class PolygonSelection(HasStrictTraits):
"""Plots, and lets the user interact with, a 2D selection.
Attributes
----------
polygon : Instance(numpy.ndarray)
The polygon vertices
view : Instance(IView)
the IView that this view is wrapping. I suggest that if it's another
ISelectionView, that its `interactive` property remain False. >.>
interactive : Bool
is this view interactive? Ie, can the user set the polygon verticies
with mouse clicks?
"""
id = "edu.mit.synbio.cytoflow.views.polygon"
friendly_id = "Polygon Selection"
view = Instance(IView, transient = True)
interactive = Bool(False, transient = True)
vertices = List((Float, Float))
# internal state.
_cursor = Instance(Cursor, transient = True)
_path = Instance(mpl.path.Path, transient = True)
_patch = Instance(mpl.patches.PathPatch, transient = True)
_line = Instance(mpl.lines.Line2D, transient = True)
_drawing = Bool(transient = True)
def plot(self, experiment, **kwargs):
"""Plot self.view, and then plot the selection on top of it."""
self.view.plot(experiment, **kwargs)
self._draw_poly()
def is_valid(self, experiment):
"""If the decorated view is valid, we are too."""
return self.view.is_valid(experiment)
@on_trait_change('vertices')
def _draw_poly(self):
ca = plt.gca()
if self._patch and self._patch in ca.patches:
self._patch.remove()
if self._drawing or not self.vertices or len(self.vertices) < 3 \
or any([len(x) != 2 for x in self.vertices]):
return
patch_vert = np.concatenate((np.array(self.vertices),
np.array((0,0), ndmin = 2)))
self._patch = \
mpl.patches.PathPatch(mpl.path.Path(patch_vert, closed = True),
edgecolor="black",
linewidth = 1.5,
fill = False)
ca.add_patch(self._patch)
plt.gcf().canvas.draw()
@on_trait_change('interactive')
def _interactive(self):
if self.interactive:
ax = plt.gca()
self._cursor = Cursor(ax, horizOn = False, vertOn = False)
self._cursor.connect_event('button_press_event', self._onclick)
self._cursor.connect_event('motion_notify_event', self._onmove)
else:
self._cursor.disconnect_events()
self._cursor = None
def _onclick(self, event):
"""Update selection traits"""
if(self._cursor.ignore(event)):
return
if event.dblclick:
self._drawing = False
self.vertices = map(tuple, self._path.vertices)
self._path = None
return
ca = plt.gca()
self._drawing = True
if self._patch and self._patch in ca.patches:
self._patch.remove()
if self._path:
vertices = np.concatenate((self._path.vertices,
np.array((event.xdata, event.ydata), ndmin = 2)))
else:
vertices = np.array((event.xdata, event.ydata), ndmin = 2)
self._path = mpl.path.Path(vertices, closed = False)
self._patch = mpl.patches.PathPatch(self._path,
edgecolor = "black",
fill = False)
ca.add_patch(self._patch)
plt.gcf().canvas.draw()
def _onmove(self, event):
if(self._cursor.ignore(event)
or not self._drawing
or not self._path
or self._path.vertices.shape[0] == 0
or not event.xdata
or not event.ydata):
return
ca = plt.gca()
if not ca:
return
if self._line and self._line in ca.lines:
self._line.remove()
xdata = [self._path.vertices[-1, 0], event.xdata]
ydata = [self._path.vertices[-1, 1], event.ydata]
self._line = mpl.lines.Line2D(xdata, ydata, linewidth = 1, color = "black")
ca.add_line(self._line)
plt.gcf().canvas.draw()
class QuadSelection(cytoflow.views.ScatterplotView):
"""Plots, and lets the user interact with, a quadrant gate.
Attributes
----------
op : Instance(Range2DOp)
The instance of Range2DOp that we're viewing / editing
huefacet : Str
The conditioning variable to plot multiple colors
subset : Str
The string passed to `Experiment.query()` to subset the data before
plotting
interactive : Bool
is this view interactive? Ie, can the user set the threshold with a
mouse click?
Notes
-----
We inherit `xfacet` and `yfacet` from `cytoflow.views.ScatterplotView`, but
they must both be unset!
Examples
--------
In an IPython notebook with `%matplotlib notebook`
>>> q = flow.QuadOp(name = "Quad",
... xchannel = "V2-A",
... ychannel = "Y2-A"))
>>> qv = q.default_view()
>>> qv.interactive = True
>>> qv.plot(ex2)
"""
id = Constant('edu.mit.synbio.cytoflow.views.quad')
friendly_id = Constant("Quadrant Selection")
op = Instance(IOperation)
name = DelegatesTo('op')
xchannel = DelegatesTo('op')
ychannel = DelegatesTo('op')
interactive = Bool(False, transient = True)
# internal state.
_ax = Any(transient = True)
_hline = Instance(Line2D, transient = True)
_vline = Instance(Line2D, transient = True)
_cursor = Instance(Cursor, transient = True)
def plot(self, experiment, **kwargs):
"""Plot the underlying scatterplot and then plot the selection on top of it."""
if not experiment:
raise util.CytoflowOpError("No experiment specified")
if not experiment:
raise util.CytoflowViewError("No experiment specified")
if self.xfacet:
raise util.CytoflowViewError("RangeSelection.xfacet must be empty or `Undefined`")
if self.yfacet:
raise util.CytoflowViewError("RangeSelection.yfacet must be empty or `Undefined`")
super(QuadSelection, self).plot(experiment, **kwargs)
self._ax = plt.gca()
self._draw_lines()
self._interactive()
@on_trait_change('op.xthreshold, op.ythreshold', post_init = True)
def _draw_lines(self):
if not self._ax:
return
if self._hline and self._hline in self._ax.lines:
self._hline.remove()
if self._vline and self._vline in self._ax.lines:
self._vline.remove()
if self.op.xthreshold and self.op.ythreshold:
self._hline = plt.axhline(self.op.ythreshold,
linewidth = 3,
color = 'blue')
self._vline = plt.axvline(self.op.xthreshold,
linewidth = 3,
color = 'blue')
plt.draw_if_interactive()
@on_trait_change('interactive', post_init = True)
def _interactive(self):
if self._ax and self.interactive:
self._cursor = Cursor(self._ax,
horizOn = True,
vertOn = True,
color = 'blue')
self._cursor.connect_event('button_press_event', self._onclick)
elif self._cursor:
self._cursor.disconnect_events()
self._cursor = None
def _onclick(self, event):
"""Update the threshold location"""
self.op.xthreshold = event.xdata
self.op.ythreshold = event.ydata
class ECE4012:
def __init__(self, figure, filename, toolbar):
self.dfCal = None
self.fig = figure
self.toolbar = toolbar
self.filename = filename
self.rect = None
# Function used to setup graph after class is created or after new data is loaded
def initializer(self, type):
self.fig.clear()
print("clear figure")
self.fig.subplots_adjust(hspace=1.0)
self.annoteText = "annotated"
self.isAnnotate = False
self.fig.canvas.mpl_connect('button_release_event', self.onrelease)
self.fig.canvas.mpl_connect('button_press_event', self.onclick)
self.fig.canvas.mpl_connect('key_press_event', self.onpress)
self.fig.canvas.mpl_connect('pick_event', self.onpick)
if type == "DB":
self.searchOpenCalibration(self.filename)
self.conn = self.getConnection(self.filename)
t = time.time()
df = pd.read_sql_query("select * from acc;", self.conn)
elapsed = time.time() - t
print("time taken to read data was {:f}".format(elapsed))
elif type == "CSV":
print("CSV getting Calibration")
self.searchOpenCalibration(self.filename)
print("CSV opening file")
df = pd.read_csv(self.filename)
print("CSV opened file")
print("Starting")
# Apply calibration if calibration data is loaded
if self.dfCal is not None:
df["valuex"] = np.subtract(df["valuex"], self.dfCal['Values'][
self.XOffset]) / self.dfCal['Values'][self.XGain]
df["valuey"] = np.subtract(df["valuey"], self.dfCal['Values'][
self.YOffset]) / self.dfCal['Values'][self.YGain]
df["valuez"] = np.subtract(df["valuez"], self.dfCal['Values'][
self.ZOffset]) / self.dfCal['Values'][self.ZGain]
self.fig.subplots_adjust(bottom=0.3, left=0.2, hspace=1.0)
# setup some constants to be used in Scale Selection panel
self.labels = ['30 sec', '5 min', '30 min', '1 hr', '2 hr']
sec30 = pd.Timedelta(30, unit='s')
min5 = pd.Timedelta(5, unit='m')
min30 = pd.Timedelta(30, unit='m')
hr1 = pd.Timedelta(1, unit='h')
hr2 = pd.Timedelta(2, unit='h')
# Scale Selection panel made from Radio Buttons
self.scaleDeltaArray = [sec30, min5, min30, hr1, hr2]
self.rax = self.fig.add_axes([0.02, 0.7, 0.11, 0.15])
self.rax.set_title('Scale')
self.check = RadioButtons(self.rax, self.labels)
self.fig.canvas.mpl_connect('button_press_event', self.onclick)
self.check.on_clicked(self.changeScale)
# Data Set Selection Check Box
self.rcbax = self.fig.add_axes([0.02, 0.25, 0.11, 0.15])
self.rcbax.set_title('DataSet')
self.checkBox = CheckButtons(self.rcbax,
('valuex', 'valuey', 'valuez', 'mag'),
(True, True, True, True))
self.checkBox.on_clicked(self.oncheck)
xs = np.linspace(15, 21, 200)
horiz_line_dataz = np.array([0.41 for i in range(len(xs))])
self.rcbax.plot(xs, horiz_line_dataz, 'C3-')
horiz_line_datam = np.array([0.26 for i in range(len(xs))])
self.rcbax.plot(xs, horiz_line_datam, 'C0-')
horiz_line_datay = np.array([0.58 for i in range(len(xs))])
self.rcbax.plot(xs, horiz_line_datay, 'C2-')
horiz_line_datax = np.array([0.73 for i in range(len(xs))])
self.rcbax.plot(xs, horiz_line_datax, 'C1-')
# Create magnitude value of acceleration data in a dataframe and substract 1g to eliminate gravity
df["mag"] = np.sqrt(np.square(df["valuex"]) + np.square(df['valuey']) + \
np.square(df["valuez"]))-1.0
print("Normalize")
ya_min = df.loc[:, "mag"].min() - 0.1
ya_max = df.loc[:, "mag"].max() + 0.1
print("y limit (max={:f},min={:f})".format(ya_max, ya_min))
print("Convert Date Time")
print(df["epoch"].iloc[0])
print(df["epoch"].iloc[1])
# Convert epoch to datetime
if type == "DB":
print("epoch type", df.dtypes[0])
df['epoch'] = pd.to_datetime(df['epoch'], unit='ms')
elif type == "CSV":
print("epoch type", df.dtypes[0])
if 'annotated' not in df.columns:
df['epoch'] = pd.to_datetime(df['epoch'], unit='ms')
else:
df['epoch'] = pd.to_datetime(df['epoch'])
print("epoch type after", df.dtypes[0])
# Adjusting epoch time to be in Eastern Time Zone
df['epoch'] = df['epoch'].dt.tz_localize('UTC').dt.tz_convert(
'America/New_York')
# Create external numpy array to manage timestamp data to be sure that data will be datetime
vepoch = df['epoch']
self.datevalues = vepoch.dt.to_pydatetime()
# Create annotated and colorHex columns in the dataframe for capturing annotation
if 'annotated' not in df.columns:
charArr = np.chararray((len(df["mag"], )), unicode=True)
charArr[:] = ' '
df["annotated"] = pd.DataFrame(charArr)
df["colorHex"] = pd.DataFrame(charArr)
# Define format for graph ticks
self.hoursFmt = mdates.DateFormatter('%a-%m-%d %H:%M:%S')
self.HMSFmt = mdates.DateFormatter('%H:%M:%S')
# Get total time of the data in hours
startDate = df["epoch"].iloc[0]
self.startDate = startDate
endDate = df["epoch"].iloc[-1]
totaltime = int(endDate.timestamp() * 1000) - \
int(startDate.timestamp() * 1000)
total_hours = totaltime / 1000 / 3600 #totaltime in hours
total_minutes = total_hours * 60
print("total hours {:f}".format(total_hours))
# Create variable to track drag time
self.timeTrack = 0
# Create variable to track initial click xpos
self.xpos = 0
# Create class attribute with the data to be used in the rest of class functions
self.df = df
print("Creating Top Graph")
# First axis representing Top Graph
self.ax = self.fig.add_subplot(2, 1, 1)
# Second axis representing Bottom Graph
print("Creating Bottom Graph")
self.ax2 = self.fig.add_subplot(2, 1, 2)
# Adjust distance between toolbar and graph to give more space
self.fig.subplots_adjust(bottom=0.145)
# Adjust distance between toolbar and graph if data is 24 hours or more
if total_hours > 24:
self.fig.subplots_adjust(hspace=1.3)
print("Start Plot Setting")
# Set axis titles to graphs
self.ax.set_xlabel("Time")
self.ax2.set_xlabel("Time")
self.ax.set_ylabel("Acceleration (g)")
self.ax2.set_ylabel("Acceleration (g)")
# Adjust y-axis range to maximum and minimum of magnitude
self.ax.set_ylim(ya_min, ya_max)
self.ax2.set_ylim(ya_min, ya_max)
# Set title with word Calibrated if calibration was applied
bottomtitle = 'Magnitude Graph for Start Date ' + "{:%Y-%m-%d}".format(
startDate)
if self.dfCal is not None:
bottomtitle = 'Calibrated ' + bottomtitle
self.ax.set_title(bottomtitle)
toptitle = 'Zoomed-In Graph for Start Date ' + "{:%Y-%m-%d}".format(
startDate)
if self.dfCal is not None:
toptitle = 'Calibrated ' + toptitle
self.ax2.set_title(toptitle)
# Prepare x-axis range to display initially in bottom graph
start_time = df["epoch"].iloc[0]
print("start time={v}".format(v=start_time))
# If data loaded is longer than 1 hour, GUI will show the first hour on bottom graph
if total_hours > 1:
end_time = start_time + hr1
elif total_minutes > 30:
end_time = start_time + min30
elif total_minutes > 5:
end_time = start_time + min5
else:
end_time = start_time + sec30
print("end time={v}".format(v=end_time))
self.startX = start_time
self.endX = end_time
# Set x-axis limit with previous selection
self.ax2.set_xlim(start_time, end_time)
print("Set Limit")
# Create data mask with informaton being displayed
mask = (df["epoch"] >= start_time) & (df["epoch"] <= end_time)
print("Plotting")
# Plot top graph
t = time.time()
# To increase speed to graph, only plot first 4 points and then
# substitute the data with function set_data, this saves several seconds of load time
self.plotTop, = self.ax.plot(df["epoch"].iloc[0:3],
df["mag"].iloc[0:3],
visible=True)
self.plotTop.set_data(self.datevalues, df["mag"])
self.ax.relim()
self.ax.autoscale_view(True, True, True)
self.fig.canvas.draw()
elapsed = time.time() - t
print("time taken to top graph magnitude was {:f}".format(elapsed))
print(len(df.loc[mask, "epoch"]))
# Plot bottom graph
t = time.time()
# Initially graphs only magnitude
# To increase speed to graph, only plot first 4 points and then
# substitute the data with function set_data, this saves several seconds of load time
self.lm, = self.ax2.plot(df["epoch"].iloc[0:3],
df["mag"].iloc[0:3],
visible=True)
self.lm.set_data(self.datevalues, df["mag"])
self.ax2.relim()
self.ax2.autoscale_view(True, True, True)
self.fig.canvas.draw()
elapsed = time.time() - t
print("time taken to bottom graph magnitude was {:f}".format(elapsed))
t = time.time()
# Create thread to plot x value in the bottom graph in background mode
# to avoid startup delay
try:
thread1 = myThread(1, "valuex", self)
thread1.start()
except:
print("Error: unable to start thread")
elapsed = time.time() - t
print("time taken to bottom graph valuex was {:f}".format(elapsed))
t = time.time()
# Create thread to plot y value in the bottom graph in background mode
# to avoid startup delay
try:
thread2 = myThread(2, "valuey", self)
thread2.start()
except:
print("Error: unable to start thread")
elapsed = time.time() - t
print("time taken to bottom graph valuey was {:f}".format(elapsed))
t = time.time()
# Create thread to plot z value in the bottom graph in background mode
# to avoid startup delay
try:
thread3 = myThread(3, "valuez", self)
thread3.start()
except:
print("Error: unable to start thread")
elapsed = time.time() - t
print("time taken to bottom graph valuez was {:f}".format(elapsed))
# x in the range
tX = df.loc[mask, "epoch"]
self.ax2.set_xlim(tX.iloc[0], tX.iloc[len(tX) - 1])
# Set tick format and number on top graph
self.ax.xaxis.set_major_formatter(self.HMSFmt)
self.ax.get_xaxis().set_major_locator(LinearLocator(numticks=12))
# Setup format of ticks to Weekday month/day if data is 24 hours or more
if total_hours > 24:
self.ax.xaxis.set_major_formatter(self.hoursFmt)
# Rotate labels on x-axis 45 degrees and set font size to 8
self.ax.tick_params(axis='x', labelsize=8, rotation=45)
# Select initial random color for random annotation
self.color = self.colorChoose(random.randint(0, 255),
random.randint(0, 255),
random.randint(0, 255))
self.removedObj = None
# Refresh the graph
self.fig.canvas.draw()
# Prepare graph to display red cursor on top graph
self.fig.canvas.mpl_connect('motion_notify_event', self.onmouseover)
self.cursor = Cursor(self.ax,
useblit=True,
horizOn=False,
color='red',
linewidth=2)
self.cursor.connect_event('button_press_event', self.cursorOnclick)
# Setup initial value for the scale to 30 seconds
self.currentDelta = pd.Timedelta(30, unit='s')
# Set tick format and number on bottom graph
self.ax2.xaxis.set_major_formatter(self.HMSFmt)
self.ax2.get_xaxis().set_major_locator(LinearLocator(numticks=7))
# Set function to format coordinates to be displayed on bottom right corner
self.ax.format_coord = self.format_coord
# Call function to search for annotation in the data
# if it was loaded from CSV file and graph them
if type == "CSV" and 'annotated' in df.columns:
print("calling searchForAnnotation")
self.searchForAnnotation()
# Function that derives values to be shown on bottom right corner.
# It will display Timestamp and magnitude of where cursor is located
def format_coord(self, x, y):
dateclickOn = mdates.num2date(x)
idx = self.df['epoch'].searchsorted(dateclickOn)
idx = idx - 1
vx = self.df['valuex'].values[idx][0]
vy = self.df['valuey'].values[idx][0]
vz = self.df['valuez'].values[idx][0]
vm = self.df['mag'].values[idx][0]
return "{:%H:%M:%S} M:{:1.3f}".format(dateclickOn, vm)
# Function to read calibrationResultsXXXXXXXXXXXX.csv
# to obtain offset and gain values of x,y, and z-axis
# from MetaWear device
def readCalibration(self, filename):
self.dfCal = pd.read_csv(filename)
print('Results: %s', self.dfCal)
print('title: %s', self.dfCal['Titles'])
print('values: %s', self.dfCal['Values'])
print('ZGain: %s', self.dfCal['Values'][1])
self.ZOffset = 0
self.ZGain = 1
self.YOffset = 2
self.YGain = 3
self.XOffset = 4
self.XGain = 5
# Function used to redraw top and bottom graphs
# with calibrated values applied to x, y, and z values
def redrawAfterCalibrate(self):
print("Computing new data")
#Computes new x, y, and z values with calibration
if self.dfCal is not None:
self.df["valuex"] = np.subtract(
self.df["valuex"], self.dfCal['Values'][
self.XOffset]) / self.dfCal['Values'][self.XGain]
self.df["valuey"] = np.subtract(
self.df["valuey"], self.dfCal['Values'][
self.YOffset]) / self.dfCal['Values'][self.YGain]
self.df["valuez"] = np.subtract(
self.df["valuez"], self.dfCal['Values'][
self.ZOffset]) / self.dfCal['Values'][self.ZGain]
print("Computing new mag")
self.df["mag"] = np.sqrt(np.square(self.df["valuex"]) + np.square(self.df['valuey']) + \
np.square(self.df["valuez"]))-1.0
print("setting titles")
# Bottom Title changed to say Calibrated
bottomtitle = 'Magnitude Graph for Start Date ' + "{:%Y-%m-%d}".format(
self.startDate)
if self.dfCal is not None:
bottomtitle = 'Calibrated ' + bottomtitle
self.ax.set_title(bottomtitle)
# Top Title changed to say Calibrated
toptitle = 'Zoomed-In Graph for Start Date ' + "{:%Y-%m-%d}".format(
self.startDate)
if self.dfCal is not None:
toptitle = 'Calibrated ' + toptitle
self.ax2.set_title(toptitle)
print("redraw graph")
# Refreshes graphs with new data values
self.plotTop.set_ydata(self.df["mag"])
self.lm.set_ydata(self.df["mag"])
self.lx.set_ydata(self.df["valuex"])
self.ly.set_ydata(self.df["valuey"])
self.lz.set_ydata(self.df["valuez"])
self.fig.canvas.draw()
# Function used to determine where mouse event occurs
def onmouseover(self, event):
if event.inaxes == self.rax:
None
if event.inaxes == self.ax:
self.cursor.onmove(event)
# Function used to determine if calibration file is found in same directory
# as GUI application
def searchOpenCalibration(self, filename):
directory = os.path.dirname(filename)
print("directory=" + directory)
tosearch = re.compile('^calibrationResults.*')
for sChild in os.listdir(directory):
print("file=" + sChild)
if tosearch.match(sChild) is not None:
if directory == "":
directory = "."
calibfilename = directory + "/" + sChild
print("calibfilename=" + calibfilename)
self.readCalibration(calibfilename)
break
# Function used to determine if annotations have been applied to
# recently opened csv file
def searchForAnnotation(self):
colorKick = self.colorChoose(255, 0, 0)
colorSleep = self.colorChoose(0, 0, 255)
colorRandom = self.colorChoose(0, 255, 0)
randomColor = self.color
maskKick = self.df['annotated'] == "Kick"
maskSleep = self.df['annotated'] == "Sleep"
maskRandom = self.df['annotated'] == "Random"
maskColorRandom = self.df['annotated'] == "annotated"
print("masked found")
# Creates mask of locations of annotations
# Calls reDrawAnnotation to replot rectangles on graphs
if len(self.df.loc[maskKick, 'epoch']) > 0:
self.reDrawAnnotation(maskKick, colorKick)
if len(self.df.loc[maskSleep, 'epoch']) > 0:
self.reDrawAnnotation(maskSleep, colorSleep)
if len(self.df.loc[maskRandom, 'epoch']) > 0:
self.reDrawAnnotation(maskRandom, colorRandom)
if len(self.df.loc[maskColorRandom, 'epoch']) > 0:
self.reDrawAnnotation(maskColorRandom, randomColor)
# Function used to redraw all annotations seen when
# opening csv file that has annotations
def reDrawAnnotation(self, mask, color):
[ymin, ymax] = self.ax.get_ylim()
height = ymax - ymin
# Determines index positions of annotations
positionKick = np.array(self.df.index[mask].tolist())
# Determines where gaps between annotations occur
diff = np.subtract(positionKick[1:-1], positionKick[0:-2])
maskcuts = diff > 1
posInCuts = np.where(maskcuts)
arrposcut = posInCuts[0]
arrpostcut1 = arrposcut + 1
# Initializes first seen annotation
xmin = self.df.loc[mask, 'epoch'].iloc[0]
xmax = self.df.loc[mask, 'epoch'].iloc[-1]
xmin = xmin.to_pydatetime()
xmax = xmax.to_pydatetime()
# converts values to proper time format
print("xmin={v1} xmax={v2}".format(v1=xmin, v2=xmax))
xmin = mdates.date2num(xmin)
xmax = mdates.date2num(xmax)
print("len(posInCuts)", len(posInCuts[0]))
print("xmin={v1} xmax={v2}".format(v1=xmin, v2=xmax))
# For loop used to run through and create rectangles to plot for annotations
for idx in range(len(posInCuts[0])):
print("idx=", idx)
print("xmin={v1} xmax={v2}".format(
v1=xmin,
v2=self.df['epoch'].iloc[positionKick[arrposcut[idx]]]))
rectmin = xmin
rectmax = self.df['epoch'].iloc[positionKick[arrposcut[idx]]]
rectmax = rectmax.to_pydatetime()
rectmax = mdates.date2num(rectmax)
width = rectmax - rectmin
rect = ECERectangle(rectmin,
ymin,
width,
height,
color=color,
index=1)
rect2 = ECERectangle(xmin,
ymin,
width,
height,
color=color,
index=2)
rect.setNext(rect2)
rect2.setPrev(rect)
self.ax.add_patch(rect)
self.ax2.add_patch(rect2)
self.fig.canvas.draw()
xmin = self.df['epoch'].iloc[positionKick[arrpostcut1[idx]]]
xmin = xmin.to_pydatetime()
xmin = mdates.date2num(xmin)
rectmin = xmin
rectmax = xmax
width = rectmax - rectmin
rect = ECERectangle(rectmin, ymin, width, height, color=color, index=1)
rect2 = ECERectangle(xmin, ymin, width, height, color=color, index=2)
rect.setNext(rect2)
rect2.setPrev(rect)
self.ax.add_patch(rect)
self.ax2.add_patch(rect2)
print("xmin={v1} xmax={v2}".format(v1=xmin, v2=xmax))
self.fig.canvas.draw()
# Sets up sqlite3 connection to database file
def getConnection(self, filename):
"""
get the connection of sqlite given file name
:param filename:
:return: sqlite3 connection
"""
conn = sqlite3.connect(filename)
return conn
# Old Function used to read calibration file. No longer relevant
def readCalibration(self, filename):
self.dfCal = pd.read_csv(filename)
print('Results: %s', self.dfCal)
print('title: %s', self.dfCal['Titles'])
print('values: %s', self.dfCal['Values'])
print('ZGain: %s', self.dfCal['Values'][1])
self.ZOffset = 0
self.ZGain = 1
self.YOffset = 2
self.YGain = 3
self.XOffset = 4
self.XGain = 5
# Function used to create calibration button. No longer relevant
def createCalibrationAction(self):
image_file = 'square-upload'
callback = self.toolbar.importCal
text = "Calibrate"
tooltip_text = "Calibrate"
a = self.toolbar.addAction(self.toolbar._icon(image_file + '.png'),
text, callback)
print("action created")
self.toolbar._actions[callback] = a
print("action added to array")
a.setToolTip(tooltip_text)
# Function to execute query
def executeQuery(self, query):
return None
# Function used to set range of colors
def colorChoose(self, r, g, b):
"""
create a normalized color map give r, g, b in 0-255 scale
:param r: red
:param g: green
:param b: blue
:return: tuple of color that can be used for matplotlib
"""
if self.rangeOff(r) or self.rangeOff(g) or self.rangeOff(r):
return (0, 0, 0)
return r / 255.0, g / 255.0, b / 255.0
# Function to set range off
def rangeOff(self, val):
return (val > 255) or (val < 0)
# Function to determine event of creating annotations
def onpick(self, event):
print("pick event")
if isinstance(event.artist, Rectangle):
patch = event.artist
# patch.remove()
self.removedObj = patch
print('onpick1 patch:', patch.get_path())
else:
print(event.artist.get_xdata())
print(event.artist.get_xdata())
print(len(event.artist.get_ydata()))
# Function used to check if annotation is selected
def onclick(self, event):
if not self.toolbar._actions['zoom'].isChecked(
) and event.button == 1: # left = 1, middle = 2, right = 3
self.timeTrack = time.time()
print("clicked {}".format(self.timeTrack))
print("clicked X: {}".format(event.xdata))
self.xpos = event.xdata
# Function used to determine when annotation event occurs
def onrelease(self, event):
if not self.toolbar._actions['zoom'].isChecked() \
and event.button == 1 and self.isAnnotate:
curTime = time.time()
if (curTime - self.timeTrack) > PRE_DEF_CLICK_TIME:
print("dragged")
xmin = self.xpos
xmax = event.xdata
width = xmax - xmin
[ymin, ymax] = self.ax.get_ylim()
height = ymax - ymin
self.create_annotation(xmin, xmax)
rect = ECERectangle(xmin,
ymin,
width,
height,
color=self.color,
index=1)
rect2 = ECERectangle(xmin,
ymin,
width,
height,
color=self.color,
index=2)
rect.setNext(rect2)
rect2.setPrev(rect)
self.ax.add_patch(rect)
self.ax2.add_patch(rect2)
self.fig.canvas.draw()
# Key commands running from keyboard
def onpress(self, event):
# print(event.key())
print(event.key)
if event.key == 'r':
self.annoteText = "Kick"
self.color = self.colorChoose(255, 0, 0)
elif event.key == 'b':
self.annoteText = "Sleep"
self.color = self.colorChoose(0, 0, 255)
elif event.key == 'g':
self.annoteText = "Random"
self.color = self.colorChoose(0, 255, 0)
elif event.key == "right":
print("right pressed")
self.startX += self.currentDelta
self.endX += self.currentDelta
self.ax2.set_xlim(self.startX, self.endX)
self.run()
elif event.key == "left":
# TODO check left and right limit
print("left pressed")
self.startX -= self.currentDelta
self.endX -= self.currentDelta
self.ax2.set_xlim(self.startX, self.endX)
self.run()
elif event.key == "delete":
print("delete")
if self.removedObj is not None:
if isinstance(self.removedObj, ECERectangle):
print("deleting ECERect")
rect_min_x = self.removedObj.get_x()
rect_max_x = rect_min_x + self.removedObj.get_width()
self.remove_annotation(rect_min_x, rect_max_x)
ind = self.removedObj.getIndex()
self.removedObj.remove()
if ind == 1:
nextRect = self.removedObj.getNext()
else:
nextRect = self.removedObj.getPrev()
self.removedObj = None
if nextRect.axes is not None:
nextRect.remove()
self.fig.canvas.draw()
# Redraws graphs
def run(self):
self.fig.canvas.draw()
# Creates annotation to dataframe
def create_annotation(self, xmin, xmax):
print("Annoated")
cond = self.get_x_in_ranges(xmin, xmax)
self.df.loc[cond, 'annotated'] = self.annoteText
self.df.loc[cond, 'colorHex'] = self.get_color_in_hex()
# Deletes annotation labels
def remove_annotation(self, xmin, xmax):
cond = self.get_x_in_ranges(xmin, xmax)
self.df.loc[cond, 'annotated'] = " "
self.df.loc[cond, 'colorHex'] = " "
# Obtain mask of range of x values
def get_x_in_ranges(self, xmin, xmax):
return (self.df["epoch"] <= mdates.num2date(xmax)) \
& (self.df["epoch"] >= mdates.num2date(xmin))
# Get hexdecimal color
def get_color_in_hex(self):
return "#{:02X}{:02X}{:02X}".format(int(self.color[0] * 255),
int(self.color[1] * 255),
int(self.color[2] * 255))
# Unselect annotation when not active
def setSelect(self):
self.isAnnotate = not self.isAnnotate
# Function used to determine what click and hold effect does for annotations
def cursorOnclick(self, event):
'on button press we will see if the mouse is over us '
if (self.ax == event.inaxes) and (not self.isAnnotate):
xdata = event.xdata
dateclicked = mdates.num2date(xdata)
self.startX = dateclicked
dateEnd = dateclicked + self.currentDelta
self.endX = dateEnd
mask = (self.df["epoch"] >= dateclicked) & (self.df["epoch"] <=
dateEnd)
tX = self.df.loc[mask, "epoch"]
self.ax2.set_xlim(tX.iloc[0], tX.iloc[len(tX) - 1])
self.ax2.get_xaxis().set_major_locator(LinearLocator(numticks=12))
self.ax2.autoscale_view(True, True, True)
width = mdates.date2num(dateEnd) - xdata
[ymin, ymax] = self.ax.get_ylim()
height = ymax - ymin
if self.rect is not None:
self.rect.remove()
self.rect = Rectangle((xdata, ymin),
width,
height,
fill=True,
alpha=0.4,
color=(1, 0, 0),
picker=False)
self.ax.add_patch(self.rect)
self.fig.canvas.draw()
# Sets checks on visibility of x,y, and z -axis plots
def oncheck(self, label):
if label == 'valuex':
self.lx.set_visible(not self.lx.get_visible())
elif label == 'valuey':
self.ly.set_visible(not self.ly.get_visible())
elif label == 'valuez':
self.lz.set_visible(not self.lz.get_visible())
elif label == 'mag':
self.lm.set_visible(not self.lm.get_visible())
self.fig.canvas.draw()
# Adjust time scale values to plot on bottom graph
def changeScale(self, label):
index = self.labels.index(label)
self.currentDelta = self.scaleDeltaArray[index]
class ThresholdSelection(cytoflow.views.HistogramView):
"""
Plots, and lets the user interact with, a threshold on the X axis.
TODO - beautify!
Attributes
----------
op : Instance(ThresholdOp)
the ThresholdOp we're working on.
huefacet : Str
The conditioning variable to show multiple colors on this plot
subset : Str
the string passed to Experiment.subset() defining the subset we plot
interactive : Bool
is this view interactive?
Notes
-----
We inherit `xfacet` and `yfacet` from `cytoflow.views.HistogramView`, but
they must both be unset!
Examples
--------
In an IPython notebook with `%matplotlib notebook`
>>> t = flow.ThresholdOp(name = "Threshold",
... channel = "Y2-A")
>>> tv = t.default_view()
>>> tv.plot(ex2)
>>> tv.interactive = True
>>> # .... draw a threshold on the plot
>>> ex3 = thresh.apply(ex2)
"""
id = Constant('edu.mit.synbio.cytoflow.views.threshold')
friendly_id = Constant("Threshold Selection")
op = Instance(IOperation)
name = DelegatesTo('op')
channel = DelegatesTo('op')
interactive = Bool(False, transient = True)
# internal state
_ax = Any(transient = True)
_line = Instance(Line2D, transient = True)
_cursor = Instance(Cursor, transient = True)
def plot(self, experiment, **kwargs):
"""Plot the histogram and then plot the threshold on top of it."""
if not experiment:
raise util.CytoflowViewError("No experiment specified")
if self.xfacet:
raise util.CytoflowViewError("ThresholdSelection.xfacet must be empty")
if self.yfacet:
raise util.CytoflowViewError("ThresholdSelection.yfacet must be empty")
super(ThresholdSelection, self).plot(experiment, **kwargs)
self._ax = plt.gca()
self._draw_threshold()
self._interactive()
@on_trait_change('op.threshold', post_init = True)
def _draw_threshold(self):
if not self._ax or not self.op.threshold:
return
if self._line:
# when used in the GUI, _draw_threshold gets called *twice* without
# the plot being updated inbetween: and then the line can't be
# removed from the plot, because it was never added. so check
# explicitly first. this is likely to be an issue in other
# interactive plots, too.
if self._line and self._line in self._ax.lines:
self._line.remove()
self._line = None
if self.op.threshold:
self._line = plt.axvline(self.op.threshold, linewidth=3, color='blue')
plt.draw_if_interactive()
@on_trait_change('interactive', post_init = True)
def _interactive(self):
if self._ax and self.interactive:
self._cursor = Cursor(self._ax,
horizOn=False,
vertOn=True,
color='blue')
self._cursor.connect_event('button_press_event', self._onclick)
elif self._cursor:
self._cursor.disconnect_events()
self._cursor = None
def _onclick(self, event):
"""Update the threshold location"""
self.op.threshold = event.xdata
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
class ThresholdSelection(cytoflow.views.HistogramView):
"""
Plots, and lets the user interact with, a threshold on the X axis.
TODO - beautify!
Attributes
----------
op : Instance(ThresholdOp)
the ThresholdOp we're working on.
huefacet : Str
The conditioning variable to show multiple colors on this plot
subset : Str
the string passed to Experiment.subset() defining the subset we plot
interactive : Bool
is this view interactive?
Notes
-----
We inherit `xfacet` and `yfacet` from `cytoflow.views.HistogramView`, but
they must both be unset!
Examples
--------
In an IPython notebook with `%matplotlib notebook`
>>> t = flow.ThresholdOp(name = "Threshold",
... channel = "Y2-A")
>>> tv = t.default_view()
>>> tv.plot(ex2)
>>> tv.interactive = True
>>> # .... draw a threshold on the plot
>>> ex3 = thresh.apply(ex2)
"""
id = Constant('edu.mit.synbio.cytoflow.views.threshold')
friendly_id = Constant("Threshold Selection")
op = Instance(IOperation)
name = DelegatesTo('op')
channel = DelegatesTo('op')
threshold = DelegatesTo('op')
interactive = Bool(False, transient=True)
# internal state
_ax = Any(transient=True)
_line = Instance(Line2D, transient=True)
_cursor = Instance(Cursor, transient=True)
def plot(self, experiment, **kwargs):
"""Plot the histogram and then plot the threshold on top of it."""
if not experiment:
raise util.CytoflowViewError("No experiment specified")
if self.xfacet:
raise util.CytoflowViewError(
"ThresholdSelection.xfacet must be empty")
if self.yfacet:
raise util.CytoflowViewError(
"ThresholdSelection.yfacet must be empty")
super(ThresholdSelection, self).plot(experiment, **kwargs)
self._ax = plt.gca()
self._draw_threshold()
self._interactive()
@on_trait_change('threshold', post_init=True)
def _draw_threshold(self):
if not self._ax or not self.threshold:
return
if self._line:
# when used in the GUI, _draw_threshold gets called *twice* without
# the plot being updated inbetween: and then the line can't be
# removed from the plot, because it was never added. so check
# explicitly first. this is likely to be an issue in other
# interactive plots, too.
if self._line and self._line in self._ax.lines:
self._line.remove()
self._line = None
if self.threshold:
self._line = plt.axvline(self.threshold, linewidth=3, color='blue')
plt.draw()
@on_trait_change('interactive', post_init=True)
def _interactive(self):
if self._ax and self.interactive:
self._cursor = Cursor(self._ax,
horizOn=False,
vertOn=True,
color='blue',
useblit=True)
self._cursor.connect_event('button_press_event', self._onclick)
elif self._cursor:
self._cursor.disconnect_events()
self._cursor = None
def _onclick(self, event):
"""Update the threshold location"""
# sometimes the axes aren't set up and we don't get xdata (??)
if event.xdata:
self.threshold = event.xdata
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
class MaskEditor(ToolWindow, DoubleFileChooserDialog):
def __init__(self, *args, **kwargs):
self.mask = None
self._undo_stack = []
self._im = None
self._selector = None
self._cursor = None
self.exposureloader = None
self.plot2d = None
ToolWindow.__init__(self, *args, **kwargs)
DoubleFileChooserDialog.__init__(
self, self.widget, 'Open mask file...', 'Save mask file...', [('Mask files', '*.mat'), ('All files', '*')],
self.instrument.config['path']['directories']['mask'],
os.path.abspath(self.instrument.config['path']['directories']['mask']),
)
def init_gui(self, *args, **kwargs):
self.exposureloader = ExposureLoader(self.instrument)
self.builder.get_object('loadexposure_expander').add(self.exposureloader)
self.exposureloader.connect('open', self.on_loadexposure)
self.plot2d = PlotImageWidget()
self.builder.get_object('plotbox').pack_start(self.plot2d.widget, True, True, 0)
self.builder.get_object('toolbar').set_sensitive(False)
def on_loadexposure(self, exposureloader: ExposureLoader, im: Exposure):
if self.mask is None:
self.mask = im.mask
self._im = im
self.plot2d.set_image(im.intensity)
self.plot2d.set_mask(self.mask)
self.builder.get_object('toolbar').set_sensitive(True)
def on_new(self, button):
if self._im is None or self.mask is None:
return False
self.mask = np.ones_like(self.mask)
self.plot2d.set_mask(self.mask)
self.set_last_filename(None)
def on_open(self, button):
filename = self.get_open_filename()
if filename is not None:
mask = loadmat(filename)
self.mask = mask[[k for k in mask.keys() if not k.startswith('__')][0]]
self.plot2d.set_mask(self.mask)
def on_save(self, button):
filename = self.get_last_filename()
if filename is None:
return self.on_saveas(button)
maskname = os.path.splitext(os.path.split(filename)[1])[0]
savemat(filename, {maskname: self.mask})
def on_saveas(self, button):
filename = self.get_save_filename(None)
if filename is not None:
self.on_save(button)
def suggest_filename(self):
return 'mask_dist_{0.year:d}{0.month:02d}{0.day:02d}.mat'.format(datetime.date.today())
def on_selectcircle_toggled(self, button):
if button.get_active():
self.set_sensitive(False, 'Ellipse selection not ready',
['new_button', 'save_button', 'saveas_button', 'open_button', 'undo_button',
'selectrectangle_button', 'selectpolygon_button', 'pixelhunting_button',
'loadexposure_expander', 'close_button', self.plot2d.toolbar,
self.plot2d.settings_expander])
while self.plot2d.toolbar.mode != '':
# turn off zoom, pan, etc. modes.
self.plot2d.toolbar.zoom()
self._selector = EllipseSelector(self.plot2d.axis,
self.on_ellipse_selected,
rectprops={'facecolor': 'white', 'edgecolor': 'none', 'alpha': 0.7,
'fill': True, 'zorder': 10},
button=[1, ],
interactive=False, lineprops={'zorder': 10})
self._selector.state.add('square')
self._selector.state.add('center')
else:
assert isinstance(self._selector, EllipseSelector)
self._selector.set_active(False)
self._selector.set_visible(False)
self._selector = None
self.plot2d.replot(keepzoom=False)
self.set_sensitive(True)
def on_ellipse_selected(self, pos1, pos2):
# pos1 and pos2 are mouse button press and release events, with xdata and ydata carrying
# the two opposite corners of the bounding box of the circle. These are NOT the exact
# button presses and releases!
row = np.arange(self.mask.shape[0])[:, np.newaxis]
column = np.arange(self.mask.shape[1])[np.newaxis, :]
row0 = 0.5 * (pos1.ydata + pos2.ydata)
col0 = 0.5 * (pos1.xdata + pos2.xdata)
r2 = ((pos2.xdata - pos1.xdata) ** 2 + (pos2.ydata - pos1.ydata) ** 2) / 8
tobemasked = (row - row0) ** 2 + (column - col0) ** 2 <= r2
self._undo_stack.append(self.mask)
if self.builder.get_object('mask_button').get_active():
self.mask &= ~tobemasked
elif self.builder.get_object('unmask_button').get_active():
self.mask |= tobemasked
elif self.builder.get_object('invertmask_button').get_active():
self.mask[tobemasked] = ~self.mask[tobemasked]
else:
pass
self.builder.get_object('selectcircle_button').set_active(False)
self.plot2d.set_mask(self.mask)
def on_selectrectangle_toggled(self, button):
if button.get_active():
self.set_sensitive(False, 'Rectangle selection not ready',
['new_button', 'save_button', 'saveas_button', 'open_button', 'undo_button',
'selectcircle_button', 'selectpolygon_button', 'pixelhunting_button',
'loadexposure_expander', 'close_button', self.plot2d.toolbar,
self.plot2d.settings_expander])
while self.plot2d.toolbar.mode != '':
# turn off zoom, pan, etc. modes.
self.plot2d.toolbar.zoom()
self._selector = RectangleSelector(self.plot2d.axis,
self.on_rectangle_selected,
rectprops={'facecolor': 'white', 'edgecolor': 'none', 'alpha': 0.7,
'fill': True, 'zorder': 10},
button=[1, ],
interactive=False, lineprops={'zorder': 10})
else:
self._selector.set_active(False)
self._selector.set_visible(False)
self._selector = None
self.plot2d.replot(keepzoom=False)
self.set_sensitive(True)
def on_rectangle_selected(self, pos1, pos2):
# pos1 and pos2 are mouse button press and release events, with xdata and ydata
# carrying the two opposite corners of the bounding box of the rectangle. These
# are NOT the exact button presses and releases!
row = np.arange(self.mask.shape[0])[:, np.newaxis]
column = np.arange(self.mask.shape[1])[np.newaxis, :]
tobemasked = ((row >= min(pos1.ydata, pos2.ydata)) & (row <= max(pos1.ydata, pos2.ydata)) &
(column >= min(pos1.xdata, pos2.xdata)) & (column <= max(pos1.xdata, pos2.xdata)))
self._undo_stack.append(self.mask)
if self.builder.get_object('mask_button').get_active():
self.mask = self.mask & (~tobemasked)
elif self.builder.get_object('unmask_button').get_active():
self.mask = self.mask | tobemasked
elif self.builder.get_object('invertmask_button').get_active():
self.mask[tobemasked] = ~self.mask[tobemasked]
else:
pass
self.builder.get_object('selectrectangle_button').set_active(False)
self.plot2d.set_mask(self.mask)
def on_selectpolygon_toggled(self, button):
if button.get_active():
self.set_sensitive(False, 'Polygon selection not ready',
['new_button', 'save_button', 'saveas_button', 'open_button', 'undo_button',
'selectrectangle_button', 'selectcircle_button', 'pixelhunting_button',
'loadexposure_expander', 'close_button', self.plot2d.toolbar,
self.plot2d.settings_expander])
while self.plot2d.toolbar.mode != '':
# turn off zoom, pan, etc. modes.
self.plot2d.toolbar.zoom()
self._selector = LassoSelector(self.plot2d.axis,
self.on_polygon_selected,
lineprops={'color': 'white', 'zorder': 10},
button=[1, ],
)
else:
self._selector.set_active(False)
self._selector.set_visible(False)
self._selector = None
self.plot2d.replot(keepzoom=False)
self.set_sensitive(True)
def on_polygon_selected(self, vertices):
path = Path(vertices)
col, row = np.meshgrid(np.arange(self.mask.shape[1]),
np.arange(self.mask.shape[0]))
points = np.vstack((col.flatten(), row.flatten())).T
tobemasked = path.contains_points(points).reshape(self.mask.shape)
self._undo_stack.append(self.mask)
if self.builder.get_object('mask_button').get_active():
self.mask = self.mask & (~tobemasked)
elif self.builder.get_object('unmask_button').get_active():
self.mask = self.mask | tobemasked
elif self.builder.get_object('invertmask_button').get_active():
self.mask[tobemasked] = ~self.mask[tobemasked]
else:
pass
self.plot2d.set_mask(self.mask)
self.builder.get_object('selectpolygon_button').set_active(False)
def on_mask_toggled(self, button):
pass
def on_unmask_toggled(self, button):
pass
def on_invertmask_toggled(self, button):
pass
def on_pixelhunting_toggled(self, button):
if button.get_active():
self._cursor = Cursor(self.plot2d.axis, useblit=False, color='white', lw=1)
self._cursor.connect_event('button_press_event', self.on_cursorclick)
while self.plot2d.toolbar.mode != '':
# turn off zoom, pan, etc. modes.
self.plot2d.toolbar.zoom()
else:
self._cursor.disconnect_events()
self._cursor = None
self._undo_stack.append(self.mask)
self.plot2d.replot(keepzoom=False)
def on_cursorclick(self, event):
if (event.inaxes == self.plot2d.axis) and (self.plot2d.toolbar.mode == ''):
self.mask[round(event.ydata), round(event.xdata)] ^= True
self._cursor.disconnect_events()
self._cursor = None
self.plot2d.replot(keepzoom=True)
self.on_pixelhunting_toggled(self.builder.get_object('pixelhunting_button'))
def cleanup(self):
super().cleanup()
self._undo_stack = []
def on_undo(self, button):
try:
self.mask = self._undo_stack.pop()
except IndexError:
return
self.plot2d.set_mask(self.mask)
class PolygonSelection(cytoflow.views.ScatterplotView):
"""Plots, and lets the user interact with, a 2D polygon selection.
Attributes
----------
op : Instance(PolygonOp)
The operation on which this selection view is operating
huefacet : Str
The conditioning variable to show multiple colors on this plot
subset : Str
The string for subsetting the plot
interactive : Bool
is this view interactive? Ie, can the user set the polygon verticies
with mouse clicks?
Notes
-----
We inherit `xfacet` and `yfacet` from `cytoflow.views.ScatterPlotView`, but
they must both be unset!
Examples
--------
In an IPython notebook with `%matplotlib notebook`
>>> s = flow.ScatterplotView(xchannel = "V2-A",
... ychannel = "Y2-A")
>>> poly = s.default_view()
>>> poly.plot(ex2)
>>> poly.interactive = True
"""
id = Constant('edu.mit.synbio.cytoflow.views.polygon')
friendly_id = Constant("Polygon Selection")
op = Instance(IOperation)
name = DelegatesTo('op')
xchannel = DelegatesTo('op')
ychannel = DelegatesTo('op')
interactive = Bool(False, transient=True)
# internal state.
_ax = Any(transient=True)
_cursor = Instance(Cursor, transient=True)
_path = Instance(mpl.path.Path, transient=True)
_patch = Instance(mpl.patches.PathPatch, transient=True)
_line = Instance(mpl.lines.Line2D, transient=True)
_drawing = Bool(transient=True)
_last_draw_time = Float(0.0, transient=True)
_last_click_time = Float(0.0, transient=True)
def plot(self, experiment, **kwargs):
"""Plot self.view, and then plot the selection on top of it."""
if not experiment:
raise util.CytoflowViewError("No experiment specified")
if self.xfacet:
raise util.CytoflowViewError(
"RangeSelection.xfacet must be empty or `Undefined`")
if self.yfacet:
raise util.CytoflowViewError(
"RangeSelection.yfacet must be empty or `Undefined`")
super(PolygonSelection, self).plot(experiment, **kwargs)
self._ax = plt.gca()
self._draw_poly()
self._interactive()
@on_trait_change('op.vertices', post_init=True)
def _draw_poly(self):
if not self._ax:
return
if self._patch and self._patch in self._ax.patches:
self._patch.remove()
if self._drawing or not self.op.vertices or len(self.op.vertices) < 3 \
or any([len(x) != 2 for x in self.op.vertices]):
return
patch_vert = np.concatenate(
(np.array(self.op.vertices), np.array((0, 0), ndmin=2)))
self._patch = \
mpl.patches.PathPatch(mpl.path.Path(patch_vert, closed = True),
edgecolor="black",
linewidth = 1.5,
fill = False)
self._ax.add_patch(self._patch)
plt.draw_if_interactive()
@on_trait_change('interactive', post_init=True)
def _interactive(self):
if self._ax and self.interactive:
self._cursor = Cursor(self._ax, horizOn=False, vertOn=False)
self._cursor.connect_event('button_press_event', self._onclick)
self._cursor.connect_event('motion_notify_event', self._onmove)
elif self._cursor:
self._cursor.disconnect_events()
self._cursor = None
def _onclick(self, event):
"""Update selection traits"""
if not self._ax:
return
if (self._cursor.ignore(event)):
return
# we have to check the wall clock time because the IPython notebook
# doesn't seem to register double-clicks
if event.dblclick or (time.clock() - self._last_click_time < 0.5):
self._drawing = False
self.op.vertices = map(tuple, self._path.vertices)
self.op._xscale = plt.gca().get_xscale()
self.op._yscale = plt.gca().get_yscale()
self._path = None
return
self._last_click_time = time.clock()
self._drawing = True
if self._patch and self._patch in self._ax.patches:
self._patch.remove()
if self._path:
vertices = np.concatenate((self._path.vertices,
np.array((event.xdata, event.ydata),
ndmin=2)))
else:
vertices = np.array((event.xdata, event.ydata), ndmin=2)
self._path = mpl.path.Path(vertices, closed=False)
self._patch = mpl.patches.PathPatch(self._path,
edgecolor="black",
fill=False)
self._ax.add_patch(self._patch)
plt.draw_if_interactive()
def _onmove(self, event):
if not self._ax:
return
if (self._cursor.ignore(event) or not self._drawing or not self._path
or self._path.vertices.shape[0] == 0 or not event.xdata
or not event.ydata):
return
# only draw 5 times/sec
if (time.clock() - self._last_draw_time < 0.2):
return
self._last_draw_time = time.clock()
if self._line and self._line in self._ax.lines:
self._line.remove()
xdata = [self._path.vertices[-1, 0], event.xdata]
ydata = [self._path.vertices[-1, 1], event.ydata]
self._line = mpl.lines.Line2D(xdata, ydata, linewidth=1, color="black")
self._ax.add_line(self._line)
plt.gcf().canvas.draw()
class QuadSelection(Op2DView, ScatterplotView):
"""Plots, and lets the user interact with, a quadrant gate.
Attributes
----------
interactive : Bool
is this view interactive? Ie, can the user set the threshold with a
mouse click?
Notes
-----
We inherit :attr:`xfacet` and :attr:`yfacet` from
:class:`cytoflow.views.ScatterplotView`, but they must both be unset!
Examples
--------
In an Jupyter notebook with `%matplotlib notebook`
>>> q = flow.QuadOp(name = "Quad",
... xchannel = "V2-A",
... ychannel = "Y2-A"))
>>> qv = q.default_view()
>>> qv.interactive = True
>>> qv.plot(ex2)
"""
id = Constant('edu.mit.synbio.cytoflow.views.quad')
friendly_id = Constant("Quadrant Selection")
xfacet = Constant(None)
yfacet = Constant(None)
# override the Op2DView
xscale = util.ScaleEnum
yscale = util.ScaleEnum
xthreshold = DelegatesTo('op')
ythreshold = DelegatesTo('op')
interactive = Bool(False, transient=True)
# internal state.
_ax = Any(transient=True)
_hline = Instance(Line2D, transient=True)
_vline = Instance(Line2D, transient=True)
_cursor = Instance(Cursor, transient=True)
def plot(self, experiment, **kwargs):
"""
Plot the underlying scatterplot and then plot the selection on top of it.
Parameters
----------
"""
if experiment is None:
raise util.CytoflowViewError('experiment',
"No experiment specified")
super().plot(experiment, **kwargs)
self._ax = plt.gca()
self._draw_lines()
self._interactive()
@on_trait_change('xthreshold, ythreshold', post_init=True)
def _draw_lines(self):
if not self._ax:
return
if self._hline and self._hline in self._ax.lines:
self._hline.remove()
if self._vline and self._vline in self._ax.lines:
self._vline.remove()
if self.xthreshold and self.ythreshold:
self._hline = plt.axhline(self.ythreshold,
linewidth=3,
color='blue')
self._vline = plt.axvline(self.xthreshold,
linewidth=3,
color='blue')
plt.draw()
@on_trait_change('interactive', post_init=True)
def _interactive(self):
if self._ax and self.interactive:
self._cursor = Cursor(self._ax,
horizOn=True,
vertOn=True,
color='blue',
useblit=True)
self._cursor.connect_event('button_press_event', self._onclick)
elif self._cursor:
self._cursor.disconnect_events()
self._cursor = None
def _onclick(self, event):
"""Update the threshold location"""
self.xthreshold = event.xdata
self.ythreshold = event.ydata
class PolygonSelection(cytoflow.views.ScatterplotView):
"""Plots, and lets the user interact with, a 2D polygon selection.
Attributes
----------
op : Instance(PolygonOp)
The operation on which this selection view is operating
huefacet : Str
The conditioning variable to show multiple colors on this plot
subset : Str
The string for subsetting the plot
interactive : Bool
is this view interactive? Ie, can the user set the polygon verticies
with mouse clicks?
Notes
-----
We inherit `xfacet` and `yfacet` from `cytoflow.views.ScatterPlotView`, but
they must both be unset!
Examples
--------
In an IPython notebook with `%matplotlib notebook`
>>> s = flow.ScatterplotView(xchannel = "V2-A",
... ychannel = "Y2-A")
>>> poly = s.default_view()
>>> poly.plot(ex2)
>>> poly.interactive = True
"""
id = Constant('edu.mit.synbio.cytoflow.views.polygon')
friendly_id = Constant("Polygon Selection")
op = Instance(IOperation)
name = DelegatesTo('op')
xchannel = DelegatesTo('op')
ychannel = DelegatesTo('op')
interactive = Bool(False, transient = True)
# internal state.
_ax = Any(transient = True)
_cursor = Instance(Cursor, transient = True)
_path = Instance(mpl.path.Path, transient = True)
_patch = Instance(mpl.patches.PathPatch, transient = True)
_line = Instance(mpl.lines.Line2D, transient = True)
_drawing = Bool(transient = True)
_last_draw_time = Float(0.0, transient = True)
_last_click_time = Float(0.0, transient = True)
def plot(self, experiment, **kwargs):
"""Plot self.view, and then plot the selection on top of it."""
if not experiment:
raise util.CytoflowViewError("No experiment specified")
if self.xfacet:
raise util.CytoflowViewError("RangeSelection.xfacet must be empty or `Undefined`")
if self.yfacet:
raise util.CytoflowViewError("RangeSelection.yfacet must be empty or `Undefined`")
super(PolygonSelection, self).plot(experiment, **kwargs)
self._ax = plt.gca()
self._draw_poly()
self._interactive()
@on_trait_change('op.vertices', post_init = True)
def _draw_poly(self):
if not self._ax:
return
if self._patch and self._patch in self._ax.patches:
self._patch.remove()
if self._drawing or not self.op.vertices or len(self.op.vertices) < 3 \
or any([len(x) != 2 for x in self.op.vertices]):
return
patch_vert = np.concatenate((np.array(self.op.vertices),
np.array((0,0), ndmin = 2)))
self._patch = \
mpl.patches.PathPatch(mpl.path.Path(patch_vert, closed = True),
edgecolor="black",
linewidth = 1.5,
fill = False)
self._ax.add_patch(self._patch)
plt.draw_if_interactive()
@on_trait_change('interactive', post_init = True)
def _interactive(self):
if self._ax and self.interactive:
self._cursor = Cursor(self._ax, horizOn = False, vertOn = False)
self._cursor.connect_event('button_press_event', self._onclick)
self._cursor.connect_event('motion_notify_event', self._onmove)
elif self._cursor:
self._cursor.disconnect_events()
self._cursor = None
def _onclick(self, event):
"""Update selection traits"""
if not self._ax:
return
if(self._cursor.ignore(event)):
return
# we have to check the wall clock time because the IPython notebook
# doesn't seem to register double-clicks
if event.dblclick or (time.clock() - self._last_click_time < 0.5):
self._drawing = False
self.op.vertices = map(tuple, self._path.vertices)
self.op._xscale = plt.gca().get_xscale()
self.op._yscale = plt.gca().get_yscale()
self._path = None
return
self._last_click_time = time.clock()
self._drawing = True
if self._patch and self._patch in self._ax.patches:
self._patch.remove()
if self._path:
vertices = np.concatenate((self._path.vertices,
np.array((event.xdata, event.ydata), ndmin = 2)))
else:
vertices = np.array((event.xdata, event.ydata), ndmin = 2)
self._path = mpl.path.Path(vertices, closed = False)
self._patch = mpl.patches.PathPatch(self._path,
edgecolor = "black",
fill = False)
self._ax.add_patch(self._patch)
plt.draw_if_interactive()
def _onmove(self, event):
if not self._ax:
return
if(self._cursor.ignore(event)
or not self._drawing
or not self._path
or self._path.vertices.shape[0] == 0
or not event.xdata
or not event.ydata):
return
# only draw 5 times/sec
if(time.clock() - self._last_draw_time < 0.2):
return
self._last_draw_time = time.clock()
if self._line and self._line in self._ax.lines:
self._line.remove()
xdata = [self._path.vertices[-1, 0], event.xdata]
ydata = [self._path.vertices[-1, 1], event.ydata]
self._line = mpl.lines.Line2D(xdata, ydata, linewidth = 1, color = "black")
self._ax.add_line(self._line)
plt.gcf().canvas.draw()
class QuadSelection(cytoflow.views.ScatterplotView):
"""Plots, and lets the user interact with, a quadrant gate.
Attributes
----------
op : Instance(Range2DOp)
The instance of Range2DOp that we're viewing / editing
huefacet : Str
The conditioning variable to plot multiple colors
subset : Str
The string passed to `Experiment.query()` to subset the data before
plotting
interactive : Bool
is this view interactive? Ie, can the user set the threshold with a
mouse click?
Notes
-----
We inherit `xfacet` and `yfacet` from `cytoflow.views.ScatterplotView`, but
they must both be unset!
Examples
--------
In an IPython notebook with `%matplotlib notebook`
>>> q = flow.QuadOp(name = "Quad",
... xchannel = "V2-A",
... ychannel = "Y2-A"))
>>> qv = q.default_view()
>>> qv.interactive = True
>>> qv.plot(ex2)
"""
id = Constant('edu.mit.synbio.cytoflow.views.quad')
friendly_id = Constant("Quadrant Selection")
op = Instance(IOperation)
name = DelegatesTo('op')
xchannel = DelegatesTo('op')
ychannel = DelegatesTo('op')
interactive = Bool(False, transient=True)
# internal state.
_ax = Any(transient=True)
_hline = Instance(Line2D, transient=True)
_vline = Instance(Line2D, transient=True)
_cursor = Instance(Cursor, transient=True)
def plot(self, experiment, **kwargs):
"""Plot the underlying scatterplot and then plot the selection on top of it."""
if not experiment:
raise util.CytoflowOpError("No experiment specified")
if not experiment:
raise util.CytoflowViewError("No experiment specified")
if self.xfacet:
raise util.CytoflowViewError(
"RangeSelection.xfacet must be empty or `Undefined`")
if self.yfacet:
raise util.CytoflowViewError(
"RangeSelection.yfacet must be empty or `Undefined`")
super(QuadSelection, self).plot(experiment, **kwargs)
self._ax = plt.gca()
self._draw_lines()
self._interactive()
@on_trait_change('op.xthreshold, op.ythreshold', post_init=True)
def _draw_lines(self):
if not self._ax:
return
if self._hline and self._hline in self._ax.lines:
self._hline.remove()
if self._vline and self._vline in self._ax.lines:
self._vline.remove()
if self.op.xthreshold and self.op.ythreshold:
self._hline = plt.axhline(self.op.ythreshold,
linewidth=3,
color='blue')
self._vline = plt.axvline(self.op.xthreshold,
linewidth=3,
color='blue')
plt.draw_if_interactive()
@on_trait_change('interactive', post_init=True)
def _interactive(self):
if self._ax and self.interactive:
self._cursor = Cursor(self._ax,
horizOn=True,
vertOn=True,
color='blue')
self._cursor.connect_event('button_press_event', self._onclick)
elif self._cursor:
self._cursor.disconnect_events()
self._cursor = None
def _onclick(self, event):
"""Update the threshold location"""
self.op.xthreshold = event.xdata
self.op.ythreshold = event.ydata
class ECE4012:
def __init__(self, figure, filename, toolbar):
self.dfCal = None
self.fig = figure
self.toolbar = toolbar
self.filename = filename
self.rect = None
def initializer(self, type):
self.fig.clear()
print("celar figure")
self.fig.subplots_adjust(hspace=1.0)
self.annoteText = "annotated"
#self.fig = figure
#self.toolbar = toolbar
self.isAnnotate = False
self.fig.canvas.mpl_connect('button_release_event', self.onrelease)
self.fig.canvas.mpl_connect('button_press_event', self.onclick)
self.fig.canvas.mpl_connect('key_press_event', self.onpress)
self.fig.canvas.mpl_connect('pick_event', self.onpick)
# print(self.fig)
if type == "DB":
self.searchOpenCalibration(self.filename)
self.conn = self.getConnection(self.filename)
# df = pd.read_sql_query("select * from acc LIMIT 100000;", self.conn)
t = time.time()
df = pd.read_sql_query("select * from acc;", self.conn)
elapsed = time.time() - t
print("time taken to read data was {:f}".format(elapsed))
elif type == "CSV":
print("CSV getting Calibration")
self.searchOpenCalibration(self.filename)
print("CSV opening file")
df = pd.read_csv(self.filename)
print("CSV opened file")
print("Starting")
if self.dfCal is not None:
df["valuex"] = np.subtract(df["valuex"], self.dfCal['Values'][
self.XOffset]) / self.dfCal['Values'][self.XGain]
df["valuey"] = np.subtract(df["valuey"], self.dfCal['Values'][
self.YOffset]) / self.dfCal['Values'][self.YGain]
df["valuez"] = np.subtract(df["valuez"], self.dfCal['Values'][
self.ZOffset]) / self.dfCal['Values'][self.ZGain]
# DONE !!TODO this calibartion should change to either actual calibration from
# metawear C
# print(len(df["valuex"]))
# avgX = np.sum(df["valuex"]) / len(df["valuex"])
# avgY = np.sum(df["valuey"]) / len(df["valuey"])
# avgZ = np.sum(df["valuez"]) / len(df["valuez"])
# df["valuex"] = np.subtract(df["valuex"], avgX)
# df["valuey"] = np.subtract(df["valuey"], avgY)
# df["valuez"] = np.subtract(df["valuez"], avgZ)
#self.axTop = self.fig.add_subplot(2, 1, 1)
#self.axBottom = self.fig.add_subplot(2, 1, 2)
self.fig.subplots_adjust(bottom=0.3, left=0.2, hspace=1.0)
self.labels = ['30 sec', '5 min', '30 min', '1 hr', '2 hr']
sec30 = pd.Timedelta(30, unit='s')
min5 = pd.Timedelta(5, unit='m')
min30 = pd.Timedelta(30, unit='m')
hr1 = pd.Timedelta(1, unit='h')
hr2 = pd.Timedelta(2, unit='h')
# Scale Radio Buttons for Zoom
self.scaleDeltaArray = [sec30, min5, min30, hr1, hr2]
self.rax = self.fig.add_axes([0.02, 0.7, 0.11, 0.15])
self.rax.set_title('Scale')
self.check = RadioButtons(self.rax, self.labels)
self.fig.canvas.mpl_connect('button_press_event', self.onclick)
# Data Set Selection Check Box
self.rcbax = self.fig.add_axes([0.02, 0.25, 0.11, 0.15])
self.rcbax.set_title('DataSet')
self.checkBox = CheckButtons(self.rcbax,
('valuex', 'valuey', 'valuez', 'mag'),
(True, True, True, True))
self.checkBox.on_clicked(self.oncheck)
xs = np.linspace(15, 21, 200)
horiz_line_dataz = np.array([0.41 for i in range(len(xs))])
self.rcbax.plot(xs, horiz_line_dataz, 'C3-')
horiz_line_datam = np.array([0.26 for i in range(len(xs))])
self.rcbax.plot(xs, horiz_line_datam, 'C0-')
horiz_line_datay = np.array([0.58 for i in range(len(xs))])
self.rcbax.plot(xs, horiz_line_datay, 'C2-')
horiz_line_datax = np.array([0.73 for i in range(len(xs))])
self.rcbax.plot(xs, horiz_line_datax, 'C1-')
self.check.on_clicked(self.changeScale)
df["mag"] = np.sqrt(np.square(df["valuex"]) + np.square(df['valuey']) + \
np.square(df["valuez"]))-1.0
print("Normalize")
ya_min = df.loc[:, "mag"].min() - 0.1
ya_max = df.loc[:, "mag"].max() + 0.1
print("y limit (max={:f},min={:f})".format(ya_max, ya_min))
# print("Normalized")
# print(type(ya_min))
# print(ya_max)
# print(df["mag"])
# df["mag"] = df["mag"] - 1 # subtract 1g
#Convert epoch to datetime to see the right value
print("Convert Date Time")
print(df["epoch"].iloc[0])
print(df["epoch"].iloc[1])
if type == "DB":
print("epoch type", df.dtypes[0])
df['epoch'] = pd.to_datetime(df['epoch'], unit='ms')
elif type == "CSV":
print("epoch type", df.dtypes[0])
if 'annotated' not in df.columns:
df['epoch'] = pd.to_datetime(df['epoch'], unit='ms')
else:
df['epoch'] = pd.to_datetime(df['epoch'])
print("epoch type after", df.dtypes[0])
# Adjusting epoch time to be on Eastern Time Zone
df['epoch'] = df['epoch'].dt.tz_localize('UTC').dt.tz_convert(
'America/New_York')
vepoch = df['epoch']
self.datevalues = vepoch.dt.to_pydatetime()
if 'annotated' not in df.columns:
charArr = np.chararray((len(df["mag"], )), unicode=True)
charArr[:] = ' '
df["annotated"] = pd.DataFrame(charArr)
df["colorHex"] = pd.DataFrame(charArr)
# print(df["epoch"])
# print(type(df['epoch'][0]))
#Definition of x-axis formatter of tick
# self.hoursFmt = mdates.DateFormatter('%Y-%m-%d %H:%M:%S') #Week Month/Day H:M:S
self.hoursFmt = mdates.DateFormatter('%a-%m-%d %H:%M:%S')
self.HMSFmt = mdates.DateFormatter('%H:%M:%S')
#Get total time of the data in hours
startDate = df["epoch"].iloc[0]
self.startDate = startDate
endDate = df["epoch"].iloc[-1]
totaltime = int(endDate.timestamp() * 1000) - \
int(startDate.timestamp() * 1000)
total_hours = totaltime / 1000 / 3600 #totaltime in hours
total_minutes = total_hours * 60
print("total hours {:f}".format(total_hours))
#create variable to track drag time
self.timeTrack = 0
#create variable to track initial click xpos
self.xpos = 0
self.df = df
print("Creating Top Graph")
self.ax = self.fig.add_subplot(2, 1, 1)
# second axis
print("Creating Bottom Graph")
self.ax2 = self.fig.add_subplot(2, 1, 2)
#adjust distance between toolbar and graph to give more space
self.fig.subplots_adjust(bottom=0.145)
#adjust distance between toolbar and graph if data is 24 hours or more
if total_hours > 24:
self.fig.subplots_adjust(hspace=1.3)
print("Start Plot Setting")
# Set default values for x aixs
##changed temporary pls ignore
# self.ax.set_ylim(1, 1.1)
# self.ax2.set_ylim(1, 1.1)
#self.ax.set_ylim(0, 8)
#self.ax2.set_ylim(0, 8)
self.ax.set_xlabel("Time (H:M:S)")
self.ax2.set_xlabel("Time (H:M:S)")
self.ax.set_ylabel("Acceleration (g)")
self.ax2.set_ylabel("Acceleration (g)")
#self.ax.set_title('Scale')
self.ax.set_ylim(ya_min, ya_max)
self.ax2.set_ylim(ya_min, ya_max)
bottomtitle = 'Magnitude Graph for Start Date ' + "{:%Y-%m-%d}".format(
startDate)
if self.dfCal is not None:
bottomtitle = 'Calibrated ' + bottomtitle
self.ax.set_title(bottomtitle)
toptitle = 'Zoomed-In Graph for Start Date ' + "{:%Y-%m-%d}".format(
startDate)
if self.dfCal is not None:
toptitle = 'Calibrated ' + toptitle
self.ax2.set_title(toptitle)
# self.ya_min = ya_min
# self.ya_max = ya_max
# start date
# print(type(df["epoch"]))
# print(len(df["epoch"]))
# print(df["epoch"])
# print()
# TODO we assume time is not empty but it could be good to chek empty
start_time = df["epoch"].iloc[0]
print("start time={v}".format(v=start_time))
# print(type(start_time))
if total_hours > 1:
end_time = start_time + hr1
elif total_minutes > 30:
end_time = start_time + min30
elif total_minutes > 5:
end_time = start_time + min5
else:
end_time = start_time + sec30
print("end time={v}".format(v=end_time))
# print(type(start_time))
#end_time = start_time + pd.Timedelta(hours=1)
#print(end_time)
self.startX = start_time
self.endX = end_time
# set axis 2
self.ax2.set_xlim(start_time, end_time)
print("Set Limit")
# print(type(df["epoch"].iloc[0]))
mask = (df["epoch"] >= start_time) & (df["epoch"] <= end_time)
print("Plotting")
# print(mask)
# print(df.loc[mask, "epoch"])
# plot
t = time.time()
self.plotTop, = self.ax.plot(df["epoch"].iloc[0:3],
df["mag"].iloc[0:3],
visible=True)
self.plotTop.set_data(self.datevalues, df["mag"])
self.ax.relim()
self.ax.autoscale_view(True, True, True)
self.fig.canvas.draw()
#self.ax.plot(df["epoch"], df["mag"])
elapsed = time.time() - t
print("time taken to top graph magnitud was {:f}".format(elapsed))
# print(df.loc[mask, "epoch"])
print(len(df.loc[mask, "epoch"]))
t = time.time()
self.lm, = self.ax2.plot(df["epoch"].iloc[0:3],
df["mag"].iloc[0:3],
visible=True)
self.lm.set_data(self.datevalues, df["mag"])
self.ax2.relim()
self.ax2.autoscale_view(True, True, True)
self.fig.canvas.draw()
#self.lm, = self.ax2.plot(df["epoch"], df["mag"],visible=True)
elapsed = time.time() - t
print("time taken to bottom graph magnitud was {:f}".format(elapsed))
t = time.time()
try:
thread1 = myThread(1, "valuex", self)
thread1.start()
except:
print("Error: unable to start thread")
#self.lx, = self.ax2.plot(df["epoch"], df["valuex"],visible=False)
elapsed = time.time() - t
print("time taken to bottom graph valuex was {:f}".format(elapsed))
t = time.time()
try:
thread2 = myThread(2, "valuey", self)
thread2.start()
except:
print("Error: unable to start thread")
#self.ly, = self.ax2.plot(df["epoch"], df["valuey"],visible=False)
elapsed = time.time() - t
print("time taken to bottom graph valuey was {:f}".format(elapsed))
t = time.time()
try:
thread3 = myThread(3, "valuez", self)
thread3.start()
except:
print("Error: unable to start thread")
#self.lz, = self.ax2.plot(df["epoch"], df["valuez"],visible=False)
elapsed = time.time() - t
print("time taken to bottom graph valuez was {:f}".format(elapsed))
# x in the range
tX = df.loc[mask, "epoch"]
self.ax2.set_xlim(tX.iloc[0], tX.iloc[len(tX) - 1])
# self.ax.xaxis.set_major_formatter(self.hoursFmt)
self.ax.xaxis.set_major_formatter(self.HMSFmt)
self.ax.get_xaxis().set_major_locator(LinearLocator(numticks=12))
#setup format of ticks to Weekday month/day if data is 24 hours or more
if total_hours > 24:
self.ax.xaxis.set_major_formatter(self.hoursFmt)
#Rotate labels on x-axis 45 degrees and set font size to 8
self.ax.tick_params(axis='x', labelsize=8, rotation=45)
# self.ax.title("Magnitude")
# self.ax2.plot(df["epoch"], df["valuex"],
# color=self.colorChoose(255, 0, 255))
# self.ax2.plot(df["epoch"], df["valuey"],
# color=self.colorChoose(255, 0, 0))
# self.ax2.plot(df["epoch"], df["valuez"],
# color=self.colorChoose(255, 255, 0))
self.color = self.colorChoose(random.randint(0, 255),
random.randint(0, 255),
random.randint(0, 255))
self.removedObj = None
# self.ax.add_patch(rect)
self.fig.canvas.draw()
self.fig.canvas.mpl_connect('motion_notify_event', self.onmouseover)
self.cursor = Cursor(self.ax,
useblit=True,
horizOn=False,
color='red',
linewidth=2)
self.cursor.connect_event('button_press_event', self.cursorOnclick)
self.currentDelta = pd.Timedelta(30, unit='s')
self.ax2.xaxis.set_major_formatter(self.HMSFmt)
self.ax2.get_xaxis().set_major_locator(LinearLocator(numticks=7))
#data text axes
#self.txtax = self.fig.add_axes([0.75, 0.85, 0.11, 0.05])
#self.txtax.axis('off')
self.ax.format_coord = self.format_coord
if type == "CSV" and 'annotated' in df.columns:
print("calling searchForAnnotation")
self.searchForAnnotation()
#self.txt = self.ax.text(0.8, 1.05, 'X,Y,Z Values', transform=self.ax.transAxes)
#self.txt = self.txtax.text(0.05, 0.05, 'X,Y,Z Values', transform=self.txtax.transAxes)
def format_coord(self, x, y):
dateclickOn = mdates.num2date(x)
idx = self.df['epoch'].searchsorted(dateclickOn)
idx = idx - 1
#logger.debug("dateclickOn:%s idx=%s", dateclickOn,idx)
vx = self.df['valuex'].values[idx][0]
vy = self.df['valuey'].values[idx][0]
vz = self.df['valuez'].values[idx][0]
vm = self.df['mag'].values[idx][0]
#print("d: {:%H:%M:%S} vx:{:1.5f} vy:{:1.5f} vz:{:1.5f}".format(dateclickOn,vx,vy,vz))
#self.txt.set_text('%H:%M:%S x=%1.3f, y=%1.3f, z=%1.3f' % (dateclickOn,vx, vy,vz))
return "{:%H:%M:%S} M:{:1.3f}".format(dateclickOn, vm)
def readCalibration(self, filename):
self.dfCal = pd.read_csv(filename)
print('Results: %s', self.dfCal)
print('title: %s', self.dfCal['Titles'])
print('values: %s', self.dfCal['Values'])
print('ZGain: %s', self.dfCal['Values'][1])
self.ZOffset = 0
self.ZGain = 1
self.YOffset = 2
self.YGain = 3
self.XOffset = 4
self.XGain = 5
def redrawAfterCalibrate(self):
print("Computing new data")
if self.dfCal is not None:
self.df["valuex"] = np.subtract(
self.df["valuex"], self.dfCal['Values'][
self.XOffset]) / self.dfCal['Values'][self.XGain]
self.df["valuey"] = np.subtract(
self.df["valuey"], self.dfCal['Values'][
self.YOffset]) / self.dfCal['Values'][self.YGain]
self.df["valuez"] = np.subtract(
self.df["valuez"], self.dfCal['Values'][
self.ZOffset]) / self.dfCal['Values'][self.ZGain]
print("Computing new mag")
self.df["mag"] = np.sqrt(np.square(self.df["valuex"]) + np.square(self.df['valuey']) + \
np.square(self.df["valuez"]))-1.0
print("setting titles")
bottomtitle = 'Magnitude Graph for Start Date ' + "{:%Y-%m-%d}".format(
self.startDate)
if self.dfCal is not None:
bottomtitle = 'Calibrated ' + bottomtitle
self.ax.set_title(bottomtitle)
toptitle = 'Zoomed-In Graph for Start Date ' + "{:%Y-%m-%d}".format(
self.startDate)
if self.dfCal is not None:
toptitle = 'Calibrated ' + toptitle
self.ax2.set_title(toptitle)
print("redraw graph")
self.plotTop.set_ydata(self.df["mag"])
self.lm.set_ydata(self.df["mag"])
self.lx.set_ydata(self.df["valuex"])
self.ly.set_ydata(self.df["valuey"])
self.lz.set_ydata(self.df["valuez"])
self.fig.canvas.draw()
def onmouseover(self, event):
if event.inaxes == self.rax:
None
#logger.debug("click on radiobutton")
#self.check._clicked(event)
if event.inaxes == self.ax:
self.cursor.onmove(event)
def searchOpenCalibration(self, filename):
directory = os.path.dirname(filename)
print("directory=" + directory)
tosearch = re.compile('^calibrationResults.*')
for sChild in os.listdir(directory):
print("file=" + sChild)
if tosearch.match(sChild) is not None:
if directory == "":
directory = "."
calibfilename = directory + "/" + sChild
print("calibfilename=" + calibfilename)
self.readCalibration(calibfilename)
break
def searchForAnnotation(self):
colorKick = self.colorChoose(255, 0, 0)
colorSleep = self.colorChoose(0, 0, 255)
colorRandom = self.colorChoose(0, 255, 0)
randomColor = self.color
maskKick = self.df['annotated'] == "Kick"
maskSleep = self.df['annotated'] == "Sleep"
maskRandom = self.df['annotated'] == "Random"
maskColorRandom = self.df['annotated'] == "annotated"
print("masked found")
if len(self.df.loc[maskKick, 'epoch']) > 0:
self.reDrawAnnotation(maskKick, colorKick)
if len(self.df.loc[maskSleep, 'epoch']) > 0:
self.reDrawAnnotation(maskSleep, colorSleep)
if len(self.df.loc[maskRandom, 'epoch']) > 0:
self.reDrawAnnotation(maskRandom, colorRandom)
if len(self.df.loc[maskColorRandom, 'epoch']) > 0:
self.reDrawAnnotation(maskColorRandom, randomColor)
def reDrawAnnotation(self, mask, color):
[ymin, ymax] = self.ax.get_ylim()
height = ymax - ymin
positionKick = np.array(self.df.index[mask].tolist())
diff = np.subtract(positionKick[1:-1], positionKick[0:-2])
maskcuts = diff > 1
posInCuts = np.where(maskcuts)
arrposcut = posInCuts[0]
arrpostcut1 = arrposcut + 1
xmin = self.df.loc[mask, 'epoch'].iloc[0]
xmax = self.df.loc[mask, 'epoch'].iloc[-1]
xmin = xmin.to_pydatetime()
xmax = xmax.to_pydatetime()
#xmin=int(xmin.timestamp() * 1000)/1000
#xmax=int(xmax.timestamp() * 1000)/1000
print("xmin={v1} xmax={v2}".format(v1=xmin, v2=xmax))
xmin = mdates.date2num(xmin)
xmax = mdates.date2num(xmax)
print("len(posInCuts)", len(posInCuts[0]))
print("xmin={v1} xmax={v2}".format(v1=xmin, v2=xmax))
for idx in range(len(posInCuts[0])):
print("idx=", idx)
print("xmin={v1} xmax={v2}".format(
v1=xmin,
v2=self.df['epoch'].iloc[positionKick[arrposcut[idx]]]))
rectmin = xmin
rectmax = self.df['epoch'].iloc[positionKick[arrposcut[idx]]]
rectmax = rectmax.to_pydatetime()
rectmax = mdates.date2num(rectmax)
#rectmax=int(rectmax.timestamp() * 1000)/1000
#rectmax=mdates.num2date(rectmax)
width = rectmax - rectmin
rect = ECERectangle(rectmin,
ymin,
width,
height,
color=color,
index=1)
rect2 = ECERectangle(xmin,
ymin,
width,
height,
color=color,
index=2)
rect.setNext(rect2)
rect2.setPrev(rect)
self.ax.add_patch(rect)
self.ax2.add_patch(rect2)
self.fig.canvas.draw()
xmin = self.df['epoch'].iloc[positionKick[arrpostcut1[idx]]]
xmin = xmin.to_pydatetime()
xmin = mdates.date2num(xmin)
#xmin=int(xmin.timestamp() * 1000)/1000
#xmin=mdates.num2date(xmin)
rectmin = xmin
rectmax = xmax
#rectmax=int(rectmax.timestamp() * 1000)/1000
width = rectmax - rectmin
rect = ECERectangle(rectmin, ymin, width, height, color=color, index=1)
rect2 = ECERectangle(xmin, ymin, width, height, color=color, index=2)
rect.setNext(rect2)
rect2.setPrev(rect)
self.ax.add_patch(rect)
self.ax2.add_patch(rect2)
print("xmin={v1} xmax={v2}".format(v1=xmin, v2=xmax))
self.fig.canvas.draw()
def getConnection(self, filename):
"""
get the connection of sqlite given file name
:param filename:
:return: sqlite3 connection
"""
conn = sqlite3.connect(filename)
return conn
def readCalibration(self, filename):
self.dfCal = pd.read_csv(filename)
print('Results: %s', self.dfCal)
print('title: %s', self.dfCal['Titles'])
print('values: %s', self.dfCal['Values'])
print('ZGain: %s', self.dfCal['Values'][1])
self.ZOffset = 0
self.ZGain = 1
self.YOffset = 2
self.YGain = 3
self.XOffset = 4
self.XGain = 5
def createCalibrationAction(self):
image_file = 'square-upload'
callback = self.toolbar.importCal
text = "Calibrate"
tooltip_text = "Calibrate"
a = self.toolbar.addAction(self.toolbar._icon(image_file + '.png'),
text, callback)
print("action created")
self.toolbar._actions[callback] = a
print("action added to array")
a.setToolTip(tooltip_text)
def executeQuery(self, query):
return None
def colorChoose(self, r, g, b):
"""
create a normalized color map give r, g, b in 0-255 scale
:param r: red
:param g: green
:param b: blue
:return: tuple of color that can be used for matplotlib
"""
if self.rangeOff(r) or self.rangeOff(g) or self.rangeOff(r):
return (0, 0, 0)
return r / 255.0, g / 255.0, b / 255.0
def rangeOff(self, val):
return (val > 255) or (val < 0)
def onpick(self, event):
print("pick event")
if isinstance(event.artist, Rectangle):
patch = event.artist
# patch.remove()
self.removedObj = patch
print('onpick1 patch:', patch.get_path())
else:
print(event.artist.get_xdata())
print(event.artist.get_xdata())
print(len(event.artist.get_ydata()))
# self.fig.canvas.draw()
# def onselect(self, xmin, xmax):
# print(xmin)
# print(xmax)
# width = xmax - xmin
# [ymin, ymax] = self.ax.get_ylim()
# height = ymax - ymin
#
# rect = matpat.Rectangle((xmin, ymin), width, height,
# fill=True, alpha=0.4,
# color=self.color)
# self.ax.add_patch(rect)
def onclick(self, event):
if not self.toolbar._actions['zoom'].isChecked(
) and event.button == 1: # left = 1, middle = 2, right = 3
self.timeTrack = time.time()
print("clicked {}".format(self.timeTrack))
print("clicked X: {}".format(event.xdata))
self.xpos = event.xdata
# [ymin, ymax] = self.ax.get_ylim()
# self.ax.annotate('sth', xy=(event.xdata, event.ydata),
# xytext=(event.xdata, ymax),
# arrowprops=dict(facecolor='black', shrink=0.05),)
# self.fig.canvas.draw()
def onrelease(self, event):
if not self.toolbar._actions['zoom'].isChecked() \
and event.button == 1 and self.isAnnotate:
#and not self.toolbar._actions['pan'].isChecked() \
curTime = time.time()
if (curTime - self.timeTrack) > PRE_DEF_CLICK_TIME:
print("dragged")
xmin = self.xpos
xmax = event.xdata
width = xmax - xmin
# print(xmin)
# print(xmax)
# print(type(xmin))
# print(mdates.num2date(xmin))
# print(mdates.num2date(xmax))
# print(type(xmax))
# print(width)
[ymin, ymax] = self.ax.get_ylim()
height = ymax - ymin
#annotation problem temporary
# print(any(cond))
self.create_annotation(xmin, xmax)
# print(height)
rect = ECERectangle(xmin,
ymin,
width,
height,
color=self.color,
index=1)
rect2 = ECERectangle(xmin,
ymin,
width,
height,
color=self.color,
index=2)
# Rectangle((xmin, ymin), width, height,
# fill=True, alpha=0.4,
# color=self.color, picker=True)
rect.setNext(rect2)
rect2.setPrev(rect)
self.ax.add_patch(rect)
self.ax2.add_patch(rect2)
# self.ax2.add_patch(rect)
self.fig.canvas.draw()
def onpress(self, event):
# print(event.key())
print(event.key)
if event.key == 'r':
self.annoteText = "Kick"
self.color = self.colorChoose(255, 0, 0)
elif event.key == 'b':
self.annoteText = "Sleep"
self.color = self.colorChoose(0, 0, 255)
elif event.key == 'g':
self.annoteText = "Random"
self.color = self.colorChoose(0, 255, 0)
elif event.key == "right":
print("right pressed")
self.startX += self.currentDelta
self.endX += self.currentDelta
self.ax2.set_xlim(self.startX, self.endX)
# mask = (self.df["epoch"] >= self.startX) & \
# (self.df["epoch"] <= self.endX)
# self.ax2.plot(self.df.loc[mask, "epoch"],
# self.df.loc[mask, "mag"], '#1f77b4')
self.run()
elif event.key == "left":
# TODO check left and right limit
print("left pressed")
self.startX -= self.currentDelta
self.endX -= self.currentDelta
self.ax2.set_xlim(self.startX, self.endX)
# mask = (self.df["epoch"] >= self.startX) & \
# (self.df["epoch"] <= self.endX)
# self.ax2.plot(self.df.loc[mask, "epoch"],
# self.df.loc[mask, "mag"], '#1f77b4')
self.run()
elif event.key == "delete":
print("delete")
if self.removedObj is not None:
if isinstance(self.removedObj, ECERectangle):
print("deleting ECERect")
rect_min_x = self.removedObj.get_x()
rect_max_x = rect_min_x + self.removedObj.get_width()
self.remove_annotation(rect_min_x, rect_max_x)
ind = self.removedObj.getIndex()
self.removedObj.remove()
if ind == 1:
nextRect = self.removedObj.getNext()
else:
nextRect = self.removedObj.getPrev()
self.removedObj = None
# print(type())
if nextRect.axes is not None:
nextRect.remove()
self.fig.canvas.draw()
def run(self):
self.fig.canvas.draw()
def create_annotation(self, xmin, xmax):
print("Annoated")
cond = self.get_x_in_ranges(xmin, xmax)
self.df.loc[cond, 'annotated'] = self.annoteText
self.df.loc[cond, 'colorHex'] = self.get_color_in_hex()
def remove_annotation(self, xmin, xmax):
cond = self.get_x_in_ranges(xmin, xmax)
self.df.loc[cond, 'annotated'] = " "
self.df.loc[cond, 'colorHex'] = " "
def get_x_in_ranges(self, xmin, xmax):
return (self.df["epoch"] <= mdates.num2date(xmax)) \
& (self.df["epoch"] >= mdates.num2date(xmin))
def get_color_in_hex(self):
return "#{:02X}{:02X}{:02X}".format(int(self.color[0] * 255),
int(self.color[1] * 255),
int(self.color[2] * 255))
def setSelect(self):
self.isAnnotate = not self.isAnnotate
def cursorOnclick(self, event):
'on button press we will see if the mouse is over us '
if (self.ax == event.inaxes) and (not self.isAnnotate):
xdata = event.xdata
dateclicked = mdates.num2date(xdata)
self.startX = dateclicked
dateEnd = dateclicked + self.currentDelta
self.endX = dateEnd
# df2,epoch,endDate=self.createBottomGraph(dateclicked)
# mask = (df2["epoch"] >= dateclicked) & (df2["epoch"] <= endDate)
# self.ax2.clear()
# self.ax2.set_ylim(1, 1.1)
# self.ax2.plot(df2.loc[mask, "epoch"], df2.loc[mask, "mag"])
mask = (self.df["epoch"] >= dateclicked) & (self.df["epoch"] <=
dateEnd)
tX = self.df.loc[mask, "epoch"]
# print(tX)
self.ax2.set_xlim(tX.iloc[0], tX.iloc[len(tX) - 1])
# locator = mdates.SecondLocator(interval=120)
self.ax2.get_xaxis().set_major_locator(LinearLocator(numticks=12))
# self.ax2.xaxis.set_major_locator(locator)
# self.ax2.xaxis.set_major_formatter(mdates.DateFormatter('%H:%M:%S'))
# self.ax2.relim()
self.ax2.autoscale_view(True, True, True)
#
# x_ticks = np.append(self.ax2.get_xticks(), mdates.date2num(df2.iloc[0,0]))
# x_ticks = np.append(x_ticks,mdates.date2num(df2.iloc[-1,0]))
#self.ax2.set_xticks(x_ticks)
# #self.ax2.tick_params(axis='x', labelsize=8,rotation=45)
#
width = mdates.date2num(dateEnd) - xdata
[ymin, ymax] = self.ax.get_ylim()
height = ymax - ymin
if self.rect is not None:
self.rect.remove()
self.rect = Rectangle((xdata, ymin),
width,
height,
fill=True,
alpha=0.4,
color=(1, 0, 0),
picker=False)
self.ax.add_patch(self.rect)
self.fig.canvas.draw()
def oncheck(self, label):
if label == 'valuex':
self.lx.set_visible(not self.lx.get_visible())
elif label == 'valuey':
self.ly.set_visible(not self.ly.get_visible())
elif label == 'valuez':
self.lz.set_visible(not self.lz.get_visible())
elif label == 'mag':
self.lm.set_visible(not self.lm.get_visible())
self.fig.canvas.draw()
def changeScale(self, label):
index = self.labels.index(label)
self.currentDelta = self.scaleDeltaArray[index]