def __init__(self, wxparent=None, window=1, _larch=None, size=None, **kws):
PlotFrame.__init__(self,
parent=None,
size=size,
output_title='plot2d',
exit_callback=self.onExit,
**kws)
self.Show()
self.Raise()
self.panel.cursor_callback = self.onCursor
self.panel.cursor_mode = 'zoom'
self.window = int(window)
self._larch = _larch
self._xylims = {}
self.cursor_hist = []
self.symname = '%s.plot%i' % (MODNAME, self.window)
symtable = ensuremod(self._larch, MODNAME)
self.panel.canvas.figure.set_facecolor('#FDFDFB')
if symtable is not None:
symtable.set_symbol(self.symname, self)
if not hasattr(symtable, '%s.cursor_maxhistory' % MODNAME):
symtable.set_symbol('%s.cursor_maxhistory' % MODNAME,
MAX_CURSHIST)
if window not in PLOT_DISPLAYS:
PLOT_DISPLAYS[window] = self
def OnClick(self, event):
p = self.dos_panel.GetParams()
if p.step == 1234:
awx.tetris_game()
try:
edos = self.bands.get_dos(step=p.step, width=p.width)
except:
awx.showErrorMessage(self)
return
tot_dos, tot_idos = edos.dos_idos()
label = "$\sigma = %s, step = %s$" % (p.width, p.step)
plotframe = None
if self.replot_checkbox.GetValue() and len(self._pframes):
plotframe = self._pframes[-1]
if plotframe is None:
plotframe = PlotFrame(parent=self)
plotframe.plot(tot_dos.mesh, tot_dos.values, label=label, draw_legend=True)
plotframe.Show()
self._pframes.append(plotframe)
else:
plotframe.oplot(tot_dos.mesh, tot_dos.values, label=label, draw_legend=True)
def onProject(self, event=None, mode='y'):
wid = event.GetId()
if mode=='x':
x = self.tomo_frame[0].panel.ydata
y = self.tomo_frame[0].panel.conf.data.sum(axis=1)
x = self.tomo_frame[1].panel.ydata
y = self.tomo_frame[1].panel.conf.data.sum(axis=1)
axname = 'horizontal'
if x is None:
x = np.arange(y.shape[0])
else:
x = self.tomo_frame[0].panel.xdata
y = self.tomo_frame[0].panel.conf.data.sum(axis=0)
x = self.tomo_frame[1].panel.xdata
y = self.tomo_frame[1].panel.conf.data.sum(axis=0)
if x is None:
x = np.arange(y.shape[0])
axname = 'vertical'
title = '%s: sum along %s axis' % (self.GetTitle(), axname)
pf = PlotFrame(title=title, parent=self, size=(500, 250))
colors = RGB_COLORS
if len(y.shape) == 2 and y.shape[1] == 3:
pf.plot(x, y[:,0], color=colors[0])
pf.oplot(x, y[:,1], color=colors[1])
pf.oplot(x, y[:,2], color=colors[2])
else:
pf.plot(x, y)
pf.Raise()
pf.Show()
def raise_plotframe(self):
if self.plotframe is not None:
try:
self.plotframe.Show()
except:
self.plotframe = None
if self.plotframe is None:
self.plotframe = PlotFrame(None, size=(650, 400))
self.plotframe.Show()
def onStartProjections(self, event=None):
try:
self.xplot.Raise()
except:
self.xplot = PlotFrame(parent=self)
try:
self.yplot.Raise()
except:
self.yplot = PlotFrame(parent=self)
self.proj_start = True
self.proj_timer = wx.Timer(self)
self.Bind(wx.EVT_TIMER, self.onShowProjections, self.proj_timer)
self.proj_timer.Start(500)
def onStartProjections(self, event=None):
try:
self.xplot.Raise()
except:
self.xplot = PlotFrame(parent=self)
try:
self.yplot.Raise()
except:
self.yplot = PlotFrame(parent=self)
self.proj_start = True
self.proj_timer = wx.Timer(self)
self.Bind(wx.EVT_TIMER, self.onShowProjections, self.proj_timer)
self.proj_timer.Start(500)
def OnCompare(self, event):
"""
Callback triggered by the `compare` option in the popup menu of the panels
Plote the netcdf variable/dimension as function of the file index.
"""
# Get the name of the variable.
name, obj = event.name, event.obj
# Define the function to use the get the value of the dimension/variable.
if isinstance(obj, netCDF4.Variable):
def extract(dataset, name):
return dataset.variables[name][:]
elif isinstance(obj, netCDF4.Dimension):
def extract(dataset, name):
return np.array(len(dataset.dimensions[name]))
else:
raise ValueError("Don't know how to handle %s" % repr(obj))
# Extract data. Make sure all the shapes are equal.
data, shape = [], None
for dataset in self.datasets:
v = extract(dataset, name)
data.append(v)
if shape is None:
shape = v.shape
else:
assert shape == v.shape
# Plot data. Two Branches for scalars and arrays.
opts = self.GetPlotOptions()
is_scalar = not shape or (len(shape) == 1 and shape[0] == 1)
#print(shape)
from wxmplot import PlotFrame
if is_scalar:
frame = PlotFrame(parent=self)
xx = range(len(self.datasets))
if opts.plot_mode == "line":
frame.plot(xx, data)
else:
frame.scatterplot(xx, data)
frame.set_xlabel("File index")
frame.set_ylabel(name)
frame.Show()
else:
# Open new frame to allow the user to specify how to handle the array.
ArrayComparisonFrame(self, name, data).Show()
def show_PlotFrame(self, do_raise=True, clear=True):
"make sure plot frame is enabled, and visible"
if self.plotframe is None:
self.plotframe = PlotFrame(self, title='XRF Spectra')
try:
self.plotframe.Show()
except wx.PyDeadObjectError:
self.plotframe = PlotFrame(self, title='XRF Spectra')
self.plotframe.Show()
if do_raise:
self.plotframe.Raise()
if clear:
self.plotframe.panel.clear()
self.plotframe.reset_config()
def __init__(self, wxparent=None, window=1, _larch=None, **kws):
PlotFrame.__init__(self, parent=wxparent,
exit_callback=self.onExit, **kws)
self.Show()
self.Raise()
self.cursor_pos = None
self.panel.cursor_callback = self.onCursor
self.window = int(window)
self._larch = _larch
self.symname = '%s.plot%i' % (MODNAME, self.window)
symtable = ensuremod(self._larch)
if symtable is not None:
symtable.set_symbol(self.symname, self)
if window not in PLOT_DISPLAYS:
PLOT_DISPLAYS[window] = self
def OnClick(self, event):
method = self.method_choice.GetStringSelection()
try:
from wxmplot import PlotFrame
except ImportError:
#warnings.warn("Error while importing wxmplot. Some features won't be available")
raise
plotframe = None
if self.replot_checkbox.GetValue() and len(self._pframes):
plotframe = self._pframes[-1]
try:
if method == "None":
g = self.func1d
else:
g = getattr(self.func1d, method)()
if plotframe is None:
plotframe = PlotFrame(self)
self._pframes.append(plotframe)
plotframe.plot(g.mesh, g.values, label=method, draw_legend=True)
plotframe.Show()
else:
plotframe.oplot(g.mesh, g.values, label=method, draw_legend=True)
except:
showErrorMessage(self)
def OnClick(self, event):
method = self.method_choice.GetStringSelection()
plotframe = None
if self.replot_checkbox.GetValue() and len(self._pframes):
plotframe = self._pframes[-1]
try:
if method == "None":
g = self.func1d
else:
g = getattr(self.func1d, method)()
if plotframe is None:
plotframe = PlotFrame(self)
self._pframes.append(plotframe)
plotframe.plot(g.mesh,
g.values,
label=method,
draw_legend=True)
plotframe.Show()
else:
plotframe.oplot(g.mesh,
g.values,
label=method,
draw_legend=True)
except:
showErrorMessage(self)
def OnClick(self, event):
p = self.dos_panel.GetParams()
if p.step == 1234:
awx.tetris_game()
try:
edos = self.bands.get_edos(step=p.step, width=p.width)
except:
awx.showErrorMessage(self)
return
tot_dos, tot_idos = edos.dos_idos()
label = "$\sigma = %s, step = %s$" % (p.width, p.step)
plotframe = None
if self.replot_checkbox.GetValue() and len(self._pframes):
plotframe = self._pframes[-1]
if plotframe is None:
plotframe = PlotFrame(parent=self)
plotframe.plot(tot_dos.mesh,
tot_dos.values,
label=label,
draw_legend=True)
plotframe.Show()
self._pframes.append(plotframe)
else:
plotframe.oplot(tot_dos.mesh,
tot_dos.values,
label=label,
draw_legend=True)
def __init__(self, wxparent=None, window=1, _larch=None, **kws):
PlotFrame.__init__(self,
parent=wxparent,
exit_callback=self.onExit,
**kws)
self.Show()
self.Raise()
self.cursor_pos = None
self.panel.cursor_callback = self.onCursor
self.window = int(window)
self._larch = _larch
self.symname = '%s.plot%i' % (MODNAME, self.window)
symtable = ensuremod(self._larch)
if symtable is not None:
symtable.set_symbol(self.symname, self)
if window not in PLOT_DISPLAYS:
PLOT_DISPLAYS[window] = self
def __init__(self, wxparent=None, window=1, _larch=None, size=None, **kws):
PlotFrame.__init__(self, parent=None, size=size,
output_title='plot2d',
exit_callback=self.onExit, **kws)
self.Show()
self.Raise()
self.panel.cursor_callback = self.onCursor
self.panel.cursor_mode = 'zoom'
self.window = int(window)
self._larch = _larch
self._xylims = {}
self.symname = '%s.plot%i' % (MODNAME, self.window)
symtable = ensuremod(self._larch, MODNAME)
if symtable is not None:
symtable.set_symbol(self.symname, self)
if window not in PLOT_DISPLAYS:
PLOT_DISPLAYS[window] = self
def __init__(self, wxparent=None, window=1, _larch=None, size=None, **kws):
PlotFrame.__init__(self,
parent=None,
size=size,
output_title='plot2d',
exit_callback=self.onExit,
**kws)
self.Show()
self.Raise()
self.panel.cursor_callback = self.onCursor
self.panel.cursor_mode = 'zoom'
self.window = int(window)
self._larch = _larch
self._xylims = {}
self.symname = '%s.plot%i' % (MODNAME, self.window)
symtable = ensuremod(self._larch, MODNAME)
if symtable is not None:
symtable.set_symbol(self.symname, self)
if window not in PLOT_DISPLAYS:
PLOT_DISPLAYS[window] = self
def get_plotwindow(self, new=False, **kws):
pframe = None
if not new:
while pframe is None:
try:
pframe = self.plotters.pop()
pframe.Show()
pframe.Raise()
except IndexError:
pframe = None
break
except PyDeadObjectError:
pframe = None
if pframe is None:
pframe = PlotFrame()
pframe.Show()
pframe.Raise()
self.plotters.append(pframe)
return pframe
def OnClick(self, event):
method = self.method_choice.GetStringSelection()
plotframe = None
if self.replot_checkbox.GetValue() and len(self._pframes):
plotframe = self._pframes[-1]
try:
if method == "None":
g = self.func1d
else:
g = getattr(self.func1d, method)()
if plotframe is None:
plotframe = PlotFrame(self)
self._pframes.append(plotframe)
plotframe.plot(g.mesh, g.values, label=method, draw_legend=True)
plotframe.Show()
else:
plotframe.oplot(g.mesh, g.values, label=method, draw_legend=True)
except:
showErrorMessage(self)
def __init__(self, wxparent=None, window=1, _larch=None, size=None, **kws):
PlotFrame.__init__(self, parent=None, size=size,
output_title='plot2d',
exit_callback=self.onExit, **kws)
self.Show()
self.Raise()
self.panel.cursor_callback = self.onCursor
self.panel.cursor_mode = 'zoom'
self.window = int(window)
self._larch = _larch
self._xylims = {}
self.cursor_hist = []
self.symname = '%s.plot%i' % (_larch_name, self.window)
symtable = ensuremod(self._larch, _larch_name)
self.panel.canvas.figure.set_facecolor('#FDFDFB')
if symtable is not None:
symtable.set_symbol(self.symname, self)
if not hasattr(symtable, '%s.cursor_maxhistory' % _larch_name):
symtable.set_symbol('%s.cursor_maxhistory' % _larch_name, MAX_CURSHIST)
if window not in PLOT_DISPLAYS:
PLOT_DISPLAYS[window] = self
def onPlotData(self, event):
operators = self.panel.GetSelectedOperators()
from wxmplot import PlotFrame
frame = PlotFrame(parent=self)
xx = range(len(self.data))
for oname, op in operators.items():
#print(oname)
values = [op(arr) for arr in self.data]
frame.oplot(xx, values, label=oname)
#if opts.plot_mode == "line":
# frame.oplot(xx, values)
#else:
# frame.scatterplot(xx, values)
frame.set_xlabel("File index")
frame.set_ylabel(self.name)
frame.Show()
def onPlotData(self, event):
operators = self.panel.GetSelectedOperators()
frame = PlotFrame(parent=self)
xx = range(len(self.data))
for oname, op in operators.items():
#print(oname)
values = [op(arr) for arr in self.data]
frame.oplot(xx, values, label=oname)
#if opts.plot_mode == "line":
# frame.oplot(xx, values)
#else:
# frame.scatterplot(xx, values)
frame.set_xlabel("File index")
frame.set_ylabel(self.name)
frame.Show()
def plot_variable(self, var_name, var, dataset):
"""
Use `wxmplot` to plot the selected variables.
Args:
var_name:
Name of the variable
var:
Netcdf4 `Variable`.
dataset:
Netcdf4 `Dataset`.
"""
# Remove fake dimensions.
shape, dimensions = [], []
for num, name in zip(var.shape, var.dimensions):
if num > 1:
shape.append(num)
dimensions.append(name)
# Get data to plot.
data = np.reshape(var[:], shape)
opts = self.GetPlotOptions()
cplx_mode = opts.cplx_mode
if cplx_mode != "None":
if shape[-1] != 2:
err_msg = "cplx_mode: %s. Expecting 2 as last dimensions but got %d" % (
cplx_mode, shape[-1])
raise ValueError(err_msg)
# Convert to complex then change shape and dimensions
data = data[..., 0] + 1j*data[..., 1]
shape = shape[:-1]
dimensions = dimensions[:-1]
if cplx_mode == "Abs":
data = np.abs(data)
elif cplx_mode == "Real":
data = data.real
elif cplx_mode == "Imag":
data = data.imag
else:
raise ValueError("Wrong value for cplx_mode %s" % cplx_mode)
# Plotting a scalar?
if not shape: return
ndim = len(shape)
if ndim == 1:
# Vector
dim_name = dimensions[0]
xx = range(len(dataset.dimensions[dim_name]))
frame = PlotFrame(parent=self)
if opts.plot_mode == "line":
frame.plot(xx, data)
else:
frame.scatterplot(xx, data)
frame.set_xlabel(dim_name)
frame.set_ylabel(var_name)
frame.Show()
elif ndim == 2:
# Two dimensional array.
dim_namex, dim_namey = dimensions
xx, yy = range(len(dataset.dimensions[dim_namex])), range(len(dataset.dimensions[dim_namey]))
mode = opts.image_mode
if False:
# 3d plot
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
fig = plt.figure()
ax = Axes3D(fig)
X, Y = np.meshgrid(xx, yy, sparse=False, indexing='ij')
print(X.shape, Y.shape, data.shape)
ax.plot_surface(X, Y, data) # rstride=8, cstride=8, alpha=0.3)
plt.show()
frame = ImageFrame(parent=self)
frame.display(data, title=var_name, style=mode, x=xx, y=yy, xlabel=dim_namex, ylabel=dim_namey)
frame.Show()
else:
raise NotImplementedError()
class MapImageFrame(ImageFrame):
"""
MatPlotlib Image Display on a wx.Frame, using ImagePanel
"""
def __init__(self, parent=None, size=None, mode='intensity',
lasso_callback=None, move_callback=None, save_callback=None,
show_xsections=False, cursor_labels=None,
output_title='Image', **kws):
# instdb=None, inst_name=None,
self.det = None
self.xrmfile = None
self.map = None
self.move_callback = move_callback
self.save_callback = save_callback
ImageFrame.__init__(self, parent=parent, size=size,
lasso_callback=lasso_callback,
cursor_labels=cursor_labels, mode=mode,
output_title=output_title, **kws)
self.panel.add_cursor_mode('prof', motion = self.prof_motion,
leftdown = self.prof_leftdown,
leftup = self.prof_leftup)
self.panel.report_leftdown = self.report_leftdown
self.panel.report_motion = self.report_motion
self.prof_plotter = None
self.zoom_ini = None
self.lastpoint = [None, None]
self.this_point = None
self.rbbox = None
def display(self, map, det=None, xrmfile=None, xoff=0, yoff=0, **kws):
self.xoff = xoff
self.yoff = yoff
self.det = det
self.xrmfile = xrmfile
self.map = map
self.title = ''
if 'title' in kws:
self.title = kws['title']
ImageFrame.display(self, map, **kws)
if 'x' in kws:
self.panel.xdata = kws['x']
if 'y' in kws:
self.panel.ydata = kws['y']
if self.panel.conf.auto_contrast:
self.set_contrast_levels()
def prof_motion(self, event=None):
if not event.inaxes or self.zoom_ini is None:
return
try:
xmax, ymax = event.x, event.y
except:
return
xmin, ymin, xd, yd = self.zoom_ini
if event.xdata is not None:
self.lastpoint[0] = event.xdata
if event.ydata is not None:
self.lastpoint[1] = event.ydata
yoff = self.panel.canvas.figure.bbox.height
ymin, ymax = yoff - ymin, yoff - ymax
zdc = wx.ClientDC(self.panel.canvas)
zdc.SetLogicalFunction(wx.XOR)
zdc.SetBrush(wx.TRANSPARENT_BRUSH)
zdc.SetPen(wx.Pen('White', 2, wx.SOLID))
zdc.ResetBoundingBox()
if not is_wxPhoenix:
zdc.BeginDrawing()
# erase previous box
if self.rbbox is not None:
zdc.DrawLine(*self.rbbox)
self.rbbox = (xmin, ymin, xmax, ymax)
zdc.DrawLine(*self.rbbox)
if not is_wxPhoenix:
zdc.EndDrawing()
def prof_leftdown(self, event=None):
self.report_leftdown(event=event)
if event.inaxes and len(self.map.shape) == 2:
self.lastpoint = [None, None]
self.zoom_ini = [event.x, event.y, event.xdata, event.ydata]
def prof_leftup(self, event=None):
if len(self.map.shape) != 2:
return
if self.rbbox is not None:
zdc = wx.ClientDC(self.panel.canvas)
zdc.SetLogicalFunction(wx.XOR)
zdc.SetBrush(wx.TRANSPARENT_BRUSH)
zdc.SetPen(wx.Pen('White', 2, wx.SOLID))
zdc.ResetBoundingBox()
if not is_wxPhoenix:
zdc.BeginDrawing()
zdc.DrawLine(*self.rbbox)
if not is_wxPhoenix:
zdc.EndDrawing()
self.rbbox = None
if self.zoom_ini is None or self.lastpoint[0] is None:
return
x0 = int(self.zoom_ini[2])
x1 = int(self.lastpoint[0])
y0 = int(self.zoom_ini[3])
y1 = int(self.lastpoint[1])
dx, dy = abs(x1-x0), abs(y1-y0)
self.lastpoint, self.zoom_ini = [None, None], None
if dx < 2 and dy < 2:
self.zoom_ini = None
return
outdat = []
if dy > dx:
_y0 = min(int(y0), int(y1+0.5))
_y1 = max(int(y0), int(y1+0.5))
for iy in range(_y0, _y1):
ix = int(x0 + (iy-int(y0))*(x1-x0)/(y1-y0))
outdat.append((ix, iy))
else:
_x0 = min(int(x0), int(x1+0.5))
_x1 = max(int(x0), int(x1+0.5))
for ix in range(_x0, _x1):
iy = int(y0 + (ix-int(x0))*(y1-y0)/(x1-x0))
outdat.append((ix, iy))
x, y, z = [], [], []
for ix, iy in outdat:
x.append(ix)
y.append(iy)
z.append(self.panel.conf.data[iy,ix])
self.prof_dat = dy>dx, outdat
if self.prof_plotter is not None:
try:
self.prof_plotter.Raise()
self.prof_plotter.clear()
except (AttributeError, PyDeadObjectError):
self.prof_plotter = None
if self.prof_plotter is None:
self.prof_plotter = PlotFrame(self, title='Profile')
self.prof_plotter.panel.report_leftdown = self.prof_report_coords
xlabel, y2label = 'Pixel (x)', 'Pixel (y)'
if dy > dx:
x, y = y, x
xlabel, y2label = y2label, xlabel
self.prof_plotter.panel.clear() # reset_config()
if len(self.title) < 1:
self.title = os.path.split(self.xrmfile.filename)[1]
opts = dict(linewidth=2, marker='+', markersize=3,
show_legend=True, xlabel=xlabel)
self.prof_plotter.plot(x, z, title=self.title, color='blue',
zorder=20, xmin=min(x)-3, xmax=max(x)+3,
ylabel='counts', label='counts', **opts)
self.prof_plotter.oplot(x, y, y2label=y2label, label=y2label,
zorder=3, side='right', color='#771111', **opts)
self.prof_plotter.panel.unzoom_all()
self.prof_plotter.Show()
self.zoom_ini = None
self.zoom_mode.SetSelection(0)
self.panel.cursor_mode = 'zoom'
def prof_report_coords(self, event=None):
"""override report leftdown for profile plotter"""
if event is None:
return
ex, ey = event.x, event.y
msg = ''
plotpanel = self.prof_plotter.panel
axes = plotpanel.fig.get_axes()[0]
write = plotpanel.write_message
try:
x, y = axes.transData.inverted().transform((ex, ey))
except:
x, y = event.xdata, event.ydata
if x is None or y is None:
return
_point = 0, 0, 0, 0, 0
for ix, iy in self.prof_dat[1]:
if (int(x) == ix and not self.prof_dat[0] or
int(x) == iy and self.prof_dat[0]):
_point = (ix, iy,
self.panel.xdata[ix],
self.panel.ydata[iy],
self.panel.conf.data[iy, ix])
msg = "Pixel [%i, %i], X, Y = [%.4f, %.4f], Intensity= %g" % _point
write(msg, panel=0)
def onCursorMode(self, event=None, mode='zoom'):
self.panel.cursor_mode = mode
if event is not None:
if 1 == event.GetInt():
self.panel.cursor_mode = 'lasso'
elif 2 == event.GetInt():
self.panel.cursor_mode = 'prof'
def report_leftdown(self, event=None):
if event is None:
return
if event.xdata is None or event.ydata is None:
return
ix, iy = round(event.xdata), round(event.ydata)
conf = self.panel.conf
if conf.flip_ud: iy = conf.data.shape[0] - iy
if conf.flip_lr: ix = conf.data.shape[1] - ix
self.this_point = None
msg = ''
if (ix >= 0 and ix < conf.data.shape[1] and
iy >= 0 and iy < conf.data.shape[0]):
pos = ''
pan = self.panel
# print( 'has xdata? ', pan.xdata is not None, pan.ydata is not None)
labs, vals = [], []
if pan.xdata is not None:
labs.append(pan.xlab)
vals.append(pan.xdata[ix])
if pan.ydata is not None:
labs.append(pan.ylab)
vals.append(pan.ydata[iy])
pos = ', '.join(labs)
vals =', '.join(['%.4g' % v for v in vals])
pos = '%s = [%s]' % (pos, vals)
dval = conf.data[iy, ix]
if len(pan.data_shape) == 3:
dval = "%.4g, %.4g, %.4g" % tuple(dval)
else:
dval = "%.4g" % dval
if pan.xdata is not None and pan.ydata is not None:
self.this_point = (ix, iy)
msg = "Pixel [%i, %i], %s, Intensity=%s " % (ix, iy, pos, dval)
self.panel.write_message(msg, panel=0)
def report_motion(self, event=None):
return
def onLasso(self, data=None, selected=None, mask=None, **kws):
if hasattr(self.lasso_callback , '__call__'):
self.lasso_callback(data=data, selected=selected, mask=mask,
xoff=self.xoff, yoff=self.yoff,
det=self.det, xrmfile=self.xrmfile, **kws)
self.zoom_mode.SetSelection(0)
self.panel.cursor_mode = 'zoom'
def CustomConfig(self, panel, sizer, irow):
"""config panel for left-hand-side of frame"""
conf = self.panel.conf
lpanel = panel
lsizer = sizer
labstyle = wx.ALIGN_LEFT|wx.LEFT|wx.TOP|wx.EXPAND
self.zoom_mode = wx.RadioBox(panel, -1, "Cursor Mode:",
wx.DefaultPosition, wx.DefaultSize,
('Zoom to Rectangle',
'Pick Area for XRF Spectrum',
'Show Line Profile'),
1, wx.RA_SPECIFY_COLS)
self.zoom_mode.Bind(wx.EVT_RADIOBOX, self.onCursorMode)
sizer.Add(self.zoom_mode, (irow, 0), (1, 4), labstyle, 3)
if self.save_callback is not None:
self.pos_name = wx.TextCtrl(panel, -1, '', size=(175, -1),
style=wx.TE_PROCESS_ENTER)
self.pos_name.Bind(wx.EVT_TEXT_ENTER, self.onSavePixel)
label = SimpleText(panel, label='Save Position:',
size=(-1, -1))
# sbutton = Button(panel, 'Save Position', size=(100, -1),
# action=self.onSavePixel)
sizer.Add(label, (irow+1, 0), (1, 2), labstyle, 3)
sizer.Add(self.pos_name, (irow+1, 2), (1, 2), labstyle, 3)
# sizer.Add(sbutton, (irow+2, 0), (1, 2), labstyle, 3)
if self.move_callback is not None:
mbutton = Button(panel, 'Move to Position', size=(100, -1),
action=self.onMoveToPixel)
irow = irow + 2
sizer.Add(mbutton, (irow+1, 0), (1, 2), labstyle, 3)
def onMoveToPixel(self, event=None):
if self.this_point is not None and self.move_callback is not None:
p1 = float(self.panel.xdata[self.this_point[0]])
p2 = float(self.panel.ydata[self.this_point[1]])
self.move_callback(p1, p2)
def onSavePixel(self, event=None):
if self.this_point is not None and self.save_callback is not None:
name = str(event.GetString().strip())
# name = str(self.pos_name.GetValue().strip())
ix, iy = self.this_point
x = float(self.panel.xdata[ix])
y = float(self.panel.ydata[iy])
self.save_callback(name, ix, iy, x=x, y=y,
title=self.title, datafile=self.xrmfile)
def prof_leftup(self, event=None):
if len(self.map.shape) != 2:
return
if self.rbbox is not None:
zdc = wx.ClientDC(self.panel.canvas)
zdc.SetLogicalFunction(wx.XOR)
zdc.SetBrush(wx.TRANSPARENT_BRUSH)
zdc.SetPen(wx.Pen('White', 2, wx.SOLID))
zdc.ResetBoundingBox()
if not is_wxPhoenix:
zdc.BeginDrawing()
zdc.DrawLine(*self.rbbox)
if not is_wxPhoenix:
zdc.EndDrawing()
self.rbbox = None
if self.zoom_ini is None or self.lastpoint[0] is None:
return
x0 = int(self.zoom_ini[2])
x1 = int(self.lastpoint[0])
y0 = int(self.zoom_ini[3])
y1 = int(self.lastpoint[1])
dx, dy = abs(x1-x0), abs(y1-y0)
self.lastpoint, self.zoom_ini = [None, None], None
if dx < 2 and dy < 2:
self.zoom_ini = None
return
outdat = []
if dy > dx:
_y0 = min(int(y0), int(y1+0.5))
_y1 = max(int(y0), int(y1+0.5))
for iy in range(_y0, _y1):
ix = int(x0 + (iy-int(y0))*(x1-x0)/(y1-y0))
outdat.append((ix, iy))
else:
_x0 = min(int(x0), int(x1+0.5))
_x1 = max(int(x0), int(x1+0.5))
for ix in range(_x0, _x1):
iy = int(y0 + (ix-int(x0))*(y1-y0)/(x1-x0))
outdat.append((ix, iy))
x, y, z = [], [], []
for ix, iy in outdat:
x.append(ix)
y.append(iy)
z.append(self.panel.conf.data[iy,ix])
self.prof_dat = dy>dx, outdat
if self.prof_plotter is not None:
try:
self.prof_plotter.Raise()
self.prof_plotter.clear()
except (AttributeError, PyDeadObjectError):
self.prof_plotter = None
if self.prof_plotter is None:
self.prof_plotter = PlotFrame(self, title='Profile')
self.prof_plotter.panel.report_leftdown = self.prof_report_coords
xlabel, y2label = 'Pixel (x)', 'Pixel (y)'
if dy > dx:
x, y = y, x
xlabel, y2label = y2label, xlabel
self.prof_plotter.panel.clear() # reset_config()
if len(self.title) < 1:
self.title = os.path.split(self.xrmfile.filename)[1]
opts = dict(linewidth=2, marker='+', markersize=3,
show_legend=True, xlabel=xlabel)
self.prof_plotter.plot(x, z, title=self.title, color='blue',
zorder=20, xmin=min(x)-3, xmax=max(x)+3,
ylabel='counts', label='counts', **opts)
self.prof_plotter.oplot(x, y, y2label=y2label, label=y2label,
zorder=3, side='right', color='#771111', **opts)
self.prof_plotter.panel.unzoom_all()
self.prof_plotter.Show()
self.zoom_ini = None
self.zoom_mode.SetSelection(0)
self.panel.cursor_mode = 'zoom'
class XRD2D_DisplayFrame(ImageFrame):
"""
MatPlotlib Image Display on a wx.Frame, using ImagePanel
"""
def __init__(self, _larch=None, parent=None, size=None, mode='intensity',
move_callback=None, save_callback=None,
show_xsections=False, cursor_labels=None,
output_title='Image', **kws):
self.xrmfile = None
self.map = None
self.move_callback = move_callback
self.save_callback = save_callback
self.larch = _larch
if self.larch is None:
self.init_larch()
ImageFrame.__init__(self, parent=parent, size=size,
cursor_labels=cursor_labels, mode=mode,
output_title=output_title, **kws)
self.panel.cursor_mode = 'zoom'
self.panel.xaxis = 'q'
self.panel.report_leftdown = self.report_leftdown
self.panel.report_motion = self.report_motion
self.prof_plotter = None
self.zoom_ini = None
self.lastpoint = [None, None]
self.this_point = None
self.rbbox = None
def display(self, map, xrmfile=None, ai=None, mask=None, **kws):
self.xrmfile = xrmfile
self.map = map
self.title = ''
if 'title' in kws:
self.title = kws['title']
ImageFrame.display(self, map, **kws)
if self.panel.conf.auto_contrast:
self.set_contrast_levels()
self.ai = ai
self.mask = mask
if np.shape(self.mask) == np.shape(map):
self.masked_map = map * (np.ones(np.shape(self.mask))-mask.value)
self.panel.xdata = np.arange(map.shape[0])
self.panel.ydata = np.arange(map.shape[0])
def init_larch(self):
if self.larch is None:
self.larch = Interpreter()
def prof_motion(self, event=None):
if not event.inaxes or self.zoom_ini is None:
return
try:
xmax, ymax = event.x, event.y
except:
return
xmin, ymin, xd, yd = self.zoom_ini
if event.xdata is not None:
self.lastpoint[0] = event.xdata
if event.ydata is not None:
self.lastpoint[1] = event.ydata
yoff = self.panel.canvas.figure.bbox.height
ymin, ymax = yoff - ymin, yoff - ymax
zdc = wx.ClientDC(self.panel.canvas)
zdc.SetLogicalFunction(wx.XOR)
zdc.SetBrush(wx.TRANSPARENT_BRUSH)
zdc.SetPen(wx.Pen('White', 2, wx.SOLID))
zdc.ResetBoundingBox()
if not is_wxPhoenix:
zdc.BeginDrawing()
# erase previous box
if self.rbbox is not None:
zdc.DrawLine(*self.rbbox)
self.rbbox = (xmin, ymin, xmax, ymax)
zdc.DrawLine(*self.rbbox)
if not is_wxPhoenix:
zdc.EndDrawing()
def prof_leftdown(self, event=None):
self.report_leftdown(event=event)
if event.inaxes and len(self.map.shape) == 2:
self.lastpoint = [None, None]
self.zoom_ini = [event.x, event.y, event.xdata, event.ydata]
def prof_leftup(self, event=None):
if len(self.map.shape) != 2:
return
if self.rbbox is not None:
zdc = wx.ClientDC(self.panel.canvas)
zdc.SetLogicalFunction(wx.XOR)
zdc.SetBrush(wx.TRANSPARENT_BRUSH)
zdc.SetPen(wx.Pen('White', 2, wx.SOLID))
zdc.ResetBoundingBox()
if not is_wxPhoenix:
zdc.BeginDrawing()
zdc.DrawLine(*self.rbbox)
if not is_wxPhoenix:
zdc.EndDrawing()
self.rbbox = None
if self.zoom_ini is None or self.lastpoint[0] is None:
return
x0 = int(self.zoom_ini[2])
x1 = int(self.lastpoint[0])
y0 = int(self.zoom_ini[3])
y1 = int(self.lastpoint[1])
dx, dy = abs(x1-x0), abs(y1-y0)
self.lastpoint, self.zoom_ini = [None, None], None
if dx < 2 and dy < 2:
self.zoom_ini = None
return
outdat = []
if dy > dx:
_y0 = min(int(y0), int(y1+0.5))
_y1 = max(int(y0), int(y1+0.5))
for iy in range(_y0, _y1):
ix = int(x0 + (iy-int(y0))*(x1-x0)/(y1-y0))
outdat.append((ix, iy))
else:
_x0 = min(int(x0), int(x1+0.5))
_x1 = max(int(x0), int(x1+0.5))
for ix in range(_x0, _x1):
iy = int(y0 + (ix-int(x0))*(y1-y0)/(x1-x0))
outdat.append((ix, iy))
x, y, z = [], [], []
for ix, iy in outdat:
x.append(ix)
y.append(iy)
z.append(self.panel.conf.data[iy,ix])
self.prof_dat = dy>dx, outdat
if self.prof_plotter is not None:
try:
self.prof_plotter.Raise()
self.prof_plotter.clear()
except (AttributeError, PyDeadObjectError):
self.prof_plotter = None
if self.prof_plotter is None:
self.prof_plotter = PlotFrame(self, title='Profile')
self.prof_plotter.panel.report_leftdown = self.prof_report_coords
xlabel, y2label = 'Pixel (x)', 'Pixel (y)'
if dy > dx:
x, y = y, x
xlabel, y2label = y2label, xlabel
self.prof_plotter.panel.clear() # reset_config()
if len(self.title) < 1:
self.title = os.path.split(self.xrmfile.filename)[1]
opts = dict(linewidth=2, marker='+', markersize=3,
show_legend=True, xlabel=xlabel)
self.prof_plotter.plot(x, z, title=self.title, color='blue',
zorder=20, xmin=min(x)-3, xmax=max(x)+3,
ylabel='counts', label='counts', **opts)
self.prof_plotter.oplot(x, y, y2label=y2label, label=y2label,
zorder=3, side='right', color='#771111', **opts)
self.prof_plotter.panel.unzoom_all()
self.prof_plotter.Show()
self.zoom_ini = None
self.panel.cursor_mode = 'zoom'
def prof_report_coords(self, event=None):
"""override report leftdown for profile plotter"""
if event is None:
return
ex, ey = event.x, event.y
msg = ''
plotpanel = self.prof_plotter.panel
axes = plotpanel.fig.get_axes()[0]
write = plotpanel.write_message
try:
x, y = axes.transData.inverted().transform((ex, ey))
except:
x, y = event.xdata, event.ydata
if x is None or y is None:
return
if self.ai is None:
_point = 0, 0, 0
for ix, iy in self.prof_dat[1]:
if (int(x) == ix and not self.prof_dat[0] or
int(x) == iy and self.prof_dat[0]):
_point = (ix, iy,
self.panel.conf.data[iy, ix])
msg = "Pixel [%i, %i], Intensity= %g" % _point
else:
ai = self.ai
xcenter = ai._poni2/ai.detector.pixel2 ## units pixels
ycenter = ai._poni1/ai.detector.pixel1 ## units pixels
_point = 0, 0, 0, 0, 0
for ix, iy in self.prof_dat[1]:
if (int(x) == ix and not self.prof_dat[0] or
int(x) == iy and self.prof_dat[0]):
x_pix = ix - xcenter ## units pixels
y_pix = iy - ycenter ## units pixels
x_m = x_pix * ai.detector.pixel2 ## units m
y_m = y_pix * ai.detector.pixel1 ## units m
twth = np.arctan2(math.sqrt(x_m**2 + y_m**2),ai._dist) ## radians
twth = np.degrees(twth) ## units degrees
eta = np.arctan2(y_m,x_m) ## units radians
eta = np.degrees(eta) ## units degrees
_point = (ix, iy, twth, eta, self.panel.conf.data[iy, ix])
msg = 'Pixel [%i, %i], 2TH=%.2f, ETA=%.1f, Intensity= %g' % _point
write(msg, panel=0)
def report_leftdown(self, event=None):
if event is None:
return
if event.xdata is None or event.ydata is None:
return
ix, iy = int(round(event.xdata)), int(round(event.ydata))
conf = self.panel.conf
if conf.flip_ud: iy = conf.data.shape[0] - iy
if conf.flip_lr: ix = conf.data.shape[1] - ix
self.this_point = None
msg = ''
if (ix >= 0 and ix < conf.data.shape[1] and
iy >= 0 and iy < conf.data.shape[0]):
pos = ''
pan = self.panel
labs, vals = [], []
if pan.xdata is not None:
labs.append(pan.xlab)
vals.append(pan.xdata[ix])
if pan.ydata is not None:
labs.append(pan.ylab)
vals.append(pan.ydata[iy])
dval = conf.data[iy, ix]
if len(pan.data_shape) == 3:
dval = "%.4g, %.4g, %.4g" % tuple(dval)
else:
dval = "%.4g" % dval
if pan.xdata is not None and pan.ydata is not None:
self.this_point = (ix, iy)
if self.ai is None:
msg = "Pixel [%i, %i], Intensity=%s " % (ix, iy, dval)
else:
ai = self.ai
xcenter = ai._poni2/ai.detector.pixel2 ## units pixels
ycenter = ai._poni1/ai.detector.pixel1 ## units pixels
x_pix = ix - xcenter ## units pixels
y_pix = iy - ycenter ## units pixels
x_m = x_pix * ai.detector.pixel2 ## units m
y_m = y_pix * ai.detector.pixel1 ## units m
twth = np.arctan2(math.sqrt(x_m**2 + y_m**2),ai._dist) ## radians
twth = np.degrees(twth) ## units degrees
eta = np.arctan2(y_m,x_m) ## units radians
eta = np.degrees(eta) ## units degrees
msg = 'Pixel [%i, %i], 2TH=%.2f deg., ETA=%.1f deg., Intensity= %s' % (ix,
iy, twth, eta, dval)
self.panel.write_message(msg, panel=0)
def report_motion(self, event=None):
return
def CustomConfig(self, panel, sizer, irow):
"""config panel for left-hand-side of frame"""
conf = self.panel.conf
lpanel = panel
lsizer = sizer
labstyle = wx.ALIGN_LEFT|wx.LEFT|wx.TOP|wx.EXPAND
self.MskCkBx = wx.CheckBox(panel, label='Apply mask?')
self.MskCkBx.Bind(wx.EVT_CHECKBOX, self.onApplyMask)
sizer.Add(self.MskCkBx, (irow+1,0), (1,4), labstyle, 3)
self.LoadBtn = wx.Button(panel, label='Load New Mask')
self.LoadBtn.Bind(wx.EVT_BUTTON, self.onLoadMask)
sizer.Add(self.LoadBtn, (irow+2,0), (1,4), labstyle, 3)
self.ReCalc1D = wx.Button(panel, label='Replot 1DXRD')
self.ReCalc1D.Bind(wx.EVT_BUTTON, self.onReplot1DXRD)
sizer.Add(self.ReCalc1D, (irow+3,0), (1,4), labstyle, 3)
def onApplyMask(self, event):
'''
Applies mask to 2DXRD map
mkak 2016.09.29
'''
if event.GetEventObject().GetValue():
if self.masked_map is None:
print('Mask file not defined.')
question = 'No mask found in map file. Would you like to load a new file now?'
caption = 'Load mask file?'
dlg = wx.MessageDialog(self, question, caption, wx.YES_NO | wx.ICON_QUESTION)
print( 'answer:', dlg.ShowModal()) # == wx.ID_YES
read = dlg.ShowModal()
dlg.Destroy()
if read == wx.ID_YES:
self.onLoadMask()
self.MskCkBx.SetValue(False)
else:
ImageFrame.display(self, self.masked_map)
else:
ImageFrame.display(self, self.map)
def onLoadMask(self, evt=None):
wildcards = 'pyFAI mask (*.edf)|*.edf|All files (*.*)|*.*'
dlg = wx.FileDialog(self, message='Choose XRD mask file',
defaultDir=os.getcwd(),
wildcard=wildcards, style=wx.FD_OPEN)
edffile, read = None, False
if dlg.ShowModal() == wx.ID_OK:
read = True
edffile = dlg.GetPath().replace('\\', '/')
dlg.Destroy()
if read:
print('Reading mask file: %s' % edffile)
try:
import fabio
self.mask = fabio.open(edffile).data
self.masked_map = self.map * (np.ones(np.shape(self.mask))-self.mask)
self.MskCkBx.SetValue(True)
ImageFrame.display(self, self.masked_map)
except:
print('File must be .edf format; user must have fabio installed.')
## Can this be called here?
#readEDFfile(self,name='mask',keyword='maskfile')
#add_calibration()
def onReplot1DXRD(self, evt=None):
print('Not yet implemented.')
class StageFrame(wx.Frame):
htmllog = 'SampleStage.html'
html_header = """<html><head><title>Sample Stage Log</title></head>
<meta http-equiv='Pragma' content='no-cache'>
<meta http-equiv='Refresh' content='300'>
<body>
"""
def __init__(self, inifile='SampleStage.ini', size=(1600, 800),
ask_workdir=True, orientation='landscape'):
super(StageFrame, self).__init__(None, wx.ID_ANY,
style=wx.DEFAULT_FRAME_STYLE,
size=size)
self.SetFont(wx.Font(10, wx.SWISS, wx.NORMAL, wx.BOLD, False))
self.read_config(configfile=inifile, get_dir=ask_workdir)
self.overlay_frame = None
self.last_pixel = None
self.xhair_pixel = None
self.create_frame(size=size, orientation=orientation)
self.xplot = None
self.yplot = None
self.imgpanel.Start()
def create_frame(self, size=(1600, 800), orientation='landscape'):
"build main frame"
self.statusbar = self.CreateStatusBar(2, wx.CAPTION)
self.statusbar.SetStatusWidths([-4, -1])
for index in range(2):
self.statusbar.SetStatusText('', index)
config = self.config
opts = dict(writer=self.write_framerate,
leftdown_cb=self.onSelectPixel,
motion_cb=self.onPixelMotion,
xhair_cb=self.onShowCrosshair,
center_cb=self.onMoveToCenter,
autosave_file=self.autosave_file)
if self.cam_type.startswith('fly2'):
opts['camera_id'] = int(self.cam_fly2id)
opts['output_pv'] = config['camera'].get('output_pv', None)
ImagePanel, ConfPanel = ImagePanel_Fly2, ConfPanel_Fly2
elif self.cam_type.startswith('area'):
opts['prefix'] = self.cam_adpref
ImagePanel, ConfPanel = ImagePanel_EpicsAD, ConfPanel_EpicsAD
elif self.cam_type.startswith('webcam'):
opts['url'] = self.cam_weburl
ImagePanel, ConfPanel = ImagePanel_URL, ConfPanel_URL
self.imgpanel = ImagePanel(self, **opts)
self.imgpanel.SetMinSize((285, 250))
if orientation.lower().startswith('land'):
size = (1600, 800)
self.cpanel = wx.CollapsiblePane(self, label='Show Controls',
style=wx.CP_DEFAULT_STYLE|wx.CP_NO_TLW_RESIZE)
self.Bind(wx.EVT_COLLAPSIBLEPANE_CHANGED, self.OnPaneChanged, self.cpanel)
ppanel = wx.Panel(self.cpanel.GetPane())
self.pospanel = PositionPanel(ppanel, self, config=config['scandb'])
self.pospanel.SetMinSize((250, 700))
self.ctrlpanel = ControlPanel(ppanel,
groups=config['stage_groups'],
config=config['stages'],
autofocus=self.onAutoFocus)
self.confpanel = ConfPanel(ppanel,
image_panel=self.imgpanel, **opts)
msizer = wx.GridBagSizer(2, 2)
msizer.Add(self.ctrlpanel, (0, 0), (1, 1), ALL_EXP|LEFT_TOP, 1)
msizer.Add(self.confpanel, (1, 0), (1, 1), ALL_EXP|LEFT_TOP, 1)
msizer.Add(self.pospanel, (0, 1), (2, 1), ALL_EXP|LEFT_TOP, 2)
pack(ppanel, msizer)
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.AddMany([(self.imgpanel, 5, ALL_EXP|LEFT_CEN, 0),
(self.cpanel, 1, ALL_EXP|LEFT_CEN|wx.GROW, 1)])
pack(self, sizer)
self.cpanel.Collapse(False)
self.cpanel.SetLabel('Hide Controls')
else: # portrait mode
size = (900, 1500)
ppanel = wx.Panel(self)
self.pospanel = PositionPanel(ppanel, self, config=config['scandb'])
self.pospanel.SetMinSize((250, 450))
self.ctrlpanel = ControlPanel(ppanel,
groups=config['stage_groups'],
config=config['stages'],
autofocus=self.onAutoFocus)
self.confpanel = ConfPanel(ppanel,
image_panel=self.imgpanel, **opts)
msizer = wx.GridBagSizer(3, 3)
msizer.Add(self.ctrlpanel, (0, 0), (1, 1), ALL_EXP|LEFT_TOP, 1)
msizer.Add(self.pospanel, (0, 1), (2, 1), ALL_EXP|LEFT_TOP, 2)
msizer.Add(self.confpanel, (0, 2), (1, 1), ALL_EXP|LEFT_TOP, 1)
pack(ppanel, msizer)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.AddMany([(self.imgpanel, 5, ALL_EXP|LEFT_CEN, 0),
(ppanel, 1, ALL_EXP|LEFT_CEN|wx.GROW, 1)])
pack(self, sizer)
self.imgpanel.confpanel = self.confpanel
self.SetSize(size)
if len(self.iconfile) > 0:
self.SetIcon(wx.Icon(self.iconfile, wx.BITMAP_TYPE_ICO))
ex = [{'shape':'circle', 'color': (255, 0, 0),
'width': 1.5, 'args': (0.5, 0.5, 0.007)},
{'shape':'line', 'color': (200, 100, 0),
'width': 2.0, 'args': (0.7, 0.97, 0.97, 0.97)}]
self.create_menus()
self.Bind(wx.EVT_CLOSE, self.onClose)
self.init_timer = wx.Timer(self)
self.Bind(wx.EVT_TIMER, self.onInitTimer, self.init_timer)
self.init_timer.Start(1000)
def OnPaneChanged(self, evt=None):
self.Layout()
if self.cpanel.IsExpanded():
self.cpanel.SetLabel('Hide Controls')
else:
self.cpanel.SetLabel('Show Controls')
self.imgpanel.Refresh()
def onInitTimer(self, event=None, **kws):
if self.imgpanel.full_size is not None:
if 'overlays' in self.config:
olays = self.config['overlays']
sbar = [float(x) for x in olays['scalebar'].split()]
circ = [float(x) for x in olays['circle'].split()]
img_x, img_y = self.imgpanel.full_size
pix_x = float(self.config['camera']['calib_x'])
iscale = 0.5/abs(pix_x * img_x)
ssiz, sx, sy, swid, scolr, scolg, scolb = sbar
csiz, cx, cy, cwid, ccolr, ccolg, ccolb = circ
cargs = [cx, cy, csiz*iscale]
sargs = [sx - ssiz*iscale, sy, sx + ssiz*iscale, sy]
scol = wx.Colour(int(scolr), int(scolg), int(scolb))
ccol = wx.Colour(int(ccolr), int(ccolg), int(ccolb))
dobjs = [dict(shape='Line', width=swid,
style=wx.SOLID, color=scol, args=sargs),
dict(shape='Circle', width=cwid,
style=wx.SOLID, color=ccol, args=cargs)]
if self.xhair_pixel is not None:
xwid, xcolr, xcolg, xcolb = swid, scolr, scolg, scolb
xcol = wx.Colour(int(xcolr), int(xcolg), int(xcolb))
xcol = wx.Colour(int(20), int(300), int(250))
hx = self.xhair_pixel['x']
hy = self.xhair_pixel['y']
xargs = [hx - ssiz*iscale, hy - ssiz*iscale, hx + ssiz*iscale, hy + ssiz*iscale]
dobjs.append(dict(shape='Line', width=2,
style=wx.SOLID, color=xcol, args=xargs))
#print "Showing xhair: ", xargs
# print 'Draw Objects ', dobjs
self.imgpanel.draw_objects = dobjs
self.init_timer.Stop()
def onChangeCamera(self, evt=None):
if not self.cam_type.startswith('area'):
print 'How did that happen?'
return
name = self.cam_adpref
prefix = None
dlg = wx.TextEntryDialog(self, 'Enter PV for Area Detector',
caption='Enter PV for Area Detector',
defaultValue=name)
dlg.Raise()
if dlg.ShowModal() == wx.ID_OK:
prefix = dlg.GetValue()
dlg.Destroy()
if prefix is not None:
self.imgpanel.set_prefix(prefix)
self.confpanel.set_prefix(prefix)
self.cam_adpref = prefix
def create_menus(self):
"Create the menubar"
mbar = wx.MenuBar()
fmenu = wx.Menu()
pmenu = wx.Menu()
omenu = wx.Menu()
add_menu(self, fmenu, label="&Read Config", text="Read Configuration",
action = self.onReadConfig)
add_menu(self, fmenu, label="&Save Config", text="Save Configuration",
action = self.onSaveConfig)
add_menu(self, fmenu, label="Show Projections\tCtrl+G",
text="Start Projection Plots",
action = self.onStartProjections)
add_menu(self, fmenu, label="Print Blurriness\tCtrl+B",
text="print blurriness",
action = self.onReportBlurry)
add_menu(self, fmenu, label="Stop Projection\tCtrl+C",
text="Stop Projection Plots",
action = self.onStopProjections)
add_menu(self, fmenu, label="Select &Working Directory\tCtrl+W",
text="change Working Folder",
action = self.onChangeWorkdir)
if self.cam_type.startswith('area'):
add_menu(self, fmenu, label="Change AreaDetector",
text="Change Camera to different AreaDetector",
action = self.onChangeCamera)
fmenu.AppendSeparator()
add_menu(self, fmenu, label="E&xit\tCtrl+x", text="Quit Program",
action = self.onClose)
add_menu(self, pmenu, label="Export Positions", text="Export Positions",
action = self.onExportPositions)
add_menu(self, pmenu, label="Import Positions", text="Import Positions",
action = self.onImportPositions)
add_menu(self, pmenu, label="Erase Many Positions\tCtrl+E",
text="Select Multiple Positions to Erase",
action = self.onEraseMany)
add_menu(self, omenu, label="Image Overlays",
text="Setup Image Overlays",
action = self.onConfigOverlays)
vmove = wx.NewId()
verase = wx.NewId()
vreplace = wx.NewId()
cenfine = wx.NewId()
self.menu_opts = {vmove: 'v_move', verase: 'v_erase',
vreplace: 'v_replace',
cenfine: 'center_with_fine_stages'}
mitem = omenu.Append(vmove, "Verify Go To ",
"Prompt to Verify Moving with 'Go To'",
wx.ITEM_CHECK)
mitem.Check()
self.Bind(wx.EVT_MENU, self.onMenuOption, mitem)
mitem = omenu.Append(verase, "Verify Erase",
"Prompt to Verify Erasing Positions", wx.ITEM_CHECK)
mitem.Check()
self.Bind(wx.EVT_MENU, self.onMenuOption, mitem)
mitem = omenu.Append(vreplace, "Verify Overwrite",
"Prompt to Verify Overwriting Positions", wx.ITEM_CHECK)
mitem.Check()
self.Bind(wx.EVT_MENU, self.onMenuOption, mitem)
mitem = omenu.Append(cenfine, "Center With Fine Stages",
"Bring to Center will move the Fine Stages", wx.ITEM_CHECK)
mitem.Check(0)
self.Bind(wx.EVT_MENU, self.onMenuOption, mitem)
omenu.AppendSeparator()
# print 'Create Menus ', self.ctrlpanel.subpanels
# for key, val in self.config['stages'].items():
# print key, val
for name, panel in self.ctrlpanel.subpanels.items():
show = 0
label = 'Enable %s' % name
mid = wx.NewId()
self.menu_opts[mid] = label
for mname, data in self.config['stages'].items():
if data['group'] == name:
show = show + data['show']
mitem = omenu.Append(mid, label, label, wx.ITEM_CHECK)
if show > 0 :
mitem.Check()
self.Bind(wx.EVT_MENU, Closure(self.onShowHide, name=name, panel=panel), mitem)
mbar.Append(fmenu, '&File')
mbar.Append(omenu, '&Options')
mbar.Append(pmenu, 'Positions')
if len(self.config['scandb'].get('offline', '')):
cmenu = wx.Menu()
# add_menu(self, cmenu, label="Calibrate Microscope",
# text="Calibrate to Offline Microscope",
# action = self.pospanel.onMicroscopeCalibrate)
add_menu(self, cmenu, label="Copy Positions from Offline Microscope",
text="Copy Positions from Offline Microscope",
action = self.pospanel.onMicroscopeTransfer)
mbar.Append(cmenu, 'Offline Microscope')
self.SetMenuBar(mbar)
def onShowHide(self, event=None, panel=None, name='---'):
showval = {True:1, False:0}[event.Checked()]
if showval:
panel.Enable()
else:
panel.Disable()
for mname, data in self.config['stages'].items():
if data['group'] == name:
data['show'] = showval
def onEraseMany(self, evt=None, **kws):
self.pospanel.onEraseMany(event=evt)
evt.Skip()
def onConfigOverlays(self, evt=None, **kws):
shown = False
if self.overlay_frame is not None:
try:
self.overlay_frame.Raise()
shown = True
except:
del self.overlay_frame
if not shown:
self.overlayframe = OverlayFrame(image_panel=self.imgpanel,
config=self.config)
def onMenuOption(self, evt=None):
"""events for options menu: move, erase, overwrite """
setattr(self, self.menu_opts[evt.GetId()], evt.Checked())
def read_config(self, configfile=None, get_dir=False):
"open/read ini config file"
if get_dir:
ret = SelectWorkdir(self)
if ret is None:
self.Destroy()
os.chdir(ret)
self.cnf = StageConfig(configfile)
self.config = self.cnf.config
gui = self.config['gui']
self.workdir_file = gui.get('workdir_file', 'sampleviewer_workdir.txt')
self.iconfile = gui.get('icon_file', '')
self.autosave_file = gui.get('autosave_file', 'SampleStage_autosave.ini')
self.v_move = gui.get('verify_move', True)
self.v_erase = gui.get('verify_erase', True)
self.v_replace = gui.get('verify_overwrite', True)
self.center_with_fine_stages = gui.get('center_with_fine_stages', False)
self.SetTitle(gui.get('title', 'Microscope'))
cam = self.config['camera']
self.imgdir = cam.get('image_folder', 'Sample_Images')
self.cam_type = cam.get('type', 'fly2').lower()
self.cam_fly2id = cam.get('fly2_id', 0)
self.cam_adpref = cam.get('ad_prefix', '')
self.cam_adform = cam.get('ad_format', 'JPEG')
self.cam_weburl = cam.get('web_url', 'http://164.54.160.115/jpg/2/image.jpg')
self.get_cam_calib()
try:
pref = self.imgdir.split('_')[0]
except:
pref = 'Sample'
self.htmllog = '%sStage.html' % pref
if not os.path.exists(self.imgdir):
os.makedirs(self.imgdir)
if not os.path.exists(self.htmllog):
self.begin_htmllog()
self.config = self.cnf.config
self.stages = OrderedDict()
for mname, data in self.config.get('stages', {}).items():
mot = Motor(name=mname)
if data['prec'] is None:
data['prec'] = mot.precision
if data['desc'] is None:
data['desc'] = mot.description
if data['maxstep'] is None:
data['maxstep'] = (mot.high_limit - mot.low_limit)/2.10
self.stages[mname] = data
def get_cam_calib(self):
cam = self.config['camera']
cx = self.cam_calibx = float(cam.get('calib_x', 0.001))
cy = self.cam_caliby = float(cam.get('calib_y', 0.001))
return cx, cy
def begin_htmllog(self):
"initialize log file"
fout = open(self.htmllog, 'w')
fout.write(self.html_header)
fout.close()
def save_image(self, fname):
"save image to file"
imgdata = self.imgpanel.SaveImage(fname)
if imgdata is None:
self.write_message('could not save image to %s' % fname)
else:
self.write_message('saved image to %s' % fname)
return imgdata
def autosave(self, positions=None):
self.cnf.Save(self.autosave_file, positions=positions)
def write_htmllog(self, name, thispos):
stages = self.config['stages']
img_folder = self.config['camera']['image_folder']
junk, img_file = os.path.split(thispos['image'])
imgfile = os.path.join(img_folder, img_file)
txt = []
html_fmt ="""<hr>
<table><tr><td><a href='%s'> <img src='%s' width=350></a></td>
<td><table><tr><td>Position:</td><td>%s</td><td>%s</td></tr>
<tr><td>Motor Name</td><td>PV Name</td><td>Value</td></tr>
%s
</table></td></tr></table>"""
pos_fmt =" <tr><td> %s </td><td> %s </td><td> %f</td></tr>"
for pvname, value in thispos['position'].items():
txt.append(pos_fmt % (stages[pvname]['desc'], pvname, value))
fout = open(self.htmllog, 'a')
fout.write(html_fmt % (imgfile, imgfile, name,
thispos['timestamp'], '\n'.join(txt)))
fout.close()
def write_message(self, msg='', index=0):
"write to status bar"
self.statusbar.SetStatusText(msg, index)
def write_framerate(self, msg):
"write to status bar"
self.statusbar.SetStatusText(msg, 1)
def onShowCrosshair(self, event=None, show=True, **kws):
self.xhair_pixel = None
if show:
self.xhair_pixel = self.last_pixel
print "Set XHAIR ", self.xhair_pixel
def onAFTimer(self, event=None, **kws):
if self.af_done:
self.af_thread.join()
self.af_timer.Stop()
if self.ctrlpanel.af_message is not None:
self.ctrlpanel.af_message.SetLabel('')
self.ctrlpanel.af_button.Enable()
def onAutoFocus(self, event=None, **kws):
self.af_done = False
self.ctrlpanel.af_button.Disable()
self.af_thread = Thread(target=self.do_autofocus)
self.af_timer = wx.Timer(self)
self.Bind(wx.EVT_TIMER, self.onAFTimer, self.af_timer)
self.af_timer.Start(2000)
self.af_thread.start()
def do_autofocus(self):
report = None
if self.ctrlpanel.af_message is not None:
report = self.ctrlpanel.af_message.SetLabel
if report is not None:
report('Auto-setting exposure')
self.imgpanel.AutoSetExposureTime()
report('Auto-focussing start')
zstage = self.ctrlpanel.motors['z']._pvs['VAL']
start_pos = zstage.get()
min_pos = start_pos - 2.50
max_pos = start_pos + 2.50
step, min_step = 0.004*(81), 0.002
# start trying both directions:
score_start = image_blurriness(self.imgpanel)
zstage.put(start_pos+step/2.0, wait=True)
time.sleep(0.15)
score_plus = image_blurriness(self.imgpanel)
direction = 1
if score_start < score_plus:
direction = -1
print("Start Scores: ", score_start, score_plus, direction)
best_score = score_start
best_pos = start_pos
zstage.put(start_pos, wait=True)
count = 0
report('Auto-focussing finding focus')
posvals = []
scores = []
while step >= min_step and count < 32:
self.imgpanel.Refresh()
count += 1
pos = zstage.get() + step * direction
if pos < min_pos or pos > max_pos:
break
zstage.put(pos, wait=True, timeout=3.0)
time.sleep(0.15)
score = image_blurriness(self.imgpanel)
# print(" step : ", step, direction, score_plus)
report('Auto-focussing step=%.3f' % step)
# print 'Focus %i: %.3f %.3f %.3f %.3f %.3f %.1f' % (
# count, pos, score, best_pos, best_score, step, direction)
posvals.append(pos)
scores.append(score)
if score < best_score:
best_score = score
best_pos = pos
else:
# best_score = score
step = step / 3.0
if step < min_step:
break
direction = -direction
zstage.put(best_pos, wait=True, timeout=3.0)
time.sleep(0.15)
last_score = score
zstage.put(best_pos)
self.af_done = True
report('Auto-focussing done.')
def onMoveToCenter(self, event=None, **kws):
"bring last pixel to image center"
p = self.last_pixel
if p is None:
return
cal_x, cal_y = self.get_cam_calib()
dx = 0.001*cal_x*(p['x']-p['xmax']/2.0)
dy = 0.001*cal_y*(p['y']-p['ymax']/2.0)
mots = self.ctrlpanel.motors
xmotor, ymotor = 'x', 'y'
if self.center_with_fine_stages and 'finex' in mots:
xmotor, ymotor = 'finex', 'finey'
xscale, yscale = 1.0, 1.0
for stage_info in self.stages.values():
if stage_info['desc'].lower() == xmotor:
xscale = stage_info['scale']
if stage_info['desc'].lower() == ymotor:
yscale = stage_info['scale']
mots[xmotor].VAL += dx*xscale
mots[ymotor].VAL += dy*yscale
self.onSelectPixel(p['xmax']/2.0, p['ymax']/2.0,
xmax=p['xmax'], ymax=p['ymax'])
def onSelectPixel(self, x, y, xmax=100, ymax=100):
" select a pixel from image "
self.last_pixel = dict(x=x, y=y, xmax=xmax, ymax=ymax)
cal_x, cal_y = self.get_cam_calib()
self.confpanel.on_selected_pixel(x, y, xmax, ymax,
cam_calibx=cal_x,
cam_caliby=cal_y)
def onPixelMotion(self, x, y, xmax=100, ymax=100):
" select a pixel from image "
fmt = """Pixel=(%i, %i) (%.1f, %.1f)um from center, (%.1f, %.1f)um from selected"""
if x > 0 and x < xmax and y > 0 and y < ymax:
dx = abs(self.cam_calibx*(x-xmax/2.0))
dy = abs(self.cam_caliby*(y-ymax/2.0))
ux, uy = 0, 0
if self.last_pixel is not None:
lastx = self.last_pixel['x']
lasty = self.last_pixel['y']
ux = abs(self.cam_calibx*(x-lastx))
uy = abs(self.cam_caliby*(y-lasty))
pix_msg = fmt % (x, y, dx, dy, ux, uy)
self.write_message(pix_msg)
if not self.confpanel.img_size_shown:
self.confpanel.img_size.SetLabel("(%i, %i)" % (xmax, ymax))
self.confpanel.img_size_shown = True
def onClose(self, event=None):
if wx.ID_YES == popup(self, "Really Quit?", "Exit Sample Stage?",
style=wx.YES_NO|wx.NO_DEFAULT|wx.ICON_QUESTION):
fout = open(self.workdir_file, 'w')
fout.write("%s\n" % os.path.abspath(os.curdir))
fout.close()
self.imgpanel.Stop()
try:
self.overlay_frame.Destroy()
except:
pass
self.Destroy()
def onExportPositions(self, event=None):
fname = FileSave(self, 'Export Positions File',
wildcard='Position Files (*.pos)|*.pos|All files (*.*)|*.*',
default_file='Save.pos')
if fname is not None:
self.pospanel.SavePositions(fname)
self.write_message('Saved Positions File %s' % fname)
def onImportPositions(self, event=None):
fname = FileOpen(self, 'Import Positions File',
wildcard='Position Files (*.pos)|*.pos|All files (*.*)|*.*',
default_file='Save.pos')
if fname is not None:
self.pospanel.LoadPositions(fname)
self.write_message('Loaded Positions from File %s' % fname)
def onChangeWorkdir(self, event=None):
ret = SelectWorkdir(self)
if ret is None:
return
os.chdir(ret)
cam = self.config['camera']
self.imgdir = cam.get('image_folder', 'Sample_Images')
if not os.path.exists(self.imgdir):
os.makedirs(self.imgdir)
if not os.path.exists(self.htmllog):
self.begin_htmllog()
def onReportBlurry(self, event=None):
score = image_blurriness(self.imgpanel, full=True)
tscore = -(5*score[0] - score[1])
print(" blurriness: %.3f %.3f -> %.3f " % (score[0], score[1], tscore))
def onStartProjections(self, event=None):
try:
self.xplot.Raise()
except:
self.xplot = PlotFrame(parent=self)
try:
self.yplot.Raise()
except:
self.yplot = PlotFrame(parent=self)
self.proj_start = True
self.proj_timer = wx.Timer(self)
self.Bind(wx.EVT_TIMER, self.onShowProjections, self.proj_timer)
self.proj_timer.Start(500)
def onStopProjections(self, event=None):
self.proj_timer.Stop()
def onShowProjections(self, event=None):
dat = self.imgpanel.grab_data()
shape = dat.shape
if len(shape) == 3:
dat = dat.sum(axis=2)
cx, cy = self.get_cam_calib()
kws = dict(ylabel='intensity',
xlabel='distance ($\mu\mathrm{m}$)',
marker='+', markersize=4)
_y = (np.arange(shape[0]) - shape[0]/2.0) *abs(cx)
_x = (np.arange(shape[1]) - shape[1]/2.0) *abs(cy)
_xi = dat.sum(axis=0)
_yi = dat.sum(axis=1)
ymin = min((min(_xi), min(_yi)))
ymax = max((max(_xi), max(_yi)))
if self.proj_start:
self.xplot.plot(_x, _xi, title='X projection', **kws)
self.yplot.plot(_y, _yi, title='Y projection', **kws)
self.xplot.Show()
self.yplot.Show()
self.proj_start = False
else:
self.xplot.panel.update_line(0, _x, _xi, draw=True, update_limits=True)
self.yplot.panel.update_line(0, _y, _yi, draw=True, update_limits=True)
self.xplot.panel.axes.set_ylim((ymin, ymax), emit=True)
self.yplot.panel.axes.set_ylim((ymin, ymax), emit=True)
# print 'X lims: ', self.xplot.panel.conf.zoom_lims, xlims
# self.xplot.panel.set_xylims(xlims)
# self.yplot.panel.set_xylims(ylims)
def onSaveConfig(self, event=None):
fname = FileSave(self, 'Save Configuration File',
wildcard='INI (*.ini)|*.ini|All files (*.*)|*.*',
default_file='SampleStage.ini')
if fname is not None:
self.cnf.Save(fname)
self.write_message('Saved Configuration File %s' % fname)
def onReadConfig(self, event=None):
fname = FileOpen(self, 'Read Configuration File',
wildcard='INI (*.ini)|*.ini|All files (*.*)|*.*',
default_file='SampleStage.ini')
if fname is not None:
self.read_config(fname)
self.connect_motors()
self.pospanel.set_positions(self.config['positions'])
self.write_message('Read Configuration File %s' % fname)
def prof_leftup(self, event=None):
if len(self.map.shape) != 2:
return
if self.rbbox is not None:
zdc = wx.ClientDC(self.panel.canvas)
zdc.SetLogicalFunction(wx.XOR)
zdc.SetBrush(wx.TRANSPARENT_BRUSH)
zdc.SetPen(wx.Pen('White', 2, wx.SOLID))
zdc.ResetBoundingBox()
if not is_wxPhoenix:
zdc.BeginDrawing()
zdc.DrawLine(*self.rbbox)
if not is_wxPhoenix:
zdc.EndDrawing()
self.rbbox = None
if self.zoom_ini is None or self.lastpoint[0] is None:
return
x0 = int(self.zoom_ini[2])
x1 = int(self.lastpoint[0])
y0 = int(self.zoom_ini[3])
y1 = int(self.lastpoint[1])
dx, dy = abs(x1-x0), abs(y1-y0)
self.lastpoint, self.zoom_ini = [None, None], None
if dx < 2 and dy < 2:
self.zoom_ini = None
return
outdat = []
if dy > dx:
_y0 = min(int(y0), int(y1+0.5))
_y1 = max(int(y0), int(y1+0.5))
for iy in range(_y0, _y1):
ix = int(x0 + (iy-int(y0))*(x1-x0)/(y1-y0))
outdat.append((ix, iy))
else:
_x0 = min(int(x0), int(x1+0.5))
_x1 = max(int(x0), int(x1+0.5))
for ix in range(_x0, _x1):
iy = int(y0 + (ix-int(x0))*(y1-y0)/(x1-x0))
outdat.append((ix, iy))
x, y, z = [], [], []
for ix, iy in outdat:
x.append(ix)
y.append(iy)
z.append(self.panel.conf.data[iy,ix])
self.prof_dat = dy>dx, outdat
if self.prof_plotter is not None:
try:
self.prof_plotter.Raise()
self.prof_plotter.clear()
except (AttributeError, PyDeadObjectError):
self.prof_plotter = None
if self.prof_plotter is None:
self.prof_plotter = PlotFrame(self, title='Profile')
self.prof_plotter.panel.report_leftdown = self.prof_report_coords
xlabel, y2label = 'Pixel (x)', 'Pixel (y)'
if dy > dx:
x, y = y, x
xlabel, y2label = y2label, xlabel
self.prof_plotter.panel.clear() # reset_config()
if len(self.title) < 1:
self.title = os.path.split(self.xrmfile.filename)[1]
opts = dict(linewidth=2, marker='+', markersize=3,
show_legend=True, xlabel=xlabel)
self.prof_plotter.plot(x, z, title=self.title, color='blue',
zorder=20, xmin=min(x)-3, xmax=max(x)+3,
ylabel='counts', label='counts', **opts)
self.prof_plotter.oplot(x, y, y2label=y2label, label=y2label,
zorder=3, side='right', color='#771111', **opts)
self.prof_plotter.panel.unzoom_all()
self.prof_plotter.Show()
self.zoom_ini = None
self.zoom_mode.SetSelection(0)
self.panel.cursor_mode = 'zoom'
def OnCompare(self, event):
"""
Callback triggered by the `compare` option in the popup menu of the panels
Plote the netcdf variable/dimension as function of the file index.
"""
# Get the name of the variable.
name, obj = event.name, event.obj
# Define the function to use the get the value of the dimension/variable.
if isinstance(obj, netCDF4.Variable):
def extract(dataset, name):
return dataset.variables[name][:]
elif isinstance(obj, netCDF4.Dimension):
def extract(dataset, name):
return np.array(len(dataset.dimensions[name]))
else:
raise ValueError("Don't know how to handle %s" % repr(obj))
# Extract data. Make sure all the shapes are equal.
data, shape = [], None
for dataset in self.datasets:
v = extract(dataset, name)
data.append(v)
if shape is None:
shape = v.shape
else:
assert shape == v.shape
# Plot data. Two Branches for scalars and arrays.
opts = self.GetPlotOptions()
is_scalar = not shape or (len(shape) == 1 and shape[0] == 1)
#print(shape)
from wxmplot import PlotFrame
if is_scalar:
frame = PlotFrame(parent=self)
xx = range(len(self.datasets))
if opts.plot_mode == "line":
frame.plot(xx, data)
else:
frame.scatterplot(xx, data)
frame.set_xlabel("File index")
frame.set_ylabel(name)
frame.Show()
else:
# Open new frame to allow the user to specify how to handle the array.
ArrayComparisonFrame(self, name, data).Show()
def plot_variable(self, var_name, var, dataset):
"""
Use `wxmplot` to plot the selected variables.
Args:
var_name:
Name of the variable
var:
Netcdf4 `Variable`.
dataset:
Netcdf4 `Dataset`.
"""
# Remove fake dimensions.
shape, dimensions = [], []
for num, name in zip(var.shape, var.dimensions):
if num > 1:
shape.append(num)
dimensions.append(name)
# Get data to plot.
data = np.reshape(var[:], shape)
opts = self.GetPlotOptions()
cplx_mode = opts.cplx_mode
if cplx_mode != "None":
if shape[-1] != 2:
err_msg = "cplx_mode: %s. Expecting 2 as last dimensions but got %d" % (
cplx_mode, shape[-1])
raise ValueError(err_msg)
# Convert to complex then change shape and dimensions
data = data[..., 0] + 1j * data[..., 1]
shape = shape[:-1]
dimensions = dimensions[:-1]
if cplx_mode == "Abs":
data = np.abs(data)
elif cplx_mode == "Real":
data = data.real
elif cplx_mode == "Imag":
data = data.imag
else:
raise ValueError("Wrong value for cplx_mode %s" % cplx_mode)
# Plotting a scalar?
if not shape: return
ndim = len(shape)
if ndim == 1:
# Vector
dim_name = dimensions[0]
xx = range(len(dataset.dimensions[dim_name]))
from wxmplot import PlotFrame
frame = PlotFrame(parent=self)
if opts.plot_mode == "line":
frame.plot(xx, data)
else:
frame.scatterplot(xx, data)
frame.set_xlabel(dim_name)
frame.set_ylabel(var_name)
frame.Show()
elif ndim == 2:
# Two dimensional array.
dim_namex, dim_namey = dimensions
xx, yy = range(len(dataset.dimensions[dim_namex])), range(
len(dataset.dimensions[dim_namey]))
mode = opts.image_mode
if False:
# 3d plot
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
fig = plt.figure()
ax = Axes3D(fig)
X, Y = np.meshgrid(xx, yy, sparse=False, indexing='ij')
print(X.shape, Y.shape, data.shape)
ax.plot_surface(X, Y, data) # rstride=8, cstride=8, alpha=0.3)
plt.show()
from wxmplot import ImageFrame
frame = ImageFrame(parent=self)
frame.display(data,
title=var_name,
style=mode,
x=xx,
y=yy,
xlabel=dim_namex,
ylabel=dim_namey)
frame.Show()
else:
raise NotImplementedError()
class StageFrame(wx.Frame):
htmllog = 'SampleStage.html'
html_header = """<html><head><title>Sample Stage Log</title></head>
<meta http-equiv='Pragma' content='no-cache'>
<meta http-equiv='Refresh' content='300'>
<body>
"""
def __init__(self,
inifile='SampleStage.ini',
size=(1600, 800),
ask_workdir=True,
orientation='landscape'):
super(StageFrame, self).__init__(None,
wx.ID_ANY,
style=wx.DEFAULT_FRAME_STYLE,
size=size)
self.SetFont(wx.Font(10, wx.SWISS, wx.NORMAL, wx.BOLD, False))
self.read_config(configfile=inifile, get_dir=ask_workdir)
self.overlay_frame = None
self.last_pixel = None
self.xhair_pixel = None
self.create_frame(size=size, orientation=orientation)
self.xplot = None
self.yplot = None
self.imgpanel.Start()
def create_frame(self, size=(1600, 800), orientation='landscape'):
"build main frame"
self.statusbar = self.CreateStatusBar(2, wx.CAPTION)
self.statusbar.SetStatusWidths([-4, -1])
for index in range(2):
self.statusbar.SetStatusText('', index)
config = self.config
opts = dict(writer=self.write_framerate,
leftdown_cb=self.onSelectPixel,
motion_cb=self.onPixelMotion,
xhair_cb=self.onShowCrosshair,
center_cb=self.onMoveToCenter,
autosave_file=self.autosave_file)
autofocus_cb = self.onAutoFocus
if self.cam_type.startswith('fly2'):
opts['camera_id'] = int(self.cam_fly2id)
opts['output_pv'] = config['camera'].get('output_pv', None)
ImagePanel, ConfPanel = ImagePanel_Fly2, ConfPanel_Fly2
elif self.cam_type.startswith('adfly'):
opts['prefix'] = self.cam_adpref
ImagePanel, ConfPanel = ImagePanel_Fly2AD, ConfPanel_Fly2AD
autofocus_cb = None
elif self.cam_type.startswith('area'):
opts['prefix'] = self.cam_adpref
ImagePanel, ConfPanel = ImagePanel_EpicsAD, ConfPanel_EpicsAD
elif self.cam_type.startswith('webcam'):
opts['url'] = self.cam_weburl
ImagePanel, ConfPanel = ImagePanel_URL, ConfPanel_URL
self.imgpanel = ImagePanel(self, **opts)
self.imgpanel.SetMinSize((285, 250))
if orientation.lower().startswith('land'):
size = (1600, 800)
self.cpanel = wx.CollapsiblePane(self,
label='Show Controls',
style=wx.CP_DEFAULT_STYLE
| wx.CP_NO_TLW_RESIZE)
self.Bind(wx.EVT_COLLAPSIBLEPANE_CHANGED, self.OnPaneChanged,
self.cpanel)
ppanel = wx.Panel(self.cpanel.GetPane())
self.pospanel = PositionPanel(ppanel,
self,
config=config['scandb'])
self.pospanel.SetMinSize((250, 700))
self.ctrlpanel = ControlPanel(ppanel,
groups=config['stage_groups'],
config=config['stages'],
autofocus=autofocus_cb)
self.confpanel = ConfPanel(ppanel,
image_panel=self.imgpanel,
**opts)
msizer = wx.GridBagSizer(2, 2)
msizer.Add(self.ctrlpanel, (0, 0), (1, 1), ALL_EXP | LEFT_TOP, 1)
msizer.Add(self.confpanel, (1, 0), (1, 1), ALL_EXP | LEFT_TOP, 1)
msizer.Add(self.pospanel, (0, 1), (2, 1), ALL_EXP | LEFT_TOP, 2)
pack(ppanel, msizer)
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.AddMany([(self.imgpanel, 5, ALL_EXP | LEFT_CEN, 0),
(self.cpanel, 1, ALL_EXP | LEFT_CEN | wx.GROW, 1)])
pack(self, sizer)
self.cpanel.Collapse(False)
self.cpanel.SetLabel('Hide Controls')
else: # portrait mode
size = (900, 1500)
ppanel = wx.Panel(self)
self.pospanel = PositionPanel(ppanel,
self,
config=config['scandb'])
self.pospanel.SetMinSize((250, 450))
self.ctrlpanel = ControlPanel(ppanel,
groups=config['stage_groups'],
config=config['stages'],
autofocus=autofocus_cb)
self.confpanel = ConfPanel(ppanel,
image_panel=self.imgpanel,
**opts)
msizer = wx.GridBagSizer(3, 3)
msizer.Add(self.ctrlpanel, (0, 0), (1, 1), ALL_EXP | LEFT_TOP, 1)
msizer.Add(self.pospanel, (0, 1), (2, 1), ALL_EXP | LEFT_TOP, 2)
msizer.Add(self.confpanel, (0, 2), (1, 1), ALL_EXP | LEFT_TOP, 1)
pack(ppanel, msizer)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.AddMany([(self.imgpanel, 5, ALL_EXP | LEFT_CEN, 0),
(ppanel, 1, ALL_EXP | LEFT_CEN | wx.GROW, 1)])
pack(self, sizer)
self.imgpanel.confpanel = self.confpanel
self.SetSize(size)
if len(self.iconfile) > 0:
self.SetIcon(wx.Icon(self.iconfile, wx.BITMAP_TYPE_ICO))
ex = [{
'shape': 'circle',
'color': (255, 0, 0),
'width': 1.5,
'args': (0.5, 0.5, 0.007)
}, {
'shape': 'line',
'color': (200, 100, 0),
'width': 2.0,
'args': (0.7, 0.97, 0.97, 0.97)
}]
self.create_menus()
self.Bind(wx.EVT_CLOSE, self.onClose)
self.init_timer = wx.Timer(self)
self.Bind(wx.EVT_TIMER, self.onInitTimer, self.init_timer)
self.init_timer.Start(1000)
def OnPaneChanged(self, evt=None):
self.Layout()
if self.cpanel.IsExpanded():
self.cpanel.SetLabel('Hide Controls')
else:
self.cpanel.SetLabel('Show Controls')
self.imgpanel.Refresh()
def onInitTimer(self, event=None, **kws):
if self.imgpanel.full_size is not None:
if 'overlays' in self.config:
olays = self.config['overlays']
sbar = [float(x) for x in olays['scalebar'].split()]
circ = [float(x) for x in olays['circle'].split()]
img_x, img_y = self.imgpanel.full_size
pix_x = float(self.config['camera']['calib_x'])
iscale = 0.5 / abs(pix_x * img_x)
ssiz, sx, sy, swid, scolr, scolg, scolb = sbar
csiz, cx, cy, cwid, ccolr, ccolg, ccolb = circ
cargs = [cx, cy, csiz * iscale]
sargs = [sx - ssiz * iscale, sy, sx + ssiz * iscale, sy]
scol = wx.Colour(int(scolr), int(scolg), int(scolb))
ccol = wx.Colour(int(ccolr), int(ccolg), int(ccolb))
dobjs = [
dict(shape='Line',
width=swid,
style=wx.SOLID,
color=scol,
args=sargs),
dict(shape='Circle',
width=cwid,
style=wx.SOLID,
color=ccol,
args=cargs)
]
if self.xhair_pixel is not None:
xwid, xcolr, xcolg, xcolb = swid, scolr, scolg, scolb
xcol = wx.Colour(int(xcolr), int(xcolg), int(xcolb))
xcol = wx.Colour(int(20), int(300), int(250))
hx = self.xhair_pixel['x']
hy = self.xhair_pixel['y']
xargs = [
hx - ssiz * iscale, hy - ssiz * iscale,
hx + ssiz * iscale, hy + ssiz * iscale
]
dobjs.append(
dict(shape='Line',
width=2,
style=wx.SOLID,
color=xcol,
args=xargs))
#print( "Showing xhair: ", xargs)
# print('Draw Objects ', dobjs)
self.imgpanel.draw_objects = dobjs
self.init_timer.Stop()
def onChangeCamera(self, evt=None):
if not self.cam_type.startswith('area'):
print('How did that happen?')
return
name = self.cam_adpref
prefix = None
dlg = wx.TextEntryDialog(self,
'Enter PV for Area Detector',
caption='Enter PV for Area Detector',
defaultValue=name)
dlg.Raise()
if dlg.ShowModal() == wx.ID_OK:
prefix = dlg.GetValue()
dlg.Destroy()
if prefix is not None:
self.imgpanel.set_prefix(prefix)
self.confpanel.set_prefix(prefix)
self.cam_adpref = prefix
def create_menus(self):
"Create the menubar"
mbar = wx.MenuBar()
fmenu = wx.Menu()
pmenu = wx.Menu()
omenu = wx.Menu()
add_menu(self,
fmenu,
label="&Read Config",
text="Read Configuration",
action=self.onReadConfig)
add_menu(self,
fmenu,
label="&Save Config",
text="Save Configuration",
action=self.onSaveConfig)
add_menu(self,
fmenu,
label="Show Projections\tCtrl+G",
text="Start Projection Plots",
action=self.onStartProjections)
add_menu(self,
fmenu,
label="Print Blurriness\tCtrl+B",
text="print blurriness",
action=self.onReportBlurry)
add_menu(self,
fmenu,
label="Stop Projection\tCtrl+C",
text="Stop Projection Plots",
action=self.onStopProjections)
add_menu(self,
fmenu,
label="Select &Working Directory\tCtrl+W",
text="change Working Folder",
action=self.onChangeWorkdir)
if self.cam_type.startswith('area'):
add_menu(self,
fmenu,
label="Change AreaDetector",
text="Change Camera to different AreaDetector",
action=self.onChangeCamera)
fmenu.AppendSeparator()
add_menu(self,
fmenu,
label="E&xit\tCtrl+x",
text="Quit Program",
action=self.onClose)
add_menu(self,
pmenu,
label="Export Positions",
text="Export Positions",
action=self.onExportPositions)
add_menu(self,
pmenu,
label="Import Positions",
text="Import Positions",
action=self.onImportPositions)
add_menu(self,
pmenu,
label="Erase Many Positions\tCtrl+E",
text="Select Multiple Positions to Erase",
action=self.onEraseMany)
add_menu(self,
omenu,
label="Image Overlays",
text="Setup Image Overlays",
action=self.onConfigOverlays)
vmove = wx.NewId()
verase = wx.NewId()
vreplace = wx.NewId()
cenfine = wx.NewId()
self.menu_opts = {
vmove: 'v_move',
verase: 'v_erase',
vreplace: 'v_replace',
cenfine: 'center_with_fine_stages'
}
mitem = omenu.Append(vmove, "Verify Go To ",
"Prompt to Verify Moving with 'Go To'",
wx.ITEM_CHECK)
mitem.Check()
self.Bind(wx.EVT_MENU, self.onMenuOption, mitem)
mitem = omenu.Append(verase, "Verify Erase",
"Prompt to Verify Erasing Positions",
wx.ITEM_CHECK)
mitem.Check()
self.Bind(wx.EVT_MENU, self.onMenuOption, mitem)
mitem = omenu.Append(vreplace, "Verify Overwrite",
"Prompt to Verify Overwriting Positions",
wx.ITEM_CHECK)
mitem.Check()
self.Bind(wx.EVT_MENU, self.onMenuOption, mitem)
mitem = omenu.Append(cenfine, "Center With Fine Stages",
"Bring to Center will move the Fine Stages",
wx.ITEM_CHECK)
mitem.Check(0)
self.Bind(wx.EVT_MENU, self.onMenuOption, mitem)
omenu.AppendSeparator()
# print( 'Create Menus ', self.ctrlpanel.subpanels)
# for key, val in self.config['stages'].items():
# print( key, val)
for name, panel in self.ctrlpanel.subpanels.items():
show = 0
label = 'Enable %s' % name
mid = wx.NewId()
self.menu_opts[mid] = label
for mname, data in self.config['stages'].items():
if data['group'] == name:
show = show + data['show']
mitem = omenu.Append(mid, label, label, wx.ITEM_CHECK)
if show > 0:
mitem.Check()
self.Bind(wx.EVT_MENU,
Closure(self.onShowHide, name=name, panel=panel), mitem)
mbar.Append(fmenu, '&File')
mbar.Append(omenu, '&Options')
mbar.Append(pmenu, 'Positions')
if len(self.config['scandb'].get('offline', '')):
cmenu = wx.Menu()
# add_menu(self, cmenu, label="Calibrate Microscope",
# text="Calibrate to Offline Microscope",
# action = self.pospanel.onMicroscopeCalibrate)
add_menu(self,
cmenu,
label="Copy Positions from Offline Microscope",
text="Copy Positions from Offline Microscope",
action=self.pospanel.onMicroscopeTransfer)
mbar.Append(cmenu, 'Offline Microscope')
self.SetMenuBar(mbar)
def onShowHide(self, event=None, panel=None, name='---'):
showval = {True: 1, False: 0}[event.IsChecked()]
if showval:
panel.Enable()
else:
panel.Disable()
for mname, data in self.config['stages'].items():
if data['group'] == name:
data['show'] = showval
def onEraseMany(self, evt=None, **kws):
self.pospanel.onEraseMany(event=evt)
evt.Skip()
def onConfigOverlays(self, evt=None, **kws):
shown = False
if self.overlay_frame is not None:
try:
self.overlay_frame.Raise()
shown = True
except:
del self.overlay_frame
if not shown:
self.overlayframe = OverlayFrame(image_panel=self.imgpanel,
config=self.config)
def onMenuOption(self, evt=None):
"""events for options menu: move, erase, overwrite """
setattr(self, self.menu_opts[evt.GetId()], evt.IsChecked())
def read_config(self, configfile=None, get_dir=False):
"open/read ini config file"
if get_dir:
ret = SelectWorkdir(self)
if ret is None:
self.Destroy()
os.chdir(ret)
self.cnf = StageConfig(configfile)
self.config = self.cnf.config
gui = self.config['gui']
self.workdir_file = gui.get('workdir_file', 'sampleviewer_workdir.txt')
self.iconfile = gui.get('icon_file', '')
self.autosave_file = gui.get('autosave_file',
'SampleStage_autosave.ini')
self.v_move = gui.get('verify_move', True)
self.v_erase = gui.get('verify_erase', True)
self.v_replace = gui.get('verify_overwrite', True)
self.center_with_fine_stages = gui.get('center_with_fine_stages',
False)
self.SetTitle(gui.get('title', 'Microscope'))
cam = self.config['camera']
self.imgdir = cam.get('image_folder', 'Sample_Images')
self.cam_type = cam.get('type', 'fly2').lower()
self.cam_fly2id = cam.get('fly2_id', 0)
self.cam_adpref = cam.get('ad_prefix', '')
self.cam_adform = cam.get('ad_format', 'JPEG')
self.cam_weburl = cam.get('web_url',
'http://164.54.160.115/jpg/2/image.jpg')
self.get_cam_calib()
try:
pref = self.imgdir.split('_')[0]
except:
pref = 'Sample'
self.htmllog = '%sStage.html' % pref
if not os.path.exists(self.imgdir):
os.makedirs(self.imgdir)
if not os.path.exists(self.htmllog):
self.begin_htmllog()
self.config = self.cnf.config
self.stages = OrderedDict()
for mname, data in self.config.get('stages', {}).items():
mot = Motor(name=mname)
if data['prec'] is None:
data['prec'] = mot.precision
if data['desc'] is None:
data['desc'] = mot.description
if data['maxstep'] is None:
data['maxstep'] = (mot.high_limit - mot.low_limit) / 2.10
self.stages[mname] = data
def get_cam_calib(self):
cam = self.config['camera']
cx = self.cam_calibx = float(cam.get('calib_x', 0.001))
cy = self.cam_caliby = float(cam.get('calib_y', 0.001))
return cx, cy
def begin_htmllog(self):
"initialize log file"
fout = open(self.htmllog, 'w')
fout.write(self.html_header)
fout.close()
def save_image(self, fname):
"save image to file"
imgdata = self.imgpanel.SaveImage(fname)
if imgdata is None:
self.write_message('could not save image to %s' % fname)
else:
self.write_message('saved image to %s' % fname)
return imgdata
def autosave(self, positions=None):
self.cnf.Save(self.autosave_file, positions=positions)
def write_htmllog(self, name, thispos):
stages = self.config['stages']
img_folder = self.config['camera']['image_folder']
junk, img_file = os.path.split(thispos['image'])
imgfile = os.path.join(img_folder, img_file)
txt = []
html_fmt = """<hr>
<table><tr><td><a href='%s'> <img src='%s' width=350></a></td>
<td><table><tr><td>Position:</td><td>%s</td><td>%s</td></tr>
<tr><td>Motor Name</td><td>PV Name</td><td>Value</td></tr>
%s
</table></td></tr></table>"""
pos_fmt = " <tr><td> %s </td><td> %s </td><td> %f</td></tr>"
for pvname, value in thispos['position'].items():
txt.append(pos_fmt % (stages[pvname]['desc'], pvname, value))
fout = open(self.htmllog, 'a')
fout.write(
html_fmt %
(imgfile, imgfile, name, thispos['timestamp'], '\n'.join(txt)))
fout.close()
def write_message(self, msg='', index=0):
"write to status bar"
self.statusbar.SetStatusText(msg, index)
def write_framerate(self, msg):
"write to status bar"
self.statusbar.SetStatusText(msg, 1)
def onShowCrosshair(self, event=None, show=True, **kws):
self.xhair_pixel = None
if show:
self.xhair_pixel = self.last_pixel
def onAFTimer(self, event=None, **kws):
if self.af_done:
self.af_thread.join()
self.af_timer.Stop()
if self.ctrlpanel.af_message is not None:
self.ctrlpanel.af_message.SetLabel('')
self.ctrlpanel.af_button.Enable()
def onAutoFocus(self, event=None, **kws):
self.af_done = False
self.ctrlpanel.af_button.Disable()
self.af_thread = Thread(target=self.do_autofocus)
self.af_timer = wx.Timer(self)
self.Bind(wx.EVT_TIMER, self.onAFTimer, self.af_timer)
self.af_timer.Start(2000)
self.af_thread.start()
def do_autofocus(self):
report = None
if self.ctrlpanel.af_message is not None:
report = self.ctrlpanel.af_message.SetLabel
if report is not None:
report('Auto-setting exposure')
self.imgpanel.AutoSetExposureTime()
report('Auto-focussing start')
def make_fibs(max=3000):
f = [1., 1.]
i = 0
while True:
val = f[i] + f[i + 1]
if val > max:
break
f.append(val)
i += 1
return f
zstage = self.ctrlpanel.motors['z']._pvs['VAL']
start_pos = zstage.get()
focus_data = []
def get_score(pos):
zpos = start_pos + pos * 0.001
zstage.put(zpos, wait=True)
time.sleep(0.2)
score = image_blurriness(self.imgpanel)
dat = (pos, zstage.get(), score)
focus_data.append(dat)
return score
# step 1: take up to 15 steps of 250 microns
# while score is still improving
report('Auto-focussing finding rough focus')
scores = []
NMAX = 15
step = 250.0
score0 = get_score(0)
scorep = get_score(step)
scorem = get_score(-step)
sign = None
best = 0.0
if scorem < score0:
score0 = scorem
sign = -1.0
elif scorep < score0:
score0 = scorep
sign = 1.0
if sign is not None:
i = 1
while i < NMAX:
i = i + 1
tmp = sign * step * (i + 1)
score = get_score(tmp)
if score > score0:
break
score0, best = score, tmp
zstage.put(start_pos + best * 0.001, wait=True)
# now refine
start_pos = zstage.get()
report('Auto-focussing refining focus')
start, stop = -300, 300
fibs = make_fibs(max=abs(stop - start))
nfibs = len(fibs)
step = fibs[nfibs - 3] / fibs[nfibs - 1]
best = (start + stop) / 2
z1, z2 = int(start + step * (stop - start)), int(stop - step *
(stop - start))
score1, score2 = get_score(z1), get_score(z2)
for i in range(nfibs - 2):
step = fibs[nfibs - i - 3] / fibs[nfibs - i - 1]
report("Auto-focussing refining focus %i " % (i + 1))
if score1 > score2:
start = z1
best = int(stop - step * (stop - start))
z1, z2 = z2, best
score1, score2 = score2, get_score(best)
else:
stop = z2
best = int(start + step * (stop - start))
z1, z2 = best, z1
score1, score2 = get_score(best), score1
if abs(z1 - z2) < 2:
break
get_score(best)
report('Auto-focussing done. ')
self.ctrlpanel.af_button.Enable()
def onMoveToCenter(self, event=None, **kws):
"bring last pixel to image center"
p = self.last_pixel
if p is None:
return
cal_x, cal_y = self.get_cam_calib()
dx = 0.001 * cal_x * (p['x'] - p['xmax'] / 2.0)
dy = 0.001 * cal_y * (p['y'] - p['ymax'] / 2.0)
mots = self.ctrlpanel.motors
xmotor, ymotor = 'x', 'y'
if self.center_with_fine_stages and 'finex' in mots:
xmotor, ymotor = 'finex', 'finey'
xscale, yscale = 1.0, 1.0
for stage_info in self.stages.values():
if stage_info['desc'].lower() == xmotor:
xscale = stage_info['scale']
if stage_info['desc'].lower() == ymotor:
yscale = stage_info['scale']
mots[xmotor].VAL += dx * xscale
mots[ymotor].VAL += dy * yscale
self.onSelectPixel(p['xmax'] / 2.0,
p['ymax'] / 2.0,
xmax=p['xmax'],
ymax=p['ymax'])
def onSelectPixel(self, x, y, xmax=100, ymax=100):
" select a pixel from image "
self.last_pixel = dict(x=x, y=y, xmax=xmax, ymax=ymax)
cal_x, cal_y = self.get_cam_calib()
self.confpanel.on_selected_pixel(x,
y,
xmax,
ymax,
cam_calibx=cal_x,
cam_caliby=cal_y)
def onPixelMotion(self, x, y, xmax=100, ymax=100):
" select a pixel from image "
fmt = """Pixel=(%i, %i) (%.1f, %.1f)um from center, (%.1f, %.1f)um from selected"""
if x > 0 and x < xmax and y > 0 and y < ymax:
dx = abs(self.cam_calibx * (x - xmax / 2.0))
dy = abs(self.cam_caliby * (y - ymax / 2.0))
ux, uy = 0, 0
if self.last_pixel is not None:
lastx = self.last_pixel['x']
lasty = self.last_pixel['y']
ux = abs(self.cam_calibx * (x - lastx))
uy = abs(self.cam_caliby * (y - lasty))
pix_msg = fmt % (x, y, dx, dy, ux, uy)
self.write_message(pix_msg)
if not self.confpanel.img_size_shown:
self.confpanel.img_size.SetLabel("(%i, %i)" % (xmax, ymax))
self.confpanel.img_size_shown = True
def onClose(self, event=None):
if wx.ID_YES == popup(self,
"Really Quit?",
"Exit Sample Stage?",
style=wx.YES_NO | wx.NO_DEFAULT
| wx.ICON_QUESTION):
fout = open(self.workdir_file, 'w')
fout.write("%s\n" % os.path.abspath(os.curdir))
fout.close()
self.imgpanel.Stop()
try:
self.overlay_frame.Destroy()
except:
pass
self.Destroy()
def onExportPositions(self, event=None):
curpath = os.getcwd()
fname = FileSave(
self,
'Export Positions File',
wildcard='Position Files (*.pos)|*.pos|All files (*.*)|*.*',
default_file='Save.pos')
if fname is not None:
self.pospanel.SavePositions(fname)
self.write_message('Saved Positions File %s' % fname)
os.chdir(curpath)
def onImportPositions(self, event=None):
curpath = os.getcwd()
fname = FileOpen(
self,
'Import Positions File',
wildcard='Position Files (*.pos)|*.pos|All files (*.*)|*.*',
default_file='Save.pos')
if fname is not None:
self.pospanel.LoadPositions(fname)
self.write_message('Loaded Positions from File %s' % fname)
os.chdir(curpath)
def onChangeWorkdir(self, event=None):
ret = SelectWorkdir(self)
if ret is None:
return
os.chdir(ret)
cam = self.config['camera']
self.imgdir = cam.get('image_folder', 'Sample_Images')
if not os.path.exists(self.imgdir):
os.makedirs(self.imgdir)
if not os.path.exists(self.htmllog):
self.begin_htmllog()
def onReportBlurry(self, event=None):
score = image_blurriness(self.imgpanel)
print(" blurriness = %.3f" % (score))
def onStartProjections(self, event=None):
try:
self.xplot.Raise()
except:
self.xplot = PlotFrame(parent=self)
try:
self.yplot.Raise()
except:
self.yplot = PlotFrame(parent=self)
self.proj_start = True
self.proj_timer = wx.Timer(self)
self.Bind(wx.EVT_TIMER, self.onShowProjections, self.proj_timer)
self.proj_timer.Start(500)
def onStopProjections(self, event=None):
self.proj_timer.Stop()
def onShowProjections(self, event=None):
dat = self.imgpanel.grab_data()
shape = dat.shape
if len(shape) == 3:
dat = dat.sum(axis=2)
cx, cy = self.get_cam_calib()
kws = dict(ylabel='intensity',
xlabel='distance ($\mu\mathrm{m}$)',
marker='+',
markersize=4)
_y = (np.arange(shape[0]) - shape[0] / 2.0) * abs(cx)
_x = (np.arange(shape[1]) - shape[1] / 2.0) * abs(cy)
_xi = dat.sum(axis=0)
_yi = dat.sum(axis=1)
ymin = min((min(_xi), min(_yi)))
ymax = max((max(_xi), max(_yi)))
if self.proj_start:
self.xplot.plot(_x, _xi, title='X projection', **kws)
self.yplot.plot(_y, _yi, title='Y projection', **kws)
self.xplot.Show()
self.yplot.Show()
self.proj_start = False
else:
self.xplot.panel.update_line(0,
_x,
_xi,
draw=True,
update_limits=True)
self.yplot.panel.update_line(0,
_y,
_yi,
draw=True,
update_limits=True)
self.xplot.panel.axes.set_ylim((ymin, ymax), emit=True)
self.yplot.panel.axes.set_ylim((ymin, ymax), emit=True)
# print('X lims: ', self.xplot.panel.conf.zoom_lims, xlims)
# self.xplot.panel.set_xylims(xlims)
# self.yplot.panel.set_xylims(ylims)
def onSaveConfig(self, event=None):
fname = FileSave(self,
'Save Configuration File',
wildcard='INI (*.ini)|*.ini|All files (*.*)|*.*',
default_file='SampleStage.ini')
if fname is not None:
self.cnf.Save(fname)
self.write_message('Saved Configuration File %s' % fname)
def onReadConfig(self, event=None):
curpath = os.getcwd()
fname = FileOpen(self,
'Read Configuration File',
wildcard='INI (*.ini)|*.ini|All files (*.*)|*.*',
default_file='SampleStage.ini')
if fname is not None:
self.read_config(fname)
self.connect_motors()
self.pospanel.set_positions(self.config['positions'])
self.write_message('Read Configuration File %s' % fname)
os.chdir(curpath)
class XRD2D_DisplayFrame(ImageFrame):
"""
MatPlotlib Image Display on a wx.Frame, using ImagePanel
"""
def __init__(self, _larch=None, parent=None, size=None, mode='intensity',
move_callback=None, save_callback=None,
show_xsections=False, cursor_labels=None,
output_title='Image', **kws):
self.xrmfile = None
self.map = None
self.move_callback = move_callback
self.save_callback = save_callback
self.larch = _larch
if self.larch is None:
self.init_larch()
ImageFrame.__init__(self, parent=parent, size=size,
cursor_labels=cursor_labels, mode=mode,
output_title=output_title, **kws)
self.panel.cursor_mode = 'zoom'
self.panel.xaxis = 'q'
self.panel.report_leftdown = self.report_leftdown
self.panel.report_motion = self.report_motion
self.prof_plotter = None
self.zoom_ini = None
self.lastpoint = [None, None]
self.this_point = None
self.rbbox = None
def display(self, map, xrmfile=None, ai=None, mask=None, **kws):
self.xrmfile = xrmfile
self.map = map
self.title = ''
if 'title' in kws:
self.title = kws['title']
ImageFrame.display(self, map, **kws)
if self.panel.conf.auto_contrast:
self.set_contrast_levels()
self.ai = ai
self.mask = mask
if np.shape(self.mask) == np.shape(map):
self.masked_map = map * (np.ones(np.shape(self.mask))-mask.value)
self.panel.xdata = np.arange(map.shape[0])
self.panel.ydata = np.arange(map.shape[0])
def init_larch(self):
if self.larch is None:
self.larch = Interpreter()
def prof_motion(self, event=None):
if not event.inaxes or self.zoom_ini is None:
return
try:
xmax, ymax = event.x, event.y
except:
return
xmin, ymin, xd, yd = self.zoom_ini
if event.xdata is not None:
self.lastpoint[0] = event.xdata
if event.ydata is not None:
self.lastpoint[1] = event.ydata
yoff = self.panel.canvas.figure.bbox.height
ymin, ymax = yoff - ymin, yoff - ymax
zdc = wx.ClientDC(self.panel.canvas)
zdc.SetLogicalFunction(wx.XOR)
zdc.SetBrush(wx.TRANSPARENT_BRUSH)
zdc.SetPen(wx.Pen('White', 2, wx.SOLID))
zdc.ResetBoundingBox()
if not is_wxPhoenix:
zdc.BeginDrawing()
# erase previous box
if self.rbbox is not None:
zdc.DrawLine(*self.rbbox)
self.rbbox = (xmin, ymin, xmax, ymax)
zdc.DrawLine(*self.rbbox)
if not is_wxPhoenix:
zdc.EndDrawing()
def prof_leftdown(self, event=None):
self.report_leftdown(event=event)
if event.inaxes and len(self.map.shape) == 2:
self.lastpoint = [None, None]
self.zoom_ini = [event.x, event.y, event.xdata, event.ydata]
def prof_leftup(self, event=None):
if len(self.map.shape) != 2:
return
if self.rbbox is not None:
zdc = wx.ClientDC(self.panel.canvas)
zdc.SetLogicalFunction(wx.XOR)
zdc.SetBrush(wx.TRANSPARENT_BRUSH)
zdc.SetPen(wx.Pen('White', 2, wx.SOLID))
zdc.ResetBoundingBox()
if not is_wxPhoenix:
zdc.BeginDrawing()
zdc.DrawLine(*self.rbbox)
if not is_wxPhoenix:
zdc.EndDrawing()
self.rbbox = None
if self.zoom_ini is None or self.lastpoint[0] is None:
return
x0 = int(self.zoom_ini[2])
x1 = int(self.lastpoint[0])
y0 = int(self.zoom_ini[3])
y1 = int(self.lastpoint[1])
dx, dy = abs(x1-x0), abs(y1-y0)
self.lastpoint, self.zoom_ini = [None, None], None
if dx < 2 and dy < 2:
self.zoom_ini = None
return
outdat = []
if dy > dx:
_y0 = min(int(y0), int(y1+0.5))
_y1 = max(int(y0), int(y1+0.5))
for iy in range(_y0, _y1):
ix = int(x0 + (iy-int(y0))*(x1-x0)/(y1-y0))
outdat.append((ix, iy))
else:
_x0 = min(int(x0), int(x1+0.5))
_x1 = max(int(x0), int(x1+0.5))
for ix in range(_x0, _x1):
iy = int(y0 + (ix-int(x0))*(y1-y0)/(x1-x0))
outdat.append((ix, iy))
x, y, z = [], [], []
for ix, iy in outdat:
x.append(ix)
y.append(iy)
z.append(self.panel.conf.data[iy,ix])
self.prof_dat = dy>dx, outdat
if self.prof_plotter is not None:
try:
self.prof_plotter.Raise()
self.prof_plotter.clear()
except (AttributeError, PyDeadObjectError):
self.prof_plotter = None
if self.prof_plotter is None:
self.prof_plotter = PlotFrame(self, title='Profile')
self.prof_plotter.panel.report_leftdown = self.prof_report_coords
xlabel, y2label = 'Pixel (x)', 'Pixel (y)'
if dy > dx:
x, y = y, x
xlabel, y2label = y2label, xlabel
self.prof_plotter.panel.clear() # reset_config()
if len(self.title) < 1:
self.title = os.path.split(self.xrmfile.filename)[1]
opts = dict(linewidth=2, marker='+', markersize=3,
show_legend=True, xlabel=xlabel)
self.prof_plotter.plot(x, z, title=self.title, color='blue',
zorder=20, xmin=min(x)-3, xmax=max(x)+3,
ylabel='counts', label='counts', **opts)
self.prof_plotter.oplot(x, y, y2label=y2label, label=y2label,
zorder=3, side='right', color='#771111', **opts)
self.prof_plotter.panel.unzoom_all()
self.prof_plotter.Show()
self.zoom_ini = None
self.panel.cursor_mode = 'zoom'
def prof_report_coords(self, event=None):
"""override report leftdown for profile plotter"""
if event is None:
return
ex, ey = event.x, event.y
msg = ''
plotpanel = self.prof_plotter.panel
axes = plotpanel.fig.get_axes()[0]
write = plotpanel.write_message
try:
x, y = axes.transData.inverted().transform((ex, ey))
except:
x, y = event.xdata, event.ydata
if x is None or y is None:
return
if self.ai is None:
_point = 0, 0, 0
for ix, iy in self.prof_dat[1]:
if (int(x) == ix and not self.prof_dat[0] or
int(x) == iy and self.prof_dat[0]):
_point = (ix, iy,
self.panel.conf.data[iy, ix])
msg = "Pixel [%i, %i], Intensity= %g" % _point
else:
ai = self.ai
xcenter = ai._poni2/ai.detector.pixel2 ## units pixels
ycenter = ai._poni1/ai.detector.pixel1 ## units pixels
_point = 0, 0, 0, 0, 0
for ix, iy in self.prof_dat[1]:
if (int(x) == ix and not self.prof_dat[0] or
int(x) == iy and self.prof_dat[0]):
x_pix = ix - xcenter ## units pixels
y_pix = iy - ycenter ## units pixels
x_m = x_pix * ai.detector.pixel2 ## units m
y_m = y_pix * ai.detector.pixel1 ## units m
twth = np.arctan2(math.sqrt(x_m**2 + y_m**2),ai._dist) ## radians
twth = np.degrees(twth) ## units degrees
eta = np.arctan2(y_m,x_m) ## units radians
eta = np.degrees(eta) ## units degrees
_point = (ix, iy, twth, eta, self.panel.conf.data[iy, ix])
msg = 'Pixel [%i, %i], 2TH=%.2f, ETA=%.1f, Intensity= %g' % _point
write(msg, panel=0)
def report_leftdown(self, event=None):
if event is None:
return
if event.xdata is None or event.ydata is None:
return
ix, iy = int(round(event.xdata)), int(round(event.ydata))
conf = self.panel.conf
if conf.flip_ud: iy = conf.data.shape[0] - iy
if conf.flip_lr: ix = conf.data.shape[1] - ix
self.this_point = None
msg = ''
if (ix >= 0 and ix < conf.data.shape[1] and
iy >= 0 and iy < conf.data.shape[0]):
pos = ''
pan = self.panel
labs, vals = [], []
if pan.xdata is not None:
labs.append(pan.xlab)
vals.append(pan.xdata[ix])
if pan.ydata is not None:
labs.append(pan.ylab)
vals.append(pan.ydata[iy])
dval = conf.data[iy, ix]
if len(pan.data_shape) == 3:
dval = "%.4g, %.4g, %.4g" % tuple(dval)
else:
dval = "%.4g" % dval
if pan.xdata is not None and pan.ydata is not None:
self.this_point = (ix, iy)
if self.ai is None:
msg = "Pixel [%i, %i], Intensity=%s " % (ix, iy, dval)
else:
ai = self.ai
xcenter = ai._poni2/ai.detector.pixel2 ## units pixels
ycenter = ai._poni1/ai.detector.pixel1 ## units pixels
x_pix = ix - xcenter ## units pixels
y_pix = iy - ycenter ## units pixels
x_m = x_pix * ai.detector.pixel2 ## units m
y_m = y_pix * ai.detector.pixel1 ## units m
twth = np.arctan2(math.sqrt(x_m**2 + y_m**2),ai._dist) ## radians
twth = np.degrees(twth) ## units degrees
eta = np.arctan2(y_m,x_m) ## units radians
eta = np.degrees(eta) ## units degrees
msg = 'Pixel [%i, %i], 2TH=%.2f deg., ETA=%.1f deg., Intensity= %s' % (ix,
iy, twth, eta, dval)
self.panel.write_message(msg, panel=0)
def report_motion(self, event=None):
return
def CustomConfig(self, panel, sizer, irow):
"""config panel for left-hand-side of frame"""
conf = self.panel.conf
lpanel = panel
lsizer = sizer
labstyle = wx.ALIGN_LEFT|wx.LEFT|wx.TOP|wx.EXPAND
self.MskCkBx = wx.CheckBox(panel, label='Apply mask?')
self.MskCkBx.Bind(wx.EVT_CHECKBOX, self.onApplyMask)
sizer.Add(self.MskCkBx, (irow+1,0), (1,4), labstyle, 3)
self.LoadBtn = wx.Button(panel, label='Load New Mask')
self.LoadBtn.Bind(wx.EVT_BUTTON, self.onLoadMask)
sizer.Add(self.LoadBtn, (irow+2,0), (1,4), labstyle, 3)
self.ReCalc1D = wx.Button(panel, label='Replot 1DXRD')
self.ReCalc1D.Bind(wx.EVT_BUTTON, self.onReplot1DXRD)
sizer.Add(self.ReCalc1D, (irow+3,0), (1,4), labstyle, 3)
def onApplyMask(self, event):
'''
Applies mask to 2DXRD map
mkak 2016.09.29
'''
if event.GetEventObject().GetValue():
if self.masked_map is None:
print('Mask file not defined.')
question = 'No mask found in map file. Would you like to load a new file now?'
caption = 'Load mask file?'
dlg = wx.MessageDialog(self, question, caption, wx.YES_NO | wx.ICON_QUESTION)
print 'answer:', dlg.ShowModal() # == wx.ID_YES
read = dlg.ShowModal()
dlg.Destroy()
if read == wx.ID_YES:
self.onLoadMask()
self.MskCkBx.SetValue(False)
else:
ImageFrame.display(self, self.masked_map)
else:
ImageFrame.display(self, self.map)
def onLoadMask(self, evt=None):
wildcards = 'pyFAI mask (*.edf)|*.edf|All files (*.*)|*.*'
dlg = wx.FileDialog(self, message='Choose XRD mask file',
defaultDir=os.getcwd(),
wildcard=wildcards, style=wx.FD_OPEN)
edffile, read = None, False
if dlg.ShowModal() == wx.ID_OK:
read = True
edffile = dlg.GetPath().replace('\\', '/')
dlg.Destroy()
if read:
print('Reading mask file: %s' % edffile)
try:
import fabio
self.mask = fabio.open(edffile).data
self.masked_map = self.map * (np.ones(np.shape(self.mask))-self.mask)
self.MskCkBx.SetValue(True)
ImageFrame.display(self, self.masked_map)
except:
print('File must be .edf format; user must have fabio installed.')
## Can this be called here?
#readEDFfile(self,name='mask',keyword='maskfile')
#add_calibration()
def onReplot1DXRD(self, evt=None):
print('Not yet implemented.')
class EditColumnFrame(wx.Frame):
"""Set Column Labels for a file"""
def __init__(self,
parent,
group=None,
last_array_sel=None,
read_ok_cb=None,
edit_groupname=True):
self.parent = parent
self.dgroup = group
if not hasattr(self.dgroup, 'is_xas'):
try:
self.dgroup.is_xas = 'energ' in self.dgroup.array_labels[
0].lower()
except:
self.dgroup.is_xas = False
self.read_ok_cb = read_ok_cb
self.array_sel = {
'xpop': '',
'xarr': None,
'ypop': '',
'yop': '/',
'yarr1': None,
'yarr2': None,
'use_deriv': False
}
if last_array_sel is not None:
self.array_sel.update(last_array_sel)
if self.array_sel['yarr2'] is None and 'i0' in self.dgroup.array_labels:
self.array_sel['yarr2'] = 'i0'
if self.array_sel['yarr1'] is None:
if 'itrans' in self.dgroup.array_labels:
self.array_sel['yarr1'] = 'itrans'
elif 'i1' in self.dgroup.array_labels:
self.array_sel['yarr1'] = 'i1'
message = "Build Arrys from Data Columns for %s" % self.dgroup.filename
wx.Frame.__init__(self,
None,
-1,
'Build Arrays from Data Columns for %s' %
self.dgroup.filename,
style=FRAMESTYLE)
self.SetFont(Font(10))
panel = scrolled.ScrolledPanel(self)
self.SetMinSize((600, 600))
self.colors = GUIColors()
self.plotframe = None
# title row
title = SimpleText(panel,
message,
font=Font(13),
colour=self.colors.title,
style=LCEN)
opts = dict(action=self.onColumnChoice, size=(120, -1))
arr_labels = self.dgroup.array_labels
yarr_labels = arr_labels + ['1.0', '0.0', '']
xarr_labels = arr_labels + ['<index>']
self.xarr = Choice(panel, choices=xarr_labels, **opts)
self.yarr1 = Choice(panel, choices=arr_labels, **opts)
self.yarr2 = Choice(panel, choices=yarr_labels, **opts)
opts['size'] = (90, -1)
self.xpop = Choice(panel, choices=XPRE_OPS, **opts)
self.ypop = Choice(panel, choices=YPRE_OPS, **opts)
opts['size'] = (50, -1)
self.yop = Choice(panel, choices=ARR_OPS, **opts)
ylab = SimpleText(panel, 'Y = ')
xlab = SimpleText(panel, 'X = ')
self.xsuf = SimpleText(panel, '')
self.ysuf = SimpleText(panel, '')
self.xpop.SetStringSelection(self.array_sel['xpop'])
self.ypop.SetStringSelection(self.array_sel['ypop'])
self.yop.SetStringSelection(self.array_sel['yop'])
if '(' in self.array_sel['ypop']:
self.ysuf.SetLabel(')')
ixsel, iysel, iy2sel = 0, 1, len(yarr_labels) - 1
if self.array_sel['xarr'] in xarr_labels:
ixsel = xarr_labels.index(self.array_sel['xarr'])
if self.array_sel['yarr1'] in arr_labels:
iysel = arr_labels.index(self.array_sel['yarr1'])
if self.array_sel['yarr2'] in yarr_labels:
iy2sel = yarr_labels.index(self.array_sel['yarr2'])
self.xarr.SetSelection(ixsel)
self.yarr1.SetSelection(iysel)
self.yarr2.SetSelection(iy2sel)
opts['size'] = (150, -1)
self.use_deriv = Check(panel,
label='use derivative',
default=self.array_sel['use_deriv'],
**opts)
self.is_xas = Check(panel,
label='use as XAS data',
default=self.dgroup.is_xas,
**opts)
bpanel = wx.Panel(panel)
bsizer = wx.BoxSizer(wx.HORIZONTAL)
bsizer.Add(Button(bpanel, 'Preview', action=self.onColumnChoice), 4)
bsizer.Add(Button(bpanel, 'OK', action=self.onOK), 4)
bsizer.Add(Button(bpanel, 'Cancel', action=self.onCancel), 4)
pack(bpanel, bsizer)
sizer = wx.GridBagSizer(4, 8)
sizer.Add(title, (0, 0), (1, 7), LCEN, 5)
ir = 1
sizer.Add(xlab, (ir, 0), (1, 1), CEN, 0)
sizer.Add(self.xpop, (ir, 1), (1, 1), CEN, 0)
sizer.Add(self.xarr, (ir, 2), (1, 1), CEN, 0)
sizer.Add(self.xsuf, (ir, 3), (1, 1), CEN, 0)
ir += 1
sizer.Add(ylab, (ir, 0), (1, 1), CEN, 0)
sizer.Add(self.ypop, (ir, 1), (1, 1), CEN, 0)
sizer.Add(self.yarr1, (ir, 2), (1, 1), CEN, 0)
sizer.Add(self.yop, (ir, 3), (1, 1), CEN, 0)
sizer.Add(self.yarr2, (ir, 4), (1, 1), CEN, 0)
sizer.Add(self.ysuf, (ir, 5), (1, 1), CEN, 0)
ir += 1
sizer.Add(self.use_deriv, (ir, 0), (1, 3), LCEN, 0)
ir += 1
sizer.Add(self.is_xas, (ir, 0), (1, 3), LCEN, 0)
self.wid_groupname = None
if edit_groupname:
wid_grouplab = SimpleText(panel, 'Use Group Name: ')
self.wid_groupname = wx.TextCtrl(panel,
value=self.dgroup._groupname,
size=(100, -1))
ir += 1
sizer.Add(wid_grouplab, (ir, 0), (1, 2), LCEN, 3)
sizer.Add(self.wid_groupname, (ir, 2), (1, 3), LCEN, 3)
ir += 1
sizer.Add(bpanel, (ir, 0), (1, 5), LCEN, 3)
pack(panel, sizer)
ftext = wx.TextCtrl(self,
style=wx.TE_MULTILINE | wx.TE_READONLY,
size=(-1, 150))
try:
m = open(self.dgroup.filename, 'r')
text = m.read()
m.close()
except:
text = "The file '%s'\n was not found" % self.dgroup.filename
ftext.SetValue(text)
ftext.SetFont(Font(9))
mainsizer = wx.BoxSizer(wx.VERTICAL)
mainsizer.Add(panel, 0, wx.GROW | wx.ALL, 2)
mainsizer.Add(ftext, 1, LCEN | wx.GROW, 2)
pack(self, mainsizer)
self.Show()
self.Raise()
def onOK(self, event=None):
""" build arrays according to selection """
if not hasattr(self.dgroup, '_xdat'):
self.onColumnChoice()
if self.wid_groupname is not None:
self.dgroup._groupname = fix_varname(self.wid_groupname.GetValue())
if self.plotframe is not None:
try:
self.plotframe.Destroy()
except:
pass
if self.read_ok_cb is not None:
self.read_ok_cb(self.dgroup, self.array_sel)
self.Destroy()
def onCancel(self, event=None):
self.dgroup.import_ok = False
if self.plotframe is not None:
self.plotframe.Destroy()
self.Destroy()
def onColumnChoice(self, evt=None):
"""column selections changed calc _xdat and _ydat"""
# dtcorr = self.dtcorr.IsChecked()
dtcorr = False
use_deriv = self.use_deriv.IsChecked()
dgroup = self.dgroup
ix = self.xarr.GetSelection()
xname = self.xarr.GetStringSelection()
if xname == '<index>':
xname = self.dgroup.array_labels[0]
dgroup._index = 1.0 * np.arange(len(getattr(dgroup, xname)))
xname = '_index'
dgroup.is_xas = self.is_xas.IsChecked()
dgroup._xdat = getattr(dgroup, xname)
def do_preop(opwid, arr):
opstr = opwid.GetStringSelection().strip()
suf = ''
if opstr in ('-log(', 'log('):
suf = ')'
if opstr == 'log(':
arr = np.log(arr)
elif opstr == '-log(':
arr = -np.log(arr)
return suf, opstr, arr
xsuf, xpop, dgroup._xdat = do_preop(self.xpop, dgroup._xdat)
self.xsuf.SetLabel(xsuf)
try:
xunits = dgroup.array_units[ix].strip()
xlabel = '%s (%s)' % (xname, xunits)
except:
xlabel = xname
def get_data(group, arrayname, correct=False):
if hasattr(group, 'get_data'):
return group.get_data(arrayname, correct=correct)
return getattr(group, arrayname, None)
yname1 = self.yarr1.GetStringSelection().strip()
yname2 = self.yarr2.GetStringSelection().strip()
yop = self.yop.GetStringSelection().strip()
ylabel = yname1
if len(yname2) == 0:
yname2, yop = '1.0', '*'
else:
ylabel = "%s%s%s" % (ylabel, yop, yname2)
yarr1 = get_data(dgroup, yname1, correct=dtcorr)
if yname2 in ('0.0', '1.0'):
yarr2 = float(yname2)
if yop == '/': yarr2 = 1.0
else:
yarr2 = get_data(dgroup, yname2, correct=dtcorr)
dgroup._ydat = yarr1
if yop == '+':
dgroup._ydat = yarr1.__add__(yarr2)
elif yop == '-':
dgroup._ydat = yarr1.__sub__(yarr2)
elif yop == '*':
dgroup._ydat = yarr1.__mul__(yarr2)
elif yop == '/':
dgroup._ydat = yarr1.__truediv__(yarr2)
ysuf, ypop, dgroup._ydat = do_preop(self.ypop, dgroup._ydat)
self.ysuf.SetLabel(ysuf)
if use_deriv:
try:
dgroup._ydat = np.gradient(dgroup._ydat) / np.gradient(
dgroup._xdat)
except:
pass
self.array_sel = {
'xpop': xpop,
'xarr': xname,
'ypop': ypop,
'yop': yop,
'yarr1': yname1,
'yarr2': yname2,
'use_deriv': use_deriv
}
try:
npts = min(len(dgroup._xdat), len(dgroup._ydat))
except AttributeError:
print('Error calculating arrays (npts not correct)')
return
dgroup._npts = npts
dgroup.plot_xlabel = xlabel
dgroup.plot_ylabel = ylabel
dgroup._xdat = np.array(dgroup._xdat[:npts])
dgroup._ydat = np.array(dgroup._ydat[:npts])
if dgroup.is_xas:
dgroup.energy = dgroup._xdat
dgroup.mu = dgroup._ydat
self.raise_plotframe()
ppanel = self.plotframe.panel
popts = {}
path, fname = os.path.split(dgroup.filename)
popts['label'] = "%s: %s" % (fname, dgroup.plot_ylabel)
popts['title'] = fname
popts['ylabel'] = dgroup.plot_ylabel
popts['xlabel'] = dgroup.plot_xlabel
ppanel.plot(dgroup._xdat, dgroup._ydat, **popts)
def raise_plotframe(self):
if self.plotframe is not None:
try:
self.plotframe.Show()
except:
self.plotframe = None
if self.plotframe is None:
self.plotframe = PlotFrame(None, size=(650, 400))
self.plotframe.Show()
class MapImageFrame(ImageFrame):
"""
MatPlotlib Image Display on a wx.Frame, using ImagePanel
"""
def __init__(self, parent=None, size=(650, 650), mode='intensity',
lasso_callback=None, move_callback=None, save_callback=None,
show_xsections=False, cursor_labels=None,
with_savepos=True,output_title='Image', **kws):
# instdb=None, inst_name=None,
self.det = None
self.xrmfile = None
self.map = None
self.move_callback = move_callback
self.save_callback = save_callback
self.with_savepos = with_savepos
ImageFrame.__init__(self, parent=parent, size=size,
lasso_callback=lasso_callback,
cursor_labels=cursor_labels, mode=mode,
output_title=output_title, **kws)
self.panel.add_cursor_mode('prof', motion = self.prof_motion,
leftdown = self.prof_leftdown,
leftup = self.prof_leftup)
self.panel.report_leftdown = self.report_leftdown
self.panel.report_motion = self.report_motion
w0, h0 = self.GetSize()
w1, h1 = self.GetBestSize()
self.SetSize((max(w0, w1)+5, max(h0, h1)+5))
self.SetMinSize((500, 500))
self.prof_plotter = None
self.zoom_ini = None
self.lastpoint = [None, None]
self.this_point = None
self.rbbox = None
def display(self, map, det=None, xrmfile=None, xoff=0, yoff=0,
with_savepos=True, **kws):
self.xoff = xoff
self.yoff = yoff
self.det = det
self.xrmfile = xrmfile
self.map = map
self.title = ''
if 'title' in kws:
self.title = kws['title']
ImageFrame.display(self, map, **kws)
if 'x' in kws:
self.panel.xdata = kws['x']
if 'y' in kws:
self.panel.ydata = kws['y']
self.set_contrast_levels()
if self.save_callback is not None and hasattr(self, 'pos_name'):
self.pos_name.Enable(with_savepos)
sd = kws.get('subtitles', None)
if sd is not None:
for i, name in enumerate(('red', 'green', 'blue')):
sub = sd.get(name, None)
if sub is not None:
self.cmap_panels[i].title.SetLabel(sub)
def prof_motion(self, event=None):
if not event.inaxes or self.zoom_ini is None:
return
try:
xmax, ymax = event.x, event.y
except:
return
xmin, ymin, xd, yd = self.zoom_ini
if event.xdata is not None:
self.lastpoint[0] = event.xdata
if event.ydata is not None:
self.lastpoint[1] = event.ydata
yoff = self.panel.canvas.figure.bbox.height
ymin, ymax = yoff - ymin, yoff - ymax
zdc = wx.ClientDC(self.panel.canvas)
zdc.SetLogicalFunction(wx.XOR)
zdc.SetBrush(wx.TRANSPARENT_BRUSH)
zdc.SetPen(wx.Pen('White', 2, wx.SOLID))
zdc.ResetBoundingBox()
if not is_wxPhoenix:
zdc.BeginDrawing()
# erase previous box
if self.rbbox is not None:
zdc.DrawLine(*self.rbbox)
self.rbbox = (xmin, ymin, xmax, ymax)
zdc.DrawLine(*self.rbbox)
if not is_wxPhoenix:
zdc.EndDrawing()
def prof_leftdown(self, event=None):
self.report_leftdown(event=event)
if event.inaxes: # and len(self.map.shape) == 2:
self.lastpoint = [None, None]
self.zoom_ini = [event.x, event.y, event.xdata, event.ydata]
def prof_leftup(self, event=None):
# print("Profile Left up ", self.map.shape, self.rbbox)
if self.rbbox is not None:
zdc = wx.ClientDC(self.panel.canvas)
zdc.SetLogicalFunction(wx.XOR)
zdc.SetBrush(wx.TRANSPARENT_BRUSH)
zdc.SetPen(wx.Pen('White', 2, wx.SOLID))
zdc.ResetBoundingBox()
if not is_wxPhoenix:
zdc.BeginDrawing()
zdc.DrawLine(*self.rbbox)
if not is_wxPhoenix:
zdc.EndDrawing()
self.rbbox = None
if self.zoom_ini is None or self.lastpoint[0] is None:
return
x0 = int(self.zoom_ini[2])
x1 = int(self.lastpoint[0])
y0 = int(self.zoom_ini[3])
y1 = int(self.lastpoint[1])
dx, dy = abs(x1-x0), abs(y1-y0)
self.lastpoint, self.zoom_ini = [None, None], None
if dx < 2 and dy < 2:
self.zoom_ini = None
return
outdat = []
if dy > dx:
_y0 = min(int(y0), int(y1+0.5))
_y1 = max(int(y0), int(y1+0.5))
for iy in range(_y0, _y1):
ix = int(x0 + (iy-int(y0))*(x1-x0)/(y1-y0))
outdat.append((ix, iy))
else:
_x0 = min(int(x0), int(x1+0.5))
_x1 = max(int(x0), int(x1+0.5))
for ix in range(_x0, _x1):
iy = int(y0 + (ix-int(x0))*(y1-y0)/(x1-x0))
outdat.append((ix, iy))
x, y, z = [], [], []
for ix, iy in outdat:
x.append(ix)
y.append(iy)
z.append(self.panel.conf.data[iy, ix])
self.prof_dat = dy>dx, outdat
if self.prof_plotter is not None:
try:
self.prof_plotter.Raise()
self.prof_plotter.clear()
except (AttributeError, PyDeadObjectError):
self.prof_plotter = None
if self.prof_plotter is None:
self.prof_plotter = PlotFrame(self, title='Profile')
self.prof_plotter.panel.report_leftdown = self.prof_report_coords
xlabel, y2label = 'Pixel (x)', 'Pixel (y)'
x = np.array(x)
y = np.array(y)
z = np.array(z)
if dy > dx:
x, y = y, x
xlabel, y2label = y2label, xlabel
self.prof_plotter.panel.clear()
if len(self.title) < 1:
self.title = os.path.split(self.xrmfile.filename)[1]
opts = dict(linewidth=2, marker='+', markersize=3,
show_legend=True, xlabel=xlabel)
if isinstance(z[0], np.ndarray) and len(z[0]) == 3: # color plot
rlab = self.subtitles['red']
glab = self.subtitles['green']
blab = self.subtitles['blue']
self.prof_plotter.plot(x, z[:, 0], title=self.title, color='red',
zorder=20, xmin=min(x)-3, xmax=max(x)+3,
ylabel='counts', label=rlab, **opts)
self.prof_plotter.oplot(x, z[:, 1], title=self.title, color='darkgreen',
zorder=20, xmin=min(x)-3, xmax=max(x)+3,
ylabel='counts', label=glab, **opts)
self.prof_plotter.oplot(x, z[:, 2], title=self.title, color='blue',
zorder=20, xmin=min(x)-3, xmax=max(x)+3,
ylabel='counts', label=blab, **opts)
else:
self.prof_plotter.plot(x, z, title=self.title, color='blue',
zorder=20, xmin=min(x)-3, xmax=max(x)+3,
ylabel='counts', label='counts', **opts)
self.prof_plotter.oplot(x, y, y2label=y2label, label=y2label,
zorder=3, side='right', color='black', **opts)
self.prof_plotter.panel.unzoom_all()
self.prof_plotter.Show()
self.zoom_ini = None
self.zoom_mode.SetSelection(0)
self.panel.cursor_mode = 'zoom'
def prof_report_coords(self, event=None):
"""override report leftdown for profile plotter"""
if event is None:
return
ex, ey = event.x, event.y
msg = ''
plotpanel = self.prof_plotter.panel
axes = plotpanel.fig.properties()['axes'][0]
write = plotpanel.write_message
try:
x, y = axes.transData.inverted().transform((ex, ey))
except:
x, y = event.xdata, event.ydata
if x is None or y is None:
return
_point = 0, 0, 0, 0, 0
for ix, iy in self.prof_dat[1]:
if (int(x) == ix and not self.prof_dat[0] or
int(x) == iy and self.prof_dat[0]):
_point = (ix, iy,
self.panel.xdata[ix],
self.panel.ydata[iy],
self.panel.conf.data[iy, ix])
msg = "Pixel [%i, %i], X, OME = [%.4f mm, %.4f deg], Intensity= %g" % _point
write(msg, panel=0)
def onCursorMode(self, event=None, mode='zoom'):
self.panel.cursor_mode = mode
choice = self.zoom_mode.GetString(self.zoom_mode.GetSelection())
if event is not None:
if choice.startswith('Pick Area'):
#if 1 == event.GetInt():
self.panel.cursor_mode = 'lasso'
elif choice.startswith('Show Line'):
#elif 2 == event.GetInt():
self.panel.cursor_mode = 'prof'
def report_leftdown(self, event=None):
if event is None:
return
if event.xdata is None or event.ydata is None:
return
ix, iy = int(round(event.xdata)), int(round(event.ydata))
conf = self.panel.conf
if conf.flip_ud: iy = conf.data.shape[0] - iy
if conf.flip_lr: ix = conf.data.shape[1] - ix
self.this_point = None
msg = ''
if (ix >= 0 and ix < conf.data.shape[1] and
iy >= 0 and iy < conf.data.shape[0]):
pos = ''
pan = self.panel
labs, vals = [], []
if pan.xdata is not None:
labs.append(pan.xlab)
vals.append(pan.xdata[ix])
if pan.ydata is not None:
labs.append(pan.ylab)
vals.append(pan.ydata[iy])
pos = ', '.join(labs)
vals =', '.join(['%.4g' % v for v in vals])
pos = '%s = [%s]' % (pos, vals)
dval = conf.data[iy, ix]
if len(pan.data_shape) == 3:
dval = "%.4g, %.4g, %.4g" % tuple(dval)
else:
dval = "%.4g" % dval
if pan.xdata is not None and pan.ydata is not None:
self.this_point = (ix, iy)
msg = "Pixel [%i, %i], %s, Intensity=%s " % (ix, iy, pos, dval)
self.panel.write_message(msg, panel=0)
def report_motion(self, event=None):
return
def onLasso(self, data=None, selected=None, mask=None, **kws):
if hasattr(self.lasso_callback , '__call__'):
self.lasso_callback(data=data, selected=selected, mask=mask,
xoff=self.xoff, yoff=self.yoff, det=self.det,
xrmfile=self.xrmfile, **kws)
self.zoom_mode.SetSelection(0)
self.panel.cursor_mode = 'zoom'
def CustomConfig(self, panel, sizer=None, irow=0):
"""config panel for left-hand-side of frame"""
labstyle = wx.ALIGN_LEFT|wx.LEFT|wx.TOP|wx.EXPAND
if self.lasso_callback is None:
zoom_opts = ('Zoom to Rectangle',
'Show Line Profile')
else:
zoom_opts = ('Zoom to Rectangle',
'Pick Area for XRF Spectrum',
'Show Line Profile')
cpanel = wx.Panel(panel)
if sizer is None:
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(SimpleText(cpanel, label='Cursor Modes', style=labstyle),
0, labstyle, 3)
self.zoom_mode = wx.RadioBox(cpanel, -1, "",
wx.DefaultPosition, wx.DefaultSize,
zoom_opts, 1, wx.RA_SPECIFY_COLS)
self.zoom_mode.Bind(wx.EVT_RADIOBOX, self.onCursorMode)
sizer.Add(self.zoom_mode, 1, labstyle, 4)
if self.save_callback is not None:
sizer.Add(SimpleText(cpanel, label='Save Position:', style=labstyle),
0, labstyle, 3)
self.pos_name = wx.TextCtrl(cpanel, -1, '', size=(155, -1),
style=wx.TE_PROCESS_ENTER)
self.pos_name.Bind(wx.EVT_TEXT_ENTER, self.onSavePixel)
sizer.Add(self.pos_name, 0, labstyle, 3)
pack(cpanel, sizer)
return cpanel
def onMoveToPixel(self, event=None):
pass
def onSavePixel(self, event=None):
if self.this_point is not None and self.save_callback is not None:
name = str(event.GetString().strip())
# name = str(self.pos_name.GetValue().strip())
ix, iy = self.this_point
x = float(self.panel.xdata[int(ix)])
y = float(self.panel.ydata[int(iy)])
self.save_callback(name, ix, iy, x=x, y=y,
title=self.title, xrmfile=self.xrmfile)
class TomographyFrame(BaseFrame):
### COPY OF ImageFrame(BaseFrame) with portions of ImageMatrixFrame(BaseFrame)
'''
MatPlotlib Image Display ons a wx.Frame, using ImagePanel
'''
help_msg = '''Quick help:
Left-Click: to display X,Y coordinates and Intensity
Left-Drag: to zoom in on region
Right-Click: display popup menu with choices:
Zoom out 1 level
Zoom all the way out
--------------------
Rotate Image
Save Image
Keyboard Shortcuts: (For Mac OSX, replace 'Ctrl' with 'Apple')
Saving Images:
Ctrl-S: Save image to file
Ctrl-C: Copy image to clipboard
Ctrl-P: Print Image
Zooming:
Ctrl-Z: Zoom all the way out
Rotating/Flipping:
Ctrl-R: Rotate Clockwise
Ctrl-T: Flip Top/Bottom
Ctrl-F: Flip Left/Right
Image Enhancement:
Ctrl-L: Log-Scale Intensity
Ctrl-E: Enhance Contrast
'''
def __init__(self, parent=None, size=None, mode='intensity',
lasso_callback=None,
output_title='Tomography Display Frame', subtitles=None,
user_menus=None, **kws):
if size is None: size = (1500, 600)
self.lasso_callback = lasso_callback
self.user_menus = user_menus
self.cursor_menulabels = {}
self.cursor_menulabels.update(CURSOR_MENULABELS)
self.title = output_title
self.det = None
self.xrmfile = None
self.wxmplot_version = get_wxmplot_version()
BaseFrame.__init__(self, parent=parent,
title = output_title,
output_title=output_title,
size=size, **kws)
self.cmap_panels = {}
self.subtitles = {}
self.config_mode = None
if subtitles is not None:
self.subtitles = subtitles
sbar_widths = [-2, -1, -1]
sbar = self.CreateStatusBar(len(sbar_widths), wx.CAPTION)
sfont = sbar.GetFont()
sfont.SetWeight(wx.BOLD)
sfont.SetPointSize(10)
sbar.SetFont(sfont)
self.SetStatusWidths(sbar_widths)
self.optional_menus = []
self.bgcol = rgb2hex(self.GetBackgroundColour()[:3])
splitter = wx.SplitterWindow(self, style=wx.SP_LIVE_UPDATE)
splitter.SetMinimumPaneSize(225)
self.config_panel = wx.Panel(splitter)
self.main_panel = wx.Panel(splitter)
img_opts = dict(size = (700, 525),
dpi = 100,
data_callback = self.onDataChange,
lasso_callback = self.onLasso,
output_title = self.output_title)
self.tomo_frame = [TomoFrameClass(panel=ImagePanel(self.main_panel, **img_opts),
label='Sinogram'),
TomoFrameClass(panel=ImagePanel(self.main_panel, **img_opts),
label='Tomograph')]
for iframe in self.tomo_frame:
iframe.panel.nstatusbar = sbar.GetFieldsCount()
self.BuildMenu()
self.SetBackgroundColour('#F8F8F4')
self.imin_val = {}
self.imax_val = {}
self.islider_range = {}
self.config_mode = 'int'
if mode.lower().startswith('rgb'):
self.config_mode = 'rgb'
self.Build_ConfigPanel()
for iframe in self.tomo_frame:
kwargs = {'frame':iframe}
iframe.panel.add_cursor_mode('prof',
motion = partial(self.prof_motion, **kwargs),
leftdown = partial(self.prof_leftdown, **kwargs),
leftup = partial(self.prof_leftup, **kwargs))
iframe.panel.report_leftdown = partial(self.report_leftdown, **kwargs)
iframe.panel.messenger = self.write_message
self.prof_plotter = None
self.zoom_ini = None
self.lastpoint = [None, None]
self.this_point = None
self.rbbox = None
lsty = wx.ALIGN_LEFT|wx.LEFT|wx.TOP|wx.EXPAND
gsizer = wx.GridSizer(1, 2, 2, 2)
lsty |= wx.GROW|wx.ALL|wx.EXPAND|wx.ALIGN_CENTER|wx.ALIGN_CENTER_VERTICAL
gsizer.Add(self.tomo_frame[0].panel, 1, lsty, 2)
gsizer.Add(self.tomo_frame[1].panel, 1, lsty, 2)
pack(self.main_panel, gsizer)
splitter.SplitVertically(self.config_panel, self.main_panel, 1)
mainsizer = wx.BoxSizer(wx.VERTICAL)
mainsizer.Add(splitter, 1, wx.GROW|wx.ALL, 5)
pack(self, mainsizer)
def display(self, map1, map2, title=None, colormap=None, style='image',
subtitles=None, name1='Sinogram', name2='Tomograph',
xlabel='x', ylabel='y', rotlabel='theta',
x=None, y=None, rot=None,
**kws):
'''plot after clearing current plot
'''
map1 = np.array(map1)
map2 = np.array(map2)
if len(map1.shape) != len(map2.shape):
return
self.tomo_frame[0].label, self.tomo_frame[1].label = name1, name2
self.xdata, self.ydata, self.rotdata = x, y, rot
self.xlabel, self.ylabel, self.rotlabel = xlabel, ylabel, rotlabel
if title is not None:
self.SetTitle(title)
if subtitles is not None:
self.subtitles = subtitles
cmode = self.config_mode.lower()[:3]
# make sure 3d image is shaped (NY, NX, 3)
if len(map1.shape) == 3:
ishape = map1.shape
if ishape[2] != 3:
if ishape[0] == 3:
map1 = map1.swapaxes(0, 1).swapaxes(1, 2)
elif ishape[1] == 3:
map1 = map1.swapaxes(1, 2)
if len(map2.shape) == 3:
ishape = map2.shape
if ishape[2] != 3:
if ishape[0] == 3:
map2 = map2.swapaxes(0, 1).swapaxes(1, 2)
elif ishape[1] == 3:
map2 = map2.swapaxes(1, 2)
self.xzoom = self.yzoom = slice(0, map1.shape[1]+1)
self.rotzoom = slice(0, map1.shape[0]+1)
## sets config_mode to single or tri color and builds panel accordingly
if len(map1.shape) == 3 and len(map2.shape) == 3:
if cmode != 'rgb':
for comp in self.config_panel.Children:
comp.Destroy()
self.config_mode = 'rgb'
self.tomo_frame[0].panel.conf.tricolor_mode = 'rgb'
self.Build_ConfigPanel()
else: ##if len(map1.shape) == 2 and len(map2.shape) == 2:
if cmode != 'int':
for comp in self.config_panel.Children:
comp.Destroy()
self.config_mode = 'int'
self.Build_ConfigPanel()
for map,iframe in zip([map1,map2],self.tomo_frame):
iframe.map = map
iframe.panel.display(iframe.map, style=style, **kws)
iframe.panel.conf.title = iframe.label
if colormap is not None and self.config_mode == 'int':
self.cmap_panels[0].set_colormap(name=colormap)
if subtitles is not None:
if isinstance(subtitles, dict):
self.set_subtitles(**subtitles)
elif self.config_mode == 'int':
self.set_subtitles(red=subtitles)
contour_value = 0
if style == 'contour':
contour_value = 1
self.set_contrast_levels()
for iframe in self.tomo_frame:
iframe.panel.redraw()
self.config_panel.Refresh()
self.SendSizeEvent()
wx.CallAfter(self.EnableMenus)
def prof_motion(self, event=None, frame=None):
if not event.inaxes or self.zoom_ini is None:
return
try:
xmax, ymax = event.x, event.y
except:
return
if frame is None:
frame = self.tomo_frame[0]
xmin, ymin, xd, yd = self.zoom_ini
if event.xdata is not None:
self.lastpoint[0] = event.xdata
if event.ydata is not None:
self.lastpoint[1] = event.ydata
yoff = frame.panel.canvas.figure.bbox.height
ymin, ymax = yoff - ymin, yoff - ymax
zdc = wx.ClientDC(frame.panel.canvas)
zdc.SetLogicalFunction(wx.XOR)
zdc.SetBrush(wx.TRANSPARENT_BRUSH)
zdc.SetPen(wx.Pen('White', 2, wx.SOLID))
zdc.ResetBoundingBox()
if not is_wxPhoenix:
zdc.BeginDrawing()
# erase previous box
if self.rbbox is not None:
zdc.DrawLine(*self.rbbox)
self.rbbox = (xmin, ymin, xmax, ymax)
zdc.DrawLine(*self.rbbox)
if not is_wxPhoenix:
zdc.EndDrawing()
def prof_leftdown(self, event=None, frame=None):
if frame is None:
frame = self.tomo_frame[0]
self.report_leftdown(event=event,frame=frame)
if event.inaxes: # and len(self.map.shape) == 2:
self.lastpoint = [None, None]
self.zoom_ini = [event.x, event.y, event.xdata, event.ydata]
def prof_leftup(self, event=None, frame=None):
# print("Profile Left up ", self.map.shape, self.rbbox)
if frame is None:
frame = self.tomo_frame[0]
if self.rbbox is not None:
zdc = wx.ClientDC(frame.panel.canvas)
zdc.SetLogicalFunction(wx.XOR)
zdc.SetBrush(wx.TRANSPARENT_BRUSH)
zdc.SetPen(wx.Pen('White', 2, wx.SOLID))
zdc.ResetBoundingBox()
if not is_wxPhoenix:
zdc.BeginDrawing()
zdc.DrawLine(*self.rbbox)
if not is_wxPhoenix:
zdc.EndDrawing()
self.rbbox = None
if self.zoom_ini is None or self.lastpoint[0] is None:
return
x0 = int(self.zoom_ini[2])
x1 = int(self.lastpoint[0])
y0 = int(self.zoom_ini[3])
y1 = int(self.lastpoint[1])
dx, dy = abs(x1-x0), abs(y1-y0)
self.lastpoint, self.zoom_ini = [None, None], None
if dx < 2 and dy < 2:
self.zoom_ini = None
return
outdat = []
if dy > dx:
_y0 = min(int(y0), int(y1+0.5))
_y1 = max(int(y0), int(y1+0.5))
for iy in range(_y0, _y1):
ix = int(x0 + (iy-int(y0))*(x1-x0)/(y1-y0))
outdat.append((ix, iy))
else:
_x0 = min(int(x0), int(x1+0.5))
_x1 = max(int(x0), int(x1+0.5))
for ix in range(_x0, _x1):
iy = int(y0 + (ix-int(x0))*(y1-y0)/(x1-x0))
outdat.append((ix, iy))
x, y, z = [], [], []
for ix, iy in outdat:
x.append(ix)
y.append(iy)
z.append(frame.panel.conf.data[iy, ix])
self.prof_dat = dy>dx, outdat
if self.prof_plotter is not None:
try:
self.prof_plotter.Raise()
self.prof_plotter.clear()
except (AttributeError, PyDeadObjectError):
self.prof_plotter = None
if self.prof_plotter is None:
self.prof_plotter = PlotFrame(self, title='Profile')
self.prof_plotter.panel.report_leftdown = self.prof_report_coords
xlabel, y2label = 'Pixel (x)', 'Pixel (y)'
x = np.array(x)
y = np.array(y)
z = np.array(z)
if dy > dx:
x, y = y, x
xlabel, y2label = y2label, xlabel
self.prof_plotter.panel.clear()
if len(self.title) < 1:
self.title = os.path.split(self.xrmfile.filename)[1]
opts = dict(linewidth=2, marker='+', markersize=3,
show_legend=True, xlabel=xlabel)
if isinstance(z[0], np.ndarray) and len(z[0]) == 3: # color plot
rlab = self.subtitles['red']
glab = self.subtitles['green']
blab = self.subtitles['blue']
self.prof_plotter.plot(x, z[:, 0], title=self.title, color='red',
zorder=20, xmin=min(x)-3, xmax=max(x)+3,
ylabel='counts', label=rlab, **opts)
self.prof_plotter.oplot(x, z[:, 1], title=self.title, color='darkgreen',
zorder=20, xmin=min(x)-3, xmax=max(x)+3,
ylabel='counts', label=glab, **opts)
self.prof_plotter.oplot(x, z[:, 2], title=self.title, color='blue',
zorder=20, xmin=min(x)-3, xmax=max(x)+3,
ylabel='counts', label=blab, **opts)
else:
self.prof_plotter.plot(x, z, color='blue', title=self.title.split(':')[-1], #title=self.title,
zorder=20, xmin=min(x)-3, xmax=max(x)+3,
ylabel='counts', label='counts', **opts)
try:
self.prof_plotter.oplot(x, y, y2label=y2label, label=y2label,
zorder=3, side='right', color='black', **opts)
except:
pass
self.prof_plotter.panel.unzoom_all()
self.prof_plotter.Show()
self.zoom_ini = None
self.zoom_mode.SetSelection(0)
frame.panel.cursor_mode = 'zoom'
def prof_report_coords(self, event=None, frame=None):
"""override report leftdown for profile plotter"""
if event is None:
return
ex, ey = event.x, event.y
msg = ''
if frame is None:
frame = self.tomo_frame[0]
plotpanel = self.prof_plotter.panel
axes = plotpanel.fig.properties()['axes'][0]
write = plotpanel.write_message
try:
x, y = axes.transData.inverted().transform((ex, ey))
except:
x, y = event.xdata, event.ydata
if x is None or y is None:
return
_point = 0, 0, 0, 0, 0
for ix, iy in self.prof_dat[1]:
if (int(x) == ix and not self.prof_dat[0] or
int(x) == iy and self.prof_dat[0]):
_point = (ix, iy,
frame.panel.xdata[ix],
frame.panel.ydata[iy],
frame.panel.conf.data[iy, ix])
msg = "Pixel [%i, %i], X, OME = [%.4f mm, %.4f deg], Intensity= %g" % _point
write(msg, panel=0)
def report_leftdown(self,event=None, frame=None):
if event is None:
return
if event.xdata is None or event.ydata is None:
return
if frame is None:
frame = self.tomo_frame[0]
ix, iy = int(round(event.xdata)), int(round(event.ydata))
if (ix >= 0 and ix < frame.map.shape[1] and
iy >= 0 and iy < frame.map.shape[0]):
pos = ''
if self.xdata is not None:
pos = ' %s=%.4g,' % (self.xlabel, self.xdata[ix])
if self.ydata is not None:
pos = '%s %s=%.4g,' % (pos, self.ylabel, self.ydata[iy])
if len(frame.map.shape) > 2:
msg = 'Pixel [%i, %i],%s %s=(%.4g, %.4g, %.4g)' % (ix, iy, pos,
frame.label, frame.map[iy,ix,0],
frame.map[iy,ix,1], frame.map[iy,ix,2])
else:
msg = 'Pixel [%i, %i],%s %s=%.4g' % (ix, iy, pos,
frame.label, frame.map[iy, ix])
self.write_message(msg, panel=0)
#if callable(self.cursor_callback):
# self.cursor_callback(x=event.xdata, y=event.ydata)
def set_subtitles(self, red=None, green=None, blue=None, **kws):
if self.config_mode.startswith('int') and red is not None:
self.cmap_panels[0].title.SetLabel(red)
if self.config_mode.startswith('rgb') and red is not None:
self.cmap_panels[0].title.SetLabel(red)
if self.config_mode.startswith('rgb') and green is not None:
self.cmap_panels[1].title.SetLabel(green)
if self.config_mode.startswith('rgb') and blue is not None:
self.cmap_panels[2].title.SetLabel(blue)
def EnableMenus(self, evt=None):
is_3color = len(self.tomo_frame[0].panel.conf.data.shape) > 2
for menu, on_3color in self.optional_menus:
menu.Enable(is_3color==on_3color)
def unzoom_all(self):
self.tomo_frame[0].panel.unzoom()
self.tomo_frame[1].panel.unzoom()
def BuildMenu(self):
# file menu
mfile = self.Build_FileMenu(extras=(('Save Image of Colormap',
'Save Image of Colormap',
self.onCMapSave),))
# options menu
mview = self.view_menu = wx.Menu()
MenuItem(self, mview, 'Zoom Out\tCtrl+Z',
'Zoom out to full data range',
self.unzoom_all)
m = MenuItem(self, mview, 'Toggle Background Color (Black/White)\tCtrl+W',
'Toggle background color for 3-color images',
self.onTriColorBG, kind=wx.ITEM_CHECK)
self.optional_menus.append((m, True))
mview.AppendSeparator()
MenuItem(self, mview, 'Rotate clockwise\tCtrl+R', '',
partial(self.onFlip, mode='rot_cw'))
MenuItem(self, mview, 'Flip Top/Bottom\tCtrl+T', '',
partial(self.onFlip, mode='flip_ud'))
MenuItem(self, mview, 'Flip Left/Right\tCtrl+F', '',
partial(self.onFlip, mode='flip_lr'))
mview.AppendSeparator()
MenuItem(self, mview, 'Projet Horizontally\tCtrl+X', '',
partial(self.onProject, mode='x'))
MenuItem(self, mview, 'Projet Vertically\tCtrl+Y', '',
partial(self.onProject, mode='y'))
mview.AppendSeparator()
m = MenuItem(self, mview, 'As Contour', 'Shown as contour map',
self.onContourToggle, kind=wx.ITEM_CHECK)
m.Check(False)
self.optional_menus.append((m, False))
m = MenuItem(self, mview, 'Configure Contours', 'Configure Contours',
self.onContourConfig)
self.optional_menus.append((m, False))
# intensity contrast
mint =self.intensity_menu = wx.Menu()
# MenuItem(self, mint, 'Log Scale Intensity\tCtrl+L',
# 'use logarithm to set intensity scale',
# self.onLogScale, kind=wx.ITEM_CHECK)
MenuItem(self, mint, 'Toggle Contrast Enhancement\tCtrl+E',
'Toggle contrast between auto-scale and full-scale',
self.onEnhanceContrast, kind=wx.ITEM_CHECK)
MenuItem(self, mint, 'Set Auto-Contrast Level',
'Set auto-contrast scale',
self.onContrastConfig)
# smoothing
msmoo = wx.Menu()
for itype in Interp_List:
wid = wx.NewId()
msmoo.AppendRadioItem(wid, itype, itype)
self.Bind(wx.EVT_MENU, partial(self.onInterp, name=itype), id=wid)
# help
mhelp = wx.Menu()
MenuItem(self, mhelp, 'Quick Reference',
'Quick Reference for WXMPlot', self.onHelp)
MenuItem(self, mhelp, 'About', 'About WXMPlot', self.onAbout)
# add all sub-menus, including user-added
submenus = [('File', mfile),
('Image', mview),
('Contrast', mint),
('Smoothing', msmoo)]
if self.user_menus is not None:
submenus.extend(self.user_menus)
submenus.append(('&Help', mhelp))
mbar = wx.MenuBar()
for title, menu in submenus:
mbar.Append(menu, title)
self.SetMenuBar(mbar)
self.Bind(wx.EVT_CLOSE,self.onExit)
def onInterp(self, evt=None, name=None):
if name not in Interp_List:
name = Interp_List[0]
for iframe in self.tomo_frame:
iframe.panel.conf.interp = name
iframe.panel.redraw()
def onCursorMode(self, event=None, mode='zoom'):
choice = self.zoom_mode.GetString(self.zoom_mode.GetSelection())
for iframe in self.tomo_frame:
iframe.panel.cursor_mode = mode
if event is not None:
if choice.startswith('Pick Area'):
iframe.panel.cursor_mode = 'lasso'
elif choice.startswith('Show Line'):
iframe.panel.cursor_mode = 'prof'
def onProject(self, event=None, mode='y'):
wid = event.GetId()
if mode=='x':
x = self.tomo_frame[0].panel.ydata
y = self.tomo_frame[0].panel.conf.data.sum(axis=1)
x = self.tomo_frame[1].panel.ydata
y = self.tomo_frame[1].panel.conf.data.sum(axis=1)
axname = 'horizontal'
if x is None:
x = np.arange(y.shape[0])
else:
x = self.tomo_frame[0].panel.xdata
y = self.tomo_frame[0].panel.conf.data.sum(axis=0)
x = self.tomo_frame[1].panel.xdata
y = self.tomo_frame[1].panel.conf.data.sum(axis=0)
if x is None:
x = np.arange(y.shape[0])
axname = 'vertical'
title = '%s: sum along %s axis' % (self.GetTitle(), axname)
pf = PlotFrame(title=title, parent=self, size=(500, 250))
colors = RGB_COLORS
if len(y.shape) == 2 and y.shape[1] == 3:
pf.plot(x, y[:,0], color=colors[0])
pf.oplot(x, y[:,1], color=colors[1])
pf.oplot(x, y[:,2], color=colors[2])
else:
pf.plot(x, y)
pf.Raise()
pf.Show()
def onFlip(self, event=None, mode=None):
for iframe in self.tomo_frame:
conf = iframe.panel.conf
if mode == 'flip_lr':
conf.flip_lr = not conf.flip_lr
elif mode == 'flip_ud':
conf.flip_ud = not conf.flip_ud
elif mode == 'flip_orig':
conf.flip_lr, conf.flip_ud = False, False
elif mode == 'rot_cw':
conf.rot = True
iframe.panel.unzoom_all()
def Build_ConfigPanel(self):
'''config panel for left-hand-side of frame: RGB Maps'''
csizer = wx.BoxSizer(wx.VERTICAL)
lsty = wx.ALIGN_LEFT|wx.LEFT|wx.TOP|wx.EXPAND
icol = 0
if self.config_mode == 'rgb':
for iframe in self.tomo_frame:
for ic,col in enumerate(RGB_COLORS):
self.cmap_panels[icol] = ColorMapPanel(self.config_panel,
iframe.panel,
title='%s - %s: ' % (iframe.label,col.title()),
color=ic,
default=col,
colormap_list=None)
csizer.Add(self.cmap_panels[icol], 0, lsty, 2)
csizer.Add(wx.StaticLine(self.config_panel, size=(100, 2),
style=wx.LI_HORIZONTAL), 0, lsty, 2)
icol += 1
else:
for iframe in self.tomo_frame:
self.cmap_panels[icol] = ColorMapPanel(self.config_panel,
iframe.panel,
title='%s: ' % iframe.label,
default='gray',
colormap_list=ColorMap_List)
csizer.Add(self.cmap_panels[icol], 0, lsty, 1)
csizer.Add(wx.StaticLine(self.config_panel, size=(100, 2),
style=wx.LI_HORIZONTAL), 0, lsty, 2)
icol += 1
cust = self.CustomConfig(self.config_panel, None, 0)
if cust is not None:
csizer.Add(cust, 0, lsty, 1)
pack(self.config_panel, csizer)
def clear_highlight_area(self):
for iframe in self.tomo_frame:
for area in iframe.panel.conf.highlight_areas:
for w in area.collections + area.labelTexts:
w.remove()
iframe.panel.conf.highlight_areas = []
iframe.panel.redraw()
def add_highlight_area(self, mask0, label=None, col=0):
"""add a highlighted area -- outline an arbitrarily shape --
as if drawn from a Lasso event.
This takes a mask, which should be a boolean array of the
same shape as the image.
"""
panel = None
for iframe in self.tomo_frame:
imap_size = iframe.map.shape[:2]
for imask in (mask0,np.swapaxes(mask0,0,1)):
if imap_size == imask.shape:
panel = iframe.panel
mask = imask
if panel is not None:
patch = mask * np.ones(mask.shape) * 0.9
cmap = panel.conf.cmap[col]
area = panel.axes.contour(patch, cmap=cmap, levels=[0, 1])
panel.conf.highlight_areas.append(area)
col = None
if hasattr(cmap, '_lut'):
rgb = [int(i*240)^255 for i in cmap._lut[0][:3]]
col = '#%02x%02x%02x' % (rgb[0], rgb[1], rgb[2])
if label is not None:
def fmt(*args, **kws): return label
panel.axes.clabel(area, fontsize=9, fmt=fmt,
colors=col, rightside_up=True)
if col is not None:
for l in area.collections:
l.set_color(col)
panel.canvas.draw()
def CustomConfig(self, panel, sizer=None, irow=0):
'''
override to add custom config panel items
to bottom of config panel
'''
labstyle = wx.ALIGN_LEFT|wx.LEFT|wx.TOP|wx.EXPAND
if self.lasso_callback is None:
zoom_opts = ('Zoom to Rectangle',
'Show Line Profile')
else:
zoom_opts = ('Zoom to Rectangle',
'Pick Area for XRM Spectra',
'Show Line Profile')
if self.wxmplot_version > 0.921:
cpanel = wx.Panel(panel)
if sizer is None:
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(SimpleText(cpanel, label='Cursor Modes', style=labstyle), 0, labstyle, 3)
self.zoom_mode = wx.RadioBox(cpanel, -1, '',
wx.DefaultPosition, wx.DefaultSize,
zoom_opts, 1, wx.RA_SPECIFY_COLS)
self.zoom_mode.Bind(wx.EVT_RADIOBOX, self.onCursorMode)
sizer.Add(self.zoom_mode, 1, labstyle, 4)
pack(cpanel, sizer)
return cpanel
else: # support older versions of wxmplot, will be able to deprecate
conf = self.tomo_frame[0].panel.conf # self.panel.conf
lpanel = panel
lsizer = sizer
self.zoom_mode = wx.RadioBox(panel, -1, 'Cursor Mode:',
wx.DefaultPosition, wx.DefaultSize,
zoom_opts, 1, wx.RA_SPECIFY_COLS)
self.zoom_mode.Bind(wx.EVT_RADIOBOX, self.onCursorMode)
sizer.Add(self.zoom_mode, (irow, 0), (1, 4), labstyle, 3)
def onContrastConfig(self, event=None):
for iframe in self.tomo_frame:
dlg = AutoContrastDialog(parent=self, conf=iframe.panel.conf)
dlg.CenterOnScreen()
val = dlg.ShowModal()
if val == wx.ID_OK:
pass
dlg.Destroy()
def onContourConfig(self, event=None):
for icol,iframe in enumerate(self.tomo_frame):
conf = iframe.panel.conf
dlg = ContourDialog(parent=self, conf=conf)
dlg.CenterOnScreen()
val = dlg.ShowModal()
if val == wx.ID_OK:
pass
dlg.Destroy()
if conf.style != 'contour':
return
if self.config_mode == 'int':
self.cmap_panels[icol].set_colormap()
iframe.panel.axes.cla()
iframe.panel.display(conf.data, x=iframe.panel.xdata, y = iframe.panel.ydata,
xlabel=iframe.panel.xlab, ylabel=iframe.panel.ylab,
contour_labels=conf.contour_labels,
nlevels=conf.ncontour_levels, style='contour')
iframe.panel.redraw()
def onContourToggle(self, event=None):
for icol,iframe in enumerate(self.tomo_frame):
if len(iframe.panel.conf.data.shape) > 2:
return
conf = iframe.panel.conf
conf.style = 'image'
if event.IsChecked():
conf.style = 'contour'
nlevels = int(conf.ncontour_levels)
if self.config_mode == 'int':
self.cmap_panels[0].set_colormap()
iframe.panel.axes.cla()
iframe.panel.display(conf.data, x=iframe.panel.xdata, y = iframe.panel.ydata,
nlevels=nlevels, contour_labels=conf.contour_labels,
xlabel=iframe.panel.xlab, ylabel=iframe.panel.ylab,
style=conf.style)
iframe.panel.redraw()
def onTriColorBG(self, event=None):
bgcol = {True:'white', False:'black'}[event.IsChecked()]
icol = 0
for iframe in self.tomo_frame:
conf = iframe.panel.conf
if bgcol == conf.tricolor_bg:
return
conf.tricolor_bg = bgcol
cmaps = colors = RGB_COLORS
if bgcol.startswith('wh'):
cmaps = ('Reds', 'Greens', 'Blues')
for i in range(3):
self.cmap_panels[icol].set_colormap(name=cmaps[i])
icol += 1
iframe.panel.redraw()
def onLasso(self, data=None, selected=None, mask=None, **kws):
## orients mask correctly to match with raw data shape
## mkak 2018.01.24
mask = np.swapaxes(mask,0,1)
if hasattr(self.lasso_callback , '__call__'):
self.lasso_callback(data=data, selected=selected, mask=mask, **kws)
def onDataChange(self, data, x=None, y=None, col='int', **kw):
icol = 0
for iframe in self.tomo_frame:
conf = iframe.panel.conf
if len(data.shape) == 2: # intensity map
imin, imax = data.min(), data.max()
conf.int_lo[0] = imin
conf.int_hi[0] = imax
cpan = self.cmap_panels[0]
cpan.cmap_lo.SetValue(imin)
cpan.cmap_hi.SetValue(imax)
cpan.imin_val.SetValue('%.4g' % imin)
cpan.imax_val.SetValue('%.4g' % imax)
cpan.imin_val.Enable()
cpan.imax_val.Enable()
else:
for ix in range(3):
imin, imax = data[:,:,ix].min(), data[:,:,ix].max()
conf.int_lo[ix] = imin
conf.int_hi[ix] = imax
self.cmap_panels[icol].imin_val.SetValue('%.4g' % imin)
self.cmap_panels[icol].imax_val.SetValue('%.4g' % imax)
self.cmap_panels[icol].imin_val.Enable()
self.cmap_panels[icol].imax_val.Enable()
icol += 1
def onEnhanceContrast(self, event=None):
'''change image contrast, using scikit-image exposure routines'''
for iframe in self.tomo_frame:
iframe.panel.conf.auto_contrast = event.IsChecked()
self.set_contrast_levels()
for iframe in self.tomo_frame:
iframe.panel.redraw()
def set_contrast_levels(self):
'''enhance contrast levels, or use full data range
according to value of iframe.panel.conf.auto_contrast
'''
def set_panel_contrast(icol,conf,ix=-1):
if ix < 0:
ix = icol
img = conf.data
else:
img = conf.data[:,:,ix]
jmin = imin = img.min()
jmax = imax = img.max()
self.cmap_panels[icol].imin_val.SetValue('%.4g' % imin)
self.cmap_panels[icol].imax_val.SetValue('%.4g' % imax)
conf.int_lo[ix] = imin
conf.int_hi[ix] = imax
if conf.auto_contrast:
jmin, jmax = np.percentile(img, [ conf.auto_contrast_level,
100.0-conf.auto_contrast_level])
if imax == imin:
imax = imin + 0.5
conf.cmap_lo[ix] = xlo = (jmin-imin)*conf.cmap_range/(imax-imin)
conf.cmap_hi[ix] = xhi = (jmax-imin)*conf.cmap_range/(imax-imin)
self.cmap_panels[icol].cmap_hi.SetValue(xhi)
self.cmap_panels[icol].cmap_lo.SetValue(xlo)
str = 'Shown: [ %.4g : %.4g ]' % (jmin, jmax)
self.cmap_panels[icol].islider_range.SetLabel(str)
self.cmap_panels[icol].redraw_cmap()
icol = 0
for iframe in self.tomo_frame:
conf = iframe.panel.conf
if len(conf.data.shape) == 2: # intensity map
set_panel_contrast(icol,conf)
icol += 1
elif len(conf.data.shape) == 3: # rgb map
for ix in range(3):
set_panel_contrast(icol,conf,ix=ix)
icol += 1
iframe.panel.redraw()
def onLogScale(self, event=None):
for iframe in self.tomo_frame:
iframe.panel.conf.log_scale = not iframe.panel.conf.log_scale
iframe.panel.redraw()
def onCMapSave(self, event=None, col='int'):
'''save color table image'''
file_choices = 'PNG (*.png)|*.png'
ofile = 'Colormap.png'
dlg = wx.FileDialog(self, message='Save Colormap as...',
defaultDir=os.getcwd(),
defaultFile=ofile,
wildcard=file_choices,
style=wx.FD_SAVE|wx.FD_CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
self.cmap_panels[0].cmap_canvas.print_figure(dlg.GetPath(), dpi=600)
def save_figure(self,event=None, transparent=True, dpi=600):
''' save figure image to file'''
for iframe in self.tomo_frame:
if iframe.panel is not None:
iframe.panel.save_figure(event=event, transparent=transparent, dpi=dpi)
class with_profile_mode:
def prof_motion(self, event=None):
if not event.inaxes or self.zoom_ini is None:
return
try:
xmax, ymax = event.x, event.y
except:
return
xmin, ymin, xd, yd = self.zoom_ini
if event.xdata is not None:
self.lastpoint[0] = event.xdata
if event.ydata is not None:
self.lastpoint[1] = event.ydata
yoff = self.panel.canvas.figure.bbox.height
ymin, ymax = yoff - ymin, yoff - ymax
zdc = wx.ClientDC(self.panel.canvas)
zdc.SetLogicalFunction(wx.XOR)
zdc.SetBrush(wx.TRANSPARENT_BRUSH)
zdc.SetPen(wx.Pen('White', 2, wx.SOLID))
zdc.ResetBoundingBox()
if not is_wxPhoenix:
zdc.BeginDrawing()
# erase previous box
if self.rbbox is not None:
zdc.DrawLine(*self.rbbox)
self.rbbox = (xmin, ymin, xmax, ymax)
zdc.DrawLine(*self.rbbox)
if not is_wxPhoenix:
zdc.EndDrawing()
def prof_leftdown(self, event=None):
self.report_leftdown(event=event)
if event.inaxes: # and len(self.map.shape) == 2:
self.lastpoint = [None, None]
self.zoom_ini = [event.x, event.y, event.xdata, event.ydata]
def prof_leftup(self, event=None):
# print("Profile Left up ", self.map.shape, self.rbbox)
if self.rbbox is not None:
zdc = wx.ClientDC(self.panel.canvas)
zdc.SetLogicalFunction(wx.XOR)
zdc.SetBrush(wx.TRANSPARENT_BRUSH)
zdc.SetPen(wx.Pen('White', 2, wx.SOLID))
zdc.ResetBoundingBox()
if not is_wxPhoenix:
zdc.BeginDrawing()
zdc.DrawLine(*self.rbbox)
if not is_wxPhoenix:
zdc.EndDrawing()
self.rbbox = None
if self.zoom_ini is None or self.lastpoint[0] is None:
return
x0 = int(self.zoom_ini[2])
x1 = int(self.lastpoint[0])
y0 = int(self.zoom_ini[3])
y1 = int(self.lastpoint[1])
dx, dy = abs(x1-x0), abs(y1-y0)
self.lastpoint, self.zoom_ini = [None, None], None
if dx < 2 and dy < 2:
self.zoom_ini = None
return
outdat = []
if dy > dx:
_y0 = min(int(y0), int(y1+0.5))
_y1 = max(int(y0), int(y1+0.5))
for iy in range(_y0, _y1):
ix = int(x0 + (iy-int(y0))*(x1-x0)/(y1-y0))
outdat.append((ix, iy))
else:
_x0 = min(int(x0), int(x1+0.5))
_x1 = max(int(x0), int(x1+0.5))
for ix in range(_x0, _x1):
iy = int(y0 + (ix-int(x0))*(y1-y0)/(x1-x0))
outdat.append((ix, iy))
x, y, z = [], [], []
for ix, iy in outdat:
x.append(ix)
y.append(iy)
z.append(self.panel.conf.data[iy, ix])
self.prof_dat = dy>dx, outdat
if self.prof_plotter is not None:
try:
self.prof_plotter.Raise()
self.prof_plotter.clear()
except (AttributeError, PyDeadObjectError):
self.prof_plotter = None
if self.prof_plotter is None:
self.prof_plotter = PlotFrame(self, title='Profile')
self.prof_plotter.panel.report_leftdown = self.prof_report_coords
xlabel, y2label = 'Pixel (x)', 'Pixel (y)'
x = np.array(x)
y = np.array(y)
z = np.array(z)
if dy > dx:
x, y = y, x
xlabel, y2label = y2label, xlabel
self.prof_plotter.panel.clear()
if len(self.title) < 1:
self.title = os.path.split(self.xrmfile.filename)[1]
opts = dict(linewidth=2, marker='+', markersize=3,
show_legend=True, xlabel=xlabel)
if isinstance(z[0], np.ndarray) and len(z[0]) == 3: # color plot
rlab = self.subtitles['red']
glab = self.subtitles['green']
blab = self.subtitles['blue']
self.prof_plotter.plot(x, z[:, 0], title=self.title, color='red',
zorder=20, xmin=min(x)-3, xmax=max(x)+3,
ylabel='counts', label=rlab, **opts)
self.prof_plotter.oplot(x, z[:, 1], title=self.title, color='darkgreen',
zorder=20, xmin=min(x)-3, xmax=max(x)+3,
ylabel='counts', label=glab, **opts)
self.prof_plotter.oplot(x, z[:, 2], title=self.title, color='blue',
zorder=20, xmin=min(x)-3, xmax=max(x)+3,
ylabel='counts', label=blab, **opts)
else:
self.prof_plotter.plot(x, z, title=self.title, color='blue',
zorder=20, xmin=min(x)-3, xmax=max(x)+3,
ylabel='counts', label='counts', **opts)
self.prof_plotter.oplot(x, y, y2label=y2label, label=y2label,
zorder=3, side='right', color='black', **opts)
self.prof_plotter.panel.unzoom_all()
self.prof_plotter.Show()
self.zoom_ini = None
self.zoom_mode.SetSelection(0)
self.panel.cursor_mode = 'zoom'
def prof_report_coords(self, event=None):
"""override report leftdown for profile plotter"""
if event is None:
return
ex, ey = event.x, event.y
msg = ''
plotpanel = self.prof_plotter.panel
axes = plotpanel.fig.properties()['axes'][0]
write = plotpanel.write_message
try:
x, y = axes.transData.inverted().transform((ex, ey))
except:
x, y = event.xdata, event.ydata
if x is None or y is None:
return
_point = 0, 0, 0, 0, 0
for ix, iy in self.prof_dat[1]:
if (int(x) == ix and not self.prof_dat[0] or
int(x) == iy and self.prof_dat[0]):
_point = (ix, iy,
self.panel.xdata[ix],
self.panel.ydata[iy],
self.panel.conf.data[iy, ix])
msg = "Pixel [%i, %i], X, OME = [%.4f mm, %.4f deg], Intensity= %g" % _point
write(msg, panel=0)
class MapImageFrame(ImageFrame):
"""
MatPlotlib Image Display on a wx.Frame, using ImagePanel
"""
def __init__(self, parent=None, size=None, mode='intensity',
lasso_callback=None, move_callback=None, save_callback=None,
show_xsections=False, cursor_labels=None,
output_title='Image', **kws):
# instdb=None, inst_name=None,
self.det = None
self.xrmfile = None
self.map = None
self.move_callback = move_callback
self.save_callback = save_callback
ImageFrame.__init__(self, parent=parent, size=size,
lasso_callback=lasso_callback,
cursor_labels=cursor_labels, mode=mode,
output_title=output_title, **kws)
self.panel.add_cursor_mode('prof', motion = self.prof_motion,
leftdown = self.prof_leftdown,
leftup = self.prof_leftup)
self.panel.report_leftdown = self.report_leftdown
self.panel.report_motion = self.report_motion
self.prof_plotter = None
self.zoom_ini = None
self.lastpoint = [None, None]
self.this_point = None
self.rbbox = None
def display(self, map, det=None, xrmfile=None, xoff=0, yoff=0, **kws):
self.xoff = xoff
self.yoff = yoff
self.det = det
self.xrmfile = xrmfile
self.map = map
self.title = ''
if 'title' in kws:
self.title = kws['title']
ImageFrame.display(self, map, **kws)
if 'x' in kws:
self.panel.xdata = kws['x']
if 'y' in kws:
self.panel.ydata = kws['y']
if self.panel.conf.auto_contrast:
self.set_contrast_levels()
def prof_motion(self, event=None):
if not event.inaxes or self.zoom_ini is None:
return
try:
xmax, ymax = event.x, event.y
except:
return
xmin, ymin, xd, yd = self.zoom_ini
if event.xdata is not None:
self.lastpoint[0] = event.xdata
if event.ydata is not None:
self.lastpoint[1] = event.ydata
yoff = self.panel.canvas.figure.bbox.height
ymin, ymax = yoff - ymin, yoff - ymax
zdc = wx.ClientDC(self.panel.canvas)
zdc.SetLogicalFunction(wx.XOR)
zdc.SetBrush(wx.TRANSPARENT_BRUSH)
zdc.SetPen(wx.Pen('White', 2, wx.SOLID))
zdc.ResetBoundingBox()
if not is_wxPhoenix:
zdc.BeginDrawing()
# erase previous box
if self.rbbox is not None:
zdc.DrawLine(*self.rbbox)
self.rbbox = (xmin, ymin, xmax, ymax)
zdc.DrawLine(*self.rbbox)
if not is_wxPhoenix:
zdc.EndDrawing()
def prof_leftdown(self, event=None):
self.report_leftdown(event=event)
if event.inaxes and len(self.map.shape) == 2:
self.lastpoint = [None, None]
self.zoom_ini = [event.x, event.y, event.xdata, event.ydata]
def prof_leftup(self, event=None):
if len(self.map.shape) != 2:
return
if self.rbbox is not None:
zdc = wx.ClientDC(self.panel.canvas)
zdc.SetLogicalFunction(wx.XOR)
zdc.SetBrush(wx.TRANSPARENT_BRUSH)
zdc.SetPen(wx.Pen('White', 2, wx.SOLID))
zdc.ResetBoundingBox()
if not is_wxPhoenix:
zdc.BeginDrawing()
zdc.DrawLine(*self.rbbox)
if not is_wxPhoenix:
zdc.EndDrawing()
self.rbbox = None
if self.zoom_ini is None or self.lastpoint[0] is None:
return
x0 = int(self.zoom_ini[2])
x1 = int(self.lastpoint[0])
y0 = int(self.zoom_ini[3])
y1 = int(self.lastpoint[1])
dx, dy = abs(x1-x0), abs(y1-y0)
self.lastpoint, self.zoom_ini = [None, None], None
if dx < 2 and dy < 2:
self.zoom_ini = None
return
outdat = []
if dy > dx:
_y0 = min(int(y0), int(y1+0.5))
_y1 = max(int(y0), int(y1+0.5))
for iy in range(_y0, _y1):
ix = int(x0 + (iy-int(y0))*(x1-x0)/(y1-y0))
outdat.append((ix, iy))
else:
_x0 = min(int(x0), int(x1+0.5))
_x1 = max(int(x0), int(x1+0.5))
for ix in range(_x0, _x1):
iy = int(y0 + (ix-int(x0))*(y1-y0)/(x1-x0))
outdat.append((ix, iy))
x, y, z = [], [], []
for ix, iy in outdat:
x.append(ix)
y.append(iy)
z.append(self.panel.conf.data[iy,ix])
self.prof_dat = dy>dx, outdat
if self.prof_plotter is not None:
try:
self.prof_plotter.Raise()
self.prof_plotter.clear()
except (AttributeError, PyDeadObjectError):
self.prof_plotter = None
if self.prof_plotter is None:
self.prof_plotter = PlotFrame(self, title='Profile')
self.prof_plotter.panel.report_leftdown = self.prof_report_coords
xlabel, y2label = 'Pixel (x)', 'Pixel (y)'
if dy > dx:
x, y = y, x
xlabel, y2label = y2label, xlabel
self.prof_plotter.panel.clear() # reset_config()
if len(self.title) < 1:
self.title = os.path.split(self.xrmfile.filename)[1]
opts = dict(linewidth=2, marker='+', markersize=3,
show_legend=True, xlabel=xlabel)
self.prof_plotter.plot(x, z, title=self.title, color='blue',
zorder=20, xmin=min(x)-3, xmax=max(x)+3,
ylabel='counts', label='counts', **opts)
self.prof_plotter.oplot(x, y, y2label=y2label, label=y2label,
zorder=3, side='right', color='#771111', **opts)
self.prof_plotter.panel.unzoom_all()
self.prof_plotter.Show()
self.zoom_ini = None
self.zoom_mode.SetSelection(0)
self.panel.cursor_mode = 'zoom'
def prof_report_coords(self, event=None):
"""override report leftdown for profile plotter"""
if event is None:
return
ex, ey = event.x, event.y
msg = ''
plotpanel = self.prof_plotter.panel
axes = plotpanel.fig.get_axes()[0]
write = plotpanel.write_message
try:
x, y = axes.transData.inverted().transform((ex, ey))
except:
x, y = event.xdata, event.ydata
if x is None or y is None:
return
_point = 0, 0, 0, 0, 0
for ix, iy in self.prof_dat[1]:
if (int(x) == ix and not self.prof_dat[0] or
int(x) == iy and self.prof_dat[0]):
_point = (ix, iy,
self.panel.xdata[ix],
self.panel.ydata[iy],
self.panel.conf.data[iy, ix])
msg = "Pixel [%i, %i], X, Y = [%.4f, %.4f], Intensity= %g" % _point
write(msg, panel=0)
def onCursorMode(self, event=None, mode='zoom'):
self.panel.cursor_mode = mode
if event is not None:
if 1 == event.GetInt():
self.panel.cursor_mode = 'lasso'
elif 2 == event.GetInt():
self.panel.cursor_mode = 'prof'
def report_leftdown(self, event=None):
if event is None:
return
if event.xdata is None or event.ydata is None:
return
ix, iy = int(round(event.xdata)), int(round(event.ydata))
conf = self.panel.conf
if conf.flip_ud: iy = conf.data.shape[0] - iy
if conf.flip_lr: ix = conf.data.shape[1] - ix
self.this_point = None
msg = ''
if (ix >= 0 and ix < conf.data.shape[1] and
iy >= 0 and iy < conf.data.shape[0]):
pos = ''
pan = self.panel
# print( 'has xdata? ', pan.xdata is not None, pan.ydata is not None)
labs, vals = [], []
if pan.xdata is not None:
labs.append(pan.xlab)
vals.append(pan.xdata[ix])
if pan.ydata is not None:
labs.append(pan.ylab)
vals.append(pan.ydata[iy])
pos = ', '.join(labs)
vals =', '.join(['%.4g' % v for v in vals])
pos = '%s = [%s]' % (pos, vals)
dval = conf.data[iy, ix]
if len(pan.data_shape) == 3:
dval = "%.4g, %.4g, %.4g" % tuple(dval)
else:
dval = "%.4g" % dval
if pan.xdata is not None and pan.ydata is not None:
self.this_point = (ix, iy)
msg = "Pixel [%i, %i], %s, Intensity=%s " % (ix, iy, pos, dval)
self.panel.write_message(msg, panel=0)
def report_motion(self, event=None):
return
def onLasso(self, data=None, selected=None, mask=None, **kws):
if hasattr(self.lasso_callback , '__call__'):
self.lasso_callback(data=data, selected=selected, mask=mask,
xoff=self.xoff, yoff=self.yoff,
det=self.det, xrmfile=self.xrmfile, **kws)
self.zoom_mode.SetSelection(0)
self.panel.cursor_mode = 'zoom'
def CustomConfig(self, panel, sizer, irow):
"""config panel for left-hand-side of frame"""
conf = self.panel.conf
lpanel = panel
lsizer = sizer
labstyle = wx.ALIGN_LEFT|wx.LEFT|wx.TOP|wx.EXPAND
self.zoom_mode = wx.RadioBox(panel, -1, "Cursor Mode:",
wx.DefaultPosition, wx.DefaultSize,
('Zoom to Rectangle',
'Pick Area for XRF Spectrum',
'Show Line Profile'),
1, wx.RA_SPECIFY_COLS)
self.zoom_mode.Bind(wx.EVT_RADIOBOX, self.onCursorMode)
sizer.Add(self.zoom_mode, (irow, 0), (1, 4), labstyle, 3)
if self.save_callback is not None:
self.pos_name = wx.TextCtrl(panel, -1, '', size=(175, -1),
style=wx.TE_PROCESS_ENTER)
self.pos_name.Bind(wx.EVT_TEXT_ENTER, self.onSavePixel)
label = SimpleText(panel, label='Save Position:',
size=(-1, -1))
# sbutton = Button(panel, 'Save Position', size=(100, -1),
# action=self.onSavePixel)
sizer.Add(label, (irow+1, 0), (1, 2), labstyle, 3)
sizer.Add(self.pos_name, (irow+1, 2), (1, 2), labstyle, 3)
# sizer.Add(sbutton, (irow+2, 0), (1, 2), labstyle, 3)
if self.move_callback is not None:
mbutton = Button(panel, 'Move to Position', size=(100, -1),
action=self.onMoveToPixel)
irow = irow + 2
sizer.Add(mbutton, (irow+1, 0), (1, 2), labstyle, 3)
def onMoveToPixel(self, event=None):
if self.this_point is not None and self.move_callback is not None:
p1 = float(self.panel.xdata[self.this_point[0]])
p2 = float(self.panel.ydata[self.this_point[1]])
self.move_callback(p1, p2)
def onSavePixel(self, event=None):
if self.this_point is not None and self.save_callback is not None:
name = str(event.GetString().strip())
# name = str(self.pos_name.GetValue().strip())
ix, iy = self.this_point
x = float(self.panel.xdata[int(ix)])
y = float(self.panel.ydata[int(iy)])
self.save_callback(name, ix, iy, x=x, y=y,
title=self.title, datafile=self.xrmfile)
class ScanViewerFrame(wx.Frame):
_about = """Scan 2D Plotter
Matt Newville <newville @ cars.uchicago.edu>
"""
def __init__(self, _larch=None, **kws):
wx.Frame.__init__(self, None, -1, style=FRAMESTYLE)
self.file_groups = {}
self.file_paths = []
title = "Column Data File Viewer"
self.larch = _larch
self.larch_buffer = None
self.subframes = {}
self.plotframe = None
self.groupname = None
self.SetTitle(title)
self.SetSize((850, 650))
self.SetFont(Font(10))
self.config = {'chdir_on_fileopen': True}
self.createMainPanel()
self.createMenus()
self.statusbar = self.CreateStatusBar(2, 0)
self.statusbar.SetStatusWidths([-3, -1])
statusbar_fields = ["Initializing....", " "]
for i in range(len(statusbar_fields)):
self.statusbar.SetStatusText(statusbar_fields[i], i)
read_workdir('scanviewer.dat')
def createMainPanel(self):
splitter = wx.SplitterWindow(self, style=wx.SP_LIVE_UPDATE)
splitter.SetMinimumPaneSize(225)
self.filelist = wx.ListBox(splitter)
self.filelist.SetBackgroundColour(wx.Colour(255, 255, 255))
self.filelist.Bind(wx.EVT_LISTBOX, self.ShowFile)
self.detailspanel = self.createDetailsPanel(splitter)
splitter.SplitVertically(self.filelist, self.detailspanel, 1)
wx.CallAfter(self.init_larch)
def createDetailsPanel(self, parent):
mainpanel = wx.Panel(parent)
mainsizer = wx.BoxSizer(wx.VERTICAL)
panel = wx.Panel(mainpanel)
sizer = wx.GridBagSizer(8, 7)
self.title = SimpleText(panel, 'initializing...')
ir = 0
sizer.Add(self.title, (ir, 0), (1, 6), LCEN, 2)
# x-axis
self.xarr = Choice(panel,
choices=[],
action=self.onColumnChoices,
size=(120, -1))
self.xop = Choice(panel,
choices=('', 'log'),
action=self.onColumnChoices,
size=(90, -1))
ir += 1
sizer.Add(SimpleText(panel, 'X = '), (ir, 0), (1, 1), CEN, 0)
sizer.Add(self.xop, (ir, 1), (1, 1), CEN, 0)
sizer.Add(SimpleText(panel, '('), (ir, 2), (1, 1), CEN, 0)
sizer.Add(self.xarr, (ir, 3), (1, 1), RCEN, 0)
sizer.Add(SimpleText(panel, ')'), (ir, 4), (1, 1), CEN, 0)
self.yops = []
self.yarr = []
opts = {
'choices': [],
'size': (120, -1),
'action': self.onColumnChoices
}
for i in range(3):
self.yarr.append(Choice(panel, **opts))
for opts, sel, siz in ((PRE_OPS, 0, 90), (ARR_OPS, 3, 50), (ARR_OPS, 3,
50)):
w1 = Choice(panel,
choices=opts,
action=self.onColumnChoices,
size=(siz, -1))
w1.SetSelection(sel)
self.yops.append(w1)
ir += 1
label = 'Y = '
sizer.Add(SimpleText(panel, label), (ir, 0), (1, 1), CEN, 0)
sizer.Add(self.yops[0], (ir, 1), (1, 1), CEN, 0)
sizer.Add(SimpleText(panel, '[('), (ir, 2), (1, 1), CEN, 0)
sizer.Add(self.yarr[0], (ir, 3), (1, 1), CEN, 0)
sizer.Add(self.yops[1], (ir, 4), (1, 1), CEN, 0)
sizer.Add(self.yarr[1], (ir, 5), (1, 1), CEN, 0)
sizer.Add(SimpleText(panel, ')'), (ir, 6), (1, 1), LCEN, 0)
ir += 1
sizer.Add(self.yops[2], (ir, 4), (1, 1), CEN, 0)
sizer.Add(self.yarr[2], (ir, 5), (1, 1), CEN, 0)
sizer.Add(SimpleText(panel, ']'), (ir, 6), (1, 1), LCEN, 0)
self.use_deriv = Check(panel,
default=False,
label='Use Derivative?',
action=self.onColumnChoices)
self.dtcorr = Check(panel,
default=True,
label='correct deadtime?',
action=self.onColumnChoices)
ir += 1
sizer.Add(self.use_deriv, (ir, 0), (1, 3), LCEN, 0)
sizer.Add(self.dtcorr, (ir, 3), (1, 3), LCEN, 0)
pack(panel, sizer)
self.nb = flat_nb.FlatNotebook(mainpanel, -1, agwStyle=FNB_STYLE)
self.nb.SetTabAreaColour(wx.Colour(248, 248, 240))
self.nb.SetActiveTabColour(wx.Colour(254, 254, 195))
self.nb.SetNonActiveTabTextColour(wx.Colour(40, 40, 180))
self.nb.SetActiveTabTextColour(wx.Colour(80, 0, 0))
self.xas_panel = self.CreateXASPanel(self.nb) # mainpanel)
self.fit_panel = self.CreateFitPanel(self.nb) # mainpanel)
self.nb.AddPage(self.fit_panel, ' General Analysis ', True)
self.nb.AddPage(self.xas_panel, ' XAS Processing ', True)
mainsizer.Add(panel, 0, LCEN | wx.EXPAND, 2)
btnbox = wx.Panel(mainpanel)
btnsizer = wx.BoxSizer(wx.HORIZONTAL)
for ttl, opt in (('New Plot', 'new'), ('Over Plot (left)', 'left'),
('Over Plot (right)', 'right')):
btnsizer.Add(
Button(btnbox,
ttl,
size=(135, -1),
action=partial(self.onPlot, opt=opt)), LCEN, 1)
pack(btnbox, btnsizer)
mainsizer.Add(btnbox, 0, LCEN, 2)
mainsizer.Add(self.nb, 1, LCEN | wx.EXPAND, 2)
pack(mainpanel, mainsizer)
return mainpanel
def CreateFitPanel(self, parent):
panel = wx.Panel(parent)
tpan = wx.Panel(panel)
self.fit_model = Choice(tpan,
size=(100, -1),
choices=('Gaussian', 'Lorentzian', 'Voigt',
'Linear', 'Quadratic', 'Step',
'Rectangle', 'Exponential'))
self.fit_bkg = Choice(tpan,
size=(100, -1),
choices=('None', 'constant', 'linear',
'quadratic'))
self.fit_step = Choice(tpan,
size=(100, -1),
choices=('linear', 'error function', 'arctan'))
tsizer = wx.GridBagSizer(10, 4)
tsizer.Add(SimpleText(tpan, 'Fit Model: '), (0, 0), (1, 1), LCEN)
tsizer.Add(self.fit_model, (0, 1), (1, 1), LCEN)
tsizer.Add(SimpleText(tpan, 'Background: '), (0, 2), (1, 1), LCEN)
tsizer.Add(self.fit_bkg, (0, 3), (1, 1), LCEN)
tsizer.Add(
Button(tpan, 'Show Fit', size=(100, -1), action=self.onFitPeak),
(1, 1), (1, 1), LCEN)
tsizer.Add(SimpleText(tpan, 'Step Form: '), (1, 2), (1, 1), LCEN)
tsizer.Add(self.fit_step, (1, 3), (1, 1), LCEN)
pack(tpan, tsizer)
self.fit_report = RichTextCtrl(panel,
size=(525, 250),
style=wx.VSCROLL | wx.NO_BORDER)
self.fit_report.SetEditable(False)
self.fit_report.SetFont(Font(9))
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(tpan, 0, wx.GROW | wx.ALL, 2)
sizer.Add(self.fit_report, 1, LCEN | wx.GROW, 2)
pack(panel, sizer)
return panel
def InitializeXASPanel(self):
if self.groupname is None:
lgroup = None
lgroup = getattr(self.larch.symtable, self.groupname)
self.xas_e0.SetValue(getattr(lgroup, 'e0', 0))
self.xas_step.SetValue(getattr(lgroup, 'edge_step', 0))
self.xas_pre1.SetValue(getattr(lgroup, 'pre1', -200))
self.xas_pre2.SetValue(getattr(lgroup, 'pre2', -30))
self.xas_nor1.SetValue(getattr(lgroup, 'norm1', 50))
self.xas_nor2.SetValue(getattr(lgroup, 'norm2', -10))
self.xas_vict.SetSelection(getattr(lgroup, 'nvict', 1))
self.xas_nnor.SetSelection(getattr(lgroup, 'nnorm', 2))
def CreateXASPanel(self, parent):
p = panel = wx.Panel(parent)
self.xas_autoe0 = Check(panel, default=True, label='auto?')
self.xas_showe0 = Check(panel, default=True, label='show?')
self.xas_autostep = Check(panel, default=True, label='auto?')
self.xas_op = Choice(
panel,
size=(225, -1),
choices=('Raw Data', 'Normalized', 'Derivative',
'Normalized + Derivative', 'Pre-edge subtracted',
'Raw Data With Pre-edge/Post-edge Curves'),
action=self.onXASChoice)
opts = {
'size': (95, -1),
'precision': 3
} # , 'action': self.onXASChoice}
self.xas_e0 = FloatCtrl(panel, value=0, **opts)
self.xas_step = FloatCtrl(panel, value=0, **opts)
opts['precision'] = 1
self.xas_pre1 = FloatCtrl(panel, value=-200, **opts)
self.xas_pre2 = FloatCtrl(panel, value=-30, **opts)
self.xas_nor1 = FloatCtrl(panel, value=50, **opts)
self.xas_nor2 = FloatCtrl(panel, value=-50, **opts)
opts = {
'size': (50, -1),
'choices': ('0', '1', '2', '3'),
'action': self.onXASChoice
}
self.xas_vict = Choice(panel, **opts)
self.xas_nnor = Choice(panel, **opts)
self.xas_vict.SetSelection(1)
self.xas_nnor.SetSelection(2)
sizer = wx.GridBagSizer(10, 4)
sizer.Add(SimpleText(p, 'Plot XAS as: '), (0, 0), (1, 1), LCEN)
sizer.Add(SimpleText(p, 'E0 : '), (1, 0), (1, 1), LCEN)
sizer.Add(SimpleText(p, 'Edge Step: '), (2, 0), (1, 1), LCEN)
sizer.Add(SimpleText(p, 'Pre-edge range: '), (3, 0), (1, 1), LCEN)
sizer.Add(SimpleText(p, 'Normalization range: '), (4, 0), (1, 1), LCEN)
sizer.Add(self.xas_op, (0, 1), (1, 3), LCEN)
sizer.Add(self.xas_e0, (1, 1), (1, 1), LCEN)
sizer.Add(self.xas_step, (2, 1), (1, 1), LCEN)
sizer.Add(self.xas_pre1, (3, 1), (1, 1), LCEN)
sizer.Add(SimpleText(p, ':'), (3, 2), (1, 1), LCEN)
sizer.Add(self.xas_pre2, (3, 3), (1, 1), LCEN)
sizer.Add(self.xas_nor1, (4, 1), (1, 1), LCEN)
sizer.Add(SimpleText(p, ':'), (4, 2), (1, 1), LCEN)
sizer.Add(self.xas_nor2, (4, 3), (1, 1), LCEN)
sizer.Add(self.xas_autoe0, (1, 2), (1, 2), LCEN)
sizer.Add(self.xas_showe0, (1, 4), (1, 2), LCEN)
sizer.Add(self.xas_autostep, (2, 2), (1, 2), LCEN)
sizer.Add(SimpleText(p, 'Victoreen:'), (3, 4), (1, 1), LCEN)
sizer.Add(self.xas_vict, (3, 5), (1, 1), LCEN)
sizer.Add(SimpleText(p, 'PolyOrder:'), (4, 4), (1, 1), LCEN)
sizer.Add(self.xas_nnor, (4, 5), (1, 1), LCEN)
pack(panel, sizer)
return panel
def onFitPeak(self, evt=None):
gname = self.groupname
dtext = []
model = self.fit_model.GetStringSelection().lower()
dtext.append('Fit Model: %s' % model)
bkg = self.fit_bkg.GetStringSelection()
if bkg == 'None':
bkg = None
if bkg is None:
dtext.append('No Background')
else:
dtext.append('Background: %s' % bkg)
step = self.fit_step.GetStringSelection().lower()
if model in ('step', 'rectangle'):
dtext.append('Step form: %s' % step)
try:
lgroup = getattr(self.larch.symtable, gname)
x = lgroup._xdat_
y = lgroup._ydat_
except AttributeError:
self.write_message('need data to fit!')
return
if step.startswith('error'):
step = 'erf'
elif step.startswith('arctan'):
step = 'atan'
pgroup = fit_peak(x,
y,
model,
background=bkg,
step=step,
_larch=self.larch)
dtext = '\n'.join(dtext)
dtext = '%s\n%s\n' % (
dtext, fit_report(
pgroup.params, min_correl=0.25, _larch=self.larch))
self.fit_report.SetEditable(True)
self.fit_report.SetValue(dtext)
self.fit_report.SetEditable(False)
popts1 = dict(style='solid', linewidth=3, marker='None', markersize=4)
popts2 = dict(style='short dashed',
linewidth=2,
marker='None',
markersize=4)
lgroup.plot_yarrays = [(lgroup._ydat_, popts1, lgroup.plot_ylabel)]
if bkg is None:
lgroup._fit = pgroup.fit[:]
lgroup.plot_yarrays.append((lgroup._fit, popts2, 'fit'))
else:
lgroup._fit = pgroup.fit[:]
lgroup._fit_bgr = pgroup.bkg[:]
lgroup.plot_yarrays.append((lgroup._fit, popts2, 'fit'))
lgroup.plot_yarrays.append((lgroup._fit_bgr, popts2, 'background'))
self.onPlot()
def xas_process(self, gname, new_mu=False, **kws):
""" process (pre-edge/normalize) XAS data from XAS form, overwriting
larch group '_y1_' attribute to be plotted
"""
out = self.xas_op.GetStringSelection().lower() # raw, pre, norm, flat
preopts = {'group': gname, 'e0': None}
lgroup = getattr(self.larch.symtable, gname)
dtcorr = self.dtcorr.IsChecked()
if new_mu:
try:
del lgroup.e0, lgroup.edge_step
except:
pass
if not self.xas_autoe0.IsChecked():
e0 = self.xas_e0.GetValue()
if e0 < max(lgroup._xdat_) and e0 > min(lgroup._xdat_):
preopts['e0'] = e0
if not self.xas_autostep.IsChecked():
preopts['step'] = self.xas_step.GetValue()
dt = debugtime()
preopts['pre1'] = self.xas_pre1.GetValue()
preopts['pre2'] = self.xas_pre2.GetValue()
preopts['norm1'] = self.xas_nor1.GetValue()
preopts['norm2'] = self.xas_nor2.GetValue()
preopts['nvict'] = self.xas_vict.GetSelection()
preopts['nvict'] = self.xas_vict.GetSelection()
preopts['nnorm'] = self.xas_nnor.GetSelection()
preopts['make_flat'] = 'False'
preopts['group'] = gname
preopts = ", ".join(["%s=%s" % (k, v) for k, v in preopts.items()])
preedge_cmd = "pre_edge(%s._xdat_, %s._ydat_, %s)"
self.larch(preedge_cmd % (gname, gname, preopts))
if self.xas_autoe0.IsChecked():
self.xas_e0.SetValue(lgroup.e0)
if self.xas_autostep.IsChecked():
self.xas_step.SetValue(lgroup.edge_step)
details_group = lgroup
try:
details_group = lgroup.pre_edge_details
except:
pass
self.xas_pre1.SetValue(details_group.pre1)
self.xas_pre2.SetValue(details_group.pre2)
self.xas_nor1.SetValue(details_group.norm1)
self.xas_nor2.SetValue(details_group.norm2)
popts1 = dict(style='solid', linewidth=3, marker='None', markersize=4)
popts2 = dict(style='short dashed',
linewidth=2,
zorder=-5,
marker='None',
markersize=4)
poptsd = dict(style='solid',
linewidth=2,
zorder=-5,
side='right',
y2label='derivative',
marker='None',
markersize=4)
lgroup.plot_yarrays = [(lgroup._ydat_, popts1, lgroup.plot_ylabel)]
y4e0 = lgroup._ydat_
if out.startswith('raw data with'):
lgroup.plot_yarrays = [(lgroup._ydat_, popts1, lgroup.plot_ylabel),
(lgroup.pre_edge, popts2, 'pre edge'),
(lgroup.post_edge, popts2, 'post edge')]
elif out.startswith('pre'):
self.larch('%s.pre_edge_sub = %s.norm * %s.edge_step' %
(gname, gname, gname))
lgroup.plot_yarrays = [(lgroup.pre_edge_sub, popts1,
'pre edge subtracted XAFS')]
y4e0 = lgroup.pre_edge_sub
elif 'norm' in out and 'deriv' in out:
lgroup.plot_yarrays = [(lgroup.norm, popts1, 'normalized XAFS'),
(lgroup.dmude, poptsd, 'derivative')]
y4e0 = lgroup.norm
elif out.startswith('norm'):
lgroup.plot_yarrays = [(lgroup.norm, popts1, 'normalized XAFS')]
y4e0 = lgroup.norm
elif out.startswith('deriv'):
lgroup.plot_yarrays = [(lgroup.dmude, popts1, 'derivative')]
y4e0 = lgroup.dmude
lgroup.plot_ymarkers = []
if self.xas_showe0.IsChecked():
ie0 = index_of(lgroup._xdat_, lgroup.e0)
lgroup.plot_ymarkers = [(lgroup.e0, y4e0[ie0], {'label': 'e0'})]
return
def init_larch(self):
t0 = time.time()
if self.larch is None:
self.larch = Interpreter()
self.larch.symtable.set_symbol('_sys.wx.wxapp', wx.GetApp())
self.larch.symtable.set_symbol('_sys.wx.parent', self)
self.SetStatusText('ready')
self.datagroups = self.larch.symtable
self.title.SetLabel('')
def write_message(self, s, panel=0):
"""write a message to the Status Bar"""
self.SetStatusText(s, panel)
def get_data(self, group, arrayname, correct=False):
if hasattr(group, 'get_data'):
return group.get_data(arrayname, correct=correct)
return getattr(group, arrayname, None)
def onXASChoice(self, evt=None, **kws):
if self.groupname is None:
return
self.xas_process(self.groupname, **kws)
self.onPlot()
def onColumnChoices(self, evt=None):
"""column selections changed ..
recalculate _xdat_ and _ydat_
arrays for this larch group"""
dtcorr = self.dtcorr.IsChecked()
use_deriv = self.use_deriv.IsChecked()
ix = self.xarr.GetSelection()
x = self.xarr.GetStringSelection()
xop = self.xop.GetStringSelection()
op1 = self.yops[0].GetStringSelection()
op2 = self.yops[1].GetStringSelection()
op3 = self.yops[2].GetStringSelection()
y1 = self.yarr[0].GetStringSelection()
y2 = self.yarr[1].GetStringSelection()
y3 = self.yarr[2].GetStringSelection()
array_sel = {
'xop': xop,
'xarr': x,
'op1': op1,
'op2': op2,
'op3': op3,
'y1': y1,
'y2': y2,
'y3': y3,
'dtcorr': dtcorr,
'use_deriv': use_deriv
}
try:
gname = self.groupname
lgroup = getattr(self.larch.symtable, gname)
except:
gname = SCANGROUP
lgroup = getattr(self.larch.symtable, gname)
xlabel = x
try:
xunits = lgroup.array_units[ix]
except:
xunits = ''
if xop != '':
xlabel = "%s(%s)" % (xop, xlabel)
if xunits != '':
xlabel = '%s (%s)' % (xlabel, xunits)
ylabel = y1
if y2 == '':
y2, op2 = '1.0', '*'
else:
ylabel = "%s%s%s" % (ylabel, op2, y2)
if y3 == '':
y3, op3 = '1.0', '*'
else:
ylabel = "(%s)%s%s" % (ylabel, op3, y3)
if op1 != '':
ylabel = "%s(%s)" % (op1, ylabel)
if y1 in ('0.0', '1.0'):
y1 = float(yl1)
else:
y1 = self.get_data(lgroup, y1, correct=dtcorr)
if y2 in ('0.0', '1.0'):
y2 = float(y2)
if op2 == '/': y2 = 1.0
else:
y2 = self.get_data(lgroup, y2, correct=dtcorr)
if y3 in ('0.0', '1.0'):
y3 = float(y3)
if op3 == '/': y3 = 1.0
else:
y3 = self.get_data(lgroup, y3, correct=dtcorr)
if x not in ('0', '1'):
x = self.get_data(lgroup, x)
lgroup._x = x
lgroup._y1 = y1
lgroup._y2 = y2
lgroup._y3 = y3
self.larch("%s._xdat_ = %s(%s._x)" % (gname, xop, gname))
try:
yexpr = "%s._ydat_ = %s((%s._y1 %s %s._y2) %s %s._y3)" % (
gname, op1, gname, op2, gname, op3, gname)
self.larch(yexpr)
except RuntimeWarning:
self.larch("%s._ydat_ = %s._y1")
try:
if use_deriv:
d_calc = "%s._ydat_ = gradient(%s._ydat_)/gradient(%s._xdat_)"
self.larch(d_calc % (gname, gname, gname))
except:
pass
try:
npts = min(len(lgroup._xdat_), len(lgroup._ydat_))
except AttributeError:
print('Error calculating arrays (npts not correct)')
return
del lgroup._x, lgroup._y1, lgroup._y2, lgroup._y3
lgroup.array_sel = array_sel
lgroup.plot_xlabel = xlabel
lgroup.plot_ylabel = ylabel
lgroup._xdat_ = np.array(lgroup._xdat_[:npts])
lgroup._ydat_ = np.array(lgroup._ydat_[:npts])
if (self.nb.GetCurrentPage() == self.xas_panel):
self.xas_process(self.groupname, new_mu=True)
else:
lgroup.plot_yarrays = [(lgroup._ydat_, {}, None)]
def onPlot(self, evt=None, opt='new', npts=None, reprocess=False):
try:
self.plotframe.Show()
except: # wx.PyDeadObjectError
self.plotframe = PlotFrame(None, size=(650, 400))
self.plotframe.Show()
self.plotpanel = self.plotframe.panel
if reprocess:
if (self.nb.GetCurrentPage() == self.xas_panel):
self.xas_process(self.groupname, new_mu=True)
side = 'left'
update = False
plotcmd = self.plotpanel.plot
if opt in ('left', 'right'):
side = opt
plotcmd = self.plotpanel.oplot
elif opt == 'update' and npts > 4:
plotcmd = self.plotpanel.update_line
update = True
if 'new' in opt:
self.plotpanel.clear()
popts = {'side': side}
try:
gname = self.groupname
lgroup = getattr(self.larch.symtable, gname)
except:
gname = SCANGROUP
lgroup = getattr(self.larch.symtable, gname)
return
if not hasattr(lgroup, '_xdat_'):
self.onColumnChoices()
lgroup._xdat_ = np.array(lgroup._xdat_[:npts])
plot_yarrays = [(lgroup._ydat_, {}, None)]
if hasattr(lgroup, 'plot_yarrays'):
plot_yarrays = lgroup.plot_yarrays
#for yarr in plot_yarrays:
# yarr = np.array(yarr[:npts])
path, fname = os.path.split(lgroup.filename)
popts['label'] = "%s: %s" % (fname, lgroup.plot_ylabel)
if side == 'right':
popts['y2label'] = lgroup.plot_ylabel
else:
popts['ylabel'] = lgroup.plot_ylabel
if plotcmd == self.plotpanel.plot:
popts['title'] = fname
if update:
self.plotpanel.set_xlabel(lgroup.plot_xlabel)
self.plotpanel.set_ylabel(lgroup.plot_ylabel)
for itrace, yarr, label in enumerate(plot_yarrays):
plotcmd(itrace,
lgroup._xdat_,
yarr[0],
draw=True,
update_limits=((npts < 5) or (npts % 5 == 0)),
**yarr[1])
self.plotpanel.set_xylims(
(min(lgroup._xdat_), max(lgroup._xdat_), min(yarr),
max(yarr)))
else:
for yarr in plot_yarrays:
popts.update(yarr[1])
if yarr[2] is not None:
popts['label'] = yarr[2]
plotcmd(lgroup._xdat_, yarr[0], **popts)
plotcmd = self.plotpanel.oplot
if hasattr(lgroup, 'plot_ymarkers'):
for x, y, opts in lgroup.plot_ymarkers:
popts = {'marker': 'o', 'markersize': 4}
popts.update(opts)
self.plotpanel.oplot([x], [y], **popts)
self.plotpanel.canvas.draw()
def onShowLarchBuffer(self, evt=None):
if self.larch_buffer is None:
self.larch_buffer = larchframe.LarchFrame(_larch=self.larch)
self.larch_buffer.Show()
self.larch_buffer.Raise()
def ShowFile(self, evt=None, groupname=None, **kws):
if groupname is None and evt is not None:
fpath = self.file_paths[evt.GetInt()]
groupname = self.file_groups[fpath]
if not hasattr(self.datagroups, groupname):
print('Error reading file ', groupname)
return
self.groupname = groupname
self.lgroup = getattr(self.datagroups, groupname, None)
if groupname == SCANGROUP:
self.lgroup.filename = filename
elif self.lgroup is not None:
if hasattr(self.lgroup, 'array_labels'):
array_labels = self.lgroup.array_labels[:]
elif hasattr(self.lgroup, 'column_labels'):
array_labels = self.lgroup.column_labels[:]
else:
array_labels = []
for attr in dir(self.lgroup):
if isinstance(getattr(self.lgroup, attr), np.ndarray):
array_labels.append(attr)
self.lgroup.array_labels = array_labels
self.set_array_labels()
if hasattr(self.lgroup, 'array_sel'):
sel = self.lgroup.array_sel
try:
self.xarr.SetStringSelection(sel['xarr'])
self.xop.SetStringSelection(sel['xop'])
self.yops[0].SetStringSelection(sel['op1'])
self.yops[1].SetStringSelection(sel['op2'])
self.yops[2].SetStringSelection(sel['op3'])
self.yarr[0].SetStringSelection(sel['y1'])
self.yarr[1].SetStringSelection(sel['y2'])
self.yarr[2].SetStringSelection(sel['y3'])
self.dtcorr.SetValue({True: 1, False: 0}[sel['dtcorr']])
self.use_deriv.SetValue({
True: 1,
False: 0
}[sel['use_deriv']])
except:
pass
def set_array_labels(self, labels=None):
"""set choices for array dropdowns from array labels"""
array_labels = self.lgroup.array_labels
xcols = array_labels[:]
ycols = array_labels[:]
y2cols = array_labels[:] + ['1.0', '0.0', '']
ncols = len(xcols)
self.title.SetLabel(self.lgroup.filename)
_xarr = self.xarr.GetStringSelection()
if len(_xarr) < 1 or _xarr not in xcols:
_xarr = xcols[0]
_yarr = [[], [], []]
for j in range(3):
_yarr[j] = self.yarr[j].GetStringSelection()
if _yarr[j] not in ycols:
_yarr[j] = ''
self.xarr.SetItems(xcols)
self.xarr.SetStringSelection(_xarr)
for j in range(3):
if j == 0:
self.yarr[j].SetItems(ycols)
if _yarr[j] in ycols and len(_yarr[j]) > 0:
self.yarr[j].SetStringSelection(_yarr[j])
elif ycols[0] == _xarr and len(ycols) > 1:
self.yarr[j].SetStringSelection(ycols[1])
else:
self.yarr[j].SetItems(y2cols)
self.yarr[j].SetStringSelection(_yarr[j])
inb = 0
for colname in xcols:
if 'energ' in colname.lower():
inb = 1
self.nb.SetSelection(inb)
if inb == 1:
self.InitializeXASPanel()
def createMenus(self):
# ppnl = self.plotpanel
self.menubar = wx.MenuBar()
#
fmenu = wx.Menu()
MenuItem(self, fmenu, "&Open Data File\tCtrl+O", "Read Scan File",
self.onReadScan)
MenuItem(self, fmenu, "Show Larch Buffer",
"Show Larch Programming Buffer", self.onShowLarchBuffer)
fmenu.AppendSeparator()
MenuItem(self, fmenu, "&Quit\tCtrl+Q", "Quit program", self.onClose)
self.menubar.Append(fmenu, "&File")
omenu = wx.Menu()
MenuItem(self, omenu, "Edit Column Labels\tCtrl+E",
"Edit Column Labels", self.onEditColumnLabels)
self.menubar.Append(omenu, "Options")
# fmenu.AppendSeparator()
# MenuItem(self, fmenu, "&Copy\tCtrl+C",
# "Copy Figure to Clipboard", self.onClipboard)
# MenuItem(self, fmenu, "&Save\tCtrl+S", "Save Figure", self.onSaveFig)
# MenuItem(self, fmenu, "&Print\tCtrl+P", "Print Figure", self.onPrint)
# MenuItem(self, fmenu, "Page Setup", "Print Page Setup", self.onPrintSetup)
# MenuItem(self, fmenu, "Preview", "Print Preview", self.onPrintPreview)
#
#MenuItem(self, pmenu, "Unzoom\tCtrl+Z", "Unzoom Plot", self.onUnzoom)
##pmenu.AppendSeparator()
#MenuItem(self, pmenu, "Toggle Legend\tCtrl+L",
# "Toggle Legend on Plot", self.onToggleLegend)
#MenuItem(self, pmenu, "Toggle Grid\tCtrl+G",
# "Toggle Grid on Plot", self.onToggleGrid)
# self.menubar.Append(pmenu, "Plot Options")
self.SetMenuBar(self.menubar)
self.Bind(wx.EVT_CLOSE, self.onClose)
def onAbout(self, evt):
dlg = wx.MessageDialog(self, self._about, "About Epics StepScan",
wx.OK | wx.ICON_INFORMATION)
dlg.ShowModal()
dlg.Destroy()
def onClose(self, evt):
save_workdir('scanviewer.dat')
try:
self.plotframe.Destroy()
except:
pass
if self.larch_buffer is not None:
try:
self.larch_buffer.onClose()
except:
pass
for nam in dir(self.larch.symtable._sys.wx):
obj = getattr(self.larch.symtable._sys.wx, nam)
del obj
self.Destroy()
def show_subframe(self, name, frameclass):
shown = False
if name in self.subframes:
try:
self.subframes[name].Raise()
shown = True
except:
del self.subframes[name]
if not shown:
self.subframes[name] = frameclass(self)
def onEditColumnLabels(self, evt=None):
self.show_subframe('coledit', EditColumnFrame)
def onReadScan(self, evt=None):
dlg = wx.FileDialog(self,
message="Load Column Data File",
defaultDir=os.getcwd(),
wildcard=FILE_WILDCARDS,
style=wx.FD_OPEN)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
path = path.replace('\\', '/')
if path in self.file_groups:
if wx.ID_YES != popup(self, "Re-read file '%s'?" % path,
'Re-read file?'):
return
gname = '_sview0001'
count, maxcount = 1, 9999
while hasattr(self.datagroups, gname) and count < maxcount:
count += 1
gname = '_sview%4.4i' % count
if hasattr(self.datagroups, gname):
gname = randname()
parent, fname = os.path.split(path)
if self.config['chdir_on_fileopen']:
os.chdir(parent)
fh = open(path, 'r')
line1 = fh.readline().lower()
fh.close()
reader = 'read_ascii'
if 'epics scan' in line1:
reader = 'read_gsescan'
elif 'xdi' in line1:
reader = 'read_xdi'
if 'epics stepscan file' in line1:
reader = 'read_gsexdi'
self.larch("%s = %s('%s')" % (gname, reader, path))
self.larch("%s.path = '%s'" % (gname, path))
self.filelist.Append(fname)
self.file_paths.append(path)
self.file_groups[path] = gname
self.ShowFile(groupname=gname)
dlg.Destroy()
def onPlot(self, evt=None, opt='new', npts=None, reprocess=False):
try:
self.plotframe.Show()
except: # wx.PyDeadObjectError
self.plotframe = PlotFrame(None, size=(650, 400))
self.plotframe.Show()
self.plotpanel = self.plotframe.panel
if reprocess:
if (self.nb.GetCurrentPage() == self.xas_panel):
self.xas_process(self.groupname, new_mu=True)
side = 'left'
update = False
plotcmd = self.plotpanel.plot
if opt in ('left', 'right'):
side = opt
plotcmd = self.plotpanel.oplot
elif opt == 'update' and npts > 4:
plotcmd = self.plotpanel.update_line
update = True
if 'new' in opt:
self.plotpanel.clear()
popts = {'side': side}
try:
gname = self.groupname
lgroup = getattr(self.larch.symtable, gname)
except:
gname = SCANGROUP
lgroup = getattr(self.larch.symtable, gname)
return
if not hasattr(lgroup, '_xdat_'):
self.onColumnChoices()
lgroup._xdat_ = np.array(lgroup._xdat_[:npts])
plot_yarrays = [(lgroup._ydat_, {}, None)]
if hasattr(lgroup, 'plot_yarrays'):
plot_yarrays = lgroup.plot_yarrays
#for yarr in plot_yarrays:
# yarr = np.array(yarr[:npts])
path, fname = os.path.split(lgroup.filename)
popts['label'] = "%s: %s" % (fname, lgroup.plot_ylabel)
if side == 'right':
popts['y2label'] = lgroup.plot_ylabel
else:
popts['ylabel'] = lgroup.plot_ylabel
if plotcmd == self.plotpanel.plot:
popts['title'] = fname
if update:
self.plotpanel.set_xlabel(lgroup.plot_xlabel)
self.plotpanel.set_ylabel(lgroup.plot_ylabel)
for itrace, yarr, label in enumerate(plot_yarrays):
plotcmd(itrace,
lgroup._xdat_,
yarr[0],
draw=True,
update_limits=((npts < 5) or (npts % 5 == 0)),
**yarr[1])
self.plotpanel.set_xylims(
(min(lgroup._xdat_), max(lgroup._xdat_), min(yarr),
max(yarr)))
else:
for yarr in plot_yarrays:
popts.update(yarr[1])
if yarr[2] is not None:
popts['label'] = yarr[2]
plotcmd(lgroup._xdat_, yarr[0], **popts)
plotcmd = self.plotpanel.oplot
if hasattr(lgroup, 'plot_ymarkers'):
for x, y, opts in lgroup.plot_ymarkers:
popts = {'marker': 'o', 'markersize': 4}
popts.update(opts)
self.plotpanel.oplot([x], [y], **popts)
self.plotpanel.canvas.draw()
class MapViewerFrame(wx.Frame):
_about = """XRF Map Viewer
Matt Newville <newville @ cars.uchicago.edu>
"""
def __init__(self, conffile=None, **kwds):
kwds["style"] = wx.DEFAULT_FRAME_STYLE
wx.Frame.__init__(self, None, -1, size=(700, 400), **kwds)
self.data = None
self.filemap = {}
self.im_displays = []
self.larch = None
self.plotframe = None
self.Font14=wx.Font(14, wx.SWISS, wx.NORMAL, wx.BOLD, 0, "")
self.Font12=wx.Font(12, wx.SWISS, wx.NORMAL, wx.BOLD, 0, "")
self.Font11=wx.Font(11, wx.SWISS, wx.NORMAL, wx.BOLD, 0, "")
self.Font10=wx.Font(10, wx.SWISS, wx.NORMAL, wx.BOLD, 0, "")
self.Font9 =wx.Font(9, wx.SWISS, wx.NORMAL, wx.BOLD, 0, "")
self.SetTitle("GSE XRM MapViewer")
self.SetFont(self.Font9)
self.createMainPanel()
self.createMenus()
self.statusbar = self.CreateStatusBar(2, 0)
self.statusbar.SetStatusWidths([-3, -1])
statusbar_fields = ["Initializing....", " "]
for i in range(len(statusbar_fields)):
self.statusbar.SetStatusText(statusbar_fields[i], i)
def createMainPanel(self):
sizer = wx.BoxSizer(wx.VERTICAL)
splitter = wx.SplitterWindow(self, style=wx.SP_LIVE_UPDATE)
splitter.SetMinimumPaneSize(175)
self.filelist = EditableListBox(splitter, self.ShowFile)
# self.detailspanel = self.createViewOptsPanel(splitter)
dpanel = self.detailspanel = wx.Panel(splitter)
dpanel.SetMinSize((575, 350))
self.createNBPanels(dpanel)
splitter.SplitVertically(self.filelist, self.detailspanel, 1)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(splitter, 1, wx.GROW|wx.ALL, 5)
wx.CallAfter(self.init_larch)
pack(self, sizer)
def createNBPanels(self, parent):
self.title = SimpleText(parent, 'initializing...')
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(self.title, 0, ALL_CEN)
self.nb = flat_nb.FlatNotebook(parent, wx.ID_ANY, agwStyle=FNB_STYLE)
self.nb.SetBackgroundColour('#FCFCFA')
self.SetBackgroundColour('#F0F0E8')
self.nbpanels = {}
for name, key, creator in (('Simple ROI Map', 'roimap', SimpleMapPanel),
('3-Color ROI Map', '3color', TriColorMapPanel)):
# ('2x2 Grid', self.MapGridPanel)):
# print 'panel ' , name, parent, creator
p = creator(parent, owner=self)
self.nb.AddPage(p, name, True)
self.nbpanels[key] = p
self.nb.SetSelection(0)
sizer.Add(self.nb, 1, wx.ALL|wx.EXPAND)
pack(parent, sizer)
def lassoHandler(self, data=None, selected=None, det=None, mask=None, **kws):
mask.shape = data.shape
energy = self.current_file.xrfmap['detsum/energy'].value
spectra = self.current_file.xrfmap['detsum/data'].value
spectra = spectra.swapaxes(0, 1)[mask].sum(axis=0)
self.show_PlotFrame()
spectra[np.where(spectra<1)] = 1
self.plotframe.plot(energy, spectra, ylog_scale=True)
def show_PlotFrame(self, do_raise=True, clear=True):
"make sure plot frame is enabled, and visible"
if self.plotframe is None:
self.plotframe = PlotFrame(self, title='XRF Spectra')
try:
self.plotframe.Show()
except wx.PyDeadObjectError:
self.plotframe = PlotFrame(self, title='XRF Spectra')
self.plotframe.Show()
if do_raise:
self.plotframe.Raise()
if clear:
self.plotframe.panel.clear()
self.plotframe.reset_config()
def add_imdisplay(self, title, det=None, config_on_frame=True):
on_lasso = Closure(self.lassoHandler, det=det)
self.im_displays.append(ImageFrame(output_title=title,
lasso_callback=on_lasso,
config_on_frame=config_on_frame))
def display_map(self, map, title='', info='', x=None, y=None, det=None,
with_config=True):
"""display a map in an available image display"""
displayed = False
while not displayed:
try:
imd = self.im_displays.pop()
imd.display(map, title=title, x=x, y=y)
displayed = True
except IndexError:
on_lasso = Closure(self.lassoHandler, det=det)
imd = ImageFrame(output_title=title,
lasso_callback=on_lasso,
config_on_frame=with_config)
imd.display(map, title=title, x=x, y=y)
displayed = True
except PyDeadObjectError:
displayed = False
self.im_displays.append(imd)
imd.SetStatusText(info, 1)
imd.Show()
imd.Raise()
def init_larch(self):
t0 = time.time()
from larch import Interpreter
from larch.wxlib import inputhook
self.larch = Interpreter()
self.larch.symtable.set_symbol('_sys.wx.wxapp', wx.GetApp())
self.larch.symtable.set_symbol('_sys.wx.parent', self)
self.SetStatusText('ready')
self.datagroups = self.larch.symtable
self.title.SetLabel('')
def onPlot(self, evt): self.do_plot(newplot=True)
def onOPlot(self, evt): self.do_plot(newplot=False)
def do_plot(self, newplot=False):
ix = self.x_choice.GetSelection()
x = self.x_choice.GetStringSelection()
if self.data is None and ix > -1:
self.SetStatusText( 'cannot plot - no valid data')
xop = self.x_op.GetStringSelection()
yop1 = self.y_op1.GetStringSelection()
yop2 = self.y_op2.GetStringSelection()
yop3 = self.y_op3.GetStringSelection()
y1 = self.y1_choice.GetStringSelection()
y2 = self.y2_choice.GetStringSelection()
y3 = self.y3_choice.GetStringSelection()
if y1 == '': y1 = '1'
if y2 == '': y2 = '1'
if y3 == '': y3 = '1'
gname = self.groupname
lgroup = getattr(self.larch.symtable, gname)
xlabel_ = xlabel = x
xunits = lgroup.column_units[ix]
if xunits != '':
xlabel = '%s (%s)' % (xlabel, xunits)
x = "%s.get_data('%s')" % (gname, x)
if xop == 'log': x = "log(%s)" % x
ylabel = "[%s%s%s]%s%s" % (y1, yop2, y2, yop3, y3)
if y2 == '1' and yop2 in ('*', '/') or y2 == '0' and yop2 in ('+', '-'):
ylabel = "(%s%s%s" % (y1, yop3, y3)
if y3 == '1' and yop3 in ('*', '/') or y3 == '0' and yop3 in ('+', '-'):
ylabel = "%s" % (y1)
elif y3 == '1' and yop3 in ('*', '/') or y3 == '0' and yop3 in ('+', '-'):
ylabel = "%s%s%s" % (y1, yop2, y2)
if yop1 != '':
yoplab = yop1.replace('deriv', 'd')
ylabel = '%s(%s)' % (yoplab, ylabel)
if '(' in yop1: ylabel = "%s)" % ylabel
y1 = y1 if y1 in ('0, 1') else "%s.get_data('%s')" % (gname, y1)
y2 = y2 if y2 in ('0, 1') else "%s.get_data('%s')" % (gname, y2)
y3 = y3 if y3 in ('0, 1') else "%s.get_data('%s')" % (gname, y3)
y = "%s((%s %s %s) %s (%s))" % (yop1, y1, yop2, y2, yop3, y3)
if '(' in yop1: y = "%s)" % y
if 'deriv' in yop1:
y = "%s/deriv(%s)" % (y, x)
ylabel = '%s/d(%s)' % (ylabel, xlabel_)
fmt = "plot(%s, %s, label='%s', xlabel='%s', ylabel='%s', new=%s)"
cmd = fmt % (x, y, self.data.fname, xlabel, ylabel, repr(newplot))
self.larch(cmd)
def ShowFile(self, evt=None, filename=None, **kws):
if filename is None and evt is not None:
filename = evt.GetString()
if self.check_ownership(filename):
self.filemap[filename].process()
self.current_file = self.filemap[filename]
self.title.SetLabel("%s" % filename)
rois = list(self.filemap[filename].xrfmap['roimap/sum_name'])
rois_extra = [''] + rois
set_choices(self.nbpanels['roimap'].roi1, rois)
set_choices(self.nbpanels['roimap'].roi2, rois_extra)
set_choices(self.nbpanels['3color'].rchoice, rois)
set_choices(self.nbpanels['3color'].gchoice, rois)
set_choices(self.nbpanels['3color'].bchoice, rois)
def createMenus(self):
self.menubar = wx.MenuBar()
fmenu = wx.Menu()
add_menu(self, fmenu, "&Open Map File\tCtrl+O",
"Read Map File", self.onReadFile)
add_menu(self, fmenu, "&Open Map Folder\tCtrl+F",
"Read Map Folder", self.onReadFolder)
fmenu.AppendSeparator()
add_menu(self, fmenu, "&Quit\tCtrl+Q",
"Quit program", self.onClose)
self.menubar.Append(fmenu, "&File")
self.SetMenuBar(self.menubar)
def onAbout(self,evt):
dlg = wx.MessageDialog(self, self._about,"About GSEXRM MapViewer",
wx.OK | wx.ICON_INFORMATION)
dlg.ShowModal()
dlg.Destroy()
def onClose(self,evt):
for xrmfile in self.filemap.values():
xrmfile.close()
for imd in self.im_displays:
try:
imd.Destroy()
except:
pass
for nam in dir(self.larch.symtable._plotter):
obj = getattr(self.larch.symtable._plotter, nam)
try:
obj.Destroy()
except:
pass
for nam in dir(self.larch.symtable._sys.wx):
obj = getattr(self.larch.symtable._sys.wx, nam)
del obj
self.Destroy()
def onReadFolder(self, evt=None):
dlg = wx.DirDialog(self, message="Read Map Folder",
defaultPath=os.getcwd(),
style=wx.OPEN)
path, read = None, False
if dlg.ShowModal() == wx.ID_OK:
read = True
path = dlg.GetPath().replace('\\', '/')
dlg.Destroy()
if read:
try:
xrmfile = GSEXRM_MapFile(folder=str(path))
except:
popup(self, NOT_GSEXRM_FOLDER % fname,
"Not a Map folder")
return
fname = xrmfile.filename
if fname not in self.filemap:
self.filemap[fname] = xrmfile
if fname not in self.filelist.GetItems():
self.filelist.Append(fname)
if self.check_ownership(fname):
self.process_file(fname)
self.ShowFile(filename=fname)
def onReadFile(self, evt=None):
dlg = wx.FileDialog(self, message="Read Map File",
defaultDir=os.getcwd(),
wildcard=FILE_WILDCARDS,
style=wx.OPEN)
path, read = None, False
if dlg.ShowModal() == wx.ID_OK:
read = True
path = dlg.GetPath().replace('\\', '/')
if path in self.filemap:
read = popup(self, "Re-read file '%s'?" % path, 'Re-read file?',
style=wx.YES_NO)
dlg.Destroy()
if read:
try:
parent, fname = os.path.split(path)
xrmfile = GSEXRM_MapFile(fname)
except:
popup(self, NOT_GSEXRM_FILE % fname,
"Not a Map file!")
return
if fname not in self.filemap:
self.filemap[fname] = xrmfile
if fname not in self.filelist.GetItems():
self.filelist.Append(fname)
if self.check_ownership(fname):
self.process_file(fname)
self.ShowFile(filename=fname)
def onGSEXRM_Data(self, **kws):
print 'Saw GSEXRM_Data ', kws
def process_file(self, filename):
"""Request processing of map file.
This can take awhile, so is done in a separate thread,
with updates displayed in message bar
"""
xrm_map = self.filemap[filename]
if xrm_map.status == GSEXRM_FileStatus.created:
xrm_map.initialize_xrfmap()
if xrm_map.dimension is None and isGSEXRM_MapFolder(self.folder):
xrm_map.read_master()
if self.filemap[filename].folder_has_newdata():
print 'PROCESS ', filename, xrm_map.folder_has_newdata()
dthread = Thread(target=self.new_mapdata, args=(filename,))
dthread.start()
dthread.join()
def new_mapdata(self, filename):
xrm_map = self.filemap[filename]
nrows = len(xrm_map.rowdata)
if xrm_map.folder_has_newdata():
irow = xrm_map.last_row + 1
while irow < nrows:
row = xrm_map.read_rowdata(irow)
if row is not None:
xrm_map.add_rowdata(row)
irow = irow + 1
time.sleep(.001)
wx.Yield()
xrm_map.resize_arrays(xrm_map.last_row+1)
xrm_map.h5root.flush()
def OLDprocess_file(self, filename):
"""Request processing of map file.
This can take awhile, so is done in a separate thread,
with updates displayed in message bar
"""
xrm_map = self.filemap[filename]
def on_process(row=0, maxrow=0, filename=None, status='unknown'):
print 'on process ', row, maxrow, filename, status
if maxrow < 1 or filename is None:
return
#self.SetStatusText('processing row=%i / %i for %s [%s]' %
# (row, maxrow, fname, status))
if xrm_map.folder_has_newdata():
print 'PROCESS ', filename, xrm_map.folder_has_newdata()
dthread = Thread(target=self.filemap[filename].process,
kwargs={'callback': on_process},
name='process_thread')
dthread.start()
dthread.join()
def check_ownership(self, fname):
"""
check whether we're currently owner of the file.
this is important!! HDF5 files can be corrupted.
"""
if not self.filemap[fname].check_hostid():
if popup(self, NOT_OWNER_MSG % fname,
'Not Owner of HDF5 File', style=wx.YES_NO):
self.filemap[fname].claim_hostid()
return self.filemap[fname].check_hostid()