def loadData(self, path):
if not hasattr(self, 'panelOn'):
# Initialize the panels
self.notebook.DeleteAllPages()
self.panelOn = self.res.LoadPanel(self.notebook,
'panelReconstructOn')
self.panelOff = self.res.LoadPanel(self.notebook,
'panelReconstructOff')
self.panelRatios = self.res.LoadPanel(self.notebook,
'panelRatios')
self.panelOn.Init(self.res, self, on=True)
self.panelOff.Init(self.res, self, on=False)
self.panelRatios.Init(self.res, self)
self.notebook.AddPage(self.panelOn, "Probe on")
self.notebook.AddPage(self.panelOff, "Probe off")
self.notebook.AddPage(self.panelRatios, "Enhancement Ratios")
self.panelOn.Update()
self.panelOff.Update()
self.panelRatios.Update()
# Open the Loading progress dialog
dialog = wx.ProgressDialog("Data loading progress", "Loading...", 100,
style=wx.PD_APP_MODAL | wx.PD_ELAPSED_TIME | wx.PD_REMAINING_TIME)
dialog.SetSize((300, 200))
dialog.Update(0, newmsg="Loading data from disk")
# Do the actual data loading from file
self.bimg = BeatingImage(path=path, no_bleach=no_bleach)
# Show measure metadata
self.lblAcquired.SetLabel(self.bimg.acquired)
str_pixel_f = "{0} Hz".format(self.bimg.pixel_frequency)
self.lblPixelFrequency.SetLabel(str_pixel_f)
str_shutter_f = "{0} Hz".format(self.bimg.shutter_frequency)
self.lblShutterFrequency.SetLabel(str_shutter_f)
self.lblRepetitions.SetLabel(str(self.bimg.repetitions))
# Let's reconstruct the image
manager = multiprocessing.Manager()
queue = manager.Queue()
self.bimg.reconstruct_with_update(queue=queue, dialog=dialog)
# Loading complete, progress dialog is not needed anymore
dialog.Update(100, newmsg="Complete")
dialog.Destroy()
# Keep a reference to the data
self.rec_on = self.bimg.reconstructed_on
self.rec_off = self.bimg.reconstructed_off
self.ratios = self.bimg.ratios
self.taus = self.bimg.taus
# Prepare main figure and details figure
self.panelOn.prepare(data=self.rec_on, max_rate=self.rec_on.max())
self.panelOff.prepare(data=self.rec_off, max_rate=self.rec_on.max())
self.panelRatios.prepare(data=self.ratios)
self.prepare_details()
# Paint it!
self.panelOn.Replot(data=self.rec_on)
self.panelOff.Replot(data=self.rec_off)
self.panelRatios.Replot(data=self.ratios)
# Resize stuff
self.canvas.mpl_connect('resize_event', self.OnResize)
# Threshold stuff
self.sliderThresOn = XRCCTRL(self.panelOn, 'sliderThresholdOn')
self.sliderThresOff = XRCCTRL(self.panelOff, 'sliderThresholdOff')
maxThresOn = self.rec_on.mean()
maxThresOff = self.rec_off.mean()
self.sliderThresOn.SetRange(0.0, maxThresOn * 100)
self.sliderThresOff.SetRange(0.0, maxThresOff * 100)
self.sliderThresOn.SetTickFreq(5)
self.lblThresOn = XRCCTRL(self.panelOn, 'lblThresholdOn')
self.lblThresOff = XRCCTRL(self.panelOff, 'lblThresholdOff')
self.Bind(wx.EVT_COMMAND_SCROLL_THUMBTRACK,
self.OnSliderOn, self.sliderThresOn)
self.Bind(wx.EVT_COMMAND_SCROLL_THUMBTRACK,
self.OnSliderOff, self.sliderThresOff)
# Enable the Save menu
self.menuMain.Enable(XRCID('menuSave'), True)
# Update the stats
self.update_stats()
class MainFrame(wx.Frame):
def __init__(self, parent, id, title, res):
wx.Frame.__init__(self, parent, id, title, pos=wx.DefaultPosition,
size=(900, 700), style=wx.DEFAULT_FRAME_STYLE)
# set up resource file and config file
self.res = res
# Load the main panel for the program
self.panelGeneral = self.res.LoadPanel(self, 'panelGeneral')
# Attach the details graph panel
self.panelDetails = wxmpl.PlotPanel(self.panelGeneral, -1,
size=(1, 2), dpi=68, crosshairs=True, autoscaleUnzoom=False)
self.res.AttachUnknownControl('panelDetails', self.panelDetails, self)
self.x, self.y = None, None
self.InitDetails()
# Initialize the General panel controls
self.notebook = XRCCTRL(self, 'notebook')
self.lblAcquired = XRCCTRL(self, 'lblAcquired')
self.lblPixelFrequency = XRCCTRL(self, 'lblPixelFrequency')
self.lblRepetitions = XRCCTRL(self, 'lblRepetitions')
self.lblShutterFrequency = XRCCTRL(self, 'lblShutterFrequency')
# Get the references for the stats panel
self.choiceStatistics = XRCCTRL(self, 'choiceStatistics')
self.caption = []
self.lbl = []
self.unit = []
for i in range(5):
self.caption.append(XRCCTRL(self, 'caption{0}'.format(i)))
self.lbl.append(XRCCTRL(self, 'lbl{0}'.format(i)))
self.unit.append(XRCCTRL(self, 'unit{0}'.format(i)))
self.Bind(wx.EVT_CHOICE, self.OnChoice)
self.bimg = None
# Setup the layout for the frame
mainGrid = wx.BoxSizer(wx.VERTICAL)
hGrid = wx.BoxSizer(wx.HORIZONTAL)
hGrid.Add(self.panelGeneral, 1, flag=wx.EXPAND|wx.ALL|wx.ALIGN_CENTRE,
border=4)
mainGrid.Add(hGrid, 1, flag=wx.EXPAND|wx.ALL|wx.ALIGN_CENTRE)
# Load the menu for the frame
self.menuMain = self.res.LoadMenuBar('menuMain')
# Bind menu events to the proper methods
wx.EVT_MENU(self, XRCID('menuOpen'), self.OnOpenMeasure)
wx.EVT_MENU(self, XRCID('menuSave'), self.OnSave)
wx.EVT_MENU(self, XRCID('menuExit'), self.OnClose)
# Set the menu as the default menu for this frame
self.SetMenuBar(self.menuMain)
self.SetSizer(mainGrid)
self.Layout()
#Set the Minumum size
self.SetMinSize((900, 700))
self.Centre(wx.BOTH)
# Initialize the welcome notebook tab
panelWelcome = self.res.LoadPanel(self.notebook, 'panelWelcome')
self.notebook.AddPage(panelWelcome, 'Welcome')
def InitDetails(self):
self.old_coord = (None, None)
self.fig = self.panelDetails.get_figure()
self.fig.set_edgecolor('white')
self.ax_top = self.fig.add_subplot(211,
title="Row Repetitions")
self.ax_bottom = self.fig.add_subplot(212,
title="Point Repetitions")
self.ax_bottom.grid()
self.fig.subplots_adjust(hspace=0.3)
self.canvas = self.fig.canvas
self.empty_details = True
self.canvas.draw()
def prepare_details(self):
x, y = self.x, self.y
ax_top, ax_bottom = self.ax_top, self.ax_bottom
# Set axes limits
self.det_im = ax_top.imshow(
zeros((self.bimg.repetitions, self.bimg.width)),
cmap=rate_color_map, interpolation='nearest',
vmin=0.0, vmax=self.rec_on.max(), animated=True)
self.axis = ax_top.get_xaxis()
self.ax_bottom.set_xlim(0.0, self.bimg.repetitions)
self.ax_bottom.set_ylim(0.0, self.bimg.unbleached_array.max())
self.canvas.draw()
pos = arange(self.bimg.repetitions)
values = zeros_like(pos)
self.det_plt, = ax_bottom.plot(pos, values, 'k', animated=True)
self.det_plt_on, = ax_bottom.plot(pos, values, 'r', animated=True)
self.det_plt_off, = ax_bottom.plot(pos, values, 'b', animated=True)
self.det_thr_on = ax_bottom.axhline(y=0, color='r', animated=True)
self.det_thr_off = ax_bottom.axhline(y=0, color='b', animated=True)
# Copy the plot backgrounds for later reuse
self.bg = self.canvas.copy_from_bbox(self.fig.bbox)
self.canvas.draw()
def ReplotDetails(self, e=None):
x, y = self.x, self.y
ax_top, ax_bottom = self.ax_top, self.ax_bottom
# clear the axes and replot everything
# Do the drawing
if x is not None and y is not None and (x,y) != self.old_coord:
# Restore background
self.canvas.restore_region(self.bg)
# Top panel
self.det_im.set_data(self.bimg.unbleached_array[y,:,:])
self.axis.set_ticks([x])
self.axis.set_tick_params(direction='out',
length=6, width=2, colors='r')
self.axis.set_animated(True)
self.axis.set_ticklabels([""])
ax_top.draw_artist(self.det_im)
ax_top.draw_artist(self.axis)
# Bottom panel
# Update data
values = self.bimg.unbleached_array[y,:,x]
width = len(values)
pos = arange(width)
mask_off = self.bimg.rows[y].beating_mask[:,x]
mask_on = ones(mask_off.shape) - mask_off
val_off = ma.array(values, mask=mask_off)
val_on = ma.array(values, mask=mask_on)
# Update line image and line data
self.det_plt.set_ydata(values)
self.det_plt_on.set_ydata(val_on)
self.det_plt_off.set_ydata(val_off)
self.det_thr_on.set_ydata(self.bimg.thresOn)
self.det_thr_off.set_ydata(self.bimg.thresOff)
# Tell those slacking artists to draw
ax_bottom.draw_artist(self.det_plt)
ax_bottom.draw_artist(self.det_plt_on)
ax_bottom.draw_artist(self.det_plt_off)
ax_bottom.draw_artist(self.det_thr_on)
ax_bottom.draw_artist(self.det_thr_off)
# Blit, and we're done
self.canvas.blit(self.fig.bbox)
self.old_coord = (x,y)
def OnOpenMeasure(self, evt):
wildcard = "Data file (*.dat)|*.dat|" \
"Ago file (*.ago)|*.ago|" \
"All files (*.*)|*.*"
dialog = wx.FileDialog(None, "Choose a measure file", os.getcwd(),
"", wildcard, wx.OPEN)
if dialog.ShowModal() == wx.ID_OK:
print("Opening: {0}".format(dialog.GetPath()))
self.loadData(dialog.GetPath())
dialog.Destroy()
def loadData(self, path):
if not hasattr(self, 'panelOn'):
# Initialize the panels
self.notebook.DeleteAllPages()
self.panelOn = self.res.LoadPanel(self.notebook,
'panelReconstructOn')
self.panelOff = self.res.LoadPanel(self.notebook,
'panelReconstructOff')
self.panelRatios = self.res.LoadPanel(self.notebook,
'panelRatios')
self.panelOn.Init(self.res, self, on=True)
self.panelOff.Init(self.res, self, on=False)
self.panelRatios.Init(self.res, self)
self.notebook.AddPage(self.panelOn, "Probe on")
self.notebook.AddPage(self.panelOff, "Probe off")
self.notebook.AddPage(self.panelRatios, "Enhancement Ratios")
self.panelOn.Update()
self.panelOff.Update()
self.panelRatios.Update()
# Open the Loading progress dialog
dialog = wx.ProgressDialog("Data loading progress", "Loading...", 100,
style=wx.PD_APP_MODAL | wx.PD_ELAPSED_TIME | wx.PD_REMAINING_TIME)
dialog.SetSize((300, 200))
dialog.Update(0, newmsg="Loading data from disk")
# Do the actual data loading from file
self.bimg = BeatingImage(path=path, no_bleach=no_bleach)
# Show measure metadata
self.lblAcquired.SetLabel(self.bimg.acquired)
str_pixel_f = "{0} Hz".format(self.bimg.pixel_frequency)
self.lblPixelFrequency.SetLabel(str_pixel_f)
str_shutter_f = "{0} Hz".format(self.bimg.shutter_frequency)
self.lblShutterFrequency.SetLabel(str_shutter_f)
self.lblRepetitions.SetLabel(str(self.bimg.repetitions))
# Let's reconstruct the image
manager = multiprocessing.Manager()
queue = manager.Queue()
self.bimg.reconstruct_with_update(queue=queue, dialog=dialog)
# Loading complete, progress dialog is not needed anymore
dialog.Update(100, newmsg="Complete")
dialog.Destroy()
# Keep a reference to the data
self.rec_on = self.bimg.reconstructed_on
self.rec_off = self.bimg.reconstructed_off
self.ratios = self.bimg.ratios
self.taus = self.bimg.taus
# Prepare main figure and details figure
self.panelOn.prepare(data=self.rec_on, max_rate=self.rec_on.max())
self.panelOff.prepare(data=self.rec_off, max_rate=self.rec_on.max())
self.panelRatios.prepare(data=self.ratios)
self.prepare_details()
# Paint it!
self.panelOn.Replot(data=self.rec_on)
self.panelOff.Replot(data=self.rec_off)
self.panelRatios.Replot(data=self.ratios)
# Resize stuff
self.canvas.mpl_connect('resize_event', self.OnResize)
# Threshold stuff
self.sliderThresOn = XRCCTRL(self.panelOn, 'sliderThresholdOn')
self.sliderThresOff = XRCCTRL(self.panelOff, 'sliderThresholdOff')
maxThresOn = self.rec_on.mean()
maxThresOff = self.rec_off.mean()
self.sliderThresOn.SetRange(0.0, maxThresOn * 100)
self.sliderThresOff.SetRange(0.0, maxThresOff * 100)
self.sliderThresOn.SetTickFreq(5)
self.lblThresOn = XRCCTRL(self.panelOn, 'lblThresholdOn')
self.lblThresOff = XRCCTRL(self.panelOff, 'lblThresholdOff')
self.Bind(wx.EVT_COMMAND_SCROLL_THUMBTRACK,
self.OnSliderOn, self.sliderThresOn)
self.Bind(wx.EVT_COMMAND_SCROLL_THUMBTRACK,
self.OnSliderOff, self.sliderThresOff)
# Enable the Save menu
self.menuMain.Enable(XRCID('menuSave'), True)
# Update the stats
self.update_stats()
def update_stats(self, on=None):
choice = self.choiceStatistics.GetCurrentSelection()
if choice == 0:
caption = ["Width:", "Height:",
"Pixel Width:", "Pixel Height:", "Over Threshold:"]
if self.bimg is not None:
lbl = [self.bimg.w_step * self.bimg.width,
self.bimg.h_step * self.bimg.height,
self.bimg.w_step, self.bimg.h_step,
"{:.2%}".format(float(
self.ratios.count()) / self.ratios.size)]
else:
lbl = ["-"] * 5
unit = ["µm", "µm", "µm", "µm", "%"]
else:
if self.bimg is not None:
if on is None:
data = self.ratios
elif on is False:
data = self.rec_off
else:
data = self.rec_on
if choice == 1:
caption = ["Max:", "Min:", "Mean:", "Bleach Time:", "-"]
lbl = []
if self.bimg is not None \
and self.x is not None and self.y is not None:
row = data[self.y].compressed()
taus = self.taus[self.y].compressed()
if len(row) > 0:
lbl.append("{:.2f}".format(row.max()))
lbl.append("{:.2f}".format(row.min()))
lbl.append("{:.2f}".format(row.mean()))
if len(taus) > 0:
tau = taus.mean()
stddev = taus.std()
lbl.append("{:.2f} ± {:.2f}".format(tau, stddev))
else:
lbl.append("-")
lbl.append("-")
else:
lbl = ["-"] * 5
else:
lbl = ["-"] * 5
unit = ["Hz", "Hz", "Hz", "ms", "-"]
if choice == 2:
caption = ["Max:", "Min:", "Mean:", "Bleach Time:", "-"]
lbl = []
if self.bimg is not None \
and self.x is not None and self.y is not None:
col = data[:,self.x].compressed()
taus = self.taus[:,self.x].compressed()
if len(col) > 0:
lbl.append("{:.2f}".format(col.max()))
lbl.append("{:.2f}".format(col.min()))
lbl.append("{:.2f}".format(col.mean()))
if len(taus) > 0:
tau = taus.mean()
stddev = taus.std()
lbl.append("{:.2f} ± {:.2f}".format(tau, stddev))
else:
lbl.append("-")
lbl.append("-")
else:
lbl = ["-"] * 5
else:
lbl = ["-"] * 5
unit = ["Hz", "Hz", "Hz", "ms", "-"]
for i in range(5):
self.caption[i].SetLabel(str(caption[i]))
self.lbl[i].SetLabel(str(lbl[i]))
self.unit[i].SetLabel(str(unit[i]))
self.lbl[i].Parent.Layout()
def OnChoice(self, e):
self.update_stats()
def OnResize(self, e):
self.prepare_details()
def OnSliderOn(self, e):
threshold = float(self.sliderThresOn.GetValue()) / 100
self.lblThresOn.SetLabel("{:.2f} Hz".format(threshold))
self.bimg.thresOn = threshold
self.rec_on = self.bimg.reconstructed_on
self.panelOn.Replot(data=self.rec_on)
self.ratios = self.bimg.ratios
self.panelRatios.Replot(data=self.ratios)
self.taus = self.bimg.taus
self.update_stats()
def OnSliderOff(self, e):
threshold = float(self.sliderThresOff.GetValue()) / 100
self.lblThresOff.SetLabel("{:.2f} Hz".format(threshold))
self.bimg.thresOff = threshold
self.rec_off = self.bimg.reconstructed_off
self.panelOff.Replot(data=self.rec_off)
self.ratios = self.bimg.ratios
self.panelRatios.Replot(data=self.ratios)
self.taus = self.bimg.taus
self.update_stats()
def OnSave(self, e):
wildcard = "Data file (.dat)|*.dat|PNG file (.png)|*.png"
dialog = wx.FileDialog(None, message="Choose a prefix", defaultDir="",
defaultFile="output", wildcard=wildcard, style=wx.SAVE)
if dialog.ShowModal() == wx.ID_OK:
print("Saving. Prefix: {0}. Format: {1}".format(
dialog.GetPath(), dialog.GetFilterIndex()))
self.saveData(dialog.GetPath(), dialog.GetFilterIndex())
dialog.Destroy()
def saveData(self, path, index):
if index == 0:
savetxt(path + "-on.dat", self.rec_on,
fmt="%10.5f", delimiter="\t")
savetxt(path + "-off.dat", self.rec_off,
fmt="%10.5f", delimiter="\t")
savetxt(path + "-ratios.dat", self.ratios,
fmt="%10.5f", delimiter="\t")
else:
self.panelOn.fig.savefig(path + "-on.png", dpi=300)
self.panelOff.fig.savefig(path + "-off.png", dpi=300)
self.panelRatios.fig.savefig(path + "-ratios.png", dpi=300)
def OnClose(self, _):
self.Destroy()
