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')
from mpl_toolkits.axisartist import Subplot
from mpl_toolkits.axisartist.grid_helper_curvelinear import \
GridHelperCurveLinear
def tr(x, y): # source (data) to target (rectilinear plot) coordinates
x, y = numpy.asarray(x), numpy.asarray(y)
return x + 0.2 * y, y - x
def inv_tr(x, y):
x, y = numpy.asarray(x), numpy.asarray(y)
return x - 0.2 * y, y + x
grid_helper = GridHelperCurveLinear((tr, inv_tr))
ax6 = Subplot(fig, nrow, ncol, 6, grid_helper=grid_helper)
fig.add_subplot(ax6)
ax6.set_title('non-ortho axes')
xx, yy = tr([3, 6], [5.0, 10.])
ax6.plot(xx, yy)
ax6.set_aspect(1.)
ax6.set_xlim(0, 10.)
ax6.set_ylim(0, 10.)
ax6.axis["t"] = ax6.new_floating_axis(0, 3.)
ax6.axis["t2"] = ax6.new_floating_axis(1, 7.)
ax6.grid(True)
plt.show()
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()
"""
class SliceViewerDataView(QWidget):
"""The view for the data portion of the sliceviewer"""
def __init__(self, presenter: IDataViewSubscriber, dims_info, can_normalise, parent=None, conf=None):
super().__init__(parent)
self.presenter = presenter
self.image = None
self.line_plots_active = False
self.can_normalise = can_normalise
self.nonortho_transform = None
self.conf = conf
self._line_plots = None
self._image_info_tracker = None
self._region_selection_on = False
self._orig_lims = None
# Dimension widget
self.dimensions_layout = QGridLayout()
self.dimensions = DimensionWidget(dims_info, parent=self)
self.dimensions.dimensionsChanged.connect(self.presenter.dimensions_changed)
self.dimensions.valueChanged.connect(self.presenter.slicepoint_changed)
self.dimensions_layout.addWidget(self.dimensions, 1, 0, 1, 1)
self.colorbar_layout = QVBoxLayout()
self.colorbar_layout.setContentsMargins(0, 0, 0, 0)
self.colorbar_layout.setSpacing(0)
self.image_info_widget = ImageInfoWidget(self)
self.image_info_widget.setToolTip("Information about the selected pixel")
self.track_cursor = QCheckBox("Track Cursor", self)
self.track_cursor.setToolTip(
"Update the image readout table when the cursor is over the plot. "
"If unticked the table will update only when the plot is clicked")
self.dimensions_layout.setHorizontalSpacing(10)
self.dimensions_layout.addWidget(self.track_cursor, 0, 1, Qt.AlignRight)
self.dimensions_layout.addWidget(self.image_info_widget, 1, 1)
self.track_cursor.setChecked(True)
self.track_cursor.stateChanged.connect(self.on_track_cursor_state_change)
# normalization options
if can_normalise:
self.norm_label = QLabel("Normalization")
self.colorbar_layout.addWidget(self.norm_label)
self.norm_opts = QComboBox()
self.norm_opts.addItems(["None", "By bin width"])
self.norm_opts.setToolTip("Normalization options")
self.colorbar_layout.addWidget(self.norm_opts)
# MPL figure + colorbar
self.fig = Figure()
self.ax = None
self.image = None
self._grid_on = False
self.fig.set_facecolor(self.palette().window().color().getRgbF())
self.canvas = SliceViewerCanvas(self.fig)
self.canvas.mpl_connect('button_release_event', self.mouse_release)
self.canvas.mpl_connect('button_press_event', self.presenter.canvas_clicked)
self.colorbar_label = QLabel("Colormap")
self.colorbar_layout.addWidget(self.colorbar_label)
norm_scale = self.get_default_scale_norm()
self.colorbar = ColorbarWidget(self, norm_scale)
self.colorbar.cmap.setToolTip("Colormap options")
self.colorbar.crev.setToolTip("Reverse colormap")
self.colorbar.norm.setToolTip("Colormap normalisation options")
self.colorbar.powerscale.setToolTip("Power colormap scale")
self.colorbar.cmax.setToolTip("Colormap maximum limit")
self.colorbar.cmin.setToolTip("Colormap minimum limit")
self.colorbar.autoscale.setToolTip("Automatically changes colormap limits when zooming on the plot")
self.colorbar_layout.addWidget(self.colorbar)
self.colorbar.colorbarChanged.connect(self.update_data_clim)
self.colorbar.scaleNormChanged.connect(self.scale_norm_changed)
# make width larger to fit image readout table
self.colorbar.setMaximumWidth(200)
# MPL toolbar
self.toolbar_layout = QHBoxLayout()
self.mpl_toolbar = SliceViewerNavigationToolbar(self.canvas, self, False)
self.mpl_toolbar.gridClicked.connect(self.toggle_grid)
self.mpl_toolbar.linePlotsClicked.connect(self.on_line_plots_toggle)
self.mpl_toolbar.regionSelectionClicked.connect(self.on_region_selection_toggle)
self.mpl_toolbar.homeClicked.connect(self.on_home_clicked)
self.mpl_toolbar.nonOrthogonalClicked.connect(self.on_non_orthogonal_axes_toggle)
self.mpl_toolbar.zoomPanClicked.connect(self.presenter.zoom_pan_clicked)
self.mpl_toolbar.zoomPanFinished.connect(self.on_data_limits_changed)
self.toolbar_layout.addWidget(self.mpl_toolbar)
# Status bar
self.status_bar = QStatusBar(parent=self)
self.status_bar.setStyleSheet('QStatusBar::item {border: None;}') # Hide spacers between button and label
self.status_bar_label = QLabel()
self.help_button = QToolButton()
self.help_button.setText("?")
self.status_bar.addWidget(self.help_button)
self.status_bar.addWidget(self.status_bar_label)
# layout
layout = QGridLayout(self)
layout.setSpacing(1)
layout.addLayout(self.dimensions_layout, 0, 0, 1, 2)
layout.addLayout(self.toolbar_layout, 1, 0, 1, 1)
layout.addLayout(self.colorbar_layout, 1, 1, 3, 1)
layout.addWidget(self.canvas, 2, 0, 1, 1)
layout.addWidget(self.status_bar, 3, 0, 1, 1)
layout.setRowStretch(2, 1)
@property
def grid_on(self):
return self._grid_on
@property
def line_plotter(self):
return self._line_plots
@property
def nonorthogonal_mode(self):
return self.nonortho_transform is not None
def create_axes_orthogonal(self, redraw_on_zoom=False):
"""Create a standard set of orthogonal axes
:param redraw_on_zoom: If True then when scroll zooming the canvas is redrawn immediately
"""
self.clear_figure()
self.nonortho_transform = None
self.ax = self.fig.add_subplot(111, projection='mantid')
self.enable_zoom_on_mouse_scroll(redraw_on_zoom)
if self.grid_on:
self.ax.grid(self.grid_on)
if self.line_plots_active:
self.add_line_plots()
self.plot_MDH = self.plot_MDH_orthogonal
self.canvas.draw_idle()
def create_axes_nonorthogonal(self, transform):
self.clear_figure()
self.set_nonorthogonal_transform(transform)
self.ax = CurveLinearSubPlot(self.fig,
1,
1,
1,
grid_helper=GridHelperCurveLinear(
(transform.tr, transform.inv_tr)))
# don't redraw on zoom as the data is rebinned and has to be redrawn again anyway
self.enable_zoom_on_mouse_scroll(redraw=False)
self.set_grid_on()
self.fig.add_subplot(self.ax)
self.plot_MDH = self.plot_MDH_nonorthogonal
self.canvas.draw_idle()
def enable_zoom_on_mouse_scroll(self, redraw):
"""Enable zoom on scroll the mouse wheel for the created axes
:param redraw: Pass through to redraw option in enable_zoom_on_scroll
"""
self.canvas.enable_zoom_on_scroll(self.ax,
redraw=redraw,
toolbar=self.mpl_toolbar,
callback=self.on_data_limits_changed)
def add_line_plots(self, toolcls, exporter):
"""Assuming line plots are currently disabled, enable them on the current figure
The image axes must have been created first.
:param toolcls: Use this class to handle creating the plots
:param exporter: Object defining methods to export cuts/roi
"""
if self.line_plots_active:
return
self.line_plots_active = True
self._line_plots = toolcls(LinePlots(self.ax, self.colorbar), exporter)
self.status_bar_label.setText(self._line_plots.status_message())
self.canvas.setFocus()
self.mpl_toolbar.set_action_checked(ToolItemText.LINEPLOTS, True, trigger=False)
def switch_line_plots_tool(self, toolcls, exporter):
"""Assuming line plots are currently enabled then switch the tool used to
generate the plot curves.
:param toolcls: Use this class to handle creating the plots
"""
if not self.line_plots_active:
return
# Keep the same set of line plots axes but swap the selection tool
plotter = self._line_plots.plotter
plotter.delete_line_plot_lines()
self._line_plots.disconnect()
self._line_plots = toolcls(plotter, exporter)
self.status_bar_label.setText(self._line_plots.status_message())
self.canvas.setFocus()
self.canvas.draw_idle()
def remove_line_plots(self):
"""Assuming line plots are currently enabled, remove them from the current figure
"""
if not self.line_plots_active:
return
self._line_plots.plotter.close()
self.status_bar_label.clear()
self._line_plots = None
self.line_plots_active = False
def plot_MDH_orthogonal(self, ws, **kwargs):
"""
clears the plot and creates a new one using a MDHistoWorkspace
"""
self.clear_image()
self.image = self.ax.imshow(ws,
origin='lower',
aspect='auto',
transpose=self.dimensions.transpose,
norm=self.colorbar.get_norm(),
**kwargs)
# ensure the axes data limits are updated to match the
# image. For example if the axes were zoomed and the
# swap dimensions was clicked we need to restore the
# appropriate extents to see the image in the correct place
extent = self.image.get_extent()
self.ax.set_xlim(extent[0], extent[1])
self.ax.set_ylim(extent[2], extent[3])
# Set the original data limits which get passed to the ImageInfoWidget so that
# the mouse projection to data space is correct for MDH workspaces when zoomed/changing slices
self._orig_lims = self.get_axes_limits()
self.on_track_cursor_state_change(self.track_cursor_checked())
self.draw_plot()
def plot_MDH_nonorthogonal(self, ws, **kwargs):
self.clear_image()
self.image = pcolormesh_nonorthogonal(self.ax,
ws,
self.nonortho_transform.tr,
transpose=self.dimensions.transpose,
norm=self.colorbar.get_norm(),
**kwargs)
self.on_track_cursor_state_change(self.track_cursor_checked())
# swapping dimensions in nonorthogonal mode currently resets back to the
# full data limits as the whole axes has been recreated so we don't have
# access to the original limits
# pcolormesh clears any grid that was previously visible
if self.grid_on:
self.ax.grid(self.grid_on)
self.draw_plot()
def plot_matrix(self, ws, **kwargs):
"""
clears the plot and creates a new one using a MatrixWorkspace keeping
the axes limits that have already been set
"""
# ensure view is correct if zoomed in while swapping dimensions
# compute required extent and just have resampling imshow deal with it
old_extent = None
if self.image is not None:
old_extent = self.image.get_extent()
if self.image.transpose != self.dimensions.transpose:
e1, e2, e3, e4 = old_extent
old_extent = e3, e4, e1, e2
self.clear_image()
self.image = self.ax.imshow(ws,
origin='lower',
aspect='auto',
interpolation='none',
transpose=self.dimensions.transpose,
norm=self.colorbar.get_norm(),
extent=old_extent,
**kwargs)
self.on_track_cursor_state_change(self.track_cursor_checked())
self.draw_plot()
def clear_image(self):
"""Removes any image from the axes"""
if self.image is not None:
if self.line_plots_active:
self._line_plots.plotter.delete_line_plot_lines()
self.image_info_widget.cursorAt(DBLMAX, DBLMAX, DBLMAX)
if hasattr(self.ax, "remove_artists_if"):
self.ax.remove_artists_if(lambda art: art == self.image)
else:
self.image.remove()
self.image = None
def clear_figure(self):
"""Removes everything from the figure"""
if self.line_plots_active:
self._line_plots.plotter.close()
self.line_plots_active = False
self.image = None
self.canvas.disable_zoom_on_scroll()
self.fig.clf()
self.ax = None
def draw_plot(self):
self.ax.set_title('')
self.canvas.draw()
if self.image:
self.colorbar.set_mappable(self.image)
self.colorbar.update_clim()
self.mpl_toolbar.update() # clear nav stack
if self.line_plots_active:
self._line_plots.plotter.delete_line_plot_lines()
self._line_plots.plotter.update_line_plot_labels()
def export_region(self, limits, cut):
"""
React to a region selection that should be exported
:param limits: 2-tuple of ((left, right), (bottom, top))
:param cut: A str denoting which cuts to export.
"""
self.presenter.export_region(limits, cut)
def update_plot_data(self, data):
"""
This just updates the plot data without creating a new plot. The extents
can change if the data has been rebinned.
"""
if self.nonortho_transform:
self.image.set_array(data.T.ravel())
else:
self.image.set_data(data.T)
self.colorbar.update_clim()
def track_cursor_checked(self):
return self.track_cursor.isChecked() if self.track_cursor else False
def on_track_cursor_state_change(self, state):
"""
Called to notify the current state of the track cursor box
"""
if self._image_info_tracker is not None:
self._image_info_tracker.disconnect()
if self._line_plots is not None and not self._region_selection_on:
self._line_plots.disconnect()
self._image_info_tracker = ImageInfoTracker(image=self.image,
transform=self.nonortho_transform,
do_transform=self.nonorthogonal_mode,
widget=self.image_info_widget,
cursor_transform=self._orig_lims)
if state:
self._image_info_tracker.connect()
if self._line_plots and not self._region_selection_on:
self._line_plots.connect()
else:
self._image_info_tracker.disconnect()
if self._line_plots and not self._region_selection_on:
self._line_plots.disconnect()
def on_home_clicked(self):
"""Reset the view to encompass all of the data"""
self.presenter.show_all_data_clicked()
def on_line_plots_toggle(self, state):
"""Switch state of the line plots"""
self.presenter.line_plots(state)
def on_region_selection_toggle(self, state):
"""Switch state of the region selection"""
self.presenter.region_selection(state)
self._region_selection_on = state
# If state is off and track cursor is on, make sure line plots are re-connected to move cursor
if not state and self.track_cursor_checked():
if self._line_plots:
self._line_plots.connect()
def on_non_orthogonal_axes_toggle(self, state):
"""
Switch state of the non-orthognal axes on/off
"""
self.presenter.nonorthogonal_axes(state)
def on_data_limits_changed(self):
"""
React to when the data limits have changed
"""
self.presenter.data_limits_changed()
def deactivate_and_disable_tool(self, tool_text):
"""Deactivate a tool as if the control had been pressed and disable the functionality"""
self.deactivate_tool(tool_text)
self.disable_tool_button(tool_text)
def activate_tool(self, tool_text):
"""Activate a given tool as if the control had been pressed"""
self.mpl_toolbar.set_action_checked(tool_text, True)
def deactivate_tool(self, tool_text):
"""Deactivate a given tool as if the tool button had been pressed"""
self.mpl_toolbar.set_action_checked(tool_text, False)
def enable_tool_button(self, tool_text):
"""Set a given tool button enabled so it can be interacted with"""
self.mpl_toolbar.set_action_enabled(tool_text, True)
def disable_tool_button(self, tool_text):
"""Set a given tool button disabled so it cannot be interacted with"""
self.mpl_toolbar.set_action_enabled(tool_text, False)
def get_axes_limits(self):
"""
Return the limits on the image axes transformed into the nonorthogonal frame if appropriate
"""
if self.image is None:
return None
else:
xlim, ylim = self.ax.get_xlim(), self.ax.get_ylim()
if self.nonorthogonal_mode:
inv_tr = self.nonortho_transform.inv_tr
# viewing axis y not aligned with plot axis
xmin_p, ymax_p = inv_tr(xlim[0], ylim[1])
xmax_p, ymin_p = inv_tr(xlim[1], ylim[0])
xlim, ylim = (xmin_p, xmax_p), (ymin_p, ymax_p)
return xlim, ylim
def get_full_extent(self):
"""
Return the full extent of image - only applicable for plots of matrix workspaces
"""
if self.image and isinstance(self.image, samplingimage.SamplingImage):
return self.image.get_full_extent()
else:
return None
def set_axes_limits(self, xlim, ylim):
"""
Set the view limits on the image axes to the given extents. Assume the
limits are in the orthogonal frame.
:param xlim: 2-tuple of (xmin, xmax)
:param ylim: 2-tuple of (ymin, ymax)
"""
self.ax.set_xlim(xlim)
self.ax.set_ylim(ylim)
def set_grid_on(self):
"""
If not visible sets the grid visibility
"""
if not self._grid_on:
self._grid_on = True
self.mpl_toolbar.set_action_checked(ToolItemText.GRID, state=self._grid_on)
def set_nonorthogonal_transform(self, transform):
"""
Set the transform for nonorthogonal axes mode
:param transform: An object with a tr method to transform from nonorthognal
coordinates to display coordinates
"""
self.nonortho_transform = transform
def show_temporary_status_message(self, msg, timeout_ms):
"""
Show a message in the status bar that disappears after a set period
:param msg: A str message to display
:param timeout_ms: Timeout in milliseconds to display the message for
"""
self.status_bar.showMessage(msg, timeout_ms)
def toggle_grid(self, state):
"""
Toggle the visibility of the grid on the axes
"""
self._grid_on = state
self.ax.grid(self._grid_on)
self.canvas.draw_idle()
def mouse_release(self, event):
if event.inaxes != self.ax:
return
self.canvas.setFocus()
if event.button == 1:
self._image_info_tracker.on_cursor_at(event.xdata, event.ydata)
if self.line_plots_active and not self._region_selection_on:
self._line_plots.on_cursor_at(event.xdata, event.ydata)
if event.button == 3:
self.on_home_clicked()
def deactivate_zoom_pan(self):
self.deactivate_tool(ToolItemText.PAN)
self.deactivate_tool(ToolItemText.ZOOM)
def update_data_clim(self):
self.image.set_clim(self.colorbar.colorbar.mappable.get_clim())
if self.line_plots_active:
self._line_plots.plotter.update_line_plot_limits()
self.canvas.draw_idle()
def set_normalization(self, ws, **kwargs):
normalize_by_bin_width, _ = get_normalize_by_bin_width(ws, self.ax, **kwargs)
is_normalized = normalize_by_bin_width or ws.isDistribution()
self.presenter.normalization = is_normalized
if is_normalized:
self.norm_opts.setCurrentIndex(1)
else:
self.norm_opts.setCurrentIndex(0)
def get_default_scale_norm(self):
scale = 'Linear'
if self.conf is None:
return scale
if self.conf.has(SCALENORM):
scale = self.conf.get(SCALENORM)
if scale == 'Power' and self.conf.has(POWERSCALE):
exponent = self.conf.get(POWERSCALE)
scale = (scale, exponent)
scale = "SymmetricLog10" if scale == 'Log' else scale
return scale
def scale_norm_changed(self):
if self.conf is None:
return
scale = self.colorbar.norm.currentText()
self.conf.set(SCALENORM, scale)
if scale == 'Power':
exponent = self.colorbar.powerscale_value
self.conf.set(POWERSCALE, exponent)
class SliceViewerDataView(QWidget):
"""The view for the data portion of the sliceviewer"""
def __init__(self, presenter, dims_info, can_normalise, parent=None):
super().__init__(parent)
self.presenter = presenter
self.image = None
self.line_plots = False
self.can_normalise = can_normalise
self.nonortho_tr = None
# Dimension widget
self.dimensions_layout = QHBoxLayout()
self.dimensions = DimensionWidget(dims_info, parent=self)
self.dimensions.dimensionsChanged.connect(
self.presenter.dimensions_changed)
self.dimensions.valueChanged.connect(self.presenter.slicepoint_changed)
self.dimensions_layout.addWidget(self.dimensions)
self.colorbar_layout = QVBoxLayout()
# normalization options
if can_normalise:
self.norm_layout = QHBoxLayout()
self.norm_label = QLabel("Normalization =")
self.norm_layout.addWidget(self.norm_label)
self.norm_opts = QComboBox()
self.norm_opts.addItems(["None", "By bin width"])
self.norm_opts.setToolTip("Normalization options")
self.norm_layout.addWidget(self.norm_opts)
self.colorbar_layout.addLayout(self.norm_layout)
# MPL figure + colorbar
self.mpl_layout = QHBoxLayout()
self.fig = Figure()
self.ax = None
self._grid_on = False
self.fig.set_facecolor(self.palette().window().color().getRgbF())
self.canvas = FigureCanvas(self.fig)
self.canvas.mpl_connect('motion_notify_event', self.mouse_move)
self.create_axes_orthogonal()
self.mpl_layout.addWidget(self.canvas)
self.colorbar = ColorbarWidget(self)
self.colorbar_layout.addWidget(self.colorbar)
self.colorbar.colorbarChanged.connect(self.update_data_clim)
self.colorbar.colorbarChanged.connect(self.update_line_plot_limits)
self.mpl_layout.addLayout(self.colorbar_layout)
# MPL toolbar
self.mpl_toolbar = SliceViewerNavigationToolbar(self.canvas, self)
self.mpl_toolbar.gridClicked.connect(self.toggle_grid)
self.mpl_toolbar.linePlotsClicked.connect(self.line_plots_toggle)
self.mpl_toolbar.plotOptionsChanged.connect(
self.colorbar.mappable_changed)
self.mpl_toolbar.nonOrthogonalClicked.connect(
self.non_orthogonal_axes_toggle)
# layout
self.layout = QGridLayout(self)
self.layout.addLayout(self.dimensions_layout, 0, 0)
self.layout.addWidget(self.mpl_toolbar, 1, 0)
self.layout.addLayout(self.mpl_layout, 2, 0)
@property
def grid_on(self):
return self._grid_on
@property
def nonorthogonal_mode(self):
return self.nonortho_tr is not None
def create_axes_orthogonal(self):
self.clear_figure()
self.nonortho_tr = None
self.ax = self.fig.add_subplot(111, projection='mantid')
if self.grid_on:
self.ax.grid()
if self.line_plots:
self.add_line_plots()
self.plot_MDH = self.plot_MDH_orthogonal
self.canvas.draw_idle()
def create_axes_nonorthogonal(self, transform):
self.clear_figure()
self.set_nonorthogonal_transform(transform)
self.ax = CurveLinearSubPlot(self.fig,
1,
1,
1,
grid_helper=GridHelperCurveLinear(
(self.nonortho_tr, transform.inv_tr)))
self.set_grid_on()
self.fig.add_subplot(self.ax)
self.plot_MDH = self.plot_MDH_nonorthogonal
self.canvas.draw_idle()
def add_line_plots(self):
"""Assuming line plots are currently disabled, enable them on the current figure
The image axes must have been created first.
"""
if self.line_plots:
return
image_axes = self.ax
if image_axes is None:
return
# Create a new GridSpec and reposition the existing image Axes
gs = gridspec.GridSpec(2,
2,
width_ratios=[1, 4],
height_ratios=[4, 1],
wspace=0.0,
hspace=0.0)
image_axes.set_position(gs[1].get_position(self.fig))
image_axes.xaxis.set_visible(False)
image_axes.yaxis.set_visible(False)
self.axx = self.fig.add_subplot(gs[3], sharex=image_axes)
self.axx.yaxis.tick_right()
self.axy = self.fig.add_subplot(gs[0], sharey=image_axes)
self.axy.xaxis.tick_top()
self.mpl_toolbar.update() # sync list of axes in navstack
self.canvas.draw_idle()
def remove_line_plots(self):
"""Assuming line plots are currently enabled, remove them from the current figure
"""
if not self.line_plots:
return
image_axes = self.ax
if image_axes is None:
return
self.clear_line_plots()
all_axes = self.fig.axes
# The order is defined by the order of the add_subplot calls so we always want to remove
# the last two Axes. Do it backwards to cope with the container size change
all_axes[2].remove()
all_axes[1].remove()
gs = gridspec.GridSpec(1, 1)
image_axes.set_position(gs[0].get_position(self.fig))
image_axes.xaxis.set_visible(True)
image_axes.yaxis.set_visible(True)
self.axx, self.axy = None, None
self.mpl_toolbar.update() # sync list of axes in navstack
self.canvas.draw_idle()
def plot_MDH_orthogonal(self, ws, **kwargs):
"""
clears the plot and creates a new one using a MDHistoWorkspace
"""
self.clear_image()
self.image = self.ax.imshow(ws,
origin='lower',
aspect='auto',
transpose=self.dimensions.transpose,
norm=self.colorbar.get_norm(),
**kwargs)
self.draw_plot()
def plot_MDH_nonorthogonal(self, ws, **kwargs):
self.clear_image()
self.image = pcolormesh_nonorthogonal(
self.ax,
ws,
self.nonortho_tr,
transpose=self.dimensions.transpose,
norm=self.colorbar.get_norm(),
**kwargs)
# pcolormesh clears any grid that was previously visible
if self.grid_on:
self.ax.grid()
self.draw_plot()
def plot_matrix(self, ws, **kwargs):
"""
clears the plot and creates a new one using a MatrixWorkspace
"""
self.clear_image()
self.image = imshow_sampling(self.ax,
ws,
origin='lower',
aspect='auto',
interpolation='none',
transpose=self.dimensions.transpose,
norm=self.colorbar.get_norm(),
**kwargs)
self.image._resample_image()
self.draw_plot()
def clear_image(self):
"""Removes any image from the axes"""
if self.image is not None:
self.image.remove()
self.image = None
def clear_figure(self):
"""Removes everything from the figure"""
self.image = None
self._grid_on = False
self.fig.clf()
def draw_plot(self):
self.ax.set_title('')
self.colorbar.set_mappable(self.image)
self.colorbar.update_clim()
self.mpl_toolbar.update() # clear nav stack
self.clear_line_plots()
self.canvas.draw_idle()
def update_plot_data(self, data):
"""
This just updates the plot data without creating a new plot
"""
if self.nonortho_tr:
self.image.set_array(data.T.ravel())
else:
self.image.set_data(data.T)
self.colorbar.update_clim()
def line_plots_toggle(self, state):
self.presenter.line_plots(state)
self.line_plots = state
def non_orthogonal_axes_toggle(self, state):
"""
Switch state of the non-orthognal axes on/off
"""
self.presenter.nonorthogonal_axes(state)
def enable_lineplots_button(self):
"""
Enables line plots functionality
"""
self.mpl_toolbar.set_action_enabled(ToolItemText.LINEPLOTS, True)
def disable_lineplots_button(self):
"""
Disabled line plots functionality
"""
self.mpl_toolbar.set_action_enabled(ToolItemText.LINEPLOTS, False)
def enable_peaks_button(self):
"""
Enables line plots functionality
"""
self.mpl_toolbar.set_action_enabled(ToolItemText.OVERLAYPEAKS, True)
def disable_peaks_button(self):
"""
Disables line plots functionality
"""
self.mpl_toolbar.set_action_enabled(ToolItemText.OVERLAYPEAKS, False)
def disable_nonorthogonal_axes_button(self):
"""
Disables non-orthorognal axes functionality
"""
self.mpl_toolbar.set_action_enabled(ToolItemText.NONORTHOGONAL_AXES,
False)
def clear_line_plots(self):
try: # clear old plots
del self.xfig
del self.yfig
except AttributeError:
pass
def update_data_clim(self):
self.image.set_clim(self.colorbar.colorbar.mappable.get_clim())
self.canvas.draw_idle()
def update_line_plot_limits(self):
if self.line_plots:
self.axx.set_ylim(self.colorbar.cmin_value,
self.colorbar.cmax_value)
self.axy.set_xlim(self.colorbar.cmin_value,
self.colorbar.cmax_value)
def set_grid_on(self):
"""
If not visible sets the grid visibility
"""
if not self._grid_on:
self.toggle_grid()
def set_nonorthogonal_transform(self, transform):
"""
Set the transform for nonorthogonal axes mode
:param transform: An object with a tr method to transform from nonorthognal
coordinates to display coordinates
"""
self.nonortho_tr = transform.tr
def toggle_grid(self):
"""
Toggle the visibility of the grid on the axes
"""
self.ax.grid()
self._grid_on = not self._grid_on
self.canvas.draw_idle()
def mouse_move(self, event):
if self.line_plots and event.inaxes == self.ax:
self.update_line_plots(event.xdata, event.ydata)
def plot_x_line(self, x, y):
try:
self.xfig[0].set_data(x, y)
except (AttributeError, IndexError):
self.axx.clear()
self.xfig = self.axx.plot(x, y)
self.axx.set_xlabel(self.ax.get_xlabel())
self.update_line_plot_limits()
self.canvas.draw_idle()
def plot_y_line(self, x, y):
try:
self.yfig[0].set_data(y, x)
except (AttributeError, IndexError):
self.axy.clear()
self.yfig = self.axy.plot(y, x)
self.axy.set_ylabel(self.ax.get_ylabel())
self.update_line_plot_limits()
self.canvas.draw_idle()
def update_line_plots(self, x, y):
xmin, xmax, ymin, ymax = self.image.get_extent()
arr = self.image.get_array()
data_extent = Bbox([[ymin, xmin], [ymax, xmax]])
array_extent = Bbox([[0, 0], arr.shape[:2]])
trans = BboxTransform(boxin=data_extent, boxout=array_extent)
point = trans.transform_point([y, x])
if any(np.isnan(point)):
return
i, j = point.astype(int)
if 0 <= i < arr.shape[0]:
self.plot_x_line(np.linspace(xmin, xmax, arr.shape[1]), arr[i, :])
if 0 <= j < arr.shape[1]:
self.plot_y_line(np.linspace(ymin, ymax, arr.shape[0]), arr[:, j])
def set_normalization(self, ws, **kwargs):
normalize_by_bin_width, _ = get_normalize_by_bin_width(
ws, self.ax, **kwargs)
is_normalized = normalize_by_bin_width or ws.isDistribution()
if is_normalized:
self.presenter.normalization = mantid.api.MDNormalization.VolumeNormalization
self.norm_opts.setCurrentIndex(1)
else:
self.presenter.normalization = mantid.api.MDNormalization.NoNormalization
self.norm_opts.setCurrentIndex(0)
class SliceViewerDataView(QWidget):
"""The view for the data portion of the sliceviewer"""
def __init__(self, presenter, dims_info, can_normalise, parent=None):
super().__init__(parent)
self.presenter = presenter
self.image = None
self.line_plots = False
self.can_normalise = can_normalise
self.nonortho_tr = None
self.ws_type = dims_info[0]['type']
# Dimension widget
self.dimensions_layout = QGridLayout()
self.dimensions = DimensionWidget(dims_info, parent=self)
self.dimensions.dimensionsChanged.connect(
self.presenter.dimensions_changed)
self.dimensions.valueChanged.connect(self.presenter.slicepoint_changed)
self.dimensions_layout.addWidget(self.dimensions, 1, 0, 1, 1)
self.colorbar_layout = QVBoxLayout()
self.colorbar_layout.setContentsMargins(0, 0, 0, 0)
self.colorbar_layout.setSpacing(0)
self.image_info_widget = ImageInfoWidget(self.ws_type, self)
self.track_cursor = QCheckBox("Track Cursor", self)
self.track_cursor.setToolTip(
"Update the image readout table when the cursor is over the plot. "
"If unticked the table will update only when the plot is clicked")
if self.ws_type == 'MDE':
self.colorbar_layout.addWidget(self.image_info_widget,
alignment=Qt.AlignCenter)
self.colorbar_layout.addWidget(self.track_cursor)
else:
self.dimensions_layout.setHorizontalSpacing(10)
self.dimensions_layout.addWidget(self.track_cursor, 0, 1,
Qt.AlignRight)
self.dimensions_layout.addWidget(self.image_info_widget, 1, 1)
self.track_cursor.setChecked(True)
# normalization options
if can_normalise:
self.norm_label = QLabel("Normalization")
self.colorbar_layout.addWidget(self.norm_label)
self.norm_opts = QComboBox()
self.norm_opts.addItems(["None", "By bin width"])
self.norm_opts.setToolTip("Normalization options")
self.colorbar_layout.addWidget(self.norm_opts)
# MPL figure + colorbar
self.fig = Figure()
self.ax = None
self.axx, self.axy = None, None
self.image = None
self._grid_on = False
self.fig.set_facecolor(self.palette().window().color().getRgbF())
self.canvas = SliceViewerCanvas(self.fig)
self.canvas.mpl_connect('motion_notify_event', self.mouse_move)
self.canvas.mpl_connect('axes_leave_event', self.mouse_outside_image)
self.canvas.mpl_connect('button_press_event', self.mouse_click)
self.canvas.mpl_connect('button_release_event', self.mouse_release)
self.colorbar_label = QLabel("Colormap")
self.colorbar_layout.addWidget(self.colorbar_label)
self.colorbar = ColorbarWidget(self)
self.colorbar_layout.addWidget(self.colorbar)
self.colorbar.colorbarChanged.connect(self.update_data_clim)
self.colorbar.colorbarChanged.connect(self.update_line_plot_limits)
# make width larger to fit image readout table
if self.ws_type == 'MDE':
self.colorbar.setMaximumWidth(155)
# MPL toolbar
self.toolbar_layout = QHBoxLayout()
self.mpl_toolbar = SliceViewerNavigationToolbar(
self.canvas, self, False)
self.mpl_toolbar.gridClicked.connect(self.toggle_grid)
self.mpl_toolbar.linePlotsClicked.connect(self.on_line_plots_toggle)
self.mpl_toolbar.homeClicked.connect(self.on_home_clicked)
self.mpl_toolbar.plotOptionsChanged.connect(
self.colorbar.mappable_changed)
self.mpl_toolbar.nonOrthogonalClicked.connect(
self.on_non_orthogonal_axes_toggle)
self.mpl_toolbar.zoomPanFinished.connect(self.on_data_limits_changed)
self.toolbar_layout.addWidget(self.mpl_toolbar)
# layout
layout = QGridLayout(self)
layout.setSpacing(1)
layout.addLayout(self.dimensions_layout, 0, 0, 1, 2)
layout.addLayout(self.toolbar_layout, 1, 0, 1, 2)
layout.addWidget(self.canvas, 2, 0, 1, 1)
layout.addLayout(self.colorbar_layout, 1, 1, 2, 1)
layout.setRowStretch(2, 1)
@property
def grid_on(self):
return self._grid_on
@property
def nonorthogonal_mode(self):
return self.nonortho_tr is not None
def create_axes_orthogonal(self, redraw_on_zoom=False):
"""Create a standard set of orthogonal axes
:param redraw_on_zoom: If True then when scroll zooming the canvas is redrawn immediately
"""
self.clear_figure()
self.nonortho_tr = None
self.ax = self.fig.add_subplot(111, projection='mantid')
self.enable_zoom_on_mouse_scroll(redraw_on_zoom)
if self.grid_on:
self.ax.grid(self.grid_on)
if self.line_plots:
self.add_line_plots()
self.plot_MDH = self.plot_MDH_orthogonal
self.canvas.draw_idle()
def create_axes_nonorthogonal(self, transform):
self.clear_figure()
self.set_nonorthogonal_transform(transform)
self.ax = CurveLinearSubPlot(self.fig,
1,
1,
1,
grid_helper=GridHelperCurveLinear(
(self.nonortho_tr, transform.inv_tr)))
# don't redraw on zoom as the data is rebinned and has to be redrawn again anyway
self.enable_zoom_on_mouse_scroll(redraw=False)
self.set_grid_on()
self.fig.add_subplot(self.ax)
self.plot_MDH = self.plot_MDH_nonorthogonal
self.canvas.draw_idle()
def enable_zoom_on_mouse_scroll(self, redraw):
"""Enable zoom on scroll the mouse wheel for the created axes
:param redraw: Pass through to redraw option in enable_zoom_on_scroll
"""
self.canvas.enable_zoom_on_scroll(self.ax,
redraw=redraw,
toolbar=self.mpl_toolbar,
callback=self.on_data_limits_changed)
def add_line_plots(self):
"""Assuming line plots are currently disabled, enable them on the current figure
The image axes must have been created first.
"""
if self.line_plots:
return
self.line_plots = True
image_axes = self.ax
if image_axes is None:
return
# Create a new GridSpec and reposition the existing image Axes
gs = gridspec.GridSpec(2,
2,
width_ratios=[1, 4],
height_ratios=[4, 1],
wspace=0.0,
hspace=0.0)
image_axes.set_position(gs[1].get_position(self.fig))
set_artist_property(image_axes.get_xticklabels(), visible=False)
set_artist_property(image_axes.get_yticklabels(), visible=False)
self.axx = self.fig.add_subplot(gs[3], sharex=image_axes)
self.axx.yaxis.tick_right()
self.axy = self.fig.add_subplot(gs[0], sharey=image_axes)
self.axy.xaxis.tick_top()
self.update_line_plot_labels()
self.mpl_toolbar.update() # sync list of axes in navstack
self.canvas.draw_idle()
def remove_line_plots(self):
"""Assuming line plots are currently enabled, remove them from the current figure
"""
if not self.line_plots:
return
self.line_plots = False
image_axes = self.ax
if image_axes is None:
return
self.delete_line_plot_lines()
all_axes = self.fig.axes
# The order is defined by the order of the add_subplot calls so we always want to remove
# the last two Axes. Do it backwards to cope with the container size change
all_axes[2].remove()
all_axes[1].remove()
gs = gridspec.GridSpec(1, 1)
image_axes.set_position(gs[0].get_position(self.fig))
image_axes.xaxis.tick_bottom()
image_axes.yaxis.tick_left()
self.axx, self.axy = None, None
self.mpl_toolbar.update() # sync list of axes in navstack
self.canvas.draw_idle()
def plot_MDH_orthogonal(self, ws, **kwargs):
"""
clears the plot and creates a new one using a MDHistoWorkspace
"""
self.clear_image()
self.image = self.ax.imshow(ws,
origin='lower',
aspect='auto',
transpose=self.dimensions.transpose,
norm=self.colorbar.get_norm(),
**kwargs)
# ensure the axes data limits are updated to match the
# image. For example if the axes were zoomed and the
# swap dimensions was clicked we need to restore the
# appropriate extents to see the image in the correct place
extent = self.image.get_extent()
self.ax.set_xlim(extent[0], extent[1])
self.ax.set_ylim(extent[2], extent[3])
self.draw_plot()
def plot_MDH_nonorthogonal(self, ws, **kwargs):
self.clear_image()
self.image = pcolormesh_nonorthogonal(
self.ax,
ws,
self.nonortho_tr,
transpose=self.dimensions.transpose,
norm=self.colorbar.get_norm(),
**kwargs)
# swapping dimensions in nonorthogonal mode currently resets back to the
# full data limits as the whole axes has been recreated so we don't have
# access to the original limits
# pcolormesh clears any grid that was previously visible
if self.grid_on:
self.ax.grid(self.grid_on)
self.draw_plot()
def plot_matrix(self, ws, **kwargs):
"""
clears the plot and creates a new one using a MatrixWorkspace keeping
the axes limits that have already been set
"""
# ensure view is correct if zoomed in while swapping dimensions
# compute required extent and just have resampling imshow deal with it
old_extent = None
if self.image is not None:
old_extent = self.image.get_extent()
if self.image.transpose != self.dimensions.transpose:
e1, e2, e3, e4 = old_extent
old_extent = e3, e4, e1, e2
self.clear_image()
self.image = imshow_sampling(self.ax,
ws,
origin='lower',
aspect='auto',
interpolation='none',
transpose=self.dimensions.transpose,
norm=self.colorbar.get_norm(),
extent=old_extent,
**kwargs)
self.draw_plot()
def clear_image(self):
"""Removes any image from the axes"""
if self.image is not None:
if self.line_plots:
self.delete_line_plot_lines()
self.image_info_widget.updateTable(DBLMAX, DBLMAX, DBLMAX)
self.image.remove()
self.image = None
def clear_figure(self):
"""Removes everything from the figure"""
if self.line_plots:
self.delete_line_plot_lines()
self.axx, self.axy = None, None
self.image = None
self.canvas.disable_zoom_on_scroll()
self.fig.clf()
self.ax = None
def draw_plot(self):
self.ax.set_title('')
self.colorbar.set_mappable(self.image)
self.colorbar.update_clim()
self.mpl_toolbar.update() # clear nav stack
self.delete_line_plot_lines()
self.update_line_plot_labels()
self.canvas.draw_idle()
def select_zoom(self):
"""Select the zoom control on the toolbar"""
self.mpl_toolbar.zoom()
def update_plot_data(self, data):
"""
This just updates the plot data without creating a new plot. The extents
can change if the data has been rebinned
"""
if self.nonortho_tr:
self.image.set_array(data.T.ravel())
else:
self.image.set_data(data.T)
self.colorbar.update_clim()
def on_home_clicked(self):
"""Reset the view to encompass all of the data"""
self.presenter.show_all_data_requested()
def on_line_plots_toggle(self, state):
self.presenter.line_plots(state)
def on_non_orthogonal_axes_toggle(self, state):
"""
Switch state of the non-orthognal axes on/off
"""
self.presenter.nonorthogonal_axes(state)
def on_data_limits_changed(self):
"""
React to when the data limits have changed
"""
self.presenter.data_limits_changed()
def enable_lineplots_button(self):
"""
Enables line plots functionality
"""
self.mpl_toolbar.set_action_enabled(ToolItemText.LINEPLOTS, True)
def disable_lineplots_button(self):
"""
Disabled line plots functionality
"""
self.mpl_toolbar.set_action_enabled(ToolItemText.LINEPLOTS, False)
def enable_peaks_button(self):
"""
Enables line plots functionality
"""
self.mpl_toolbar.set_action_enabled(ToolItemText.OVERLAYPEAKS, True)
def disable_peaks_button(self):
"""
Disables line plots functionality
"""
self.mpl_toolbar.set_action_enabled(ToolItemText.OVERLAYPEAKS, False)
def enable_nonorthogonal_axes_button(self):
"""
Enables access to non-orthogonal axes functionality
"""
self.mpl_toolbar.set_action_enabled(ToolItemText.NONORTHOGONAL_AXES,
True)
def disable_nonorthogonal_axes_button(self):
"""
Disables non-orthorognal axes functionality
"""
self.mpl_toolbar.set_action_enabled(ToolItemText.NONORTHOGONAL_AXES,
state=False)
def delete_line_plot_lines(self):
try: # clear old plots
try:
self.xfig.remove()
self.yfig.remove()
except ValueError:
pass
del self.xfig
del self.yfig
except AttributeError:
pass
def get_axes_limits(self):
"""
Return the limits of the image axes or None if no image yet exists
"""
if self.image is None:
return None
else:
return self.ax.get_xlim(), self.ax.get_ylim()
def set_axes_limits(self, xlim, ylim):
"""
Set the view limits on the image axes to the given extents
:param xlim: 2-tuple of (xmin, xmax)
:param ylim: 2-tuple of (ymin, ymax)
"""
self.ax.set_xlim(xlim)
self.ax.set_ylim(ylim)
def set_grid_on(self):
"""
If not visible sets the grid visibility
"""
if not self._grid_on:
self._grid_on = True
self.mpl_toolbar.set_action_checked(ToolItemText.GRID,
state=self._grid_on)
def set_nonorthogonal_transform(self, transform):
"""
Set the transform for nonorthogonal axes mode
:param transform: An object with a tr method to transform from nonorthognal
coordinates to display coordinates
"""
self.nonortho_tr = transform.tr
def toggle_grid(self, state):
"""
Toggle the visibility of the grid on the axes
"""
self._grid_on = state
self.ax.grid(self._grid_on)
self.canvas.draw_idle()
def mouse_move(self, event):
if event.inaxes == self.ax:
signal = self.update_image_data(event.xdata, event.ydata,
self.line_plots)
if self.track_cursor.checkState() == Qt.Checked:
self.update_image_table_widget(event.xdata, event.ydata,
signal)
def mouse_outside_image(self, _):
"""
Indicates that the mouse have moved outside of an axes.
We clear the line plots so that it is not confusing what they mean.
"""
if self.line_plots:
self.delete_line_plot_lines()
self.canvas.draw_idle()
def mouse_click(self, event):
if self.track_cursor.checkState() == Qt.Unchecked \
and event.inaxes == self.ax and event.button == 1:
signal = self.update_image_data(event.xdata, event.ydata)
self.update_image_table_widget(event.xdata, event.ydata, signal)
def mouse_release(self, event):
if event.button == 3 and event.inaxes == self.ax:
self.on_home_clicked()
def update_image_table_widget(self, xdata, ydata, signal):
if signal is not None:
if self.dimensions.transpose and self.ws_type == "MATRIX":
self.image_info_widget.updateTable(ydata, xdata, signal)
else:
self.image_info_widget.updateTable(xdata, ydata, signal)
def plot_x_line(self, x, y):
try:
self.xfig.set_data(x, y)
except (AttributeError, IndexError):
self.axx.clear()
self.xfig = self.axx.plot(x, y, scalex=False)[0]
self.update_line_plot_labels()
self.update_line_plot_limits()
self.canvas.draw_idle()
def plot_y_line(self, x, y):
try:
self.yfig.set_data(y, x)
except (AttributeError, IndexError):
self.axy.clear()
self.yfig = self.axy.plot(y, x, scaley=False)[0]
self.update_line_plot_labels()
self.update_line_plot_limits()
self.canvas.draw_idle()
def update_data_clim(self):
self.image.set_clim(self.colorbar.colorbar.mappable.get_clim())
self.canvas.draw_idle()
def update_line_plot_limits(self):
try: # set line plot intensity axes to match colorbar limits
self.axx.set_ylim(self.colorbar.cmin_value,
self.colorbar.cmax_value)
self.axy.set_xlim(self.colorbar.cmin_value,
self.colorbar.cmax_value)
except AttributeError:
pass
def update_line_plot_labels(self):
try: # ensure plot labels are in sync with main axes
self.axx.set_xlabel(self.ax.get_xlabel())
self.axy.set_ylabel(self.ax.get_ylabel())
except AttributeError:
pass
def update_image_data(self, x, y, update_line_plot=False):
xmin, xmax, ymin, ymax = self.image.get_extent()
arr = self.image.get_array()
data_extent = Bbox([[ymin, xmin], [ymax, xmax]])
array_extent = Bbox([[0, 0], arr.shape[:2]])
trans = BboxTransform(boxin=data_extent, boxout=array_extent)
point = trans.transform_point([y, x])
if any(np.isnan(point)):
return
i, j = point.astype(int)
if update_line_plot:
if 0 <= i < arr.shape[0]:
self.plot_x_line(np.linspace(xmin, xmax, arr.shape[1]),
arr[i, :])
if 0 <= j < arr.shape[1]:
self.plot_y_line(np.linspace(ymin, ymax, arr.shape[0]), arr[:,
j])
# Clip the coordinates at array bounds
if not (0 <= i < arr.shape[0]) or not (0 <= j < arr.shape[1]):
return None
else:
return arr[i, j]
def set_normalization(self, ws, **kwargs):
normalize_by_bin_width, _ = get_normalize_by_bin_width(
ws, self.ax, **kwargs)
is_normalized = normalize_by_bin_width or ws.isDistribution()
if is_normalized:
self.presenter.normalization = mantid.api.MDNormalization.VolumeNormalization
self.norm_opts.setCurrentIndex(1)
else:
self.presenter.normalization = mantid.api.MDNormalization.NoNormalization
self.norm_opts.setCurrentIndex(0)
def plot_univariate_inequality(xdata,
inclusive=False,
raycolor='blue',
bgcolor='white',
xlim=None,
figsize=(5, 0.5),
figure=None,
title=None,
**kwargs):
"""Plot a chart of a univariate inequality ray with matplotlib
Args:
xdata (list, tuple): endpoints of the ray: ``[start, ..., end]``
Kwargs:
inclusive (bool): if True, draw a filled circle; if False, draw a circle without fill
raycolor (str): matplotlib color of the line and markers
bgcolor (str): matplotlib color for the background and circle without fill
xlim (None, True, or list/tuple): if True, calculate defaults for xmin and xmax of the x-axis
figsize (tuple): matplotlib figsize
figure (None or matplotlib.figure.Figure): Figure to add a plot to
title (None or str): Title to add the the plot
kwargs: all other kwargs will be passed to `plt.figure()`
Returns:
matplotlib.figure.Figure: inequality figure
"""
_xdata = sorted(xdata)
xstart = _xdata[0]
xend = _xdata[-1]
lefttoright = xstart <= xend
lefttoright2 = xdata[0] <= xdata[-1]
fig1 = figure or plt.figure(figsize=figsize, facecolor=bgcolor, **kwargs)
ax1 = Subplot(fig1, 111)
fig1.add_subplot(ax1)
style = {}
style['linewidth'] = 4
style['linestyle'] = 'solid'
style['color'] = raycolor
style['marker'] = 'o'
style['markersize'] = 12
style['markevery'] = [0] if lefttoright else [-1]
style['markerfacecolor'] = raycolor if inclusive else bgcolor
style['markeredgecolor'] = raycolor
style['markeredgewidth'] = 4
arrowstyle = {}
arrowstyle['marker'] = '>' if lefttoright2 else '<'
arrowstyle['markersize'] = 12
arrowstyle['markerfacecolor'] = raycolor
arrowstyle['markeredgecolor'] = raycolor
arrowy = xdata[-1] if lefttoright else xdata[0]
ax1.set(ylim=(-0.5, 1))
if xlim is True:
xlim = (float(xstart - 1), float(xend + 0.5))
if xlim:
ax1.set(xlim=xlim)
ax1.axis["left"].set_visible(False)
ax1.axis["right"].set_visible(False)
ax1.axis["top"].set_visible(False)
#ax1.axis["bottom"].set_axisline_style(axisline_style="->", size=2)
ax1.plot(1, -0.5, ">k", transform=ax1.get_yaxis_transform(), clip_on=False)
ax1.plot(0, -0.5, "<k", transform=ax1.get_yaxis_transform(), clip_on=False)
_x = [xval for xval in xdata]
_y = [0 for xval in xdata]
plt.plot(_x, _y, **style)
if title:
ax1.set_title(title)
plt.plot(arrowy, 0, **arrowstyle)
return fig1