class PlotFigure(wx.Window):
#============================================================================
def __init__(self,parent,size=wx.DefaultSize, filename=None, options=None):
wx.Window.__init__( self, parent, id=-1, style=wx.NO_BORDER)
self.fig = Figure((21,21),60)
self.canvas = FigureCanvas(self, -1, self.fig)
self.toolbar = Toolbar(self.canvas)
self.choice=PlotChoice(self)
self.choice.mode="Standard"
self.toolbar.Realize()
self.parent=parent
# On Windows, default frame size behaviour is incorrect
# you don't need this under Linux
tw, th = self.toolbar.GetSizeTuple()
fw, fh = self.canvas.GetSizeTuple()
self.toolbar.SetSize(wx.Size(fw, th))
# Create a figure manager to manage things
self.figmgr = FigureManager(self.canvas, 1, self)
self.Fit()
self.filename=filename
if DEBUG :
DEBUG_MSG("plot :"+filename)
self.n=0
self.ni=0
self.vl=0
self.vl1=0
self.sw=0
self.sw1=0
self.flag_sum=False
try:
[dirname,shortfilename]=os.path.split(filename)
[basename,extension]=os.path.splitext(shortfilename)
self.title=basename
self.filename=dirname+"\\"+basename+".spe"
if not options:
self.options={'units': 'ppm',
'titles': 'no',
'yoffset': '0.001',
'yaxis': 'yes'}
self.grid=False
except:
pass
def GetToolBar(self):
# You will need to override GetToolBar if you are using an
# unmanaged toolbar in your frame
return self.toolbar
def read_spectra(self):
#frequency=(i+1)*sw/n-sw/2.
#ppm=frequency*1.e6/abs(vl)
DEBUG_MSG("read_spectra : "+self.filename)
try: #Handling filename error (Correction of a bug for NEw in file menu)
f=open(self.filename,"rb")
except:
return False
try: # Handling opening erros
#first the header
line=f.readline() # PULSAR string
DEBUG_MSG(rtn(line))
line=f.readline() # NP string
DEBUG_MSG(rtn(line))
items=line.split('=')
n=int(items[1])
line=f.readline() # SW string
DEBUG_MSG(rtn(line))
items=line.split('=')
sw=float(items[1])
line=f.readline() # VL
DEBUG_MSG(rtn(line))
items=line.split('=')
vl=float(items[1])
line=f.readline() # NI or LB string?
DEBUG_MSG(rtn(line))
items=line.split('=')
ni=1 #by default
if string.strip(items[0])=="NI":
ni=int(items[1])
line=f.readline() #SW1
DEBUG_MSG(rtn(line))
items=line.split('=')
sw1=float(items[1])
line=f.readline() #VL1
DEBUG_MSG(rtn(line))
items=line.split('=')
vl1=float(items[1])
line=f.readline() #SUM
DEBUG_MSG(rtn(line))
items=line.split('=')
flag_sum=eval(string.upper(items[1]))
line=f.readline() # LB string
DEBUG_MSG(rtn(line))
items=line.split('=')
#now we have to read LB
self.lb=[]
self.lb.append(float(items[1]))
#and GB
line=f.readline()
DEBUG_MSG(rtn(line))
items=line.split('=')
self.gb=[]
self.gb.append(float(items[1]))
#and CONCENTRATION
line=f.readline()
DEBUG_MSG(rtn(line))
items=line.split('=')
self.concentration=[]
self.concentration.append(float(items[1]))
if ni>1:
for j in range(ni-1):
line=f.readline() #LB
DEBUG_MSG(rtn(line))
items=line.split('=')
self.lb.append(float(items[1]))
line=f.readline() #GB
DEBUG_MSG(rtn(line))
items=line.split('=')
self.gb.append(float(items[1]))
line=f.readline() #concentration
DEBUG_MSG(rtn(line))
items=line.split('=')
self.concentration.append(float(items[1]))
self.ydata = []
self.spec = []
line=f.readline() # read TYPE
DEBUG_MSG(rtn(line))
line=f.readline() # read YDATA or XDATA
DEBUG_MSG(rtn(line))
except: # There was an error
WRITE_STRING("***ERROR***: Badly formatted header")
f.close()
return false
if string.find(line,"YDATA")>-1: # check if there is a YDATA directive
try:
self.label=string.join(string.split(line)[1:],' ')
print self.label
print ni
for j in range(ni):
line=f.readline()
if not isinstance(line,str):
self.ydata.append(float(line))
else:
self.ydata.append(line)
except:
WRITE_ERROR("bad YDATA labels")
f.close()
return false
line=f.readline()
DEBUG_MSG(rtn(line)) # read XDATA
try:
for j in range(ni):
DEBUG_MSG("\treading spectrum"+str(j+1))
xy = []
DEBUG_MSG("n %13i"%n)
for i in range(n):
line=f.readline()
items=line.split(' ')
x=float(items[0])
y=float(items[1])
xy.append(complex(x,y)*self.concentration[j])
DEBUG_MSG("end reading "+str(j+1))
self.spec.append(array(xy))
line=f.readline()
DEBUG_MSG(rtn(line))
if string.find(line,"END")>-1:
DEBUG_MSG("reading file success!")
except:
WRITE_STRING("***ERROR***: problem when reading X,Y data in the *.spe file!")
f.close()
return false
self.frequency, self.ppm = [], []
for i in range(n):
self.frequency.append((i+1)*sw/n-sw/2.)
self.ppm.append(((i+1)*sw/n-sw/2.)*1.e6/abs(vl))
#save some data as class properties
self.n=n
self.ni=ni
self.vl=vl
self.sw=sw
if ni > 1:
self.vl1=vl1
self.sw1=sw1
self.flag_sum=flag_sum
#perform the fft and broadening
addlb(ni, self.spec, self.sw, self.lb, self.gb, self.concentration)
#sum of the spectra
if self.flag_sum:
p=[]
for i in range (n):
sum=complex(0.,0.)
for j in range(ni):
sum=sum+self.spec[j][i]
p.append(sum)
self.spec.append(array(p))
self.ni=ni+1
return True
#------------------------------------------------
def plot_data(self,mode=None, offset=None):
#------------------------------------------------
""" PLOT_SPECTRA:
Plot one or more 1D spectra on the same figure
"""
if not mode or mode=='reset':
try:
if not self.read_spectra(): return False
except:
return False
self.maxi=0
for j in range(self.ni):
mxi=max(map(abs,self.spec[j]))
self.maxi=max(mxi,self.maxi)
self.offset=0
if self.ni<6:
mode='standard'
else:
mode='popt'
else:
mode= string.lower(mode)
## if mode == 'reset' :
## try:
## if not self.read_spectra(): return False
## except:
## return False
##
## self.maxi=0
## for j in range(self.ni):
## mxi=max(map(abs,self.spec[j]))
## self.maxi=max(mxi,self.maxi)
## self.offset=0
mx=self.ni+1
self.dlg = wx.ProgressDialog("Spectrum plotting",
"...wait...",
maximum = mx+1,
parent=self,
# style = wx.PD_CAN_ABORT
#| wx.PD_APP_MODAL
#| wx.PD_ELAPSED_TIME
#| wx.PD_ESTIMATED_TIME
#| wx.PD_REMAINING_TIME
)
keepGoing = True
count = 0
self.fig.clear()
self.plotdata = self.fig.add_subplot(111)
if offset :
self.offset=offset
else:
self.offset=0
#------------------
if mode == "popt":
if self.ni == 1:
mode=="standard"
else:
self.fig.clear()
self.plotdat=None
self.plotdata = self.fig.add_subplot(111)
xticks=[]
xtickslabel=[]
spacing=10*(round(log10(self.ni))-1)
DEBUG_MSG("%5i %5i"%(self.ni, spacing))
if spacing<2: spacing=2
for i in range(self.ni):
X=[float(self.n-j-1+i*self.n)/self.n for j in range(self.n)]
if self.ydata:
if i%spacing==0:
xticks.append(float(self.n/2+i*self.n)/self.n)
if not isinstance(self.ydata[i],str):
xtickslabel.append(string.strip(str('%10.3f'%float(self.ydata[i]))))
else:
xtickslabel.append(string.strip(str('%s'%self.ydata[i])))
Y=[k.real for k in self.spec[i]]
self.plotdata.plot(X, array(Y))
count += 1
keepGoing = self.dlg.Update(count)
self.plotdata.set_xlabel('Index')
if self.ydata:
self.plotdata.set_xticks(xticks)
self.plotdata.set_xticklabels(xtickslabel)
self.plotdata.set_xlabel(self.label)
self.plotdata.set_ylabel('Intensity (a.u.)\n\n')
self.plotdata.set_title("POPT display, "+self.title)
self.plotdata.grid(self.grid)
#------------------
if mode == "popt 2d":
if self.ni == 1:
mode=="standard"
else:
self.fig.clear()
self.plotdata = self.fig.add_subplot(111)
count += 1
keepGoing = self.dlg.Update(count)
X=[]
Y=[]
Z=[]
X=self.ppm
Y=range(self.ni)
yticks=[]
ytickslabel=[]
spacing=10*(round(log10(self.ni))-1)
if spacing<2: spacing=2
maxi=0.
mini=0.
for i in range(self.ni):
Zt=[k.real for k in self.spec[i]]
mxi=max(map(abs,Zt))
mni=min(map(abs,Zt))
maxi=max(maxi,mxi)
mini=min(mini,mni)
Z.append(array(Zt))
if self.ydata:
if i%spacing==0:
yticks.append(i)
ytickslabel.append(string.strip(str('%10.3f'%self.ydata[i])))
amp=(maxi-mini)
levels=arange(mini-amp*.05,maxi+amp*.05,amp/self.ni)
print mini,maxi
cmap=pylab.cm.get_cmap('jet', len(levels)-1)
cset = self.plotdata.contourf(X, Y, Z, levels, cmap=cmap,)
#cset2 = self.plotdata.contour(X, Y, Z, cset.levels,
# colors = 'k',
# hold='on')
self.plotdata.set_xlim(self.ppm[len(self.ppm)-1],self.ppm[0])
self.plotdata.set_xlabel('Chemical shift (ppm)')
self.plotdata.set_ylabel('Index\n')
if self.ydata:
self.plotdata.set_yticks(yticks)
self.plotdata.set_yticklabels(ytickslabel)
self.plotdata.set_ylabel(self.label+'\n')
self.plotdata.set_title("POPT 2D display, "+self.title)
## clabels=[mini,0.,maxi]
## self.fig.colorbar(cset,clabels=clabels)
## #self.plotdata.grid(self.grid)
if mode == 'reset' or mode=="standard" :
#print string.lower(self.options['units'])
if string.lower(self.options['units'])=="hz":
for i in range(self.ni):
spec=[]
shift=(i+1)*self.offset*self.maxi
spec=[shift + x.real for x in self.spec[i]]
self.plotdata.plot(self.frequency, array(spec))
count += 1
keepGoing = self.dlg.Update(count)
self.plotdata.set_xlim(self.frequency[len(self.frequency)-1],self.frequency[0])
self.plotdata.set_xlabel('Frequency (Hz)')
else:
for i in range(self.ni):
shift=(i+1)*self.offset*self.maxi
spec=[shift + x.real for x in self.spec[i]]
self.plotdata.plot(self.ppm, array(spec))
count += 1
keepGoing = self.dlg.Update(count)
self.plotdata.set_xlim(self.ppm[len(self.ppm)-1],self.ppm[0])
self.plotdata.set_xlabel('Chemical shift (ppm)')
if string.lower(self.options['yaxis'])!="no":
self.plotdata.set_ylabel('Intensity (a.u.)\n')
else:
self.plotdata.set_yticks([])
self.plotdata.set_yticklabels([])
self.plotdata.set_title(self.title)
self.plotdata.grid(self.grid)
#update everything and exit
self.canvas.draw()
self.toolbar.update()
self.dlg.Destroy()
return True
class Plot(wx.Frame):
def __init__(self, parent, id=-1, dpi=None, **kwargs):
# begin wxGlade: MyFrame.__init__
kwargs["style"] = wx.DEFAULT_FRAME_STYLE
kwargs["size"] = (600, 600)
wx.Frame.__init__(self, parent, id=id, **kwargs)
# create figure
self.figure = mpl.figure.Figure(dpi=dpi, figsize=(2, 2))
self.canvas = Canvas(self, -1, self.figure)
#self.toolbar = Toolbar(self.canvas)
#self.toolbar.Realize()
self.add_toolbar()
#self.axes = self.figure.gca()
self.PNL_AXES = wx.Panel(parent=self)
# additional controls
xAxisDataLabel = wx.StaticText(parent=self.PNL_AXES, label='X data:')
yAxisDataLabel = wx.StaticText(parent=self.PNL_AXES, label='Y data:')
self.xAxisData = wx.Choice(self.PNL_AXES)
self.yAxisData = wx.Choice(self.PNL_AXES)
self.xAxisScale = wx.Choice(self.PNL_AXES)
self.xAxisScale.AppendItems(["linear scale", "log10 scale"])
self.xAxisScale.Select(0)
self.yAxisScale = wx.Choice(self.PNL_AXES)
self.yAxisScale.AppendItems(["linear scale", "log10 scale"])
self.yAxisScale.Select(0)
axesPanelSizer = wx.FlexGridSizer(rows=0, cols=3, vgap=0, hgap=0)
axesPanelSizer.Add(xAxisDataLabel, 0, wx.LEFT)
axesPanelSizer.Add(self.xAxisData, 0, wx.LEFT)
axesPanelSizer.Add(self.xAxisScale, 0, wx.LEFT)
axesPanelSizer.Add(yAxisDataLabel, 0, wx.LEFT)
axesPanelSizer.Add(self.yAxisData, 0, wx.LEFT)
axesPanelSizer.Add(self.yAxisScale, 0, wx.LEFT)
self.PNL_AXES.SetSizer(axesPanelSizer)
self.PNL_AXES.SetAutoLayout(True)
axesPanelSizer.Fit(self.PNL_AXES)
axesPanelSizer.SetSizeHints(self.PNL_AXES)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(self.canvas, 1, wx.EXPAND)
sizer.Add(self.toolbar, 0, wx.LEFT | wx.EXPAND)
sizer.Add(self.PNL_AXES, 0, wx.LEFT | wx.EXPAND)
self.SetSizer(sizer)
self.Layout()
#self.__set_properties()
# couple the EVENTS
# self.Bind(wx.EVT_CHECKBOX, self.stop, self.check_run)
self.Bind(event=wx.EVT_CLOSE, handler=self.OnClose)
self.Bind(event=wx.EVT_CHOICE,
handler=self.OnSetXlabel,
source=self.xAxisData)
self.Bind(event=wx.EVT_CHOICE,
handler=self.OnSetYlabel,
source=self.yAxisData)
self.Bind(event=wx.EVT_CHOICE,
handler=self.OnSetXScale,
source=self.xAxisScale)
self.Bind(event=wx.EVT_CHOICE,
handler=self.OnSetYScale,
source=self.yAxisScale)
self.acquizitionRunning = True
# create queue instance for the plot handling:
self.plottingThread = Queue.Queue(1)
# create redrawing deamon who will eat the queue
self.backgndDraw = threading.Thread(target=self._redrawPlot)
self.backgndDraw.setDaemon(True)
self.backgndDraw.start()
self.getPoints = threading.Thread(target=self._checkData)
self.getPoints.setDaemon(True)
return
def add_toolbar(self):
self.toolbar = Toolbar(self.canvas)
self.toolbar.Realize()
if wx.Platform == '__WXMAC__':
# Mac platform (OSX 10.3, MacPython) does not seem to cope with
# having a toolbar in a sizer. This work-around gets the buttons
# back, but at the expense of having the toolbar at the top
self.SetToolBar(self.toolbar)
else:
# On Windows platform, default window size is incorrect, so set
# toolbar width to figure width.
tw, th = self.toolbar.GetSizeTuple()
fw, fh = self.canvas.GetSizeTuple()
# By adding toolbar in sizer, we are able to put it at the bottom
# of the frame - so appearance is closer to GTK version.
# As noted above, doesn't work for Mac.
self.toolbar.SetSize(wx.Size(fw, th))
#self.sizer.Add(self.toolbar, 0, wx.LEFT | wx.EXPAND)
# update the axes menu on the toolbar
self.toolbar.update()
def set_my_title(self, title):
# begin wxGlade: MyFrame.__set_properties
self.SetTitle(title)
axes = self.figure.gca()
axes.set_title(title, visible=True)
# end wxGlade
def bind_data(self, datastore):
self.datagram = datastore.get_datagram()
self.graphTitle = datastore.dataFileName[-50:]
self.set_my_title(self.graphTitle)
self.lastDataRow = 0
self.xAxisData.Clear()
self.xAxisData.AppendItems(self.datagram.extract_header())
self.xAxisData.Select(0)
self.xIndex = self.xAxisData.GetStringSelection()
self.yAxisData.Clear()
self.yAxisData.AppendItems(self.datagram.extract_header())
self.yAxisData.Select(0)
self.yIndex = self.yAxisData.GetStringSelection()
#self.timer.start()
# update the axis label
axes = self.figure.gca()
axes.set_ylabel(self.yIndex, visible=True)
axes.set_xlabel(self.xIndex, visible=True)
def start_acquizition(self):
self.acquizitionRunning = True
self.getPoints.start()
def _checkData(self):
"""
periodically check for new data acquired
"""
while self.acquizitionRunning:
currentRow = self.datagram.get_current_data_row()
if currentRow > self.lastDataRow:
xFrom = 0
xTo = currentRow
try:
self.plottingThread.put(item=(xFrom, xTo),
block=False,
timeout=0)
except:
pass
time.sleep(0.1)
def reloadData(self, xFrom=0, xTo=None):
# which axes to plot in?
axes = self.figure.gca()
axes.clear()
# get data:
index = self.datagram.extract_data(key=self.xIndex,
from_to=(xFrom, xTo))
# check the scales:
xScale = self.xAxisScale.GetStringSelection()
if xScale == "log10 scale":
index = log10(abs(index))
axes.set_xlabel(('(log10(abs( %s ))' % self.xIndex), visible=True)
if xScale == "linear scale":
axes.set_xlabel(self.xIndex, visible=True)
values = self.datagram.extract_data(key=self.yIndex,
from_to=(xFrom, xTo))
# check the scales:
yScale = self.yAxisScale.GetStringSelection()
if yScale == "log10 scale":
values = log10(abs(values))
axes.set_ylabel(('(log10(abs( %s ))' % self.yIndex), visible=True)
if yScale == "linear scale":
axes.set_ylabel(self.yIndex, visible=True)
# plot and show the graph
axes.set_title(self.graphTitle, visible=True)
axes.scatter(
index,
values,
s=10,
c='r',
marker='+',
)
axes.autoscale_view()
self.canvas.draw()
def _redrawPlot(self):
while self.acquizitionRunning:
(xFrom,
xTo) = self.plottingThread.get(block=True) # obtain data to plot
self.reloadData(xFrom, xTo)
#self.timer.start()
time.sleep(0.1)
def OnClose(self, event):
self.Show(False)
return
def OnPaint(self, event):
self.canvas.draw()
return
def OnSetXlabel(self, event):
self.xIndex = event.GetString()
# update the axis label
#axes = self.figure.gca()
#axes.set_xlabel(self.xIndex,visible=True)
if not self.acquizitionRunning:
self.reloadData()
return
def OnSetYlabel(self, event):
self.yIndex = event.GetString()
# update the axis label
#axes = self.figure.gca()
#axes.set_ylabel(self.yIndex,visible=True)
if not self.acquizitionRunning:
self.reloadData()
return
def OnSetXScale(self, event):
scale = event.GetString()
# update the axis label
#axes = self.figure.gca()
#axes.set_xlabel(self.xIndex,visible=True)
if not self.acquizitionRunning:
self.reloadData()
return
def OnSetYScale(self, event):
scale = event.GetString()
# update the axis label
#axes = self.figure.gca()
#axes.set_ylabel(self.yIndex,visible=True)
if not self.acquizitionRunning:
self.reloadData()
return
