def __init__(self, img_path):
super().__init__()
#
# Load image data
#
base_path = os.path.splitext(img_path)[0]
lenslet_path = base_path + '-lenslet.txt'
optics_path = base_path + '-optics.txt'
with open(lenslet_path) as f:
tmp = eval(f.readline())
x_offset, y_offset, right_dx, right_dy, down_dx, down_dy = \
np.array(tmp, dtype=np.float32)
with open(optics_path) as f:
for line in f:
name, val = line.strip().split()
try:
setattr(self, name, np.float32(val))
except:
pass
max_angle = math.atan(self.pitch/2/self.flen)
#
# Prepare image
#
im_pil = Image.open(img_path)
if im_pil.mode == 'RGB':
self.NCHANNELS = 3
w, h = im_pil.size
im = np.zeros((h, w, 4), dtype=np.float32)
im[:, :, :3] = np.array(im_pil).astype(np.float32)
self.LF_dim = (ceil(h/down_dy), ceil(w/right_dx), 3)
else:
self.NCHANNELS = 1
im = np.array(im_pil.getdata()).reshape(im_pil.size[::-1]).astype(np.float32)
h, w = im.shape
self.LF_dim = (ceil(h/down_dy), ceil(w/right_dx))
x_start = x_offset - int(x_offset / right_dx) * right_dx
y_start = y_offset - int(y_offset / down_dy) * down_dy
x_ratio = self.flen * right_dx / self.pitch
y_ratio = self.flen * down_dy / self.pitch
#
# Generate the cuda kernel
#
mod_LFview = pycuda.compiler.SourceModule(
_kernel_tpl.render(
newiw=self.LF_dim[1],
newih=self.LF_dim[0],
oldiw=w,
oldih=h,
x_start=x_start,
y_start=y_start,
x_ratio=x_ratio,
y_ratio=y_ratio,
x_step=right_dx,
y_step=down_dy,
NCHANNELS=self.NCHANNELS
)
)
self.LFview_func = mod_LFview.get_function("LFview_kernel")
self.texref = mod_LFview.get_texref("tex")
#
# Now generate the cuda texture
#
if self.NCHANNELS == 3:
cuda.bind_array_to_texref(
cuda.make_multichannel_2d_array(im, order="C"),
self.texref
)
else:
cuda.matrix_to_texref(im, self.texref, order="C")
#
# We could set the next if we wanted to address the image
# in normalized coordinates ( 0 <= coordinate < 1.)
# texref.set_flags(cuda.TRSF_NORMALIZED_COORDINATES)
#
self.texref.set_filter_mode(cuda.filter_mode.LINEAR)
#
# Prepare the traits
#
self.add_trait('X_angle', Range(-max_angle, max_angle, 0.0))
self.add_trait('Y_angle', Range(-max_angle, max_angle, 0.0))
self.plotdata = ArrayPlotData(LF_img=self.sampleLF())
self.LF_img = Plot(self.plotdata)
if self.NCHANNELS == 3:
self.LF_img.img_plot("LF_img")
else:
self.LF_img.img_plot("LF_img", colormap=gray)
def _create_plot_component(self):
self.data = ArrayPlotData()
self.data["frequency"] = np.linspace(0.,
SAMPLING_RATE / 2.0,
num=NUM_SAMPLES / 2)
for i in xrange(NUM_LINES):
self.data['amplitude%d' % i] = np.zeros(NUM_SAMPLES / 2)
self.data["time"] = np.linspace(0.,
float(NUM_SAMPLES) / SAMPLING_RATE,
num=NUM_SAMPLES)
self.data['time_amplitude'] = np.zeros(NUM_SAMPLES)
self.data['imagedata'] = np.zeros(
(NUM_SAMPLES / 2, SPECTROGRAM_LENGTH))
spectrum_plot = Plot(self.data)
for i in xrange(NUM_LINES):
if i == NUM_LINES - 1:
linewidth = 2
color = (1, 0, 0)
else:
linewidth = 1
c = (NUM_LINES - i - 1) / float(NUM_LINES)
color = (1, 0.5 + c / 2, c)
spectrum_plot.plot(("frequency", "amplitude%d" % i),
name="Spectrum%d" % i,
color=color,
line_width=linewidth)
spectrum_plot.padding_bottom = 20
spectrum_plot.padding_top = 20
spec_range = spectrum_plot.plots.values()[0][0].value_mapper.range
spec_range.low = -90
spec_range.high = 0.0
spectrum_plot.index_axis.title = 'Frequency(Hz)'
spectrum_plot.value_axis.title = 'Amplitude(dB)'
time_plot = Plot(self.data)
time_plot.plot(("time", "time_amplitude"), name="Time", color="blue")
time_plot.padding_top = 20
time_plot.padding_bottom = 20
time_plot.index_axis.title = 'Time (seconds)'
time_plot.value_axis.title = 'Amplitude'
time_range = time_plot.plots.values()[0][0].value_mapper.range
time_range.low = -1.5
time_range.high = 1.5
spectrogram_plot = Plot(self.data)
spectrogram_time = (0.0, SPECTROGRAM_LENGTH * NUM_SAMPLES /
float(SAMPLING_RATE))
spectrogram_freq = (0.0, SAMPLING_RATE / 2.0)
spectrogram_plot.img_plot(
'imagedata',
name='Spectrogram',
xbounds=spectrogram_time,
ybounds=spectrogram_freq,
colormap=cm.reverse(cm.Blues),
)
range_obj = spectrogram_plot.plots['Spectrogram'][0].value_mapper.range
range_obj.high = -20
range_obj.low = -60
spectrogram_plot.padding_bottom = 20
spectrogram_plot.padding_top = 20
container = VPlotContainer()
container.add(time_plot)
container.add(spectrum_plot)
container.add(spectrogram_plot)
return container
def _create_plot_window(self):
# Create the model
min_value = 350
max_value = self.max_data
image_value_range = DataRange1D(low=min_value, high=max_value)
self.cmap = jet(range=image_value_range)
self._update_model()
datacube = self.colorcube
# Create the plot
self.plotdata = ArrayPlotData()
self.plotdataVoxel = ArrayPlotData()
self.plotdataSlices = ArrayPlotData()
self.plotdataVoxelFFT = ArrayPlotData()
self.plotdataPC = ArrayPlotData()
self._update_images()
# Top Left plot
centerplot = Plot(self.plotdata,
resizable='hv',
padding=20,
title="Slice_X")
imgplot = centerplot.img_plot("yz",
xbounds=None,
ybounds=None,
colormap=self.cmap)[0]
centerplot.x_axis.title = "Y"
centerplot.y_axis.title = "Z"
self._add_plot_tools(imgplot, "yz")
self.cursorYZ = CursorTool(imgplot, drag_button='left', color='white')
self.cursorYZ.current_position = self.slice_y, self.slice_z
imgplot.overlays.append(self.cursorYZ)
self.center = imgplot
# Top Right Plot
rightplot = Plot(self.plotdata,
resizable='hv',
padding=20,
title="Slice_Y")
rightplot.x_axis.title = "X"
rightplot.y_axis.title = "Z"
imgplot = rightplot.img_plot("xz",
xbounds=None,
ybounds=None,
colormap=self.cmap)[0]
self._add_plot_tools(imgplot, "xz")
self.cursorXZ = CursorTool(imgplot, drag_button='left', color='white')
self.cursorXZ.current_position = self.slice_x, self.slice_z
imgplot.overlays.append(self.cursorXZ)
self.right = imgplot
# Bottom LeftPlot
bottomplot = Plot(self.plotdata,
resizable='hv',
padding=20,
title="Slice_Z")
bottomplot.x_axis.title = "Y"
bottomplot.y_axis.title = "X"
imgplot = bottomplot.img_plot("xy",
xbounds=None,
ybounds=None,
colormap=self.cmap)[0]
"""bottomplot.contour_plot("xy",
type="poly",
xbounds=None,
ybounds=None)[0]"""
self._add_plot_tools(imgplot, "xy")
self.cursorXY = CursorTool(imgplot, drag_button='left', color='white')
self.cursorXY.current_position = self.slice_y, self.slice_x
imgplot.overlays.append(self.cursorXY)
self.bottom = imgplot
""" # Create a colorbar
cbar_index_mapper = LinearMapper(range=image_value_range)
self.colorbar = ColorBar(index_mapper=cbar_index_mapper,
plot=centerplot,
padding_top=centerplot.padding_top,
padding_bottom=centerplot.padding_bottom,
padding_right=40,
resizable='v',
width=30, height = 100)"""
# Create data series to plot
timeplot = Plot(self.plotdataVoxel, resizable='hv', padding=20)
timeplot.x_axis.title = "Frames"
timeplot.plot("TimeVoxel",
color='lightblue',
line_width=1.0,
bgcolor="white",
name="Time")[0]
# for i in range(len(self.tasks)):
# timeplot.plot(self.timingNames[i+2],color=tuple(COLOR_PALETTE[i]),
# line_width=1.0, bgcolor = "white", border_visible=True, name = self.timingNames[i+2])[0]
timeplot.legend.visible = True
timeplot.plot("time",
type="scatter",
color=tuple(COLOR_PALETTE[2]),
line_width=1,
bgcolor="white",
border_visible=True,
name="time")[0]
self.timePlot = timeplot
# Create data series to plot
timeplotBig = Plot(self.plotdataVoxel, resizable='hv', padding=20)
timeplotBig.x_axis.title = "Frames"
timeplotBig.plot("TimeVoxel",
color='lightblue',
line_width=1.5,
bgcolor="white",
name="Time")[0]
timeplotBig.legend.visible = True
timeplotBig.plot("time",
type="scatter",
color=tuple(COLOR_PALETTE[2]),
line_width=1,
bgcolor="white",
border_visible=True,
name="time")[0]
self.timePlotBig = timeplotBig
# Create data series to plot
freqplotBig = Plot(self.plotdataVoxelFFT, resizable='hv', padding=20)
freqplotBig.x_axis.title = "Frequency (Hz)"
freqplotBig.plot("FreqVoxel",
color='lightblue',
line_width=1.5,
bgcolor="white",
name="Abs(Y)")[0]
freqplotBig.legend.visible = True
freqplotBig.plot("peaks",
type="scatter",
color=tuple(COLOR_PALETTE[2]),
line_width=1,
bgcolor="white",
border_visible=True,
name="peaks")[0]
self.freqPlotBig = freqplotBig
# Create data series to plot
PCplotBig = Plot(self.plotdataPC, resizable='hv', padding=20)
PCplotBig.x_axis.title = "Frames"
PCplotBig.plot("Principal Component",
color='lightblue',
line_width=1.5,
bgcolor="white",
name="Principal Component")[0]
PCplotBig.legend.visible = True
PCplotBig.plot("time",
type="scatter",
color=tuple(COLOR_PALETTE[2]),
line_width=1,
bgcolor="white",
border_visible=True,
name="time")[0]
self.PCplotBig = PCplotBig
#self.time = time
# Create a GridContainer to hold all of our plots
container = GridContainer(padding=10,
fill_padding=True,
bgcolor="white",
use_backbuffer=True,
shape=(2, 2),
spacing=(10, 10))
containerTime = GridContainer(padding=10,
fill_padding=True,
bgcolor="white",
use_backbuffer=True,
shape=(1, 1),
spacing=(5, 5))
containerFreq = GridContainer(padding=10,
fill_padding=True,
bgcolor="white",
use_backbuffer=True,
shape=(1, 1),
spacing=(5, 5))
containerPC = GridContainer(padding=10,
fill_padding=True,
bgcolor="white",
use_backbuffer=True,
shape=(1, 1),
spacing=(5, 5))
container.add(centerplot)
container.add(rightplot)
container.add(bottomplot)
container.add(timeplot)
containerTime.add(timeplotBig)
containerFreq.add(freqplotBig)
containerPC.add(PCplotBig)
"""container = GridContainer(padding=10, fill_padding=True,
bgcolor="white", use_backbuffer=True,
shape=(3,3), spacing=(10,10))
for i in range(14,23):
slicePlot = Plot(self.plotdataSlices, resizable= 'hv', padding=20,title = "slice " + str(i),bgcolor = "white")
slicePlot.img_plot("slice " + str(i),xbounds= None, ybounds= None, colormap=self.cmap,bgcolor = "white")[0]
container.add(slicePlot)"""
self.container = container
self.nb.DeleteAllPages()
self.window = Window(self.nb, -1, component=container)
self.windowTime = Window(self.nb, -1, component=containerTime)
self.windowFreq = Window(self.nb, -1, component=containerFreq)
self.windowPC = Window(self.nb, -1, component=containerPC)
self.sizer.Detach(self.topsizer)
self.sizer.Detach(self.pnl2)
self.topsizer.Clear()
self.topsizer.Add(self.pnl3, 0, wx.ALL, 10)
self.nb.AddPage(self.window.control, "fMRI Slices")
self.nb.AddPage(self.windowTime.control, "Time Voxel")
self.nb.AddPage(self.windowFreq.control, "Frequency Voxel")
self.nb.AddPage(self.windowPC.control, "Principal Component")
self.topsizer.Add(self.nb, 1, wx.EXPAND)
self.sizer.Add(self.topsizer, 1, wx.EXPAND)
self.sizer.Add(self.pnl2,
flag=wx.EXPAND | wx.BOTTOM | wx.TOP,
border=10)
self.SetSizer(self.sizer)
self.Centre()
self.Show(True)
