def _createPlot(self,
title,
xTitle,
yTitle,
fnOutput,
mdLabelX,
mdLabelY,
color='g',
figure=None):
xplotter = XmippPlotter(figure=figure)
xplotter.plot_title_fontsize = 11
ax = xplotter.createSubPlot(title, xTitle, yTitle, 1, 1)
ax.set_yscale('log')
ax.set_xscale('log')
#plot noise and related errorbar
fnOutputN = self.protocol._defineResultsNoiseName()
md = xmipp.MetaData(fnOutputN)
xValueN = md.getColumnValues(xmipp.MDL_COUNT)
yValueN = md.getColumnValues(xmipp.MDL_AVG)
plt.plot(xValueN,
yValueN,
'--',
color='r',
label='Aligned gaussian noise')
# putting error bar
md = xmipp.MetaData(fnOutputN)
yErrN = md.getColumnValues(xmipp.MDL_STDDEV)
xValueNe = md.getColumnValues(xmipp.MDL_COUNT)
yValueNe = md.getColumnValues(xmipp.MDL_AVG)
plt.errorbar(xValueNe, yValueNe, yErrN, fmt='o', color='k')
#plot real data-set
fnOutput = self.protocol._defineResultsName()
md = xmipp.MetaData(fnOutput)
xValue = md.getColumnValues(xmipp.MDL_COUNT)
yValue = md.getColumnValues(xmipp.MDL_AVG)
plt.plot(xValue, yValue, color='g', label='Aligned particles')
# putting error bar
md = xmipp.MetaData(fnOutput)
yErr = md.getColumnValues(xmipp.MDL_STDDEV)
xValue = md.getColumnValues(xmipp.MDL_COUNT)
yValue = md.getColumnValues(xmipp.MDL_AVG)
plt.errorbar(xValue, yValue, yErr, fmt='o')
plt.legend(loc='upper right', fontsize=11)
return xplotter
def _createPlot(self, figure=None):
xplotter = XmippPlotter(figure=figure)
xplotter.plot_title_fontsize = 11
title = 'Validation 3D Reconstruction (Overfitting)'
xTitle = '# Particles'
yTitle = 'Resolution in A'
ax = xplotter.createSubPlot(title, xTitle, yTitle, 1, 1)
ax.set_yscale('log')
ax.set_xscale('log')
# plot real data-set
fnOutput = self.protocol._defineResultsTxt()
if exists(fnOutput):
fileValues = open(fnOutput, 'r')
xVal = []
yVal = []
yErr = []
for line in fileValues:
values = line.split()
xVal.append(float(values[0]))
yVal.append(float(values[1]))
yErr.append(float(values[2]))
plt.plot(xVal, yVal, color='g', label='Aligned particles')
plt.errorbar(xVal, yVal, yErr, fmt='o')
plt.legend(loc='upper right', fontsize=11)
# plot noise and related errorbar
fnOutputN = self.protocol._defineResultsNoiseTxt()
if exists(fnOutputN):
fileNoise = open(fnOutputN, 'r')
yValN = []
yErrN = []
for line in fileNoise:
values = line.split()
yValN.append(float(values[1]))
yErrN.append(float(values[2]))
plt.plot(xVal,
yValN,
'--',
color='r',
label='Aligned gaussian noise')
plt.errorbar(xVal, yValN, yErrN, fmt='o', color='k')
return xplotter
def _createPlotInv(self, figure=None):
xplotter = XmippPlotter(figure=figure)
xplotter.plot_title_fontsize = 11
title = 'Validation 3D Reconstruction (Overfitting)'
xTitle = 'log10(# Particles)'
yTitle = '1/Resolution^2 in 1/A^2'
ax = xplotter.createSubPlot(title, xTitle, yTitle, 1, 1)
# plot real data-set
fnOutput = self.protocol._defineResultsTxt()
if exists(fnOutput):
fileValues = open(fnOutput, 'r')
xValInv = []
yValInv = []
yErrInv = []
for line in fileValues:
values = line.split()
xValInv.append(log10(float(values[0])))
yValInv.append(float(values[3]))
yErrInv.append(float(values[4]))
plt.plot(xValInv, yValInv, color='g', label='Aligned particles')
plt.errorbar(xValInv, yValInv, yErrInv, fmt='o')
plt.legend(loc='upper right', fontsize=11)
# plot noise and related errorbar
fnOutputN = self.protocol._defineResultsNoiseTxt()
if exists(fnOutputN):
fileNoise = open(fnOutputN, 'r')
yValNInv = []
yErrNInv = []
for line in fileNoise:
values = line.split()
yValNInv.append(float(values[3]))
yErrNInv.append(float(values[4]))
plt.plot(xValInv,
yValNInv,
'--',
color='r',
label='Aligned gaussian noise')
plt.errorbar(xValInv, yValNInv, yErrNInv, fmt='o', color='k')
return xplotter
def _createPlot(self, title, xTitle, yTitle, fnOutput, mdLabelX,
mdLabelY, color = 'g', figure=None):
xplotter = XmippPlotter(figure=figure)
xplotter.plot_title_fontsize = 11
ax=xplotter.createSubPlot(title, xTitle, yTitle, 1, 1)
ax.set_yscale('log')
ax.set_xscale('log')
#plot noise and related errorbar
fnOutputN = self.protocol._defineResultsNoiseName()
md = xmipp.MetaData(fnOutputN)
xValueN = md.getColumnValues(xmipp.MDL_COUNT)
yValueN = md.getColumnValues(xmipp.MDL_AVG)
plt.plot(xValueN, yValueN, '--', color='r',
label='Aligned gaussian noise')
# putting error bar
md = xmipp.MetaData(fnOutputN)
yErrN = md.getColumnValues(xmipp.MDL_STDDEV)
xValueNe = md.getColumnValues(xmipp.MDL_COUNT)
yValueNe = md.getColumnValues(xmipp.MDL_AVG)
plt.errorbar(xValueNe, yValueNe, yErrN, fmt='o', color='k')
#plot real data-set
fnOutput = self.protocol._defineResultsName()
md = xmipp.MetaData(fnOutput)
xValue = md.getColumnValues(xmipp.MDL_COUNT)
yValue = md.getColumnValues(xmipp.MDL_AVG)
plt.plot(xValue, yValue, color='g', label='Aligned particles')
# putting error bar
md = xmipp.MetaData(fnOutput)
yErr = md.getColumnValues(xmipp.MDL_STDDEV)
xValue = md.getColumnValues(xmipp.MDL_COUNT)
yValue = md.getColumnValues(xmipp.MDL_AVG)
plt.errorbar(xValue, yValue, yErr, fmt='o')
plt.legend(loc='upper right' , fontsize = 11)
return xplotter
def _visualize(self, e=None):
fnOutput1 = self.protocol._defineResultsName1()
fnOutput2 = self.protocol._defineResultsName2()
fnOutput3 = self.protocol._defineResultsName3()
if not os.path.exists(fnOutput3):
return [
self.errorMessage(
'The necessary metadata was not produced\n'
'Execute again the protocol\n',
title='Missing result file')
]
volList = [vol.clone() for vol in self.protocol._iterInputVolumes()]
# 1 Dimension
data1 = []
fnCoordinate1 = open(fnOutput1, "r")
for line in fnCoordinate1:
fields = line.split()
rowdata = map(float, fields)
data1.extend(rowdata)
data1N = [[0 for i in range(1)] for i in volList]
count = 0
for i in volList:
data1N[count][0] = data1[count]
count += 1
data1N = np.array(data1N)
# 2 Dimensions
data2 = []
fnCoordinate2 = open(fnOutput2, "r")
for line in fnCoordinate2:
fields = line.split()
rowdata = map(float, fields)
data2.extend(rowdata)
count = 0
data2N = [[0 for i in range(2)] for i in volList]
nVolj = 1
for j in range(2):
nVoli = 1
for i in volList:
data2N[(nVoli - 1)][(nVolj - 1)] = data2[count]
count += 1
nVoli += 1
nVolj += 1
data2N = np.array(data2N)
# 3 Dimensions
data3 = []
fnCoordinate3 = open(fnOutput3, "r")
for line in fnCoordinate3:
fields = line.split()
rowdata = map(float, fields)
data3.extend(rowdata)
count = 0
data3N = [[0 for i in range(3)] for i in volList]
nVolj = 1
for j in range(3):
nVoli = 1
for i in volList:
data3N[(nVoli - 1)][(nVolj - 1)] = data3[count]
count += 1
nVoli += 1
nVolj += 1
data3N = np.array(data3N)
count = 0
labels = []
for voli in volList:
if not voli.getObjLabel():
count += 1
labels.append("vol_%02d" % count)
else:
labels.append("%s" % voli.getObjLabel())
count += 1
nComponent = self.numberOfDimensions.get()
if nComponent == 1:
AX = plt.subplot(111)
val = 0
plot = plt.plot(data1N[:, 0],
np.zeros_like(data1N[:, 0]) + val,
'o',
c='g')
plt.xlabel('Dimension 1', fontsize=11)
AX.set_yticks([1])
plt.title('StructMap')
for label, x, y in zip(labels, data1N[:, 0],
np.zeros_like(data1N[:, 0]) + val):
plt.annotate(label,
xy=(x, y),
xytext=(-8, 8),
textcoords='offset points',
ha='right',
va='bottom',
fontsize=9,
bbox=dict(boxstyle='round,pad=0.3',
fc='yellow',
alpha=0.3))
plt.show()
elif nComponent == 2:
plot = plt.scatter(data2N[:, 0], data2N[:, 1], marker='o', c='g')
plt.xlabel('Dimension 1', fontsize=11)
plt.ylabel('Dimension 2', fontsize=11)
plt.title('StructMap')
for label, x, y in zip(labels, data2N[:, 0], data2N[:, 1]):
plt.annotate(label,
xy=(x, y),
xytext=(-8, 8),
textcoords='offset points',
ha='right',
va='bottom',
fontsize=9,
bbox=dict(boxstyle='round,pad=0.3',
fc='yellow',
alpha=0.3))
plt.grid(True)
plt.show()
else:
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.scatter(data3N[:, 0],
data3N[:, 1],
data3N[:, 2],
marker='o',
c='g')
ax.set_xlabel('Dimension 1', fontsize=11)
ax.set_ylabel('Dimension 2', fontsize=11)
ax.set_zlabel('Dimension 3', fontsize=11)
ax.text2D(0.05, 0.95, "StructMap", transform=ax.transAxes)
tX, tY, _ = proj3d.proj_transform(data3N[:, 0], data3N[:, 1],
data3N[:, 2], ax.get_proj())
Labels = []
for i in range(len(data3N[:, 0])):
text = labels[i]
label = ax.annotate(text,
xycoords='data',
xy=(tX[i], tY[i]),
xytext=(-8, 8),
textcoords='offset points',
ha='right',
va='bottom',
fontsize=9,
bbox=dict(boxstyle='round,pad=0.5',
fc='yellow',
alpha=0.5))
Labels.append(label)
def update_position(e):
x2, y2, _ = proj3d.proj_transform(data3N[:, 0], data3N[:, 1],
data3N[:, 2], ax.get_proj())
for i in range(len(data3N[:, 0])):
label = Labels[i]
label.xy = x2[i], y2[i]
label.update_positions(fig.canvas.renderer)
fig.canvas.draw()
fig.canvas.mpl_connect('button_release_event', update_position)
plt.show()
return plot
def _visualize(self, e=None):
nDim = self.numberOfDimensions.get()
fnOutput = self.protocol._defineResultsName(nDim)
if not os.path.exists(fnOutput):
return [
self.errorMessage(
'The necessary metadata was not produced\n'
'Execute again the protocol\n',
title='Missing result file')
]
coordinates = np.loadtxt(fnOutput)
# Create labels
count = 0
labels = []
for voli in self.protocol._iterInputVolumes():
if not voli.getObjLabel():
count += 1
labels.append("vol_%02d" % count)
else:
labels.append("%s" % voli.getObjLabel())
count += 1
val = 0
if nDim == 1:
AX = plt.subplot(111)
plot = plt.plot(coordinates,
np.zeros_like(coordinates) + val,
'o',
c='g')
plt.xlabel('Dimension 1', fontsize=11)
AX.set_yticks([1])
plt.title('StructMap')
for label, x, y in zip(labels, coordinates,
np.zeros_like(coordinates)):
plt.annotate(label,
xy=(x, y),
xytext=(x + val, y + val),
textcoords='data',
ha='right',
va='bottom',
fontsize=9,
bbox=dict(boxstyle='round,pad=0.3',
fc='yellow',
alpha=0.3))
plt.grid(True)
plt.show()
elif nDim == 2:
plot = plt.scatter(coordinates[:, 0],
coordinates[:, 1],
marker='o',
c='g')
plt.xlabel('Dimension 1', fontsize=11)
plt.ylabel('Dimension 2', fontsize=11)
plt.title('StructMap')
for label, x, y in zip(labels, coordinates[:, 0], coordinates[:,
1]):
plt.annotate(label,
xy=(x, y),
xytext=(x + val, y + val),
textcoords='data',
ha='right',
va='bottom',
fontsize=9,
bbox=dict(boxstyle='round,pad=0.3',
fc='yellow',
alpha=0.3))
plt.grid(True)
plt.show()
else:
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.scatter(coordinates[:, 0],
coordinates[:, 1],
coordinates[:, 2],
marker='o',
c='g')
ax.set_xlabel('Dimension 1', fontsize=11)
ax.set_ylabel('Dimension 2', fontsize=11)
ax.set_zlabel('Dimension 3', fontsize=11)
ax.text2D(0.05, 0.95, "StructMap", transform=ax.transAxes)
x2, y2, _ = proj3d.proj_transform(coordinates[:, 0],
coordinates[:, 1],
coordinates[:, 2], ax.get_proj())
Labels = []
for i in range(len(coordinates[:, 0])):
text = labels[i]
label = ax.annotate(text,
xycoords='data',
xy=(x2[i], y2[i]),
xytext=(x2[i] + val, y2[i] + val),
textcoords='data',
ha='right',
va='bottom',
fontsize=9,
bbox=dict(boxstyle='round,pad=0.3',
fc='yellow',
alpha=0.3))
Labels.append(label)
def update_position(e):
x2, y2, _ = proj3d.proj_transform(coordinates[:, 0],
coordinates[:, 1],
coordinates[:, 2],
ax.get_proj())
for i in range(len(coordinates[:, 0])):
label = Labels[i]
label.xytext = (x2[i], y2[i])
label.update_positions(fig.canvas.get_renderer())
fig.canvas.draw()
fig.canvas.mpl_connect('button_release_event', update_position)
plt.show()
return plot
def _visualize(self, e=None):
fnOutput1 = self.protocol._defineResultsName1()
fnOutput2 = self.protocol._defineResultsName2()
fnOutput3 = self.protocol._defineResultsName3()
if not os.path.exists(fnOutput3):
return [self.errorMessage('The necessary metadata was not produced\n'
'Execute again the protocol\n',
title='Missing result file')]
volList = [vol.clone() for vol in self.protocol._iterInputVolumes()]
# 1 Dimension
data1 = []
fnCoordinate1 = open(fnOutput1, "r")
for line in fnCoordinate1:
fields = line.split()
rowdata = map(float, fields)
data1.extend(rowdata)
data1N = [[0 for i in range(1)] for i in volList]
count = 0
for i in volList:
data1N[count][0] = data1[count]
count += 1
data1N = np.array (data1N)
# 2 Dimensions
data2 = []
fnCoordinate2 = open(fnOutput2, "r")
for line in fnCoordinate2:
fields = line.split()
rowdata = map(float, fields)
data2.extend(rowdata)
count = 0
data2N = [[0 for i in range(2)] for i in volList]
nVolj = 1
for j in range(2):
nVoli = 1
for i in volList:
data2N[(nVoli-1)][(nVolj-1)] = data2[count]
count += 1
nVoli += 1
nVolj += 1
data2N = np.array (data2N)
# 3 Dimensions
data3 = []
fnCoordinate3 = open(fnOutput3, "r")
for line in fnCoordinate3:
fields = line.split()
rowdata = map(float, fields)
data3.extend(rowdata)
count = 0
data3N = [[0 for i in range(3)] for i in volList]
nVolj = 1
for j in range(3):
nVoli = 1
for i in volList:
data3N[(nVoli-1)][(nVolj-1)] = data3[count]
count += 1
nVoli += 1
nVolj += 1
data3N = np.array (data3N)
count = 0
labels = []
for voli in volList:
if not voli.getObjLabel():
count+=1
labels.append("vol_%02d"%count)
else:
labels.append("%s"%voli.getObjLabel())
count += 1
nComponent = self.numberOfDimensions.get()
if nComponent == 1:
AX = plt.subplot(111)
val = 0
plot = plt.plot(data1N[:, 0], np.zeros_like(data1N[:, 0]) + val, 'o', c='g')
plt.xlabel('Dimension 1', fontsize=11)
AX.set_yticks([1])
plt.title('StructMap')
for label, x, y in zip(labels, data1N[:, 0], np.zeros_like(data1N[:, 0 ]) + val):
plt.annotate(
label,
xy = (x, y), xytext = (-8, 8),
textcoords = 'offset points', ha = 'right', va = 'bottom',fontsize=9,
bbox = dict(boxstyle = 'round,pad=0.3', fc = 'yellow', alpha = 0.3))
plt.show()
elif nComponent == 2:
plot = plt.scatter(data2N[:, 0], data2N[:, 1], marker='o', c='g')
plt.xlabel('Dimension 1', fontsize=11)
plt.ylabel('Dimension 2', fontsize=11)
plt.title('StructMap')
for label, x, y in zip(labels, data2N[:, 0], data2N[:, 1]):
plt.annotate(
label,
xy = (x, y), xytext = (-8, 8),
textcoords = 'offset points', ha = 'right', va = 'bottom',fontsize=9,
bbox = dict(boxstyle = 'round,pad=0.3', fc = 'yellow', alpha = 0.3))
plt.grid(True)
plt.show()
else:
fig = plt.figure()
ax = fig.add_subplot(111, projection = '3d')
ax.scatter(data3N[:, 0], data3N[:, 1], data3N[:, 2], marker = 'o', c='g')
ax.set_xlabel('Dimension 1', fontsize=11)
ax.set_ylabel('Dimension 2', fontsize=11)
ax.set_zlabel('Dimension 3', fontsize=11)
ax.text2D(0.05, 0.95, "StructMap", transform=ax.transAxes)
tX, tY, _ = proj3d.proj_transform(data3N[:, 0], data3N[:, 1],
data3N[:, 2], ax.get_proj())
Labels = []
for i in range(len(data3N[:, 0])):
text = labels[i]
label = ax.annotate(text,
xycoords='data',
xy = (tX[i], tY[i]), xytext = (-8, 8),
textcoords = 'offset points', ha = 'right',
va = 'bottom', fontsize=9,
bbox = dict(boxstyle = 'round,pad=0.5',
fc = 'yellow', alpha = 0.5))
Labels.append(label)
def update_position(e):
x2, y2, _ = proj3d.proj_transform(data3N[:, 0], data3N[:, 1],
data3N[:, 2], ax.get_proj())
for i in range(len(data3N[:, 0])):
label = Labels[i]
label.xy = x2[i],y2[i]
label.update_positions(fig.canvas.renderer)
fig.canvas.draw()
fig.canvas.mpl_connect('button_release_event', update_position)
plt.show()
return plot
def _visualize(self, e=None):
nDim = self.numberOfDimensions.get()
fnOutput = self.protocol._defineResultsName(nDim)
if not os.path.exists(fnOutput):
return [
self.errorMessage(
'The necessary metadata was not produced\n'
'Execute again the protocol\n',
title='Missing result file')
]
coordinates = np.loadtxt(fnOutput)
# Create labels
count = 0
labels = []
for voli in self.protocol._iterInputVolumes():
if not voli.getObjLabel():
count += 1
labels.append("vol_%02d" % count)
else:
labels.append("%s" % voli.getObjLabel())
count += 1
val = 0
if nDim == 1:
AX = plt.subplot(111)
plot = plt.plot(coordinates,
np.zeros_like(coordinates) + val,
'o',
c='g')
plt.xlabel('Dimension 1', fontsize=11)
AX.set_yticks([1])
plt.title('StructMap')
for label, x, y in zip(labels, coordinates,
np.zeros_like(coordinates)):
plt.annotate(label,
xy=(x, y),
xytext=(x + val, y + val),
textcoords='data',
ha='right',
va='bottom',
fontsize=9,
bbox=dict(boxstyle='round,pad=0.3',
fc='yellow',
alpha=0.3))
plt.grid(True)
plt.show()
elif nDim == 2:
plot = plt.scatter(coordinates[:, 0],
coordinates[:, 1],
marker='o',
c='g')
plt.xlabel('Dimension 1', fontsize=11)
plt.ylabel('Dimension 2', fontsize=11)
plt.title('StructMap')
for label, x, y in zip(labels, coordinates[:, 0], coordinates[:,
1]):
plt.annotate(label,
xy=(x, y),
xytext=(x + val, y + val),
textcoords='data',
ha='right',
va='bottom',
fontsize=9,
bbox=dict(boxstyle='round,pad=0.3',
fc='yellow',
alpha=0.3))
plt.grid(True)
plt.show()
else:
fig = figure()
ax = Axes3D(fig)
for i in range(len(coordinates[:, 0])):
ax.scatter(coordinates[i, 0],
coordinates[i, 1],
coordinates[i, 2],
marker='o',
s=50,
c='g')
ax.text(coordinates[i, 0],
coordinates[i, 1],
coordinates[i, 2],
' %s' % (labels[i]),
size=15,
zorder=1,
color='k')
ax.set_xlabel('Dimension 1', fontsize=15)
ax.set_ylabel('Dimension 2', fontsize=15)
ax.set_zlabel('Dimension 3', fontsize=15)
ax.xaxis.labelpad = 10
ax.yaxis.labelpad = 10
ax.zaxis.labelpad = 10
ax.text2D(0.05,
0.95,
"StructMap",
transform=ax.transAxes,
fontsize=15)
plt.show()
return plot