def getpgcmap(cmp='BuRd'):
import pyqtgraph as pg
import numpy as np
if cmp =='bryw':
STEPS = np.array([0.0, 0.2, 0.6, 1.0])
CLRS = ['k', 'r', 'y', 'w']
## Create a ColorMap
clrmp = pg.ColorMap(STEPS, np.array([pg.colorTuple(pg.Color(c)) for c in CLRS]))
## Get the LookupTable
lut = clrmp.getLookupTable()
elif cmp == 'TrmBlk':
pos = np.array([0.0, 0.5, 1.0])
color = np.array([[0,0,0,255], [255,128,0,255], [255,255,0,255]], dtype=np.ubyte)
map = pg.ColorMap(pos, color)
lut = map.getLookupTable(0.0, 1.0, 256)
elif cmp == 'RdBu':
pos = np.array([0.0,0.5,1.0])
color = np.array([[255,0,0,0],[255,255,255,255],[0,0,255,0]],dtype=np.ubyte)
map = pg.ColorMap(pos,color)
lut = map.getLookupTable(0.0,1.0,256)
elif cmp == 'BuRd':
pos = np.array([0.0,0.5,1.0])
color = np.array([[0,0,255,0],[255,255,255,255],[255,0,0,0]],dtype=np.ubyte)
map = pg.ColorMap(pos,color)
lut = map.getLookupTable(0.0,1.0,256)
return lut
def __init__(self, parent=None):
pyqtgraph.setConfigOption('background', 'k') #before loading widget
super(HyperSpecApp, self).__init__(parent)
self.setupUi(self)
self.updateBtn.clicked.connect(self.update)
#self.view = pyqtgraph.ViewBox(self.gView0)
#self.scene = pyqtgraph.ImageItem(self.view)
STEPS = np.array([0.0, 0.2, 0.6, 1.0])
CLRS = ['k', 'r', 'y', 'w']
clrmp = pyqtgraph.ColorMap(
STEPS,
np.array([pyqtgraph.colorTuple(pyqtgraph.Color(c)) for c in CLRS]))
data = np.random.normal(size=(100, 200, 200))
#imv = pyqtgraph.image(data)
self.ImageView2.setImage(data)
#self.ImageView2.ui.histogram.gradient.setColorMap(clrmp)
#self.img_array = np.zeros((1000, CHUNKSZ / 2 + 1))
# bipolar colormap
#pos = np.array([0., 1., 0.5, 0.25, 0.75])
#color = np.array([[0, 255, 255, 255], [255, 255, 0, 255], [0, 0, 0, 255], (0, 0, 255, 255), (255, 0, 0, 255)],
# dtype=np.ubyte)
#cmap = pyqtgraph.ColorMap(pos, color)
#lut = cmap.getLookupTable(0.0, 1.0, 256)
#self.img.setLookupTable(lut)
self.pltView1.plotItem.showGrid(True, True, 0.7)
self.pltView2.plotItem.showGrid(True, True, 0.7)
def init_ui(self):
""""""
from vnpy.app.realtime_monitor.ui.baseQtItems import MarketDataChartWidget
self.setWindowTitle(self.title)
self.resize(1300, 800)
vbox = QtWidgets.QVBoxLayout()
klineWidget = MarketDataChartWidget()
klineWidget.update_all(self.marketData, self.tradeData, [])
if not self.record_df.empty:
record = self.record_df.asof(
klineWidget.dt_ix_map.keys()).fillna(0)
ixs = []
for _dt in record.index:
ixs.append(klineWidget.dt_ix_map[_dt])
record.index = ixs
candle = klineWidget.get_plot('candle')
for n, s in record.items():
c = pg.PlotCurveItem()
candle.addItem(c)
h = sha256()
h.update(n.encode())
c.setData(s.index.values,
s.values,
pen=pg.Color(int(h.hexdigest(), base=16)))
vbox.addWidget(klineWidget)
self.setLayout(vbox)
def plotPulses(self, t_start, t_end):
# print('PlotCurrents')
self.clear() # clear plot
self.setBackground('w')
# self.s
d_plot = self.addPlot()
d_plot.addLegend()
d_plot.getAxis('left').setPen(pg.Color('k'))
d_plot.getAxis('bottom').setPen(pg.Color('k'))
d_plot.showGrid(x=True)
digital_list = [] # list of active digital channels
# print("Current channels_data", self.parent.channels_data)
t_first = min(
min([1000] + [x[0] for x in value if x[0] > 0])
for name, value in self.parent.channels_data.items()
if 'C' in name)
t_last = t_end
# t_last = max(max(x[0] for x in value if x[0] > 0) for name, value in
# self.globals['pulses'].items() if 'D' in name and len(value)>1) + 10
digital_counter = 0
for name in sorted(self.parent.channels_data.keys(), reverse=True):
if 'C' not in name:
continue
digital_list.append(name)
value = self.parent.channels_data[name]
xx = []
yy = []
# construct points to show
for i, point in enumerate(value):
if i == 0:
xx.append(t_first - (100 if t_first > 100 else t_first))
yy.append(point[1])
continue
# if not i == len(value) - 1:
xx.append(point[0])
yy.append(value[i - 1][1])
xx.append(point[0])
yy.append(point[1])
xx.append(t_last)
yy.append(point[1])
d_plot.plot(np.array(xx),
np.array(yy),
pen=pg.mkPen(pg.intColor(digital_counter, hues=5),
width=2),
name=name) # plot data
digital_counter += 1
def scanStarted(self):
self.new_scan_started = False # flag to handle new scanse in series
self.dataD = {}
self.folder = self.globals['current_measurement_folder']
self.meas_type, self.conf_params, self.x_lbl, self.y_lbl, self.xaxis_calib = impr.get_x_calibration(
self.folder, [])
# if self.meas_type =='T':
# self.fit_data_index=2
# else:
# self.fit_data_index=0
self.fit_data_index = int(self.index_box.currentText())
self.single_meas_plot.setLabel('left', text=self.y_lbl)
self.single_meas_plot.setLabel('bottom', text=self.x_lbl)
self.single_meas_plot.setTitle(self.folder.split('/')[-1],
color=pg.Color('k'))
self.curve1.setData([], [])
self.curve2.setData([], [])
self.curve3.setData([], [])
self.curve4.setData([], [])
self.single_meas_plot.removeItem(self.plot_info)
self.single_meas_plot.setXRange(
self.xaxis_calib(min(self.globals['active_params_list'][0][0])),
self.xaxis_calib(max(self.globals['active_params_list'][0][0])))
from misura.canon.indexer import SharedFile
from misura.canon.reference import get_node_reference
try:
import pyqtgraph as pg
import pyqtgraph.opengl as gl
except:
pg = False
gl = False
STEPS = np.array([0.0, 0.33, 0.66, 1.0])
CLRS = ['b', 'r', 'y', 'w']
if pg:
clrmp = pg.ColorMap(STEPS,
np.array([pg.colorTuple(pg.Color(c)) for c in CLRS]))
#TODO: add decoding
def read_file(profile, start=3500, end=-1, max_layers=1000, cut=0):
xs = []
ys = []
zs = []
colors = []
c = 0.
n = len(profile)
if end < 0:
end += n
n = end - start + 1
step = max(n // max_layers, 1)
def plotPulses(self, t_start, t_end):
print('PlotAnalogIn')
self.clear() # clear plot
self.setBackground('w')
# self.s
d_plot = self.addPlot()
d_plot.getAxis('left').setPen(pg.Color('k'))
d_plot.getAxis('bottom').setPen(pg.Color('k'))
d_plot.showGrid(x=True)
digital_height = 1.2 # place for each curve of height=1graphic
digital_counter = 0 # number of plotted channel
digital_list = [] # list of active digital channels
# print(self.globals["pulses"])
if self.parent.channels_data == {}:
return
t_first = min(
min(x[0] for x in value if x[0] > 0)
for name, value in self.parent.channels_data.items()
if 'I' in name)
t_last = t_end
# t_last = max(max(x[0] for x in value if x[0] > 0) for name, value in
# self.globals['pulses'].items() if 'D' in name and len(value)>1) + 10
pulse_counter = 0
for name in sorted(self.parent.channels_data.keys(), reverse=True):
if 'I' not in name:
continue
digital_list.append(name)
value = self.parent.channels_data[name]
# construct points to show
for i, pulse in enumerate(value):
xx = [
t_first - (100 if t_first > 100 else t_first), pulse[0],
pulse[0], pulse[1], pulse[1], t_last - t_start
]
yy = [0, 0, 1, 1, 0, 0]
# xx.append(t_first-(100 if t_first > 100 else t_first))
# yy.append(0)
# xx.append(pulse[0])
# yy.append(1)
# xx.append(pulse[1])
# yy.append(0)
# xx.append(t_last-t_start)
# yy.append(0)
d_plot.plot(np.array(xx),
np.array(yy) + digital_counter * digital_height,
pen=pg.mkPen(pg.intColor(pulse_counter),
width=2)) # plot data
pulse_counter += 1
d_plot.plot(np.array(xx),
np.ones_like(xx) * digital_counter * digital_height,
pen=pg.mkPen(width=0.5,
style=Qt.DashLine)) # plot zero
digital_counter += 1
# set ticks names
tick_names = digital_list
d_plot.getAxis('left').setTicks([
list(
zip((np.arange(len(digital_list)) + 1 / 2) * digital_height,
tick_names))
])
def __init__(self, parent=None, signals=None, globals=None):
super().__init__()
self.dataD = {}
self.fits_list = []
self.mdb_client = MongoClient(
'mongodb://192.168.1.59:27017/') # or IP of MongoDB server
self.meas_database = self.mdb_client.measData.meas_data
self.cb_axis_items = ['fit1D_x', 'fit1D_y', 'fit2D']
self.cb_index_items = ['0', '1', '2', '3', '4']
self.parent = parent
self.signals = signals
self.globals = globals
self.signals.scanStarted.connect(self.scanStarted)
self.signals.singleScanFinished.connect(self.onSingleScanFinished)
self.signals.imageProcessed.connect(
self.newDataArrived
) # replace signal by one emmited when image processing is over
self.min_n_to_avr = 3 # minimal number of good images to start everaging
main_layout = QHBoxLayout()
info_layout = QVBoxLayout()
info_layout.addWidget(QLabel('Fit'))
self.axis_box = QComboBox()
self.axis_box.addItems(self.cb_axis_items)
self.axis_box.setCurrentIndex(1)
self.axis_box.currentIndexChanged.connect(self.onFitParamChanged)
info_layout.addWidget(self.axis_box)
info_layout.addWidget(QLabel('Index'))
self.index_box = QComboBox()
self.index_box.addItems(self.cb_index_items)
self.index_box.setCurrentIndex(0)
self.index_box.currentIndexChanged.connect(self.onFitParamChanged)
info_layout.addWidget(self.index_box)
info_layout.addWidget(QLabel('Fit_func'))
self.fit_func_box = QComboBox()
self.fit_func_box.addItems(
[s for s in dir(fit_func_lib) if s[0] != '_'])
self.fit_func_box.setCurrentText('gaussian2')
self.fit_func_box.currentIndexChanged.connect(self.onFitParamChanged)
info_layout.addWidget(self.fit_func_box)
info_layout.addWidget(QLabel('p0'))
self.p0_line = QLineEdit()
self.p0_line.setMaximumWidth(200)
self.p0_line.editingFinished.connect(self.p0Edited)
info_layout.addWidget(self.p0_line)
info_layout.addWidget(QLabel('drop points (by #)'))
self.drop_points_line = QLineEdit()
self.drop_points_line.setMaximumWidth(200)
self.drop_points_line.editingFinished.connect(self.dropPointsEdited)
info_layout.addWidget(self.drop_points_line)
info_layout.addStretch(1)
main_layout.addLayout(info_layout)
self.single_meas_plot = pg.PlotWidget(background='w',
pen=pg.Color('k'))
# self.single_meas_plot.setMaximumWidth(400)
# self.single_meas_plot.showGrid(x=True, y=True,alpha=0.5)
self.single_meas_plot.getAxis('left').setPen(pg.Color('k'))
self.single_meas_plot.getAxis('bottom').setPen(pg.Color('k'))
self.curve1 = self.single_meas_plot.plot(np.array([]),
pen=None,
symbol='o',
symbolPen=None,
symbolBrush=(0, 255, 0),
symbolSize=7)
self.curve2 = self.single_meas_plot.plot(np.array([]),
pen=None,
symbol='o',
symbolPen=None,
symbolBrush=(255, 0, 0),
symbolSize=7)
self.curve3 = self.single_meas_plot.plot(np.array([]),
pen=None,
symbol='+',
symbolPen=None,
symbolBrush=pg.Color('b'),
symbolSize=15)
self.curve4 = self.single_meas_plot.plot(np.array([]), pen=(0, 0, 255))
self.plot_info = pg.TextItem(' ', anchor=(0, 1), color=pg.Color('k'))
main_layout.addWidget(self.single_meas_plot)
# self.single_meas_plot2 = pg.PlotWidget(background='w',pen=pg.Color('k'))
# self.single_meas_plot2.setMaximumWidth(400)
# # self.single_meas_plot.showGrid(x=True, y=True,alpha=0.5)
# self.single_meas_plot2.getAxis('left').setPen(pg.Color('k'))
# self.single_meas_plot2.getAxis('bottom').setPen(pg.Color('k'))
# self.curve21 = self.single_meas_plot2.plot(np.array([]), pen=None,symbol='o',
# symbolPen=None,symbolBrush=(0,255,0),symbolSize=7)
# self.curve22 = self.single_meas_plot2.plot(np.array([]), pen=None,symbol='o',
# symbolPen=None,symbolBrush=(255,0,0),symbolSize=7)
# self.curve23 = self.single_meas_plot2.plot(np.array([]), pen=None, symbol='+',
# symbolPen=None,symbolBrush=pg.Color('b'),symbolSize=15)
# self.curve24 = self.single_meas_plot2.plot(np.array([]), pen=(0,0,255))
# self.plot_info = pg.TextItem(' ', anchor=(0,1),color=pg.Color('k'))
# main_layout.addWidget(self.single_meas_plot2)
self.setLayout(main_layout)
def setColor(self, *args):
"""Set the color of the box. Arguments are the same as those accepted by functions.mkColor()"""
self.__color = pg.Color(*args)
def __init__(self,map='map'):
prefileMeas = sorted([x for x in [y for y in os.listdir("./")] if re.search("axion.m.[0-9]{5}$", x)])
fileMeas = []
for maes in prefileMeas:
try:
with h5py.File(maes, 'r') as f:
if (map in f) :
fileMeas.append(maes)
except:
print('Error opening file: %s'%maes)
fileHdf5 = h5py.File(fileMeas[0], "r")
self.Lx = fileHdf5["/"].attrs.get("Size")
self.Ly = fileHdf5["/"].attrs.get("Size")
self.Lz = fileHdf5["/"].attrs.get("Depth")
self.z = fileHdf5["/"].attrs.get("z")
self.R = self.z
fileHdf5.close()
self.allData = []
self.step = 1
self.tStep = 100
self.pause = False
self.timer = pg.QtCore.QTimer()
# Read all data
self.i = 0
self.size = 0
# if os.path.exists("./Strings.PyDat"):
# fp = gzip.open("./Strings.PyDat", "rb")
# self.allData = pickle.load(fp)
# fp.close()
# self.size = len(self.allData)
# else:
for meas in fileMeas:
# print(meas)
fileHdf5 = h5py.File(meas, "r")
Lx = fileHdf5["/"].attrs.get("Size")
Ly = fileHdf5["/"].attrs.get("Size")
Lz = fileHdf5["/"].attrs.get("Depth")
zR = fileHdf5["/"].attrs.get("z")
R = zR
if 'R' in fileHdf5:
R = fileHdf5["/"].attrs.get("R")
fl = fileHdf5["/"].attrs.get("Field type").decode()
if self.Lx != Lx or self.Ly != Ly or self.Lz != Lz:
print("Error: Size mismatch (%d %d %d) vs (%d %d %d)\nAre you mixing files?\n" % (Lx, Ly, Lz, self.Lx, self.Ly, self.Lz))
exit()
if fl == "Saxion":
mTmp = fileHdf5[map]['m'].value.reshape(Ly,Lx,2)
rData = np.sqrt(mTmp[:,:,0]**2 + mTmp[:,:,1]**2)
rMax = np.amax(rData)
rData = rData/R
aData = (np.arctan2(mTmp[:,:,1], mTmp[:,:,0]) + 2*np.pi)/(4.*np.pi)
elif fl == "Axion":
aData = fileHdf5[map]['m'].value.reshape(Ly,Lx)
# pm = np.amax(aData)
# print ("BMax %f" % pm)
aData = aData/R
rData = np.ones(aData.shape)
pData = np.ones(aData.shape)*(2*np.pi)
aData = (aData + pData)/(4.*np.pi)
# iData = np.trunc(aData/(2*np.pi))
# aData = aData - iData*(2*np.pi)
# aData = aData - pData
# pm = np.amax(aData)
# print ("AMax %f" % pm)
rMax = R
else:
print("Unrecognized field type %s" % fl)
exit()
self.allData.append([rData, aData, zR, rMax])
fileHdf5.close()
self.size = self.size + 1
# fp = gzip.open("Strings.PyDat", "wb")
# pickle.dump(self.allData, fp, protocol=2)
# fp.close()
self.app = QtGui.QApplication([])
self.pWin = pg.GraphicsLayoutWidget()
self.pWin.setWindowTitle('Axion / Saxion evolution')
self.pWin.resize(1600,1600)
pg.setConfigOptions(antialias=True)
self.aPlot = self.pWin.addPlot(row=0, col=0)
self.sPlot = self.pWin.addPlot(row=0, col=1)
self.aPlot.setXRange(0,Lx*1.2)
self.aPlot.setYRange(0,Lx*1.2)
self.sPlot.setXRange(0,Lx*1.2)
self.sPlot.setYRange(0,Lx*1.2)
self.zAtxt = pg.TextItem("z=0.000000")
self.zStxt = pg.TextItem("z=0.000000")
data = self.allData[0]
aPos = np.array([0.00, 0.10, 0.25, 0.4, 0.5, 0.6, 0.75, 0.9, 1.0 ])
aCol = ['#006600', 'b', 'w', 'r', 'k', 'b', 'w', 'r', '#006600']
vb = self.aPlot.getViewBox()
aSzeX = vb.size().width()*0.96
aSzeY = vb.size().height()*0.8
self.aMap = pg.ColorMap(aPos, np.array([pg.colorTuple(pg.Color(c)) for c in aCol]))
self.aLut = self.aMap.getLookupTable()
self.aLeg = pg.GradientLegend((aSzeX/20, aSzeY), (aSzeX, aSzeY/12.))
self.aLeg.setLabels({ "-pi": 0.0, "-pi/2": 0.25, "0.0": 0.50, "+pi/2": 0.75, "+pi": 1.00 })
self.aLeg.setParentItem(self.aPlot)
self.aLeg.gradient.setColorAt(0.00, QtGui.QColor(255,255,255))
self.aLeg.gradient.setColorAt(0.25, QtGui.QColor(255, 0, 0))
self.aLeg.gradient.setColorAt(0.50, QtGui.QColor( 0, 0, 0))
self.aLeg.gradient.setColorAt(0.75, QtGui.QColor( 0, 0,255))
self.aLeg.gradient.setColorAt(1.00, QtGui.QColor(255,255,255))
self.aImg = pg.ImageItem(lut=self.aLut)
self.aPlot.addItem(self.aImg)
self.aPlot.addItem(self.zAtxt)
# sPos = np.linspace(0.0, data[3], 5)
sPos = np.array([0.00, 0.25, 0.50, 0.75, 1.00])
sLab = ["%.2f" % mod for mod in sPos]
sCol = ['w', 'r', 'y', 'c', 'k']
vs = self.sPlot.getViewBox()
sSzeX = vs.size().width()*0.96
sSzeY = vs.size().height()*0.8
self.sMap = pg.ColorMap(sPos, np.array([pg.colorTuple(pg.Color(c)) for c in sCol]))
self.s**t = self.sMap.getLookupTable()
self.sLeg = pg.GradientLegend((sSzeX/20, sSzeY), (aSzeX/0.96 + sSzeX, sSzeY/12.))
self.sLeg.setLabels({ sLab[0]: 0.0, sLab[1]: 0.25, sLab[2]: 0.50, sLab[3]: 0.75, sLab[4]: 1.00 })
self.sLeg.setParentItem(self.sPlot)
self.sLeg.gradient.setColorAt(0.00, QtGui.QColor(255,255,255))
self.sLeg.gradient.setColorAt(0.25, QtGui.QColor(255, 0, 0))
self.sLeg.gradient.setColorAt(0.50, QtGui.QColor(255,255, 0))
self.sLeg.gradient.setColorAt(0.75, QtGui.QColor( 0,255,255))
self.sLeg.gradient.setColorAt(1.00, QtGui.QColor( 0, 0, 0))
self.sImg = pg.ImageItem(lut=self.s**t)
self.sPlot.addItem(self.sImg)
self.sPlot.addItem(self.zStxt)
self.sImg.setImage(data[0], levels=(0.,1.))
self.aImg.setImage(data[1], levels=(0.,1.))
self.pWin.show()
self.baseKeyPress = self.pWin.keyPressEvent
