def OnPlotProfile(self, event=None):
from PYME.Analysis.profile_extraction import extract_profile
lx, ly, hx, hy = self.do.GetSliceSelection()
w = int(self.do.selectionWidth)
try:
names = self.image.mdh.getEntry('ChannelNames')
except:
names = ['Channel %d' % d for d in range(self.image.data.shape[3])]
try:
voxx = self.image.mdh.getEntry('voxelsize.x')
except:
voxx = 1
plots = []
n_chans = self.image.data_xyztc.shape[4]
for chanNum in range(n_chans):
img = self.image.data_xyztc[:, :, self.do.zp, self.do.tp,
chanNum].squeeze()
p = extract_profile(img, lx, ly, hx, hy, w)
plots.append(p.reshape(-1, 1, 1, 1))
#plt.legend(names)
t = np.arange(p.size)
im = ImageStack(plots, titleStub='New Profile')
im.xvals = t * voxx
if not voxx == 1:
im.xlabel = 'Distance [um]'
else:
im.xlabel = 'Distance [pixels]'
im.ylabel = 'Intensity'
im.defaultExt = '.txt'
im.mdh['voxelsize.x'] = voxx
im.mdh['ChannelNames'] = names
im.mdh['Profile.XValues'] = im.xvals
im.mdh['Profile.XLabel'] = im.xlabel
im.mdh['Profile.YLabel'] = im.ylabel
im.mdh['Profile.StartX'] = lx
im.mdh['Profile.StartY'] = ly
im.mdh['Profile.EndX'] = hx
im.mdh['Profile.EndY'] = hy
im.mdh['Profile.Width'] = 2 * w + 1
im.mdh['OriginalImage'] = self.image.filename
ViewIm3D(im, mode='graph', parent=wx.GetTopLevelParent(self.dsviewer))
def OnPlotWavyProfile(self, event=None):
#lx, ly, hx, hy = self.do.GetSliceSelection()
pts = np.array(self.do.selection_trace)
w = int(np.floor(0.5 * self.do.selectionWidth))
try:
names = self.image.mdh.getEntry('ChannelNames')
except:
names = ['Channel %d' % d for d in range(self.image.data.shape[3])]
try:
voxx = self.image.mdh.getEntry('voxelsize.x')
except:
voxx = 1
plots = []
t = np.arange(np.ceil(len(pts)))
n_chans = self.image.data_xyztc.shape[4]
for chanNum in range(n_chans):
p = ndimage.map_coordinates(
self.image.data_xyztc[:, :, self.do.zp, self.do.tp,
chanNum].squeeze(), pts.T)
plots.append(p.reshape(-1, 1, 1, 1))
#plt.legend(names)
im = ImageStack(plots, titleStub='New Profile')
im.xvals = t * voxx
if not voxx == 1:
im.xlabel = 'Distance [um]'
else:
im.xlabel = 'Distance [pixels]'
im.ylabel = 'Intensity'
im.defaultExt = '.txt'
im.mdh['voxelsize.x'] = voxx
im.mdh['ChannelNames'] = names
im.mdh['Profile.XValues'] = im.xvals
im.mdh['Profile.XLabel'] = im.xlabel
im.mdh['Profile.YLabel'] = im.ylabel
#im.mdh['Profile.StartX'] = lx
#im.mdh['Profile.StartY'] = ly
#im.mdh['Profile.EndX'] = hx
#im.mdh['Profile.EndY'] = hy
#im.mdh['Profile.Width'] = 2*w + 1
im.mdh['OriginalImage'] = self.image.filename
ViewIm3D(im, mode='graph')
def OnPlotProfile(self, event=None):
try:
names = self.image.mdh.getEntry('ChannelNames')
except:
names = ['Channel %d' % d for d in range(self.image.data.shape[3])]
#print lx, hx, ly, hy
#pylab.figure()
plots = []
for chanNum in range(self.image.data.shape[3]):
tmin = self.do.Offs[chanNum]
tmax = tmin + 1. / self.do.Gains[chanNum]
d = self.image.data[:, :, :, chanNum].squeeze()
trange = np.linspace(tmin, tmax)
p = np.array([ndimage.label(d > t)[1] for t in trange])
plots.append(p.reshape(-1, 1, 1))
#pylab.legend(names)
im = ImageStack(plots, titleStub='New Threshold Range')
im.xvals = trange
im.xlabel = 'Threshold'
im.ylabel = 'Num Objects'
im.defaultExt = '.txt'
#im.mdh['voxelsize.x'] = voxx
im.mdh['ChannelNames'] = names
im.mdh['Profile.XValues'] = im.xvals
im.mdh['Profile.XLabel'] = im.xlabel
im.mdh['Profile.YLabel'] = im.ylabel
im.mdh['OriginalImage'] = self.image.filename
ViewIm3D(im, mode='graph', parent=wx.GetTopLevelParent(self.dsviewer))
def OnBinProperty(self, event=None):
# these are the defaults
avProperty = 'nPhotons'
byProperty = 'x'
binwidth = 100
# traitsui dialog to set the event properties etc
pChoice = propertyChoice()
pChoice.add_channels(sorted(self.pipeline.keys()))
# select defaults if these event properties exist
if avProperty in pChoice.clist:
pChoice.EventProperty = avProperty
if byProperty in pChoice.clist:
pChoice.BinByProperty = byProperty
if pChoice.configure_traits(kind='modal'):
avProperty = pChoice.EventProperty
byProperty = pChoice.BinByProperty
binwidth = pChoice.BinWidth
else:
return
avp = self.pipeline[avProperty]
byp = self.pipeline[byProperty]
bypmin = byp.min()
bypmax = byp.max()
nbins = int((bypmax - bypmin) / binwidth)
bins = bypmin + np.arange(nbins + 1) * binwidth
binctrs = 0.5 * (bins[0:-1] + bins[1:])
avbin, abins = np.histogram(byp, bins=bins, weights=avp)
bybin, bybins = np.histogram(byp, bins=bins)
good = bybin > 0
bad = bybin <= 0
avmean = np.zeros_like(avbin, dtype='float64')
avmean[good] = avbin[good] / bybin[good]
avmean[bad] = np.nan
# direct matplotlib plotting scrapped for ImageStack approach
# which allows saving of data
#plt.figure()
#plt.plot(binctrs, avmean)
#plt.xlabel(byProperty)
#plt.ylabel('mean of %s' % avProperty)
plots = []
plots.append(avmean.reshape(-1, 1, 1))
im = ImageStack(plots, titleStub='mean of %s' % avProperty)
im.xvals = binctrs
im.xlabel = byProperty
im.ylabel = 'mean of %s' % avProperty
im.defaultExt = '*.txt'
im.mdh['voxelsize.x'] = binwidth
im.mdh['ChannelNames'] = [avProperty]
im.mdh['Profile.XValues'] = im.xvals
im.mdh['Profile.XLabel'] = im.xlabel
im.mdh['Profile.YLabel'] = im.ylabel
im.mdh['OriginalImage'] = self.pipeline.filename
ViewIm3D(im, mode='graph', parent=wx.GetTopLevelParent(self.visFr))
def OnColoc(self, event=None, restrict_z=False, coloc_vs_z = False):
from PYME.Analysis.Colocalisation import correlationCoeffs, edtColoc
from scipy import interpolate
voxelsize = self.image.voxelsize_nm
names = self.image.names
if not getattr(self.image, 'labels', None) is None:
have_mask = True
mask = (self.image.labels > 0.5).squeeze()
else:
have_mask = False
mask = None
if not restrict_z:
dlg = ColocSettingsDialog(self.dsviewer, voxelsize[0], names, have_mask=have_mask)
else:
dlg = ColocSettingsDialog(self.dsviewer, voxelsize[0], names, have_mask=have_mask, z_size=self.image.data.shape[2])
dlg.ShowModal()
bins = dlg.GetBins()
chans = dlg.GetChans()
use_mask = dlg.GetUseMask()
zs, ze = (0, self.image.data.shape[2])
if (self.image.data.shape[2] > 1) and restrict_z:
zs, ze = dlg.GetZrange()
zs,ze = (0,1)
if self.image.data.shape[2] > 1:
zs,ze = dlg.GetZrange()
dlg.Destroy()
print('Use mask: %s' % use_mask)
if not use_mask:
mask=None
#assume we have exactly 2 channels #FIXME - add a selector
#grab image data
imA = self.image.data[:,:,zs:ze,chans[0]].squeeze()
imB = self.image.data[:,:,zs:ze,chans[1]].squeeze()
#assume threshold is half the colour bounds - good if using threshold mode
tA = self.do.Offs[chans[0]] + .5/self.do.Gains[chans[0]] #plt.mean(self.ivps[0].clim)
tB = self.do.Offs[chans[1]] + .5/self.do.Gains[chans[1]] #plt.mean(self.ivps[0].clim)
nameA = names[chans[0]]
nameB = names[chans[1]]
voxelsize = voxelsize[:imA.ndim] #trunctate to number of dimensions
print('Calculating Pearson and Manders coefficients ...')
pearson = correlationCoeffs.pearson(imA, imB, roi_mask=mask)
MA, MB = correlationCoeffs.thresholdedManders(imA, imB, tA, tB, roi_mask=mask)
if coloc_vs_z:
MAzs, MBzs = ([],[])
FAzs, FBzs = ([],[])
if self.image.data.shape[2] > 1:
for z in range(self.image.data.shape[2]):
imAz = self.image.data[:,:,z,chans[0]].squeeze()
imBz = self.image.data[:,:,z,chans[1]].squeeze()
MAz, MBz = correlationCoeffs.thresholdedManders(imAz, imBz, tA, tB)
FAz, FBz = correlationCoeffs.maskFractions(imAz, imBz, tA, tB)
MAzs.append(MAz)
MBzs.append(MBz)
FAzs.append(FAz)
FBzs.append(FBz)
print("M(A->B) %s" % MAzs)
print("M(B->A) %s" % MBzs)
print("Species A: %s, Species B: %s" %(nameA,nameB))
plt.figure()
plt.subplot(211)
if 'filename' in self.image.__dict__:
plt.title(self.image.filename)
# nameB with nameA
cAB, = plt.plot(MAzs,'o', label = '%s with %s' %(nameB,nameA))
# nameA with nameB
cBA, = plt.plot(MBzs,'*', label = '%s with %s' %(nameA,nameB))
plt.legend([cBA,cAB])
plt.xlabel('z slice level')
plt.ylabel('Manders coloc fraction')
plt.ylim(0,None)
plt.subplot(212)
if 'filename' in self.image.__dict__:
plt.title(self.image.filename)
# nameB with nameA
fA, = plt.plot(FAzs,'o', label = '%s mask fraction' %(nameA))
# nameA with nameB
fB, = plt.plot(FBzs,'*', label = '%s mask fraction' %(nameB))
plt.legend([fA,fB])
plt.xlabel('z slice level')
plt.ylabel('Mask fraction')
plt.ylim(0,None)
plt.show()
print('Performing distance transform ...')
#bnA, bmA, binsA = edtColoc.imageDensityAtDistance(imB, imA > tA, voxelsize, bins, roi_mask=mask)
#bnAA, bmAA, binsA = edtColoc.imageDensityAtDistance(imA, imA > tA, voxelsize, bins, roi_mask=mask)
bins_, enrichment_BA, enclosed_BA, enclosed_area_A = edtColoc.image_enrichment_and_fraction_at_distance(imB, imA > tA, voxelsize,
bins, roi_mask=mask)
bins_, enrichment_AA, enclosed_AA, _ = edtColoc.image_enrichment_and_fraction_at_distance(imA, imA > tA, voxelsize,
bins, roi_mask=mask)
print('Performing distance transform (reversed) ...')
#bnB, bmB, binsB = edtColoc.imageDensityAtDistance(imA, imB > tB, voxelsize, bins, roi_mask=mask)
#bnBB, bmBB, binsB = edtColoc.imageDensityAtDistance(imB, imB > tB, voxelsize, bins, roi_mask=mask)
bins_, enrichment_AB, enclosed_AB, enclosed_area_B = edtColoc.image_enrichment_and_fraction_at_distance(imA, imB > tB, voxelsize,
bins, roi_mask=mask)
bins_, enrichment_BB, enclosed_BB, _ = edtColoc.image_enrichment_and_fraction_at_distance(imB, imB > tB, voxelsize,
bins, roi_mask=mask)
#print binsB, bmB
plots = []
pnames = []
# B from mA
####################
plots_ = {}
#plots_['Frac. %s from mask(%s)' % (nameB, nameA)] =
plots.append(enclosed_BA.reshape(-1, 1, 1))
pnames.append('Frac. %s from mask(%s)' % (nameB, nameA))
plots.append(enrichment_BA.reshape(-1, 1, 1))
pnames.append('Enrichment of %s at distance from mask(%s)' % (nameB, nameA))
edtColoc.plot_image_dist_coloc_figure(bins_, enrichment_BA, enrichment_AA, enclosed_BA, enclosed_AA, enclosed_area_A, pearson, MA, MB, nameA, nameB)
plots.append(enclosed_AB.reshape(-1, 1, 1))
pnames.append('Frac. %s from mask(%s)' % (nameA, nameB))
plots.append(enrichment_AB.reshape(-1, 1, 1))
pnames.append('Enrichment of %s at distance from mask(%s)' % (nameA, nameB))
edtColoc.plot_image_dist_coloc_figure(bins_, enrichment_AB, enrichment_BB, enclosed_AB, enclosed_BB, enclosed_area_B, pearson,
MA, MB, nameB, nameA)
plt.show()
im = ImageStack(plots, titleStub='Radial Distribution')
im.xvals = bins[:-1]
im.xlabel = 'Distance [nm]'
im.ylabel = 'Fraction'
im.defaultExt = '.txt'
im.mdh['voxelsize.x'] = (bins[1] - bins[0])*1e-3
im.mdh['ChannelNames'] = pnames
im.mdh['Profile.XValues'] = im.xvals
im.mdh['Profile.XLabel'] = im.xlabel
im.mdh['Profile.YLabel'] = im.ylabel
im.mdh['Colocalisation.Channels'] = names
im.mdh['Colocalisation.Thresholds'] = [tA, tB]
im.mdh['Colocalisation.Pearson'] = pearson
im.mdh['Colocalisation.Manders'] = [MA, MB]
try:
im.mdh['Colocalisation.ThresholdMode'] = self.do.ThreshMode
except:
pass
im.mdh['OriginalImage'] = self.image.filename
ViewIm3D(im, mode='graph')
def OnPlotAxialProfile(self, event=None):
lx, ly, hx, hy = self.do.GetSliceSelection()
try:
names = self.image.mdh.getEntry('ChannelNames')
except:
names = ['Channel %d' % d for d in range(self.image.data.shape[3])]
plots = []
t = np.arange(self.image.data.shape[2])
try:
stack = (self.image.mdh['AcquisitionType'] == 'Stack')
except:
stack = False
if stack:
dt = self.image.mdh['voxelsize.z']
else:
try:
dt = self.image.mdh['Camera.CycleTime']
except:
dt = 1
for chanNum in range(self.image.data.shape[3]):
plots.append(np.zeros((len(t), 1, 1)))
dlg = wx.ProgressDialog('Extracting Axial Profile', 'Progress',
max(len(t) - 1, 1))
for i in t:
for chanNum in range(self.image.data.shape[3]):
plots[chanNum][i] = self.image.data[lx:hx, ly:hy, i,
chanNum].mean()
if (i % 10) == 0:
dlg.Update(i, '%d of %d frames' % (i, t.size))
dlg.Destroy()
#plt.legend(names)
#TODO: Is this really sensible???
# fix so that we can even plot stacks of depth 1 (i.e. data that is not really a stack)
# works by replicating the single plane twice simulating a stack of depth 2
if len(t) == 1:
t = np.arange(2)
plots2 = []
for chanNum in range(self.image.data.shape[3]):
plots2.append(np.zeros((len(t), 1, 1)))
for j in range(2):
plots2[chanNum][j] = plots[chanNum][0]
plots = plots2
im = ImageStack(plots, titleStub='New Profile')
im.xvals = t * dt
if stack:
im.xlabel = 'Position [um]'
elif not dt == 1:
im.xlabel = 'Time [s]'
else:
im.xlabel = 'Time [frames]'
im.ylabel = 'Intensity'
im.defaultExt = '.txt'
im.mdh['voxelsize.x'] = dt
im.mdh['ChannelNames'] = names
im.mdh['Profile.XValues'] = im.xvals
im.mdh['Profile.XLabel'] = im.xlabel
im.mdh['Profile.YLabel'] = im.ylabel
im.mdh['Profile.X1'] = lx
im.mdh['Profile.Y1'] = ly
im.mdh['Profile.X2'] = hx
im.mdh['Profile.Y2'] = hy
im.mdh['OriginalImage'] = self.image.filename
im.parent = self.image
ViewIm3D(im, mode='graph')
def _OnPlotProfile(self, event=None):
lx, ly, hx, hy = self.do.GetSliceSelection()
w = int(np.floor(0.5 * self.do.selectionWidth))
try:
names = self.image.mdh.getEntry('ChannelNames')
except:
names = ['Channel %d' % d for d in range(self.image.data.shape[3])]
try:
voxx = self.image.mdh.getEntry('voxelsize.x')
except:
voxx = 1
Dx = hx - lx
Dy = hy - ly
l = np.sqrt((Dx**2 + Dy**2))
dx = Dx / l
dy = Dy / l
if Dx == 0 and Dy == 0: #special case - profile is orthogonal to current plane
d_x = w
d_y = w
else:
d_x = w * abs(dy)
d_y = w * abs(dx)
#print lx, hx, ly, hy
#plt.figure()
plots = []
t = np.arange(np.ceil(l))
for chanNum in range(self.image.data.shape[3]):
x_0 = min(lx, hx)
y_0 = min(ly, hy)
d__x = abs(d_x) + 1
d__y = abs(d_y) + 1
print((dx, dy, d__x, d__y, w))
if (self.do.slice == self.do.SLICE_XY):
ims = self.image.data[(min(lx, hx) - d__x):(max(lx, hx) +
d__x + 1),
(min(ly, hy) - d__y):(max(ly, hy) +
d__y + 1),
self.do.zp, chanNum].squeeze()
splf = ndimage.spline_filter(ims)
p = np.zeros(len(t))
x_c = t * dx + lx - x_0
y_c = t * dy + ly - y_0
print((splf.shape))
for i in range(-w, w + 1):
#print np.vstack([x_c + d__x +i*dy, y_c + d__y + i*dx])
p += ndimage.map_coordinates(
splf,
np.vstack([x_c + d__x + i * dy, y_c + d__y - i * dx]),
prefilter=False)
p = p / (2 * w + 1)
plots.append(p.reshape(-1, 1, 1))
#plt.legend(names)
im = ImageStack(plots, titleStub='New Profile')
im.xvals = t * voxx
if not voxx == 1:
im.xlabel = 'Distance [um]'
else:
im.xlabel = 'Distance [pixels]'
im.ylabel = 'Intensity'
im.defaultExt = '.txt'
im.mdh['voxelsize.x'] = voxx
im.mdh['ChannelNames'] = names
im.mdh['Profile.XValues'] = im.xvals
im.mdh['Profile.XLabel'] = im.xlabel
im.mdh['Profile.YLabel'] = im.ylabel
im.mdh['Profile.StartX'] = lx
im.mdh['Profile.StartY'] = ly
im.mdh['Profile.EndX'] = hx
im.mdh['Profile.EndY'] = hy
im.mdh['Profile.Width'] = 2 * w + 1
im.mdh['OriginalImage'] = self.image.filename
ViewIm3D(im, mode='graph', parent=wx.GetTopLevelParent(self.dsviewer))