def __spacetime_diagram_o_frame(self):
# from (x',t') to (x,t)
def tr(x_prime, t_prime):
x_prime, t_prime = np.asarray(x_prime), np.asarray(t_prime)
return self.lorentz_transformations.transform(
x_prime, t_prime, -self.velocity)
# form (x,t) to (x',t')
def inv_tr(x, t):
x, t = np.asarray(x), np.asarray(t)
return self.lorentz_transformations.transform(x, t, self.velocity)
grid_helper = GridHelperCurveLinear((tr, inv_tr))
ax = Subplot(self.fig, 1, 2, 1, grid_helper=grid_helper) if self.showOPrime \
else Subplot(self.fig, 1, 1, 1, grid_helper=grid_helper)
self.fig.add_subplot(ax)
ax.set_xlabel("x", loc="center")
ax.set_ylabel("t", loc="center")
# O' x axis
ax.axis["x1"] = x1 = ax.new_floating_axis(1, 0)
x1.label.set_text("x'")
# O' t axis
ax.axis["t1"] = t1 = ax.new_floating_axis(0, 0)
t1.label.set_text("t'")
self.__add_x_and_y_axis(ax)
ax.format_coord = self.__format_coord_o_frame
self.__remove_ticks(ax, x1, t1)
self.world_lines_plotter.plot(plt, ax, self.velocity)
def plotISIDistributions(sessions,groups=None,sessionTypes=None,samplingRate=30000.0,save=False,fname=None,figsize=(10,6)):
"""Plots the isi distributions for all the cells in the given sessions"""
fig = plt.figure(figsize=figsize)
fig.subplots_adjust(left=0.05,right=.95)
ISIs = {}
ncells = 0
if sessionTypes != None:
sessionTypes = dict(zip(sessions,sessionTypes))
for g in groups:
for s in sessions:
dataFile = h5py.File(os.path.expanduser('~/Documents/research/data/spikesorting/hmm/p=1e-20/%sg%.4d.hdf5' % (s,g)),'r')
try:
for c in dataFile['unitTimePoints'].keys():
isi = np.log(np.diff(dataFile['unitTimePoints'][c][:]/(samplingRate/1000)))
cn = 'g%dc%d' % (g,int(c))
if cn in ISIs:
ISIs[cn]['%s' %(s,)] = isi
else:
ISIs[cn] = {'%s' %(s,): isi}
finally:
dataFile.close()
i = 1
ncells = len(ISIs.keys())
for c in ISIs.keys():
ax = Subplot(fig,1,ncells,i)
formatAxis(ax)
fig.add_axes(ax)
ax.set_title(c)
for k,v in ISIs[c].items():
if sessionTypes != None:
L = sessionTypes[k]
else:
L = k
n,b = np.histogram(v,bins=20,normed=True)
plt.plot(b[:-1],n,label=L)
i+=1
ax.set_xlabel('ISI [ms]')
xl,xh = int(np.round((b[0]-0.5)*2))/2,int(np.round((b[-1]+0.5)*2))/2
xl = -0.5
dx = np.round(10.0*(xh-xl)/4.0)/10
xt_ = np.arange(xl,xh+1,dx)
ax.set_xticks(xt_)
ax.set_xticklabels(map(lambda s: r'$10^{%.1f}$' % (s,),xt_))
fig.axes[-1].legend()
if save:
if fname == None:
fname = os.path.expanduser('~/Documents/research/figures/isi_comparison.pdf')
fig.savefig(fname,bbox='tight')
def setup_axes1(self, fig, T_ticks, subplotshape=None):
"""
A simple one.
"""
deg = -45.
self.tr = Affine2D().rotate_deg(deg)
theta_ticks = [] #np.arange(theta_min, theta_max, d_T)
grid_helper = GridHelperCurveLinear(
self.tr,
grid_locator1=FixedLocator(T_ticks),
grid_locator2=FixedLocator(theta_ticks))
if subplotshape is None:
subplotshape = (1, 1, 1)
ax1 = Subplot(fig, *subplotshape, grid_helper=grid_helper)
# ax1 will have a ticks and gridlines defined by the given
# transform (+ transData of the Axes). Note that the transform of
# the Axes itself (i.e., transData) is not affected by the given
# transform.
fig.add_subplot(ax1)
# SW, SE, NE, NW
corners = np.array([[-25., -20.], [30., 40.], [-40., 120.],
[-105., 60.]])
corners_t = self._tf(corners[:, 0], corners[:, 1])
# ax1.set_aspect(1.)
x_min, x_max = self.x_range
ax1.set_xlim(x_min, x_max)
ax1.set_ylim(*self.y_range)
ax1.set_xlabel('Temperature [C]')
ax1.set_aspect(1)
#ax1.axis["t"]=ax1.new_floating_axis(0, 0.)
#T_axis = ax1.axis['t']
#theta_axis = ax1.axis["t2"]=ax1.new_floating_axis(1, 0.)
# plot.draw()
# plot.show()
self.ax1 = ax1
def setup_axes1(self, fig, T_ticks, subplotshape=None):
"""
A simple one.
"""
deg = -45.
self.tr = Affine2D().rotate_deg(deg)
theta_ticks = [] #np.arange(theta_min, theta_max, d_T)
grid_helper = GridHelperCurveLinear(self.tr, grid_locator1=FixedLocator(T_ticks), grid_locator2=FixedLocator(theta_ticks))
if subplotshape is None:
subplotshape = (1,1,1)
ax1 = Subplot(fig, *subplotshape, grid_helper=grid_helper)
# ax1 will have a ticks and gridlines defined by the given
# transform (+ transData of the Axes). Note that the transform of
# the Axes itself (i.e., transData) is not affected by the given
# transform.
fig.add_subplot(ax1)
# SW, SE, NE, NW
corners = np.array([[-25., -20.], [30., 40.], [-40., 120.], [-105., 60.]])
corners_t = self._tf(corners[:,0], corners[:,1])
# ax1.set_aspect(1.)
x_min, x_max = self.x_range
ax1.set_xlim(x_min, x_max)
ax1.set_ylim(*self.y_range)
ax1.set_xlabel('Temperature [C]')
ax1.set_aspect(1)
#ax1.axis["t"]=ax1.new_floating_axis(0, 0.)
#T_axis = ax1.axis['t']
#theta_axis = ax1.axis["t2"]=ax1.new_floating_axis(1, 0.)
# plot.draw()
# plot.show()
self.ax1 = ax1
class DGSPlannerGUI(QtGui.QWidget):
def __init__(self, ol=None, parent=None):
# pylint: disable=unused-argument,super-on-old-class
super(DGSPlannerGUI, self).__init__(parent)
#OrientedLattice
if ValidateOL(ol):
self.ol = ol
else:
self.ol = mantid.geometry.OrientedLattice()
self.masterDict = dict() #holds info about instrument and ranges
self.updatedInstrument = False
self.updatedOL = False
self.wg = None #workspace group
self.instrumentWidget = InstrumentSetupWidget.InstrumentSetupWidget(
self)
self.setLayout(QtGui.QHBoxLayout())
controlLayout = QtGui.QVBoxLayout()
controlLayout.addWidget(self.instrumentWidget)
self.ublayout = QtGui.QHBoxLayout()
self.classic = ClassicUBInputWidget.ClassicUBInputWidget(self.ol)
self.ublayout.addWidget(self.classic,
alignment=QtCore.Qt.AlignTop,
stretch=1)
self.matrix = MatrixUBInputWidget.MatrixUBInputWidget(self.ol)
self.ublayout.addWidget(self.matrix,
alignment=QtCore.Qt.AlignTop,
stretch=1)
controlLayout.addLayout(self.ublayout)
self.dimensionWidget = DimensionSelectorWidget.DimensionSelectorWidget(
self)
controlLayout.addWidget(self.dimensionWidget)
plotControlLayout = QtGui.QGridLayout()
self.plotButton = QtGui.QPushButton("Plot", self)
self.oplotButton = QtGui.QPushButton("Overplot", self)
self.helpButton = QtGui.QPushButton("?", self)
self.colorLabel = QtGui.QLabel('Color by angle', self)
self.colorButton = QtGui.QCheckBox(self)
self.colorButton.toggle()
self.aspectLabel = QtGui.QLabel('Aspect ratio 1:1', self)
self.aspectButton = QtGui.QCheckBox(self)
self.saveButton = QtGui.QPushButton("Save Figure", self)
plotControlLayout.addWidget(self.plotButton, 0, 0)
plotControlLayout.addWidget(self.oplotButton, 0, 1)
plotControlLayout.addWidget(self.colorLabel, 0, 2,
QtCore.Qt.AlignRight)
plotControlLayout.addWidget(self.colorButton, 0, 3)
plotControlLayout.addWidget(self.aspectLabel, 0, 4,
QtCore.Qt.AlignRight)
plotControlLayout.addWidget(self.aspectButton, 0, 5)
plotControlLayout.addWidget(self.helpButton, 0, 6)
plotControlLayout.addWidget(self.saveButton, 0, 7)
controlLayout.addLayout(plotControlLayout)
self.layout().addLayout(controlLayout)
#figure
self.figure = Figure()
self.figure.patch.set_facecolor('white')
self.canvas = FigureCanvas(self.figure)
self.grid_helper = GridHelperCurveLinear((self.tr, self.inv_tr))
self.trajfig = Subplot(self.figure,
1,
1,
1,
grid_helper=self.grid_helper)
self.trajfig.hold(True)
self.figure.add_subplot(self.trajfig)
self.layout().addWidget(self.canvas)
self.needToClear = False
self.saveDir = ''
#connections
self.matrix.UBmodel.changed.connect(self.updateUB)
self.matrix.UBmodel.changed.connect(self.classic.updateOL)
self.classic.changed.connect(self.matrix.UBmodel.updateOL)
self.classic.changed.connect(self.updateUB)
self.instrumentWidget.changed.connect(self.updateParams)
self.dimensionWidget.changed.connect(self.updateParams)
self.plotButton.clicked.connect(self.updateFigure)
self.oplotButton.clicked.connect(self.updateFigure)
self.helpButton.clicked.connect(self.help)
self.saveButton.clicked.connect(self.save)
#force an update of values
self.instrumentWidget.updateAll()
self.dimensionWidget.updateChanges()
#help
self.assistantProcess = QtCore.QProcess(self)
# pylint: disable=protected-access
self.collectionFile = os.path.join(mantid._bindir,
'../docs/qthelp/MantidProject.qhc')
version = ".".join(mantid.__version__.split(".")[:2])
self.qtUrl = 'qthelp://org.sphinx.mantidproject.' + version + '/doc/interfaces/DGSPlanner.html'
self.externalUrl = 'http://docs.mantidproject.org/nightly/interfaces/DGSPlanner.html'
#control for cancel button
self.iterations = 0
self.progress_canceled = False
@QtCore.pyqtSlot(mantid.geometry.OrientedLattice)
def updateUB(self, ol):
self.ol = ol
self.updatedOL = True
self.trajfig.clear()
@QtCore.pyqtSlot(dict)
def updateParams(self, d):
if self.sender() is self.instrumentWidget:
self.updatedInstrument = True
if d.has_key('dimBasis') and self.masterDict.has_key(
'dimBasis') and d['dimBasis'] != self.masterDict['dimBasis']:
self.needToClear = True
if d.has_key('dimIndex') and self.masterDict.has_key(
'dimIndex') and d['dimIndex'] != self.masterDict['dimIndex']:
self.needToClear = True
self.masterDict.update(copy.deepcopy(d))
def help(self):
try:
import pymantidplot
pymantidplot.proxies.showCustomInterfaceHelp('DGSPlanner')
except ImportError:
self.assistantProcess.close()
self.assistantProcess.waitForFinished()
helpapp = QtCore.QLibraryInfo.location(
QtCore.QLibraryInfo.BinariesPath) + QtCore.QDir.separator()
helpapp += 'assistant'
args = [
'-enableRemoteControl', '-collectionFile', self.collectionFile,
'-showUrl', self.qtUrl
]
if os.path.isfile(helpapp):
self.assistantProcess.close()
self.assistantProcess.waitForFinished()
self.assistantProcess.start(helpapp, args)
else:
QtGui.QDesktopServices.openUrl(QtCore.QUrl(self.externalUrl))
def closeEvent(self, event):
self.assistantProcess.close()
self.assistantProcess.waitForFinished()
event.accept()
# pylint: disable=too-many-locals
def updateFigure(self):
# pylint: disable=too-many-branches
if self.updatedInstrument or self.progress_canceled:
self.progress_canceled = False
#get goniometer settings first
gonioAxis0values = numpy.arange(
self.masterDict['gonioMinvals'][0],
self.masterDict['gonioMaxvals'][0] +
0.1 * self.masterDict['gonioSteps'][0],
self.masterDict['gonioSteps'][0])
gonioAxis1values = numpy.arange(
self.masterDict['gonioMinvals'][1],
self.masterDict['gonioMaxvals'][1] +
0.1 * self.masterDict['gonioSteps'][1],
self.masterDict['gonioSteps'][1])
gonioAxis2values = numpy.arange(
self.masterDict['gonioMinvals'][2],
self.masterDict['gonioMaxvals'][2] +
0.1 * self.masterDict['gonioSteps'][2],
self.masterDict['gonioSteps'][2])
self.iterations = len(gonioAxis0values) * len(
gonioAxis1values) * len(gonioAxis2values)
if self.iterations > 10:
reply = QtGui.QMessageBox.warning(
self, 'Goniometer',
"More than 10 goniometer settings. This might be long.\n"
"Are you sure you want to proceed?",
QtGui.QMessageBox.Yes | QtGui.QMessageBox.No,
QtGui.QMessageBox.No)
if reply == QtGui.QMessageBox.No:
return
if self.wg != None:
mantid.simpleapi.DeleteWorkspace(self.wg)
mantid.simpleapi.LoadEmptyInstrument(
mantid.api.ExperimentInfo.getInstrumentFilename(
self.masterDict['instrument']),
OutputWorkspace="__temp_instrument")
if self.masterDict['instrument'] == 'HYSPEC':
mantid.simpleapi.AddSampleLog(Workspace="__temp_instrument",
LogName='msd',
LogText='1798.5',
LogType='Number Series')
mantid.simpleapi.AddSampleLog(Workspace="__temp_instrument",
LogName='s2',
LogText=str(
self.masterDict['S2']),
LogType='Number Series')
mantid.simpleapi.LoadInstrument(Workspace="__temp_instrument",
RewriteSpectraMap=True,
InstrumentName="HYSPEC")
#masking
if self.masterDict.has_key('maskFilename') and len(
self.masterDict['maskFilename'].strip()) > 0:
try:
__maskWS = mantid.simpleapi.Load(
self.masterDict['maskFilename'])
mantid.simpleapi.MaskDetectors(
Workspace="__temp_instrument",
MaskedWorkspace=__maskWS)
except (ValueError, RuntimeError) as e:
reply = QtGui.QMessageBox.critical(
self, 'Error',
"The following error has occured in loading the mask:\n"
+ str(e) + "\nDo you want to continue without mask?",
QtGui.QMessageBox.Yes | QtGui.QMessageBox.No,
QtGui.QMessageBox.No)
if reply == QtGui.QMessageBox.No:
return
if self.masterDict['makeFast']:
sp = range(
mantid.mtd["__temp_instrument"].getNumberHistograms())
tomask = sp[::4] + sp[1::4] + sp[2::4]
mantid.simpleapi.MaskDetectors("__temp_instrument",
SpectraList=tomask)
i = 0
groupingStrings = []
progressDialog = QtGui.QProgressDialog(self)
progressDialog.setMinimumDuration(0)
progressDialog.setCancelButtonText("&Cancel")
progressDialog.setRange(0, self.iterations)
progressDialog.setWindowTitle("DGSPlanner progress")
for g0 in gonioAxis0values:
for g1 in gonioAxis1values:
for g2 in gonioAxis2values:
name = "__temp_instrument" + str(i)
i += 1
progressDialog.setValue(i)
progressDialog.setLabelText(
"Creating workspace %d of %d..." %
(i, self.iterations))
QtGui.qApp.processEvents()
if progressDialog.wasCanceled():
self.progress_canceled = True
progressDialog.close()
return
groupingStrings.append(name)
mantid.simpleapi.CloneWorkspace("__temp_instrument",
OutputWorkspace=name)
mantid.simpleapi.SetGoniometer(
Workspace=name,
Axis0=str(g0) + "," +
self.masterDict['gonioDirs'][0] + "," +
str(self.masterDict['gonioSenses'][0]),
Axis1=str(g1) + "," +
self.masterDict['gonioDirs'][1] + "," +
str(self.masterDict['gonioSenses'][1]),
Axis2=str(g2) + "," +
self.masterDict['gonioDirs'][2] + "," +
str(self.masterDict['gonioSenses'][2]))
progressDialog.close()
mantid.simpleapi.DeleteWorkspace("__temp_instrument")
self.wg = mantid.simpleapi.GroupWorkspaces(
groupingStrings, OutputWorkspace="__temp_instrument")
self.updatedInstrument = False
#set the UB
if self.updatedOL or not self.wg[0].sample().hasOrientedLattice():
mantid.simpleapi.SetUB(self.wg, UB=self.ol.getUB())
self.updatedOL = False
#calculate coverage
dimensions = ['Q1', 'Q2', 'Q3', 'DeltaE']
progressDialog = QtGui.QProgressDialog(self)
progressDialog.setMinimumDuration(0)
progressDialog.setCancelButtonText("&Cancel")
progressDialog.setRange(0, self.iterations)
progressDialog.setWindowTitle("DGSPlanner progress")
for i in range(self.iterations):
progressDialog.setValue(i)
progressDialog.setLabelText("Calculating orientation %d of %d..." %
(i, self.iterations))
QtGui.qApp.processEvents()
if progressDialog.wasCanceled():
self.progress_canceled = True
progressDialog.close()
return
__mdws = mantid.simpleapi.CalculateCoverageDGS(
self.wg[i],
Q1Basis=self.masterDict['dimBasis'][0],
Q2Basis=self.masterDict['dimBasis'][1],
Q3Basis=self.masterDict['dimBasis'][2],
IncidentEnergy=self.masterDict['Ei'],
Dimension1=dimensions[self.masterDict['dimIndex'][0]],
Dimension1Min=float2Input(self.masterDict['dimMin'][0]),
Dimension1Max=float2Input(self.masterDict['dimMax'][0]),
Dimension1Step=float2Input(self.masterDict['dimStep'][0]),
Dimension2=dimensions[self.masterDict['dimIndex'][1]],
Dimension2Min=float2Input(self.masterDict['dimMin'][1]),
Dimension2Max=float2Input(self.masterDict['dimMax'][1]),
Dimension2Step=float2Input(self.masterDict['dimStep'][1]),
Dimension3=dimensions[self.masterDict['dimIndex'][2]],
Dimension3Min=float2Input(self.masterDict['dimMin'][2]),
Dimension3Max=float2Input(self.masterDict['dimMax'][2]),
Dimension4=dimensions[self.masterDict['dimIndex'][3]],
Dimension4Min=float2Input(self.masterDict['dimMin'][3]),
Dimension4Max=float2Input(self.masterDict['dimMax'][3]))
if i == 0:
intensity = __mdws.getSignalArray(
)[:, :, 0, 0] * 1. #to make it writeable
else:
if self.colorButton.isChecked():
tempintensity = __mdws.getSignalArray()[:, :, 0, 0]
intensity[numpy.where(tempintensity > 0)] = i + 1.
else:
tempintensity = __mdws.getSignalArray()[:, :, 0, 0]
intensity[numpy.where(tempintensity > 0)] = 1.
progressDialog.close()
x = numpy.linspace(
__mdws.getDimension(0).getMinimum(),
__mdws.getDimension(0).getMaximum(), intensity.shape[0])
y = numpy.linspace(
__mdws.getDimension(1).getMinimum(),
__mdws.getDimension(1).getMaximum(), intensity.shape[1])
Y, X = numpy.meshgrid(y, x)
xx, yy = self.tr(X, Y)
Z = numpy.ma.masked_array(intensity, intensity == 0)
Z = Z[:-1, :-1]
#plotting
if self.sender() is self.plotButton or self.needToClear:
self.figure.clear()
self.trajfig.clear()
self.figure.add_subplot(self.trajfig)
self.needToClear = False
self.trajfig.pcolorfast(xx, yy, Z)
if self.aspectButton.isChecked():
self.trajfig.set_aspect(1.)
else:
self.trajfig.set_aspect('auto')
self.trajfig.set_xlabel(self.masterDict['dimNames'][0])
self.trajfig.set_ylabel(self.masterDict['dimNames'][1])
self.trajfig.grid(True)
self.canvas.draw()
mantid.simpleapi.DeleteWorkspace(__mdws)
def save(self):
fileName = str(
QtGui.QFileDialog.getSaveFileName(self, 'Save Plot', self.saveDir,
'*.png'))
data = "Instrument " + self.masterDict['instrument'] + '\n'
if self.masterDict['instrument'] == 'HYSPEC':
data += "S2 = " + str(self.masterDict['S2']) + '\n'
data += "Ei = " + str(self.masterDict['Ei']) + ' meV\n'
data += "Goniometer values:\n"
gonioAxis0values = numpy.arange(
self.masterDict['gonioMinvals'][0],
self.masterDict['gonioMaxvals'][0] +
0.1 * self.masterDict['gonioSteps'][0],
self.masterDict['gonioSteps'][0])
gonioAxis1values = numpy.arange(
self.masterDict['gonioMinvals'][1],
self.masterDict['gonioMaxvals'][1] +
0.1 * self.masterDict['gonioSteps'][1],
self.masterDict['gonioSteps'][1])
gonioAxis2values = numpy.arange(
self.masterDict['gonioMinvals'][2],
self.masterDict['gonioMaxvals'][2] +
0.1 * self.masterDict['gonioSteps'][2],
self.masterDict['gonioSteps'][2])
for g0 in gonioAxis0values:
for g1 in gonioAxis1values:
for g2 in gonioAxis2values:
data += " " + self.masterDict['gonioLabels'][
0] + " = " + str(g0)
data += " " + self.masterDict['gonioLabels'][
1] + " = " + str(g1)
data += " " + self.masterDict['gonioLabels'][
2] + " = " + str(g2) + '\n'
data += "Lattice parameters:\n"
data += " a = " + str(self.ol.a()) + " b = " + str(
self.ol.b()) + " c = " + str(self.ol.c()) + '\n'
data += " alpha = " + str(self.ol.alpha()) + " beta = " + str(
self.ol.beta()) + " gamma = " + str(self.ol.gamma()) + '\n'
data += "Orientation vectors:\n"
data += " u = " + str(self.ol.getuVector()) + '\n'
data += " v = " + str(self.ol.getvVector()) + '\n'
data+="Integrated "+self.masterDict['dimNames'][2]+" between "+\
str(self.masterDict['dimMin'][2])+" and "+str(self.masterDict['dimMax'][2])+'\n'
data+="Integrated "+self.masterDict['dimNames'][3]+" between "+\
str(self.masterDict['dimMin'][3])+" and "+str(self.masterDict['dimMax'][3])+'\n'
info = self.figure.text(0.2, 0, data, verticalalignment='top')
self.figure.savefig(fileName,
bbox_inches='tight',
additional_artists=info)
self.saveDir = os.path.dirname(fileName)
def tr(self, x, y):
x, y = numpy.asarray(x), numpy.asarray(y)
#one of the axes is energy
if self.masterDict['dimIndex'][0] == 3 or self.masterDict['dimIndex'][
1] == 3:
return x, y
else:
h1, k1, l1 = (float(temp) for temp in self.masterDict['dimBasis'][
self.masterDict['dimIndex'][0]].split(','))
h2, k2, l2 = (float(temp) for temp in self.masterDict['dimBasis'][
self.masterDict['dimIndex'][1]].split(','))
angle = numpy.radians(self.ol.recAngle(h1, k1, l1, h2, k2, l2))
return 1. * x + numpy.cos(angle) * y, numpy.sin(angle) * y
def inv_tr(self, x, y):
x, y = numpy.asarray(x), numpy.asarray(y)
#one of the axes is energy
if self.masterDict['dimIndex'][0] == 3 or self.masterDict['dimIndex'][
1] == 3:
return x, y
else:
h1, k1, l1 = (float(temp) for temp in self.masterDict['dimBasis'][
self.masterDict['dimIndex'][0]].split(','))
h2, k2, l2 = (float(temp) for temp in self.masterDict['dimBasis'][
self.masterDict['dimIndex'][1]].split(','))
angle = numpy.radians(self.ol.recAngle(h1, k1, l1, h2, k2, l2))
return 1. * x - y / numpy.tan(angle), y / numpy.sin(angle)
class DGSPlannerGUI(QtWidgets.QWidget):
def __init__(self, parent=None, window_flags=None, ol=None):
# pylint: disable=unused-argument,super-on-old-class
super(DGSPlannerGUI, self).__init__(parent)
if window_flags:
self.setWindowFlags(window_flags)
# OrientedLattice
if ValidateOL(ol):
self.ol = ol
else:
self.ol = mantid.geometry.OrientedLattice()
self.masterDict = dict() # holds info about instrument and ranges
self.updatedInstrument = False
self.instrumentWAND = False
self.updatedOL = False
self.wg = None # workspace group
self.instrumentWidget = InstrumentSetupWidget.InstrumentSetupWidget(
self)
self.setLayout(QtWidgets.QHBoxLayout())
controlLayout = QtWidgets.QVBoxLayout()
geometryBox = QtWidgets.QGroupBox("Instrument Geometry")
plotBox = QtWidgets.QGroupBox("Plot Axes")
geometryBoxLayout = QtWidgets.QVBoxLayout()
geometryBoxLayout.addWidget(self.instrumentWidget)
geometryBox.setLayout(geometryBoxLayout)
controlLayout.addWidget(geometryBox)
self.ublayout = QtWidgets.QHBoxLayout()
self.classic = ClassicUBInputWidget.ClassicUBInputWidget(self.ol)
self.ublayout.addWidget(self.classic,
alignment=QtCore.Qt.AlignTop,
stretch=1)
self.matrix = MatrixUBInputWidget.MatrixUBInputWidget(self.ol)
self.ublayout.addWidget(self.matrix,
alignment=QtCore.Qt.AlignTop,
stretch=1)
sampleBox = QtWidgets.QGroupBox("Sample")
sampleBox.setLayout(self.ublayout)
controlLayout.addWidget(sampleBox)
self.dimensionWidget = DimensionSelectorWidget.DimensionSelectorWidget(
self)
plotBoxLayout = QtWidgets.QVBoxLayout()
plotBoxLayout.addWidget(self.dimensionWidget)
plotControlLayout = QtWidgets.QGridLayout()
self.plotButton = QtWidgets.QPushButton("Plot", self)
self.oplotButton = QtWidgets.QPushButton("Overplot", self)
self.helpButton = QtWidgets.QPushButton("?", self)
self.colorLabel = QtWidgets.QLabel('Color by angle', self)
self.colorButton = QtWidgets.QCheckBox(self)
self.colorButton.toggle()
self.aspectLabel = QtWidgets.QLabel('Aspect ratio 1:1', self)
self.aspectButton = QtWidgets.QCheckBox(self)
self.saveButton = QtWidgets.QPushButton("Save Figure", self)
plotControlLayout.addWidget(self.plotButton, 0, 0)
plotControlLayout.addWidget(self.oplotButton, 0, 1)
plotControlLayout.addWidget(self.colorLabel, 0, 2,
QtCore.Qt.AlignRight)
plotControlLayout.addWidget(self.colorButton, 0, 3)
plotControlLayout.addWidget(self.aspectLabel, 0, 4,
QtCore.Qt.AlignRight)
plotControlLayout.addWidget(self.aspectButton, 0, 5)
plotControlLayout.addWidget(self.helpButton, 0, 6)
plotControlLayout.addWidget(self.saveButton, 0, 7)
plotBoxLayout.addLayout(plotControlLayout)
plotBox = QtWidgets.QGroupBox("Plot Axes")
plotBox.setLayout(plotBoxLayout)
controlLayout.addWidget(plotBox)
self.layout().addLayout(controlLayout)
# figure
self.figure = Figure()
self.figure.patch.set_facecolor('white')
self.canvas = FigureCanvas(self.figure)
self.grid_helper = GridHelperCurveLinear((self.tr, self.inv_tr))
self.trajfig = Subplot(self.figure,
1,
1,
1,
grid_helper=self.grid_helper)
if matplotlib.compare_versions('2.1.0', matplotlib.__version__):
self.trajfig.hold(
True) # hold is deprecated since 2.1.0, true by default
self.figure.add_subplot(self.trajfig)
self.toolbar = MantidNavigationToolbar(self.canvas, self)
figureLayout = QtWidgets.QVBoxLayout()
figureLayout.addWidget(self.toolbar, 0)
figureLayout.addWidget(self.canvas, 1)
self.layout().addLayout(figureLayout)
self.needToClear = False
self.saveDir = ''
# connections
self.matrix.UBmodel.changed.connect(self.updateUB)
self.matrix.UBmodel.changed.connect(self.classic.updateOL)
self.classic.changed.connect(self.matrix.UBmodel.updateOL)
self.classic.changed.connect(self.updateUB)
self.instrumentWidget.changed.connect(self.updateParams)
self.instrumentWidget.getInstrumentComboBox().activated[str].connect(
self.instrumentUpdateEvent)
self.instrumentWidget.getEditEi().textChanged.connect(
self.eiWavelengthUpdateEvent)
self.dimensionWidget.changed.connect(self.updateParams)
self.plotButton.clicked.connect(self.updateFigure)
self.oplotButton.clicked.connect(self.updateFigure)
self.helpButton.clicked.connect(self.help)
self.saveButton.clicked.connect(self.save)
# force an update of values
self.instrumentWidget.updateAll()
self.dimensionWidget.updateChanges()
# help
self.assistant_process = QtCore.QProcess(self)
# pylint: disable=protected-access
self.mantidplot_name = 'DGS Planner'
# control for cancel button
self.iterations = 0
self.progress_canceled = False
# register startup
mantid.UsageService.registerFeatureUsage(
mantid.kernel.FeatureType.Interface, "DGSPlanner", False)
@QtCore.Slot(mantid.geometry.OrientedLattice)
def updateUB(self, ol):
self.ol = ol
self.updatedOL = True
self.trajfig.clear()
def eiWavelengthUpdateEvent(self):
if self.masterDict['instrument'] == 'WAND\u00B2':
ei = UnitConversion.run('Wavelength', 'Energy',
self.masterDict['Ei'], 0, 0, 0, Elastic, 0)
offset = ei * 0.01
lowerBound = -offset
upperBound = offset
self.dimensionWidget.set_editMin4(lowerBound)
self.dimensionWidget.set_editMax4(upperBound)
def instrumentUpdateEvent(self):
if self.masterDict['instrument'] == 'WAND\u00B2':
self.instrumentWAND = True
# change the ui accordingly
self.dimensionWidget.toggleDeltaE(False)
self.instrumentWidget.setLabelEi('Input Wavelength')
self.instrumentWidget.setEiVal(str(1.488))
self.instrumentWidget.setGoniometerNames(['s1', 'sgl', 'sgu'])
self.instrumentWidget.setGoniometerDirections(
['0,1,0', '1,0,0', '0,0,1'])
self.instrumentWidget.setGoniometerRotationSense([1, -1, -1])
self.instrumentWidget.updateAll()
self.eiWavelengthUpdateEvent()
else:
if self.instrumentWAND:
self.instrumentWAND = False
self.dimensionWidget.toggleDeltaE(True)
self.instrumentWidget.setLabelEi('Incident Energy')
self.instrumentWidget.setEiVal(str(10.0))
self.instrumentWidget.setGoniometerNames(['psi', 'gl', 'gs'])
self.instrumentWidget.setGoniometerDirections(
['0,1,0', '0,0,1', '1,0,0'])
self.instrumentWidget.setGoniometerRotationSense([1, 1, 1])
self.instrumentWidget.updateAll()
@QtCore.Slot(dict)
def updateParams(self, d):
if self.sender() is self.instrumentWidget:
self.updatedInstrument = True
if 'dimBasis' in d and 'dimBasis' in self.masterDict and d[
'dimBasis'] != self.masterDict['dimBasis']:
self.needToClear = True
if 'dimIndex' in d and 'dimIndex' in self.masterDict and d[
'dimIndex'] != self.masterDict['dimIndex']:
self.needToClear = True
self.masterDict.update(copy.deepcopy(d))
def help(self):
show_interface_help(self.mantidplot_name,
self.assistant_process,
area='direct')
def closeEvent(self, event):
self.assistant_process.close()
self.assistant_process.waitForFinished()
event.accept()
def _create_goniometer_workspaces(self, gonioAxis0values, gonioAxis1values,
gonioAxis2values, progressDialog):
groupingStrings = []
i = 0
for g0 in gonioAxis0values:
for g1 in gonioAxis1values:
for g2 in gonioAxis2values:
name = "__temp_instrument" + str(i)
i += 1
progressDialog.setValue(i)
progressDialog.setLabelText(
"Creating workspace %d of %d..." %
(i, self.iterations))
QtWidgets.qApp.processEvents()
if progressDialog.wasCanceled():
self.progress_canceled = True
progressDialog.close()
return None
groupingStrings.append(name)
mantid.simpleapi.CloneWorkspace("__temp_instrument",
OutputWorkspace=name)
mantid.simpleapi.SetGoniometer(
Workspace=name,
Axis0=str(g0) + "," + self.masterDict['gonioDirs'][0] +
"," + str(self.masterDict['gonioSenses'][0]),
Axis1=str(g1) + "," + self.masterDict['gonioDirs'][1] +
"," + str(self.masterDict['gonioSenses'][1]),
Axis2=str(g2) + "," + self.masterDict['gonioDirs'][2] +
"," + str(self.masterDict['gonioSenses'][2]))
return groupingStrings
# pylint: disable=too-many-locals
def updateFigure(self): # noqa: C901
# pylint: disable=too-many-branches
if self.updatedInstrument or self.progress_canceled:
self.progress_canceled = False
# get goniometer settings first
gonioAxis0values = numpy.arange(
self.masterDict['gonioMinvals'][0],
self.masterDict['gonioMaxvals'][0] +
0.1 * self.masterDict['gonioSteps'][0],
self.masterDict['gonioSteps'][0])
gonioAxis1values = numpy.arange(
self.masterDict['gonioMinvals'][1],
self.masterDict['gonioMaxvals'][1] +
0.1 * self.masterDict['gonioSteps'][1],
self.masterDict['gonioSteps'][1])
gonioAxis2values = numpy.arange(
self.masterDict['gonioMinvals'][2],
self.masterDict['gonioMaxvals'][2] +
0.1 * self.masterDict['gonioSteps'][2],
self.masterDict['gonioSteps'][2])
self.iterations = len(gonioAxis0values) * len(
gonioAxis1values) * len(gonioAxis2values)
if self.iterations > 10:
reply = QtWidgets.QMessageBox.warning(
self, 'Goniometer',
"More than 10 goniometer settings. This might be long.\n"
"Are you sure you want to proceed?",
QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No,
QtWidgets.QMessageBox.No)
if reply == QtWidgets.QMessageBox.No:
return
if self.wg is not None:
mantid.simpleapi.DeleteWorkspace(self.wg)
instrumentName = self.masterDict['instrument']
if instrumentName == 'WAND\u00B2':
instrumentName = 'WAND'
mantid.simpleapi.LoadEmptyInstrument(
mantid.api.ExperimentInfo.getInstrumentFilename(
instrumentName),
OutputWorkspace="__temp_instrument")
if self.masterDict['instrument'] == 'HYSPEC':
mantid.simpleapi.AddSampleLog(Workspace="__temp_instrument",
LogName='msd',
LogText='1798.5',
LogType='Number Series')
mantid.simpleapi.AddSampleLog(Workspace="__temp_instrument",
LogName='s2',
LogText=str(
self.masterDict['S2']),
LogType='Number Series')
mantid.simpleapi.LoadInstrument(Workspace="__temp_instrument",
RewriteSpectraMap=True,
InstrumentName="HYSPEC")
elif self.masterDict['instrument'] == 'EXED':
mantid.simpleapi.RotateInstrumentComponent(
Workspace="__temp_instrument",
ComponentName='Tank',
Y=1,
Angle=str(self.masterDict['S2']),
RelativeRotation=False)
elif instrumentName == 'WAND':
mantid.simpleapi.AddSampleLog(Workspace="__temp_instrument",
LogName='HB2C:Mot:s2.RBV',
LogText=str(
self.masterDict['S2']),
LogType='Number Series')
mantid.simpleapi.AddSampleLog(Workspace="__temp_instrument",
LogName='HB2C:Mot:detz.RBV',
LogText=str(
self.masterDict['DetZ']),
LogType='Number Series')
mantid.simpleapi.LoadInstrument(Workspace="__temp_instrument",
RewriteSpectraMap=True,
InstrumentName="WAND")
# masking
if 'maskFilename' in self.masterDict and len(
self.masterDict['maskFilename'].strip()) > 0:
try:
__maskWS = mantid.simpleapi.Load(
self.masterDict['maskFilename'])
mantid.simpleapi.MaskDetectors(
Workspace="__temp_instrument",
MaskedWorkspace=__maskWS)
except (ValueError, RuntimeError) as e:
reply = QtWidgets.QMessageBox.critical(
self, 'Error',
"The following error has occurred in loading the mask:\n"
+ str(e) + "\nDo you want to continue without mask?",
QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No,
QtWidgets.QMessageBox.No)
if reply == QtWidgets.QMessageBox.No:
return
if self.masterDict['makeFast']:
sp = list(
range(
mantid.mtd["__temp_instrument"].getNumberHistograms()))
tomask = sp[1::4] + sp[2::4] + sp[3::4]
mantid.simpleapi.MaskDetectors("__temp_instrument",
SpectraList=tomask)
progressDialog = QtWidgets.QProgressDialog(self)
progressDialog.setMinimumDuration(0)
progressDialog.setCancelButtonText("&Cancel")
progressDialog.setRange(0, self.iterations)
progressDialog.setWindowTitle("DGSPlanner progress")
groupingStrings = self._create_goniometer_workspaces(
gonioAxis0values, gonioAxis1values, gonioAxis2values,
progressDialog)
if groupingStrings is None:
return
progressDialog.close()
mantid.simpleapi.DeleteWorkspace("__temp_instrument")
self.wg = mantid.simpleapi.GroupWorkspaces(
groupingStrings, OutputWorkspace="__temp_instrument")
self.updatedInstrument = False
# set the UB
if self.updatedOL or not self.wg[0].sample().hasOrientedLattice():
mantid.simpleapi.SetUB(self.wg, UB=self.ol.getUB())
self.updatedOL = False
# calculate coverage
dimensions = ['Q1', 'Q2', 'Q3', 'DeltaE']
progressDialog = QtWidgets.QProgressDialog(self)
progressDialog.setMinimumDuration(0)
progressDialog.setCancelButtonText("&Cancel")
progressDialog.setRange(0, self.iterations)
progressDialog.setWindowTitle("DGSPlanner progress")
if self.masterDict['instrument'] == 'WAND\u00B2':
ei = UnitConversion.run('Wavelength', 'Energy',
self.masterDict['Ei'], 0, 0, 0, Elastic, 0)
else:
ei = self.masterDict['Ei']
for i in range(self.iterations):
progressDialog.setValue(i)
progressDialog.setLabelText("Calculating orientation %d of %d..." %
(i, self.iterations))
QtWidgets.qApp.processEvents()
if progressDialog.wasCanceled():
self.progress_canceled = True
progressDialog.close()
return
__mdws = mantid.simpleapi.CalculateCoverageDGS(
self.wg[i],
Q1Basis=self.masterDict['dimBasis'][0],
Q2Basis=self.masterDict['dimBasis'][1],
Q3Basis=self.masterDict['dimBasis'][2],
IncidentEnergy=ei,
Dimension1=dimensions[self.masterDict['dimIndex'][0]],
Dimension1Min=float2Input(self.masterDict['dimMin'][0]),
Dimension1Max=float2Input(self.masterDict['dimMax'][0]),
Dimension1Step=float2Input(self.masterDict['dimStep'][0]),
Dimension2=dimensions[self.masterDict['dimIndex'][1]],
Dimension2Min=float2Input(self.masterDict['dimMin'][1]),
Dimension2Max=float2Input(self.masterDict['dimMax'][1]),
Dimension2Step=float2Input(self.masterDict['dimStep'][1]),
Dimension3=dimensions[self.masterDict['dimIndex'][2]],
Dimension3Min=float2Input(self.masterDict['dimMin'][2]),
Dimension3Max=float2Input(self.masterDict['dimMax'][2]),
Dimension4=dimensions[self.masterDict['dimIndex'][3]],
Dimension4Min=float2Input(self.masterDict['dimMin'][3]),
Dimension4Max=float2Input(self.masterDict['dimMax'][3]))
if i == 0:
intensity = __mdws.getSignalArray(
)[:, :, 0, 0] * 1. # to make it writeable
else:
if self.colorButton.isChecked():
tempintensity = __mdws.getSignalArray()[:, :, 0, 0]
intensity[numpy.where(tempintensity > 0)] = i + 1.
else:
tempintensity = __mdws.getSignalArray()[:, :, 0, 0]
intensity[numpy.where(tempintensity > 0)] = 1.
progressDialog.close()
x = numpy.linspace(
__mdws.getDimension(0).getMinimum(),
__mdws.getDimension(0).getMaximum(), intensity.shape[0])
y = numpy.linspace(
__mdws.getDimension(1).getMinimum(),
__mdws.getDimension(1).getMaximum(), intensity.shape[1])
Y, X = numpy.meshgrid(y, x)
xx, yy = self.tr(X, Y)
Z = numpy.ma.masked_array(intensity, intensity == 0)
Z = Z[:-1, :-1]
# plotting
if self.sender() is self.plotButton or self.needToClear:
self.figure.clear()
self.trajfig.clear()
self.figure.add_subplot(self.trajfig)
self.needToClear = False
self.trajfig.pcolorfast(xx, yy, Z)
if self.aspectButton.isChecked():
self.trajfig.set_aspect(1.)
else:
self.trajfig.set_aspect('auto')
self.trajfig.set_xlabel(self.masterDict['dimNames'][0])
self.trajfig.set_ylabel(self.masterDict['dimNames'][1])
self.trajfig.grid(True)
self.canvas.draw()
mantid.simpleapi.DeleteWorkspace(__mdws)
def save(self):
fileName = QtWidgets.QFileDialog.getSaveFileName(
self, 'Save Plot', self.saveDir, '*.png')
if isinstance(fileName, tuple):
fileName = fileName[0]
if not fileName:
return
data = "Instrument " + self.masterDict['instrument'] + '\n'
if self.masterDict['instrument'] == 'HYSPEC':
data += "S2 = " + str(self.masterDict['S2']) + '\n'
data += "Ei = " + str(self.masterDict['Ei']) + ' meV\n'
data += "Goniometer values:\n"
gonioAxis0values = numpy.arange(
self.masterDict['gonioMinvals'][0],
self.masterDict['gonioMaxvals'][0] +
0.1 * self.masterDict['gonioSteps'][0],
self.masterDict['gonioSteps'][0])
gonioAxis1values = numpy.arange(
self.masterDict['gonioMinvals'][1],
self.masterDict['gonioMaxvals'][1] +
0.1 * self.masterDict['gonioSteps'][1],
self.masterDict['gonioSteps'][1])
gonioAxis2values = numpy.arange(
self.masterDict['gonioMinvals'][2],
self.masterDict['gonioMaxvals'][2] +
0.1 * self.masterDict['gonioSteps'][2],
self.masterDict['gonioSteps'][2])
for g0 in gonioAxis0values:
for g1 in gonioAxis1values:
for g2 in gonioAxis2values:
data += " " + self.masterDict['gonioLabels'][
0] + " = " + str(g0)
data += " " + self.masterDict['gonioLabels'][
1] + " = " + str(g1)
data += " " + self.masterDict['gonioLabels'][
2] + " = " + str(g2) + '\n'
data += "Lattice parameters:\n"
data += " a = " + str(self.ol.a()) + " b = " + str(
self.ol.b()) + " c = " + str(self.ol.c()) + '\n'
data += " alpha = " + str(self.ol.alpha()) + " beta = " + str(
self.ol.beta()) + " gamma = " + str(self.ol.gamma()) + '\n'
data += "Orientation vectors:\n"
data += " u = " + str(self.ol.getuVector()) + '\n'
data += " v = " + str(self.ol.getvVector()) + '\n'
data += "Integrated " + self.masterDict['dimNames'][2] + " between " + \
str(self.masterDict['dimMin'][2]) + " and " + str(self.masterDict['dimMax'][2]) + '\n'
data += "Integrated " + self.masterDict['dimNames'][3] + " between " + \
str(self.masterDict['dimMin'][3]) + " and " + str(self.masterDict['dimMax'][3]) + '\n'
info = self.figure.text(0.2, 0, data, verticalalignment='top')
self.figure.savefig(fileName,
bbox_inches='tight',
additional_artists=info)
self.saveDir = os.path.dirname(fileName)
def tr(self, x, y):
x, y = numpy.asarray(x), numpy.asarray(y)
# one of the axes is energy
if self.masterDict['dimIndex'][0] == 3 or self.masterDict['dimIndex'][
1] == 3:
return x, y
else:
h1, k1, l1 = (float(temp) for temp in self.masterDict['dimBasis'][
self.masterDict['dimIndex'][0]].split(','))
h2, k2, l2 = (float(temp) for temp in self.masterDict['dimBasis'][
self.masterDict['dimIndex'][1]].split(','))
angle = numpy.radians(self.ol.recAngle(h1, k1, l1, h2, k2, l2))
return 1. * x + numpy.cos(angle) * y, numpy.sin(angle) * y
def inv_tr(self, x, y):
x, y = numpy.asarray(x), numpy.asarray(y)
# one of the axes is energy
if self.masterDict['dimIndex'][0] == 3 or self.masterDict['dimIndex'][
1] == 3:
return x, y
else:
h1, k1, l1 = (float(temp) for temp in self.masterDict['dimBasis'][
self.masterDict['dimIndex'][0]].split(','))
h2, k2, l2 = (float(temp) for temp in self.masterDict['dimBasis'][
self.masterDict['dimIndex'][1]].split(','))
angle = numpy.radians(self.ol.recAngle(h1, k1, l1, h2, k2, l2))
return 1. * x - y / numpy.tan(angle), y / numpy.sin(angle)
class DGSPlannerGUI(QtGui.QWidget):
def __init__(self,ol=None,parent=None):
# pylint: disable=unused-argument,super-on-old-class
super(DGSPlannerGUI,self).__init__(parent)
#OrientedLattice
if ValidateOL(ol):
self.ol=ol
else:
self.ol=mantid.geometry.OrientedLattice()
self.masterDict=dict() #holds info about instrument and ranges
self.updatedInstrument=False
self.updatedOL=False
self.wg=None #workspace group
self.instrumentWidget=InstrumentSetupWidget.InstrumentSetupWidget(self)
self.setLayout(QtGui.QHBoxLayout())
controlLayout=QtGui.QVBoxLayout()
controlLayout.addWidget(self.instrumentWidget)
self.ublayout=QtGui.QHBoxLayout()
self.classic=ClassicUBInputWidget.ClassicUBInputWidget(self.ol)
self.ublayout.addWidget(self.classic,alignment=QtCore.Qt.AlignTop,stretch=1)
self.matrix=MatrixUBInputWidget.MatrixUBInputWidget(self.ol)
self.ublayout.addWidget(self.matrix,alignment=QtCore.Qt.AlignTop,stretch=1)
controlLayout.addLayout(self.ublayout)
self.dimensionWidget=DimensionSelectorWidget.DimensionSelectorWidget(self)
controlLayout.addWidget(self.dimensionWidget)
plotControlLayout=QtGui.QGridLayout()
self.plotButton=QtGui.QPushButton("Plot",self)
self.oplotButton=QtGui.QPushButton("Overplot",self)
self.helpButton=QtGui.QPushButton("?",self)
self.colorLabel=QtGui.QLabel('Color by angle',self)
self.colorButton=QtGui.QCheckBox(self)
self.colorButton.toggle()
self.aspectLabel=QtGui.QLabel('Aspect ratio 1:1',self)
self.aspectButton=QtGui.QCheckBox(self)
self.saveButton=QtGui.QPushButton("Save Figure",self)
plotControlLayout.addWidget(self.plotButton,0,0)
plotControlLayout.addWidget(self.oplotButton,0,1)
plotControlLayout.addWidget(self.colorLabel,0,2,QtCore.Qt.AlignRight)
plotControlLayout.addWidget(self.colorButton,0,3)
plotControlLayout.addWidget(self.aspectLabel,0,4,QtCore.Qt.AlignRight)
plotControlLayout.addWidget(self.aspectButton,0,5)
plotControlLayout.addWidget(self.helpButton,0,6)
plotControlLayout.addWidget(self.saveButton,0,7)
controlLayout.addLayout(plotControlLayout)
self.layout().addLayout(controlLayout)
#figure
self.figure=Figure()
self.figure.patch.set_facecolor('white')
self.canvas=FigureCanvas(self.figure)
self.grid_helper = GridHelperCurveLinear((self.tr, self.inv_tr))
self.trajfig = Subplot(self.figure, 1, 1, 1, grid_helper=self.grid_helper)
self.trajfig.hold(True)
self.figure.add_subplot(self.trajfig)
self.layout().addWidget(self.canvas)
self.needToClear=False
self.saveDir=''
#connections
self.matrix.UBmodel.changed.connect(self.updateUB)
self.matrix.UBmodel.changed.connect(self.classic.updateOL)
self.classic.changed.connect(self.matrix.UBmodel.updateOL)
self.classic.changed.connect(self.updateUB)
self.instrumentWidget.changed.connect(self.updateParams)
self.dimensionWidget.changed.connect(self.updateParams)
self.plotButton.clicked.connect(self.updateFigure)
self.oplotButton.clicked.connect(self.updateFigure)
self.helpButton.clicked.connect(self.help)
self.saveButton.clicked.connect(self.save)
#force an update of values
self.instrumentWidget.updateAll()
self.dimensionWidget.updateChanges()
#help
self.assistantProcess = QtCore.QProcess(self)
# pylint: disable=protected-access
self.collectionFile=os.path.join(mantid._bindir,'../docs/qthelp/MantidProject.qhc')
version = ".".join(mantid.__version__.split(".")[:2])
self.qtUrl='qthelp://org.sphinx.mantidproject.'+version+'/doc/interfaces/DGSPlanner.html'
self.externalUrl='http://docs.mantidproject.org/nightly/interfaces/DGSPlanner.html'
#control for cancel button
self.iterations=0
self.progress_canceled=False
#register startup
mantid.UsageService.registerFeatureUsage("Interface","DGSPlanner",False)
@QtCore.pyqtSlot(mantid.geometry.OrientedLattice)
def updateUB(self,ol):
self.ol=ol
self.updatedOL=True
self.trajfig.clear()
@QtCore.pyqtSlot(dict)
def updateParams(self,d):
if self.sender() is self.instrumentWidget:
self.updatedInstrument=True
if 'dimBasis' in d and 'dimBasis' in self.masterDict and d['dimBasis']!=self.masterDict['dimBasis']:
self.needToClear=True
if 'dimIndex' in d and 'dimIndex' in self.masterDict and d['dimIndex']!=self.masterDict['dimIndex']:
self.needToClear=True
self.masterDict.update(copy.deepcopy(d))
def help(self):
try:
import pymantidplot
pymantidplot.proxies.showCustomInterfaceHelp('DGSPlanner')
except ImportError:
self.assistantProcess.close()
self.assistantProcess.waitForFinished()
helpapp = QtCore.QLibraryInfo.location(QtCore.QLibraryInfo.BinariesPath) + QtCore.QDir.separator()
helpapp += 'assistant'
args = ['-enableRemoteControl', '-collectionFile',self.collectionFile,'-showUrl',self.qtUrl]
if os.path.isfile(helpapp) and os.path.isfile(self.collectionFile):
self.assistantProcess.close()
self.assistantProcess.waitForFinished()
self.assistantProcess.start(helpapp, args)
else:
mqt.MantidQt.API.MantidDesktopServices.openUrl(QtCore.QUrl(self.externalUrl))
def closeEvent(self,event):
self.assistantProcess.close()
self.assistantProcess.waitForFinished()
event.accept()
# pylint: disable=too-many-locals
def updateFigure(self):
# pylint: disable=too-many-branches
if self.updatedInstrument or self.progress_canceled:
self.progress_canceled=False
#get goniometer settings first
gonioAxis0values=numpy.arange(self.masterDict['gonioMinvals'][0],self.masterDict['gonioMaxvals'][0]
+0.1*self.masterDict['gonioSteps'][0],self.masterDict['gonioSteps'][0])
gonioAxis1values=numpy.arange(self.masterDict['gonioMinvals'][1],self.masterDict['gonioMaxvals'][1]
+0.1*self.masterDict['gonioSteps'][1],self.masterDict['gonioSteps'][1])
gonioAxis2values=numpy.arange(self.masterDict['gonioMinvals'][2],self.masterDict['gonioMaxvals'][2]
+0.1*self.masterDict['gonioSteps'][2],self.masterDict['gonioSteps'][2])
self.iterations=len(gonioAxis0values)*len(gonioAxis1values)*len(gonioAxis2values)
if self.iterations>10:
reply = QtGui.QMessageBox.warning(self, 'Goniometer',"More than 10 goniometer settings. This might be long.\n"
"Are you sure you want to proceed?", QtGui.QMessageBox.Yes | QtGui.QMessageBox.No,
QtGui.QMessageBox.No)
if reply==QtGui.QMessageBox.No:
return
if self.wg is not None:
mantid.simpleapi.DeleteWorkspace(self.wg)
mantid.simpleapi.LoadEmptyInstrument(mantid.api.ExperimentInfo.getInstrumentFilename(self.masterDict['instrument']),
OutputWorkspace="__temp_instrument")
if self.masterDict['instrument']=='HYSPEC':
mantid.simpleapi.AddSampleLog(Workspace="__temp_instrument",LogName='msd',LogText='1798.5',LogType='Number Series')
mantid.simpleapi.AddSampleLog(Workspace="__temp_instrument",LogName='s2',
LogText=str(self.masterDict['S2']),LogType='Number Series')
mantid.simpleapi.LoadInstrument(Workspace="__temp_instrument", RewriteSpectraMap=True, InstrumentName="HYSPEC")
#masking
if 'maskFilename' in self.masterDict and len(self.masterDict['maskFilename'].strip())>0:
try:
__maskWS=mantid.simpleapi.Load(self.masterDict['maskFilename'])
mantid.simpleapi.MaskDetectors(Workspace="__temp_instrument",MaskedWorkspace=__maskWS)
except (ValueError,RuntimeError) as e:
reply = QtGui.QMessageBox.critical(self, 'Error',"The following error has occured in loading the mask:\n"+
str(e)+"\nDo you want to continue without mask?",
QtGui.QMessageBox.Yes | QtGui.QMessageBox.No, QtGui.QMessageBox.No)
if reply==QtGui.QMessageBox.No:
return
if self.masterDict['makeFast']:
sp=range(mantid.mtd["__temp_instrument"].getNumberHistograms())
tomask=sp[::4]+sp[1::4]+sp[2::4]
mantid.simpleapi.MaskDetectors("__temp_instrument",SpectraList=tomask)
i=0
groupingStrings=[]
progressDialog = QtGui.QProgressDialog(self)
progressDialog.setMinimumDuration(0)
progressDialog.setCancelButtonText("&Cancel")
progressDialog.setRange(0, self.iterations)
progressDialog.setWindowTitle("DGSPlanner progress")
for g0 in gonioAxis0values:
for g1 in gonioAxis1values:
for g2 in gonioAxis2values:
name="__temp_instrument"+str(i)
i+=1
progressDialog.setValue(i)
progressDialog.setLabelText("Creating workspace %d of %d..." % (i, self.iterations))
QtGui.qApp.processEvents()
if progressDialog.wasCanceled():
self.progress_canceled=True
progressDialog.close()
return
groupingStrings.append(name)
mantid.simpleapi.CloneWorkspace("__temp_instrument",OutputWorkspace=name)
mantid.simpleapi.SetGoniometer(Workspace=name,
Axis0=str(g0)+","+self.masterDict['gonioDirs'][0]+
","+str(self.masterDict['gonioSenses'][0]),
Axis1=str(g1)+","+self.masterDict['gonioDirs'][1]+
","+str(self.masterDict['gonioSenses'][1]),
Axis2=str(g2)+","+self.masterDict['gonioDirs'][2]+
","+str(self.masterDict['gonioSenses'][2]))
progressDialog.close()
mantid.simpleapi.DeleteWorkspace("__temp_instrument")
self.wg=mantid.simpleapi.GroupWorkspaces(groupingStrings,OutputWorkspace="__temp_instrument")
self.updatedInstrument=False
#set the UB
if self.updatedOL or not self.wg[0].sample().hasOrientedLattice():
mantid.simpleapi.SetUB(self.wg,UB=self.ol.getUB())
self.updatedOL=False
#calculate coverage
dimensions=['Q1','Q2','Q3','DeltaE']
progressDialog = QtGui.QProgressDialog(self)
progressDialog.setMinimumDuration(0)
progressDialog.setCancelButtonText("&Cancel")
progressDialog.setRange(0, self.iterations)
progressDialog.setWindowTitle("DGSPlanner progress")
for i in range(self.iterations):
progressDialog.setValue(i)
progressDialog.setLabelText("Calculating orientation %d of %d..." % (i, self.iterations))
QtGui.qApp.processEvents()
if progressDialog.wasCanceled():
self.progress_canceled=True
progressDialog.close()
return
__mdws=mantid.simpleapi.CalculateCoverageDGS(self.wg[i],
Q1Basis=self.masterDict['dimBasis'][0],
Q2Basis=self.masterDict['dimBasis'][1],
Q3Basis=self.masterDict['dimBasis'][2],
IncidentEnergy=self.masterDict['Ei'],
Dimension1=dimensions[self.masterDict['dimIndex'][0]],
Dimension1Min=float2Input(self.masterDict['dimMin'][0]),
Dimension1Max=float2Input(self.masterDict['dimMax'][0]),
Dimension1Step=float2Input(self.masterDict['dimStep'][0]),
Dimension2=dimensions[self.masterDict['dimIndex'][1]],
Dimension2Min=float2Input(self.masterDict['dimMin'][1]),
Dimension2Max=float2Input(self.masterDict['dimMax'][1]),
Dimension2Step=float2Input(self.masterDict['dimStep'][1]),
Dimension3=dimensions[self.masterDict['dimIndex'][2]],
Dimension3Min=float2Input(self.masterDict['dimMin'][2]),
Dimension3Max=float2Input(self.masterDict['dimMax'][2]),
Dimension4=dimensions[self.masterDict['dimIndex'][3]],
Dimension4Min=float2Input(self.masterDict['dimMin'][3]),
Dimension4Max=float2Input(self.masterDict['dimMax'][3]))
if i==0:
intensity=__mdws.getSignalArray()[:,:,0,0]*1. #to make it writeable
else:
if self.colorButton.isChecked():
tempintensity= __mdws.getSignalArray()[:,:,0,0]
intensity[numpy.where( tempintensity>0)]=i+1.
else:
tempintensity= __mdws.getSignalArray()[:,:,0,0]
intensity[numpy.where( tempintensity>0)]=1.
progressDialog.close()
x = numpy.linspace(__mdws.getDimension(0).getMinimum(), __mdws.getDimension(0).getMaximum(),intensity.shape[0] )
y = numpy.linspace(__mdws.getDimension(1).getMinimum(), __mdws.getDimension(1).getMaximum(),intensity.shape[1] )
Y,X = numpy.meshgrid(y,x)
xx, yy = self.tr(X, Y)
Z=numpy.ma.masked_array(intensity,intensity==0)
Z = Z[:-1, :-1]
#plotting
if self.sender() is self.plotButton or self.needToClear:
self.figure.clear()
self.trajfig.clear()
self.figure.add_subplot(self.trajfig)
self.needToClear=False
self.trajfig.pcolorfast(xx,yy,Z)
if self.aspectButton.isChecked():
self.trajfig.set_aspect(1.)
else:
self.trajfig.set_aspect('auto')
self.trajfig.set_xlabel(self.masterDict['dimNames'][0])
self.trajfig.set_ylabel(self.masterDict['dimNames'][1])
self.trajfig.grid(True)
self.canvas.draw()
mantid.simpleapi.DeleteWorkspace(__mdws)
def save(self):
fileName = str(QtGui.QFileDialog.getSaveFileName(self, 'Save Plot', self.saveDir,'*.png'))
data = "Instrument "+self.masterDict['instrument']+'\n'
if self.masterDict['instrument']=='HYSPEC':
data+= "S2 = "+str(self.masterDict['S2'])+'\n'
data+= "Ei = "+str(self.masterDict['Ei'])+' meV\n'
data+= "Goniometer values:\n"
gonioAxis0values=numpy.arange(self.masterDict['gonioMinvals'][0],self.masterDict['gonioMaxvals'][0]
+0.1*self.masterDict['gonioSteps'][0],self.masterDict['gonioSteps'][0])
gonioAxis1values=numpy.arange(self.masterDict['gonioMinvals'][1],self.masterDict['gonioMaxvals'][1]
+0.1*self.masterDict['gonioSteps'][1],self.masterDict['gonioSteps'][1])
gonioAxis2values=numpy.arange(self.masterDict['gonioMinvals'][2],self.masterDict['gonioMaxvals'][2]
+0.1*self.masterDict['gonioSteps'][2],self.masterDict['gonioSteps'][2])
for g0 in gonioAxis0values:
for g1 in gonioAxis1values:
for g2 in gonioAxis2values:
data+=" "+self.masterDict['gonioLabels'][0]+" = "+str(g0)
data+=" "+self.masterDict['gonioLabels'][1]+" = "+str(g1)
data+=" "+self.masterDict['gonioLabels'][2]+" = "+str(g2)+'\n'
data+= "Lattice parameters:\n"
data+=" a = "+str(self.ol.a())+" b = "+str(self.ol.b())+" c = "+str(self.ol.c())+'\n'
data+=" alpha = "+str(self.ol.alpha())+" beta = "+str(self.ol.beta())+" gamma = "+str(self.ol.gamma())+'\n'
data+= "Orientation vectors:\n"
data+=" u = "+str(self.ol.getuVector())+'\n'
data+=" v = "+str(self.ol.getvVector())+'\n'
data+="Integrated "+self.masterDict['dimNames'][2]+" between "+\
str(self.masterDict['dimMin'][2])+" and "+str(self.masterDict['dimMax'][2])+'\n'
data+="Integrated "+self.masterDict['dimNames'][3]+" between "+\
str(self.masterDict['dimMin'][3])+" and "+str(self.masterDict['dimMax'][3])+'\n'
info=self.figure.text(0.2,0,data,verticalalignment='top')
self.figure.savefig(fileName,bbox_inches='tight',additional_artists=info)
self.saveDir=os.path.dirname(fileName)
def tr(self,x, y):
x, y = numpy.asarray(x), numpy.asarray(y)
#one of the axes is energy
if self.masterDict['dimIndex'][0]==3 or self.masterDict['dimIndex'][1]==3:
return x,y
else:
h1,k1,l1=(float(temp) for temp in self.masterDict['dimBasis'][self.masterDict['dimIndex'][0]].split(','))
h2,k2,l2=(float(temp) for temp in self.masterDict['dimBasis'][self.masterDict['dimIndex'][1]].split(','))
angle=numpy.radians(self.ol.recAngle(h1,k1,l1,h2,k2,l2))
return 1.*x+numpy.cos(angle)*y, numpy.sin(angle)*y
def inv_tr(self,x,y):
x, y = numpy.asarray(x), numpy.asarray(y)
#one of the axes is energy
if self.masterDict['dimIndex'][0]==3 or self.masterDict['dimIndex'][1]==3:
return x,y
else:
h1,k1,l1=(float(temp) for temp in self.masterDict['dimBasis'][self.masterDict['dimIndex'][0]].split(','))
h2,k2,l2=(float(temp) for temp in self.masterDict['dimBasis'][self.masterDict['dimIndex'][1]].split(','))
angle=numpy.radians(self.ol.recAngle(h1,k1,l1,h2,k2,l2))
return 1.*x-y/numpy.tan(angle), y/numpy.sin(angle)
def plotSpikeCountDistributions(sessions,groups=None,sessionTypes=None,samplingRate=30000.0,save=False,windowSize=40,fname=None,figsize=(10,6)):
"""Plots the isi distributions for all the cells in the given sessions"""
fig = plt.figure(figsize=figsize)
fig.subplots_adjust(left=0.05,right=.95)
spikeCounts = {}
ncells = 0
nz = {}
if sessionTypes != None:
sessionTypes = dict(zip(sessions,sessionTypes))
for g in groups:
for s in sessions:
dataFile = h5py.File(os.path.expanduser('~/Documents/research/data/spikesorting/hmm/p=1e-20/%sg%.4d.hdf5' % (s,g)),'r')
try:
for c in dataFile['unitTimePoints'].keys():
sptrain = dataFile['unitTimePoints'][c][:]/(samplingRate/1000)
nbins = sptrain.max()/windowSize
bins,bs = np.linspace(0,sptrain.max(),nbins,retstep=True)
sc,bins = np.histogram(sptrain,bins)
cn = 'g%dc%d' % (g,int(c))
sl = s
if sessionTypes != None:
sl = sessionTypes[s]
if cn in spikeCounts:
spikeCounts[cn]['%s' %(s,)] = {'counts': sc, 'bins':bins}
nz[cn]['%s' %( sl,)] = 1.0*sum(sc==0)/len(sc)
else:
spikeCounts[cn] = {'%s' %(s,): {'counts':sc,'bins':bins}}
nz[cn] = {'%s' %(sl,): 1.0*sum(sc==0)/len(sc)}
finally:
dataFile.close()
i = 1
ncells = len(spikeCounts.keys())
nsessions = len(sessions)
colors = ['b','r','g','y','c','m']
for c in spikeCounts.keys():
ax = Subplot(fig,1,ncells,i)
formatAxis(ax)
fig.add_axes(ax)
ax.set_title(c)
j = 0
for k,v in spikeCounts[c].items():
#n,b = np.histogram(v['counts'],bins=20,normed=True)
#plt.plot(b[:-1],n,label=k)
if sessionTypes != None:
L = sessionTypes[k]
else:
L = k
n = np.bincount(v['counts'])
b = np.unique(v['counts'])
b = np.arange(b[0],len(n))
ax.bar(b+j*0.2,1.0*n/n.sum(),align='center',width=0.3,fc=colors[j],label=L)
j+=1
i+=1
ax.set_xlabel('Spike counts')
fig.axes[-1].legend()
if save:
if fname == None:
fname = os.path.expanduser('~/Documents/research/figures/isi_comparison.pdf')
fig.savefig(fname,bbox='tight')
return nz
def plotSpikes(qdata,save=False,fname='hmmSorting.pdf',tuning=False,figsize=(10,6)):
allSpikes = qdata['allSpikes']
unitSpikes = qdata['unitSpikes']
spikeIdx = qdata['spikeIdx']
spikeIdx = qdata['unitTimePoints']
units = qdata['unitTimePoints']
spikeForms = qdata['spikeForms']
channels = qdata['channels']
uniqueIdx = qdata['uniqueIdx']
samplingRate = qdata.get('samplingRate',30000.0)
"""
mustClose = False
if isinstance(dataFile,str):
dataFile = h5py.File(dataFile,'r')
mustClose = True
data = dataFile['data'][:]
"""
keys = np.array(units.keys())
x = np.arange(32)[None,:] + 42*np.arange(spikeForms.shape[1])[:,None]
xt = np.linspace(0,31,spikeForms.shape[-1])[None,:] + 42*np.arange(spikeForms.shape[1])[:,None]
xch = 10 + 42*np.arange(len(channels))
for c in units.keys():
ymin,ymax = (5000,-5000)
fig = plt.figure(figsize=figsize)
fig.subplots_adjust(hspace=0.3)
print "Unit: %s " %(str(c),)
print "\t Plotting waveforms..."
sys.stdout.flush()
#allspikes = data[units[c][:,None]+np.arange(-10,22)[None,:],:]
#allspikes = allSpikes[spikeIdx[c]]
allspikes = qdata['unitSpikes'][c]
otherunits = keys[keys!=c]
#nonOverlapIdx = np.prod(np.array([~np.lib.arraysetops.in1d(spikeIdx[c],spikeIdx[c1]) for c1 in otherunits]),axis=0).astype(np.bool)
#nonOverlapIdx = np.prod(np.array([pdist_threshold(spikeIdx[c],spikeIdx[c1],3) for c1 in otherunits]),axis=0).astype(np.bool)
#nonOverlapIdx = uniqueIdx[c]
nonOverlapIdx = qdata['nonOverlapIdx'][c]
overlapIdx = np.lib.arraysetops.setdiff1d(np.arange(qdata['unitTimePoints'][c].shape[0]),nonOverlapIdx)
#allspikes = allSpikes[np.lib.arraysetops.union1d(nonOverlapIdx,overlapIdx)]
ax = Subplot(fig,2,3,1)
fig.add_axes(ax)
formatAxis(ax)
#plt.plot(x.T,sp,'b')
m = allspikes[:].mean(0)
s = allspikes[:].std(0)
plt.plot(x.T,m,'k',lw=1.5)
#find the minimum point for this template
ich = spikeForms[int(c)].min(1).argmin()
ix = spikeForms[int(c)][ich,:].argmin()
#plt.plot(x.T,spikeForms[int(c)][:,ix-10:ix+22].T,'r')
plt.plot(x.T,np.roll(spikeForms[int(c)],10-ix,axis=1)[:,:32].T,'r')
for i in xrange(x.shape[0]):
plt.fill_between(x[i],m[:,i]-s[:,i],m[:,i]+s[:,i],color='b',alpha=0.5)
yl = ax.get_ylim()
ymin = min(ymin,yl[0])
ymax = max(ymax,yl[1])
ax.set_title('All spikes (%d)' % (allspikes.shape[0],))
ax = Subplot(fig,2,3,2)
fig.add_axes(ax)
formatAxis(ax)
if len(nonOverlapIdx)>0:
m = allspikes[:][nonOverlapIdx,:,:].mean(0)
s = allspikes[:][nonOverlapIdx,:,:].std(0)
plt.plot(x.T,m,'k',lw=1.5)
for i in xrange(x.shape[0]):
plt.fill_between(x[i],m[:,i]-s[:,i],m[:,i]+s[:,i],color='b',alpha=0.5)
#plt.plot(x.T,spikeForms[int(c)][:,ix-10:ix+22].T,'r')
plt.plot(x.T,np.roll(spikeForms[int(c)],10-ix,axis=1)[:,:32].T,'r')
yl = ax.get_ylim()
ymin = min(ymin,yl[0])
ymax = max(ymax,yl[1])
#for sp in allspikes[nonOverlapIdx,:,:]:
# plt.plot(x.T,sp,'r')
ax.set_title('Non-overlap spikes (%d)' %(nonOverlapIdx.shape[0],))
ax = Subplot(fig,2,3,3)
fig.add_axes(ax)
formatAxis(ax)
if len(overlapIdx)>0:
m = allspikes[:][overlapIdx,:,:].mean(0)
s = allspikes[:][overlapIdx,:,:].std(0)
plt.plot(x.T,m,'k',lw=1.5)
for i in xrange(x.shape[0]):
plt.fill_between(x[i],m[:,i]-s[:,i],m[:,i]+s[:,i],color='b',alpha=0.5)
#plt.plot(x.T,spikeForms[int(c)][:,ix-10:ix+22].T,'r')
plt.plot(x.T,np.roll(spikeForms[int(c)],10-ix,axis=1)[:,:32].T,'r')
yl = ax.get_ylim()
ymin = min(ymin,yl[0])
ymax = max(ymax,yl[1])
#for sp in allspikes[~nonOverlapIdx,:,:]:
# plt.plot(x.T,sp,'g')
ax.set_title('Overlap spikes (%d)' % ((overlapIdx).shape[0],))
for a in fig.axes:
a.set_ylim((ymin,ymax))
a.set_xticks(xch)
a.set_xticklabels(map(str,channels))
a.set_xlabel('Channels')
for a in fig.axes[1:]:
a.set_yticklabels([])
fig.axes[0].set_ylabel('Amplitude')
"""
isi distribution
"""
print "\t ISI distribution..."
sys.stdout.flush()
timepoints = qdata['unitTimePoints'][c][:]/(samplingRate/1000)
if len(timepoints)<2:
print "Too few spikes. Aborting..."
continue
isi = np.log(np.diff(timepoints))
n,b = np.histogram(isi,100)
ax = Subplot(fig,2,3,4)
fig.add_axes(ax)
formatAxis(ax)
ax.plot(b[:-1],n,'k')
yl = ax.get_ylim()
ax.vlines(0.0,0,yl[1],'r',lw=1.5)
ax.set_xlabel('ISI [ms]')
#get xticklabels
xl,xh = int(np.round((b[0]-0.5)*2))/2,int(np.round((b[-1]+0.5)*2))/2
xl = -0.5
dx = np.round(10.0*(xh-xl)/5.0)/10
xt_ = np.arange(xl,xh+1,dx)
ax.set_xticks(xt_)
ax.set_xticklabels(map(lambda s: r'$10^{%.1f}$' % (s,),xt_))
"""
auto-correlogram
"""
print "\t auto-correllogram..."
sys.stdout.flush()
if not 'autoCorr' in qdata:
if isinstance(qdata,dict):
qdata['autoCorr'] = {}
else:
qdata.create_group('autoCorr')
if not c in qdata['autoCorr']:
C = pdist_threshold2(timepoints,timepoints,50)
qdata['autoCorr'][c] = C
if not isinstance(qdata,dict):
qdata.flush()
else:
C = qdata['autoCorr'][c][:]
n,b = np.histogram(C[C!=0],np.arange(-50,50))
ax = Subplot(fig,2,3,5)
fig.add_axes(ax)
formatAxis(ax)
ax.plot(b[:-1],n,'k')
ax.fill_betweenx([0,n.max()],-1.0,1.0,color='r',alpha=0.3)
ax.set_xlabel('Lag [ms]')
if tuning:
print "\tPlotting tuning..."
sys.stdout.flush()
#attempt to get tuning for the current session, based on PWD
stimCounts,isiCounts,angles,spikedata = gt.getTuning(sptrain=timepoints)
#reshape to number of orientations X number of reps, collapsing
#across everything else
#angles = np.append(angles,[angles[0]])
C = stimCounts['0'].transpose((1,0,2,3))
C = C.reshape(C.shape[0],C.size/C.shape[0])
ax = plt.subplot(2,3,6,polar=True)
ax.errorbar(angles*np.pi/180,C.mean(1),C.std(1))
if save:
if not os.path.isabs(fname):
fn = os.path.expanduser('~/Documents/research/figures/SpikeSorting/hmm/%s' % (fname.replace('.pdf','Unit%s.pdf' %(str(c),)),))
else:
fn = fname.replace('.pdf','Unit%s.pdf' %(str(c),))
fig.savefig(fn,bbox='tight')
if not save:
plt.draw()
"""
Theta_E = (T * (1000 / p)**(k_dry)) * np.exp((L * w_s) / (c_wd * T))
return Theta_E
def theta_e_field(T, p, p_0=1000.0):
"""Produce the equiv potential temp field"""
x = theta_e(T + C_to_K, p)
return x
theta_e_mesh = theta_e_field(mesh_T, mesh_p)
skew_grid_helper = GridHelperCurveLinear((from_thermo, to_thermo))
fig = plt.figure(figsize=(12, 12))
ax = Subplot(fig, 1, 1, 1, grid_helper=skew_grid_helper)
ax.set_xlabel('Temperature (deg C)')
ax.set_ylabel('Pressure (hPa)')
fig.add_subplot(ax)
for yi in y_p_levels:
ax.plot((x_min, x_max), (yi, yi), color=(1.0, 0.8, 0.8))
for x_T in x_T_levels:
ax.plot(x_T, y_all_p, color=(1.0, 0.5, 0.5))
for x_theta in x_thetas:
ax.plot(x_theta, y_all_p, color=(1.0, 0.7, 0.7))
for x_mixing_ratio in x_mixing_ratios:
good = p_all >= 600 # restrict mixing ratio lines to below 600 mb
ax.plot(x_mixing_ratio[good], y_all_p[good], color=(0.8, 0.8, 0.6))
