def savePlotTrace(parent, dirname, Page, uselatex=False, verbose=False):
""" Save trace plot from Page into file
Parameters:
*parent* the parent window
*dirname* directory to set on saving
*Page* Page containing all variables
*uselatex* Whether to use latex for the ploting or not.
This function uses a hack in misc.py to change the function
for saving the final figure. We wanted save in the same directory
as PyCorrFit was working and the filename should be the tabtitle.
"""
# Close all other plots before commencing
try:
plt.close()
except:
pass
# Trace must be displayed in s
timefactor = 1e-3
tabtitle = Page.tabtitle.GetValue()
if tabtitle.strip() == "":
tabtitle = "page" + str(Page.counter).strip().strip(":")
# Intensity trace in kHz may stay the same
if len(Page.corr.traces) == 0:
return
traces = Page.corr.traces
labels = list()
for ii, tr in enumerate(traces):
labels.append("Channel {}: {}".format(ii + 1, tr.name))
## Check if we can use latex for plotting:
r1 = find_program("latex")[0]
r2 = find_program("dvipng")[0]
# Ghostscript
r31 = find_program("gs")[0]
r32 = find_program("mgs")[0]
r3 = max(r31, r32)
if r1 + r2 + r3 < 3:
uselatex = False
if uselatex == True:
rcParams['text.usetex'] = True
rcParams['text.latex.unicode'] = True
rcParams['font.family'] = 'serif'
rcParams['text.latex.preamble'] = [r"\usepackage{amsmath}"]
for i in np.arange(len(labels)):
labels[i] = ur"{\normalsize " + escapechars(labels[i]) + r"}"
else:
rcParams['text.usetex'] = False
# create plot
# plt.plot(x, y, '.', label = 'original data', markersize=5)
fig = plt.figure(figsize=(10, 3))
wtit = "Trace #{:04d}_{}".format(int(Page.counter.strip(":# ")),
Page.title.strip())
fig.canvas.set_window_title(wtit)
ax = plt.subplot(111)
for i in np.arange(len(traces)):
# Columns
time = traces[i][:, 0] * timefactor
intensity = traces[i][:, 1]
plt.plot(time, intensity, '-', label=labels[i], lw=1)
# set plot boundaries
maxy = -np.infty
miny = np.infty
for tr in traces:
maxy = max(np.max(tr[:, 1]), maxy)
miny = min(np.min(tr[:, 1]), miny)
ax.set_ylim(miny, maxy)
plt.ylabel('count rate [kHz]')
plt.xlabel('time [s]')
# Legend outside of plot
# Decrease size of plot to fit legend
box = ax.get_position()
ax.set_position(
[box.x0, box.y0 + box.height * 0.2, box.width, box.height * 0.9])
plt.legend(
loc='upper center',
bbox_to_anchor=(0.5, -0.35),
prop={'size': 9},
)
## Hack
# We need this for hacking. See edclasses.
fig.canvas.HACK_parent = parent
fig.canvas.HACK_fig = fig
fig.canvas.HACK_Page = Page
fig.canvas.HACK_append = "_trace.png"
plt.tight_layout(rect=(.001, .34, .999, 1.0))
if verbose == True:
plt.show()
else:
# If WXAgg is not used for some reason, then our hack does not work
# and we must use e.g. TkAgg
try:
fig.canvas.toolbar.save()
except AttributeError:
fig.canvas.toolbar.save_figure()
# Close all other plots before commencing
try:
plt.close()
except:
pass
def savePlotTrace(parent, dirname, Page, uselatex=False, verbose=False):
""" Save trace plot from Page into file
Parameters:
*parent* the parent window
*dirname* directory to set on saving
*Page* Page containing all variables
*uselatex* Whether to use latex for the ploting or not.
This function uses a hack in misc.py to change the function
for saving the final figure. We wanted save in the same directory
as PyCorrFit was working and the filename should be the tabtitle.
"""
# Close all other plots before commencing
try:
plt.close()
except:
pass
# Trace must be displayed in s
timefactor = 1e-3
tabtitle = Page.tabtitle.GetValue()
if tabtitle.strip() == "":
tabtitle = "page"+str(Page.counter).strip().strip(":")
# Intensity trace in kHz may stay the same
if len(Page.corr.traces) == 0:
return
traces = Page.corr.traces
labels = list()
for ii, tr in enumerate(traces):
labels.append("Channel {}: {}".format(ii+1, tr.name))
## Check if we can use latex for plotting:
r1 = find_program("latex")[0]
r2 = find_program("dvipng")[0]
# Ghostscript
r31 = find_program("gs")[0]
r32 = find_program("mgs")[0]
r3 = max(r31,r32)
if r1+r2+r3 < 3:
uselatex = False
if uselatex == True:
rcParams['text.usetex']=True
rcParams['text.latex.unicode']=True
rcParams['font.family']='serif'
rcParams['text.latex.preamble']=[r"\usepackage{amsmath}"]
for i in np.arange(len(labels)):
labels[i] = ur"{\normalsize "+escapechars(labels[i])+r"}"
else:
rcParams['text.usetex']=False
# create plot
# plt.plot(x, y, '.', label = 'original data', markersize=5)
fig=plt.figure(figsize=(10,3))
wtit = "Trace #{:04d}_{}".format(int(Page.counter.strip(":# ")),
Page.title.strip())
fig.canvas.set_window_title(wtit)
ax = plt.subplot(111)
for i in np.arange(len(traces)):
# Columns
time = traces[i][:,0]*timefactor
intensity = traces[i][:,1]
plt.plot(time, intensity, '-',
label = labels[i],
lw=1)
# set plot boundaries
maxy = -np.infty
miny = np.infty
for tr in traces:
maxy = max(np.max(tr[:,1]), maxy)
miny = min(np.min(tr[:,1]), miny)
ax.set_ylim(miny, maxy)
plt.ylabel('count rate [kHz]')
plt.xlabel('time [s]')
# Legend outside of plot
# Decrease size of plot to fit legend
box = ax.get_position()
ax.set_position([box.x0, box.y0 + box.height * 0.2,
box.width, box.height * 0.9])
plt.legend(loc='upper center',
bbox_to_anchor=(0.5, -0.35),
prop={'size':9},
)
## Hack
# We need this for hacking. See edclasses.
fig.canvas.HACK_parent = parent
fig.canvas.HACK_fig = fig
fig.canvas.HACK_Page = Page
fig.canvas.HACK_append = "_trace.png"
plt.tight_layout(rect=(.001,.34,.999,1.0))
if verbose == True:
plt.show()
else:
# If WXAgg is not used for some reason, then our hack does not work
# and we must use e.g. TkAgg
try:
fig.canvas.toolbar.save()
except AttributeError:
fig.canvas.toolbar.save_figure()
# Close all other plots before commencing
try:
plt.close()
except:
pass
def savePlotCorrelation(parent,
dirname,
Page,
uselatex=False,
verbose=False,
show_weights=True):
""" Save plot from Page into file
Parameters:
*parent* the parent window
*dirname* directory to set on saving
*Page* Page containing all variables
*uselatex* Whether to use latex for the ploting or not.
This function uses a hack in misc.py to change the function
for saving the final figure. We wanted save in the same directory
as PyCorrFit was working and the filename should be the tabtitle.
"""
# Close all other plots before commencing
try:
plt.close()
except:
pass
# get data
corr = Page.corr
dataexp = corr.correlation_plot
resid = corr.residuals_plot
fit = corr.modeled_plot
weights = Page.weights_plot_fill_area
tabtitle = Page.tabtitle.GetValue()
#fitlabel = ur"Fit model: "+str(mdls.modeldict[Page.modelid][0])
fitlabel = Page.corr.fit_model.name
labelweights = ur"Weights of fit"
labels, parms = mdls.GetHumanReadableParms(Page.modelid,
corr.fit_parameters)
if dataexp is None:
if tabtitle.strip() == "":
fitlabel = Page.corr.fit_model.name
else:
fitlabel = tabtitle
else:
if tabtitle.strip() == "":
tabtitle = "page" + str(Page.counter).strip().strip(":")
if Page.corr.normparm is not None:
fitlabel += ur", normalized to " + Page.corr.fit_model.parameters[0][
Page.corr.normparm]
## Check if we can use latex for plotting:
r1 = find_program("latex")[0]
r2 = find_program("dvipng")[0]
# Ghostscript
r31 = find_program("gs")[0]
r32 = find_program("mgs")[0] # from miktex
r3 = max(r31, r32)
if r1 + r2 + r3 < 3:
uselatex = False
if uselatex == True:
rcParams['text.usetex'] = True
rcParams['text.latex.unicode'] = True
rcParams['font.family'] = 'serif'
rcParams['text.latex.preamble'] = [
r"""\usepackage{amsmath}
\usepackage[utf8x]{inputenc}
\usepackage{amssymb}
\usepackage{siunitx}"""
]
fitlabel = ur"{\normalsize " + escapechars(fitlabel) + r"}"
tabtitle = ur"{\normalsize " + escapechars(tabtitle) + r"}"
labelweights = ur"{\normalsize " + escapechars(labelweights) + r"}"
else:
rcParams['text.usetex'] = False
# create plot
# plt.plot(x, y, '.', label = 'original data', markersize=5)
fig = plt.figure()
wtit = "Correlation #{:04d}_{}".format(int(Page.counter.strip(":# ")),
Page.title.strip())
fig.canvas.set_window_title(wtit)
if resid is not None:
gs = gridspec.GridSpec(2, 1, height_ratios=[5, 1])
ax = plt.subplot(gs[0])
else:
ax = plt.subplot(111)
# ax = plt.axes()
ax.semilogx()
# plot fit first
plt.plot(fit[:, 0], fit[:, 1], '-', label=fitlabel, lw=1.5, color="blue")
if dataexp is not None:
plt.plot(dataexp[:, 0],
dataexp[:, 1],
'-',
color="black",
alpha=.7,
label=tabtitle,
lw=1)
else:
plt.xlabel(ur'lag time $\tau$ [ms]')
if weights is not None and show_weights is True:
plt.fill_between(weights[0][:, 0],
weights[0][:, 1],
weights[1][:, 1],
color='cyan')
# fake legend:
p = plt.Rectangle((0, 0), 0, 0, color='cyan', label=labelweights)
ax.add_patch(p)
plt.ylabel('correlation')
if dataexp is not None:
mind = np.min([dataexp[:, 1], fit[:, 1]])
maxd = np.max([dataexp[:, 1], fit[:, 1]])
else:
mind = np.min(fit[:, 1])
maxd = np.max(fit[:, 1])
ymin = mind - (maxd - mind) / 20.
ymax = maxd + (maxd - mind) / 20.
ax.set_ylim(bottom=ymin, top=ymax)
xmin = np.min(fit[:, 0])
xmax = np.max(fit[:, 0])
ax.set_xlim(xmin, xmax)
# Add some nice text:
if uselatex == True and len(parms) != 0:
text = r""
text += r'\[' #every line is a separate raw string...
text += r'\begin{split}' # ...but they are all concatenated
# by the interpreter :-)
for i in np.arange(len(parms)):
text += ur' {} &= {:.3g} \\'.format(latexmath(labels[i]), parms[i])
## According to issue #54, we remove fitting errors from plots
#if errparms is not None:
# keys = errparms.keys()
# keys.sort()
# for key in keys:
# text += r' \Delta '+latexmath(key)+r" &= " + str(errparms[key]) +r' \\ '
text += r' \end{split} '
text += r' \] '
else:
text = ur""
for i in np.arange(len(parms)):
text += u"{} = {:.3g}\n".format(labels[i], parms[i])
## According to issue #54, we remove fitting errors from plots
#if errparms is not None:
# keys = errparms.keys()
# keys.sort()
# for key in keys:
# text += "Err "+key+" = " + str(errparms[key]) +"\n"
logmax = np.log10(xmax)
logmin = np.log10(xmin)
logtext = 0.6 * (logmax - logmin) + logmin
xt = 10**(logtext)
yt = 0.3 * ymax
plt.text(xt, yt, text, size=12)
if resid is not None:
ax2 = plt.subplot(gs[1])
#ax2 = plt.axes()
ax2.semilogx()
if Page.corr.is_weighted_fit:
if uselatex == True:
lb = r"\newline \indent "
else:
lb = "\n"
yLabelRes = "weighted " + lb + "residuals"
else:
yLabelRes = "residuals"
minx = np.min(resid[:, 0])
maxx = np.max(resid[:, 0])
miny = np.min(resid[:, 1])
maxy = np.max(resid[:, 1])
plt.hlines(0, minx, maxx, colors="orange")
plt.plot(resid[:, 0],
resid[:, 1],
'-',
color="black",
alpha=.85,
label=yLabelRes,
lw=1)
plt.xlabel(r'lag time $\tau$ [ms]')
plt.ylabel(yLabelRes, multialignment='center')
ax2.set_xlim(minx, maxx)
maxy = max(abs(maxy), abs(miny))
ax2.set_ylim(-maxy, maxy)
ticks = ax2.get_yticks()
ax2.set_yticks([ticks[0], ticks[-1], 0])
## Hack
# We need this for hacking. See edclasses.
fig.canvas.HACK_parent = parent
fig.canvas.HACK_fig = fig
fig.canvas.HACK_Page = Page
fig.canvas.HACK_append = ".png"
# Legend outside of plot
# Decrease size of plot to fit legend
box = ax.get_position()
ax.set_position(
[box.x0, box.y0 + box.height * 0.2, box.width, box.height * 0.9])
if resid is not None:
box2 = ax2.get_position()
ax2.set_position(
[box2.x0, box2.y0 + box.height * 0.2, box2.width, box2.height])
ax.legend(loc='upper center',
bbox_to_anchor=(0.5, -0.55),
prop={'size': 9})
if verbose == True:
plt.show()
else:
# If WXAgg is not used for some reason, then our hack does not work
# and we must use e.g. TkAgg
try:
fig.canvas.toolbar.save()
except AttributeError:
fig.canvas.toolbar.save_figure()
# Close all other plots before commencing
try:
plt.close()
except:
pass
def savePlotCorrelation(parent, dirname, Page, uselatex=False,
verbose=False, show_weights=True):
""" Save plot from Page into file
Parameters:
*parent* the parent window
*dirname* directory to set on saving
*Page* Page containing all variables
*uselatex* Whether to use latex for the ploting or not.
This function uses a hack in misc.py to change the function
for saving the final figure. We wanted save in the same directory
as PyCorrFit was working and the filename should be the tabtitle.
"""
# Close all other plots before commencing
try:
plt.close()
except:
pass
# get data
corr = Page.corr
dataexp = corr.correlation_plot
resid = corr.residuals_plot
fit = corr.modeled_plot
weights = Page.weights_plot_fill_area
tabtitle = Page.tabtitle.GetValue()
#fitlabel = ur"Fit model: "+str(mdls.modeldict[Page.modelid][0])
fitlabel = Page.corr.fit_model.name
labelweights = ur"Weights of fit"
labels, parms = mdls.GetHumanReadableParms(Page.modelid,
corr.fit_parameters)
if dataexp is None:
if tabtitle.strip() == "":
fitlabel = Page.corr.fit_model.name
else:
fitlabel = tabtitle
else:
if tabtitle.strip() == "":
tabtitle = "page"+str(Page.counter).strip().strip(":")
if Page.corr.normparm is not None:
fitlabel += ur", normalized to "+Page.corr.fit_model.parameters[0][Page.corr.normparm]
## Check if we can use latex for plotting:
r1 = find_program("latex")[0]
r2 = find_program("dvipng")[0]
# Ghostscript
r31 = find_program("gs")[0]
r32 = find_program("mgs")[0] # from miktex
r3 = max(r31,r32)
if r1+r2+r3 < 3:
uselatex = False
if uselatex == True:
rcParams['text.usetex']=True
rcParams['text.latex.unicode']=True
rcParams['font.family']='serif'
rcParams['text.latex.preamble']=[r"""\usepackage{amsmath}
\usepackage[utf8x]{inputenc}
\usepackage{amssymb}
\usepackage{siunitx}"""]
fitlabel = ur"{\normalsize "+escapechars(fitlabel)+r"}"
tabtitle = ur"{\normalsize "+escapechars(tabtitle)+r"}"
labelweights = ur"{\normalsize "+escapechars(labelweights)+r"}"
else:
rcParams['text.usetex']=False
# create plot
# plt.plot(x, y, '.', label = 'original data', markersize=5)
fig=plt.figure()
wtit = "Correlation #{:04d}_{}".format(int(Page.counter.strip(":# ")),
Page.title.strip())
fig.canvas.set_window_title(wtit)
if resid is not None:
gs = gridspec.GridSpec(2, 1, height_ratios=[5,1])
ax = plt.subplot(gs[0])
else:
ax = plt.subplot(111)
# ax = plt.axes()
ax.semilogx()
# plot fit first
plt.plot(fit[:,0], fit[:,1], '-', label=fitlabel, lw=1.5,
color="blue")
if dataexp is not None:
plt.plot(dataexp[:,0], dataexp[:,1], '-', color="black",
alpha=.7, label=tabtitle, lw=1)
else:
plt.xlabel(ur'lag time $\tau$ [ms]')
if weights is not None and show_weights is True:
plt.fill_between(weights[0][:,0],weights[0][:,1],weights[1][:,1],
color='cyan')
# fake legend:
p = plt.Rectangle((0, 0), 0, 0, color='cyan',
label=labelweights)
ax.add_patch(p)
plt.ylabel('correlation')
if dataexp is not None:
mind = np.min([ dataexp[:,1], fit[:,1]])
maxd = np.max([ dataexp[:,1], fit[:,1]])
else:
mind = np.min(fit[:,1])
maxd = np.max(fit[:,1])
ymin = mind - (maxd - mind)/20.
ymax = maxd + (maxd - mind)/20.
ax.set_ylim(bottom=ymin, top=ymax)
xmin = np.min(fit[:,0])
xmax = np.max(fit[:,0])
ax.set_xlim(xmin, xmax)
# Add some nice text:
if uselatex == True and len(parms) != 0:
text = r""
text += r'\[' #every line is a separate raw string...
text += r'\begin{split}' # ...but they are all concatenated
# by the interpreter :-)
for i in np.arange(len(parms)):
text += ur' {} &= {:.3g} \\'.format(latexmath(labels[i]), parms[i])
## According to issue #54, we remove fitting errors from plots
#if errparms is not None:
# keys = errparms.keys()
# keys.sort()
# for key in keys:
# text += r' \Delta '+latexmath(key)+r" &= " + str(errparms[key]) +r' \\ '
text += r' \end{split} '
text += r' \] '
else:
text = ur""
for i in np.arange(len(parms)):
text += u"{} = {:.3g}\n".format(labels[i], parms[i])
## According to issue #54, we remove fitting errors from plots
#if errparms is not None:
# keys = errparms.keys()
# keys.sort()
# for key in keys:
# text += "Err "+key+" = " + str(errparms[key]) +"\n"
logmax = np.log10(xmax)
logmin = np.log10(xmin)
logtext = 0.6*(logmax-logmin)+logmin
xt = 10**(logtext)
yt = 0.3*ymax
plt.text(xt,yt,text, size=12)
if resid is not None:
ax2 = plt.subplot(gs[1])
#ax2 = plt.axes()
ax2.semilogx()
if Page.corr.is_weighted_fit:
if uselatex == True:
lb = r"\newline \indent "
else:
lb = "\n"
yLabelRes = "weighted "+ lb +"residuals"
else:
yLabelRes = "residuals"
minx = np.min(resid[:,0])
maxx = np.max(resid[:,0])
miny = np.min(resid[:,1])
maxy = np.max(resid[:,1])
plt.hlines(0, minx, maxx, colors="orange")
plt.plot(resid[:,0], resid[:,1], '-', color="black",
alpha=.85, label=yLabelRes, lw=1)
plt.xlabel(r'lag time $\tau$ [ms]')
plt.ylabel(yLabelRes, multialignment='center')
ax2.set_xlim(minx, maxx)
maxy = max(abs(maxy), abs(miny))
ax2.set_ylim(-maxy, maxy)
ticks = ax2.get_yticks()
ax2.set_yticks([ticks[0], ticks[-1], 0])
## Hack
# We need this for hacking. See edclasses.
fig.canvas.HACK_parent = parent
fig.canvas.HACK_fig = fig
fig.canvas.HACK_Page = Page
fig.canvas.HACK_append = ".png"
# Legend outside of plot
# Decrease size of plot to fit legend
box = ax.get_position()
ax.set_position([box.x0, box.y0 + box.height * 0.2,
box.width, box.height * 0.9])
if resid is not None:
box2 = ax2.get_position()
ax2.set_position([box2.x0, box2.y0 + box.height * 0.2,
box2.width, box2.height])
ax.legend(loc='upper center', bbox_to_anchor=(0.5, -0.55),
prop={'size':9})
if verbose == True:
plt.show()
else:
# If WXAgg is not used for some reason, then our hack does not work
# and we must use e.g. TkAgg
try:
fig.canvas.toolbar.save()
except AttributeError:
fig.canvas.toolbar.save_figure()
# Close all other plots before commencing
try:
plt.close()
except:
pass
