class VisualizerWindow:
root = []
dataMgr = []
#graphs
fig = []
ax1 = []
ax2 = []
ax3 = []
ax4 = []
ylim_ax1 = []
ylim_ax2 = []
ylim_ax3 = []
#data
x = []
usage_manual = []
#debug
show_debug_msg = False
#autosave (-1 for disable)
autosave_period = 30
load_autosave_file = False
def __init__(self, filename):
self.root = Tk.Tk()
self.root.wm_title("EMG-Visualization-Tool")
self.root.protocol("WM_DELETE_WINDOW", self._quit)
if not filename:
filename = askopenfilename()
if not filename:
sys.exit(0)
while not os.path.isfile(filename):
showerror("File not found", "Sorry, file '{}' was not found, try again".format(filename))
filename = askopenfilename()
if not filename:
sys.exit(0)
if filename[-19:] == '_usage_autosave.pkl':
self.autosave_file = filename
print('Input file is an Auto-Save file "{}"'.format(self.autosave_file))
filename = filename[:-19] + '.csv'
if not os.path.isfile(filename):
showerror('Could not find file "{}" (matching to provided auto-save file "{}")'.format(filename, self.autosave_file))
print('Error: matching file not found (expected "{}")'.format(filename))
print('EXIT')
sys.exit(0)
else:
self.load_autosave_file = True
else:
self.autosave_file = filename.rsplit(".", 1)[0] + "_usage_autosave.pkl"
if os.path.isfile(self.autosave_file):
print('Auto-Save file "{}" already exists'.format(self.autosave_file))
if askyesno('Auto-Save file found', 'Auto-Save file "{}" found. Load it instead? ("No" will result in automatical overwriting of the file when auto-saving)'.format(self.autosave_file)):
self.load_autosave_file = True
self.root.wm_title("EMG-Visualization-Tool: {}".format(filename))
self.dataMgr = DataManager(filename)
self.csv_out_file = filename.rsplit(".", 1)[0] + "_usage.csv"
while os.path.isfile(self.csv_out_file):
print('File "{}" already exists'.format(self.csv_out_file))
if askyesno('Overwrite File?', 'File "{}" already exists. Overwrite?'.format(self.csv_out_file)):
print('overwriting "{}"'.format(self.csv_out_file))
break
else:
new_out_file = asksaveasfilename(initialfile=self.csv_out_file)
if new_out_file:
self.csv_out_file = new_out_file
print('New Output file "{}"'.format(self.csv_out_file))
else:
sys.exit(0)
print("csv-out-file: {}".format(self.csv_out_file))
self.configFrame = Tk.Frame(self.root, height=500, width=400)
Tk.Label(self.configFrame, text="\r\nPlot 1").pack()
self.plot1_select = ttk.Combobox(self.configFrame, values=self.dataMgr.plot_columns, state="readonly")
self.plot1_select.pack()
if '"f"' in self.dataMgr.plot_columns:
self.plot1_select.current(self.dataMgr.plot_columns.index('"f"'))
else:
self.plot1_select.current(0)
Tk.Label(self.configFrame, text="Plot 2").pack()
self.plot2_select = ttk.Combobox(self.configFrame, values=self.dataMgr.plot_columns, state="readonly")
self.plot2_select.pack()
if '"rmsd"' in self.dataMgr.plot_columns:
self.plot2_select.current(self.dataMgr.plot_columns.index('"rmsd"'))
else:
self.plot2_select.current(0)
Tk.Label(self.configFrame, text="Plot 3").pack()
self.plot3_select = ttk.Combobox(self.configFrame, values=self.dataMgr.plot_columns, state="readonly")
self.plot3_select.pack()
if '"beat"' in self.dataMgr.plot_columns:
self.plot3_select.current(self.dataMgr.plot_columns.index('"beat"'))
else:
self.plot3_select.current(0)
Tk.Label(self.configFrame, text="\r\nUsage Plot").pack()
self.usage_plots = {}
for usg in self.dataMgr.usage_columns:
if not usg == '"usage_manual"':
chkbx_var = Tk.IntVar()
chkbx_var.set(1)
usg_check = ttk.Checkbutton(self.configFrame, text=usg, variable=chkbx_var)
usg_check.pack()
self.usage_plots[usg] = chkbx_var
Tk.Label(self.configFrame, text="\r\nLoad/copy \"usage_manual\" from").pack()
if self.load_autosave_file:
Tk.Label(self.configFrame, text="provided Auto-Save file").pack()
else:
self.usg_man_select = ttk.Combobox(self.configFrame, values=self.dataMgr.usage_columns, state="readonly")
self.usg_man_select.pack()
if '"usage_manual"' in self.dataMgr.usage_columns:
self.usg_man_select.current(self.dataMgr.usage_columns.index('"usage_manual"'))
elif '"usage_total"' in self.dataMgr.usage_columns:
self.usg_man_select.current(self.dataMgr.usage_columns.index('"usage_total"'))
else:
if len(self.dataMgr.usage_columns) > 0:
self.usg_man_select.current(0)
Tk.Label(self.configFrame, text="\r\nJump Column").pack()
if len(self.dataMgr.jump_columns) == 0:
self.jmp_select = ttk.Combobox(self.configFrame, values=['--none--'], state="readonly")
self.jmp_select.current(0)
else:
self.jmp_select = ttk.Combobox(self.configFrame, values=self.dataMgr.jump_columns, state="readonly")
if '"jump_ibi"' in self.dataMgr.jump_columns:
self.jmp_select.current(self.dataMgr.jump_columns.index('"jump_ibi"'))
else:
self.jmp_select.current(0)
self.jmp_select.pack()
Tk.Label(self.configFrame, text="").pack()
button_continue = Tk.Button(self.configFrame, text='Continue', command=self._CfgContinue)
button_continue.pack()
Tk.Label(self.configFrame, text="").pack()
self.loading_label = Tk.Label(self.configFrame, text="")
self.loading_label.pack()
self.configFrame.pack()
self.visualizerFrame = Tk.Frame(self.root)
# Figure with Subplots
self.fig = plt.figure(figsize=(17,8), dpi=80, tight_layout=True)
gs = gridspec.GridSpec(4,1, height_ratios=[3,2,2,1])
self.ax1 = plt.subplot(gs[0])
self.ax2 = plt.subplot(gs[1], sharex=self.ax1)
self.ax3 = plt.subplot(gs[2], sharex=self.ax1)
self.ax4 = plt.subplot(gs[3], sharex=self.ax1)
canvas = FigureCanvasTkAgg(self.fig, master=self.visualizerFrame)
canvas.show()
canvas.mpl_connect('key_press_event', self.on_key_event)
canvas.mpl_connect('button_press_event', self.on_button_event)
# GUI Elements
self.mode_label = Tk.Label(self.visualizerFrame, text="Mode: ADD", background="green")
self.progress_label = Tk.Label(self.visualizerFrame, text="Page {}/{}".format(self.dataMgr.current_page, self.dataMgr.num_pages))
button_prev = Tk.Button(master=self.visualizerFrame, text='Prev', command=self._prev)
button_next = Tk.Button(master=self.visualizerFrame, text='Next', command=self._next)
button_zoom_in = Tk.Button(master=self.visualizerFrame, text='Zoom In', command=self._zoom_in)
button_zoom_out = Tk.Button(master=self.visualizerFrame, text='Zoom Out', command=self._zoom_out)
button_add = Tk.Button(master=self.visualizerFrame, text='Add', command=self._add)
button_del = Tk.Button(master=self.visualizerFrame, text='Del', command=self._del)
saveFrame = Tk.Frame(self.visualizerFrame)
button_autosave = Tk.Button(master=saveFrame, text='Auto-Save', command=self._autosave)
button_save = Tk.Button(master=saveFrame, text='Save', command=self._save)
button_autosave.grid(column=0, row=0)
button_save.grid(column=1, row=0)
button_quit = Tk.Button(master=self.visualizerFrame, text='Quit', command=self._quit)
# Selection
self.multi_cursor = MultiCursor(self.fig.canvas, (self.ax1, self.ax2, self.ax3, self.ax4), useblit=True, horizOn=False, vertOn=True, color='g', lw=1)
self.span1 = SpanSelector(self.ax1, self.onselectAdd, 'horizontal', useblit=True,
rectprops=dict(alpha=0.5, facecolor='green') )
self.span2 = SpanSelector(self.ax2, self.onselectAdd, 'horizontal', useblit=True,
rectprops=dict(alpha=0.5, facecolor='green') )
self.span3 = SpanSelector(self.ax3, self.onselectAdd, 'horizontal', useblit=True,
rectprops=dict(alpha=0.5, facecolor='green') )
self.span4 = SpanSelector(self.ax4, self.onselectAdd, 'horizontal', useblit=True,
rectprops=dict(alpha=0.5, facecolor='green') )
# GUI Layout
button_zoom_in.grid(column=0, row=0)
button_zoom_out.grid(column=1, row=0)
button_prev.grid(column=3, row=0)
self.progress_label.grid(column=4, row=0)
button_next.grid(column=5, row=0)
canvas.get_tk_widget().grid(column=0, row=1, columnspan=6)
canvas._tkcanvas.grid(column=0, row=1, columnspan=6)
button_add.grid(column=0, row=2)
button_del.grid(column=1, row=2)
self.mode_label.grid(column=2, row=2, columnspan=2)
saveFrame.grid(column=4, row=2)
button_quit.grid(column=5, row=2)
Tk.mainloop()
def _CfgContinue(self):
self.loading_label['text'] = 'loading ...'
self.loading_label.update()
self.plot_names = [self.plot1_select.get(),
self.plot2_select.get(),
self.plot3_select.get()]
self.plot_cols = []
for pn in self.plot_names:
self.plot_cols.append(self.dataMgr.header_columns.index(pn))
self.usage_names = []
self.usage_cols = []
for k,v in self.usage_plots.items():
if v.get() == 1:
self.usage_names.append(k)
self.usage_cols.append(self.dataMgr.header_columns.index(k))
if self.load_autosave_file:
usg_manual_col = -1
else:
if self.usg_man_select.get() in self.dataMgr.header_columns:
usg_manual_col = self.dataMgr.header_columns.index(self.usg_man_select.get())
else:
usg_manual_col = -1
if self.jmp_select.get() in self.dataMgr.jump_columns:
jmp_col = self.dataMgr.header_columns.index(self.jmp_select.get())
else:
jmp_col = -1
[self.x, self.plot_data, self.usage_data, self.usage_manual, self.jump_positions] = self.dataMgr.readData(self.plot_cols,self.usage_cols,self.loading_label, usg_manual_col, jmp_col)
if self.load_autosave_file:
infile = open(self.autosave_file, 'rb')
self.usage_manual = pickle.load(infile)
infile.close()
self.configFrame.pack_forget()
self.visualizerFrame.pack()
print("displaying plots")
self.ylim_ax1 = self.calc_ylims(self.plot_data[0])
self.ylim_ax2 = self.calc_ylims(self.plot_data[1])
self.ylim_ax3 = self.calc_ylims(self.plot_data[2])
self.loadPage(1)
def HMS(seconds, pos):
"""Customized x-axis ticks
Keyword arguments:
seconds -- input in secs
pos -- somehow required argument (matplotlib)
"""
seconds = int(seconds)
hours = seconds / 3600
seconds -= 3600 * hours
minutes = seconds / 60
seconds -= 60 * minutes
if hours == 0:
if minutes == 0:
return "%ds" % (seconds)
return "%dm%02ds" % (minutes, seconds)
return "%dh%02dm" % (hours, minutes)
def calc_ylims(self, data):
[cnt, edge] = np.histogram(data, 25)
s = len(data)
thres = 0.975*s
i = 0
j = len(cnt)-1
while True:
if cnt[i] < cnt[j]:
if s-cnt[i] < thres:
break
else:
s -= cnt[i]
i += 1
else:
if s-cnt[j] < thres:
break
else:
s -= cnt[j]
j -= 1
return [min(0, edge[i]), max(1, edge[j+1])]
def plotPage(self):
index_low = self.dataMgr.low_Idx()
index_high = self.dataMgr.high_Idx()
if self.show_debug_msg:
print("index_low: {} | index_high: {}".format(index_low, index_high))
self.ax1.clear()
self.ax1.xaxis.set_major_formatter(plt.FuncFormatter(self.HMS))
self.ax1.plot(self.x[index_low:index_high], np.array(self.plot_data[0][index_low:index_high]))
self.ax1.set_ylim(self.ylim_ax1)
self.ax1.set_title(self.plot_names[0])
self.ax2.clear()
self.ax2.plot(self.x[index_low:index_high], self.plot_data[1][index_low:index_high])
self.ax2.set_ylim(self.ylim_ax2)
self.ax2.set_title(self.plot_names[1])
self.ax3.clear()
self.ax3.plot(self.x[index_low:index_high], self.plot_data[2][index_low:index_high])
self.ax3.set_ylim(self.ylim_ax3)
self.ax3.set_title(self.plot_names[2])
self.plotUsages()
self.fig.canvas.draw()
def plotUsages(self):
index_low = self.dataMgr.low_Idx()
index_high = self.dataMgr.high_Idx()
self.ax4.clear()
self.ax4.set_ylim(0,len(self.usage_names)+2)
self.ax4.set_yticks([], minor=False)
colors = ['#483D8B', '#228B22', '#B22222', '#8A2BE2', '#808000', '#FF4500', '#DA70D6', '#FFA500']
self.ax4.fill_between(self.x[index_low:index_high], 0, (len(self.usage_names)+2)*np.array(self.usage_manual[index_low:index_high]), facecolor='#7fbf7f', edgecolor='None')
self.ax4.plot(self.jump_positions, [len(self.usage_names)+1]*len(self.jump_positions), 'r*')
for u in range(0,len(self.usage_data)):
self.ax4.fill_between(self.x[index_low:index_high], u, u+np.array(self.usage_data[u][index_low:index_high]), facecolor=colors[u], edgecolor='None')
patches = [mpatches.Patch(color='green', alpha=0.5, label='usage_manual')]
for i in range(0,len(self.usage_names)):
patches.append(mpatches.Patch(color=colors[i], label=self.usage_names[i]))
plt.legend(bbox_to_anchor=(0., 1.0, 1., .102), loc=3,
ncol=5, mode="expand", borderaxespad=0., handles=patches)
self.ax1.set_xlim(self.dataMgr.low_Xlimit(),self.dataMgr.high_Xlimit())
def onselectAdd(self, xmin, xmax):
minIdx = max(0, round(xmin*500))
maxIdx = min(self.dataMgr.file_length-1, round(xmax*500))
if self.show_debug_msg:
print("ADD: xmin: {} | xmax: {}".format(xmin, xmax))
print("ADD: minIdx: {} | maxIdx: {}".format(minIdx, maxIdx))
self.usage_manual[minIdx:maxIdx] = 1
self.plotUsages()
self.fig.canvas.draw()
def onselectDel(self, xmin, xmax):
minIdx = max(0, round(xmin*500))
maxIdx = min(self.dataMgr.file_length-1, round(xmax*500))
if self.show_debug_msg:
print("DEL: xmin: {} | xmax: {}".format(xmin, xmax))
print("DEL: minIdx: {} | maxIdx: {}".format(minIdx, maxIdx))
self.usage_manual[minIdx:maxIdx] = 0
self.plotUsages()
self.fig.canvas.draw()
def onselectZoom(self, xmin, xmax):
if self.show_debug_msg:
print("ZOOM: xmin: {} | xmax: {}".format(xmin, xmax))
self.plotUsages()
self.ax1.set_xlim(xmin,xmax)
self.fig.canvas.draw()
def on_key_event(self, event):
if self.show_debug_msg:
print('you pressed %s'%event.key)
if event.key == 'a':
self._prev()
elif event.key == 'd':
self._next()
elif event.key == 'w':
self._add()
elif event.key == 's':
self._del()
elif event.key == 'q':
self._zoom_in()
elif event.key == 'e':
self._zoom_out()
elif event.key == 'r':
self._save()
elif event.key == 'f':
self._autosave()
elif event.key == 'x':
self._prevJump()
elif event.key == 'c':
self._nextJump()
elif event.key == 'left':
self._prev()
elif event.key == 'right':
self._next()
elif event.key == 'up':
self._add()
elif event.key == 'down':
self._del()
def on_button_event(self, event):
if self.show_debug_msg:
print('you clicked %s'%event.button)
if event.button == 3: #right mouse button
self._zoom_out()
elif event.button == 2: #middle mouse button (scroll wheel)
self._zoom_in()
def _quit(self):
self.root.quit() # stops mainloop
self.root.destroy() # this is necessary on Windows to prevent
# Fatal Python Error: PyEval_RestoreThread: NULL tstate
def _prev(self):
if self.show_debug_msg:
print('_prev()')
if self.dataMgr.current_page > 1:
self.loadPage(self.dataMgr.current_page-1)
def _next(self):
if self.show_debug_msg:
print('next()')
if self.dataMgr.current_page < self.dataMgr.num_pages:
self.loadPage(self.dataMgr.current_page+1)
def _prevJump(self):
if self.show_debug_msg:
print('_prevJump()')
if self.dataMgr.current_page > 1:
for p in reversed(self.jump_positions):
num = self.dataMgr.getPageNumByX(p)
if num < self.dataMgr.current_page:
self.loadPage(num)
break
def _nextJump(self):
if self.show_debug_msg:
print('nextJump()')
if self.dataMgr.current_page < self.dataMgr.num_pages:
for p in self.jump_positions:
num = self.dataMgr.getPageNumByX(p)
if num > self.dataMgr.current_page:
self.loadPage(num)
break
def loadPage(self, page_num):
if self.autosave_period > -1 and page_num % self.autosave_period == 0:
if self.show_debug_msg:
print('autosaving on page {}'.format(page_num))
self._autosave()
self.dataMgr.current_page = min(max(1, page_num), self.dataMgr.num_pages)
if self.show_debug_msg:
print('loadPage(): {}'.format(self.dataMgr.current_page))
self.plotPage()
self.progress_label["text"] ="Page {}/{}".format(self.dataMgr.current_page, self.dataMgr.num_pages)
def _add(self):
if self.show_debug_msg:
print('_add()')
if float(matplotlib.__version__[0:3])>=1.4:
self.multi_cursor.disconnect()
self.multi_cursor = MultiCursor(self.fig.canvas, (self.ax1, self.ax2, self.ax3, self.ax4), useblit=True, horizOn=False, vertOn=True, color='g', lw=1)
self.span1.disconnect_events()
self.span2.disconnect_events()
self.span3.disconnect_events()
self.span4.disconnect_events()
self.span1 = SpanSelector(self.ax1, self.onselectAdd, 'horizontal', useblit=True,
rectprops=dict(alpha=0.5, facecolor='green') )
self.span2 = SpanSelector(self.ax2, self.onselectAdd, 'horizontal', useblit=True,
rectprops=dict(alpha=0.5, facecolor='green') )
self.span3 = SpanSelector(self.ax3, self.onselectAdd, 'horizontal', useblit=True,
rectprops=dict(alpha=0.5, facecolor='green') )
self.span4 = SpanSelector(self.ax4, self.onselectAdd, 'horizontal', useblit=True,
rectprops=dict(alpha=0.5, facecolor='green') )
self.mode_label['text'] = 'Mode: ADD'
self.mode_label['bg'] = 'green'
self.fig.canvas.draw()
def _del(self):
if self.show_debug_msg:
print('_del()')
if float(matplotlib.__version__[0:3])>=1.4:
self.multi_cursor.disconnect()
self.multi_cursor = MultiCursor(self.fig.canvas, (self.ax1, self.ax2, self.ax3, self.ax4), useblit=True, horizOn=False, vertOn=True, color='r', lw=1)
self.span1.disconnect_events()
self.span1.disconnect_events()
self.span2.disconnect_events()
self.span3.disconnect_events()
self.span4.disconnect_events()
self.span1 = SpanSelector(self.ax1, self.onselectDel, 'horizontal', useblit=True,
rectprops=dict(alpha=0.5, facecolor='red') )
self.span2 = SpanSelector(self.ax2, self.onselectDel, 'horizontal', useblit=True,
rectprops=dict(alpha=0.5, facecolor='red') )
self.span3 = SpanSelector(self.ax3, self.onselectDel, 'horizontal', useblit=True,
rectprops=dict(alpha=0.5, facecolor='red') )
self.span4 = SpanSelector(self.ax4, self.onselectDel, 'horizontal', useblit=True,
rectprops=dict(alpha=0.5, facecolor='red') )
self.mode_label['text'] = 'Mode: DEL'
self.mode_label['bg'] = 'red'
self.fig.canvas.draw()
def _zoom_in(self):
if self.show_debug_msg:
print('_zoom_in()')
if float(matplotlib.__version__[0:3])>=1.4:
self.multi_cursor.disconnect()
self.multi_cursor = MultiCursor(self.fig.canvas, (self.ax1, self.ax2, self.ax3, self.ax4), useblit=True, horizOn=False, vertOn=True, color='b', lw=1)
self.span1.disconnect_events()
self.span1.disconnect_events()
self.span2.disconnect_events()
self.span3.disconnect_events()
self.span4.disconnect_events()
self.span1 = SpanSelector(self.ax1, self.onselectZoom, 'horizontal', useblit=True,
rectprops=dict(alpha=0.5, facecolor='blue') )
self.span2 = SpanSelector(self.ax2, self.onselectZoom, 'horizontal', useblit=True,
rectprops=dict(alpha=0.5, facecolor='blue') )
self.span3 = SpanSelector(self.ax3, self.onselectZoom, 'horizontal', useblit=True,
rectprops=dict(alpha=0.5, facecolor='blue') )
self.span4 = SpanSelector(self.ax4, self.onselectZoom, 'horizontal', useblit=True,
rectprops=dict(alpha=0.5, facecolor='blue') )
self.mode_label['text'] = 'Mode: ZOOM'
self.mode_label['bg'] = 'blue'
self.fig.canvas.draw()
def _zoom_out(self):
if self.show_debug_msg:
print('_zoom_out()')
self.plotUsages()
self.fig.canvas.draw()
def _save(self):
if self.show_debug_msg:
print('_save()')
savetxt = plt.text(20, 20, 'saving...', fontsize=46, color='r', weight='bold', ha='center', va='top')
self.fig.canvas.draw()
self.dataMgr.writeCSV(self.csv_out_file, self.usage_manual)
savetxt.remove()
self.fig.canvas.draw()
if os.path.isfile(self.autosave_file):
archive_filename = self.autosave_file.rsplit(".", 1)[0] + "_old.pkl"
print('renaming autosave file from "{}" to "{}"'.format(self.autosave_file, archive_filename))
if os.path.isfile(archive_filename):
os.unlink(archive_filename)
os.rename(self.autosave_file, archive_filename)
def _autosave(self):
if self.show_debug_msg:
print('_autosave()')
savetxt = plt.text(20, 20, 'autosaving...', fontsize=46, color='r', weight='bold', ha='center', va='top')
self.fig.canvas.draw()
self.dataMgr.writeAutoSave(self.autosave_file, self.usage_manual)
savetxt.remove()
self.fig.canvas.draw()
class DisplayWindow(object):
global CdMeOTPRef, MeOTPRef
color_list = deque(['b','g','r','c','m','y','k'])
current_checker = None
def __init__(self, master,ax = None):
self.rootref = master
self.master = Toplevel()
self.checker_frame=Tkinter.Frame(master = self.master)#,yscrollcommand=self.scroll.set)
#self.scroll.config(command=self.checker_frame.yview)
self.frame = Frame(master = self.master)
self.Plot = Figure(figsize=(6,3))
self.channel_list = []
self.array_list = []
self.Plot.a = self.Plot.add_subplot(111)
self.Plot.a.set_xlabel('Raman Shift (cm$^{-1}$)')
self.Plot.a.set_ylabel('Intensity (a.u.)')
self.Plot.a.legend([])
self.Plot.a.get_legend().set_visible(False)
self.checker_list = self.Plot.a.lines
self.legend_var = IntVar()
self.legend_var.set(1)
self.legendbox = Checkbutton(self.frame,
variable=self.legend_var,
command=self.update_legend,text='Legend')
# self.legend_label=Label(self.master, bd=1, anchor=W)
# self.legend_label.config(text = "Legend")
self.statusbar = Label(self.master, bd=1, relief=SUNKEN, anchor=W)
self.statusbar.config(text = "Ready")
self.canvas = FigureCanvasTkAgg(self.Plot,master = self.frame)
self.canvas.show()
self.master.protocol("WM_DELETE_WINDOW", self.quitproc)
self.master.title(string = "RamanViewer")
#self.scroll = Tkinter.Scrollbar(self.frame)
#self.scroll.pack(side = Tkinter.RIGHT, fill = Tkinter.BOTH)
self.checker_frame=Tkinter.Frame(master = self.master)#,yscrollcommand=self.scroll.set)
#self.scroll.config(command=self.checker_frame.yview)
self.menubar = Menu(self.master)
self.filemenu = Menu(self.menubar, tearoff=0)
self.filemenu.add_command(label="New window", command = lambda: DisplayWindow(self.rootref))
self.filemenu.add_command(label="Open", command = self.DisplaySpectrum)
self.filemenu.add_command(label="Save",command = self.SaveSpectrum)
self.filemenu.add_command(label="SaveFig",command = self.SaveFigure)
self.filemenu.add_command(label="ViewNotebook",command = self.ViewNotebook)
self.filemenu.add_command(label="Exit", command = self.quitproc)
self.menubar.add_cascade(label="File", menu=self.filemenu)
# create more pulldown menus
self.editmenu = Menu(self.menubar, tearoff=0)
self.editmenu.add_command(label="Smooth", command = self.SmoothSpectrum)
self.filemenu.add_command(label="Fitting window", command = lambda:FittingWindow(Toplevel(),ramanspectrum=self.current_checker.spectrum))#, kwargs = {'ramanspectrum':self.current_checker.channel.spec_array})
self.editmenu.add_command(label="Calc Noise", command = self.start_calc_noise)
self.editmenu.add_command(label="Calc Area", command = self.start_calc_area)
self.editmenu.add_command(label="Basline", command = self.start_autobaseline)
self.editmenu.add_command(label="disconnect", command = self.disconnect)
self.editmenu.add_command(label='Quick Scan',command = self.open_next_spectrum_in_folder)
self.editmenu.add_command(label='Normalize All',command = self.normalizeall)
self.editmenu.add_command(label='Zero All',command = self.zeroall)
self.editmenu.add_command(label = 'FFT process', command=self.FFT)
self.editmenu.add_command(label = 'Remove noise', command = self.removenoise)
self.editmenu.add_command(label="Copy")
self.editmenu.add_command(label="Paste")
self.menubar.add_cascade(label="Edit", menu=self.editmenu)
self.correctionmenu = Menu(self.menubar,tearoff=0)
self.correctionmenu.add_command(label='SPID633', command = self.SPIDcorrect633)
self.correctionmenu.add_command(label='SPID785', command = self.SPIDcorrect785)
self.menubar.add_cascade(label = 'Corrections', menu = self.correctionmenu)
self.notesmenu =Menu(self.menubar, tearoff=0)
self.notesmenu.add_command(label = "Notes", command = self.ViewNotebook)
self.notesmenu.add_command(label = "Spectrum Info", command = self.showinfo)
self.menubar.add_cascade(label = 'Info', menu = self.notesmenu)
self.refsmenu =Menu(self.menubar, tearoff=0)
self.refsmenu.add_command(label = "chloroform", command = None)
self.refsmenu.add_command(label = "CdMeOTP", command = lambda:self.AddChannel(CdMeOTPRef))
self.refsmenu.add_command(label = "MeOTP", command = lambda:self.AddChannel(MeOTPRef))
self.refsmenu.add_command(label = "ClTP", command = lambda:self.AddChannel(ClTPRef))
self.refsmenu.add_command(label = "BrTP", command = lambda:self.AddChannel(BrTPRef))
self.refsmenu.add_command(label = "FTP", command = lambda:self.AddChannel(FTPRef))
self.refsmenu.add_command(label = "MethylTP", command = lambda:self.AddChannel(MethylTPRef))
self.refsmenu.add_command(label = "CdODPA", command = lambda:self.AddChannel(CdODPARef))
self.refsmenu.add_command(label = "toluene", command = lambda:self.AddChannel(tolueneRef))
self.refsmenu.add_command(label = "CdMethylTP", command = lambda:self.AddChannel(CdMethylTPRef))
self.menubar.add_cascade(label = 'References', menu = self.refsmenu)
self.master.config(menu= self.menubar)
self.left_click_menu = Menu(self.frame, tearoff=0)
self.left_click_menu.add_command(label="open", command = self.DisplaySpectrum)
# self.left_click_menu.add_command(label="blue", command=lambda:self.change_color('b'))
# self.left_click_menu.add_command(label="black", command=lambda:self.change_color('k'))
# self.left_click_menu.add_command(label="yellow", command=lambda:self.change_color('y'))
# self.canvas._tkcanvas.bind("<Button-3>", self.popup)
self.frame.pack(side = TOP, expand=1, fill=BOTH)#(row = 0, column = 0, padx = 25, pady = 25)
self.legendbox.pack(side=BOTTOM)
self.statusbar.pack(side = BOTTOM,expand=1,fill=X)
self.checker_frame.pack(side=BOTTOM,expand = 1,fill=X)#(row=1,column=0)
self.canvas._tkcanvas.pack( expand = 1, fill = BOTH)
self.toolbar = NavigationToolbar2TkAgg(self.canvas, self.frame)
self.toolbar.update()
self.toolbar.pack(side= BOTTOM,expand =True)
self.canvas.draw()
list_of_display_windows.append(self)
if ax is not None:
for line in ax.lines:
self.Plot.a.add_line(checker(self,line,color = line.get_color()))
self.Plot.a.relim()
self.Plot.a.autoscale_view(tight = False)
self.Plot.canvas.draw()
self.current_checker = self.Plot.a.lines[-1]
plt.close(ax.get_figure())
return None
def popup(self,event):
print event.x_root, event.y_root
self.left_click_menu.post(event.x_root, event.y_root)
def update_legend(self):
if self.legend_var.get() == 0:
self.Plot.a.get_legend().set_visible(False)
else:
l = list()
for entry in self.checker_list:
if True:#entry.get_visible():
l.append(entry.commentbox.get())
self.Plot.a.legend(l)
self.Plot.canvas.draw()
return 0
def showinfo(self):
tkMessageBox.showinfo('Spectrum info',self.current_checker.spectrum.info)
return 0
def getcolor(self):
self.color_list.rotate(1)
return self.color_list[0]
def DisplaySpectrum(self):
import re
options = {}
#options['defaultextension'] = '.SPE'
options['filetypes'] = [('all files','.*'),('SPE','.spe'),('txt', '.txt'),('csv','.csv')]
options['multiple'] = True
options['title'] = 'Open Spectrum...'
options['parent'] = self.master
str_name_list = tkFileDialog.askopenfilenames(**options)
if type(str_name_list) == tuple:
for name in str_name_list:
if 'notes' in name:
SFG_Notebook.SFG_NotebookWindow(target_file = name)
elif name =='':
continue
else:
newspectrum = RamanSpectrum(name)
self.Plot.a.add_line(checker(self,newspectrum,color = self.getcolor()))
self.Plot.a.relim()
self.Plot.a.autoscale_view(tight = False)
self.Plot.canvas.draw()
self.current_checker = self.Plot.a.lines[-1]
elif str_name_list == '':
return 0
elif type(str_name_list) == list:
for name in re.split(' ',str_name_list):
newspectrum = RamanSpectrum(name)
self.Plot.a.add_line(checker(self,newspectrum,color = self.getcolor()))
self.Plot.a.relim()
self.Plot.a.autoscale_view(tight = False)
self.Plot.canvas.draw()
self.current_checker = self.Plot.a.lines[-1]
return 0
def SaveSpectrum(self):
file_opt = options = {}
options['defaultextension'] = '.txt'
options['filetypes'] = [('all files', '.*')]
options['title'] = 'Open Spectrum...'
options['initialfile'] = os.path.basename(self.current_checker.name)
options['parent'] = self.master
if self.current_checker == None:
return 0
str_filename = tkFileDialog.asksaveasfilename(**options)
if str_filename == '':
return 0
else:
data = transpose([self.current_checker.get_xdata(),self.current_checker.get_ydata()])
savetxt(str_filename,data,delimiter = ',',comments = '#'+str(self.current_checker.spectrum.info))#SaveSpectrum(self.current_checker.channel.spec_array,str_filename)
os.chdir(os.path.dirname(str_filename))
return 0
def ViewNotebook(self):
print os.path.dirname(self.current_checker.name)
try:
SFG_Notebook.SFG_NotebookWindow(target_dir = os.path.dirname(self.current_checker.name))
except IOError:
tkSimpleDialog.Message('no file found')
return 0
def zeroall(self):
for c in self.Plot.a.lines:
c.set_ydata(c.get_ydata()-min(c.get_ydata()))
self.Plot.a.relim()
self.Plot.a.autoscale_view(tight = False)
self.Plot.canvas.draw()
return 0
def SmoothSpectrum(self):
if self.current_checker == None:
return 0
newspectrum = smooth(self.current_checker.spectrum)
self.Plot.a.add_line(checker(self,newspectrum,color = self.getcolor(),operations = 'sp = smooth(sp)\n'))
self.Plot.a.relim()
self.Plot.a.autoscale_view(tight = False)
self.Plot.canvas.draw()
self.current_checker = self.Plot.a.lines[-1]
return 0
def SPIDcorrect785(self):
if self.current_checker == None:
return 0
else:
newspectrum = SPIDcorrect785(self.current_checker.spectrum)
self.Plot.a.add_line(checker(self,newspectrum,color = self.getcolor(),operations = 'sp = SPIDcorrect785(sp)\n'))
self.Plot.a.relim()
self.Plot.a.autoscale_view(tight = False)
self.Plot.canvas.draw()
self.current_checker = self.Plot.a.lines[-1]
return 0
def SPIDcorrect633(self):
if self.current_checker == None:
return 0
else:
newspectrum = SPIDcorrect633(self.current_checker.spectrum)
self.Plot.a.add_line(checker(self,newspectrum,color = self.getcolor(),operations = 'sp = SPIDcorrect633(sp)\n'))
self.Plot.a.relim()
self.Plot.a.autoscale_view(tight = False)
self.Plot.canvas.draw()
self.current_checker = self.Plot.a.lines[-1]
return 0
def open_next_spectrum_in_folder(self):
self.Plot.canvas.mpl_connect('key_press_event',self.open_next_spectrum)
for c in self.checker_list[1:]:
self.RemoveSpectrum(self.checker)
self.checker_list[0].set_current(0)
return 0
def open_next_spectrum(self,event):
directory_index = os.listdir(os.path.dirname(os.path.abspath(self.current_checker.channel.spec_array.name)))
for x in directory_index:
if 'txt' not in x:
directory_index.remove(x)
directory_index.sort()
i=directory_index.index(os.path.basename(self.current_checker.channel.spec_array.name))
if i>len(directory_index)-2:
i=-1
if 'txt' not in directory_index[1+1]:
i+=1
if event.key == 'right':
i+=1
elif event.key == 'left':
i-=1
try:
newspectrum = RamanSpectrum(directory_index[i])
except:
print 'error'
print 'i=',i
return -1
self.RemoveSpectrum(self.current_checker)
self.AddChannel(self.newspectrum)
self.checker_list[0].set_current(0)
return 0
def normalizeall(self):
for check in self.checker_list:
data = check.get_ydata()
data[:]-=min(data)
data/=max(data)
check.set_ydata(data)
self.Plot.a.relim()
self.Plot.a.set_ylim(-0.5,1.5)
self.Plot.a.autoscale_view(tight = False)
self.Plot.canvas.draw()
return 0
def start_calc_noise(self):
self.span = SpanSelector(self.Plot.a, self.calc_noise, 'horizontal')
self.span.connect_event('pick_event',self.calc_noise)
gcf().canvas.mpl_connect('button_press_event',self.disconnect)
return 0
def start_calc_area(self):
self.span = SpanSelector(self.Plot.a, self.calc_area, 'horizontal')
self.span.connect_event('pick_event',self.calc_area)
gcf().canvas.mpl_connect('button_press_event',self.disconnect)
return 0
def start_autobaseline(self):
# self.toolbar.release(None)
self.span = SpanSelector(self.Plot.a, self.autobaseline, 'horizontal')
self.span.connect_event('pick_event',self.autobaseline)
gcf().canvas.mpl_connect('button_press_event',self.disconnect)
return 0
def autobaseline(self,start,end):
order = int(tkSimpleDialog.askinteger('Fit order', 'Choose the polynomial order.'))
if order == None:
return 0
if self.current_checker == None:
return 0
newspectrum = autobaseline(self.current_checker.spectrum,(start,end),order = order)
self.Plot.a.add_line(checker(self,newspectrum,color = self.getcolor(),operations = 'sp = autobaseline(sp), ('+str(start)+','+str(end)+'), order ='+str(order)+')\n'))
self.Plot.a.relim()
self.Plot.a.autoscale_view(tight = False)
self.Plot.canvas.draw()
self.current_checker = self.Plot.a.lines[-1]
self.span.disconnect_events()
return 0
def calc_noise(self,start,end):
try:
print "STD =", calc_noise(pandas.Series(self.current_checker.channel.get_ydata(),self.current_checker.channel.get_xdata()),(start,end))
except:
print 'error'
return 0
def calc_area(self, start,end):
try:
print "Area =", calc_area(pandas.Series(self.current_checker.channel.get_ydata(),self.current_checker.channel.get_xdata()),(start,end))
except:
print 'error'
return 0
def disconnect(self):
#print event.button#gcf().canvas.mpl_disconnect(self.cid)
self.span.disconnect_events()
return 0
def removenoise(self):
newspectrum = removecorrelatednoise(self.current_checker.spectrum)
self.Plot.a.add_line(checker(self,newspectrum,operations = 'sp = removecorrelatednoise(sp)',color=self.getcolor()))
self.Plot.a.relim()
self.Plot.a.autoscale_view(tight = False)
self.Plot.canvas.draw()
self.current_checker = self.Plot.a.lines[-1]
return None
def AddChannel(self,spectrum):
self.Plot.a.add_line(checker(self,spectrum))
self.Plot.a.lines[-1].set_color(self.getcolor())
self.Plot.a.relim()
self.Plot.a.autoscale_view(tight = False)
self.Plot.canvas.draw()
self.current_checker = self.Plot.a.lines[-1]
return 0
def RemoveSpectrum(self,checker):
self.Plot.a.lines.remove(checker)
self.Plot.a.relim()
self.Plot.a.autoscale_view(tight = False)
self.canvas.draw()
checker.frame.pack_forget()
return 0
def SaveFigure(self):
os.chdir('/home/chris/Desktop')
self.Plot.savefig('figure.png')
f = open('/home/chris/Desktop/figure.py','wb')
for line in self.Plot.a.lines:
f.write(line.operations)
f.close()
return 0
def FFT(self):
return 0
def quitproc(self):
self.master.destroy()
list_of_display_windows.remove(self)
if len(list_of_display_windows)==0:
self.rootref.destroy()
return 0
class LSFQDialg(QWidget):
def __init__(self):
QWidget.__init__(self)
self.handles = []
self.create_canvas()
self.segments = []
vbox = QVBoxLayout()
vbox.addWidget(self.canvas)
self.setLayout(vbox)
self.resize(800, 600)
self.move(320, 75)
self.setWindowTitle("Least Square Fitting (2D)")
def create_canvas(self):
self.fig = plt.figure()
self.canvas = FigureCanvas(self.fig)
self.axes = plt.subplot(111)
self.axes.set_xlabel("Scans")
self.axes.set_ylabel("Instensity")
self.axes.set_title("Least Square Fitting(2D)", fontsize=9)
self.axes.tick_params(axis='both', labelsize=8)
plt.subplots_adjust(bottom=0.22, top=0.90, left=0.08, right=0.9)
self.span = SpanSelector(self.axes,
self.span_select_callback,
'horizontal',
minspan=0.002,
useblit=True,
rectprops=dict(alpha=0.5, facecolor='red'),
onmove_callback=None,
button=[1])
axspan = plt.axes([0.09, 0.04, 0.08, 0.075])
axundo = plt.axes([0.2, 0.04, 0.08, 0.075])
axstar = plt.axes([0.31, 0.04, 0.08, 0.075])
self.btnspan = Button(axspan, 'span')
self.btnundo = Button(axundo, 'undo')
self.btnstar = Button(axstar, 'start')
self.btnspan.on_clicked(self.span_mode)
self.btnundo.on_clicked(self.undo_mode)
self.btnstar.on_clicked(self.star_mode)
self.span.set_active(True)
self.redraw()
ymino, ymaxo = self.axes.get_ylim()
xmino, xmaxo = self.axes.get_xlim()
self.oxy = [(xmino, xmaxo), (ymino, ymaxo)]
def redraw(self):
self.canvas.draw()
self.update()
def span_mode(self, event):
self.span.connect_event('motion_notify_event', self.span.onmove)
self.span.connect_event('button_press_event', self.span.press)
self.span.connect_event('button_release_event', self.span.release)
self.span.connect_event('draw_event', self.span.update_background)
self.leftdblclick = False
self.rightdblclick = False
self.redraw()
print "span"
def undo_mode(self, event):
self.span.disconnect_events()
if len(self.segments) >= 1:
del self.axes.collections[:]
self.segments = self.segments[:-1]
self.select_inter(self.segments)
self.redraw()
print "undo"
def star_mode(self, event):
if len(self.segments) == 0:
msgBox = QMessageBox()
msgBox.setText("No selected noise region")
msgBox.exec_()
else:
fit, bas = self.backremv(self.segments)
self.show_bas(bas)
self.show_fit(fit)
self.emit(SIGNAL('after_baseline'), fit)
def show_bas(self, bas):
self.axes.plot(np.sum(bas, axis=1), lw=2, c='k', alpha=.7, picker=5)
def show_fit(self, fit):
self.axes.plot(np.sum(fit, axis=1), lw=2, c='r', alpha=.7, picker=5)
def show_org(self, x):
self.axes.plot(np.sum(x, axis=0), lw=2, c='b', alpha=.7, picker=5)
def span_select_callback(self, xmin, xmax):
cc = np.arange(0, self.x.shape[0])
indmin, indmax = np.searchsorted(cc, (xmin, xmax))
indmax = min(len(self.x) - 1, indmax)
self.segments.append((indmin, indmax))
self.axes.vlines(xmin,
self.oxy[1][0],
self.oxy[1][1],
color='r',
linestyles='--')
self.axes.vlines(xmax,
self.oxy[1][0],
self.oxy[1][1],
color='r',
linestyles='--')
self.redraw()
def updata_data(self, x):
self.xx = x
self.axes.clear()
self.axes.set_xlabel("Scans")
self.axes.set_ylabel("Instensity")
self.axes.set_title("Least Square Fitting(2D)", fontsize=9)
self.x = x['d']
self.y = np.sum(self.x, axis=1)
self.axes.plot(self.y, lw=1, c='b', alpha=.7, picker=5)
diff_y = max(self.y) - min(self.y)
self.axes.set_xlim(0, len(self.y))
self.axes.set_ylim(0, max(self.y) * 1.1)
ymino, ymaxo = self.axes.get_ylim()
xmino, xmaxo = self.axes.get_xlim()
self.oxy = [(xmino, xmaxo), (ymino, ymaxo)]
self.plotorg = True
self.redraw()
def select_inter(self, segments):
for i in range(0, len(segments)):
indmin, indmax = segments[i]
self.axes.vlines(self.x[indmin],
self.oxy[1][0],
self.oxy[1][1],
color='r',
linestyles='--')
self.axes.vlines(self.x[indmax],
self.oxy[1][0],
self.oxy[1][1],
color='r',
linestyles='--')
def backremv(self, seg):
mn = np.shape(self.x)
bak2 = np.zeros(mn)
for i in range(0, mn[1]):
tiab = []
reg = []
for j in range(0, len(seg)):
tt = range(seg[j][0], seg[j][1])
tiab.extend(self.x[tt, i])
reg.extend(np.arange(seg[j][0], seg[j][1]))
rm = reg - np.mean(reg)
tm = tiab - np.mean(tiab)
b = np.dot(np.dot(float(1) / np.dot(rm.T, rm), rm.T), tm)
s = np.mean(tiab) - np.dot(np.mean(reg), b)
b_est = s + b * np.arange(mn[0])
bak2[:, i] = self.x[:, i] - b_est
bak = self.x - bak2
self.yy = bak2
return bak2, bak
def accept(self):
self.xx['d'] = self.yy
self.close()
class TICPlot(QWidget):
def __init__(self):
QWidget.__init__(self)
self.handles = []
self.ncr = dict()
self.fileno = 0
self.segments = []
self.create_canvas()
def create_canvas(self):
self.fig = plt.figure()
self.canvas = FigureCanvas(self.fig)
self.axes = plt.subplot(111)
self.axes.set_xlabel("Retention Time")
self.axes.set_ylabel("Instensity")
self.axes.tick_params(axis='both', labelsize=8)
plt.subplots_adjust(bottom=0.25, top=0.90, left=0.08, right=0.9)
self.zoom = RectangleSelector(self.axes,
self.rectangle_select_callback,
drawtype='box',
useblit=True,
button=[1],
minspanx=5,
minspany=5,
spancoords='pixels')
self.span = SpanSelector(self.axes,
self.span_select_callback,
'horizontal',
minspan=0.002,
useblit=True,
rectprops=dict(alpha=0.5, facecolor='red'),
onmove_callback=None,
button=[1])
axbasic = plt.axes([0.59, 0.04, 0.08, 0.075])
axPan = plt.axes([0.7, 0.04, 0.08, 0.075])
axPick = plt.axes([0.81, 0.04, 0.08, 0.075])
self.btnBasic = Button(axbasic, 'Zoom')
self.btnPan = Button(axPan, 'Span')
self.btnPick = Button(axPick, 'Undo')
axtic = plt.axes([0.92, 0.825, 0.06, 0.075])
axext = plt.axes([0.92, 0.725, 0.06, 0.075])
axres = plt.axes([0.92, 0.625, 0.06, 0.075])
self.TICbutton = Button(axtic, 'TIC')
self.EXTbutton = Button(axext, 'EXT')
self.RESbutton = Button(axres, 'RES')
vbox = QVBoxLayout()
vbox.addWidget(self.canvas)
self.setLayout(vbox)
self.btnBasic.on_clicked(self.zoom_mode)
self.btnPan.on_clicked(self.span_mode)
self.btnPick.on_clicked(self.undo_mode)
self.TICbutton.on_clicked(self.slot_tic)
self.EXTbutton.on_clicked(self.slot_ext)
self.RESbutton.on_clicked(self.slot_res)
self.zoom_mode(True)
self.redraw()
ymino, ymaxo = self.axes.get_ylim()
xmino, xmaxo = self.axes.get_xlim()
self.oxy = [(xmino, xmaxo), (ymino, ymaxo)]
def slot_tic(self, event):
self.add_tic(self.ncr, self.fileno)
def slot_ext(self, event):
self.emit(SIGNAL("ext_plot"))
def slot_res(self, event):
self.emit(SIGNAL("res_plot"), )
def add_tic(self, ncr, fn):
if not len(self.segments):
self.fn = fn
self.ncr = ncr
tic = self.ncr.tic()
self.x = tic['rt']
self.y = tic['val']
self.axes.clear()
self.axes.set_xlabel("Retention Time")
self.axes.set_ylabel("Instensity")
self.axes.set_title(str(fn), fontsize=9)
self.axes.plot(self.x, self.y, lw=1, c='b', alpha=.7, picker=5)
self.axes.set_xlim(min(self.x), max(self.x))
self.axes.set_ylim(min(self.y), max(self.y) * 1.1)
ymino, ymaxo = self.axes.get_ylim()
xmino, xmaxo = self.axes.get_xlim()
self.oxy = [(xmino, xmaxo), (ymino, ymaxo)]
self.redraw()
# def add_ext(self):
def clear_data(self):
self.axes.clear()
self.axes.set_xlabel("Retention Time")
self.axes.set_ylabel("Instensity")
self.redraw()
def redraw(self):
self.canvas.draw()
self.update()
def zoom_mode(self, event):
self.zoom.set_active(True)
self.span.set_active(False)
self.cidPress = self.canvas.mpl_connect('button_press_event',
self.mouse_press_callback)
self.cidRelease = self.canvas.mpl_connect('button_release_event',
self.mouse_release_callback)
self.span.disconnect_events()
self.leftdblclick = False
self.rightdblclick = False
self.redraw()
print "zoom"
def span_mode(self, event):
self.zoom.set_active(False)
self.span.set_active(True)
self.span.connect_event('motion_notify_event', self.span.onmove)
self.span.connect_event('button_press_event', self.span.press)
self.span.connect_event('button_release_event', self.span.release)
self.span.connect_event('draw_event', self.span.update_background)
# self.span.connect_event('button_press_event', self.mouse_press_callback)
self.rightdblclick = False
self.leftdblclick = False
self.rightdblclick = False
self.redraw()
print "span"
def undo_mode(self, event):
self.zoom.set_active(True)
self.span.disconnect_events()
self.cidPress = self.canvas.mpl_connect('button_press_event',
self.mouse_press_callback)
if len(self.segments) >= 1:
self.emit(SIGNAL("delete_SELECT"), self.segments[-1])
del self.axes.collections[:]
self.segments = self.segments[:-1]
self.select_inter(self.segments)
if self.ind_right_press != 0:
self.axes.vlines(self.xdata,
self.oxy[1][0],
self.oxy[1][1],
color='g',
linestyles='-')
self.redraw()
print "undo"
def mouse_press_callback(self, event):
if (event.button == 1 and event.dblclick == True):
self.leftdblclick = True
if event.button == 3:
self.xdata = event.xdata
self.ind_right_press = np.searchsorted(self.x, event.xdata)
del self.axes.collections[:]
self.axes.vlines(event.xdata,
self.oxy[1][0],
self.oxy[1][1],
color='g',
linestyles='-')
self.select_inter(self.segments)
self.redraw()
self.emit(SIGNAL("MASS_SELECT"), self.ncr, self.ind_right_press)
def select_inter(self, segments):
for i in range(0, len(segments)):
indmin, indmax = segments[i]
self.axes.vlines(self.x[indmin],
self.oxy[1][0],
self.oxy[1][1],
color='r',
linestyles='--')
self.axes.vlines(self.x[indmax],
self.oxy[1][0],
self.oxy[1][1],
color='r',
linestyles='--')
def mouse_release_callback(self, event):
if (self.leftdblclick):
self.leftdblclick = False
self.axes.set_xlim(self.oxy[0])
self.axes.set_ylim(self.oxy[1])
self.redraw()
if (self.rightdblclick):
self.rightdblclick = False
del self.axes.collections[:]
self.redraw()
def rectangle_select_callback(self, eclick, erelease):
x1, y1 = eclick.xdata, eclick.ydata
x2, y2 = erelease.xdata, erelease.ydata
if eclick.button == 1 and erelease.button == 1:
self.axes.set_xlim(min(x1, x2), max(x1, x2))
self.axes.set_ylim(min(y1, y2), max(y1, y2))
self.redraw()
def span_select_callback(self, xmin, xmax):
indmin, indmax = np.searchsorted(self.x, (xmin, xmax))
indmax = min(len(self.x) - 1, indmax)
self.segments.append((indmin, indmax))
self.axes.vlines(xmin,
self.oxy[1][0],
self.oxy[1][1],
color='r',
linestyles='--')
self.axes.vlines(xmax,
self.oxy[1][0],
self.oxy[1][1],
color='r',
linestyles='--')
self.redraw()
self.emit(SIGNAL("range_SELECT"), self.ncr, (indmin, indmax))
def loading(self):
self.axes.clear()
self.axes.set_xlabel("Retention Time")
self.axes.set_ylabel("Instensity")
self.redraw()
self.zoom_mode(True)
ymino, ymaxo = self.axes.get_ylim()
xmino, xmaxo = self.axes.get_xlim()
self.oxy = [(xmino, xmaxo), (ymino, ymaxo)]