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silicon calibration for nscope #311

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merged 3 commits into from
Jul 24, 2024
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Merged

silicon calibration for nscope #311

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4f6715a
silicon calibration for nscope
jonwright Jul 24, 2024
d0f46f5
silicon calibration for nscope
jonwright Jul 24, 2024
690349b
Merge branch 'FABLE-3DXRD:master' into master
jonwright Jul 24, 2024
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189 changes: 97 additions & 92 deletions ImageD11/nbGui/fit_geometry.py
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Original file line number Diff line number Diff line change
@@ -1,114 +1,119 @@
import ipywidgets, pylab as pl

import ipywidgets, pylab as pl, numpy as np, time
from ImageD11 import transformer
from tkinter import *
from tkinter import filedialog
from IPython.display import display


class FitGeom(transformer.transformer):

"Gives an IPython notebook UI for the experimental calibrations"
try:
if get_ipython().__class__.__name__ == 'ZMQInteractiveShell':
interactive = True
else:
interactive = False
except NameError:
interactive = False


def __init__(self):
transformer.transformer.__init__(self)
self.vars = "y_center z_center distance tilt_y tilt_z".split()
self.steps = (1, 1, 100, 0.01, 0.01, 0)
self.nv = len(self.vars)
names = "cell__a cell__b cell__c cell_alpha cell_beta cell_gamma cell_lattice_[P,A,B,C,I,F,R]".split() +\
"distance wavelength y_size z_size y_center z_center tilt_x tilt_y tilt_z t_x t_y t_z omegasign".split() +\
"o11 o12 o21 o22 fit_tolerance".split()
self.names = names
self.gui = None

def __parCallBack( self, arg ):
self.parameterobj.parameters.update( { arg['owner'].description : arg['new'] } )
self.__drawPlot()
def parCallBack( self, arg, name ):
self.parameterobj.parameters.update( { name : arg['new'] } )
self.drawPlot()

def __fixVaryCallBack( self, arg ):
def fixVaryCallBack( self, arg, name ):
name = arg['owner'].description.split(" ")[1]
vars = self.getvars()
if arg.new and not (name in self.vars):
vars.append( name )
if name in self.vars and not arg.new:
vars.remove(name)
self.parameterobj.set_varylist(vars)
vary = arg.new
if arg.new:
if name not in self.parameterobj.varylist:
self.parameterobj.varylist.append(name)
else:
self.parameterobj.varylist.remove(name)

def __fitCallBack(self, arg):
def fitCallBack(self, arg):
""" fit call back - runs fit """
lo, hi = self.ax1.get_xlim()
self.fit( lo, hi )
self.__updateGui()

def __drawPlot(self):
tth, eta = self.compute_tth_eta()
self.pt1.set_data( tth, eta )

def __loadCallBack(self, arg):
rootTk = Tk()
rootTk.withdraw()
rootTk.call('wm', 'attributes', '.', '-topmost', True)
filename = filedialog.askopenfilename()
get_ipython().run_line_magic('gui', 'tk')
if not filename == '':
self.loadfileparameters(filename)
self.__updateGui()

def __saveCallBack(self, arg):
rootTk = Tk()
rootTk.withdraw()
rootTk.call('wm', 'attributes', '.', '-topmost', True)
filename = filedialog.asksaveasfilename()
get_ipython().run_line_magic('gui', 'tk')
if not filename == '':
self.parameterobj.saveparameters(filename)

def __updateGui(self):
for i, pname in enumerate(self.vars):
self.layout[i,0].value = self.parameterobj.get(pname)
self.__drawPlot()
self.updateGui()

def drawPlot(self):
self.compute_tth_eta()
self.addcellpeaks()
self.pt1.set_data( self.colfile.tth, self.colfile.eta )
self.pt2.set_data( self.theorytth, np.full_like(self.theorytth,0) )
self.ax1.set(title='fitted')
self.fig1.canvas.draw()
self.fig1.canvas.flush_events()

def updateGui(self):
for i, name in enumerate( self.parameterobj.varylist ):
self.valuewidgets[name].value = self.parameterobj.parameters[name]
self.drawPlot()

def __drawWidgets(self):
nv = self.nv
vars = self.vars
steps = self.steps
self.layout = ipywidgets.GridspecLayout(nv+1,3)
for i,( pname, pstep ) in enumerate( zip( vars, steps ) ) :
self.layout[i,0] = ipywidgets.FloatText( description=pname,
value = self.parameterobj.parameters.get(pname),
step=pstep)
self.layout[i,0].observe( self.__parCallBack , names='value' )
self.layout[i,1] = ipywidgets.ToggleButton( description="Vary "+pname,
value = pname in self.getvars() )
self.layout[i,1].observe( self.__fixVaryCallBack, names='value' )

self.layout[nv,0] = ipywidgets.FloatText( description='fit_tolerance',
value = self.parameterobj.parameters.get("fit_tolerance"), step=0,)
self.layout[nv,0].observe( self.__parCallBack , names='value' )

self.layout[nv,1] = ipywidgets.Button(description="Run Fit (blocks)")
self.layout[nv,1].on_click( self.__fitCallBack )

self.layout[0,2] = ipywidgets.Button(description="Load parameters")
self.layout[0,2].on_click( self.__loadCallBack )

self.layout[1,2] = ipywidgets.Button(description="Save to a file")
self.layout[1,2].on_click( self.__saveCallBack )
def drawWidgets(self):
values = {}
fix = {}
for i,name in enumerate( self.names ):
value = self.parameterobj.parameters[name]
values[name] = ipywidgets.FloatText(
description="",
value = value,
layout=ipywidgets.Layout(positioning='left'))
values[name].observe( lambda a, name=name: self.parCallBack(a, name),
names='value' )
if self.parameterobj.par_objs[name].can_vary:
fix[name] = ipywidgets.Checkbox( description="Vary "+name,
value = name in self.parameterobj.varylist,
indent=False,
layout=ipywidgets.Layout(positioning='left'))
fix[name].observe( lambda a, name=name: self.fixVaryCallBack(a, name),
names='value' )
else:
fix[name] = ipywidgets.Label(
value=name,
layout=ipywidgets.Layout(positioning='left') )
self.valuewidgets = values
self.fixwidgets = fix


def fitGui(self):
if self.__class__.interactive:
self.fig1 = pl.figure(1, figsize=(9,6))
if self.gui is not None:
return self.gui
else:
with pl.ioff():
self.fig1 = pl.figure(figsize=(9,6), constrained_layout=True)
self.ax1 = self.fig1.add_subplot()
tth, eta = self.compute_tth_eta()
self.compute_tth_eta()
self.addcellpeaks()
self.pt1, = self.ax1.plot( tth, eta, ",")
self.pt1, = self.ax1.plot( self.colfile.tth, self.colfile.eta, ".",
ms=2, zorder=1)
self.ax1.set(xlabel="tth", ylabel="eta")
self.ax1.plot( self.theorytth, [0,]*len(self.theorytth), "r|", ms=360, alpha=0.2 )
# Add controls
self.__drawWidgets()
display(self.layout)
else:
print('Sorry, this Gui works only in IPython notebooks!')



self.pt2, = self.ax1.plot( self.theorytth, np.full_like(self.theorytth,0),
"g|", ms=360, lw= 0.1, zorder=2 )

self.fitbutton = ipywidgets.Button(description="Fit x plot range",
width='auto')

self.fitbutton.on_click( self.fitCallBack )
self.drawWidgets()
self.gui = ipywidgets.GridBox(
[ ipywidgets.VBox( list(self.fixwidgets.values()) ),
ipywidgets.VBox( list(self.valuewidgets.values()) ),
ipywidgets.VBox( [ self.fitbutton, self.fig1.canvas ], ) ],
layout=ipywidgets.Layout( width='100%',
grid_template_rows='auto auto auto',
grid_template_columns='15% 15% 70%',) )
display(self.gui)
ping(self.fig1) # gets lost on run all cells otherwise




def ping(fig):
# https://github.com/matplotlib/ipympl/issues/290
canvas = fig.canvas
#display(canvas)
canvas._handle_message(canvas, {'type': 'send_image_mode'}, [])
canvas._handle_message(canvas, {'type':'refresh'}, [])
canvas._handle_message(canvas,{'type': 'initialized'},[])
canvas._handle_message(canvas,{'type': 'draw'},[])
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