ee_field.get_activation().max(
2).transpose())
self._color_space_ee_field_plot = Plot(
self._color_space_ee_field_plotdata)
self._color_space_ee_field_plot.title = 'color space ee'
self._color_space_ee_field_plot.img_plot(
'imagedata',
name='color_space_ee_field',
xbounds=(0, self.arch._color_space_ee_field_sizes[0] - 1),
ybounds=(0, self.arch._color_space_ee_field_sizes[1] - 1),
colormap=jet,
)
range_self = self._color_space_ee_field_plot.plots[
'color_space_ee_field'][0].value_mapper.range
range_self.high = color_range_max_value
range_self.low = -color_range_max_value
# spatial target
self._spatial_target_field_plotdata = ArrayPlotData()
self._spatial_target_field_plotdata.set_data(
'imagedata',
self.arch._spatial_target_field.get_activation().transpose())
self._spatial_target_field_plot = Plot(
self._spatial_target_field_plotdata)
self._spatial_target_field_plot.title = 'spatial target'
self._spatial_target_field_plot.img_plot(
'imagedata',
name='spatial_target_field',
xbounds=(0, self.arch._spatial_target_field_sizes[0] - 1),
ybounds=(0, self.arch._spatial_target_field_sizes[1] - 1),
colormap=jet,
)
range_self = self._spatial_target_field_plot.plots[
'spatial_target_field'][0].value_mapper.range
range_self.high = color_range_max_value
range_self.low = -color_range_max_value
# move head intention
self._move_head_intention_field_plotdata = ArrayPlotData()
self._move_head_intention_field_plotdata.set_data(
'imagedata',
self.arch._move_head.get_intention_field().get_activation().
transpose())
self._move_head_intention_field_plot = Plot(
self._move_head_intention_field_plotdata)
self._move_head_intention_field_plot.title = 'move head int'
self._move_head_intention_field_plot.img_plot(
'imagedata',
name='move_head_intention_field',
xbounds=(0, self.arch._move_head_field_sizes[0] - 1),
ybounds=(0, self.arch._move_head_field_sizes[1] - 1),
colormap=jet,
)
range_self = self._move_head_intention_field_plot.plots[
'move_head_intention_field'][0].value_mapper.range
range_self.high = color_range_max_value
range_self.low = -color_range_max_value
# move head cos
self._move_head_cos_field_plotdata = ArrayPlotData()
self._move_head_cos_field_plotdata.set_data(
'imagedata',
self.arch._move_head.get_cos_field().get_activation().transpose())
self._move_head_cos_field_plot = Plot(
self._move_head_cos_field_plotdata)
self._move_head_cos_field_plot.title = 'move head cos'
self._move_head_cos_field_plot.img_plot(
'imagedata',
name='move_head_cos_field',
xbounds=(0, self.arch._move_head_field_sizes[0] - 1),
ybounds=(0, self.arch._move_head_field_sizes[1] - 1),
colormap=jet,
)
range_self = self._move_head_cos_field_plot.plots[
'move_head_cos_field'][0].value_mapper.range
range_self.high = color_range_max_value
range_self.low = -color_range_max_value
# move right arm intention
self._move_right_arm_intention_field_plotdata = ArrayPlotData()
self._move_right_arm_intention_field_plotdata.set_data(
'imagedata',
self.arch._move_right_arm_intention_field.get_activation().
transpose())
self._move_right_arm_intention_field_plot = Plot(
self._move_right_arm_intention_field_plotdata)
self._move_right_arm_intention_field_plot.title = 'move right arm int'
self._move_right_arm_intention_field_plot.img_plot(
'imagedata',
name='move_right_arm_intention_field',
xbounds=(0, self.arch._move_arm_field_sizes[0] - 1),
ybounds=(0, self.arch._move_arm_field_sizes[1] - 1),
colormap=jet,
)
range_self = self._move_right_arm_intention_field_plot.plots[
'move_right_arm_intention_field'][0].value_mapper.range
range_self.high = color_range_max_value
range_self.low = -color_range_max_value
# move right arm cos
self._move_right_arm_cos_field_plotdata = ArrayPlotData()
self._move_right_arm_cos_field_plotdata.set_data(
'imagedata',
self.arch._move_arm_cos_field.get_activation().transpose())
self._move_right_arm_cos_field_plot = Plot(
self._move_right_arm_cos_field_plotdata)
self._move_right_arm_cos_field_plot.title = 'move right arm cos'
self._move_right_arm_cos_field_plot.img_plot(
'imagedata',
name='move_right_arm_cos_field',
xbounds=(0, self.arch._move_arm_field_sizes[0] - 1),
ybounds=(0, self.arch._move_arm_field_sizes[1] - 1),
colormap=jet,
)
range_self = self._move_right_arm_cos_field_plot.plots[
'move_right_arm_cos_field'][0].value_mapper.range
range_self.high = color_range_max_value
range_self.low = -color_range_max_value
# visual servoing right intention
self._visual_servoing_right_intention_field_plotdata = ArrayPlotData()
self._visual_servoing_right_intention_field_plotdata.set_data(
'imagedata',
self.arch._visual_servoing_right.get_intention_field().
get_activation().transpose())
self._visual_servoing_right_intention_field_plot = Plot(
self._visual_servoing_right_intention_field_plotdata)
self._visual_servoing_right_intention_field_plot.title = 'visual servoing right int'
self._visual_servoing_right_intention_field_plot.img_plot(
'imagedata',
name='visual_servoing_right_intention_field',
xbounds=(0, self.arch._visual_servoing_field_sizes[0] - 1),
ybounds=(0, self.arch._visual_servoing_field_sizes[1] - 1),
colormap=jet,
)
range_self = self._visual_servoing_right_intention_field_plot.plots[
'visual_servoing_right_intention_field'][0].value_mapper.range
range_self.high = color_range_max_value
range_self.low = -color_range_max_value
# visual servoing right cos
self._visual_servoing_right_cos_field_plotdata = ArrayPlotData()
self._visual_servoing_right_cos_field_plotdata.set_data(
'imagedata',
self.arch._visual_servoing_right.get_cos_field().get_activation().
transpose())
self._visual_servoing_right_cos_field_plot = Plot(
self._visual_servoing_right_cos_field_plotdata)
self._visual_servoing_right_cos_field_plot.title = 'visual servoing right cos'
self._visual_servoing_right_cos_field_plot.img_plot(
'imagedata',
name='visual_servoing_right_cos_field',
xbounds=(0, self.arch._visual_servoing_field_sizes[0] - 1),
ybounds=(0, self.arch._visual_servoing_field_sizes[1] - 1),
colormap=jet,
)
range_self = self._visual_servoing_right_cos_field_plot.plots[
'visual_servoing_right_cos_field'][0].value_mapper.range
range_self.high = color_range_max_value
range_self.low = -color_range_max_value
self._container = VPlotContainer()
self._hcontainer_top = HPlotContainer()
self._hcontainer_bottom = HPlotContainer()
self._hcontainer_bottom.add(self._camera_field_plot)
self._hcontainer_bottom.add(self._color_space_field_plot)
self._hcontainer_bottom.add(self._spatial_target_field_plot)
self._hcontainer_bottom.add(self._move_head_intention_field_plot)
self._hcontainer_bottom.add(self._move_right_arm_intention_field_plot)
# self._hcontainer_bottom.add(self._find_color_intention_field_plot)
# self._hcontainer_bottom.add(self._gripper_right_intention_field_plot)
self._hcontainer_top.add(self._color_space_ee_field_plot)
self._hcontainer_top.add(
self._visual_servoing_right_intention_field_plot)
self._hcontainer_top.add(self._visual_servoing_right_cos_field_plot)
self._hcontainer_top.add(self._move_head_cos_field_plot)
self._hcontainer_top.add(self._move_right_arm_cos_field_plot)
# self._hcontainer_top.add(self._gripper_right_cos_field_plot)
self._container.add(self._hcontainer_bottom)
self._container.add(self._hcontainer_top)
class ColorPlot(BasePlot):
def __init__(self, parent, **kw):
self._cbar_axis_format = kw.pop('cbar_axis_format', '')
self._plotname = kw.pop('plotname', 'color_plot')
# TODO: enables via kws
BasePlot.__init__(self, parent, **kw)
# defaults from cyclops config
import cyclops
if cyclops.config.has_key('plot_colors'):
cmap = cyclops.config['plot_colors'].get('colorplot_cmap',
DEFAULT_CMAP)
self.set_colormap_by_name(cmap)
### public methods
def enable_colorbar_panning(self):
self._colorbar.tools.append(PanTool(self._colorbar,
constrain_direction='y',
constrain=True))
def enable_colorbar_zooming(self):
zoom_overlay = ZoomTool(self._colorbar, axis='index', tool_mode='range',
always_on=True, drag_button='right')
self._colorbar.overlays.append(zoom_overlay)
def set_colormap_by_name(self, colormap):
if hasattr(default_colormaps, colormap):
self._colormap = getattr(default_colormaps, colormap)
value_range = self.plot.color_mapper.range
self.plot.color_mapper = self._colormap(value_range)
self._colorbar.color_mapper = self._colormap(value_range)
self.container.request_redraw()
def set_colormap(self, colormap):
self._colormap = colormap
value_range = self.plot.color_mapper.range
self.plot.color_mapper = self._colormap(value_range)
self._container.request_redraw()
def set_data(self, x, y, z, **kw):
self.data.set_data('2d_data', z)
if self.plot.plots.has_key(self._plotname):
self.plot.delplot(self._plotname)
# determine correct bounds
xstep = (x.max() - x.min())/(len(x)-1)
ystep = (y.max() - y.min())/(len(y)-1)
x0, x1 = x.min() - xstep/2, x.max() + xstep/2
y0, y1 = y.min() - ystep/2, y.max() + ystep/2
self.plot.img_plot('2d_data',
name = self._plotname,
xbounds = (x0, x1),
ybounds = (y0, y1),
colormap = self._colormap, **kw)[0]
# if we have a cursor, need to redraw
if hasattr(self, 'crosshair'):
#pos = self.crosshair.cursor_pos
self.enable_crosshair('color_plot')
#self.crosshair.cursor_pos = pos
### private methods
def _create_window(self, **kw):
self._colormap = default_colormaps.jet
self.data = ArrayPlotData()
self.plot = Plot(self.data)
x = linspace(-10, 10, 101)
y = linspace(-10, 10, 101)
z = zeros((101,101))
self.set_data(x, y, z, **kw)
# self.set_data(x,y,z)
self._create_colorbar()
self.container = HPlotContainer(use_backbuffer=True)
self.container.add(self.plot)
self.container.add(self._colorbar)
return Window(self, -1, component=self.container)
def _create_colorbar(self):
cmap = self.plot.color_mapper
self._colorbar = ColorBar(index_mapper=LinearMapper(range=cmap.range),
color_mapper=cmap,
orientation='v',
resizable='v',
width=30,
padding=30,
axis_visible=False)
self._colorbar.plot = self.plot
self._colorbar.padding_top = self.plot.padding_top
self._colorbar.padding_bottom = self.plot.padding_bottom
# create an axis as well
kwargs = {'orientation' : 'left',
'title' : 'z'}
if self._cbar_axis_format != '' :
f = lambda val: ('%s' % self._cbar_axis_format) % val
kwargs['tick_label_formatter'] = f
self.colorbar_axis = PlotAxis(self._colorbar, **kwargs)
self._colorbar.underlays.append(self.colorbar_axis)
class TemplatePicker(HasTraits):
template = Array
CC = Array
peaks = List
zero = Int(0)
tmp_size = Range(low=2, high=512, value=64, cols=4)
max_pos_x = Int(1023)
max_pos_y = Int(1023)
top = Range(low='zero', high='max_pos_x', value=20, cols=4)
left = Range(low='zero', high='max_pos_y', value=20, cols=4)
is_square = Bool
img_plot = Instance(Plot)
tmp_plot = Instance(Plot)
findpeaks = Button
peak_width = Range(low=2, high=200, value=10)
tab_selected = Event
ShowCC = Bool
img_container = Instance(Component)
container = Instance(Component)
colorbar = Instance(Component)
numpeaks_total = Int(0)
numpeaks_img = Int(0)
OK_custom = OK_custom_handler
cbar_selection = Instance(RangeSelection)
cbar_selected = Event
thresh = Trait(None, None, List, Tuple, Array)
thresh_upper = Float(1.0)
thresh_lower = Float(0.0)
numfiles = Int(1)
img_idx = Int(0)
tmp_img_idx = Int(0)
csr = Instance(BaseCursorTool)
traits_view = View(HFlow(
VGroup(Item("img_container",
editor=ComponentEditor(),
show_label=False),
Group(
Spring(),
Item("ShowCC",
editor=BooleanEditor(),
label="Show cross correlation image")),
label="Original image",
show_border=True,
trait_modified="tab_selected"),
VGroup(
Group(HGroup(
Item("left", label="Left coordinate", style="custom"),
Item("top", label="Top coordinate", style="custom"),
),
Item("tmp_size", label="Template size", style="custom"),
Item("tmp_plot",
editor=ComponentEditor(height=256, width=256),
show_label=False,
resizable=True),
label="Template",
show_border=True),
Group(Item("peak_width", label="Peak width", style="custom"),
Group(
Spring(),
Item("findpeaks",
editor=ButtonEditor(label="Find Peaks"),
show_label=False),
Spring(),
),
HGroup(
Item("thresh_lower",
label="Threshold Lower Value",
editor=TextEditor(evaluate=float,
format_str='%1.4f')),
Item("thresh_upper",
label="Threshold Upper Value",
editor=TextEditor(evaluate=float,
format_str='%1.4f')),
),
HGroup(
Item("numpeaks_img",
label="Number of Cells selected (this image)",
style='readonly'),
Spring(),
Item("numpeaks_total", label="Total", style='readonly'),
Spring(),
),
label="Peak parameters",
show_border=True),
)),
buttons=[
Action(name='OK',
enabled_when='numpeaks_total > 0'),
CancelButton
],
title="Template Picker",
handler=OK_custom,
kind='livemodal',
key_bindings=key_bindings,
width=960,
height=600)
def __init__(self, signal_instance):
super(TemplatePicker, self).__init__()
try:
import cv
except:
print "OpenCV unavailable. Can't do cross correlation without it. Aborting."
return None
self.OK_custom = OK_custom_handler()
self.sig = signal_instance
if not hasattr(self.sig.mapped_parameters, "original_files"):
self.sig.data = np.atleast_3d(self.sig.data)
self.titles = [self.sig.mapped_parameters.name]
else:
self.numfiles = len(
self.sig.mapped_parameters.original_files.keys())
self.titles = self.sig.mapped_parameters.original_files.keys()
tmp_plot_data = ArrayPlotData(
imagedata=self.sig.data[self.top:self.top + self.tmp_size,
self.left:self.left + self.tmp_size,
self.img_idx])
tmp_plot = Plot(tmp_plot_data, default_origin="top left")
tmp_plot.img_plot("imagedata", colormap=jet)
tmp_plot.aspect_ratio = 1.0
self.tmp_plot = tmp_plot
self.tmp_plotdata = tmp_plot_data
self.img_plotdata = ArrayPlotData(
imagedata=self.sig.data[:, :, self.img_idx])
self.img_container = self._image_plot_container()
self.crop_sig = None
def render_image(self):
plot = Plot(self.img_plotdata, default_origin="top left")
img = plot.img_plot("imagedata", colormap=gray)[0]
plot.title = "%s of %s: " % (self.img_idx + 1,
self.numfiles) + self.titles[self.img_idx]
plot.aspect_ratio = float(self.sig.data.shape[1]) / float(
self.sig.data.shape[0])
#if not self.ShowCC:
csr = CursorTool(img,
drag_button='left',
color='white',
line_width=2.0)
self.csr = csr
csr.current_position = self.left, self.top
img.overlays.append(csr)
# attach the rectangle tool
plot.tools.append(PanTool(plot, drag_button="right"))
zoom = ZoomTool(plot,
tool_mode="box",
always_on=False,
aspect_ratio=plot.aspect_ratio)
plot.overlays.append(zoom)
self.img_plot = plot
return plot
def render_scatplot(self):
peakdata = ArrayPlotData()
peakdata.set_data("index", self.peaks[self.img_idx][:, 0])
peakdata.set_data("value", self.peaks[self.img_idx][:, 1])
peakdata.set_data("color", self.peaks[self.img_idx][:, 2])
scatplot = Plot(peakdata,
aspect_ratio=self.img_plot.aspect_ratio,
default_origin="top left")
scatplot.plot(
("index", "value", "color"),
type="cmap_scatter",
name="my_plot",
color_mapper=jet(DataRange1D(low=0.0, high=1.0)),
marker="circle",
fill_alpha=0.5,
marker_size=6,
)
scatplot.x_grid.visible = False
scatplot.y_grid.visible = False
scatplot.range2d = self.img_plot.range2d
self.scatplot = scatplot
self.peakdata = peakdata
return scatplot
def _image_plot_container(self):
plot = self.render_image()
# Create a container to position the plot and the colorbar side-by-side
self.container = OverlayPlotContainer()
self.container.add(plot)
self.img_container = HPlotContainer(use_backbuffer=False)
self.img_container.add(self.container)
self.img_container.bgcolor = "white"
if self.numpeaks_img > 0:
scatplot = self.render_scatplot()
self.container.add(scatplot)
colorbar = self.draw_colorbar()
self.img_container.add(colorbar)
return self.img_container
def draw_colorbar(self):
scatplot = self.scatplot
cmap_renderer = scatplot.plots["my_plot"][0]
selection = ColormappedSelectionOverlay(cmap_renderer,
fade_alpha=0.35,
selection_type="range")
cmap_renderer.overlays.append(selection)
if self.thresh is not None:
cmap_renderer.color_data.metadata['selections'] = self.thresh
cmap_renderer.color_data.metadata_changed = {
'selections': self.thresh
}
# Create the colorbar, handing in the appropriate range and colormap
colormap = scatplot.color_mapper
colorbar = ColorBar(
index_mapper=LinearMapper(range=DataRange1D(low=0.0, high=1.0)),
orientation='v',
resizable='v',
width=30,
padding=20)
colorbar_selection = RangeSelection(component=colorbar)
colorbar.tools.append(colorbar_selection)
ovr = colorbar.overlays.append(
RangeSelectionOverlay(component=colorbar,
border_color="white",
alpha=0.8,
fill_color="lightgray",
metadata_name='selections'))
#ipshell('colorbar, colorbar_selection and ovr available:')
self.cbar_selection = colorbar_selection
self.cmap_renderer = cmap_renderer
colorbar.plot = cmap_renderer
colorbar.padding_top = scatplot.padding_top
colorbar.padding_bottom = scatplot.padding_bottom
self.colorbar = colorbar
return colorbar
@on_trait_change('ShowCC')
def toggle_cc_view(self):
if self.ShowCC:
self.CC = cv_funcs.xcorr(
self.sig.data[self.top:self.top + self.tmp_size,
self.left:self.left + self.tmp_size,
self.img_idx], self.sig.data[:, :, self.img_idx])
self.img_plotdata.set_data("imagedata", self.CC)
else:
self.img_plotdata.set_data("imagedata",
self.sig.data[:, :, self.img_idx])
self.redraw_plots()
@on_trait_change("img_idx")
def update_img_depth(self):
if self.ShowCC:
self.CC = cv_funcs.xcorr(
self.sig.data[self.top:self.top + self.tmp_size,
self.left:self.left + self.tmp_size,
self.img_idx], self.sig.data[:, :, self.img_idx])
self.img_plotdata.set_data("imagedata", self.CC)
else:
self.img_plotdata.set_data("imagedata",
self.sig.data[:, :, self.img_idx])
self.img_plot.title = "%s of %s: " % (
self.img_idx + 1, self.numfiles) + self.titles[self.img_idx]
self.redraw_plots()
@on_trait_change('tmp_size')
def update_max_pos(self):
max_pos_x = self.sig.data.shape[0] - self.tmp_size - 1
if self.left > max_pos_x: self.left = max_pos_x
self.max_pos_x = max_pos_x
max_pos_y = self.sig.data.shape[1] - self.tmp_size - 1
if self.top > max_pos_y: self.top = max_pos_y
self.max_pos_y = max_pos_y
return
def increase_img_idx(self, info):
if self.img_idx == (self.numfiles - 1):
self.img_idx = 0
else:
self.img_idx += 1
def decrease_img_idx(self, info):
if self.img_idx == 0:
self.img_idx = self.numfiles - 1
else:
self.img_idx -= 1
@on_trait_change('left, top')
def update_csr_position(self):
self.csr.current_position = self.left, self.top
@on_trait_change('csr:current_position')
def update_top_left(self):
self.left, self.top = self.csr.current_position
@on_trait_change('left, top, tmp_size')
def update_tmp_plot(self):
self.tmp_plotdata.set_data(
"imagedata",
self.sig.data[self.top:self.top + self.tmp_size,
self.left:self.left + self.tmp_size, self.img_idx])
grid_data_source = self.tmp_plot.range2d.sources[0]
grid_data_source.set_data(np.arange(self.tmp_size),
np.arange(self.tmp_size))
self.tmp_img_idx = self.img_idx
return
@on_trait_change('left, top, tmp_size')
def update_CC(self):
if self.ShowCC:
self.CC = cv_funcs.xcorr(
self.sig.data[self.top:self.top + self.tmp_size,
self.left:self.left + self.tmp_size,
self.tmp_img_idx], self.sig.data[:, :,
self.img_idx])
self.img_plotdata.set_data("imagedata", self.CC)
grid_data_source = self.img_plot.range2d.sources[0]
grid_data_source.set_data(np.arange(self.CC.shape[1]),
np.arange(self.CC.shape[0]))
if self.numpeaks_total > 0:
self.peaks = [np.array([[0, 0, -1]])]
@on_trait_change('cbar_selection:selection')
def update_thresh(self):
try:
thresh = self.cbar_selection.selection
self.thresh = thresh
self.cmap_renderer.color_data.metadata['selections'] = thresh
self.thresh_lower = thresh[0]
self.thresh_upper = thresh[1]
#cmap_renderer.color_data.metadata['selection_masks']=self.thresh
self.cmap_renderer.color_data.metadata_changed = {
'selections': thresh
}
self.container.request_redraw()
self.img_container.request_redraw()
except:
pass
@on_trait_change('thresh_upper,thresh_lower')
def manual_thresh_update(self):
self.thresh = [self.thresh_lower, self.thresh_upper]
self.cmap_renderer.color_data.metadata['selections'] = self.thresh
self.cmap_renderer.color_data.metadata_changed = {
'selections': self.thresh
}
self.container.request_redraw()
self.img_container.request_redraw()
@on_trait_change('peaks,cbar_selection:selection,img_idx')
def calc_numpeaks(self):
try:
thresh = self.cbar_selection.selection
self.thresh = thresh
except:
thresh = []
if thresh == [] or thresh == () or thresh == None:
thresh = (0, 1)
self.numpeaks_total = int(
np.sum([
np.sum(
np.ma.masked_inside(self.peaks[i][:, 2], thresh[0],
thresh[1]).mask)
for i in xrange(len(self.peaks))
]))
try:
self.numpeaks_img = int(
np.sum(
np.ma.masked_inside(self.peaks[self.img_idx][:, 2],
thresh[0], thresh[1]).mask))
except:
self.numpeaks_img = 0
@on_trait_change('findpeaks')
def locate_peaks(self):
from hyperspy import peak_char as pc
peaks = []
for idx in xrange(self.numfiles):
self.CC = cv_funcs.xcorr(
self.sig.data[self.top:self.top + self.tmp_size,
self.left:self.left + self.tmp_size,
self.tmp_img_idx], self.sig.data[:, :, idx])
# peak finder needs peaks greater than 1. Multiply by 255 to scale them.
pks = pc.two_dim_findpeaks(self.CC * 255,
peak_width=self.peak_width,
medfilt_radius=None)
pks[:, 2] = pks[:, 2] / 255.
peaks.append(pks)
self.peaks = peaks
def mask_peaks(self, idx):
thresh = self.cbar_selection.selection
if thresh == []:
thresh = (0, 1)
mpeaks = np.ma.asarray(self.peaks[idx])
mpeaks[:, 2] = np.ma.masked_outside(mpeaks[:, 2], thresh[0], thresh[1])
return mpeaks
@on_trait_change("peaks")
def redraw_plots(self):
oldplot = self.img_plot
self.container.remove(oldplot)
newplot = self.render_image()
self.container.add(newplot)
self.img_plot = newplot
try:
# if these haven't been created before, this will fail. wrap in try to prevent that.
oldscat = self.scatplot
self.container.remove(oldscat)
oldcolorbar = self.colorbar
self.img_container.remove(oldcolorbar)
except:
pass
if self.numpeaks_img > 0:
newscat = self.render_scatplot()
self.container.add(newscat)
self.scatplot = newscat
colorbar = self.draw_colorbar()
self.img_container.add(colorbar)
self.colorbar = colorbar
self.container.request_redraw()
self.img_container.request_redraw()
def crop_cells_stack(self):
from eelslab.signals.aggregate import AggregateCells
if self.numfiles == 1:
self.crop_sig = self.crop_cells()
return
else:
crop_agg = []
for idx in xrange(self.numfiles):
crop_agg.append(self.crop_cells(idx))
self.crop_sig = AggregateCells(*crop_agg)
return
def crop_cells(self, idx=0):
print "cropping cells..."
from hyperspy.signals.image import Image
# filter the peaks that are outside the selected threshold
peaks = np.ma.compress_rows(self.mask_peaks(idx))
tmp_sz = self.tmp_size
data = np.zeros((tmp_sz, tmp_sz, peaks.shape[0]))
if not hasattr(self.sig.mapped_parameters, "original_files"):
parent = self.sig
else:
parent = self.sig.mapped_parameters.original_files[
self.titles[idx]]
for i in xrange(peaks.shape[0]):
# crop the cells from the given locations
data[:, :, i] = self.sig.data[peaks[i, 1]:peaks[i, 1] + tmp_sz,
peaks[i,
0]:peaks[i, 0] + tmp_sz, idx]
crop_sig = Image({
'data': data,
'mapped_parameters': {
'name': 'Cropped cells from %s' % self.titles[idx],
'record_by': 'image',
'locations': peaks,
'parent': parent,
}
})
return crop_sig
# attach a class member that has the locations from which the images were cropped
print "Complete. "
def _create_plot_component(self):
# Create a plot data object and give it this data
self.pd = ArrayPlotData()
self.pd.set_data("imagedata", self.data[self.data_name])
# Create the plot
self.tplot = Plot(self.pd, default_origin="top left")
self.tplot.x_axis.orientation = "top"
self.tplot.img_plot("imagedata",
name="my_plot",
#xbounds=(0,10),
#ybounds=(0,10),
colormap=jet)
# Tweak some of the plot properties
self.tplot.title = "Matrix"
self.tplot.padding = 50
# Right now, some of the tools are a little invasive, and we need the
# actual CMapImage object to give to them
self.my_plot = self.tplot.plots["my_plot"][0]
# Attach some tools to the plot
self.tplot.tools.append(PanTool(self.tplot))
zoom = ZoomTool(component=self.tplot, tool_mode="box", always_on=False)
self.tplot.overlays.append(zoom)
# my custom tool to get the connection information
self.custtool = CustomTool(self.tplot)
self.tplot.tools.append(self.custtool)
# Create the colorbar, handing in the appropriate range and colormap
colormap = self.my_plot.color_mapper
self.colorbar = ColorBar(index_mapper=LinearMapper(range=colormap.range),
color_mapper=colormap,
plot=self.my_plot,
orientation='v',
resizable='v',
width=30,
padding=20)
self.colorbar.padding_top = self.tplot.padding_top
self.colorbar.padding_bottom = self.tplot.padding_bottom
# create a range selection for the colorbar
self.range_selection = RangeSelection(component=self.colorbar)
self.colorbar.tools.append(self.range_selection)
self.colorbar.overlays.append(RangeSelectionOverlay(component=self.colorbar,
border_color="white",
alpha=0.8,
fill_color="lightgray"))
# we also want to the range selection to inform the cmap plot of
# the selection, so set that up as well
self.range_selection.listeners.append(self.my_plot)
# Create a container to position the plot and the colorbar side-by-side
container = HPlotContainer(use_backbuffer = True)
container.add(self.tplot)
container.add(self.colorbar)
container.bgcolor = "white"
return container
def _create_plot_component(self):
# Create a plot data object and give it this data
self.pd = ArrayPlotData()
self.pd.set_data("imagedata", self.data[self.data_name])
# Create the plot
self.tplot = Plot(self.pd, default_origin="top left")
self.tplot.x_axis.orientation = "top"
self.tplot.img_plot(
"imagedata",
name="my_plot",
#xbounds=(0,10),
#ybounds=(0,10),
colormap=jet)
# Tweak some of the plot properties
self.tplot.title = "Matrix"
self.tplot.padding = 50
# Right now, some of the tools are a little invasive, and we need the
# actual CMapImage object to give to them
self.my_plot = self.tplot.plots["my_plot"][0]
# Attach some tools to the plot
self.tplot.tools.append(PanTool(self.tplot))
zoom = ZoomTool(component=self.tplot, tool_mode="box", always_on=False)
self.tplot.overlays.append(zoom)
# my custom tool to get the connection information
self.custtool = CustomTool(self.tplot)
self.tplot.tools.append(self.custtool)
# Create the colorbar, handing in the appropriate range and colormap
colormap = self.my_plot.color_mapper
self.colorbar = ColorBar(
index_mapper=LinearMapper(range=colormap.range),
color_mapper=colormap,
plot=self.my_plot,
orientation='v',
resizable='v',
width=30,
padding=20)
self.colorbar.padding_top = self.tplot.padding_top
self.colorbar.padding_bottom = self.tplot.padding_bottom
# create a range selection for the colorbar
self.range_selection = RangeSelection(component=self.colorbar)
self.colorbar.tools.append(self.range_selection)
self.colorbar.overlays.append(
RangeSelectionOverlay(component=self.colorbar,
border_color="white",
alpha=0.8,
fill_color="lightgray"))
# we also want to the range selection to inform the cmap plot of
# the selection, so set that up as well
self.range_selection.listeners.append(self.my_plot)
# Create a container to position the plot and the colorbar side-by-side
container = HPlotContainer(use_backbuffer=True)
container.add(self.tplot)
container.add(self.colorbar)
container.bgcolor = "white"
return container
def get_plot(self):
pixel_sizes = self.data_source.voxel_sizes
shape = self.data.shape
m = min(pixel_sizes)
s = [int(d * sz / m) for d, sz in zip(shape, pixel_sizes)]
if 1: # else physical aspect ratio is enabled
ss = max(s) / 4
s = [max(s, ss) for s in s]
plot_sizes = dict(xy=(s[2], s[1]),
xz=(s[2], s[0]),
zy=(s[0], s[1]),
zz=(s[0], s[0]))
plots = GridContainer(shape=(2, 2),
spacing=(3, 3),
padding=50,
aspect_ratio=1)
pxy = Plot(
self.plotdata,
padding=1,
fixed_preferred_size=plot_sizes['xy'],
x_axis=PlotAxis(orientation='top'),
)
pxz = Plot(
self.plotdata,
padding=1,
fixed_preferred_size=plot_sizes['xz'],
)
pzy = Plot(
self.plotdata,
padding=1,
fixed_preferred_size=plot_sizes['zy'],
#orientation = 'v', # cannot use 'v' because of img_plot assumes row-major ordering
x_axis=PlotAxis(orientation='top'),
y_axis=PlotAxis(orientation='right'),
)
pzz = Plot(self.plotdata,
padding=1,
fixed_preferred_size=plot_sizes['zz'])
plots.add(pxy, pzy, pxz, pzz)
self.plots = dict(
xy=pxy.img_plot('xy', colormap=bone)[0],
xz=pxz.img_plot('xz', colormap=bone)[0],
zy=pzy.img_plot('zy', colormap=bone)[0],
zz=pzz.img_plot('zz')[0],
xyp=pxy.plot(('z_x', 'z_y'),
type='scatter',
color='orange',
marker='circle',
marker_size=3,
selection_marker_size=3,
selection_marker='circle')[0],
xzp=pxz.plot(('y_x', 'y_z'),
type='scatter',
color='orange',
marker='circle',
marker_size=3,
selection_marker_size=3,
selection_marker='circle')[0],
zyp=pzy.plot(('x_z', 'x_y'),
type='scatter',
color='orange',
marker='circle',
marker_size=3,
selection_marker_size=3,
selection_marker='circle')[0],
)
for p in ['xy', 'xz', 'zy']:
self.plots[p].overlays.append(ZoomTool(self.plots[p]))
self.plots[p].tools.append(
PanTool(self.plots[p], drag_button='right'))
imgtool = ImageInspectorTool(self.plots[p])
self.plots[p].tools.append(imgtool)
overlay = ImageInspectorOverlay(component=self.plots[p],
bgcolor='white',
image_inspector=imgtool)
self.plots['zz'].overlays.append(overlay)
self.plots[p + 'p'].tools.append(
ScatterInspector(self.plots[p + 'p'], selection_mode='toggle'))
self.plots['xyp'].index.on_trait_change(self._xyp_metadata_handler,
'metadata_changed')
self.plots['xzp'].index.on_trait_change(self._xzp_metadata_handler,
'metadata_changed')
self.plots['zyp'].index.on_trait_change(self._zyp_metadata_handler,
'metadata_changed')
plot = HPlotContainer()
# todo: add colormaps
plot.add(plots)
return plot
def __init__(self):
#The delegates views don't work unless we caller the superclass __init__
super(CursorTest, self).__init__()
container = HPlotContainer(padding=0, spacing=20)
self.plot = container
#a subcontainer for the first plot.
#I'm not sure why this is required. Without it, the layout doesn't work right.
subcontainer = OverlayPlotContainer(padding=40)
container.add(subcontainer)
#make some data
index = numpy.linspace(-10,10,512)
value = numpy.sin(index)
#create a LinePlot instance and add it to the subcontainer
line = create_line_plot([index, value], add_grid=True,
add_axis=True, index_sort='ascending',
orientation = 'h')
subcontainer.add(line)
#here's our first cursor.
csr = CursorTool(line,
drag_button="left",
color='blue')
self.cursor1 = csr
#and set it's initial position (in data-space units)
csr.current_position = 0.0, 0.0
#this is a rendered component so it goes in the overlays list
line.overlays.append(csr)
#some other standard tools
line.tools.append(PanTool(line, drag_button="right"))
line.overlays.append(ZoomTool(line))
#make some 2D data for a colourmap plot
xy_range = (-5, 5)
x = numpy.linspace(xy_range[0], xy_range[1] ,100)
y = numpy.linspace(xy_range[0], xy_range[1] ,100)
X,Y = numpy.meshgrid(x, y)
Z = numpy.sin(X)*numpy.arctan2(Y,X)
#easiest way to get a CMapImagePlot is to use the Plot class
ds = ArrayPlotData()
ds.set_data('img', Z)
img = Plot(ds, padding=40)
cmapImgPlot = img.img_plot("img",
xbounds = xy_range,
ybounds = xy_range,
colormap = jet)[0]
container.add(img)
#now make another cursor
csr2 = CursorTool(cmapImgPlot,
drag_button='left',
color='white',
line_width=2.0
)
self.cursor2 = csr2
csr2.current_position = 1.0, 1.5
cmapImgPlot.overlays.append(csr2)
#add some standard tools. Note, I'm assigning the PanTool to the
#right mouse-button to avoid conflicting with the cursors
cmapImgPlot.tools.append(PanTool(cmapImgPlot, drag_button="right"))
cmapImgPlot.overlays.append(ZoomTool(cmapImgPlot))
def _create_plot_component():
# Create a scalar field to colormap# Create a scalar field to colormap
xbounds = (-2*pi, 2*pi, 600)
ybounds = (-1.5*pi, 1.5*pi, 300)
xs = linspace(*xbounds)
ys = linspace(*ybounds)
x, y = meshgrid(xs,ys)
z = jn(2, x)*y*x
# Create a plot data obect and give it this data
pd = ArrayPlotData()
pd.set_data("imagedata", z)
# Create the plot
plot = Plot(pd)
plot.img_plot("imagedata",
name="my_plot",
xbounds=xbounds[:2],
ybounds=ybounds[:2],
colormap=jet)
# Tweak some of the plot properties
plot.title = "Selectable Image Plot"
plot.padding = 50
# Right now, some of the tools are a little invasive, and we need the
# actual CMapImage object to give to them
my_plot = plot.plots["my_plot"][0]
# Attach some tools to the plot
plot.tools.append(PanTool(plot))
zoom = ZoomTool(component=plot, tool_mode="box", always_on=False)
plot.overlays.append(zoom)
# Create the colorbar, handing in the appropriate range and colormap
colormap = my_plot.color_mapper
colorbar = ColorBar(index_mapper=LinearMapper(range=colormap.range),
color_mapper=colormap,
plot=my_plot,
orientation='v',
resizable='v',
width=30,
padding=20)
colorbar.padding_top = plot.padding_top
colorbar.padding_bottom = plot.padding_bottom
# create a range selection for the colorbar
range_selection = RangeSelection(component=colorbar)
colorbar.tools.append(range_selection)
colorbar.overlays.append(RangeSelectionOverlay(component=colorbar,
border_color="white",
alpha=0.8,
fill_color="lightgray"))
# we also want to the range selection to inform the cmap plot of
# the selection, so set that up as well
range_selection.listeners.append(my_plot)
# Create a container to position the plot and the colorbar side-by-side
container = HPlotContainer(use_backbuffer = True)
container.add(plot)
container.add(colorbar)
container.bgcolor = "lightgray"
#my_plot.set_value_selection((-1.3, 6.9))
return container
class VariableMeshPannerView(HasTraits):
plot = Instance(Plot)
spawn_zoom = Button
vm_plot = Instance(VMImagePlot)
use_tools = Bool(True)
full_container = Instance(HPlotContainer)
container = Instance(OverlayPlotContainer)
traits_view = View(
Group(Item('full_container',
editor=ComponentEditor(size=(512, 512)),
show_label=False),
Item('field', show_label=False),
orientation="vertical"),
width=800,
height=800,
resizable=True,
title="Pan and Scan",
)
def _vm_plot_default(self):
return VMImagePlot(panner=self.panner)
def __init__(self, **kwargs):
super(VariableMeshPannerView, self).__init__(**kwargs)
# Create the plot
self.add_trait("field", DelegatesTo("vm_plot"))
plot = self.vm_plot.plot
img_plot = self.vm_plot.img_plot
if self.use_tools:
plot.tools.append(PanTool(img_plot))
zoom = ZoomTool(component=img_plot,
tool_mode="box",
always_on=False)
plot.overlays.append(zoom)
imgtool = ImageInspectorTool(img_plot)
img_plot.tools.append(imgtool)
overlay = ImageInspectorOverlay(component=img_plot,
image_inspector=imgtool,
bgcolor="white",
border_visible=True)
img_plot.overlays.append(overlay)
image_value_range = DataRange1D(self.vm_plot.fid)
cbar_index_mapper = LinearMapper(range=image_value_range)
self.colorbar = ColorBar(index_mapper=cbar_index_mapper,
plot=img_plot,
padding_right=40,
resizable='v',
width=30)
self.colorbar.tools.append(
PanTool(self.colorbar, constrain_direction="y", constrain=True))
zoom_overlay = ZoomTool(self.colorbar,
axis="index",
tool_mode="range",
always_on=True,
drag_button="right")
self.colorbar.overlays.append(zoom_overlay)
# create a range selection for the colorbar
range_selection = RangeSelection(component=self.colorbar)
self.colorbar.tools.append(range_selection)
self.colorbar.overlays.append(
RangeSelectionOverlay(component=self.colorbar,
border_color="white",
alpha=0.8,
fill_color="lightgray"))
# we also want to the range selection to inform the cmap plot of
# the selection, so set that up as well
range_selection.listeners.append(img_plot)
self.full_container = HPlotContainer(padding=30)
self.container = OverlayPlotContainer(padding=0)
self.full_container.add(self.colorbar)
self.full_container.add(self.container)
self.container.add(self.vm_plot.plot)
class PlotUI(HasTraits):
#Traits view definitions:
traits_view = View(
Group(Item('container',
editor=ComponentEditor(size=(800,600)),
show_label=False)),
buttons=NoButtons,
resizable=True)
plot_edit_view = View(
Group(Item('num_levels'),
Item('colormap')),
buttons=["OK","Cancel"])
num_levels = Int(15)
colormap = Enum(color_map_name_dict.keys())
#---------------------------------------------------------------------------
# Private Traits
#---------------------------------------------------------------------------
_image_index = Instance(GridDataSource)
_image_value = Instance(ImageData)
_cmap = Trait(jet, Callable)
#---------------------------------------------------------------------------
# Public View interface
#---------------------------------------------------------------------------
def __init__(self, *args, **kwargs):
super(PlotUI, self).__init__(*args, **kwargs)
self.create_plot()
def create_plot(self):
# Create the mapper, etc
self._image_index = GridDataSource(array([]),
array([]),
sort_order=("ascending","ascending"))
image_index_range = DataRange2D(self._image_index)
self._image_index.on_trait_change(self._metadata_changed,
"metadata_changed")
self._image_value = ImageData(data=array([]), value_depth=1)
image_value_range = DataRange1D(self._image_value)
# Create the contour plots
self.polyplot = ContourPolyPlot(index=self._image_index,
value=self._image_value,
index_mapper=GridMapper(range=
image_index_range),
color_mapper=\
self._cmap(image_value_range),
levels=self.num_levels)
self.lineplot = ContourLinePlot(index=self._image_index,
value=self._image_value,
index_mapper=GridMapper(range=
self.polyplot.index_mapper.range),
levels=self.num_levels)
# Add a left axis to the plot
left = PlotAxis(orientation='left',
title= "y",
mapper=self.polyplot.index_mapper._ymapper,
component=self.polyplot)
self.polyplot.overlays.append(left)
# Add a bottom axis to the plot
bottom = PlotAxis(orientation='bottom',
title= "x",
mapper=self.polyplot.index_mapper._xmapper,
component=self.polyplot)
self.polyplot.overlays.append(bottom)
# Add some tools to the plot
self.polyplot.tools.append(PanTool(self.polyplot,
constrain_key="shift"))
self.polyplot.overlays.append(ZoomTool(component=self.polyplot,
tool_mode="box", always_on=False))
self.polyplot.overlays.append(LineInspector(component=self.polyplot,
axis='index_x',
inspect_mode="indexed",
write_metadata=True,
is_listener=False,
color="white"))
self.polyplot.overlays.append(LineInspector(component=self.polyplot,
axis='index_y',
inspect_mode="indexed",
write_metadata=True,
color="white",
is_listener=False))
# Add these two plots to one container
contour_container = OverlayPlotContainer(padding=20,
use_backbuffer=True,
unified_draw=True)
contour_container.add(self.polyplot)
contour_container.add(self.lineplot)
# Create a colorbar
cbar_index_mapper = LinearMapper(range=image_value_range)
self.colorbar = ColorBar(index_mapper=cbar_index_mapper,
plot=self.polyplot,
padding_top=self.polyplot.padding_top,
padding_bottom=self.polyplot.padding_bottom,
padding_right=40,
resizable='v',
width=30)
self.pd = ArrayPlotData(line_index = array([]),
line_value = array([]),
scatter_index = array([]),
scatter_value = array([]),
scatter_color = array([]))
self.cross_plot = Plot(self.pd, resizable="h")
self.cross_plot.height = 100
self.cross_plot.padding = 20
self.cross_plot.plot(("line_index", "line_value"),
line_style="dot")
self.cross_plot.plot(("scatter_index","scatter_value","scatter_color"),
type="cmap_scatter",
name="dot",
color_mapper=self._cmap(image_value_range),
marker="circle",
marker_size=8)
self.cross_plot.index_range = self.polyplot.index_range.x_range
self.pd.set_data("line_index2", array([]))
self.pd.set_data("line_value2", array([]))
self.pd.set_data("scatter_index2", array([]))
self.pd.set_data("scatter_value2", array([]))
self.pd.set_data("scatter_color2", array([]))
self.cross_plot2 = Plot(self.pd, width = 140, orientation="v", resizable="v", padding=20, padding_bottom=160)
self.cross_plot2.plot(("line_index2", "line_value2"),
line_style="dot")
self.cross_plot2.plot(("scatter_index2","scatter_value2","scatter_color2"),
type="cmap_scatter",
name="dot",
color_mapper=self._cmap(image_value_range),
marker="circle",
marker_size=8)
self.cross_plot2.index_range = self.polyplot.index_range.y_range
# Create a container and add components
self.container = HPlotContainer(padding=40, fill_padding=True,
bgcolor = "white", use_backbuffer=False)
inner_cont = VPlotContainer(padding=0, use_backbuffer=True)
inner_cont.add(self.cross_plot)
inner_cont.add(contour_container)
self.container.add(self.colorbar)
self.container.add(inner_cont)
self.container.add(self.cross_plot2)
def update(self, model):
self.minz = model.minz
self.maxz = model.maxz
self.colorbar.index_mapper.range.low = self.minz
self.colorbar.index_mapper.range.high = self.maxz
self._image_index.set_data(model.xs, model.ys)
self._image_value.data = model.zs
self.pd.set_data("line_index", model.xs)
self.pd.set_data("line_index2", model.ys)
self.container.invalidate_draw()
self.container.request_redraw()
#---------------------------------------------------------------------------
# Event handlers
#---------------------------------------------------------------------------
def _metadata_changed(self, old, new):
""" This function takes out a cross section from the image data, based
on the line inspector selections, and updates the line and scatter
plots."""
self.cross_plot.value_range.low = self.minz
self.cross_plot.value_range.high = self.maxz
self.cross_plot2.value_range.low = self.minz
self.cross_plot2.value_range.high = self.maxz
if self._image_index.metadata.has_key("selections"):
x_ndx, y_ndx = self._image_index.metadata["selections"]
if y_ndx and x_ndx:
self.pd.set_data("line_value",
self._image_value.data[y_ndx,:])
self.pd.set_data("line_value2",
self._image_value.data[:,x_ndx])
xdata, ydata = self._image_index.get_data()
xdata, ydata = xdata.get_data(), ydata.get_data()
self.pd.set_data("scatter_index", array([xdata[x_ndx]]))
self.pd.set_data("scatter_index2", array([ydata[y_ndx]]))
self.pd.set_data("scatter_value",
array([self._image_value.data[y_ndx, x_ndx]]))
self.pd.set_data("scatter_value2",
array([self._image_value.data[y_ndx, x_ndx]]))
self.pd.set_data("scatter_color",
array([self._image_value.data[y_ndx, x_ndx]]))
self.pd.set_data("scatter_color2",
array([self._image_value.data[y_ndx, x_ndx]]))
else:
self.pd.set_data("scatter_value", array([]))
self.pd.set_data("scatter_value2", array([]))
self.pd.set_data("line_value", array([]))
self.pd.set_data("line_value2", array([]))
def _colormap_changed(self):
self._cmap = color_map_name_dict[self.colormap]
if hasattr(self, "polyplot"):
value_range = self.polyplot.color_mapper.range
self.polyplot.color_mapper = self._cmap(value_range)
value_range = self.cross_plot.color_mapper.range
self.cross_plot.color_mapper = self._cmap(value_range)
# FIXME: change when we decide how best to update plots using
# the shared colormap in plot object
self.cross_plot.plots["dot"][0].color_mapper = self._cmap(value_range)
self.cross_plot2.plots["dot"][0].color_mapper = self._cmap(value_range)
self.container.request_redraw()
def _num_levels_changed(self):
if self.num_levels > 3:
self.polyplot.levels = self.num_levels
self.lineplot.levels = self.num_levels
class ScatterPlot2(Template):
#-- Template Traits --------------------------------------------------------
# The title of the plot:
title = TStr('Dual Scatter Plots')
# The type of marker to use. This is a mapped trait using strings as the
# keys:
marker = marker_trait(template='copy', event='update')
# The pixel size of the marker (doesn't include the thickness of the
# outline):
marker_size = TRange(1, 5, 1, event='update')
# The thickness, in pixels, of the outline to draw around the marker. If
# this is 0, no outline will be drawn.
line_width = TRange(0.0, 5.0, 1.0)
# The fill color of the marker:
color = TColor('red', event='update')
# The color of the outline to draw around the marker
outline_color = TColor('black', event='update')
# The amount of space between plots:
spacing = TRange(0.0, 20.0, 0.0)
# The contained scatter plots:
scatter_plot_1 = TInstance(ScatterPlot, ())
scatter_plot_2 = TInstance(ScatterPlot, ())
#-- Derived Traits ---------------------------------------------------------
plot = TDerived
#-- Traits UI Views --------------------------------------------------------
# The scatter plot view:
template_view = View(VGroup(
Item('title',
show_label=False,
style='readonly',
editor=ThemedTextEditor(theme=Theme('@GBB', alignment='center'))),
Item('plot',
show_label=False,
resizable=True,
editor=EnableEditor(),
item_theme=Theme('@GF5', margins=0))),
resizable=True)
# The scatter plot options view:
options_view = View(
VGroup(
VGroup(Label('Scatter Plot Options',
item_theme=Theme('@GBB', alignment='center')),
show_labels=False),
VGroup(Item('title', editor=TextEditor()),
Item('marker'),
Item('marker_size', editor=ThemedSliderEditor()),
Item('line_width',
label='Line Width',
editor=ThemedSliderEditor()),
Item('spacing', editor=ThemedSliderEditor()),
Item('color', label='Fill Color'),
Item('outline_color', label='Outline Color'),
group_theme=Theme('@GF5', margins=(-5, -1)),
item_theme=Theme('@G0B', margins=0))))
#-- ITemplate Interface Implementation -------------------------------------
def activate_template(self):
""" Converts all contained 'TDerived' objects to real objects using the
template traits of the object. This method must be overridden in
subclasses.
Returns
-------
None
"""
plots = [
p for p in [self.scatter_plot_1.plot, self.scatter_plot_2.plot]
if p is not None
]
if len(plots) == 2:
self.plot = HPlotContainer(spacing=self.spacing)
self.plot.add(*plots)
elif len(plots) == 1:
self.plot = plots[0]
#-- Default Values ---------------------------------------------------------
def _scatter_plot_1_default(self):
""" Returns the default value for the first scatter plot.
"""
result = ScatterPlot()
result.index.description = 'Shared Plot Index'
result.value.description += ' 1'
return result
def _scatter_plot_2_default(self):
""" Returns the default value for the second scatter plot.
"""
result = ScatterPlot(index=self.scatter_plot_1.index)
result.value.description += ' 2'
result.value.optional = True
return result
#-- Trait Event Handlers ---------------------------------------------------
def _update_changed(self, name, old, new):
""" Handles a plot option being changed.
"""
setattr(self.scatter_plot_1, name, new)
setattr(self.scatter_plot_2, name, new)
self.plot = Undefined
def _spacing_changed(self, spacing):
""" Handles the spacing between plots being changed.
"""
self.plot = Undefined
def __init__(self,xdata=None,ydata=None,weights=None,model=None,
include_models=None,exclude_models=None,fittype=None,**traits):
"""
:param xdata: the first dimension of the data to be fit
:type xdata: array-like
:param ydata: the second dimension of the data to be fit
:type ydata: array-like
:param weights:
The weights to apply to the data. Statistically interpreted as inverse
errors (*not* inverse variance). May be any of the following forms:
* None for equal weights
* an array of points that must match `ydata`
* a 2-sequence of arrays (xierr,yierr) such that xierr matches the
`xdata` and yierr matches `ydata`
* a function called as f(params) that returns an array of weights
that match one of the above two conditions
:param model: the initial model to use to fit this data
:type model:
None, string, or :class:`pymodelfit.core.FunctionModel1D`
instance.
:param include_models:
With `exclude_models`, specifies which models should be available in
the "new model" dialog (see `models.list_models` for syntax).
:param exclude_models:
With `include_models`, specifies which models should be available in
the "new model" dialog (see `models.list_models` for syntax).
:param fittype:
The fitting technique for the initial fit (see
:class:`pymodelfit.core.FunctionModel`).
:type fittype: string
kwargs are passed in as any additional traits to apply to the
application.
"""
self.modelpanel = View(Label('empty'),kind='subpanel',title='model editor')
self.tmodel = TraitedModel(model)
if model is not None and fittype is not None:
self.tmodel.model.fittype = fittype
if xdata is None or ydata is None:
if not hasattr(self.tmodel.model,'data') or self.tmodel.model.data is None:
raise ValueError('data not provided and no data in model')
if xdata is None:
xdata = self.tmodel.model.data[0]
if ydata is None:
ydata = self.tmodel.model.data[1]
if weights is None:
weights = self.tmodel.model.data[2]
self.on_trait_change(self._paramsChanged,'tmodel.paramchange')
self.modelselector = NewModelSelector(include_models,exclude_models)
self.data = [xdata,ydata]
if weights is None:
self.weights = np.ones_like(xdata)
self.weighttype = 'equal'
else:
self.weights = np.array(weights,copy=True)
self.savews = True
weights1d = self.weights
while len(weights1d.shape)>1:
weights1d = np.sum(weights1d**2,axis=0)
pd = ArrayPlotData(xdata=self.data[0],ydata=self.data[1],weights=weights1d)
self.plot = plot = Plot(pd,resizable='hv')
self.scatter = plot.plot(('xdata','ydata','weights'),name='data',
color_mapper=_cmapblack if self.weights0rem else _cmap,
type='cmap_scatter', marker='circle')[0]
self.errorplots = None
if not isinstance(model,FunctionModel1D):
self.fitmodel = True
self.updatemodelplot = False #force plot update - generates xmod and ymod
plot.plot(('xmod','ymod'),name='model',type='line',line_style='dash',color='black',line_width=2)
del plot.x_mapper.range.sources[-1] #remove the line plot from the x_mapper source so only the data is tied to the scaling
self.on_trait_change(self._rangeChanged,'plot.index_mapper.range.updated')
self.pantool = PanTool(plot,drag_button='left')
plot.tools.append(self.pantool)
self.zoomtool = ZoomTool(plot)
self.zoomtool.prev_state_key = KeySpec('a')
self.zoomtool.next_state_key = KeySpec('s')
plot.overlays.append(self.zoomtool)
self.scattertool = None
self.scatter.overlays.append(ScatterInspectorOverlay(self.scatter,
hover_color = "black",
selection_color="black",
selection_outline_color="red",
selection_line_width=2))
self.colorbar = colorbar = ColorBar(index_mapper=LinearMapper(range=plot.color_mapper.range),
color_mapper=plot.color_mapper.range,
plot=plot,
orientation='v',
resizable='v',
width = 30,
padding = 5)
colorbar.padding_top = plot.padding_top
colorbar.padding_bottom = plot.padding_bottom
colorbar._axis.title = 'Weights'
self.plotcontainer = container = HPlotContainer(use_backbuffer=True)
container.add(plot)
container.add(colorbar)
super(FitGui,self).__init__(**traits)
self.on_trait_change(self._scale_change,'plot.value_scale,plot.index_scale')
if weights is not None and len(weights)==2:
self.weightsChanged() #update error bars
