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GlobalPolyfit.py
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GlobalPolyfit.py
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import time
tic=time.time()
import os, sys
import numpy as np
from qtpy.QtCore import *
from qtpy.QtGui import *
from qtpy.QtCore import Signal
from qtpy.QtWidgets import *
from pyqtgraph import plot, show
import pyqtgraph as pg
import flika.global_vars as g
from collections import OrderedDict
import traceback
class RectSelector(pg.ROI):
def __init__(self, origin, size):
pg.ROI.__init__(self, origin, size, translateSnap=True, scaleSnap=True)
self.setPen(QPen(QColor(255, 0, 0), 0))
## handles scaling horizontally around center
leftHandle = self.addScaleHandle([1, 0.5], [0, 0.5])
rightHandle = self.addScaleHandle([0, 0.5], [1, 0.5])
## handles scaling vertically from opposite edge
bottomHandle = self.addScaleHandle([0.5, 0], [0.5, 1])
topHandle = self.addScaleHandle([0.5, 1], [0.5, 0])
## handles scaling both vertically and horizontally
self.addScaleHandle([1, 1], [0, 0])
self.addScaleHandle([0, 0], [1, 1])
self.sigRegionChanged.connect(self.onTranslate)
self.addPolyfill()
self.traceLine = None
def setVisible(self, v):
pg.ROI.setVisible(self, v)
if g.m.currentTrace:
self.traceLine = g.m.currentTrace.rois[0]['p1trace']
def onTranslate(self):
if not self.traceLine:
return
x, y = self.pos()
if x < 0:
self.setPos([0, y])
return
w, h = self.size()
frames = len(self.traceLine.getData()[1])
if x + w >= frames:
if frames - x - 1 <= 0:
return
self.setSize([frames - x - 1, h])
return
self.redraw()
def redraw(self):
baseline = self.pos()[1]
x, y = self.getFrameTrace()
if x is None:
return
y -= baseline
ftrace = get_polyfit(x, y)
self.analyze_trace(x, y, ftrace)
self.polyDataItem.setData(x=x, y=ftrace, pen=self.polyPen, fillBrush=QColor(0, 100, 155, 100), fillLevel=0)
def addPolyfill(self):
self.polyPen = QPen(QColor(255, 0, 0), 0)
self.polyPen.setStyle(Qt.DashLine)
self.polyPen.setDashOffset(5)
self.polyDataItem = pg.PlotDataItem(pen=self.polyPen)
self.polyDataItem.setParentItem(self)
def getFrameRect(self):
origin = self.pos()
origin[0] = max(0, origin[0])
origin[1] = max(0, origin[1])
size = self.size()
if self.traceLine and origin[0] + size[0] > max(self.traceLine.getData()[0]):
size[1] = max(self.traceLine.getData()[0]) - origin[0]
return np.array([origin[0], origin[1], origin[0] + size[0], origin[1] + size[1]], int)
def getFrameTrace(self):
if not self.traceLine:
return None, None
t = np.copy(self.traceLine.getData()[1])
x1, y1, x2, y2 = self.getFrameRect()
x1 = max(0, round(x1))
x2 = min(round(x2), len(t))
t = t[x1:x2 + 1]
return (np.arange(0, x2+1 - x1), t)
def setTrace(self, t):
if t == None:
return
if self.parentWidget() != None:
self.parentWidget().removeItem(self)
t.parentWidget().addItem(self)
self.traceLine = t
self.onTranslate()
def getIntegral(self):
x1, y1, x2, y2 = self.getFrameRect()
y = self.getTrace()[x1:x2+1]
return np.trapz(y)
def baseline(self):
return self.pos()[1]
def analyze_trace(self, x, y, ftrace):
pos = self.pos()
size = self.size()
x_peak = np.argmax(y)
f_peak = np.argmax(ftrace)
self.data = OrderedDict([('Baseline', (pos[0], pos[1])), \
('Peak', (f_peak + pos[0], ftrace[f_peak])),\
('Delta Peak', (f_peak, ftrace[f_peak] - pos[1]))])
#yRiseFall = getRiseFall(x, y)
ftraceRiseFall = getRiseFall(x, ftrace)
self.data.update(OrderedDict([(k, ftraceRiseFall[k]) for k in ftraceRiseFall.keys()]))
self.data['area'] = (0, np.trapz(y), 0, np.trapz(ftrace))
def get_polyfit(x, y):
np.warnings.simplefilter('ignore', np.RankWarning)
poly=np.poly1d(np.polyfit(x, y, 20))
ftrace=poly(x)
return ftrace
def getRiseFall(x, y):
x_peak = np.where(y == max(y))[0][0]
baseline = y[0]
dPeak = (x_peak, y[x_peak]-baseline)
data = OrderedDict([('Rise 20%', [-1, -1]),
('Rise 50%', [-1, -1]), ('Rise 80%', [-1, -1]),
('Rise 100%', [-1, -1]), ('Fall 80%', [-1, -1]),
('Fall 50%', [-1, -1]), ('Fall 20%', [-1, -1])])
try:
thresh20=dPeak[1]*.2 + baseline
thresh50=dPeak[1]*.5 + baseline
thresh80=dPeak[1]*.8 + baseline
data['Rise 20%'] = [np.argwhere(y>thresh20)[0][0], thresh20]
data['Rise 50%'] = [np.argwhere(y>thresh50)[0][0], thresh50]
data['Rise 80%'] = [np.argwhere(y>thresh80)[0][0], thresh80]
data['Rise 100%'] = [np.argmax(y), max(y)]
tmp=np.squeeze(np.argwhere(y<thresh80))
data['Fall 80%'] = [tmp[tmp>data['Rise 100%'][0]][0], thresh80]
tmp=np.squeeze(np.argwhere(y<thresh50))
data['Fall 50%'] = [tmp[tmp>data['Fall 80%'][0]][0], thresh50]
tmp=np.squeeze(np.argwhere(y<thresh20))
data['Fall 20%'] = [tmp[tmp>data['Fall 50%'][0]][0], thresh20]
except Exception as e:
pass
#print("Analysis Failed: %s" % traceback.format_exc())
return data