class Basic:
def __init__(self, file_id):
fcs_file_name = file_id + '_fcs_file.fcs'
self.datafile = os.path.join(RAW_DIR, fcs_file_name)
print('Path to data file is : ' + self.datafile)
self.sample = False
self.read_data()
def read_data(self):
self.sample = FCMeasurement(ID='Test Sample', datafile=self.datafile)
# self.sample = self.sample.transform('hlog', b=500)
def plot_columns(self, col1):
self.sample.plot(col1, bins=100, alpha=0.9, color='green')
def get_channel_names(self):
return self.sample.channel_names
def get_meta(self):
return self.sample.meta
def head(self):
channelx = "HDR-T"
channely = "FSC-A"
return (self.sample.data[[channelx, channely]][:-10]).head(10)
def medians(self):
channelx = "HDR-T"
channely = "FSC-A"
print((self.sample.data[[channelx, channely]][:-10]).head(10))
print(channelx, channely)
import os
from pylab import *
import FlowCytometryTools
from FlowCytometryTools import FCMeasurement
# Locate sample data included with this package
datadir = os.path.join(FlowCytometryTools.__path__[0], 'tests', 'data',
'Plate01')
datafile = os.path.join(datadir, 'RFP_Well_A3.fcs')
# datafile = '[insert path to your own fcs file]'
# Load data
tsample = FCMeasurement(ID='Test Sample', datafile=datafile)
tsample = tsample.transform('hlog', channels=['Y2-A', 'B1-A', 'V2-A'], b=500.0)
# Plot
tsample.plot(['Y2-A', 'B1-A'], kind='scatter', alpha=0.6, color='gray')
grid(True)
#show() # <-- Uncomment when running as a script.
import os
import FlowCytometryTools
from FlowCytometryTools import FCMeasurement
from pylab import *
# Locate sample data included with this package
datadir = os.path.join(FlowCytometryTools.__path__[0], 'tests', 'data',
'Plate01')
datafile = os.path.join(datadir, 'RFP_Well_A3.fcs')
# datafile = '[insert path to your own fcs file]'
# Load data
tsample = FCMeasurement(ID='Test Sample', datafile=datafile)
tsample = tsample.transform('hlog', channels=['Y2-A', 'B1-A', 'V2-A'], b=500.0)
# Plot
tsample.plot('Y2-A', bins=100, alpha=0.9, color='green')
grid(True)
# show() # <-- Uncomment when running as a script.
from FlowCytometryTools import FCMeasurement, ThresholdGate
import os, FlowCytometryTools
from pylab import *
# Locate sample data included with this package
datadir = os.path.join(FlowCytometryTools.__path__[0], 'tests', 'data', 'Plate01')
datafile = os.path.join(datadir, 'RFP_Well_A3.fcs')
# datafile = '[insert path to your own fcs file]'
# Load data
tsample = FCMeasurement(ID='Test Sample', datafile=datafile)
tsample = tsample.transform('hlog', channels=['Y2-A', 'B1-A', 'V2-A'], b=500.0)
# Plot
tsample.plot(['Y2-A', 'B1-A'], kind='scatter', alpha=0.6, color='gray');
grid(True)
#show() # <-- Uncomment when running as a script.
import os
from pylab import *
import FlowCytometryTools
from FlowCytometryTools import FCMeasurement
# Locate sample data included with this package
datadir = os.path.join(FlowCytometryTools.__path__[0], 'tests', 'data',
'Plate01')
datafile = os.path.join(datadir, 'RFP_Well_A3.fcs')
# datafile = '[insert path to your own fcs file]'
# Load data
tsample = FCMeasurement(ID='Test Sample', datafile=datafile)
tsample = tsample.transform('hlog', channels=['Y2-A', 'B1-A', 'V2-A'], b=500.0)
# Plot
tsample.plot(['Y2-A', 'B1-A'], bins=100, alpha=0.9, cmap=cm.hot)
grid(True)
# show() # <-- Uncomment when running as a script.
import os
import FlowCytometryTools
from FlowCytometryTools import FCMeasurement
from pylab import *
# Locate sample data included with this package
datadir = os.path.join(FlowCytometryTools.__path__[0], 'tests', 'data', 'Plate01')
datafile = os.path.join(datadir, 'RFP_Well_A3.fcs')
# datafile = '[insert path to your own fcs file]'
# Load data
tsample = FCMeasurement(ID='Test Sample', datafile=datafile)
tsample = tsample.transform('hlog', channels=['Y2-A', 'B1-A', 'V2-A'], b=500.0)
# Plot
tsample.plot('Y2-A', bins=100, alpha=0.9, color='green');
grid(True)
# show() # <-- Uncomment when running as a script.
new_sample = original_sample.copy()
new_data = new_sample.data
original_data = original_sample.data
# Our transformation goes here
new_data['Y2-A'] = original_data['Y2-A'] - 0.15 * original_data['FSC-A']
new_data['FSC-A'] = original_data['FSC-A'] - 0.32 * original_data['Y2-A']
new_data = new_data.dropna() # Removes all NaN entries
new_sample.data = new_data
return new_sample
# Load data
sample = FCMeasurement(ID='Test Sample', datafile=datafile)
sample = sample.transform('hlog')
compensated_sample = sample.apply(custom_compensate)
###
# To do this with a collection (a plate):
# compensated_plate = plate.apply(compensate, output_format='collection')
#
# Plot
sample.plot(['Y2-A', 'FSC-A'], kind='scatter', color='gray', alpha=0.6, label='Original');
compensated_sample.plot(['Y2-A', 'FSC-A'], kind='scatter', color='green', alpha=0.6, label='Compensated');
legend(loc='best')
grid(True)
#show() # <-- Uncomment when running as a script.
class FCGateManager(EventGenerator):
"""Manages gate creation widgets and gates."""
def __init__(self, ax, callback_list=None):
self.gates = []
self.fig = ax.figure
self.ax = ax
self._plt_data = None
self.active_gate = None
self.sample = None
self.canvas = self.fig.canvas
self.key_handler_cid = self.canvas.mpl_connect(
'key_press_event',
lambda event: key_press_handler(event, self.canvas, self))
self.pick_event_cid = self.canvas.mpl_connect('pick_event',
self.pick_event_handler)
self.gate_num = 1
self.current_channels = 'd1', 'd2'
self.add_callback(callback_list)
def disconnect_events(self):
self.canvas.mpl_disconnect(self.key_handler_cid)
self.canvas.mpl_disconnect(self.pick_event_cid)
def pick_event_handler(self, event):
""" Handles pick events """
info = {
'options': self.get_available_channels(),
'guiEvent': event.mouseevent.guiEvent,
}
if hasattr(self, 'xlabel_artist') and (event.artist
== self.xlabel_artist):
info['axis_num'] = 0
self.callback(Event('axis_click', info))
if hasattr(self, 'ylabel_artist') and (event.artist
== self.ylabel_artist):
info['axis_num'] = 1
self.callback(Event('axis_click', info))
def add_gate(self, gate):
self.gates.append(gate)
self.set_active_gate(gate)
def remove_active_gate(self):
if self.active_gate is not None:
self.gates.remove(self.active_gate)
self.active_gate.remove()
self.active_gate = None
def set_active_gate(self, gate):
if self.active_gate is None:
self.active_gate = gate
gate.activate()
elif self.active_gate is not gate:
self.active_gate.inactivate()
self.active_gate = gate
gate.activate()
def _get_next_gate_name(self):
gate_name = 'gate{0}'.format(self.gate_num)
self.gate_num += 1
return gate_name
def _handle_gate_events(self, event):
self.set_active_gate(event.info['caller'])
def create_gate_widget(self, kind):
def clean_drawing_tools():
self._drawing_tool.disconnect_events()
self.canvas.draw_idle()
self._drawing_tool = None
def create_gate(*args):
cancelled = False # TODO allow drawing tool to cancel
verts = args[0]
ch = self.current_channels
verts = [dict(zip(ch, v)) for v in verts]
if kind == 'poly':
gate_type = PolyGate
elif 'threshold' in kind or 'quad' in kind:
gate_type = ThresholdGate
# FIXME: This is very specific implementation
if 'vertical' in kind:
verts = [{ch[0]: v[ch[0]]} for v in verts]
elif 'horizontal' in kind:
if len(ch) == 1:
cancelled = True
else:
verts = [{ch[1]: v[ch[1]]} for v in verts]
if not cancelled:
gate = BaseGate(verts,
gate_type,
name=self._get_next_gate_name(),
callback_list=self._handle_gate_events)
gate.spawn(ch, self.ax)
self.add_gate(gate)
clean_drawing_tools()
def start_drawing(kind):
if kind == 'poly':
self._drawing_tool = PolyDrawer(self.ax,
oncreated=create_gate,
lineprops=dict(color='k',
marker='o'))
elif kind == 'quad':
self._drawing_tool = Cursor(self.ax, vertOn=1, horizOn=1)
elif kind == 'horizontal threshold':
self._drawing_tool = Cursor(self.ax, vertOn=0, horizOn=1)
elif kind == 'vertical threshold':
self._drawing_tool = Cursor(self.ax, vertOn=1, horizOn=0)
if isinstance(self._drawing_tool, Cursor):
def finish_drawing(event):
self._drawing_tool.clear(None)
return create_gate([(event.xdata, event.ydata)])
self._drawing_tool.connect_event('button_press_event',
finish_drawing)
start_drawing(kind)
####################
### Loading Data ###
####################
def load_fcs(self, filepath=None, parent=None):
ax = self.ax
if parent is None:
parent = self.fig.canvas
if filepath is None:
from FlowCytometryTools.gui import dialogs
filepath = dialogs.open_file_dialog('Select an FCS file to load',
'FCS files (*.fcs)|*.fcs',
parent=parent)
if filepath is not None:
self.sample = FCMeasurement('temp', datafile=filepath)
print('WARNING: Data is raw (not transformation).')
self._sample_loaded_event()
def load_measurement(self, measurement):
self.sample = measurement.copy()
self._sample_loaded_event()
def _sample_loaded_event(self):
if self.sample is not None:
self.current_channels = list(self.sample.channel_names[0:2])
self.set_axes(self.current_channels, self.ax)
def get_available_channels(self):
return self.sample.channel_names
def change_axis(self, axis_num, channel_name):
"""
TODO: refactor that and set_axes
what to do with ax?
axis_num: int
axis number
channel_name: str
new channel to plot on that axis
"""
current_channels = list(self.current_channels)
if len(current_channels) == 1:
if axis_num == 0:
new_channels = channel_name,
else:
new_channels = current_channels[0], channel_name
else:
new_channels = list(current_channels)
new_channels[axis_num] = channel_name
self.set_axes(new_channels, self.ax)
def set_axes(self, channels, ax):
"""
channels : iterable of string
each value corresponds to a channel names
names must be unique
"""
# To make sure displayed as hist
if len(set(channels)) == 1:
channels = channels[0],
self.current_channels = channels
# Remove existing gates
for gate in self.gates:
gate.remove_spawned_gates()
##
# Has a clear axis command inside!!
# which will "force kill" spawned gates
self.plot_data()
for gate in self.gates:
sgate = gate.spawn(channels, ax)
gate._refresh_activation()
def close(self):
for gate in self.gates:
gate.remove()
self.disconnect_events()
####################
### Plotting Data ##
####################
def plot_data(self):
"""Plots the loaded data"""
# Clear the plot before plotting onto it
self.ax.cla()
if self.sample is None:
return
if self.current_channels is None:
self.current_channels = self.sample.channel_names[:2]
channels = self.current_channels
channels_to_plot = channels[0] if len(channels) == 1 else channels
self.sample.plot(channels_to_plot, ax=self.ax)
xaxis = self.ax.get_xaxis()
yaxis = self.ax.get_yaxis()
self.xlabel_artist = xaxis.get_label()
self.ylabel_artist = yaxis.get_label()
self.xlabel_artist.set_picker(5)
self.ylabel_artist.set_picker(5)
self.fig.canvas.draw()
def get_generation_code(self):
"""Return python code that generates all drawn gates."""
if len(self.gates) < 1:
code = ''
else:
import_list = set(
[gate._gencode_gate_class for gate in self.gates])
import_list = 'from FlowCytometryTools import ' + ', '.join(
import_list)
code_list = [gate.get_generation_code() for gate in self.gates]
code_list.sort()
code_list = '\n'.join(code_list)
code = import_list + 2 * '\n' + code_list
self.callback(Event('generated_code', {'code': code}))
return code
## load in the rest of the samples
halo2 = FCMeasurement(ID='halo2',
datafile= '/Users/KendraSwain/Documents/Lab Files/Experiments/flow cytometry/180125 Sgn1 FC data/Halo only 2.fcs')
sgn1 = FCMeasurement(ID='sgn1',
datafile= '/Users/KendraSwain/Documents/Lab Files/Experiments/flow cytometry/180125 Sgn1 FC data/old SGN1 1.fcs')
sgn2 = FCMeasurement(ID='sgn2',
datafile= '/Users/KendraSwain/Documents/Lab Files/Experiments/flow cytometry/180125 Sgn1 FC data/old SGN1 2.fcs')
sgn1.channel_names
# In[5]:
## plot halo control 1
halo1.plot(['FSC-A', 'SSC-A'])
plt.show()
# In[6]:
## draw gate around healthiest cells
gate1= PolyGate([(50000,0),(80000,0), (80000,45000), (50000,45000)],
('FSC-A', 'SSC-A'), region='in')
halo1.plot(['FSC-A', 'SSC-A'], gates=gate1)
plt.show()
# In[7]:
# Locate sample data included with this package
datadir = os.path.join(FlowCytometryTools.__path__[0], 'tests', 'data', 'Plate01')
datafile = os.path.join(datadir, 'RFP_Well_A3.fcs')
# datafile = '[insert path to your own fcs file]'
# Load data
tsample = FCMeasurement(ID='Test Sample', datafile=datafile)
tsample = tsample.transform('hlog', channels=['Y2-A', 'B1-A', 'V2-A'], b=500.0)
# Create a threshold gates
y2_gate = ThresholdGate(1000.0, 'Y2-A', region='above')
# Gate
gated_sample = tsample.gate(y2_gate)
# Plot
ax1 = subplot(121);
tsample.plot('Y2-A', gates=[y2_gate], bins=100, alpha=0.9);
y2_gate.plot(color='k', linewidth=4, linestyle='-')
title('Original Sample');
ax2 = subplot(122, sharey=ax1, sharex=ax1);
gated_sample.plot('Y2-A', gates=[y2_gate], bins=100, color='y', alpha=0.9);
title('Gated Sample');
tight_layout()
#show() # <-- Uncomment when running as a script.
class FCGateManager(EventGenerator):
"""Manages gate creation widgets and gates."""
def __init__(self, ax, callback_list=None):
self.gates = []
self.fig = ax.figure
self.ax = ax
self._plt_data = None
self.active_gate = None
self.sample = None
self.canvas = self.fig.canvas
self.key_handler_cid = self.canvas.mpl_connect('key_press_event',
lambda event: key_press_handler(event,
self.canvas,
self))
self.pick_event_cid = self.canvas.mpl_connect('pick_event', self.pick_event_handler)
self.gate_num = 1
self.current_channels = 'd1', 'd2'
self.add_callback(callback_list)
def disconnect_events(self):
self.canvas.mpl_disconnect(self.key_handler_cid)
self.canvas.mpl_disconnect(self.pick_event_cid)
def pick_event_handler(self, event):
""" Handles pick events """
info = {'options': self.get_available_channels(),
'guiEvent': event.mouseevent.guiEvent,
}
if hasattr(self, 'xlabel_artist') and (event.artist == self.xlabel_artist):
info['axis_num'] = 0
self.callback(Event('axis_click', info))
if hasattr(self, 'ylabel_artist') and (event.artist == self.ylabel_artist):
info['axis_num'] = 1
self.callback(Event('axis_click', info))
def add_gate(self, gate):
self.gates.append(gate)
self.set_active_gate(gate)
def remove_active_gate(self):
if self.active_gate is not None:
self.gates.remove(self.active_gate)
self.active_gate.remove()
self.active_gate = None
def set_active_gate(self, gate):
if self.active_gate is None:
self.active_gate = gate
gate.activate()
elif self.active_gate is not gate:
self.active_gate.inactivate()
self.active_gate = gate
gate.activate()
def _get_next_gate_name(self):
gate_name = 'gate{0}'.format(self.gate_num)
self.gate_num += 1
return gate_name
def _handle_gate_events(self, event):
self.set_active_gate(event.info['caller'])
def create_gate_widget(self, kind):
def clean_drawing_tools():
self._drawing_tool.disconnect_events()
self.canvas.draw_idle()
self._drawing_tool = None
def create_gate(*args):
cancelled = False # TODO allow drawing tool to cancel
verts = args[0]
ch = self.current_channels
verts = [dict(zip(ch, v)) for v in verts]
if kind == 'poly':
gate_type = PolyGate
elif 'threshold' in kind or 'quad' in kind:
gate_type = ThresholdGate
# FIXME: This is very specific implementation
if 'vertical' in kind:
verts = [{ch[0]: v[ch[0]]} for v in verts]
elif 'horizontal' in kind:
if len(ch) == 1:
cancelled = True
else:
verts = [{ch[1]: v[ch[1]]} for v in verts]
if not cancelled:
gate = BaseGate(verts, gate_type, name=self._get_next_gate_name(),
callback_list=self._handle_gate_events)
gate.spawn(ch, self.ax)
self.add_gate(gate)
clean_drawing_tools()
def start_drawing(kind):
if kind == 'poly':
self._drawing_tool = PolyDrawer(self.ax, oncreated=create_gate,
lineprops=dict(color='k', marker='o'))
elif kind == 'quad':
self._drawing_tool = Cursor(self.ax, vertOn=1, horizOn=1)
elif kind == 'horizontal threshold':
self._drawing_tool = Cursor(self.ax, vertOn=0, horizOn=1)
elif kind == 'vertical threshold':
self._drawing_tool = Cursor(self.ax, vertOn=1, horizOn=0)
if isinstance(self._drawing_tool, Cursor):
def finish_drawing(event):
self._drawing_tool.clear(None)
return create_gate([(event.xdata, event.ydata)])
self._drawing_tool.connect_event('button_press_event', finish_drawing)
start_drawing(kind)
####################
### Loading Data ###
####################
def load_fcs(self, filepath=None, parent=None):
ax = self.ax
if parent is None:
parent = self.fig.canvas
if filepath is None:
from FlowCytometryTools.gui import dialogs
filepath = dialogs.open_file_dialog('Select an FCS file to load',
'FCS files (*.fcs)|*.fcs', parent=parent)
if filepath is not None:
self.sample = FCMeasurement('temp', datafile=filepath)
print('WARNING: Data is raw (not transformation).')
self._sample_loaded_event()
def load_measurement(self, measurement):
self.sample = measurement.copy()
self._sample_loaded_event()
def _sample_loaded_event(self):
if self.sample is not None:
self.current_channels = list(self.sample.channel_names[0:2])
self.set_axes(self.current_channels, self.ax)
def get_available_channels(self):
return self.sample.channel_names
def change_axis(self, axis_num, channel_name):
"""
TODO: refactor that and set_axes
what to do with ax?
axis_num: int
axis number
channel_name: str
new channel to plot on that axis
"""
current_channels = list(self.current_channels)
if len(current_channels) == 1:
if axis_num == 0:
new_channels = channel_name,
else:
new_channels = current_channels[0], channel_name
else:
new_channels = list(current_channels)
new_channels[axis_num] = channel_name
self.set_axes(new_channels, self.ax)
def set_axes(self, channels, ax):
"""
channels : iterable of string
each value corresponds to a channel names
names must be unique
"""
# To make sure displayed as hist
if len(set(channels)) == 1:
channels = channels[0],
self.current_channels = channels
# Remove existing gates
for gate in self.gates:
gate.remove_spawned_gates()
##
# Has a clear axis command inside!!
# which will "force kill" spawned gates
self.plot_data()
for gate in self.gates:
sgate = gate.spawn(channels, ax)
gate._refresh_activation()
def close(self):
for gate in self.gates:
gate.remove()
self.disconnect_events()
####################
### Plotting Data ##
####################
def plot_data(self):
"""Plots the loaded data"""
# Clear the plot before plotting onto it
self.ax.cla()
if self.sample is None:
return
if self.current_channels is None:
self.current_channels = self.sample.channel_names[:2]
channels = self.current_channels
channels_to_plot = channels[0] if len(channels) == 1 else channels
self.sample.plot(channels_to_plot, ax=self.ax)
xaxis = self.ax.get_xaxis()
yaxis = self.ax.get_yaxis()
self.xlabel_artist = xaxis.get_label()
self.ylabel_artist = yaxis.get_label()
self.xlabel_artist.set_picker(5)
self.ylabel_artist.set_picker(5)
self.fig.canvas.draw()
def get_generation_code(self):
"""Return python code that generates all drawn gates."""
if len(self.gates) < 1:
code = ''
else:
import_list = set([gate._gencode_gate_class for gate in self.gates])
import_list = 'from FlowCytometryTools import ' + ', '.join(import_list)
code_list = [gate.get_generation_code() for gate in self.gates]
code_list.sort()
code_list = '\n'.join(code_list)
code = import_list + 2 * '\n' + code_list
self.callback(Event('generated_code',
{'code': code}))
return code
from FlowCytometryTools import FCMeasurement, ThresholdGate
import os, FlowCytometryTools
from pylab import *
# Locate sample data included with this package
datadir = os.path.join(FlowCytometryTools.__path__[0], 'tests', 'data', 'Plate01')
datafile = os.path.join(datadir, 'RFP_Well_A3.fcs')
# datafile = '[insert path to your own fcs file]'
# Load data
tsample = FCMeasurement(ID='Test Sample', datafile=datafile)
tsample = tsample.transform('hlog', channels=['Y2-A', 'B1-A', 'V2-A'], b=500.0)
# Plot
tsample.plot(['Y2-A', 'B1-A'], bins=100, alpha=0.9, cmap=cm.hot);
grid(True)
#show() # <-- Uncomment when running as a script.
return new_sample
# Load data
sample = FCMeasurement(ID='Test Sample', datafile=datafile)
sample = sample.transform('hlog')
compensated_sample = sample.apply(custom_compensate)
###
# To do this with a collection (a plate):
# compensated_plate = plate.apply(compensate, output_format='collection')
#
# Plot
sample.plot(['Y2-A', 'FSC-A'],
kind='scatter',
color='gray',
alpha=0.6,
label='Original')
compensated_sample.plot(['Y2-A', 'FSC-A'],
kind='scatter',
color='green',
alpha=0.6,
label='Compensated')
legend(loc='best')
grid(True)
#show() # <-- Uncomment when running as a script.
# Locate sample data included with this package
datadir = os.path.join(FlowCytometryTools.__path__[0], 'tests', 'data', 'Plate01')
datafile = os.path.join(datadir, 'RFP_Well_A3.fcs')
# datafile = '[insert path to your own fcs file]'
# Load data
tsample = FCMeasurement(ID='Test Sample', datafile=datafile)
tsample = tsample.transform('hlog', channels=['Y2-A', 'B1-A', 'V2-A'], b=500.0)
# Create a threshold gates
y2_gate = ThresholdGate(1000.0, 'Y2-A', region='above')
# Gate
gated_sample = tsample.gate(y2_gate)
# Plot
ax1 = subplot(121);
tsample.plot('Y2-A', gates=[y2_gate], bins=100, alpha=0.9);
y2_gate.plot(color='k', linewidth=4, linestyle='-')
title('Original Sample');
ax2 = subplot(122, sharey=ax1, sharex=ax1);
gated_sample.plot('Y2-A', gates=[y2_gate], bins=100, color='y', alpha=0.9);
title('Gated Sample');
tight_layout()
#show() # <-- Uncomment when running as a script.
# Add Axes to the Figure
#fig.add_axes([0,0,1,1])
#fig, axs = plt.subplots(3, 1)
#fig.subplots_adjust(hspace=0.0, wspace= 0.0)
plt.subplots(figsize=(2,2))
subplots_adjust(hspace=0.0, wspace= 0.0)
# Load data
datafile = r'/Users/anazuniga/Documents/phyton/FlowCytometryTools/FCplate 2 input/2MP1/export_P7R_Single Cells.fcs'
tsample = FCMeasurement(ID='Test Sample', datafile=datafile)
tsample = tsample.transform('hlog', channels=['GFP-H', 'SSC-H', 'mCherry-H', 'FSC-H', 'V1-H'], b=200.0)
ax = subplot(3,1,1)
# Plot
#tsample.plot(['YL2-H', 'SSC-H'], bins=100, alpha=2, cmap=cm.hot);
tsample.plot(['V1-H', 'SSC-H'], kind='scatter', alpha=0.05, color='black', s=1);
ax.tick_params(labelbottom=False, labelleft=False)
#ax1.set_ylim(0, 10000)
#plt.scale('log')
#logbins = np.geomspace(10, 1000000, 100)
#plt.xscale('log')
#ax1.set_yscale('log')
ax.set_ylim(1000, 10000)
#ax1.set_xlim(0, 10000)
#ax1.xaxis.set_label_position('none')
#ax.set_yticks('')
ax.set_ylabel('')
ax.set_xlabel('')
grid(False)
ax1 = subplot(3,1,2, sharey=ax, sharex=ax)
