def OnSpecAdd(self, event):
#key = self.lFluorSpecies.GetItem(self.currentFilterItem).GetText()
dlg = specAddDialog(self)
ret = dlg.ShowModal()
if ret == wx.ID_OK:
val = float(dlg.tVal.GetValue())
key = dlg.tKey.GetValue().encode()
if key == "":
return
self.pipeline.fluorSpecies[key] = val
ind = self.lFluorSpecies.InsertStringItem(sys.maxint, key)
self.lFluorSpecies.SetStringItem(ind,1, '%3.2f' % val)
#print val, (255*numpy.array(cm.gist_rainbow(val)))[:3]
self.lFluorSpecies.SetItemTextColour(ind, wx.Colour(*((128*numpy.array(cm.jet_r(val)))[:3])))
#self.visFr.mapping.setMapping('p_%s' % key, 'exp(-(%f*A - fitResults_Ag)**2/(2*fitError_Ag**2))*exp(-(%f*A - fitResults_Ar)**2/(2*fitError_Ar**2))' % (1- val, val))
#self.visFr.mapping.setMapping('p_%s' % key, 'exp(-(%f - gFrac)**2/(2*error_gFrac**2))' % (val))
#self.pipeline.mapping.setMapping('p_%s' % key, '(1.0/(ColourNorm*2*numpy.pi*fitError_Ag*fitError_Ar))*exp(-(fitResults_Ag - %f*A)**2/(2*fitError_Ag**2) - (fitResults_Ar - %f*A)**2/(2*fitError_Ar**2))' % (val, 1-val))
self.mapping.setMapping('p_%s' % key, 'exp(-(%f - gFrac)**2/(2*error_gFrac**2))/(error_gFrac*sqrt(2*numpy.pi))' % val)
self.visFr.UpdatePointColourChoices()
self.visFr.colourFilterPane.UpdateColourFilterChoices()
dlg.Destroy()
self.refresh()
def SpecFromMetadata(self, mdh):
labels = mdh.getEntry('Sample.Labelling')
structures = []
for structure, dye in labels:
if structure in structures: #duplicate structure
structure += ' A'
structures.append(structure)
ratio = dyeRatios.getRatio(dye, mdh)
if not ratio is None:
self.pipeline.colour_mapper.species_ratios[structure] = float(
ratio)
ind = self.lFluorSpecies.InsertStringItem(
UI_MAXSIZE, structure)
self.lFluorSpecies.SetStringItem(ind, 1, '%3.3f' % ratio)
self.lFluorSpecies.SetItemTextColour(
ind,
wx.Colour(*((128 * numpy.array(cm.jet_r(ratio)))[:3])))
#self.visFr.mapping.setMapping('p_%s' % key, 'exp(-(%f*A - fitResults_Ag)**2/(2*fitError_Ag**2))*exp(-(%f*A - fitResults_Ar)**2/(2*fitError_Ar**2))' % (1- val, val))
#self.visFr.mapping.setMapping('p_%s' % structure, 'exp(-(%f - gFrac)**2/(2*error_gFrac**2))' % (ratio))
#self.pipeline.mapping.setMapping('p_%s' % structure, '(1.0/(ColourNorm*2*numpy.pi*fitError_Ag*fitError_Ar))*exp(-(fitResults_Ag - %f*A)**2/(2*fitError_Ag**2) - (fitResults_Ar - %f*A)**2/(2*fitError_Ar**2))' % (ratio, 1-ratio))
#self.pipeline.mapping.setMapping('p_%s' % structure, 'exp(-(%f - gFrac)**2/(2*error_gFrac**2))/(error_gFrac*sqrt(2*numpy.pi))' % ratio)
self.pipeline.Rebuild()
self.visFr.UpdatePointColourChoices()
self.visFr.colourFilterPane.UpdateColourFilterChoices()
self.refresh()
def OnSpecGuess(self, event):
import scipy.cluster
#count number of peaks in gFrac histogram
n = (numpy.diff(
numpy.sign(
numpy.diff(
numpy.histogram(self.pipeline.filter['gFrac'],
numpy.linspace(0, 1, 20))[0]))) < 0).sum()
guesses = scipy.cluster.vq.kmeans(self.pipeline.filter['gFrac'], n)[0]
for g, i in zip(guesses, range(n)):
key = '%c' % (65 + i)
self.pipeline.colour_mapper.species_ratios[key] = float(g)
ind = self.lFluorSpecies.InsertStringItem(UI_MAXSIZE, key)
self.lFluorSpecies.SetStringItem(ind, 1, '%3.3f' % g)
self.lFluorSpecies.SetItemTextColour(
ind, wx.Colour(*((128 * numpy.array(cm.jet_r(g)))[:3])))
#self.visFr.mapping.setMapping('p_%s' % key, 'exp(-(%f*A - fitResults_Ag)**2/(2*fitError_Ag**2))*exp(-(%f*A - fitResults_Ar)**2/(2*fitError_Ar**2))' % (1- val, val))
#self.visFr.mapping.setMapping('p_%s' % key, 'exp(-(%f - gFrac)**2/(2*error_gFrac**2))' % (g))
#self.pipeline.mapping.setMapping('p_%s' % key, '(1.0/(ColourNorm*2*numpy.pi*fitError_Ag*fitError_Ar))*exp(-(fitResults_Ag - %f*A)**2/(2*fitError_Ag**2) - (fitResults_Ar - %f*A)**2/(2*fitError_Ar**2))' % (val, 1-val))
#self.pipeline.mapping.setMapping('p_%s' % key, 'exp(-(%f - gFrac)**2/(2*error_gFrac**2))/(error_gFrac*sqrt(2*numpy.pi))' % val)
self.pipeline.Rebuild()
try:
self.visFr.UpdatePointColourChoices()
self.visFr.colourFilterPane.UpdateColourFilterChoices()
except AttributeError:
pass
self.refresh()
def OnSpecChange(self, event=None):
it = self.lFluorSpecies.GetItem(event.m_itemIndex)
val = float(event.m_item.GetText())
col = event.GetColumn()
if col == 1: #frac
self.pipeline.fluorSpecies[str(it.GetText())] = val
self.lFluorSpecies.SetItemTextColour(
event.m_itemIndex,
wx.Colour(*((128 * numpy.array(cm.jet_r(val)))[:3])))
#self.visFr.mapping.setMapping('p_%s' % it.GetText(), 'exp(-(%f*A - fitResults_Ag)**2/(4*fitError_Ag**2 + 2*fitError_Ar**2))*exp(-(%f*A - fitResults_Ar)**2/(2*fitError_Ag**2 +4*fitError_Ar**2))' % (1- val, val))
#self.visFr.mapping.setMapping('p_%s' % it.GetText(), 'exp(-(%f - gFrac)**2/(2*error_gFrac**2))' % (val))
#self.pipeline.mapping.setMapping('p_%s' % it.GetText(), '(1.0/(ColourNorm*2*numpy.pi*fitError_Ag*fitError_Ar))*exp(-(fitResults_Ag - %f*A)**2/(2*fitError_Ag**2) - (fitResults_Ar - %f*A)**2/(2*fitError_Ar**2))' % (val, 1-val))
#self.pipeline.mapping.setMapping('p_%s' % it.GetText(), 'exp(-(%f - gFrac)**2/(2*error_gFrac**2))/(error_gFrac*sqrt(2*numpy.pi))' % val)
self.pipeline.Rebuild()
self.refresh()
else: #shift
axis = ['x', 'y', 'z'][col - 3]
specName = str(it.GetText())
if not specName in self.pipeline.chromaticShifts.keys():
self.pipeline.chromaticShifts[specName] = {}
self.pipeline.chromaticShifts[specName][axis] = val
self.visFr.RefreshView()
def refresh(self):
if not self.IsShown():
return
self.colPlotPan.draw()
self.lFluorSpecies.DeleteAllItems()
for key in self.pipeline.colour_mapper.species_ratios.keys():
ind = self.lFluorSpecies.InsertStringItem(UI_MAXSIZE, key)
ratio = self.pipeline.colour_mapper.species_ratios[key]
self.lFluorSpecies.SetStringItem(ind, 1, '%3.3f' % ratio)
self.lFluorSpecies.SetItemTextColour(
ind, wx.Colour(*((128 * numpy.array(cm.jet_r(ratio)))[:3])))
num_dyes = sum(self.pipeline.colourFilter._index(key))
self.lFluorSpecies.SetStringItem(ind, 2, '%d' % num_dyes)
def OnSpecGuess(self, event):
import scipy.cluster
#count number of peaks in gFrac histogram
n = (numpy.diff(numpy.sign(numpy.diff(numpy.histogram(self.pipeline.filter['gFrac'], numpy.linspace(0, 1, 20))[0]))) < 0).sum()
guesses = scipy.cluster.vq.kmeans(self.pipeline.filter['gFrac'], n)[0]
for g, i in zip(guesses, range(n)):
key = '%c' % (65 + i)
self.pipeline.fluorSpecies[key] = g
ind = self.lFluorSpecies.InsertStringItem(sys.maxint, key)
self.lFluorSpecies.SetStringItem(ind,1, '%3.3f' % g)
self.lFluorSpecies.SetItemTextColour(ind, wx.Colour(*((128*numpy.array(cm.jet_r(g)))[:3])))
#self.visFr.mapping.setMapping('p_%s' % key, 'exp(-(%f*A - fitResults_Ag)**2/(2*fitError_Ag**2))*exp(-(%f*A - fitResults_Ar)**2/(2*fitError_Ar**2))' % (1- val, val))
#self.visFr.mapping.setMapping('p_%s' % key, 'exp(-(%f - gFrac)**2/(2*error_gFrac**2))' % (g))
#self.pipeline.mapping.setMapping('p_%s' % key, '(1.0/(ColourNorm*2*numpy.pi*fitError_Ag*fitError_Ar))*exp(-(fitResults_Ag - %f*A)**2/(2*fitError_Ag**2) - (fitResults_Ar - %f*A)**2/(2*fitError_Ar**2))' % (val, 1-val))
self.mapping.setMapping('p_%s' % key, 'exp(-(%f - gFrac)**2/(2*error_gFrac**2))/(error_gFrac*sqrt(2*numpy.pi))' % val)
self.visFr.UpdatePointColourChoices()
self.visFr.colourFilterPane.UpdateColourFilterChoices()
self.refresh()
def draw(self):
if self.IsShownOnScreen():
#print self.IsShownOnScreen()
print('d')
"""Draw data."""
if self.visFrame.refv and not self.pipeline.ready or len(
self.pipeline.filter['x']) == 0:
return
print('vd')
if not hasattr(self, 'subplot1'):
self.subplot1 = self.figure.add_axes([.1, .1, .89, .89])
#self.subplot2 = self.figure.add_subplot( 122 )
self.subplot1.cla()
x, y = self.pipeline.filter['fitResults_Ag'], self.pipeline.filter[
'fitResults_Ar']
n, xedge, yedge = numpy.histogram2d(x,
y,
bins=[100, 100],
range=[(x.min(), x.max()),
(y.min(), y.max())])
l_x = len(x)
x = x[::int(max(l_x / 1e4, 1))]
y = y[::int(max(l_x / 1e4, 1))]
#facsPlot.facsPlotContour(x, y, 100)
c = -5e3 * numpy.ones(x.shape)
# print (c < -1).sum(), c.min()
cf = self.pipeline.colourFilter
for k, v in self.pipeline.fluorSpecies.items():
p_dye = self.pipeline.filter['p_%s' %
k][::int(max(l_x / 1e4, 1))]
p_other = numpy.zeros(x.shape)
#p_tot = numpy.zeros(p_dye.shape)
p_tot = cf.t_p_background * self.pipeline.filter[
'ColourNorm'][::int(max(l_x / 1e4, 1))]
for k2 in self.pipeline.fluorSpecies.keys():
p_tot += self.pipeline.filter['p_%s' %
k2][::int(max(l_x / 1e4, 1))]
if not k2 == k:
p_other = numpy.maximum(
p_other,
self.pipeline.filter['p_%s' %
k2][::int(max(l_x / 1e4, 1))])
p_dye = p_dye / p_tot
p_other = p_other / p_tot
c[(p_dye > cf.t_p_dye) * (p_other < cf.t_p_other)] = v
cs = 0.75 * cm.jet_r(c.copy())[:, :3]
cs[c < -1, :] = (0.3 * numpy.ones(cs.shape))[c < -1, :]
# print (c < -1).sum(), c.min()
# print (c < -1).sum(), cs[c < -1, :].shape
self.subplot1.scatter(x, y, s=2, c=cs, edgecolor='none')
#self.subplot1.plot(x, y, '.', ms=1, c=cs)
#n, xedge, yedge = numpy.histogram2d(x, y, bins = [100,100], range=[(x.min(), x.max()), (y.min(), y.max())])
self.subplot1.contour((xedge[:-1] + xedge[1:]) / 2,
(yedge[:-1] + yedge[1:]) / 2,
numpy.log2(n.T + .5),
7,
cmap=cm.copper_r,
linewidths=2)
self.subplot1.axis('image')
self.subplot1.set_xlabel('Channel 1')
self.subplot1.set_ylabel('Channel 2')
x.sort()
y.sort()
xl = x[int(.997 * len(x))]
yl = y[int(.997 * len(x))]
self.subplot1.set_xlim((0, xl))
self.subplot1.set_ylim((0, yl))
for k, v in self.pipeline.fluorSpecies.items():
self.subplot1.plot([0, xl], [0, ((1 - v) / v) * xl],
lw=2,
c=cm.jet_r(v))
self.canvas.draw()
def __init__(self, parent, pipeline, visFrame, id=-1):
wx.Panel.__init__(self, parent, id)
bsizer = wx.BoxSizer(wx.VERTICAL)
self.visFr = visFrame
self.pipeline = pipeline
self.colPlotPan = colourPlotPanel(self, pipeline, visFrame)
bsizer.Add(self.colPlotPan, 4,
wx.ALL | wx.ALIGN_CENTER_VERTICAL | wx.EXPAND, 5)
# hsizer = wx.BoxSizer(wx.HORIZONTAL)
# hsizer.Add(wx.StaticText(self, -1, "x' = "), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
#
# self.tXExpr = wx.TextCtrl(self, -1, self.driftExprX, size=(130, -1))
# hsizer.Add(self.tXExpr, 2,wx.ALL|wx.ALIGN_CENTER_VERTICAL|wx.EXPAND, 5)
#
# bsizer.Add(hsizer, 0, wx.ALL, 0)
#
# hsizer = wx.BoxSizer(wx.HORIZONTAL)
# hsizer.Add(wx.StaticText(self, -1, "y' = "), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
#
# self.tYExpr = wx.TextCtrl(self, -1, self.driftExprY, size=(130,-1))
# hsizer.Add(self.tYExpr, 2,wx.ALL|wx.ALIGN_CENTER_VERTICAL|wx.EXPAND, 5)
#
# bsizer.Add(hsizer, 0, wx.ALL, 0)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
vsizer = wx.StaticBoxSizer(wx.StaticBox(self, -1, 'Fluorophores'),
wx.VERTICAL)
self.lFluorSpecies = editList.EditListCtrl(
self,
-1,
style=wx.LC_REPORT | wx.LC_SINGLE_SEL | wx.SUNKEN_BORDER,
size=(450, 100))
vsizer.Add(self.lFluorSpecies, 0, wx.ALL, 5)
self.lFluorSpecies.InsertColumn(0, 'Name')
self.lFluorSpecies.InsertColumn(1, 'Ag/(Ag + Ar)')
self.lFluorSpecies.InsertColumn(2, '# Events')
self.lFluorSpecies.InsertColumn(3, 'dx')
self.lFluorSpecies.InsertColumn(4, 'dy')
self.lFluorSpecies.InsertColumn(5, 'dz')
self.lFluorSpecies.makeColumnEditable(1)
self.lFluorSpecies.makeColumnEditable(3)
self.lFluorSpecies.makeColumnEditable(4)
self.lFluorSpecies.makeColumnEditable(5)
for key, value in self.pipeline.fluorSpecies.items():
ind = self.lFluorSpecies.InsertStringItem(UI_MAXSIZE, key)
self.lFluorSpecies.SetStringItem(ind, 1, '%3.2f' % value)
self.lFluorSpecies.SetItemTextColour(
ind, wx.Colour(*((128 * numpy.array(cm.jet_r(value)))[:3])))
self.lFluorSpecies.SetColumnWidth(3, 60)
self.lFluorSpecies.SetColumnWidth(4, 60)
self.lFluorSpecies.SetColumnWidth(5, 60)
## only do this part the first time so the events are only bound once
#if not hasattr(self, "ID_FILT_ADD"):
self.ID_SPEC_ADD = wx.NewId()
self.ID_SPEC_DELETE = wx.NewId()
#self.ID_FILT_EDIT = wx.NewId()
self.Bind(wx.EVT_MENU, self.OnSpecAdd, id=self.ID_SPEC_ADD)
self.Bind(wx.EVT_MENU, self.OnSpecDelete, id=self.ID_SPEC_DELETE)
#self.Bind(wx.EVT_MENU, self.OnFilterEdit, id=self.ID_FILT_EDIT)
# for wxMSW
self.lFluorSpecies.Bind(wx.EVT_COMMAND_RIGHT_CLICK,
self.OnSpecListRightClick)
# for wxGTK
self.lFluorSpecies.Bind(wx.EVT_RIGHT_UP, self.OnSpecListRightClick)
# self.lFluorSpecies.Bind(wx.EVT_LIST_ITEM_SELECTED, self.OnSpecItemSelected)
# self.lFluorSpecies.Bind(wx.EVT_LIST_ITEM_DESELECTED, self.OnSpecItemDeselected)
#self.lFluorSpecies.Bind(wx.EVT_LIST_ITEM_ACTIVATED, self.OnFilterEdit)
self.lFluorSpecies.Bind(wx.EVT_LIST_END_LABEL_EDIT, self.OnSpecChange)
self.bGuess = wx.Button(self, -1, 'Guess')
self.bGuess.Bind(wx.EVT_BUTTON, self.OnSpecGuess)
vsizer.Add(self.bGuess, 0, wx.ALL | wx.ALIGN_CENTER_HORIZONTAL, 5)
hsizer.Add(vsizer, 0, wx.ALL, 5)
vsizer = wx.StaticBoxSizer(
wx.StaticBox(self, -1, 'Channel Assignment '), wx.VERTICAL)
hsizer2 = wx.BoxSizer(wx.HORIZONTAL)
hsizer2.Add(wx.StaticText(self, -1, 'p_dye: '), 0,
wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.tPBelong = wx.TextCtrl(
self, -1, '%3.3f' % self.pipeline.colourFilter.t_p_dye)
hsizer2.Add(self.tPBelong, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.tPBelong.Bind(wx.EVT_TEXT, self.OnChangePDye)
vsizer.Add(hsizer2, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 0)
hsizer2 = wx.BoxSizer(wx.HORIZONTAL)
hsizer2.Add(wx.StaticText(self, -1, 'p_other:'), 0,
wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.tPOther = wx.TextCtrl(
self, -1, '%3.3f' % self.pipeline.colourFilter.t_p_other)
hsizer2.Add(self.tPOther, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.tPOther.Bind(wx.EVT_TEXT, self.OnChangePOther)
vsizer.Add(hsizer2, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 0)
hsizer.Add(vsizer, 0, wx.ALL, 5)
bsizer.Add(hsizer, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.SetSizer(bsizer)
bsizer.Fit(self)
self.Bind(wx.EVT_SHOW, self.OnShow)
def draw( self ):
print('d')
"""Draw data."""
if self.visFrame.refv and not self.pipeline.ready or len(self.pipeline.filter['x']) == 0:
return
print('vd')
if not hasattr( self, 'subplot1' ):
self.subplot1 = self.figure.add_axes([.1, .1, .89, .89])
#self.subplot2 = self.figure.add_subplot( 122 )
self.subplot1.cla()
x, y = self.visFrame.pipeline['fitResults_Ag'], self.pipeline.filter['fitResults_Ar']
n, xedge, yedge = numpy.histogram2d(x, y, bins = [100,100], range=[(x.min(), x.max()), (y.min(), y.max())])
l_x = len(x)
x = x[::max(l_x/1e4, 1)]
y = y[::max(l_x/1e4, 1)]
#facsPlot.facsPlotContour(x, y, 100)
c = -5e3*numpy.ones(x.shape)
# print (c < -1).sum(), c.min()
for k, v in self.pipeline.fluorSpecies.items():
p_dye = self.pipeline.mapping['p_%s' % k][::max(l_x/1e4, 1)]
p_other = numpy.zeros(x.shape)
#p_tot = numpy.zeros(p_dye.shape)
p_tot = self.pipeline.t_p_background*self.pipeline.mapping['ColourNorm'][::max(l_x/1e4, 1)]
for k2 in self.pipeline.fluorSpecies.keys():
p_tot += self.pipeline.mapping['p_%s' % k2][::max(l_x/1e4, 1)]
if not k2 ==k:
p_other = numpy.maximum(p_other, self.pipeline.mapping['p_%s' % k2][::max(l_x/1e4, 1)])
p_dye = p_dye/p_tot
p_other = p_other/p_tot
c[(p_dye > self.pipeline.t_p_dye)*(p_other < self.pipeline.t_p_other)] = v
cs = 0.75*cm.jet_r(c.copy())[:,:3]
cs[c < -1, :] = (0.3*numpy.ones(cs.shape))[c < -1, :]
# print (c < -1).sum(), c.min()
# print (c < -1).sum(), cs[c < -1, :].shape
self.subplot1.scatter(x, y, s=2, c=cs, edgecolor='none')
#self.subplot1.plot(x, y, '.', ms=1, c=cs)
#n, xedge, yedge = numpy.histogram2d(x, y, bins = [100,100], range=[(x.min(), x.max()), (y.min(), y.max())])
self.subplot1.contour((xedge[:-1] + xedge[1:])/2, (yedge[:-1] + yedge[1:])/2, numpy.log2(n.T + .5), 7, cmap = cm.copper_r, linewidths=2)
self.subplot1.axis('image')
self.subplot1.set_xlabel('Channel 1')
self.subplot1.set_ylabel('Channel 2')
x.sort()
y.sort()
xl = x[.997*len(x)]
yl = y[.997*len(x)]
self.subplot1.set_xlim((0, xl))
self.subplot1.set_ylim((0, yl))
for k, v in self.pipeline.fluorSpecies.items():
self.subplot1.plot([0,xl], [0, ((1-v)/v)*xl], lw=2, c=cm.jet_r(v))
self.canvas.draw()
def SpecFromMetadata(self, mdh):
labels = mdh.getEntry('Sample.Labelling')
structures = []
for structure, dye in labels:
if structure in structures: #duplicate structure
structure += ' A'
structures.append(structure)
ratio = dyeRatios.getRatio(dye, mdh)
if not ratio == None:
self.pipeline.fluorSpecies[structure] = ratio
ind = self.lFluorSpecies.InsertStringItem(sys.maxint, structure)
self.lFluorSpecies.SetStringItem(ind,1, '%3.3f' % ratio)
self.lFluorSpecies.SetItemTextColour(ind, wx.Colour(*((128*numpy.array(cm.jet_r(ratio)))[:3])))
#self.visFr.mapping.setMapping('p_%s' % key, 'exp(-(%f*A - fitResults_Ag)**2/(2*fitError_Ag**2))*exp(-(%f*A - fitResults_Ar)**2/(2*fitError_Ar**2))' % (1- val, val))
#self.visFr.mapping.setMapping('p_%s' % structure, 'exp(-(%f - gFrac)**2/(2*error_gFrac**2))' % (ratio))
#self.pipeline.mapping.setMapping('p_%s' % structure, '(1.0/(ColourNorm*2*numpy.pi*fitError_Ag*fitError_Ar))*exp(-(fitResults_Ag - %f*A)**2/(2*fitError_Ag**2) - (fitResults_Ar - %f*A)**2/(2*fitError_Ar**2))' % (ratio, 1-ratio))
self.mapping.setMapping('p_%s' % structure, 'exp(-(%f - gFrac)**2/(2*error_gFrac**2))/(error_gFrac*sqrt(2*numpy.pi))' % ratio)
self.visFr.UpdatePointColourChoices()
self.visFr.colourFilterPane.UpdateColourFilterChoices()
self.refresh()
def OnSpecChange(self, event=None):
it = self.lFluorSpecies.GetItem(event.m_itemIndex)
val = float(event.m_item.GetText())
col = event.GetColumn()
if col == 1: #frac
self.pipeline.fluorSpecies[it.GetText()] = val
self.lFluorSpecies.SetItemTextColour(event.m_itemIndex, wx.Colour(*((128*numpy.array(cm.jet_r(val)))[:3])))
#self.visFr.mapping.setMapping('p_%s' % it.GetText(), 'exp(-(%f*A - fitResults_Ag)**2/(4*fitError_Ag**2 + 2*fitError_Ar**2))*exp(-(%f*A - fitResults_Ar)**2/(2*fitError_Ag**2 +4*fitError_Ar**2))' % (1- val, val))
#self.visFr.mapping.setMapping('p_%s' % it.GetText(), 'exp(-(%f - gFrac)**2/(2*error_gFrac**2))' % (val))
#self.pipeline.mapping.setMapping('p_%s' % it.GetText(), '(1.0/(ColourNorm*2*numpy.pi*fitError_Ag*fitError_Ar))*exp(-(fitResults_Ag - %f*A)**2/(2*fitError_Ag**2) - (fitResults_Ar - %f*A)**2/(2*fitError_Ar**2))' % (val, 1-val))
self.mapping.setMapping('p_%s' % it.GetText(), 'exp(-(%f - gFrac)**2/(2*error_gFrac**2))/(error_gFrac*sqrt(2*numpy.pi))' % val)
self.refresh()
else: #shift
axis = ['x', 'y', 'z'][col-3]
specName = it.GetText()
if not specName in self.pipeline.chromaticShifts.keys():
self.pipeline.chromaticShifts[specName] = {}
self.pipeline.chromaticShifts[specName][axis] = val
self.visFr.RefreshView()
def __init__(self, parent, pipeline,visFrame, id=-1):
wx.Panel.__init__(self, parent, id)
bsizer = wx.BoxSizer(wx.VERTICAL)
self.visFr = visFrame
self.pipeline = pipeline
self.colPlotPan = colourPlotPanel(self, pipeline, visFrame)
bsizer.Add(self.colPlotPan, 4,wx.ALL|wx.ALIGN_CENTER_VERTICAL|wx.EXPAND, 5)
# hsizer = wx.BoxSizer(wx.HORIZONTAL)
# hsizer.Add(wx.StaticText(self, -1, "x' = "), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
#
# self.tXExpr = wx.TextCtrl(self, -1, self.driftExprX, size=(130, -1))
# hsizer.Add(self.tXExpr, 2,wx.ALL|wx.ALIGN_CENTER_VERTICAL|wx.EXPAND, 5)
#
# bsizer.Add(hsizer, 0, wx.ALL, 0)
#
# hsizer = wx.BoxSizer(wx.HORIZONTAL)
# hsizer.Add(wx.StaticText(self, -1, "y' = "), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
#
# self.tYExpr = wx.TextCtrl(self, -1, self.driftExprY, size=(130,-1))
# hsizer.Add(self.tYExpr, 2,wx.ALL|wx.ALIGN_CENTER_VERTICAL|wx.EXPAND, 5)
#
# bsizer.Add(hsizer, 0, wx.ALL, 0)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
vsizer = wx.StaticBoxSizer(wx.StaticBox(self, -1, 'Fluorophores'), wx.VERTICAL)
self.lFluorSpecies = editList.EditListCtrl(self, -1, style=wx.LC_REPORT|wx.LC_SINGLE_SEL|wx.SUNKEN_BORDER, size=(450, 100))
vsizer.Add(self.lFluorSpecies, 0, wx.ALL, 5)
self.lFluorSpecies.InsertColumn(0, 'Name')
self.lFluorSpecies.InsertColumn(1, 'Ag/(Ag + Ar)')
self.lFluorSpecies.InsertColumn(2, '# Events')
self.lFluorSpecies.InsertColumn(3, 'dx')
self.lFluorSpecies.InsertColumn(4, 'dy')
self.lFluorSpecies.InsertColumn(5, 'dz')
self.lFluorSpecies.makeColumnEditable(1)
self.lFluorSpecies.makeColumnEditable(3)
self.lFluorSpecies.makeColumnEditable(4)
self.lFluorSpecies.makeColumnEditable(5)
for key, value in self.pipeline.fluorSpecies.items():
ind = self.lFluorSpecies.InsertStringItem(sys.maxint, key)
self.lFluorSpecies.SetStringItem(ind,1, '%3.2f' % value)
self.lFluorSpecies.SetItemTextColour(ind, wx.Colour(*((128*numpy.array(cm.jet_r(value)))[:3])))
self.lFluorSpecies.SetColumnWidth(3, 60)
self.lFluorSpecies.SetColumnWidth(4, 60)
self.lFluorSpecies.SetColumnWidth(5, 60)
## only do this part the first time so the events are only bound once
#if not hasattr(self, "ID_FILT_ADD"):
self.ID_SPEC_ADD = wx.NewId()
self.ID_SPEC_DELETE = wx.NewId()
#self.ID_FILT_EDIT = wx.NewId()
self.Bind(wx.EVT_MENU, self.OnSpecAdd, id=self.ID_SPEC_ADD)
self.Bind(wx.EVT_MENU, self.OnSpecDelete, id=self.ID_SPEC_DELETE)
#self.Bind(wx.EVT_MENU, self.OnFilterEdit, id=self.ID_FILT_EDIT)
# for wxMSW
self.lFluorSpecies.Bind(wx.EVT_COMMAND_RIGHT_CLICK, self.OnSpecListRightClick)
# for wxGTK
self.lFluorSpecies.Bind(wx.EVT_RIGHT_UP, self.OnSpecListRightClick)
# self.lFluorSpecies.Bind(wx.EVT_LIST_ITEM_SELECTED, self.OnSpecItemSelected)
# self.lFluorSpecies.Bind(wx.EVT_LIST_ITEM_DESELECTED, self.OnSpecItemDeselected)
#self.lFluorSpecies.Bind(wx.EVT_LIST_ITEM_ACTIVATED, self.OnFilterEdit)
self.lFluorSpecies.Bind(wx.EVT_LIST_END_LABEL_EDIT, self.OnSpecChange)
self.bGuess = wx.Button(self, -1, 'Guess')
self.bGuess.Bind(wx.EVT_BUTTON, self.OnSpecGuess)
vsizer.Add(self.bGuess, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5)
hsizer.Add(vsizer, 0, wx.ALL, 5)
vsizer = wx.StaticBoxSizer(wx.StaticBox(self, -1, 'Channel Assignment '), wx.VERTICAL)
hsizer2 = wx.BoxSizer(wx.HORIZONTAL)
hsizer2.Add(wx.StaticText(self, -1, 'p_dye: '), 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.tPBelong = wx.TextCtrl(self, -1, '%3.3f' % self.pipeline.t_p_dye)
hsizer2.Add(self.tPBelong, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.tPBelong.Bind(wx.EVT_TEXT, self.OnChangePDye)
vsizer.Add(hsizer2, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 0)
hsizer2 = wx.BoxSizer(wx.HORIZONTAL)
hsizer2.Add(wx.StaticText(self, -1, 'p_other:'), 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.tPOther = wx.TextCtrl(self, -1, '%3.3f' % self.pipeline.t_p_other)
hsizer2.Add(self.tPOther, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.tPOther.Bind(wx.EVT_TEXT, self.OnChangePOther)
vsizer.Add(hsizer2, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 0)
hsizer.Add(vsizer, 0, wx.ALL, 5)
bsizer.Add(hsizer, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.SetSizer(bsizer)
bsizer.Fit(self)
self.Bind(wx.EVT_SHOW, self.OnShow)