def plot_plasma(self):
P.tricontourf(self.rzt[:, 0], self.rzt[:, 1],
self.tris, self.beta, 1001, zorder=0)
cticks = P.linspace(0.0, 0.2, 5)
P.colorbar(ticks=cticks, format='%.2f')
P.jet()
def makeContourPlot(score, scores, average, HEIGHT, WIDTH, outputId, maskId, outputdir, barcodeId=-1, vmaxVal=100):
pylab.bone()
#majorFormatter = FormatStrFormatter('%.f %%')
#ax = pylab.gca()
#ax.xaxis.set_major_formatter(majorFormatter)
pylab.figure()
ax = pylab.gca()
ax.set_xlabel('<--- Width = '+str(WIDTH)+' wells --->')
ax.set_ylabel('<--- Height = '+str(HEIGHT)+' wells --->')
ax.set_yticks([0,HEIGHT/INCREMENT])
ax.set_xticks([0,WIDTH/INCREMENT])
ax.autoscale_view()
pylab.jet()
#pylab.contourf(scores, 40,origin="lower")
if vmaxVal=='auto':
vmaxVal = autoGetVmaxFromAverage(average)
pylab.imshow(scores,vmin=0, vmax=vmaxVal, origin='lower')
pylab.vmin = 0.0
pylab.vmax = 100.0
ticksVal = getTicksForMaxVal(vmaxVal)
pylab.colorbar(format='%.0f %%',ticks=ticksVal)
string_value1 = getFormatForVal(average) % average
if(barcodeId!=-1):
if(barcodeId==0): maskId = "No Barcode Match,"
else: maskId = "Barcode Id %d," % barcodeId
pylab.title(maskId+' Loading Density (Avg ~ '+string_value1+'%)')
pylab.axis('scaled')
pylab.axis([0,WIDTH/INCREMENT-1,0,HEIGHT/INCREMENT-1])
pngFn = outputdir+'/'+outputId+'_density_contour.png'
pylab.savefig(pngFn)
print "Plot saved to", pngFn;
def makeContourPlot(scores, average, HEIGHT, WIDTH, outputId, maskId, plt_title, outputdir, barcodeId=-1, vmaxVal=100):
pylab.bone()
#majorFormatter = FormatStrFormatter('%.f %%')
#ax = pylab.gca()
#ax.xaxis.set_major_formatter(majorFormatter)
pylab.figure()
ax = pylab.gca()
ax.set_xlabel(str(WIDTH) + ' wells')
ax.set_ylabel(str(HEIGHT) + ' wells')
ax.autoscale_view()
pylab.jet()
pylab.imshow(scores,vmin=0, vmax=vmaxVal, origin='lower')
pylab.vmin = 0.0
pylab.vmax = 100.0
ticksVal = getTicksForMaxVal(vmaxVal)
pylab.colorbar(format='%.0f %%',ticks=ticksVal)
print "'%s'" % average
if(barcodeId!=-1):
if(barcodeId==0): maskId = "No Barcode Match,"
else: maskId = "Barcode Id %d," % barcodeId
if plt_title != '': maskId = '%s\n%s' % (plt_title,maskId)
print "Checkpoint A"
pylab.title('%s Loading Density (Avg ~ %0.f%%)' % (maskId, average))
pylab.axis('scaled')
print "Checkpoint B"
pngFn = outputdir+'/'+outputId+'_density_contour.png'
print "Try save to", pngFn;
pylab.savefig(pngFn, bbox_inches='tight')
print "Plot saved to", pngFn;
def main():
"""Show simple use cases for functionality provided by this module."""
from mpl_toolkits.mplot3d.axes3d import Axes3D
import pylab
argv = sys.argv
if len(argv) != 3:
print >> sys.stderr, 'usage: python -m pim.sp.gauss size sigma'
sys.exit(2)
size = int(argv[1])
sigma = float(argv[2])
x, y = numpy.mgrid[-size // 2 + 1:size // 2 + 1,
-size // 2 + 1:size // 2 + 1]
fig = pylab.figure()
fig.suptitle('Some 2-D Gauss Functions')
ax = fig.add_subplot(2, 1, 1, projection='3d')
ax.plot_surface(x,
y,
fspecial_gauss(size, sigma),
rstride=1,
cstride=1,
linewidth=0,
antialiased=False,
cmap=pylab.jet())
ax = fig.add_subplot(2, 1, 2, projection='3d')
ax.plot_surface(x,
y,
gaussian2(size, sigma),
rstride=1,
cstride=1,
linewidth=0,
antialiased=False,
cmap=pylab.jet())
pylab.show()
return 0
def plot(self):
specs = pl.array( list(set([ l['spec'] for l in self.lines ])) )
specs.sort()
self.specs = specs
pl.figure()
pl.hold('on')
pl.grid('on')
pl.jet()
lines = []
lines_spec = list(pl.zeros(len(specs)))
for i in range(0,len(self.lines)):
ispc = pl.find( specs == self.lines[i]['spec'] )
self.colr = pl.cm.get_cmap()( float(ispc)/len(specs) )
wl = self.lines[i]['wave']
ri = float(self.lines[i]['rel_int'])
lines.append( pl.plot( [wl, wl], [0., ri if not isnan(ri) else 0.], '.-', color=self.colr )[0] )
lines_spec[ispc] = lines[-1]
datacursor(lines,formatter='x={x:8.3f}\ny={y:8.3f}'.format)
pl.rc('text',usetex=True)
pl.xlabel('$\lambda ~ [\AA]$')
pl.ylabel('relative intensity [arb]')
pl.title('Spectrum for '+self.spec+' from NIST ASD')
if len(specs) > 1:
pl.legend( lines_spec,specs )
pl.show()
def filter3(url):
im=image_read(url)
pylab.imshow(im)
dnaf = ndimage.gaussian_filter(im, 1)
T = mahotas.thresholding.otsu(dnaf)
labeled,nr_objects = ndimage.label(dnaf > T)
pylab.imshow(labeled)
pylab.jet()
# pylab.save("out_filter3.png")
pylab.show()
def viz2D(self, filename, directory_="./", const_dir="z", logplot=False):
"""Visualize a slice."""
directory = fixdir(directory_)
data = load_fortran_unformatted(directory + filename)
if self.param is None:
self.load_param(directory)
x = numpy.linspace(
self.param.dx / 2.0,
self.param.dx * self.param.mx - self.param.dx / 2.0,
self.param.mx,
)
y = numpy.linspace(
self.param.dy / 2.0,
self.param.dy * self.param.my - self.param.dy / 2.0,
self.param.my,
)
z = numpy.linspace(
self.param.dz / 2.0,
self.param.dz * self.param.mz - self.param.dz / 2.0,
self.param.mz,
)
if const_dir == "x":
n1 = self.param.my
n2 = self.param.mz
x1 = y
x2 = z
x1label = "y"
x2label = "z"
elif const_dir == "y":
n1 = self.param.mx
n2 = self.param.mz
x1 = x
x2 = z
x1label = "x"
x2label = "z"
else:
n1 = self.param.mx
n2 = self.param.my
x1 = x
x2 = y
x1label = "x"
x2label = "y"
data = data.reshape((n2, n1))
pylab.clf()
if logplot:
data = 20 * numpy.log10(numpy.abs(data).clip(1e-30, 1e30))
pylab.jet()
else:
pylab.hot()
pylab.contour(x1, x2, data, 64)
pylab.colorbar()
pylab.axis("image")
pylab.xlabel(x1label + " /um")
pylab.ylabel(x2label + " /um")
pylab.show()
def plot_plasma(self):
P.tricontourf(self.rzt[:, 0],
self.rzt[:, 1],
self.tris,
self.beta,
1001,
zorder=0)
cticks = P.linspace(0.0, 0.2, 5)
P.colorbar(ticks=cticks, format='%.2f')
P.jet()
def plot(self):
"""generate the plot formatting"""
if self.data == None:
print "Must load and parse data first"
sys.exit()
for k,v in self.data.iteritems():
for type, data in v.iteritems():
pylab.clf()
height = int(self.height)
width = int(self.width)
pylab.figure()
ax = pylab.gca()
ax.set_xlabel('<--- Width = %s wells --->' % str(width))
ax.set_ylabel('<--- Height = %s wells --->' % str(height))
ax.set_yticks([0,height/10])
ax.set_xticks([0,width/10])
ax.set_yticklabels([0,height])
ax.set_xticklabels([0,width])
ax.autoscale_view()
pylab.jet()
#color = self.makeColorMap()
#remove zeros for calculation of average
flattened = []
for i in data:
for j in i:
flattened.append(j)
flattened = filter(lambda x: x != 0.0, flattened)
Aver=pylab.average(flattened)
name = type.replace(" ", "_")
fave = ("%.2f") % Aver
pylab.title(k.strip().split(" ")[-1] + " Heat Map (Average = "+fave+"%)")
ticks = None
vmax = None
if type == "Region DR":
ticks = [0.0,0.2,0.4,0.6,0.8,1.0]
vmax = 1.0
else:
ticks = [0.0,0.4,0.8,1.2,1.6,2.0]
vmax = 2.0
pylab.imshow(data, vmin=0, vmax=vmax, origin='lower')
pylab.colorbar(format='%.2f %%',ticks=ticks)
pylab.vmin = 0.0
pylab.vmax = 2.0
#pylab.colorbar()
if self.savePath is None:
save = "%s_heat_map_%s.png" % (name,k)
else:
save = path.join(self.savePath,"%s_heat_map_%s.png" % (name,k))
pylab.savefig(save)
pylab.clf()
def makeRawDataPlot(scores, outputId, outputdir):
# Writes a png file containing only the data, i.e. no axes, labels, gridlines, ticks, etc.
pylab.jet()
fig = pylab.figure()
ax1 = fig.add_subplot(111)
ax1.xaxis.set_ticklabels([None])
ax1.yaxis.set_ticklabels([None])
ax1.xaxis.set_ticks([None])
ax1.yaxis.set_ticks([None])
ax1.imshow(scores,vmin=0, vmax=100, origin='lower')
pylab.savefig(outputdir+'/'+outputId+'_density_raw.png', dpi=20, transparent=True, bbox_inches='tight', pad_inches=0)
print "Plot saved to %s" % outputId+'_density_raw.png'
def graphScatter(X,
Y,
Names=['X', 'Y'],
TestName='',
Legend=[],
Caption='',
LogX=0,
RunningAvg=0,
Lines=None,
Colors=[None]):
if not graph: return
Fig = pylab.figure()
if len(X) == 6: Fmts = Formats
else: Fmts = [
'k>',
'go',
'b^',
'rs',
'y<',
]
if Colors[0]: pylab.jet()
else: Colors = [f[0] for f in Fmts]
# LegendKey = []
if Legend:
for fmt in Fmts:
pylab.plot([0], [0], fmt)
if Lines:
for x1, y1, x2, y2 in Lines:
pylab.plot([x1, x2], [y1, y2], '-')
dot = 0.1 * min(max([max(y) for y in Y]), max([max(x) for x in X]))
for (x, y, color, fmt) in zip(X, Y, Colors, Fmts):
pylab.scatter(x, y, c=color, marker=fmt[1])
# pylab.plot(x, y, fmt)
if RunningAvg:
pylab.plot(runningAverage(x, 10), runningAverage(y, 10), '.y-')
pylab.plot(runningAverage(x, 20), runningAverage(y, 20), '.g-')
#LegendKey.append(pylab.plot(10, 10, Fmt[0]))
Axes = pylab.gca()
if LogX:
for i in [
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 26, 36, 51, 76, 101,
151, 201
]:
pylab.text(math.log(i), -1.2, str(i - 1))
adornGraph(
Title='Scatter: ' + TestName,
Filename='Scatter_' + TestName,
Figure=Fig,
XLabel=Names[0],
YLabel=Names[1],
Legend=Legend,
)
def vector_flow(output_file, i_factor=1):
# DPI resolution of the image to be saved
dpi = 200
file_path_x = "example/vector_field_x_0.csv"
file_path_y = "example/vector_field_y_0.csv"
vector_field_x = np.loadtxt(file_path_x, delimiter=",")
vector_field_y = np.loadtxt(file_path_y, delimiter=",")
x_steps, y_steps = vector_field_x.shape
# Interpolation factor. For 1 no interpolation occurs.
if i_factor > 1:
vector_field_x = scipy.ndimage.zoom(vector_field_x, i_factor)
vector_field_y = scipy.ndimage.zoom(vector_field_y, i_factor)
x_steps *= i_factor
y_steps *= i_factor
# Putting data in the expected format
vectors = np.zeros((x_steps, y_steps, 2), dtype=np.float32)
vectors[...,0] += vector_field_y
vectors[...,1] += vector_field_x
texture = np.random.rand(x_steps,y_steps).astype(np.float32)
kernellen=20
kernel = np.sin(np.arange(kernellen)*np.pi/kernellen)
kernel = kernel.astype(np.float32)
image = lic_internal.line_integral_convolution(vectors, texture, kernel)
mag = np.hypot(vector_field_x, vector_field_y)
plt.jet()
plt.figure()
plt.axis('off')
plt.imshow(texture, interpolation='nearest')
plt.savefig(output_file+"-texture.png",dpi=dpi)
plt.figure()
fig = plt.quiver(vector_field_y, vector_field_x, mag)
plt.colorbar()
plt.savefig(output_file+".png",dpi=dpi)
plt.bone()
fig = plt.imshow(image, interpolation='nearest')
# plt.colorbar()
plt.savefig(output_file+"-flow.png",dpi=dpi)
def showFit(c, x, y):
mins = x.min(axis=0)
maxs = x.max(axis=0)
mx, my = np.meshgrid(np.linspace(mins[0], maxs[0]), np.linspace(mins[1], maxs[1]))
z = c.decision_function(np.c_[mx.ravel(), my.ravel()])
pl.contour(mx, my, z.reshape(mx.shape), [-1, 0, 1])
# plot data
pos = y == 1
neg = y == -1
pl.plot(x[pos,0], x[pos,1], 'r+')
pl.plot(x[neg, 0], x[neg, 1], 'b.')
pl.jet()
def showNeuronCorrelations(self):
l = len(self.neuronDFFs)
corrMat = np.zeros((l,l))
for i in range(l):
for j in range(l):
mx = np.mean(self.neuronDFFs[i])
my = np.mean(self.neuronDFFs[j])
cov = np.sum((self.neuronDFFs[i] - mx)*(self.neuronDFFs[j] - my))
corr = cov/(sqrt(np.sum((self.neuronDFFs[i] - mx)**2))*sqrt(np.sum((self.neuronDFFs[j] - my)**2)))
corrMat[i,j] = corr
plt.imshow(corrMat,interpolation='none')
plt.jet()
plt.colorbar()
plt.show()
def show_confusion_matrix(y_true, y_predicted, title=''):
# compute confusion matrix
cm = confusion_matrix(y_true, y_predicted)
print cm
# configure window
pl.matshow(cm)
pl.title(title)
pl.colorbar()
pl.ylabel('True label')
pl.xlabel('Predicted label')
pl.jet()
# show confusion matrix plot
pl.show()
def viz2D(self, filename, directory_='./', const_dir='z', logplot=False):
"""Visualize a slice."""
directory = fixdir(directory_)
data = load_fortran_unformatted(directory + filename)
if self.param is None:
self.load_param(directory)
x = numpy.linspace(self.param.dx / 2.,
self.param.dx * self.param.mx - self.param.dx / 2.,
self.param.mx)
y = numpy.linspace(self.param.dy / 2.,
self.param.dy * self.param.my - self.param.dy / 2.,
self.param.my)
z = numpy.linspace(self.param.dz / 2.,
self.param.dz * self.param.mz - self.param.dz / 2.,
self.param.mz)
if const_dir == 'x':
n1 = self.param.my
n2 = self.param.mz
x1 = y
x2 = z
x1label = 'y'
x2label = 'z'
elif const_dir == 'y':
n1 = self.param.mx
n2 = self.param.mz
x1 = x
x2 = z
x1label = 'x'
x2label = 'z'
else:
n1 = self.param.mx
n2 = self.param.my
x1 = x
x2 = y
x1label = 'x'
x2label = 'y'
data = data.reshape((n2, n1))
pylab.clf()
if logplot:
data = 20 * numpy.log10(numpy.abs(data).clip(1e-30, 1e30))
pylab.jet()
else:
pylab.hot()
pylab.contour(x1, x2, data, 64)
pylab.colorbar()
pylab.axis('image')
pylab.xlabel(x1label + ' /um')
pylab.ylabel(x2label + ' /um')
pylab.show()
def makeFullBleed(scores, outputId, outputdir):
# Writes a png file containing only the data, i.e. no axes, labels, gridlines, ticks, etc.
pylab.jet()
fig = pylab.figure(figsize=(5,5))
ax1 = fig.add_subplot(111)
ax1.xaxis.set_ticklabels([None])
ax1.yaxis.set_ticklabels([None])
ax1.xaxis.set_ticks([None])
ax1.yaxis.set_ticks([None])
ax1.set_frame_on(False)
ax1.imshow(scores,vmin=0, vmax=100, origin='lower')
for size in (20, 70, 200, 1000):
fig_path = os.path.join(outputdir, '%s_density_%d.png' %
(outputId, size))
fig.savefig(fig_path, figsize=(5,5), dpi=size/3.875, transparent=True,
bbox_inches='tight', pad_inches=0)
print("Full bleed plot saved to %s" % fig_path)
def counter(directory, sub_directory, pic_list, results_directory):
blue_images = dict()
red_images = dict()
for pic in pic_list:
try:
current_image = str(directory) + '\\' + sub_directory + '\\' + str(pic)
sky = mh.imread(current_image)
except IOError:
current_image = str(directory) + '/' + sub_directory + '/' + str(pic)
sky = mh.imread(current_image)
finally:
t = mh.thresholding.otsu(sky.astype('uint8'))
labeled, stars = mh.label(sky > t)
if args.display:
pylab.imshow(sky)
pylab.imshow(labeled)
pylab.jet()
pylab.show()
if args.save:
pylab.imshow(sky)
pylab.imshow(labeled)
pylab.jet()
pylab.savefig("{0}\\{1}_{2}.png".format(results_directory,
str(sub_directory),
str(pic)),
format='png'
)
color = color_is_red(current_image)
if color is True:
red_images[pic] = int(stars)
elif color is False:
blue_images[pic] = int(stars)
else:
pass
pylab.close()
return blue_images, red_images
def plotarr2(mat,title):
#if arr.ndim != 2:
# print('arr can only be 2d')
# return
plt.figure()
plt.imshow(mat,origin='lower',cmap=plt.jet())
plt.title(title)
plt.show()
def viz2D(self, filename, directory_="./", const_dir="z", logplot=False):
"""Visualize a slice."""
directory = fixdir(directory_)
data = load_fortran_unformatted(directory + filename)
if self.param is None:
self.load_param(directory)
x = numpy.linspace(self.param.dx / 2.0, self.param.dx * self.param.mx - self.param.dx / 2.0, self.param.mx)
y = numpy.linspace(self.param.dy / 2.0, self.param.dy * self.param.my - self.param.dy / 2.0, self.param.my)
z = numpy.linspace(self.param.dz / 2.0, self.param.dz * self.param.mz - self.param.dz / 2.0, self.param.mz)
if const_dir == "x":
n1 = self.param.my
n2 = self.param.mz
x1 = y
x2 = z
x1label = "y"
x2label = "z"
elif const_dir == "y":
n1 = self.param.mx
n2 = self.param.mz
x1 = x
x2 = z
x1label = "x"
x2label = "z"
else:
n1 = self.param.mx
n2 = self.param.my
x1 = x
x2 = y
x1label = "x"
x2label = "y"
data = data.reshape((n2, n1))
pylab.clf()
if logplot:
data = 20 * numpy.log10(numpy.abs(data).clip(1e-30, 1e30))
pylab.jet()
else:
pylab.hot()
pylab.contour(x1, x2, data, 64)
pylab.colorbar()
pylab.axis("image")
pylab.xlabel(x1label + " /um")
pylab.ylabel(x2label + " /um")
pylab.show()
def draw_workspace_graph(obs_map, goal, connect_8=False, road_rules=True):
"""Draws the individual policies and cost-to-go field for an
environment
obs_map - description of environment. Matrix with 0 indicating free
cell, 1 indicating an obstacle
goal - [[x1, y1], [x2, y2], ...] joint goal configuration
"""
graph = workspace_graph.Workspace_Graph(obs_map,
goal,
connect_8=connect_8,
road_rules=road_rules)
cost_map = [[graph.get_cost((i, j)) for j in range(len(obs_map[0]))]
for i in range(len(obs_map))]
temp = []
for i in cost_map:
temp.extend(filter(lambda x: x < workspace_graph.MAX_COST, i))
max_val = max(temp) * 1.05
for i in cost_map:
for j in xrange(len(i)):
i[j] = min(i[j], max_val)
pylab.matshow(matrix(cost_map).T)
pylab.hold(True)
X = [[0 for i in range(len(obs_map[0]))] for j in range(len(obs_map))]
Y = [[0 for i in range(len(obs_map[0]))] for j in range(len(obs_map))]
for i in range(len(obs_map)):
for j in range(len(obs_map[0])):
if cost_map[i][j] < max_val:
pos = graph.get_step((i, j))
if pos is None:
continue
X[j][i] = (pos[1] - j)
Y[j][i] = (pos[0] - i)
pylab.quiver(Y, X)
sizex = len(obs_map)
sizey = len(obs_map[0])
pylab.xlim([-.5, sizex - .5])
pylab.ylim([-.5, sizey - .5])
pylab.xticks([])
pylab.yticks([])
pylab.jet()
pylab.hold(False)
pylab.show()
def main():
"""Show simple use cases for functionality provided by this module."""
from mpl_toolkits.mplot3d.axes3d import Axes3D
import pylab
argv = sys.argv
if len(argv) != 3:
print >>sys.stderr, 'usage: python -m pim.sp.gauss size sigma'
sys.exit(2)
size = int(argv[1])
sigma = float(argv[2])
x, y = numpy.mgrid[-size//2 + 1:size//2 + 1, -size//2 + 1:size//2 + 1]
fig = pylab.figure()
fig.suptitle('Some 2-D Gauss Functions')
ax = fig.add_subplot(2, 1, 1, projection='3d')
ax.plot_surface(x, y, fspecial_gauss(size, sigma), rstride=1, cstride=1,
linewidth=0, antialiased=False, cmap=pylab.jet())
ax = fig.add_subplot(2, 1, 2, projection='3d')
ax.plot_surface(x, y, gaussian2(size, sigma), rstride=1, cstride=1,
linewidth=0, antialiased=False, cmap=pylab.jet())
pylab.show()
return 0
def _plot(self):
## pylab.clf()
## ## Added garbage collection since matplotlib objects seem to hang
## ## around and accumulate.
## import gc
## gc.collect()
mesh = self.vars[0].getMesh()
shape = mesh.getShape()
X, Y = mesh.getCellCenters()
Z = self.vars[0].getValue()
X, Y, Z = [v.reshape(shape, order="FORTRAN") for v in (X, Y, Z)]
zmin, zmax = self._autoscale(vars=self.vars,
datamin=self._getLimit(('datamin', 'zmin')),
datamax=self._getLimit(('datamax', 'zmax')))
numberOfContours = 10
smallNumber = 1e-7
diff = zmax - zmin
if diff < smallNumber:
V = numerix.arange(numberOfContours + 1) * smallNumber / numberOfContours + zmin
else:
V = numerix.arange(numberOfContours + 1) * diff / numberOfContours + zmin
import pylab
pylab.jet()
pylab.contourf(X, Y, Z, V)
pylab.xlim(xmin=self._getLimit('xmin'),
xmax=self._getLimit('xmax'))
pylab.ylim(ymin=self._getLimit('ymin'),
ymax=self._getLimit('ymax'))
def main():
arps_mo = ARPSModelObsFile("/caps1/tsupinie/3km-fixed-radar/KCYSan014400", (2, 12))
python_mo = cPickle.load(open("3km-fixed-radar/eomean.pkl014400", 'r'))
grid = goshen_3km_grid()#bounds=(slice(242, 327), slice(199, 284)))
radar_x, radar_y = grid(arps_mo._radar_lon, arps_mo._radar_lat)
print radar_x, arps_mo._radar_x
print radar_y, arps_mo._radar_y
xs, ys = grid.getXY()
bounds = grid.getBounds()
Re = 6371000.
range = np.hypot(xs - radar_x, ys - radar_y)
slant_range = Re * np.tan(range / Re)
range_mask = (range < arps_mo._range_max) & (range > arps_mo._range_min)
height_error = arps_mo._height[0][bounds] - coneHeight(range, arps_mo._elev_angles[0] + 0.06, 1867.)
height_error_masked = np.where(range < arps_mo._range_max - 12000, height_error, np.nan)
print np.nanmin(height_error_masked), np.nanmax(height_error_masked)
pylab.figure(figsize=(12,6))
pylab.subplot(121)
pylab.pcolormesh(xs, ys, arps_mo['Z'][0][bounds], vmin=10, vmax=80, cmap=pylab.jet())
# pylab.pcolormesh(xs, ys, height_error_masked, vmin=-200, vmax=200, cmap=matplotlib.cm.get_cmap('RdBu'))
pylab.colorbar()
pylab.title("ARPS")
grid.drawPolitical()
pylab.subplot(122)
pylab.pcolormesh(xs, ys, python_mo['Z'][0, 0][bounds], vmin=10, vmax=80, cmap=matplotlib.cm.get_cmap('jet'))
pylab.title("Python")
grid.drawPolitical()
pylab.savefig("model_obs_comparison.png")
pylab.close()
cPickle.dump(arps_mo._height, open("beam_height.pkl", 'w'), -1)
return
# construct individual nodes
reservoir = ReservoirNode_lyapunov(input_size, 100, lyapunov_skip=100)
readout = Oger.nodes.RidgeRegressionNode()
# build network with MDP framework
flow = mdp.Flow([reservoir, readout])
# Nested dictionary
gridsearch_parameters = {reservoir:{'input_scaling': mdp.numx.arange(0.1, 2.2, .7), 'spectral_radius':mdp.numx.arange(0.1, 2.2, .7)}}
# Instantiate an optimizer
opt = Oger.evaluation.Optimizer(gridsearch_parameters, Oger.utils.nrmse)
# Do the grid search
opt.grid_search(data, flow, cross_validate_function=Oger.evaluation.train_test_only, training_fraction=.9)
# Plot the maximal LLE for each parameter setting
lle_max = mdp.numx.zeros(opt.paramspace_dimensions)
for i in range(opt.paramspace_dimensions[0]):
for j in range(opt.paramspace_dimensions[1]):
lle_max[i, j] = mdp.numx.amax(mdp.numx.mean(mdp.numx.array(opt.probe_data[i, j][reservoir]), 0))
pylab.figure()
pylab.imshow(mdp.numx.flipud(lle_max), cmap=pylab.jet(), interpolation='nearest', aspect="auto", extent=opt.get_extent(opt.parameters))
pylab.ylabel('Spectral Radius')
pylab.xlabel('Input scaling')
pylab.suptitle('Max LLE')
pylab.colorbar()
pylab.show()
}
# Instantiate an optimizer
opt = Oger.evaluation.Optimizer(gridsearch_parameters, Oger.utils.nrmse)
# Do the grid search
opt.grid_search(data,
flow,
cross_validate_function=Oger.evaluation.train_test_only,
training_fraction=.9)
# Plot the maximal LLE for each parameter setting
lle_max = mdp.numx.zeros(opt.paramspace_dimensions)
for i in range(opt.paramspace_dimensions[0]):
for j in range(opt.paramspace_dimensions[1]):
lle_max[i, j] = mdp.numx.amax(
mdp.numx.mean(mdp.numx.array(opt.probe_data[i, j][reservoir]),
0))
pylab.figure()
pylab.imshow(mdp.numx.flipud(lle_max),
cmap=pylab.jet(),
interpolation='nearest',
aspect="auto",
extent=opt.get_extent(opt.parameters))
pylab.ylabel('Spectral Radius')
pylab.xlabel('Input scaling')
pylab.suptitle('Max LLE')
pylab.colorbar()
pylab.show()
def main(path, marked_path=None):
# images multiscale
imgs_mscale = try_pickle_load(path)
n_scales = len(imgs_mscale)
imgs_s0 = imgs_mscale[0] # scale 1
image_shape = (imgs_s0.shape[2], imgs_s0.shape[3])
images_to_show = min(IMAGES_TO_SHOW, len(imgs_s0))
print "Images shape", imgs_s0.shape
print "Number of images to show", images_to_show
print "Number of scales", n_scales
print "Requested image shape will be", image_shape
n_rows = (1 + n_scales) * 2
perturbed_imgs = [
np.empty((images_to_show, imgs.shape[1], imgs.shape[2], imgs.shape[3]))
for imgs in imgs_mscale
]
perturbed_marks = None
if marked_path is not None:
marked_imgs = try_pickle_load(marked_path)
perturbed_marks = np.empty(
(images_to_show, marked_imgs.shape[1], marked_imgs.shape[2]))
for i in xrange(images_to_show):
imgs_to_perturb = [img[i] for img in imgs_mscale]
# if we loaded markings, add marked image to list of imgs to perturb
if perturbed_marks is not None:
imgs_to_perturb.append(marked_imgs[i])
ret_list = perturb_image(imgs_to_perturb, image_shape)
for n_scale in range(n_scales):
perturbed_imgs[n_scale][i] = ret_list[n_scale]
if perturbed_marks is not None:
perturbed_marks[i] = ret_list[n_scales]
for i, imgs in enumerate(imgs_mscale):
for j in xrange(images_to_show):
pylab.subplot(n_rows, images_to_show, i * images_to_show + j + 1)
pylab.axis('off')
pylab.imshow(imgs[j, CHANNEL, :, :])
pylab.gray() # set colormap
for ind, imgs in enumerate(perturbed_imgs):
i = n_scales + ind
for j in xrange(images_to_show):
pylab.subplot(n_rows, images_to_show, i * images_to_show + j + 1)
pylab.axis('off')
pylab.imshow(imgs[j, CHANNEL, :, :])
pylab.gray()
if perturbed_marks is not None:
for j in xrange(images_to_show):
pylab.subplot(n_rows, images_to_show,
(2 * n_scales + 0) * images_to_show + j + 1)
pylab.axis('off')
pylab.imshow(marked_imgs[j, :, :])
pylab.jet()
pylab.subplot(n_rows, images_to_show,
(2 * n_scales + 1) * images_to_show + j + 1)
pylab.axis('off')
pylab.imshow(perturbed_marks[j, :, :])
pylab.jet()
pylab.show()
def schlieren_entry():
"""
console script to apply schlieren routine to xyp files
"""
usage = """ %prog [options] initial.xyp final.xyp
for 'xz' images
%prog [options] timeseries.xyp
for 'tz' images"""
parser = OptionParser(usage=usage,
version = "%prog (igwtools " + __version__ + ")")
parser.add_option("-d", action = "store_true", dest = "display",
help = "displays images for debugging purposes")
parser.add_option("-v", "--verbose",
action = "store_true", dest = "verbose",
help = "be verbose and output settings used")
parser.add_option("-T", "--mintol",
dest="mintol", type="float", default = 10,
help = "Minimum intensity difference between pixels for computation [default: %default]")
parser.add_option("--fast", action="store_true", default=False,
help = "use experimental 'fast' getdelz calculation")
parser.add_option("-t", "--dt", type="float",
help = "Time difference between frames")
parser.add_option("-n", "--ndt", type="int", default = 2,
help = "Take time difference between how many pixels [default : %default]")
parser.add_option("-s", "--sigma", dest="sigma",
type="float", default=0.3,
help = "Distance over which to fill in uncomputed points [default: %default]")
parser.add_option("-M", "--mode", default="dn2t",
help = "Schlieren mode (dz, dzt, dn2, dn2t) [default: %default]")
parser.add_option("-o", "--outputfile",
help = "Name of output file (output saved only if supplied)")
parser.add_option("-f", "--force", action="store_true",
help = "Force overwriting of anyexisting view")
parser.add_option("--nofill", action = "store_true",
help = "do not fill-in values that were not computed by interpolation by Gaussian average")
parser.add_option("--nosmooth", action = "store_true",
help = "do not smooth with uniform average filter")
parser.add_option("--Ls", type="float", default = 24.0,
help = "Distance from back of tank to screen [default: %default]")
parser.add_option("--Lt", type="float", default = 17.5,
help = "Width of tank [default: %default]")
parser.add_option("--Lp", type="float", default = 1.0,
help = "Width of tank walls [default: %default]")
parser.add_option("--Lc", type="float", default = 330.0,
help = "Distance from fron of tank to camera [default: %default]")
# look up defaults from environment
default_database = os.getenv("IGWDB")
default_experiment = os.getenv("IGWEXPT")
#OptionGroup here
parser.add_option("-D", "--database", default= default_database,
help = "Database name [default: %default]")
parser.add_option("-e", "--experiment", default=default_experiment,
help = "Experiment name [default: %default]")
parser.add_option("-L", "--load",
help = "load input from view")
parser.add_option("-S", "--save",
help = "save results as view")
(options, args) = parser.parse_args()
# Infer whether input is xz or tz images based on number of arguments
if len(args) == 1: # timeseries.xyp
options.imagetype = "tz"
elif len(args) == 2: # initial.xyp final.xyp
options.imagetype = "xz"
elif options.load != None:
# load experiment
if options.experiment[0] != '/':
options.experiment = '/' + options.experiment
h5file = tables.openFile(options.database, mode="r")
valid_expt = h5file.__contains__(options.experiment)
h5file.close()
if valid_expt:
expt = tools.Experiment(options.database, options.experiment)
else:
print(options.experiment, "not found in", options.database)
return
field = expt.load_view(options.load)
if field is None:
print("View", options.load, "not found!")
field = schlieren_field(field, options=options)
if options.save != None:
if options.verbose:
print("saving view...")
expt.save_view(field, options.save, force=options.force)
else:
print("use --save option to store result!")
expt.close()
return
else:
parser.error("incorrect number of arguments")
if options.mode not in ['dz', 'dzt', 'dn2', 'dn2t', 'qualitative']:
parser.error("invalid schlieren mode: %s" % options.mode)
import xplot
# read in data from xyp files
if options.verbose:
print('reading in XYP files...')
if options.imagetype == "xz":
reference_image = xplot.readXYplot(args[0], orientation='xz')
image = xplot.readXYplot(args[1], orientation='xz')
options.dxt = image.dx
else: # tz
image = xplot.readXYplot(args[0], orientation='tz')
options.dxt = image.dt
print(image.shape)
options.xmin = image.xmin
options.xmax = image.xmax
options.zmin = image.zmn
options.zmax = image.zmax
options.tmin = image.tmin
options.tmax = image.tmax
if ((options.mode == 'dzt') or (options.mode == 'dn2t')):
if options.imagetype == 'x':
if options.dt == None:
parser.error("mode %s and 'xz' images requires --dt option" % \
options.mode)
else:
options.dt = options.ndt * image.dt
if options.imagetype == "xz":
output = schlieren(reference_image = reference_image,
image = image, options = options)
else:
output = schlieren(image=image, options=options)
# save output
if(options.outputfile != None):
if options.verbose:
print ('saving results in xyp file')
output.save(options.outputfile)
if options.display:
# show results
vmax = 2.5*numpy.std(output)
if options.verbose:
print('plotting result')
print(' vmin = %.3f' % -vmax, 'vmax = %.3f' % vmax)
pylab.figure()
output.plot(interpolation = 'bicubic', vmin=-vmax, vmax=vmax)
pylab.colorbar()
pylab.jet()
pylab.title(options.mode)
pylab.show()
def clickScat(array2d,
array3d,
xScat=None,
xerror3d=None,
yerror3d=None,
array3d2=None,
xerror3d2=None,
yerror3d2=None,
fn=None,
xMap=None,
yMap=None,
modelError=False,
ylimScat=None):
"""
figureHandles=clickScat(array2d, array3d, xScat=None, xerror3d=None, yerror3d=None, array3d2=None, xerror3d2=None, yerror3d2=None, fn=None, xMap=None, yMap=None):
xScat: x-axis variables for Scatter Plot. Has to be the same length as last dimension of array3d.shape[2]
xerror3d: errorbars for x-axis. two sided.
fn:'annual'
"""
import insar
dateaxis = False
if xScat is None:
xScat = np.r_[0:array3d.shape[2]]
elif isinstance(xScat[0], P.matplotlib.dates.datetime.date):
xScat = P.matplotlib.dates.date2num(xScat)
dateaxis = True
def onclick(event):
P.figure(fh.number)
P.clf()
#ax = P.gca()
#inv = ax.transData.inverted()
#A=inv.transform((event.x, event.y))
#A[1]=np.int(np.round((1-A[1])*array2d.shape[1]))
#A[0]=np.int(np.round((A[0])*array2d.shape[0]))
try:
y = np.round(event.xdata)
except:
return
x = np.round(event.ydata)
#ARRAY MAPPING IS first axis y(rows) and second axis is cols (x)
if all(np.isnan(array3d[x, y, :])):
#if there are no points to plot (all nan) then return
return
#Plot second scatter data.
if array3d2 is not None:
if isinstance(array3d2, list):
if yerror3d is None:
w = np.ones(array3d[x, y, :].shape)
else:
w = basic.rescale(1. / yerror3d[x, y, :], [1, 2])
markers = ['*', '+', 's', 'd', 'x', 'v', '<', '>', '^']
m = 0
for arr in array3d2:
print("%d, %d, %d" % (x, y, m))
P.scatter(xScat, arr[x, y, :], marker=markers[m])
idx = ~(np.isnan(arr[x, y, :])
| np.isnan(array3d[x, y, :]))
#c=insar.crosscorrelate(basic.nonan(w[idx]*arr[x, y,idx]),basic.nonan(w[idx]*array3d[x, y,idx]))
slope, intercept, r_value, p_value, std_err = scipy.stats.linregress(
basic.nonan(w[idx] * arr[x, y, idx]),
basic.nonan(w[idx] * array3d[x, y, idx]))
P.annotate(str("r2[%s]: %0.2f" % (markers[m], r_value)),
(0, 0.9 - m * 0.05),
xycoords='axes fraction')
m = m + 1
else:
if xerror3d2 is None:
xerr = None
else:
xerr = xerror3d2[x, y, :]
if yerror3d2 is None:
yerr = None
else:
yerr = yerror3d2[x, y, :]
P.errorbar(xScat,
array3d2[x, y, :],
xerr=xerr,
yerr=yerr,
marker='*',
fmt='o')
#Plot function result as scatter data.
p = None
if fn is not None:
if fn == 'linear_amplitude_annual':
dataMask = ~np.isnan(array3d[x, y, :])
p0 = np.array([1, 0, 0, basic.nonan(array3d[x, y, :]).mean()])
fitfun = lambda p: (p[0] + p[1] * xScat[dataMask] / 365.
) * np.cos(2 * np.pi * xScat[dataMask] /
365. + p[2]) + p[3]
xScat2 = np.linspace(xScat.min(), xScat.max())
fitfun2 = lambda p: (p[0] + p[1] * xScat2 / 365.) * np.cos(
2 * np.pi * xScat2 / 365. + p[2]) + p[3]
#errfun=lambda p: sum(abs(basic.nonan(array3d[x, y,:])-fitfun(p)));
if yerror3d is None:
w = np.ones(array3d[x, y, :].shape)
else:
w = basic.rescale(1. / yerror3d[x, y, :], [1, 2])
errfun = lambda p: basic.nonan(w * array3d[x, y, :]) - w[
dataMask] * fitfun(p)
#p=scipy.optimize.fmin_powell(errfun, p0)
p = scipy.optimize.leastsq(errfun, p0)
p = p[0]
P.scatter(xScat[dataMask], fitfun(p), marker='^')
sortedxy = np.squeeze(np.dstack([xScat2, fitfun2(p)]))
sortedxy = sortedxy[sortedxy[:, 0].argsort(), :]
P.plot(sortedxy[:, 0], sortedxy[:, 1])
slope, intercept, r_value, p_value, std_err = scipy.stats.linregress(
basic.nonan(w * array3d[x, y, :]), w[dataMask] * fitfun(p))
P.annotate(
str("a0:%0.2f\na1:%0.2f\npha:%0.2f\nbias:%0.2f\nr2:%0.2f" %
(p[0], p[1], p[2], p[3], r_value**2.)), (0.8, 0.8),
xycoords='axes fraction')
elif fn == 'quadratic_amplitude_annual':
dataMask = ~np.isnan(array3d[x, y, :])
p0 = np.array(
[1, 0, 0, 0,
basic.nonan(array3d[x, y, :]).mean()])
fitfun = lambda p: (p[0] + p[1] * xScat[dataMask] / 365. + p[
2] * (xScat[dataMask] / 365.)**2.) * np.cos(
2 * np.pi * xScat[dataMask] / 365. + p[3]) + p[4]
xScat2 = np.linspace(xScat.min(), xScat.max())
fitfun2 = lambda p: (p[0] + p[1] * xScat2 / 365. + p[2] * (
xScat2 / 365.)**2.) * np.cos(2 * np.pi * xScat2 / 365. + p[
3]) + p[4]
#errfun=lambda p: sum(abs(basic.nonan(array3d[x, y,:])-fitfun(p)));
if yerror3d is None:
w = np.ones(array3d[x, y, :].shape)
else:
w = basic.rescale(1. / yerror3d[x, y, :], [1, 2])
errfun = lambda p: basic.nonan(w * array3d[x, y, :]) - w[
dataMask] * fitfun(p)
#p=scipy.optimize.fmin_powell(errfun, p0)
p = scipy.optimize.leastsq(errfun, p0)
p = p[0]
P.scatter(xScat[dataMask], fitfun(p), marker='^')
sortedxy = np.squeeze(np.dstack([xScat2, fitfun2(p)]))
sortedxy = sortedxy[sortedxy[:, 0].argsort(), :]
P.plot(sortedxy[:, 0], sortedxy[:, 1])
slope, intercept, r_value, p_value, std_err = scipy.stats.linregress(
basic.nonan(w * array3d[x, y, :]), w[dataMask] * fitfun(p))
P.annotate(str(
"a0:%0.2f\na1:%0.2f\na2:%0.2f\npha:%0.2f\nbias:%0.2f\nr2:%0.2f"
% (p[0], p[1], p[2], p[3], p[4], r_value**2.)), (0.8, 0.8),
xycoords='axes fraction')
elif fn == 'annual':
dataMask = ~np.isnan(array3d[x, y, :])
p0 = np.array([1, 1, basic.nonan(array3d[x, y, :]).mean()])
fitfun = lambda p: p[0] * np.cos(2 * np.pi * xScat[dataMask] /
365. + p[1]) + p[2]
xScat2 = np.linspace(xScat.min(), xScat.max())
fitfun2 = lambda p: p[0] * np.cos(2 * np.pi * xScat2 / 365. +
p[1]) + p[2]
#errfun=lambda p: sum(abs(basic.nonan(array3d[x, y,:])-fitfun(p)));
if yerror3d is None:
w = np.ones(array3d[x, y, :].shape)
else:
w = basic.rescale(1. / yerror3d[x, y, :], [1, 2])
errfun = lambda p: basic.nonan(w * array3d[x, y, :]) - w[
dataMask] * fitfun(p)
#p=scipy.optimize.fmin_powell(errfun, p0)
p = scipy.optimize.leastsq(errfun, p0)
p = p[0]
P.scatter(xScat[dataMask], fitfun(p), marker='^')
sortedxy = np.squeeze(np.dstack([xScat2, fitfun2(p)]))
sortedxy = sortedxy[sortedxy[:, 0].argsort(), :]
P.plot(sortedxy[:, 0], sortedxy[:, 1])
slope, intercept, r_value, p_value, std_err = scipy.stats.linregress(
basic.nonan(w * array3d[x, y, :]), w[dataMask] * fitfun(p))
P.annotate(str("amp:%0.2f\npha:%0.2f\nbias:%0.2f\nr2:%0.2f" %
(p[0], p[1], p[2], r_value**2.)), (0.8, 0.8),
xycoords='axes fraction')
else:
p = None
P.scatter(xScat, fn(xScat), marker='^')
#convert axis to date...
if dateaxis:
try:
P.figure(fh.number).axes[0].xaxis_date(tz=None)
P.figure(fh.number).autofmt_xdate()
except:
pass
#change x y to xMap, yMap
if yMap is not None:
xM = ya * x + yb
else:
xM = x
if xMap is not None:
yM = xa * (y) + xb
else:
yM = y
#x and y are flipped in the try/except block above. So Flip again.
#if p is not None:
# P.title("x,y,[]: " + str(yM) + ", " + str(xM) + ', ' + str(p) )
#else:
P.title("x,y,z,z.std: " + str(yM) + ", " + str(xM) + ', ' +
str(array2d[x, y]) + ', ' +
str(np.std(basic.nonan(array3d[x, y, :]))))
# rotate and align the tick labels so they look better
#P.figure(fh.number).autofmt_xdate()
# use a more precise date string for the x axis locations in the
# toolbar
#P.gca().fmt_xdata = mdates.DateFormatter('%Y-%m-%d')
if xerror3d is None:
xerr = None
else:
xerr = xerror3d[x, y, :]
if yerror3d is None:
yerr = None
else:
yerr = yerror3d[x, y, :]
if modelError:
yerr = yerror3d[x, y, :]
yerr[dataMask] = errfun(p)
P.errorbar(xScat, array3d[x, y, :], xerr=xerr, yerr=yerr, fmt='ro')
if ylimScat is not None:
P.ylim(ylimScat)
##################################
## END OF PLOTTING
##################################
s = array2d[~np.isnan(array2d)].std()
m = array2d[~np.isnan(array2d)].mean()
fig = P.figure()
ax = fig.add_subplot(111)
ax.matshow(array2d, vmin=m - s, vmax=m + s)
#fig=P.figure();ax=fig.add_subplot(111);ax.matshow(basic.wrapToInt(array2d, s), vmin=-s, vmax=s);
if xMap is not None:
ticks = ax.get_xticks()
(xa, xb) = np.polyfit(np.r_[0:len(xMap)], xMap, 1)
ax.set_xticklabels(np.around(xa * ticks + xb, 4))
if yMap is not None:
ticks = ax.get_yticks()
(ya, yb) = np.polyfit(np.r_[len(yMap):0:-1], yMap, 1)
ax.set_yticklabels(np.around(ya * ticks + yb, 4))
#P.colorbar();
cax, kw = P.matplotlib.colorbar.make_axes(ax, orientation='vertical')
P.matplotlib.colorbar.ColorbarBase(cax,
cmap=P.jet(),
norm=P.normalize(vmin=m - s,
vmax=m + s),
orientation='vertical')
fh = P.figure()
#should be accessible in child function?
fig.canvas.mpl_connect('button_press_event', onclick)
return (fig, fh)
import numpy as np
import pylab
import sys
from skimage import io
from skimage import color
from scipy import ndimage
from matplotlib import pyplot
import project_helpers as ph
from sklearn.multiclass import OneVsRestClassifier
from sklearn.svm import SVC
from sklearn import svm
from sklearn.preprocessing import LabelBinarizer
from sklearn.ensemble import RandomForestClassifier
#############
# This tutorial walks through various functions used for the project
# and some of the concepts covered in lecture.
##############
# Flag that indicates whether to show images.
VIEW = False
# Set the path to the data files.
data_path = "crchistophenotypes_2016_04_28/CRCHistoPhenotypes_2016_04_28/"
#############
#Basic image I/O
##############
#Load the ground truth labels
#Detections are stored as [x,y] and labels are positive for detected nuclei centres
img, detections, labels = ph.load_data_set(data_path,"img7")
pylab.imshow(img)
if(VIEW):
pyplot.show()
import numpy as np import pylab import sys from skimage import io from skimage import color from scipy import ndimage from matplotlib import pyplot import project_helpers as ph from sklearn.multiclass import OneVsRestClassifier from sklearn.svm import SVC from sklearn import svm from sklearn.preprocessing import LabelBinarizer from sklearn.ensemble import RandomForestClassifier ############# # This tutorial walks through various functions used for the project # and some of the concepts covered in lecture. ############## # Flag that indicates whether to show images. # When True you will need to close each window after you've looked at the output to continue VIEW = False # Set the path to the data files. data_path = "crchistophenotypes_2016_04_28/CRCHistoPhenotypes_2016_04_28/" ############# #Basic image I/O ############## #Load the ground truth labels #Detections are stored as [x,y] and labels are positive for detected nuclei centres
def disp(self,sampler,interp_type_during_visualization):
level=sampler.level
theta=sampler.theta_current
tw=self.tw
# interval=self.interval
# interval_dense=self.interval_dense
markersize = 5
fontsize=30
cpa_space = tw.ms.L_cpa_space[level]
plt.subplot(231)
sampler.plot_ll()
plt.title('ll',fontsize=fontsize)
sampler.plot_wlp()
sampler.plot_wlp_plus_ll()
if sampler.lp_func:
plt.legend(['ll','wlp','ll+wlp'])
plt.subplot(232)
sampler.plot_ar()
plt.title('accept ratio',fontsize=fontsize)
# print theta
cpa_space.theta2As(theta=theta)
tw.update_pat_from_Avees(level=level)
tw.calc_v(level=level)
tw.v_dense.gpu2cpu()
src = self.src
# dst = self.dst
transformed = self.transformed
# src_dense=self.src_dense
# transformed_dense=self.transformed_dense
# tw.calc_T(src_dense, transformed_dense, mysign=1, level=level,
#
# transformed_dense.gpu2cpu()
tw.calc_T_inv(src, transformed, level=level,
int_quality=+1)
transformed.gpu2cpu()
if interp_type_during_visualization=='gpu_linear':
my_dtype = np.float64
else:
my_dtype = np.float32 # For opencv
img_src = self.signal.src.cpu.reshape(tw.nRows,tw.nCols)
img_src = CpuGpuArray(img_src.astype(my_dtype))
img_wrapped = CpuGpuArray.zeros_like(img_src)
img_dst = self.signal.dst.cpu.reshape(tw.nRows,tw.nCols)
img_dst = CpuGpuArray(img_dst)
if interp_type_during_visualization=='gpu_linear':
tw.remap_fwd(transformed,img_src,img_wrapped)
else:
tw.remap_fwd_opencv(transformed,img_src,img_wrapped,interp_type_during_visualization)
img_wrapped.gpu2cpu()
plt.subplot(233)
plt.imshow(img_src.cpu,interpolation="None")
plt.gray()
cpa_space.plot_cells('r')
tw.config_plt(axis_on_or_off='on')
plt.title(r'$I_{\mathrm{src}}$')
plt.subplot(234)
plt.imshow(img_wrapped.cpu,interpolation="None")
plt.gray()
# cpa_space.plot_cells('w')
tw.config_plt(axis_on_or_off='on')
plt.title(r'$I_{\mathrm{src}}\circ T^{\theta}$')
plt.subplot(235)
plt.imshow(img_dst.cpu,interpolation="None")
plt.gray()
plt.title(r'$I_{\mathrm{dst}}$')
# cpa_space.plot_cells('w')
tw.config_plt(axis_on_or_off='on')
plt.subplot(2,6,11)
self.tw.imshow_vx()
pylab.jet()
tw.config_plt(axis_on_or_off='on')
plt.title(r'$v_x$')
plt.subplot(2,6,12)
self.tw.imshow_vy()
pylab.jet()
tw.config_plt(axis_on_or_off='on')
plt.title(r'$v_y$')
def schlieren_entry():
"""
console script to apply schlieren routine to xyp files
"""
usage = """ %prog [options] initial.xyp final.xyp
for 'xz' images
%prog [options] timeseries.xyp
for 'tz' images"""
parser = OptionParser(usage=usage,
version = "%prog (igwtools " + __version__ + ")")
parser.add_option("-d", action = "store_true", dest = "display",
help = "displays images for debugging purposes")
parser.add_option("-v", "--verbose",
action = "store_true", dest = "verbose",
help = "be verbose and output settings used")
parser.add_option("-T", "--mintol",
dest="mintol", type="float", default = 10,
help = "Minimum intensity difference between pixels for computation [default: %default]")
parser.add_option("--fast", action="store_true", default=False,
help = "use experimental 'fast' getdelz calculation")
parser.add_option("-t", "--dt", type="float",
help = "Time difference between frames")
parser.add_option("-n", "--ndt", type="int", default = 2,
help = "Take time difference between how many pixels [default : %default]")
parser.add_option("-s", "--sigma", dest="sigma",
type="float", default=0.3,
help = "Distance over which to fill in uncomputed points [default: %default]")
parser.add_option("-M", "--mode", default="dn2t",
help = "Schlieren mode (dz, dzt, dn2, dn2t) [default: %default]")
parser.add_option("-o", "--outputfile",
help = "Name of output file (output saved only if supplied)")
parser.add_option("-f", "--force", action="store_true",
help = "Force overwriting of anyexisting view")
parser.add_option("--nofill", action = "store_true",
help = "do not fill-in values that were not computed by interpolation by Gaussian average")
parser.add_option("--nosmooth", action = "store_true",
help = "do not smooth with uniform average filter")
parser.add_option("--Ls", type="float", default = 24.0,
help = "Distance from back of tank to screen [default: %default]")
parser.add_option("--Lt", type="float", default = 17.5,
help = "Width of tank [default: %default]")
parser.add_option("--Lp", type="float", default = 1.0,
help = "Width of tank walls [default: %default]")
parser.add_option("--Lc", type="float", default = 330.0,
help = "Distance from fron of tank to camera [default: %default]")
# look up defaults from environment
default_database = os.getenv("IGWDB")
default_experiment = os.getenv("IGWEXPT")
#OptionGroup here
parser.add_option("-D", "--database", default= default_database,
help = "Database name [default: %default]")
parser.add_option("-e", "--experiment", default=default_experiment,
help = "Experiment name [default: %default]")
parser.add_option("-L", "--load",
help = "load input from view")
parser.add_option("-S", "--save",
help = "save results as view")
(options, args) = parser.parse_args()
# Infer whether input is xz or tz images based on number of arguments
if len(args) == 1: # timeseries.xyp
options.imagetype = "tz"
elif len(args) == 2: # initial.xyp final.xyp
options.imagetype = "xz"
elif options.load != None:
# load experiment
if options.experiment[0] != '/':
options.experiment = '/' + options.experiment
h5file = tables.openFile(options.database, mode="r")
valid_expt = h5file.__contains__(options.experiment)
h5file.close()
if valid_expt:
expt = tools.Experiment(options.database, options.experiment)
else:
print options.experiment, "not found in", options.database
return
field = expt.load_view(options.load)
if field is None:
print "View", options.load, "not found!"
field = schlieren_field(field, options=options)
if options.save != None:
if options.verbose:
print "saving view..."
expt.save_view(field, options.save, force=options.force)
else:
print "use --save option to store result!"
expt.close()
return
else:
parser.error("incorrect number of arguments")
if options.mode not in ['dz', 'dzt', 'dn2', 'dn2t', 'qualitative']:
parser.error("invalid schlieren mode: %s" % options.mode)
import xplot
# read in data from xyp files
if options.verbose:
print 'reading in XYP files...'
if options.imagetype == "xz":
reference_image = xplot.readXYplot(args[0], orientation='xz')
image = xplot.readXYplot(args[1], orientation='xz')
options.dxt = image.dx
else: # tz
image = xplot.readXYplot(args[0], orientation='tz')
options.dxt = image.dt
print image.shape
options.xmin = image.xmin
options.xmax = image.xmax
options.zmin = image.zmn
options.zmax = image.zmax
options.tmin = image.tmin
options.tmax = image.tmax
if ((options.mode == 'dzt') or (options.mode == 'dn2t')):
if options.imagetype == 'x':
if options.dt == None:
parser.error("mode %s and 'xz' images requires --dt option" % \
options.mode)
else:
options.dt = options.ndt * image.dt
if options.imagetype == "xz":
output = schlieren(reference_image = reference_image,
image = image, options = options)
else:
output = schlieren(image=image, options=options)
# save output
if(options.outputfile != None):
if options.verbose:
print ('saving results in xyp file')
output.save(options.outputfile)
if options.display:
# show results
vmax = 2.5*numpy.std(output)
if options.verbose:
print 'plotting result'
print ' vmin = %.3f' % -vmax, 'vmax = %.3f' % vmax
pylab.figure()
output.plot(interpolation = 'bicubic', vmin=-vmax, vmax=vmax)
pylab.colorbar()
pylab.jet()
pylab.title(options.mode)
pylab.show()
SW = np.random.permutation(X.shape[1])
X = X[:, SW] # permute pixels
#D = np.array([np.concatenate((pixel, pixel[i%2:-i%2 or None], pixel[(i+1)%2:(i+1)%2 or None])) for i,pixel in enumerate(X.T)])
D = X.T
for metric in [
'abs_correlation', 'braycurtis', 'canberra', 'correlation', 'cosine',
'minkowski', 'seuclidean'
]:
for n_neighbors in [4, 5, 6]:
pl.figure()
results = isomap(D, n_neighbors, metric=metric)
x, y = results.real[:, 0], results.real[:, 1]
pl.scatter(x, y, c=np.arange(X.shape[1])[SW], cmap=pl.jet())
pl.title("%s n_neighbors %d" % (metric, n_neighbors))
#pl.savefig("%s.n_neighbors.%d.png" % (metric, n_neighbors))
pl.show()
exit()
print "Saving restored frames..."
name = "movie"
if not os.path.exists(name): os.mkdir(name)
for i in range(len(X)):
pl.figure(figsize=(2, 2))
pl.hexbin(x, y, gridsize=50, C=X[i], cmap=pl.gray())
pl.savefig("%s/frame.%04d.png" % (name, i))
pl.close()
print ".",
T = mahotas.thresholding.otsu(dna) pylab.imshow(dna > T) pylab.show() # Results in numpy array of bools -> b/w image # Smooth image using gaussian filter dnaf = ndimage.gaussian_filter(dna, 8) # -- Image and stdev of image T = mahotas.thresholding.otsu(dnaf) pylab.imshow(dnaf > T) pylab.show() # Deal with merged/touching nuclei labeled,nr_objects = ndimage.label(dnaf > T) print nr_objects # prints 18 pylab.imshow(labeled) pylab.jet() # resets to jet from gray-scale pylab.show() ############ STEP TWO -- Segmenting Image/Finding seeds # Smooth image->find regional maxima->use maxima as seeds for watershed # First try: dnaf = ndimage.gaussian_filter(dna, 8) rmax = pymorph.regmax(dnaf) pylab.imshow(pymorph.overlay(dna, rmax)) # Overlay returns a color image with gray level component in first argument, second arg is red pylab.show() # Second try - Increase sigma: dnaf = ndimage.gaussian_filter(dna, 16) rmax = pymorph.regmax(dnaf) pylab.imshow(pymorph.overlay(dna, rmax))
i += 1
ltrs_uly.sort()
if '-v' in sys.argv:
print voca_ham
print voca_uly
if '--norm' in sys.argv:
voca_ham = voca_ham / voca_ham.max()
voca_uly = voca_uly / voca_uly.max()
import pylab
fig_cnt += 1
pylab.figure(fig_cnt)
pylab.jet()
pylab.imshow(voca_ham, interpolation='none')
pylab.yticks(numpy.arange(len(ltrs_ham)), ltrs_ham)
pylab.xlabel(r'Radix Tree Depth')
pylab.ylabel(r'Root letter of Radix Tree')
pylab.title(r'Radix Tree Breadth of HAMLET')
pylab.colorbar()
pylab.savefig('./plots/radix_tree_hamlet.jpg')
pylab.savefig('./plots/radix_tree_hamlet.pdf')
fig_cnt += 1
pylab.figure(fig_cnt)
pylab.jet()
pylab.imshow(voca_uly, interpolation='none')
pylab.yticks(numpy.arange(len(ltrs_uly)), ltrs_uly)
pylab.xlabel(r'Radix Tree Depth')
def update(testdir=None, seed=2):
'''
Update positioner to fiber number mapping from DocDB
Options:
testdir: if not None, write files here instead of
$DESIMODEL/data/footprint/fiberpos*
seed: integer random number seed for randomization within a cartridge
Writes testdir/fiberpos* or $DESIMODEL/data/focalplane/fiberpos*
'''
from desiutil.log import get_logger
log = get_logger()
#- Download input files from DocDB
cassette_file = docdb.download(2721, 2, 'cassette_order.txt')
xls_fp_layout = docdb.download(530, 11, 'DESI-0530-v11 (Focal Plane Layout).xlsx')
platescale_file = docdb.download(329, 15, 'Echo22Platescale.txt')
#- Pick filenames in output directory
if testdir is None:
outdir = os.path.join(datadir(), 'focalplane')
else:
outdir = testdir
if not os.path.isdir(outdir):
raise ValueError("Missing directory {}".format(testdir))
#- copy platescale file
outpsfile = os.path.join(outdir, 'platescale.txt')
shutil.copy(platescale_file, outpsfile)
log.info('Wrote {}'.format(outpsfile))
#- Random but reproducible
np.random.seed(seed)
#- DESI-0530 file name (fn) and sheet name (sn) shortcuts
fn = xls_fp_layout
sn = 'PositionerAndFiducialLocations'
#- Sanity check that columns are still in the same place
rowmin, rowmax = 48, 590
headers = docdb.xls_read_row(fn, sn, rowmin-1, 'B', 'S')
assert headers[0] == 'device_location_id'
assert headers[1] == 'device_type'
assert headers[2] == 'X'
assert headers[3] == 'Y'
assert headers[4] == 'Z'
assert headers[8] == 'cassetteID'
assert headers[15] == 'Q'
assert headers[17] == 'S'
#- Read Excel table with device locations
posloc = Table()
posloc['DEVICE'] = docdb.xls_read_col(fn, sn, 'B', rowmin, rowmax, dtype=int)
posloc['DEVICE_TYPE'] = docdb.xls_read_col(fn, sn, 'C', rowmin, rowmax, dtype=str)
posloc['X'] = docdb.xls_read_col(fn, sn, 'D', rowmin, rowmax, dtype=float)
posloc['Y'] = docdb.xls_read_col(fn, sn, 'E', rowmin, rowmax, dtype=float)
posloc['Z'] = docdb.xls_read_col(fn, sn, 'F', rowmin, rowmax, dtype=float)
posloc['Q'] = docdb.xls_read_col(fn, sn, 'Q', rowmin, rowmax, dtype=float)
posloc['S'] = docdb.xls_read_col(fn, sn, 'S', rowmin, rowmax, dtype=float)
#- Cassette N/A -> -1, and parse string -> float -> int
c = docdb.xls_read_col(fn, sn, 'J', rowmin, rowmax)
not_spectro_fiber = (c == 'N/A')
c[not_spectro_fiber] = '-1'
posloc['CASSETTE'] = np.array(c, dtype=float).astype(int)
#- Sanity check on values
ndevice = len(posloc)
assert ndevice == 543 #- 543 holes have been drilled
assert len(np.unique(posloc['DEVICE'])) == len(posloc['DEVICE'])
assert set(posloc['DEVICE_TYPE']) == set(['POS', 'FIF', 'GIF', 'NON', 'OPT', 'ETC'])
assert 0 < np.min(posloc['X']) and np.max(posloc['X']) < 410
assert 0 <= np.min(posloc['Q']) and np.max(posloc['Q']) < 36.0
assert 0 <= np.min(posloc['S']) and np.max(posloc['S']) < 412.3
assert np.all(posloc['S']**2 > posloc['X']**2 + posloc['Y']**2 + posloc['Z']**2)
assert np.min(posloc['CASSETTE']) == -1
assert np.max(posloc['CASSETTE']) == 11
assert set(posloc['DEVICE_TYPE'][posloc['CASSETTE']==11]) == set(['ETC', 'OPT'])
assert set(posloc['DEVICE_TYPE'][posloc['CASSETTE']==-1]) == set(['FIF', 'GIF', 'NON'])
assert 0 not in posloc['CASSETTE']
#- Read mapping of cassettes on focal plane to fibers on slithead
colnames = ['fibermin', 'fibermax', 'sp0', 'sp1', 'sp2', 'sp3', 'sp4', 'sp5', 'sp6', 'sp7', 'sp8', 'sp9']
cassettes = Table.read(cassette_file, format='ascii', names=colnames)
#- Randomize fibers within a cassette
petals = list()
for p in range(10):
fiberpos = posloc.copy(copy_data=True)
fiberpos['FIBER'] = -1
fiberpos['PETAL'] = p
fiberpos['SLIT'] = p
fiberpos['SPECTRO'] = p
iipos = (fiberpos['DEVICE_TYPE'] == 'POS')
### fiberpos['device'] += p*len(fiberpos)
for c in range(1,11):
ii = (cassettes['sp'+str(p)] == c)
assert np.count_nonzero(ii) == 1
fibermin = p*500 + cassettes['fibermin'][ii][0]
fibermax = p*500 + cassettes['fibermax'][ii][0]
jj = iipos & (fiberpos['CASSETTE'] == c)
assert np.count_nonzero(jj) == 50
fiber = list(range(fibermin, fibermax+1))
np.random.shuffle(fiber)
fiberpos['FIBER'][jj] = fiber
#- Additional columns
fiberpos['SLITBLOCK'] = (fiberpos['FIBER'] % 500) // 25
fiberpos['BLOCKFIBER'] = (fiberpos['FIBER'] % 500) % 25
fiberpos['LOCATION'] = p*1000 + fiberpos['DEVICE']
#- Petal 0 is at the "bottom"; See DESI-0530
phi = np.radians((7*36 + 36*p)%360)
x = np.cos(phi)*fiberpos['X'] - np.sin(phi)*fiberpos['Y']
y = np.sin(phi)*fiberpos['X'] + np.cos(phi)*fiberpos['Y']
fiberpos['X'] = x
fiberpos['Y'] = y
petals.append(fiberpos)
fiberpos = vstack(petals)
fiberpos.sort('FIBER')
POS = (fiberpos['DEVICE_TYPE'] == 'POS')
#- devices that don't go to spectrographs don't have slitblock, blockfiber
fiberpos['SLITBLOCK'][~POS] = -1
fiberpos['BLOCKFIBER'][~POS] = -1
#- More sanity checks before writing output
fp = fiberpos[POS]
assert len(fp) == 5000
assert len(np.unique(fp['FIBER'])) == 5000
assert min(fp['FIBER']) == 0
assert max(fp['FIBER']) == 4999
assert len(set(fp['SPECTRO'])) == 10
assert min(fp['SPECTRO']) == 0
assert max(fp['SPECTRO']) == 9
assert len(np.unique(fiberpos['DEVICE'])) == ndevice
assert len(np.unique(fiberpos['LOCATION'])) == len(fiberpos)
#- Drop some columns we don't need
fiberpos.remove_column('CASSETTE')
#- Update i8 -> i4 for integer columns
for colname in ['FIBER', 'DEVICE', 'SPECTRO', 'PETAL', 'SLIT']:
fiberpos.replace_column(colname, fiberpos[colname].astype('i4'))
#- Reorder columns
assert set(fiberpos.colnames) == set('DEVICE DEVICE_TYPE X Y Z Q S FIBER PETAL SLIT SPECTRO SLITBLOCK BLOCKFIBER LOCATION'.split())
colnames = 'PETAL DEVICE DEVICE_TYPE LOCATION FIBER X Y Z Q S SPECTRO SLIT SLITBLOCK BLOCKFIBER'.split()
fiberpos = fiberpos[colnames]
assert fiberpos.colnames == colnames
#- Set units and descriptions; see DESI-2724
fiberpos['X'].unit = 'mm'
fiberpos['Y'].unit = 'mm'
fiberpos['Z'].unit = 'mm'
fiberpos['Q'].unit = 'deg'
fiberpos['S'].unit = 'mm'
fiberpos['X'].description = 'focal surface location [mm]'
fiberpos['Y'].description = 'focal surface location [mm]'
fiberpos['Z'].description = 'focal surface location [mm]'
fiberpos['Q'].description = 'azimuthal angle on focal surface [deg]'
fiberpos['S'].description = 'radial distance along focal surface [mm]'
fiberpos['FIBER'].description = 'fiber number [0-4999]'
fiberpos['DEVICE'].description = 'focal plane device_loc number [0-542]'
fiberpos['SPECTRO'].description = 'spectrograph number [0-9]'
fiberpos['PETAL'].description = 'focal plane petal_loc number [0-9]'
fiberpos['SLIT'].description = 'spectrograph slit number [0-9]'
fiberpos['SLITBLOCK'].description = 'id of the slitblock on the slit [0-19]'
fiberpos['BLOCKFIBER'].description = 'id of the fiber on the slitblock [0-24]'
fiberpos['LOCATION'].description = 'global location id across entire focal plane [0-9543]; has gaps in sequence'
fiberpos.meta['comments'] = [
"Coordinates at zenith: +x = East = +RA; +y = South = -dec",
"PETAL and DEVICE refer to locations, not hardware serial numbers",
"Differences from DESI-2724 naming:",
' - Drops "_ID" from column names',
' - Drops "_LOC" from "DEVICE_LOC" and "PETAL_LOC"',
" - SLITBLOCK as int [0-19] instead of string [B0-B19]",
" - BLOCKFIBER as int [0-24] instead of string [F0-F24]",
"Convenience columns:",
" - FIBER = PETAL*500 + SLITBLOCK*25 + BLOCKFIBER",
" - LOCATION = PETAL*1000 + DEVICE",
]
ecsvout = os.path.join(outdir, 'fiberpos.ecsv')
textout = os.path.join(outdir, 'fiberpos.txt')
fitsout = os.path.join(outdir, 'fiberpos.fits')
pngout = os.path.join(outdir, 'fiberpos.png')
#- Write old text format with just fiber, device, spectro, x, y, z
write_text_fiberpos(textout, fiberpos[POS])
log.info('Wrote {}'.format(textout))
#- Write all columns but only for positioners with fibers
fiberpos[POS].write(ecsvout, format='ascii.ecsv')
log.info('Wrote {}'.format(ecsvout))
fiberpos[POS].write(fitsout, format='fits', overwrite=True)
log.info('Wrote {}'.format(fitsout))
#- Write all columns and all rows, including
#- fiducials (device_type='FIF') and sky monitor (device_type='ETC')
fiberpos.sort('LOCATION')
fitsallout = fitsout.replace('.fits', '-all.fits')
ecsvallout = textout.replace('.txt', '-all.ecsv')
fiberpos.write(fitsallout, format='fits', overwrite=True)
fiberpos.write(ecsvallout, format='ascii.ecsv')
log.info('Wrote {}'.format(fitsallout))
log.info('Wrote {}'.format(ecsvallout))
#- Visualize mapping
POS = (fiberpos['DEVICE_TYPE'] == 'POS')
FIF = (fiberpos['DEVICE_TYPE'] == 'FIF')
ETC = (fiberpos['DEVICE_TYPE'] == 'ETC')
import pylab as P
P.jet() #- With apologies to viridis
P.figure(figsize=(7,7))
P.scatter(fiberpos['X'][POS], fiberpos['Y'][POS], c=fiberpos['FIBER'][POS]%500, edgecolor='none', s=20)
# P.scatter(fiberpos['x'][FIF], fiberpos['y'][FIF], s=5, color='k')
# P.plot(fiberpos['x'][ETC], fiberpos['y'][ETC], 'kx', ms=3)
P.grid(alpha=0.2, color='k')
P.xlim(-420,420)
P.ylim(-420,420)
P.xlabel('x [mm]')
P.ylabel('y [mm]')
P.title('Focal plane color coded by fiber location on slithead')
P.savefig(pngout, dpi=80)
log.info('Wrote {}'.format(pngout))
def plot_results(self,
node_param_list=None,
vmin=None,
vmax=None,
cmap=None,
log_x=False,
axes=None,
title=None,
plot_variance=True):
''' Plot the results of the optimization.
Works for 1D and 2D linear sweeps, yielding a 2D resp. 3D plot of the parameter(s) vs. the error.
Arguments:
- node_param_list: a list of (node, param_string) tuples. Before plotting, the mean will be taken over all these node.param_string combinations, which is useful to plot/reduce multi-dimensional parameter sweeps.
- vmin/vmax: can be used to truncate the errors between lower and upper bounds before plotting.
- cmap: passed as a matplotlib colormap when plotting 2D images.
- log_x: boolean to indicate if a 1D plot should use a log scale for the x-axis.
- axes: optional Axes object to use for plotting
- title: optional title for the plot
- plot_variance: should variance be plotted in case of taking the mean over certain parameters. Default True.
'''
try:
import pylab
except ImportError:
print "It looks like matplotlib isn't installed. Plotting is impossible."
return
if axes is None:
axes = pylab.axes()
errors_to_plot, var_errors, parameters = self.mean_and_var(
node_param_list)
if vmin != None:
errors_to_plot[errors_to_plot < vmin] = vmin
if vmax != None:
errors_to_plot[errors_to_plot > vmax] = vmax
# If we have ranged over only one parameter
if len(parameters) == 1:
# Get the index of the remaining parameter to plot using the correct
# parameter ranges
param_index = self.parameters.index(parameters[0])
if var_errors is not None and plot_variance:
pylab.errorbar(self.parameter_ranges[param_index],
errors_to_plot,
var_errors,
axes=axes)
else:
if log_x:
pylab.semilogx(self.parameter_ranges[param_index],
errors_to_plot,
axes=axes)
else:
pylab.plot(self.parameter_ranges[param_index],
errors_to_plot,
axes=axes)
pylab.xlabel(str(parameters[0][0]) + '.' + parameters[0][1])
pylab.ylabel(self.loss_function.__name__)
if title is not None:
pylab.title(title)
pylab.show()
elif len(parameters) == 2:
# Get the extreme values of the parameter values
p1 = self.parameters.index(parameters[0])
p2 = self.parameters.index(parameters[1])
xm = mdp.numx.amin(self.parameter_ranges[p1])
ym = mdp.numx.amin(self.parameter_ranges[p2])
xM = mdp.numx.amax(self.parameter_ranges[p1])
yM = mdp.numx.amax(self.parameter_ranges[p2])
# For optimization algorithms which have non-uniform sampling of the parameter space, we interpolate here
# This has no effect on the plot for optimizations using gridsearch
xi = mdp.numx.linspace(xm, xM, len(self.parameter_ranges[p1]))
yi = mdp.numx.linspace(ym, yM, len(self.parameter_ranges[p2]))
(x, y) = mdp.numx.meshgrid(self.parameter_ranges[p1],
self.parameter_ranges[p2])
# Create an interpolation grid
zi = mdp.numx.fliplr(
pylab.griddata(x.flatten(), y.flatten(),
errors_to_plot.flatten('F'), xi, yi)).T
pylab.imshow(zi,
cmap=pylab.jet(),
interpolation='nearest',
extent=self.get_extent(parameters),
aspect="auto",
axes=axes)
pylab.xlabel(str(parameters[1][0]) + '.' + parameters[1][1])
pylab.ylabel(str(parameters[0][0]) + '.' + parameters[0][1])
if title is not None:
pylab.suptitle(title)
pylab.colorbar()
if var_errors is not None and plot_variance:
pylab.figure()
pylab.imshow(mdp.numx.flipud(var_errors),
cmap=cmap,
interpolation='nearest',
extent=self.get_extent(parameters),
aspect="auto",
vmin=vmin,
vmax=vmax)
pylab.xlabel(str(parameters[1][0]) + '.' + parameters[1][1])
pylab.ylabel(str(parameters[0][0]) + '.' + parameters[0][1])
pylab.suptitle('variance')
pylab.colorbar()
pylab.show()
else:
raise Exception("Too many parameter dimensions to plot: " +
str(errors_to_plot.ndim))
pylab.imshow(dna > T)
pylab.show()
# apply a gaussian filter that smoothen the image
dnaf = mh.gaussian_filter(dna, 8)
dnat = dnaf > T
pylab.gray()
nuclei1 = dnat
pylab.imshow(dnat)
pylab.show()
#labelling thereshold image
labeled, nr_objects = mh.label(dnat)
print nr_objects # output number of objects
pylab.imshow(labeled)
pylab.jet() # makes image colourful
pylab.show()
dnaf = mh.gaussian_filter(dnaf, 8)
rmax = mh.regmax(dnaf)
pylab.imshow(mh.overlay(
dna, rmax)) # print dna and rmax (with second channel in red)
pylab.show() # seeds only show when image is zoomed in
dnaf = mh.gaussian_filter(dnaf,
16) # apply different filter to yield better result
rmax = mh.regmax(dnaf)
pylab.imshow(mh.overlay(dna, rmax))
pylab.show()
seeds, nr_nuclei = mh.label(rmax) # nuclei count
# component = sta_small_visual_lin[:,:,b] #STA[:,:,b] # pl.figure() # im = pl.pcolormesh( component,vmin = 0,vmax = 255, cmap=cm.jet ) # #pl.contour(component) # pl.colorbar(im) # ax = pl.axes() # ax.set_yticklabels([]) # ax.set_xticklabels([]) # #ax.annotate(str(a+1), (.1, 1.2), bbox=dict(boxstyle="round, pad=0.3", fc="w"), size=52 ) # pl.savefig(finalfolder_lin+"/Small_STA-"+str(neurontag)+"-"+str(b)+"-g_.png",format='png', bbox_inches='tight') # del component print 'Saving mean image in lineal scale...' pl.figure() im = pl.pcolormesh(MEANSTA_lin,vmin = 0,vmax = 255, cmap=cm.jet) pl.jet() pl.colorbar(im) ax = pl.axes() ax.set_yticklabels([]) ax.set_xticklabels([]) #ax.annotate(str(a+1), (.1, 1.2), bbox=dict(boxstyle="round, pad=0.3", fc="w"), size=52 ) pl.savefig(finalfolder_lin+"/MEANSTA-g_"+str(neurontag)+".png",format='png', bbox_inches='tight') # del ax print 'CELL ' + timestampName + ' FINISHED!!!' print '-----------------------END---------------------------' del STA_desp del STA del stavisual_lin del spikeframe_matrix
def main(infile):
img = mahotas.imread(infile)
infile = os.path.splitext(
os.path.basename(infile))[0]
blue_component = img[:,:,B]
pylab.gray()
k = 3
f = ndimage.gaussian_filter(blue_component, 12)
if DEBUG:
print 'Procesando imagen %s usando canal azul' % (infile)
mahotas.imsave('00%s-input.jpg' % infile, f)
clustered = segment_kmeans(f, k)
clustered[clustered == k-1] = 0
mask = ndimage.binary_fill_holes(clustered)
if DEBUG:
print 'Segmentacion inicial k-means con k=%d' % k
mahotas.imsave('01kmeans1%s.jpg' % infile, mask)
masked = f * mask
if DEBUG:
mahotas.imsave('02masked%s.jpg' % infile, masked)
k = 4
clustered2 = segment_kmeans(masked, k)
if DEBUG:
print 'Resegmentacion k-means con k=%d' % k
mahotas.imsave('03kmeans2%s.jpg' % infile, clustered2)
clustered2[(clustered2 != k-2)] = 0
clustered2[(clustered2 == k-2)] = 1
if DEBUG:
mahotas.imsave('04kmeans2binary%s.jpg' % infile, clustered2)
clustered2 = ndimage.binary_fill_holes(clustered2)
labeled, _ = mahotas.label(mask)
if DEBUG:
print 'Etiquetando imagen segmentacion inicial k-means'
mahotas.imsave('05kmeans2noholes%s.jpg' % infile, clustered2)
mahotas.imsave('06kmeans2labeled%s.jpg' % infile, labeled)
while True:
min_max = raw_input('label1 min,max? ')
try:
min_max = min_max.strip().split(',')
min_ = int(min_max[0])
max_ = int(min_max[1])
except:
break
labeled1 = remove_by_size(labeled, min_, max_)
mahotas.imsave('07labeled1f%d,%d%s.jpg' % (min_, max_, infile), labeled1)
labeled, _ = mahotas.label(clustered2)
labeled2 = remove_by_size(labeled, 1600, 23000)
if DEBUG:
print 'Etiquetando imagen re-segmentacion k-means'
mahotas.imsave('08labeled2f%s.jpg' % infile, labeled)
mahotas.imsave('09labeled2f%s.jpg' % infile, labeled2)
combined = labeled1 + labeled2
labeled_to_binary(combined)
if DEBUG:
mahotas.imsave('10combined%s.jpg' % infile, combined)
combined = ndimage.binary_fill_holes(combined)
if DEBUG:
mahotas.imsave('11combined_noholes%s.jpg' % infile, combined)
borders = mahotas.labeled.borders(mahotas.label(combined)[0])
cells = f * combined
cells[cells == 0] = 255
if DEBUG:
mahotas.imsave('12maskedcellsw%s.jpg' % infile, cells)
rmin = mahotas.regmin(cells)
seeds, nr_nuclei = mahotas.label(rmin)
if DEBUG:
mahotas.imsave(
'13gscale-final%s.jpg' % infile,
pymorph.overlay(blue_component, rmin,
borders)
)
img2 = np.copy(img)
img2[borders] = [0,0,0]
img2[rmin] = [5,250,42]
mahotas.imsave('14%s-outputcells.jpg' % (infile), img2)
#watershed
gradient = ndimage.morphology.morphological_gradient(combined, size=(3,3))
gradient = gradient.astype(np.uint8)
if DEBUG:
print 'Watershed'
mahotas.imsave('15%s-gradient.jpg' % infile, gradient)
wshed, lines = mahotas.cwatershed(gradient, seeds, return_lines=True)
pylab.jet()
if DEBUG:
mahotas.imsave('16wshed.jpg', wshed)
ncells = len(np.unique(wshed)) - 1
print '%d cells.' % ncells
borders = mahotas.labeled.borders(wshed)
img[borders] = [0,0,0]
img[rmin] = [5,250,42]
mahotas.imsave('17%s-output-%dcells.jpg' % (infile, ncells), img)
def calculaSTA(args):
start, finish = args
if finish > endUnit:
finish = endUnit
for kunit in range(start,finish):
timestampName = per_row[kunit]
if characterization[kunit] > 0:
print 'Analysing Unit ',timestampName #, ' loop :', c ,' unit n ', c + startUnit
#--------------------------------------------------------
# get spike time stamps from file
#--------------------------------------------------------
neurontag = timestampName # tag or number of cell
rastercelulatxtfile = timefolder + timestampName +'.txt'
timestamps = npy.loadtxt(rastercelulatxtfile) # text file containing time spikes in datapoints
neuronresultfolder_lin = str(neurontag)+'_lineal'
try:
os.mkdir( outputFolder+neuronresultfolder_lin ) # create the folder
except OSError:
pass
finalfolder_lin = outputFolder+neuronresultfolder_lin
#print 'size time stamps vector: ', len(timestamps) #, 'x',len(timestamps[0])
#--------------------------------------------------------
# get time spikes depending of the stimulus start (frame do not start in time=0)
#--------------------------------------------------------
#--------------------------------------------------------
# Conversion of spike times from seconds to POINTS:
#--------------------------------------------------------
vector_spikes = timestamps[:]*samplingRate # without first id zero column (1 COLUMMN)
#vector_spikes = timestamps[:] # without first id zero column (1 COLUMMN)
stimei = [] # initialize time spike index depending of image time
spikeframe_matrix = npy.zeros( (len(vector_spikes), 4) ) # [spike time, frame id, ini time frame, end time frame]
#--------------------------------------------------------
# convert stimes (SPIKE TIMES) to frame indexes (image index):
#--------------------------------------------------------
primer_frame = 0
frame_ant = 0
#print 'Get the spike triggered stimuli indices: \n'
contator = 0
contator2 = 0
totalcont = len(vector_spikes) * len(range(primer_frame, lenSyncFile))
for punto_spike in vector_spikes:
# WTF is this?
condicion = 1
for i in range(primer_frame, lenSyncFile):
if (vector_inicio_frame[i] < punto_spike) & (punto_spike <= vector_fin_frame[i]):
# if the spike time is into a frame time points (start and ends)
spikeframe_matrix[contator,0] = punto_spike
spikeframe_matrix[contator,1] = vector_fin_frame[i]
spikeframe_matrix[contator,2] = inicio_fin_frame[i,0]
spikeframe_matrix[contator,3] = inicio_fin_frame[i,1]
stimei.append(i)
frame_ant = i
break
contator += 1
# WTF is this? Comentario idiota
sys.stdout.write("\r%d%%" %contator2)
sys.stdout.flush()
contator2 = contator * 100 // ( 1.0 * len(vector_spikes) )
primer_frame = frame_ant
#print '\n'
# WTF?
limite3 = len(stimei)
print "Nro de frames: ", limite3
#print 'length frames times vector', lenSyncFile
#print "length time stamps vector: ", len(timestamps)
#print "length spike triggered stimuli time i vector: ", len(stimei)
#--------------------------------------------------------
# STA Algorithm
#--------------------------------------------------------
#------------------- ALGORITHM TYPE 1----------------------
if(tipoalgoritmo == 1):
sta_1()
#------------------- ALGORITHM TYPE 2----------------------
if(tipoalgoritmo == 2): # sequentially algorithm
sta_2()
dosmall = 0
#------------------- ALGORITHM TYPE 3----------------------
if(tipoalgoritmo == 3): # LOAD CHUNKS OF FRAMES AND CALCULATES THE STA SEQUENTIALLY
sta_3()
#===============================================================================
#------------------- ALGORITHM TYPE 4----------------------
if(tipoalgoritmo == 4): # LOAD entire matrix stimuli AND CALCULATES THE STA SEQUENTIALLY
STA , stavisual_lin , MEANSTA_lin, STA_desp, acumula = sta_4(stimei)
#----------------------------------------------------
# save spike time stamp and frame index
#----------------------------------------------------
spikeframe_matrix_array = npy.array(spikeframe_matrix)
spikeframe_filename = "spikeframe_matrix"+str(neurontag)
#print "Save spike frame matrix as mat file: ",spikeframe_filename
scipy.io.savemat(finalfolder_lin+'/'+spikeframe_filename+'.mat',mdict={'spikeframe_matrix':spikeframe_matrix_array},oned_as='column')
#----------------------------------------------------
# save true STA matrix (NON SCALED for visual plot)
#----------------------------------------------------
STA_array = npy.array(STA)
cadena_texto = "sta_array_"+str(neurontag)
#print "Saving NON rescaled STA as mat file: ",cadena_texto
scipy.io.savemat(finalfolder_lin+'/'+cadena_texto+'.mat',mdict={'STA_array':STA_array},oned_as='column')
#----------------------------------------------------
# save visual STA matrix ( RE SCALED for visual plot)
#----------------------------------------------------
stavisual_lin_array = npy.array(stavisual_lin)
cadena_texto = "stavisual_lin_array_"+str(neurontag)
#print "Saving visual STA (lineal) as mat file: ",cadena_texto
scipy.io.savemat(finalfolder_lin+'/'+cadena_texto+'.mat',mdict={'STAarray_lin':stavisual_lin_array},oned_as='column')
#print 'Saving images in lineal scale...'
plt.clf()
fig = plt.figure(1, figsize=(12,10))
ax = fig.add_subplot(3,6,1)
component = stavisual_lin[:,:,0]
ax.pcolormesh( component,vmin = 0,vmax = 255, cmap=cm.jet )
ax.set_yticklabels([])
ax.set_xticklabels([])
ax.set_aspect(1)
kcontador = 2
#casep, cambio de 17 a framesNumber-1 para prevenir "out of bounds" al procesar menos de 18+2 frames
for ksubplot in range(framesNumber-1):
ax = fig.add_subplot(3,6,kcontador)
component = stavisual_lin[:,:,kcontador-1]
ax.pcolormesh( component,vmin = 0,vmax = 255, cmap=cm.jet )
ax.set_aspect(1)
ax.set_yticklabels([])
ax.set_xticklabels([])
kcontador+=1
plt.savefig(finalfolder_lin+"/STA-"+str(neurontag)+"_.png",format='png', bbox_inches='tight')
plt.savefig(outputFolder+"STA-"+str(neurontag)+"_.png",format='png', bbox_inches='tight')
plt.show()
plt.clf()
plt.close()
#------------------------------------------------------
#print 'Saving mean image in lineal scale...'
pl.figure()
im = pl.pcolormesh(MEANSTA_lin,vmin = 0,vmax = 255, cmap=cm.jet)
pl.jet()
pl.colorbar(im)
ax = pl.axes()
ax.set_yticklabels([])
ax.set_xticklabels([])
pl.savefig(finalfolder_lin+"/MEANSTA-g_"+str(neurontag)+".png",format='png', bbox_inches='tight')
pl.close()
print 'CELL ' + timestampName + ' FINISHED!!!'
del STA_desp
del STA
del stavisual_lin
del spikeframe_matrix
del acumula
#print img_bin,stats.mode(img_bin,axis=None)
#print img_bin,np.max(img_bin)
# binary again
#img_bin = filters.maximum_filter(img_bin,7)
#img_bin = filter.threshold_adaptive(img_bin,7)
#img_bin[img_bin>0]=255
Image.fromarray(uint8(img_bin)).save('feature_points.png')
figure(); gray(); # don't use colors
# show the two pics on 1*2 frame
#subplot(1,3,1)
imshow(img_gray)
#subplot(1,3,2)
figure(); gray(); # don't use colors
imshow(img_bin)
figure(); gray(); # don't use colors
imshow(img_bin_words)
#subplot(1,3,3)
#imshow(labeled_array)
#ob = labeled_array[obj_list[100]]
figure(); gray(); # don't use colors
imshow(labeled_array)
# starts the figure GUI and raises the figure windows
jet()
show()
def clickScat(array2d, array3d, xScat=None, xerror3d=None, yerror3d=None, array3d2=None, xerror3d2=None, yerror3d2=None, fn=None, xMap=None, yMap=None,
modelError=False, ylimScat=None):
"""
figureHandles=clickScat(array2d, array3d, xScat=None, xerror3d=None, yerror3d=None, array3d2=None, xerror3d2=None, yerror3d2=None, fn=None, xMap=None, yMap=None):
xScat: x-axis variables for Scatter Plot. Has to be the same length as last dimension of array3d.shape[2]
xerror3d: errorbars for x-axis. two sided.
fn:'annual'
"""
import insar
dateaxis=False;
if xScat is None:
xScat=np.r_[0:array3d.shape[2]];
elif isinstance(xScat[0], P.matplotlib.dates.datetime.date):
xScat=P.matplotlib.dates.date2num(xScat);
dateaxis=True;
def onclick(event):
P.figure(fh.number);
P.clf();
#ax = P.gca()
#inv = ax.transData.inverted()
#A=inv.transform((event.x, event.y))
#A[1]=np.int(np.round((1-A[1])*array2d.shape[1]))
#A[0]=np.int(np.round((A[0])*array2d.shape[0]))
try:
y=np.round(event.xdata);
except:
return
x=np.round(event.ydata);
#ARRAY MAPPING IS first axis y(rows) and second axis is cols (x)
if all(np.isnan(array3d[x, y,:])):
#if there are no points to plot (all nan) then return
return
#Plot second scatter data.
if array3d2 is not None:
if isinstance(array3d2, list):
if yerror3d is None:
w=np.ones(array3d[x, y,:].shape);
else:
w=basic.rescale(1./yerror3d[x,y,:], [1,2])
markers=['*','+','s','d','x','v','<','>','^']
m=0;
for arr in array3d2:
print ("%d, %d, %d" % (x,y,m))
P.scatter(xScat, arr[x, y,:], marker=markers[m]);
idx=~( np.isnan(arr[x, y,:]) | np.isnan(array3d[x, y,:]))
#c=insar.crosscorrelate(basic.nonan(w[idx]*arr[x, y,idx]),basic.nonan(w[idx]*array3d[x, y,idx]))
slope, intercept, r_value, p_value, std_err = scipy.stats.linregress(basic.nonan(w[idx]*arr[x, y,idx]), basic.nonan(w[idx]*array3d[x, y,idx]))
P.annotate(str("r2[%s]: %0.2f" % (markers[m],r_value)), (0,0.9-m*0.05), xycoords='axes fraction')
m=m+1;
else:
if xerror3d2 is None:
xerr=None;
else:
xerr=xerror3d2[x,y,:]
if yerror3d2 is None:
yerr=None;
else:
yerr=yerror3d2[x, y,:]
P.errorbar(xScat,array3d2[x, y,:], xerr=xerr, yerr=yerr, marker='*', fmt='o');
#Plot function result as scatter data.
p=None
if fn is not None:
if fn=='linear_amplitude_annual':
dataMask=~np.isnan(array3d[x, y,:])
p0=np.array([1,0,0,basic.nonan(array3d[x, y,:]).mean() ])
fitfun=lambda p: (p[0]+p[1]*xScat[dataMask]/365. )* np.cos(2*np.pi*xScat[dataMask]/365.+p[2]) + p[3]
xScat2=np.linspace(xScat.min(),xScat.max())
fitfun2=lambda p: (p[0]+p[1]*xScat2/365.) * np.cos(2*np.pi*xScat2/365.+p[2]) + p[3]
#errfun=lambda p: sum(abs(basic.nonan(array3d[x, y,:])-fitfun(p)));
if yerror3d is None:
w=np.ones(array3d[x, y,:].shape);
else:
w=basic.rescale(1./yerror3d[x,y,:], [1,2])
errfun=lambda p: basic.nonan(w*array3d[x, y,:])-w[dataMask]*fitfun(p);
#p=scipy.optimize.fmin_powell(errfun, p0)
p=scipy.optimize.leastsq(errfun, p0);
p=p[0];
P.scatter(xScat[dataMask], fitfun(p), marker='^');
sortedxy= np.squeeze(np.dstack([xScat2, fitfun2(p)]));
sortedxy=sortedxy[sortedxy[:,0].argsort(),:]
P.plot(sortedxy[:,0], sortedxy[:,1]);
slope, intercept, r_value, p_value, std_err = scipy.stats.linregress(basic.nonan(w*array3d[x, y,:]),w[dataMask]*fitfun(p))
P.annotate(str("a0:%0.2f\na1:%0.2f\npha:%0.2f\nbias:%0.2f\nr2:%0.2f" % (p[0], p[1], p[2], p[3], r_value**2.)), (0.8,0.8), xycoords='axes fraction')
elif fn=='quadratic_amplitude_annual':
dataMask=~np.isnan(array3d[x, y,:])
p0=np.array([1,0,0,0,basic.nonan(array3d[x, y,:]).mean() ])
fitfun=lambda p: (p[0]+p[1]*xScat[dataMask]/365.+p[2]*(xScat[dataMask]/365.)**2. )* np.cos(2*np.pi*xScat[dataMask]/365.+p[3]) + p[4]
xScat2=np.linspace(xScat.min(),xScat.max())
fitfun2=lambda p: (p[0]+p[1]*xScat2/365.+p[2]*(xScat2/365.)**2.) * np.cos(2*np.pi*xScat2/365.+p[3]) + p[4]
#errfun=lambda p: sum(abs(basic.nonan(array3d[x, y,:])-fitfun(p)));
if yerror3d is None:
w=np.ones(array3d[x, y,:].shape);
else:
w=basic.rescale(1./yerror3d[x,y,:], [1,2])
errfun=lambda p: basic.nonan(w*array3d[x, y,:])-w[dataMask]*fitfun(p);
#p=scipy.optimize.fmin_powell(errfun, p0)
p=scipy.optimize.leastsq(errfun, p0);
p=p[0];
P.scatter(xScat[dataMask], fitfun(p), marker='^');
sortedxy= np.squeeze(np.dstack([xScat2, fitfun2(p)]));
sortedxy=sortedxy[sortedxy[:,0].argsort(),:]
P.plot(sortedxy[:,0], sortedxy[:,1]);
slope, intercept, r_value, p_value, std_err = scipy.stats.linregress(basic.nonan(w*array3d[x, y,:]),w[dataMask]*fitfun(p))
P.annotate(str("a0:%0.2f\na1:%0.2f\na2:%0.2f\npha:%0.2f\nbias:%0.2f\nr2:%0.2f" % (p[0], p[1], p[2], p[3], p[4], r_value**2.)), (0.8,0.8), xycoords='axes fraction')
elif fn=='annual':
dataMask=~np.isnan(array3d[x, y,:])
p0=np.array([1,1,basic.nonan(array3d[x, y,:]).mean() ])
fitfun=lambda p: p[0]* np.cos(2*np.pi*xScat[dataMask]/365.+p[1]) + p[2]
xScat2=np.linspace(xScat.min(),xScat.max())
fitfun2=lambda p: p[0]* np.cos(2*np.pi*xScat2/365.+p[1]) + p[2]
#errfun=lambda p: sum(abs(basic.nonan(array3d[x, y,:])-fitfun(p)));
if yerror3d is None:
w=np.ones(array3d[x, y,:].shape);
else:
w=basic.rescale(1./yerror3d[x,y,:], [1,2])
errfun=lambda p: basic.nonan(w*array3d[x, y,:])-w[dataMask]*fitfun(p);
#p=scipy.optimize.fmin_powell(errfun, p0)
p=scipy.optimize.leastsq(errfun, p0);
p=p[0];
P.scatter(xScat[dataMask], fitfun(p), marker='^');
sortedxy= np.squeeze(np.dstack([xScat2, fitfun2(p)]));
sortedxy=sortedxy[sortedxy[:,0].argsort(),:]
P.plot(sortedxy[:,0], sortedxy[:,1]);
slope, intercept, r_value, p_value, std_err = scipy.stats.linregress(basic.nonan(w*array3d[x, y,:]),w[dataMask]*fitfun(p))
P.annotate(str("amp:%0.2f\npha:%0.2f\nbias:%0.2f\nr2:%0.2f" % (p[0], p[1], p[2], r_value**2.)), (0.8,0.8), xycoords='axes fraction')
else:
p=None
P.scatter(xScat, fn(xScat), marker='^');
#convert axis to date...
if dateaxis:
try:
P.figure(fh.number).axes[0].xaxis_date(tz=None)
P.figure(fh.number).autofmt_xdate()
except:
pass
#change x y to xMap, yMap
if yMap is not None:
xM=ya*x+yb;
else:
xM=x;
if xMap is not None:
yM=xa*(y)+xb;
else:
yM=y;
#x and y are flipped in the try/except block above. So Flip again.
#if p is not None:
# P.title("x,y,[]: " + str(yM) + ", " + str(xM) + ', ' + str(p) )
#else:
P.title("x,y,z,z.std: " + str(yM) + ", " + str(xM) + ', ' + str(array2d[x,y]) +', ' + str(np.std(basic.nonan(array3d[x, y,:]))) )
# rotate and align the tick labels so they look better
#P.figure(fh.number).autofmt_xdate()
# use a more precise date string for the x axis locations in the
# toolbar
#P.gca().fmt_xdata = mdates.DateFormatter('%Y-%m-%d')
if xerror3d is None:
xerr=None;
else:
xerr=xerror3d[x,y,:]
if yerror3d is None:
yerr=None;
else:
yerr=yerror3d[x, y,:]
if modelError:
yerr=yerror3d[x, y,:]
yerr[dataMask]=errfun(p)
P.errorbar(xScat,array3d[x, y,:], xerr=xerr, yerr=yerr, fmt='ro');
if ylimScat is not None:
P.ylim(ylimScat);
##################################
## END OF PLOTTING
##################################
s=array2d[~np.isnan(array2d)].std();
m=array2d[~np.isnan(array2d)].mean();
fig=P.figure();ax=fig.add_subplot(111);ax.matshow(array2d, vmin=m-s, vmax=m+s);
#fig=P.figure();ax=fig.add_subplot(111);ax.matshow(basic.wrapToInt(array2d, s), vmin=-s, vmax=s);
if xMap is not None:
ticks=ax.get_xticks();
(xa,xb)=np.polyfit(np.r_[0:len(xMap)],xMap,1)
ax.set_xticklabels(np.around(xa*ticks+xb,4));
if yMap is not None:
ticks=ax.get_yticks();
(ya,yb)=np.polyfit(np.r_[len(yMap):0:-1],yMap,1)
ax.set_yticklabels(np.around(ya*ticks+yb,4));
#P.colorbar();
cax,kw=P.matplotlib.colorbar.make_axes(ax,orientation='vertical')
P.matplotlib.colorbar.ColorbarBase(cax, cmap=P.jet(),
norm=P.normalize(vmin=m-s,vmax=m+s),
orientation='vertical')
fh=P.figure(); #should be accessible in child function?
fig.canvas.mpl_connect('button_press_event', onclick);
return (fig,fh)
data = np.loadtxt('velocities.txt')
# some constants
n = 1000
a = 0
b = int(100)
h = (b - a) / n
def f(t):
# find our appropriate y values for our x's
t = int(t)
return data[t, 1]
bum = (f(a) + f(b)) / 2
glum = 0
for k in range(1, n - 1):
glum += f(a + k * h)
integral = (glum + bum) * h
print("integral =", integral)
for i in range(0, 100):
py.plot(data[i, 0], data[i, 1], 'ko')
py.jet()
py.colorbar
py.show()
#---------------------------------------
# Matrix of Frequencies
#---------------------------------------
npos = len(target_abego)
posfreq = np.zeros((npos, 20))
#print seq_pos
for pos in range(npos):
for j, aa in enumerate(aa_list):
posfreq[pos, j] = seq_pos[pos][aa]
import matplotlib.colors as colors
dim1, dim2 = posfreq.shape
#print posfreq
plt.figure()
plt.pcolor(posfreq, cmap=plt.jet())
plt.xticks(np.arange(0.5, dim2 + 0.5, 1))
plt.yticks(np.arange(0.5, dim1 + 0.5, 1))
plt.gca().set_xticklabels(aa_list)
ylabel = []
for i in range(dim1):
ylabel.append('%i.%s' % (i, target_abego[i]))
plt.gca().set_yticklabels(ylabel)
plt.colorbar()
plt.show()
for i in range(row):
for k in range(col):
# distances to point charges
# r1 coords are (4.5, 5.0)
# r2 coords are (5.5, 5.0)
r1 = sqrt((4.5 - i)**2 + (5.0 - k)**2)
r2 = sqrt((5.5 - i)**2 + (5.0 - k)**2)
field[i, k] = (q1 * k / r1) + (q2 * k / r2)
part = input(str("Enter which part (a, b, or c): "))
if part in ['a']:
clf()
imshow(field, origin='lower')
jet()
colorbar()
show()
if part in ['b']:
h = 1e-3
pdiff_x = zeros((row, col))
pdiff_y = zeros((row, col))
for i in range(2, 9):
# derivative of all values in left column two data points to one data point
pdiff_x[:, i] = ((field[:, i - 2] - field[:, i + 2]) / 12 +
(field[:, i + 1] - field[:, i - 1]) / 3) / h
# central difference derivative
# construct individual nodes
reservoir = ReservoirNode_lyapunov(input_size, 100, lyapunov_skip=100)
readout = Oger.nodes.RidgeRegressionNode()
# build network with MDP framework
flow = mdp.Flow([reservoir, readout])
# Nested dictionary
gridsearch_parameters = {reservoir:{'input_scaling': mdp.numx.arange(0.1, 2.2, .7), 'spectral_radius':mdp.numx.arange(0.1, 2.2, .7)}}
# Instantiate an optimizer
opt = Oger.evaluation.Optimizer(gridsearch_parameters, Oger.utils.nrmse)
# Do the grid search
opt.grid_search(data, flow, cross_validate_function=Oger.evaluation.train_test_only, training_fraction=.9)
# Plot the maximal LLE for each parameter setting
lle_max = mdp.numx.zeros(opt.paramspace_dimensions)
for i in range(opt.paramspace_dimensions[0]):
for j in range(opt.paramspace_dimensions[1]):
lle_max[i, j] = mdp.numx.amax(mdp.numx.mean(mdp.numx.array(opt.probe_data[i, j][reservoir]), 0))
pylab.figure()
pylab.imshow(mdp.numx.flipud(lle_max), cmap=pylab.jet(), interpolation='nearest', aspect="auto", extent=opt.get_extent(opt.parameters))
pylab.ylabel('Spectral Radius')
pylab.xlabel('Input scaling')
pylab.suptitle('Max LLE')
pylab.colorbar()
pylab.show()
def sta_each( getimagenames,openimagesandwrite,calculatemeanrf,tipoalgoritmo,timestampName ,stafolder ,imageruta ,imagefolder ,imagefiltro ,timefolder ,samplingRate ,numberframes ,numberframespost , synchronyfile ,sizex ,sizey, dolog):
#=============================================
# GET INPUTS: initial options
#=============================================
# # LOAD DE IMAGE NAME LIST WITH THE STIMULUS ENSEMBLE
# getimagenames = int(sys.argv[1]) #0
# # DO TESTS FOR READ AND WRITE IMAGES
# openimagesandwrite = int(sys.argv[2]) #0
# # LOAD ALL THE IMAGES FROM THE STIMULOS ENSEMBLE AND CALCULATE THE MEAN STIMULUS
# calculatemeanrf = int(sys.argv[3]) #0
# # defines how to do the STA process:
# # 1 for load all spike triggered stimuli, 2 for sequentially load
# tipoalgoritmo = int(sys.argv[4]) #2
# # DEFINE THE NAME OF THE TXT FILE WITH TIME STAMPS FOR LOAD:
# timestampName = (sys.argv[5]) #C1a
# =============================================
# SET OTHERS OPTIONS
# =============================================
# FOLDER NAME TO SAVE EACH FOLDER RESULTS
# stafolder = 'STA_datos0005'
# # FOLDER NAME TO LOAD STIMULUS ENSEMBLE: IMAGE STIMULUS FOLDER
# imageruta = 'D:/'
# imagefolder = 'checkImages'
# imagefiltro = '*.png'
# # SPIKE TIME STAMPS FOLDER FOR LOAD SPIKE TRAINS
# timefolder = 'TS_datos0005/'
# # SET THE ADQUISITION SAMPLING RATE OF THE RECORDS
# samplingRate = 20000 # Hz
# # SET THE NUMBER OF FRAMES BEFORE AND AFTER A SPIKE TO ANALIZE:
# # number of frames previous to each spike for STA windows
# numberframes = 13
# # number of frames posterior to each spike for STA windows
# numberframespost = 5
# # SET THE NAME OF THE STIMULUS SYNCHRONY ANALYSIS FILE
# # IT CONTAINS THE INITIAL AND FINAL TIME STAMPS OF EACH FRAME
# synchronyfile = 'inicio_fin_frame_datos0005.txt'
inicio_fin_frame = np.loadtxt(synchronyfile)
# # SET THE SIZE OF EACH FRAME IN PIXELS
# sizex = 380 #500 #750
# sizey = 380 #500 #700
# # set if do logarithm analysis for plot:
# dolog = 0
print '---------------------BEGIN---------------------------'
#--------------------------------------------------------
# creates STA result folder
# if folder "STA" don't exist, create the folder
#--------------------------------------------------------
try:
os.mkdir( stafolder )
except OSError:
pass
#============================================================
# Get the image names (optional)
# This stage is performed the first time of analysis only.
# For each different stimuli ensemble files, this list has
# been created the first time of analysis once.
#============================================================
#getimagenames = 0
if(getimagenames == 1):
#--------------------------------------------------------
# get image file names from folder
#--------------------------------------------------------
#imageruta = '../../VIRTUALWIN/cinv_datos_05-06-2013/'
#imageruta = '../cinv_datos23-4-2013/'
#imageruta = '/media/Datos/STA_RVM/Datos 13-11-2013/' #Se aplica el mismo estimulo de la semana anterior
#imageruta = 'D:\Users\ALIEN3\Desktop/'
# imageruta = 'D:/'
# #imagefolder = 'random blanco y negro, cuadrados de 40x40 pixeles'
# imagefolder = 'checkImages'
# imagefiltro = '*.png'
globstring = imageruta + imagefolder +'/'+ imagefiltro
imagefilenames = glob.glob(globstring) # get file names from folder
imagefilenames.sort()
print "\t length imagefilenames: ", len(imagefilenames)
print "\t last imagefilenames : ",imagefilenames[len(imagefilenames)-1]
#--------------------------------------------------------
# save image name list to matlab file
#--------------------------------------------------------
ifn = np.array(imagefilenames)
cadena_texto = "image_filenames"
print "\t Saving image names as mat file: ",cadena_texto
scipy.io.savemat(stafolder+'/'+cadena_texto+'.mat',mdict={'ifn':ifn},oned_as='column')
#--------------------------------------------------------
# save image name list to txt file
#--------------------------------------------------------
try:
print "\t Saving image names as mat txt: ",cadena_texto
configFile = open(stafolder+'/'+cadena_texto+'.txt', 'w')
for parameter in ifn:
configFile.write( ''+str(parameter)+' \n' )
configFile.close
except OSError:
pass
#--------------------------------------------------------
# load image file names list:
# (the file should exist before)
#--------------------------------------------------------
cadena_texto = "image_filenames"
#print "\t Loading image names from mat file: ",cadena_texto
contenedor = scipy.io.loadmat(stafolder+'/'+cadena_texto+'.mat')
ifn2 = contenedor['ifn']
del contenedor
# print "\t length imagefilenames: ", len(ifn2 )
# print "\t last imagefilenames : ",ifn2 [len(ifn2 )-1]
# print "\n"
#============================================================
# Load images and write each image as a vector:
# This stage is only a test for load and save images from
# original stimuli images.
# The important issue is to load correctly images for the
# use of all information of each frame, using grey scale or
# RGB or others channels.
#============================================================
#openimagesandwrite = 0
if(openimagesandwrite == 1):
stimuli =[] # initialize stimuli matrix to keep images as vectors
contador = 0 # to get a defined number of images (abac)
limite = 5 # define the number of images to load using the image file name list
imagefilenames = ifn2
for line in imagefilenames:
print '\t Loading stimuli: '+ line # show inline image name
#--------------------------------------------------------
# load as gray scale image:
#--------------------------------------------------------
imagen = scim.imread(line, flatten = True) # read one image as gray scale
tamanox = len(imagen)
tamanoy = len(imagen[0])
tamanomin = np.min([tamanox,tamanoy])
print '\t size imagen : ', tamanox, 'x',tamanoy
imagenvector = np.zeros( ( 1,tamanomin*tamanomin ) ) # initialize vector for keep image
k = 0
for i in range(tamanomin): # over image x,y coordinates, for keep image matrix as row vector
for j in range(tamanomin):
imagenvector[0,k] = imagen[i,j] # keep one image pixel as one vector element
k = k+1 # for next element
stimuli.append( imagenvector ) # add image row vector and a group in a big matrix [MxN]
saveplot = 1
if saveplot:
pl.figure()
im = pl.imshow(imagen,interpolation = 'none')
pl.gray() #pl.hot()
#pl.clim(mini,maxi)
pl.contour(imagen)
pl.colorbar(im)
ax = pl.axes()
ax.set_yticklabels([])
ax.set_xticklabels([])
#ax.annotate(str(a+1), (.1, 1.2), bbox=dict(boxstyle="round, pad=0.3", fc="w"), size=52 )
pl.savefig(stafolder+"/gray_frame-"+str(contador)+"-g.png",format='png', bbox_inches='tight')
contador = contador + 1 # counting images of the ensemble
if contador==limite:
break
#============================================================
# Calculate the mean frame image for the entire stimuli
# ensemble. This calculation can be performed in one big load
# or sequentially.
#============================================================
#calculatemeanrf = 0
if(calculatemeanrf==1):
#---------------------------------------------------
# get all images and calculate the mean frame image
#---------------------------------------------------
limite2 = len(ifn)-1 #100000
contador = 0
#tamanomin = 700
imagenvector = np.zeros( ( 1 ,tamanomin*tamanomin ) )
vectoracumula = imagenvector
#tamanox = 700
#tamanoy = 750
imagenacumula = np.zeros( ( tamanox , tamanoy ) )
for line in imagefilenames:
print 'load id: ', contador #,' Loading stimuli: '+line # show inline image name
#--------------------------------------------------------
# load as gray scale image:
#--------------------------------------------------------
imagen = scim.imread(line, flatten=True) # read one image as grayscale
imagenacumula = imagenacumula + imagen
#stimuli.append( imagenvector ) # add image row vector and add to bigmatrix [MxN]
contador = contador + 1 # counting images of the ensemble
if contador==limite2:
break
meanimage = imagenacumula // (limite2*1.0)
meanimagearray = np.array(meanimage)
cadena_texto = "mean_image"
print "\t Saving mean image as mat file: ",cadena_texto
scipy.io.savemat(stafolder+'/'+cadena_texto+'.mat',mdict ={'meanimagearray':meanimagearray},oned_as='column')
#--------------------------------------------------------
# save mean frame as image:
#--------------------------------------------------------
pl.figure()
#im = pl.imshow(component,interpolation='bicubic')
im = pl.imshow(meanimage,interpolation = 'none')
pl.gray() #pl.hot()
#pl.clim(mini,maxi)
pl.contour(meanimage)
pl.colorbar(im)
ax = pl.axes()
ax.set_yticklabels([])
ax.set_xticklabels([])
#ax.annotate(str(a+1), (.1, 1.2), bbox=dict(boxstyle="round, pad=0.3", fc="w"), size=52 )
pl.savefig(stafolder+"/mean_gray_frame-g.png",format='png', bbox_inches='tight')
#============================================================
# DO STA
#============================================================
#--------------------------------------------------------
# get spike time stamps from file
#--------------------------------------------------------
#timefolder = 'ss_dMCD_fs20_nb1218_f2_CINV-25-06-2013-RANDOM-1/'
# timefolder = 'TS_datos0001/'
# nb = 1218 # number of blocks
# e = 15 # 10 #9 #8 # number of electrode
# nc = 0 # 2 #0 # number of cluster
#timestampName = 'M10a'
#neurontag = 'e_'+timestampName # tag or number of cell
neurontag = timestampName # tag or number of cell
rastercelulatxtfile = timefolder + timestampName +'.txt'
#rastercelulatxtfile = timestampName
timestamps = np.loadtxt(rastercelulatxtfile) # text file containing time spikes in datapoints
#limite3 = 820 #37928 #218 #800 # limit number of spikes to analize
# neuronresultfolder_lin = 'cell_'+str(neurontag)+'_lineal'
# neuronresultfolder_log = 'cell_'+str(neurontag)+'_log'
neuronresultfolder_lin = str(neurontag)+'_lineal'
neuronresultfolder_log = str(neurontag)+'_log'
# CREATE SUBFOLDERS
try:
os.mkdir( stafolder+'/'+neuronresultfolder_lin ) # create the folder
except OSError:
pass
if dolog ==1:
try:
os.mkdir( stafolder+'/'+neuronresultfolder_log ) # create the folder
except OSError:
pass
finalfolder_lin = stafolder+'/'+neuronresultfolder_lin
finalfolder_log = stafolder+'/'+neuronresultfolder_log
#rastercelulatxtfile = timefolder+'isi_spktimes_nb'+str(nb)+'_e'+str(e)+'_nc'+str(nc)+'.txt'
#rastercelulatxtfile = timefolder+'isi_spktimes_nb90_e17_nc0.txt'
#rastercelulatxtfile = timefolder+'F1a.txt'
#timestamps = np.loadtxt(rastercelulatxtfile) # text file containing time spikes in datapoints
print 'size time stamps vector: ', len(timestamps) #, 'x',len(timestamps[0])
#--------------------------------------------------------
# set useful parameters
#--------------------------------------------------------
# samplingRate = 20000 #20000 Hz
# #frameinicio = 31199 #31855-671+2 #1.00385e6 # points, inicio de la presentacion de frames
# #frameinicioms = 5.01925e4 # ms
# #frameduracion = 334*2 #671 #668 #350 # points = (1.00455-1.0042)*10^6
# #frameduracionms = 17.5 # ms
# numberframes = 13 # number of frames previous to each spike for STA windows
# numberframespost = 5 # number of frames posterior to each spike for STA windows
# inicio_fin_frame = np.loadtxt('inicio_fin_frame_datos0001.txt')
#print (inicio_fin_frame)
#--------------------------------------------------------
# get time spikes depending of the stimulus start (frame do not start in time=0)
#--------------------------------------------------------
#timestamps2 = timestamps[timestamps[:,1]>frameinicio*2,1]
#print 'size timestamps2: ', len(timestamps2)
#stimes = (timestamps[:,1]-timeoffset)**(samplingRate/(1000*1.0)) # time spikes (second column of data) as vector
#--------------------------------------------------------
# Conversion from microseconds to seconds
#--------------------------------------------------------
#timestamps2 = timestamps[:,1]/1000000
#print timestamps2[100,1]
#--------------------------------------------------------
# Conversion of spike times from seconds to POINTS:
#--------------------------------------------------------
#vector_spikes = timestamps[:,1]*samplingRate
vector_spikes = timestamps[:]*samplingRate # without first id zero column (1 COLUMMN)
#vector_spikes = timestamps[:,1]
#print vector_spikes
#punto_spike = timestamps[:,1]
#print inicio_fin_frame[:,0]
vector_fin_frame = inicio_fin_frame[:,1]
vector_inicio_frame = inicio_fin_frame[:,0]
# initialize time spike index depending of image time
stimei = []
spikeframe_matrix = np.zeros( (len(vector_spikes), 4) ) # [spike time, frame id, ini time frame, end time frame]
#--------------------------------------------------------
# convert stimes (SPIKE TIMES) to frame indexes (image index):
#--------------------------------------------------------
primer_frame = 0
frame_ant = 0
print 'first spike pos: ',vector_spikes[0],' last spike pos: ',vector_spikes[-1]
print 'first frame begin at: ',inicio_fin_frame[0,0],' last frame ends at: ',inicio_fin_frame[-1,1]
#print 'final: ',len(vector_spikes),' x ',len(vector_fin_frame),' = ',len(vector_spikes) * len(vector_fin_frame)
print 'Get the spike triggered stimuli indices: \n'
contator = 0
contator2 = 0
totalcont = len(vector_spikes) * len(range(primer_frame, len(vector_fin_frame)))
for punto_spike in vector_spikes:
for i in range(primer_frame, len(vector_fin_frame)):
if (vector_inicio_frame[i] < punto_spike) & (punto_spike <= vector_fin_frame[i]):
# if the spike time is into a frame time points (start and ends)
#print '\npunto de inicio de frame:\t',inicio_fin_frame[i,0]
#print 'punto de spike:\t\t\t',punto_spike
#print 'punto de final de frame:\t',inicio_fin_frame[i,1]
spikeframe_matrix[contator,0] = punto_spike
spikeframe_matrix[contator,1] = vector_fin_frame[i]
spikeframe_matrix[contator,2] = inicio_fin_frame[i,0]
spikeframe_matrix[contator,3] = inicio_fin_frame[i,1]
#print '\r punto_spike: ',punto_spike, ' i: ',i
stimei.append(i)
frame_ant = i
#contator2 = contator * 100 // (1.0 * len(vector_spikes) * len(vector_fin_frame) )
#time.sleep(1)
#sys.stdout.write("\r%d%%" %contator2, "%d%%" %contator) # or print >> sys.stdout, "\r%d%%" %i,
sys.stdout.write("\r%d%%" %contator2)
sys.stdout.flush()
contator = contator + 1 #
#contator2 = contator * 100 // (1.0 * len(vector_spikes) * len(vector_fin_frame) )/47*100
contator2 = contator * 100 // ( 1.0 * len(vector_spikes) )
primer_frame = frame_ant
#print primer_frame
print '\n'
limite3 = len(stimei)
print 'length frames times vector', len(vector_fin_frame)
print "length time stamps vector: ", len(timestamps)
print "length spike triggered stimuli time i vector: ", len(stimei)
#puntos = 10
#print " timestamps: ", (timestamps[0:puntos,1])
#print " stimei: ", (stimei[0:puntos])
#--------------------------------------------------------
# load mean frame from mat file:
#--------------------------------------------------------
cadena_texto = "mean_image"
#print "\t Loading mean frame from mat file: ",cadena_texto
contenedor = scipy.io.loadmat(stafolder+'/'+cadena_texto+'.mat')
meanimagearray = contenedor['meanimagearray']
del contenedor
#--------------------------------------------------------
# STA Algorithm
#--------------------------------------------------------
#tipoalgoritmo = 2
#------------------- ALGORITHM TYPE 1----------------------
# LOAD ALL THE FRAMES ACCORDING TO THE TIME STAMPS OF THE CELL
# NOT FUNCTIONAL ANYMORE
if(tipoalgoritmo == 1):
limite3 = len(stimei)
kframe = 0
spk = np.zeros((500,500,numberframes,limite3))
for kiter in range(limite3):
kframe = stimei[kiter]
for b in range(numberframes):
print ' kiter: ',kiter, ' kframe: ',kframe, ' b: ',b
line = ifn2[kframe-(numberframes-1)+ b ]
imagen = scim.imread(line, flatten=True)
spk[:,:,b,kiter] = imagen - meanimagearray
N = len(stimei)
STA = ( np.add.reduce(spk,axis=3) / (1.0 * N) )
#sta = sum(spk, axis=1 (over column) ) / (1*Number_Spikes)
MEANSTA = ( np.add.reduce(STA,axis=2) / (1.0 * numberframes) )
#------------------- ALGORITHM TYPE 2----------------------
# LOAD EACH FRAME AND CALCULATES THE STA SEQUENTIALLY
if(tipoalgoritmo == 2): # sequentially algorithm
kframe = 0
# sizex = 380 #500 #750
# sizey = 380 #500 #700
acumula = np.zeros((sizex,sizey,numberframes+numberframespost))
#timeProcessIni = time.time()
print 'Get the spike triggered stimuli: \n '
for kiter in range(limite3):
timeProcessIni = time.time()
kframe = stimei[kiter]
for b in range(numberframes+numberframespost):
#print 'b ',b
line = ifn2[kframe-(numberframes-1)+ b]
imagen = scim.imread( line, flatten=True )
#spk[:,:,b,kiter] = imagen
acumula[:,:,b] = acumula[:,:,b] + (imagen - meanimagearray)
if kiter > len(stimei):
break
timeProcessFin = time.time()
tiempoDiferencia = timeProcessFin - timeProcessIni
#print '\r kiter: ',kiter, ' kframe: ',kframe, ' ',"%.2f" % ((kiter+1)*100.0/limite3, ), ' % ' , (limite3 -(kiter+0)) * tiempoDiferencia/60, 'min'
#sys.stdout.write("\r%d%%" %contator2)
#sys.stdout.write("\r%d%% %d%%" %((kiter+1)*100.0/limite3) %(limite3 -(kiter+0)) * tiempoDiferencia/60)
sys.stdout.write("\r%d%%" %((kiter+1)*100.0/limite3, ) )
#sys.stdout.write("\r%d%%" %((limite3 -(kiter+0)) * tiempoDiferencia/60 ) )
sys.stdout.flush()
N = limite3 # len(stimei)
STA = acumula // N
print ' \n '
minimosta = np.min(np.min(np.min(STA)))
maximosta = np.max(np.max(np.max(STA)))
#print '\nmin sta ', minimosta, ' max sta ', maximosta
if minimosta < 0:
STA_desp = STA + np.abs(minimosta) # lineal shift
if minimosta >= 0:
STA_desp = STA - np.abs(minimosta) # lineal shift
minimosta_desp = np.min(np.min(np.min(STA_desp)))
maximosta_desp = np.max(np.max(np.max(STA_desp)))
#print 'min sta with bias', minimosta_desp
#print 'max sta with bias', maximosta_desp
if dolog ==1:
STA_log = log10(STA_desp + 1) # logarithmic normalization
minimosta_log = np.min(np.min(np.min(STA_log)))
maximosta_log = np.max(np.max(np.max(STA_log)))
print 'min sta log ', minimosta_log
print 'max sta log ', maximosta_log
stavisual_lin = STA_desp*255 # it is visualized with lineal scale
stavisual_lin = stavisual_lin // (maximosta_desp *1.0) # it is normalized with lineal scale
#print 'min sta visual lineal', np.min(np.min(np.min(stavisual_lin)))
#print 'max sta visual lineal', np.min(np.max(np.max(stavisual_lin)))
if dolog ==1:
stavisual_log = STA_log*255 # it is visualized with logarithmic scale
stavisual_log = stavisual_log // (maximosta_log *1.0) # it is normalized with logarithmic scale
print 'min sta visual log', np.min(np.min(np.min(stavisual_log)))
print 'max sta visual log', np.min(np.max(np.max(stavisual_log)))
# FINAL NORMALIZATION FOR THE MEAN STA
MEANSTA_lin = ( np.add.reduce(stavisual_lin,axis=2) / (1.0 * (numberframes+numberframespost) ) )
if dolog ==1:
MEANSTA_log = ( np.add.reduce(stavisual_log,axis=2) / (1.0 * (numberframes+numberframespost) ) )
#============================================================
#============================================================
print '\nsize STA: ',len(STA),'x',len(STA[0]),'x',len(STA[0][0])
#----------------------------------------------------
# save results
#----------------------------------------------------
spikeframe_matrix_array = np.array(spikeframe_matrix)
spikeframe_filename = "spikeframe_matrix"+str(neurontag)
print "\t spikeframe_matrix as mat file: ",spikeframe_filename
scipy.io.savemat(finalfolder_lin+'/'+spikeframe_filename+'.mat',mdict={'spikeframe_matrix':spikeframe_matrix_array},oned_as='column')
stavisual_lin_array = np.array(stavisual_lin)
cadena_texto = "stavisual_lin_array_"+str(neurontag)
print "\t Saving visual STA (lineal) as mat file: ",cadena_texto
scipy.io.savemat(finalfolder_lin+'/'+cadena_texto+'.mat',mdict={'STAarray_lin':stavisual_lin_array},oned_as='column')
if dolog ==1:
stavisual_log_array = np.array(stavisual_log)
cadena_texto = "stavisual_log_array_"+str(neurontag)
print "\t Saving visual STA (logarithmic) as mat file: ",cadena_texto
scipy.io.savemat(finalfolder_log+'/'+cadena_texto+'.mat',mdict={'STAarray_log':stavisual_log_array},oned_as='column')
# MEANSTAarray_lin = np.array(MEANSTA_lin)
# cadena_texto = "MEANSTA_lin"+str(neurontag)
# print "\t Saving STA as mat file: ",cadena_texto
# scipy.io.savemat(finalfolder_lin+'/'+cadena_texto+'.mat',mdict={'MEANSTAarray_lin':MEANSTAarray_lin},oned_as='column')
# MEANSTAarray_log = np.array(MEANSTA_log)
# cadena_texto = "MEANSTA_log"+str(neurontag)
# print "\t Saving STA as mat file: ",cadena_texto
# scipy.io.savemat(finalfolder_log+'/'+cadena_texto+'.mat',mdict={'MEANSTAarray_log':MEANSTAarray_log},oned_as='column')
print '\nSaving images in lineal scale...'
for b in range(numberframes+numberframespost):
#print 'Image ', b
sys.stdout.write("\r Image %d" %(b ) )
sys.stdout.flush()
component = stavisual_lin[:,:,b] #STA[:,:,b]
pl.figure()
#im = pl.imshow(component,interpolation = 'none')
#im = pl.pcolor( component,vmin = 0,vmax = 255, cmap=cm.jet )
im = pl.pcolormesh( component,vmin = 0,vmax = 255, cmap=cm.jet )
#pl.contour(component)
pl.colorbar(im)
ax = pl.axes()
ax.set_yticklabels([])
ax.set_xticklabels([])
#ax.annotate(str(a+1), (.1, 1.2), bbox=dict(boxstyle="round, pad=0.3", fc="w"), size=52 )
pl.savefig(finalfolder_lin+"/STA-"+str(neurontag)+"-"+str(b)+"-g_.png",format='png', bbox_inches='tight')
#pl.savefig(stafolder+"/STA-"+str(neurontag)+"-"+str(b)+"-g_.jpg",format='jpg', bbox_inches='tight')
#del pl
del component
if dolog ==1:
print '\nSaving images in logarithmic scale...'
for b in range(numberframes+numberframespost):
#print 'Image ', b
sys.stdout.write("\r Image %d" %(b ) )
sys.stdout.flush()
component = stavisual_log[:,:,b] #STA[:,:,b]
pl.figure()
#im = pl.imshow(component,interpolation = 'none')
#im = pl.pcolor(component,vmin = 0,vmax = 255, cmap=cm.jet)
im = pl.pcolormesh( component,vmin = 0,vmax = 255, cmap=cm.jet )
#pl.contour(component)
pl.colorbar(im)
ax = pl.axes()
ax.set_yticklabels([])
ax.set_xticklabels([])
####ax.annotate(str(a+1), (.1, 1.2), bbox=dict(boxstyle="round, pad=0.3", fc="w"), size=52 )
pl.savefig(finalfolder_log+"/STA-"+str(neurontag)+"-"+str(b)+"-g_.png",format='png', bbox_inches='tight')
#pl.savefig(stafolder+"/STA-"+str(neurontag)+"-"+str(b)+"-g_.jpg",format='jpg', bbox_inches='tight')'''
#del pl
del component
#for b in range(numberframes+numberframespost):
# print 'Image ', b
# component = stavisual_lin[:,:,b]
# #im = pl.pcolor(component,vmin = 0,vmax = 255, cmap=cm.jet)
# misc.imsave(finalfolder_lin+"/STA-"+str(neurontag)+"-"+str(b)+"-g_.png", component)
# #plt.imshow(component)
# #plt.show()
# myImC = Image.open(finalfolder_lin+"/STA-"+str(neurontag)+"-"+str(b)+"-g_.png")
# out = ImageChops.invert(myImC)
# out.save(finalfolder_lin+"/(inv)_STA-"+str(neurontag)+"-"+str(b)+"-g_.png")
print '\nSaving mean image in lineal scale...'
pl.figure()
#im = pl.imshow(MEANSTA,interpolation = 'none')
im = pl.pcolormesh(MEANSTA_lin,vmin = 0,vmax = 255, cmap=cm.jet)
#pl.gray()
pl.jet()
#pl.contour(MEANSTA)
pl.colorbar(im)
ax = pl.axes()
ax.set_yticklabels([])
ax.set_xticklabels([])
#ax.annotate(str(a+1), (.1, 1.2), bbox=dict(boxstyle="round, pad=0.3", fc="w"), size=52 )
pl.savefig(finalfolder_lin+"/MEANSTA-g_"+str(neurontag)+".png",format='png', bbox_inches='tight')
if dolog ==1:
print 'Saving mean image in logarithmic scale...'
pl.figure()
#im = pl.imshow(MEANSTA,interpolation = 'none')
im = pl.pcolormesh(MEANSTA_log,vmin = 0,vmax = 255, cmap=cm.jet)
#pl.gray()
pl.jet()
#pl.contour(MEANSTA)
pl.colorbar(im)
ax = pl.axes()
ax.set_yticklabels([])
ax.set_xticklabels([])
#ax.annotate(str(a+1), (.1, 1.2), bbox=dict(boxstyle="round, pad=0.3", fc="w"), size=52 )
pl.savefig(finalfolder_log+"/MEANSTA-g_"+str(neurontag)+".png",format='png', bbox_inches='tight')
# '''minim = np.min(np.min(MEANSTA))
# if minim < 0:
# MEANSTA2 = MEANSTA + np.abs(minim) #lineal shift
# if minim > 0:
# MEANSTA2 = MEANSTA - np.abs(minim) #lineal shift
# else:
# MEANSTA2 = MEANSTA
# minim2 = np.min(np.min(MEANSTA2))
# maxim = np.max(np.max(MEANSTA2))
# print 'minimo ', minim2
# print 'maximo ', maxim
# meanvisual = MEANSTA2*255
# meanvisual = meanvisual // (maxim*1.0)
# #print meanvisual
# minim3 = np.min(np.min(meanvisual))
# maxim3 = np.max(np.max(meanvisual))
# print 'minimo visual', minim3
# print 'maximo visual', maxim3
# pl.figure()
# #im = pl.imshow(meanvisual,interpolation = 'none')
# im = pl.pcolor(meanvisual,vmin = 0,vmax = 255, cmap=cm.jet)
# #pl.gray()
# pl.jet()
# #pl.contour(meanvisual)
# pl.colorbar(im)
# ax = pl.axes()
# ax.set_yticklabels([])
# ax.set_xticklabels([])
# #ax.annotate(str(a+1), (.1, 1.2), bbox=dict(boxstyle="round, pad=0.3", fc="w"), size=52 )
# pl.savefig(finalfolder+"/MEANSTA2-g_"+str(neurontag)+".png",format='png', bbox_inches='tight')'''
print 'CELL ' + timestampName + ' FINISHED!!!'
print '-----------------------END---------------------------'
del STA_desp
del STA
del stavisual_lin
del spikeframe_matrix
del imagen
del acumula
# levels=levels, colors='gray')
P.plot(r_floops, z_floops, 'ro')
#P.plot(-r_floops, z_floops, 'ro')
if 'tris' not in dir():
rzt, tris, pt = t3dinp('hitpops.05.t3d')
#do_conf = False
do_conf = True
if do_conf:
P.tricontourf(rzt[:, 0], rzt[:, 1], tris, beta, 1001, zorder=0)
cticks = P.linspace(0.0, 0.2, 5)
P.colorbar(ticks=cticks, format='%.2f')
P.jet()
#no_text = True
no_text = False
# whether to annotate in MA or MW
show_MA = True
if not no_text:
# annotate coil powers
for ii in xrange(n_b_coils):
if i_floops[ii] >= 0:
signum = '+'
else:
signum = '-'
if show_MA:
tdata = 1e-6 * i_floops[ii]
def main(path, marked_path=None):
# images multiscale
imgs_mscale = try_pickle_load(path)
n_scales = len(imgs_mscale)
imgs_s0 = imgs_mscale[0] # scale 1
image_shape = (imgs_s0.shape[2], imgs_s0.shape[3])
images_to_show = min(IMAGES_TO_SHOW, len(imgs_s0))
print "Images shape", imgs_s0.shape
print "Number of images to show", images_to_show
print "Number of scales", n_scales
print "Requested image shape will be", image_shape
n_rows = (1 + n_scales) * 2
perturbed_imgs = [np.empty((images_to_show, imgs.shape[1],
imgs.shape[2], imgs.shape[3]))
for imgs in imgs_mscale]
perturbed_marks = None
if marked_path is not None:
marked_imgs = try_pickle_load(marked_path)
perturbed_marks = np.empty((images_to_show, marked_imgs.shape[1],
marked_imgs.shape[2]))
for i in xrange(images_to_show):
imgs_to_perturb = [img[i] for img in imgs_mscale]
# if we loaded markings, add marked image to list of imgs to perturb
if perturbed_marks is not None:
imgs_to_perturb.append(marked_imgs[i])
ret_list = perturb_image(imgs_to_perturb, image_shape)
for n_scale in range(n_scales):
perturbed_imgs[n_scale][i] = ret_list[n_scale]
if perturbed_marks is not None:
perturbed_marks[i] = ret_list[n_scales]
for i, imgs in enumerate(imgs_mscale):
for j in xrange(images_to_show):
pylab.subplot(n_rows, images_to_show, i * images_to_show + j + 1)
pylab.axis('off')
pylab.imshow(imgs[j, CHANNEL, :, :])
pylab.gray() # set colormap
for ind, imgs in enumerate(perturbed_imgs):
i = n_scales + ind
for j in xrange(images_to_show):
pylab.subplot(n_rows, images_to_show, i * images_to_show + j + 1)
pylab.axis('off')
pylab.imshow(imgs[j, CHANNEL, :, :])
pylab.gray()
if perturbed_marks is not None:
for j in xrange(images_to_show):
pylab.subplot(n_rows, images_to_show, (2*n_scales+0) * images_to_show + j + 1)
pylab.axis('off')
pylab.imshow(marked_imgs[j, :, :])
pylab.jet()
pylab.subplot(n_rows, images_to_show, (2*n_scales+1) * images_to_show + j + 1)
pylab.axis('off')
pylab.imshow(perturbed_marks[j, :, :])
pylab.jet()
pylab.show()
#! populations recorded.
vmn = [-80, -80, -80, -80]
vmx = [-50, -50, -50, -50]
nest.Simulate(Params['sim_interval'])
#! loop over simulation intervals
for t in pylab.arange(Params['sim_interval'], Params['simtime'],
Params['sim_interval']):
# do the simulation
nest.Simulate(Params['sim_interval'])
# clear figure and choose colormap
pylab.clf()
pylab.jet()
# now plot data from each recorder in turn, assume four recorders
for name, r in recorders.iteritems():
rec = r[0]
sp = r[1]
pylab.subplot(2, 2, sp)
d = nest.GetStatus(rec)[0]['events']['V_m']
if len(d) != Params['N']**2:
# cortical layer with two neurons in each location, take average
d = 0.5 * (d[::2] + d[1::2])
# clear data from multimeter
nest.SetStatus(rec, {'n_events': 0})
pylab.imshow(pylab.reshape(d, (Params['N'], Params['N'])),
def main():
# Load and show original images
pylab.gray() # set gray scale mode
print
print "0. Reading and formatting images..."
images = {f: loadAndFormat(f) for f in IMAGE_FILES}
for f in IMAGE_FILES:
mShow(images[f])
###########################
# -----> Thresholding
print
print "1. Thresholding images..."
thresholdedImages = {f: getThresholdedImage(images[f]) for f in IMAGE_FILES}
for name in IMAGE_FILES:
mShow(thresholdedImages[name])
###########################
# -----> Count objects
# 1st attempt: label the thresholded image from task 1
print
print "2. Object counting"
pylab.jet() # back to color mode
print "\t1st approach: Label thresholded images"
for name in IMAGE_FILES:
labeled, nrRegions = ndimage.label(thresholdedImages[name])
print "\t" + name + ": " + str(nrRegions)
mShow(labeled)
# 2nd attempt: Changing threshold level
print
print "\t2nd approach: Tuned thresholds"
# For 'objects.png' some objects are very small (e.g.: screw) or
# have many shades (e.g.: spoon) which makes them disappear or appear
# fragmented after thresholding.
# The advantage of this image is that the background is very dark,
# so we can try using a lower threshold to make all shapes more definite
objImage = images['objects.png']
T = mahotas.thresholding.otsu(objImage)
thresholdedImage = objImage > T * 0.7
# Looks better, but...
labeled, nrRegions = ndimage.label(thresholdedImage)
print '\tobjects.png' + ": " + str(nrRegions)
# it returns 18!
# 3rd attempt: Smoothing before thresholding
print
print "\t3rd approach: Smoothing + Tuned threshold"
# Let's apply some Gaussian smoothing AND a lower threshold
smoothImage = ndimage.gaussian_filter(objImage, 3)
T = mahotas.thresholding.otsu(smoothImage)
thresholdedImage = smoothImage > T * 0.7
labeled, nrRegions = ndimage.label(thresholdedImage)
print '\tobjects.png' + ": " + str(nrRegions)
# it worked! Let's save the labeled images for later
# (we will use them for center calculation)
labeledImages = {}
labeledImages['objects.png'] = (labeled, nrRegions)
mShow(labeled)
# Let's see if this approach works on the other images
for name in ['circles.png', 'peppers.png']:
img = images[name]
smoothImage = ndimage.gaussian_filter(img, 3)
T = mahotas.thresholding.otsu(smoothImage)
thresholdedImage = smoothImage > T * 0.7
labeled, nrRegions = ndimage.label(thresholdedImage)
print '\t' + name + ": " + str(nrRegions)
# Again no luck with the circles!
# (We will take a closer look at the peppers later)
# 4th attempt:
# 'circles.png': The problem is that some circles appear "glued together".
# Let's try another technique:
# - smoothing the picture with a Gaussian filter
# - then searching for local maxima and counting regions
# (smoothing avoids having many scatter maxima and a higher level
# must be used than in the previous attempt)
# - use watershed with the maxima as seeds over the thresholded image
# to complete the labelling of circles
print
print "\t4th approach: Smoothing + Local maxima + Watershed"
smoothImage = ndimage.gaussian_filter(images['circles.png'], 10)
localmaxImage = pymorph.regmax(smoothImage)
# A distance transform must be applied before doing the watershed
dist = ndimage.distance_transform_edt(thresholdedImages['circles.png'])
dist = dist.max() - dist
dist -= dist.min()
dist = dist / float(dist.ptp()) * 255
dist = dist.astype(np.uint8)
seeds, nrRegions = ndimage.label(localmaxImage)
labeled = pymorph.cwatershed(dist, seeds)
print "\t" + 'circles.png' + ": " + str(nrRegions)
# worked right only for 'circles.png' !
labeledImages['circles.png'] = (labeled, nrRegions)
mShow(labeled)
print
print "\t5th approach: Smoothing + Multi-threshold +" +\
" Morphology labeling + Size filtering"
# 5th approach (only peppers left!)
imagePeppers = images['peppers.png']
# Problems with peppers are:
# - very different colours, they cause thresholding to work poorly
# - each pepper has some brighter parts which are detected as local maxima
# We propose to address those issues as follows:
# - gaussian filter to smooth regions of light or shadow within each pepper
smoothImage = ndimage.gaussian_filter(imagePeppers, 2)
# - instead of thresholding to create a binary image,
# create multiple thresholds to separate the most frequent colors.
# In this case, 3 thresholds will be enough
mthrImagePeppers = multiThreshold(smoothImage, 3)
# - ndimage.label didn't give good results, we try another
# labelling algorithm
from skimage import morphology
labeled = morphology.label(mthrImagePeppers)
nrRegions = np.max(labeled) + 1
print "\t\tTotal number of regions"
print "\t\t\t" + 'peppers.png' + ": " + str(nrRegions)
# - after counting regions, filter to keep only the sufficiently big ones
filtered, nrRegions = filterRegions(labeled, 0.05)
print "\t\tBig enough regions"
print "\t\t\t" + 'peppers.png' + ": " + str(nrRegions)
labeledImages['peppers.png'] = (filtered, nrRegions)
mShow(filtered)
###########################
# -----> Find center points
print
print "3. Centers for objects"
for img in IMAGE_FILES:
labeledImage, nr_objects = labeledImages[img]
CenterOfMass = ndimage.measurements.center_of_mass
labels = range(1, nr_objects + 1)
centers = CenterOfMass(labeledImage, labeledImage, labels)
centers = [(int(round(x)), int(round(y))) for (x, y) in centers]
print '\t' + img + ": " + str(centers)