#%TITLE% SPECFITSERVER.MAC
#%NAME%
# Macros to interface SpecfitServer (Device server interface to Specfit).
#%DESCRIPTION%
# This macro set allows Spec to call the Specfit modules for peak search
# and fit.
#%SETUP%
# The name of the device server has to be given to specfitserversetup
# In database less mode, the server can be started as:
# python SpecfitServer.py
# That will create a TACO device server of the form:
# //machine.esrf.fr/SpecfitServer?5000003
# %BR%
# To get peak search working, play first with the following configuration:%BR%
# fitcon["AutoFwhm"] = 0 %BR%
# fitcon["AutoScaling"] = 1 %BR%
# fitcon["Sensitivity"] = 2.5 %BR%
# fitcon["Yscaling"] = 1 %BR%
# fitcon["fitbkg"] = "Linear" %BR%
# fitcon["fittheory"] = "Area Gaussians" %BR%
# %BR%
# Supported theories are : "Gaussians","Lorentz","Area Gaussians",
# "Area Lorentz","Pseudo-Voigt Line","Area Pseudo-Voigt","Step Down",
# "Step Up","Slit","Hypermet"
# %BR%
#Supported backgrounds are : "Constant","Exponential","Linear","Internal"
#%END%
#%UU% [specfitdevicename]
#%MDESC%
# Set the variable SPECFIT_DEV and set the device server in mode "tcp"
def specfitserversetup '
global SPECFIT_DEV SPECFIT_CONFIG
if ($# < 1){
print "Usage: specfitserversetup deviceservername"
}else{
SPECFIT_DEV="$1"
}
esrf_io(SPECFIT_DEV,"tcp")
esrf_io(SPECFIT_DEV,"timeout",10)
SPECFIT_CONFIG = specfitservergetconf(SPECFIT_DEV)
'
#%UU% (specfitdevicename)
#%MDESC%
# Give back an associative array with the FULL specfit configuration
def specfitservergetconf(specfitdevice) '{
local conf[]
local n
local i
local configuration
configuration[0] = "-1"
n=esrf_io(specfitdevice,"SpecfitGetConfig",conf)
if (conf[0] == "-1"){
printf("Error getting %s configuration\n",specfitdevice)
}else{
for (i=0;i<(n/2);i++){
configuration[conf[2*i]] = conf[2 * i + 1]
}
delete configuration[0]
}
return(configuration)
}'
#%UU% (specfitdevicename,configuration)
#%MDESC%
# Configure the keys of the associative array configuration recognized
# by the device server.
def specfitserversetconf(specfitdevice,parameters) '{
local i
local key
local conf[]
local errors
i = 0
for (key in parameters) {
conf[i] = key
i++
conf[i] = sprintf("%s",parameters[key])
i++
}
errors=esrf_io(specfitdevice,"SpecfitSetConfig",conf)
if (errors == -1){
print "Error in configuration"
}
return(errors)
}'
#%UU% (specfitdevicename,two_col_array)
#%MDESC%
# Perform a quick estimation of two_col_array and gives back
# an associative array with the form:%BR%
# tmp[0] = Number of peaks%BR%
# tmp[1] = Position_1%BR%
# tmp[2] = Position_2%BR%
# ...%BR%
# tmp[n] = Position_n
def specfitserversearch(specfitdevice,yourdata) '{
local argout
argout[0] = argout[0]
esrf_io(specfitdevice,"SpecfitSearchArray",yourdata,argout)
if (argout[0] < 0) {
print "Exception occurred"
}
return(argout)
}'
#%UU% (specfitdevicename,two_col_array)
#%MDESC%
# Perform a quick estimation of two_col_array and gives back
# an associative array with the form:%BR%
# tmp[0] = Number of parameters %BR%
# tmp[1] = Name of parameter 1 %BR%
# tmp[2] = Value of parameter 1 %BR%
# ... %BR%
# tmp[n] = Value of parameter n
def specfitserverfit(specfitdevice,yourdata) '{
local argout,i
local finalargout
argout[0] = -1
finalargout[0] = -1
esrf_io(specfitdevice,"SpecfitFitArray",yourdata,argout)
if (argout[0] < 0) {
print "Exception occurred"
return finalargout
}
i = 0
finalargout[0] = argout[0] * 1.0
for (i=1;i<finalargout[0]*2+1;i++){
if ((i % 2) == 0){
finalargout[i] = argout[i] * 1.0
}else{
finalargout[i] = argout[i]
}
}
return(finalargout)
}'
#%UU% (specfitdevice,counter,parameters)
#%MDESC%
# fit the last scan on "counter" and return the fit result.
# If no fit parameters are given the default values are: %BR%
# fitcon["AutoFwhm"] = 0 %BR%
# fitcon["AutoScaling"] = 1 %BR%
# fitcon["Sensitivity"] = 2.5 %BR%
# fitcon["fitbkg"] = "Linear" %BR%
# fitcon["fittheory"] = "Area Gaussians"
def specfitserver_fitscan(specfitdevice,counter,parameters) '{
local fitcon[]
if (cnt_num(counter)==-1) {
print "Invalid counter mnemonic"
exit
}
if (whatis("parameters") & 0x01000000)
specfitserversetconf(specfitdevice,parameters)
else {
fitcon["AutoFwhm"] = 0
fitcon["AutoScaling"] = 1
fitcon["Sensitivity"] = 2.5
fitcon["fitbkg"] = "Linear"
fitcon["fittheory"] = "Area Gaussians"
specfitserversetconf(specfitdevice,fitcon)
}
return specfitserverfit(specfitdevice,SCAN_D[0:NPTS-1][0,cnt_num(counter)+1])
}'
#%UU% (specfitdevice,counter,parameters)
#%MDESC%
# fit the last scan on "counter" plot the fitted data then return the fit result.
# If no fit parameters are given the default values are: %BR%
# fitcon["AutoFwhm"] = 0 %BR%
# fitcon["AutoScaling"] = 1 %BR%
# fitcon["Sensitivity"] = 2.5 %BR%
# fitcon["fitbkg"] = "Linear" %BR%
# fitcon["fittheory"] = "Area Gaussians"
def specfitserver_plotfitscan(specfitdevice, counter, parameters) '{
#first fit the scan
#local fitres[]
local t
splot
array gendata[NPTS][2]
fitres[0]=-1
fitres = specfitserver_fitscan(specfitdevice,counter,parameters)
p fitres
if (fitres[0] < 3) {print "fit not found "; exit}
gendata[:][0]=SCAN_D[0:NPTS-1][0]
esrf_io(specfitdevice,"SpecfitGenData",gendata[:][0],gendata[:][1])
plot_cntl("addline")
symbcolor = plot_cntl("colors[4]")
plot_cntl("colors=::::3") #use magenta color for the fit plot
array_plot(gendata)
plot_cntl(t="colors=::::"symbcolor)
return fitres
}'
#%UU%
#%MDESC% fit the last scan, return the fit data and plot the fitting curve.
def fitnow 'specfitserver_plotfitscan(SPECFIT_DEV,PLOT_SEL[0])'
def fitgaussian 'fitgaussians'
def fitgauss 'fitgaussians'
def fitvoigt 'fitpvoigt'
#%UU%
#%MDESC% fit the last scan, return the fit data and plot the fitting curve.
def fitgaussians ' {
local parameters[]
parameters["AutoFwhm"] = 0
parameters["AutoScaling"] = 1
parameters["Sensitivity"] = 2.5
parameters["fitbkg"] = "Linear"
parameters["fittheory"] = "Gaussians"
parameters["PositionFlag"] = "1"
parameters["QuotedPositionFlag"] = "1"
specfitserver_plotfitscan(SPECFIT_DEV,PLOT_SEL[0],parameters)
}'
#%UU%
#%MDESC% fit the last scan, return the fit data and plot the fitting curve.
def fitlorentz ' {
local parameters[]
parameters["AutoFwhm"] = 0
parameters["AutoScaling"] = 1
parameters["Sensitivity"] = 2.5
parameters["fitbkg"] = "Linear"
parameters["fittheory"] = "Lorentz"
parameters["PositionFlag"] = "1"
parameters["QuotedPositionFlag"] = "1"
specfitserver_plotfitscan(SPECFIT_DEV,PLOT_SEL[0],parameters)
}'
#%UU%
#%MDESC% fit the last scan, return the fit data and plot the fitting curve.
def fitpvoigt ' {
local parameters[]
parameters["AutoFwhm"] = 0
parameters["AutoScaling"] = 1
parameters["Sensitivity"] = 2.5
parameters["fitbkg"] = "Linear"
parameters["fittheory"] = "Pseudo-Voigt Line"
parameters["PositionFlag"] = "1"
parameters["QuotedPositionFlag"] = "1"
specfitserver_plotfitscan(SPECFIT_DEV,PLOT_SEL[0],parameters)
}'
#%UU%
#%MDESC% fit the last scan, return the fit data and plot the fitting curve.
def fitslit ' {
local parameters[]
parameters["AutoFwhm"] = 0
parameters["AutoScaling"] = 1
parameters["Sensitivity"] = 2.5
parameters["fitbkg"] = "Constant"
parameters["fittheory"] = "Slit"
parameters["PositionFlag"] = "1"
parameters["QuotedPositionFlag"] = "1"
specfitserver_plotfitscan(SPECFIT_DEV,PLOT_SEL[0],parameters)
}'
#%UU%
#%MDESC% fit the last scan, return the fit data and plot the fitting curve.
def fitstepup ' {
local parameters[]
parameters["AutoFwhm"] = 0
parameters["AutoScaling"] = 1
parameters["Sensitivity"] = 2.5
parameters["fitbkg"] = "Constant"
parameters["fittheory"] = "Step Up"
parameters["PositionFlag"] = "1"
parameters["QuotedPositionFlag"] = "1"
specfitserver_plotfitscan(SPECFIT_DEV,PLOT_SEL[0],parameters)
}'
#%UU%
#%MDESC% fit the last scan, return the fit data and plot the fitting curve.
def fitstepdown ' {
local parameters[]
parameters["AutoFwhm"] = 0
parameters["AutoScaling"] = 1
parameters["Sensitivity"] = 2.5
parameters["fitbkg"] = "Constant"
parameters["fittheory"] = "Step Down"
parameters["PositionFlag"] = "1"
parameters["QuotedPositionFlag"] = "1"
specfitserver_plotfitscan(SPECFIT_DEV,PLOT_SEL[0],parameters)
}'
#%UU%
#%MDESC% fit the last scan, return the fit data and plot the fitting curve.
def fithypermet ' {
local parameters[]
local flag
flag = 15
if ($# > 0){
flag = int($1)
}
parameters["AutoFwhm"] = 0
parameters["AutoScaling"] = 1
parameters["Sensitivity"] = 2.5
parameters["fitbkg"] = "Linear"
parameters["fittheory"] = "Hypermet"
parameters["PositionFlag"] = "1"
parameters["QuotedPositionFlag"] = "1"
if ((flag > 0) && (flag < 16)){
parameters["HypermetTails"]=flag
}else{
print "0 < HypermetFlag < 16"
exit
}
specfitserver_plotfitscan(SPECFIT_DEV,PLOT_SEL[0],parameters)
}'
#%MDESC% Force a single gaussian fit taken SPEC parameters as starting parameters.
#Return the fit data and plot the fitting curve.
def fitforcedgaussian '{
local counter
local height
local position
local fwhm
local array gendata[NPTS][2]
local fitres
local parameters
local constraints[]
counter = PLOT_SEL[0]
height = pl_MAX - pl_MIN
position = pl_xMAX
fwhm = pl_FWHM
parameters["Height1"] = height
parameters["Position1"] = position
parameters["FWHM1"] = fwhm
constraints["Height1"] ["code"] = "POSITIVE"
constraints["Position1"]["code"] = "QUOTED"
constraints["Position1"]["cons1"] = pl_MINX
constraints["Position1"]["cons2"] = pl_MAXX
constraints["FWHM1"] ["code"] = "POSITIVE"
fitres = _fitforcedgaussian(SPECFIT_DEV, \
SCAN_D[0:NPTS-1][0,cnt_num(counter)+1],\
parameters,constraints)
print fitres
if (fitres[0]==-1) {print "fit not found "; exit}
gendata[:][0]=SCAN_D[0:NPTS-1][0]
esrf_io(SPECFIT_DEV,"SpecfitGenData",gendata[:][0],gendata[:][1])
plot_cntl("addline")
symbcolor = plot_cntl("colors[4]")
plot_cntl("colors=::::3") #use magenta color for the fit plot
array_plot(gendata)
plot_cntl(t="colors=::::"symbcolor)
}'
#%IU%
def _fitforcedgaussian(specfitdev,yourdata,parameters,constraints0)'{
local fitcon[]
local estimate[]
local constraints[]
local argout[]
local i
local key
#configure a gaussian fit plus linear background
fitcon["AutoFwhm"] = 0
fitcon["AutoScaling"] = 1
fitcon["Sensitivity"] = 2.5
fitcon["fitbkg"] = "Linear"
fitcon["fittheory"] = "Gaussians"
specfitserversetconf(specfitdev,fitcon)
esrf_io(specfitdev,"SpecfitSetData",yourdata)
estimate=specfitservergetestimate(specfitdev)
for (key in parameters){
estimate[key] = parameters[key]
}
specfitserversetestimate(specfitdev,estimate)
constraints = specfitservergetconstraints(specfitdev)
if (whatis("constraints0") != 1211105284){
for (key in constraints0){
constraints[key] = constraints0[key]
}
}
specfitserversetconstraints(specfitdev, constraints)
#print "Estimate prior to fit= ",specfitservergetestimate(SPECFIT_DEV)
esrf_io(specfitdev,"SpecfitFit",argout)
if (argout[0] < 0) {
print "Exception occurred"
return -1
}
i = 0
for (i=0;i<argout[0];i++){
finalargout[argout[2*i+1]] = argout[2*i + 2]
}
return finalargout
}'
#%UU% (specfitdevicename)
#%MDESC%
# Give back an associative array with the FULL specfit configuration
def specfitservergetestimate(specfitdevice) '{
local conf[]
local n
local i
local configuration
configuration[0] = "-1"
n=esrf_io(specfitdevice,"SpecfitGetEstimate",conf)
if (conf[0] == "-1"){
printf("Error getting %s estimate\n",specfitdevice)
}else{
for (i=1;i<(n/2);i++){
configuration[conf[2*(i-1)+1]] = conf[2 * i]
}
configuration[0]="0"
}
return(configuration)
}'
#%UU% (specfitdevicename,configuration)
#%MDESC%
# Configure the keys of the associative array configuration recognized
# by the device server.
def specfitserversetestimate(specfitdevice,parameters) '{
local i
local key
local conf[]
local errors
parameters[0] = parameters[0]
delete parameters[0]
i = 0
for (key in parameters) {
conf[i] = key
i++
conf[i] = sprintf("%s",parameters[key])
i++
}
errors=esrf_io(specfitdevice,"SpecfitSetEstimate",conf)
if (errors == -1){
print "Error setting estimate"
}
return(errors)
}'
#%UU% (specfitdevicename)
#%MDESC%
# Give back an associative array with the FULL specfit configuration
def specfitservergetconstraints(specfitdevice) '{
local conf[]
local n
local i
local j
local configuration
configuration[0] = "-1"
n=esrf_io(specfitdevice,"SpecfitGetConstraints",conf)
if (conf[0] == "-1"){
printf("Error getting %s constraints\n",specfitdevice)
}else{
for (i=0;i<=(n-1)/5;i++){
j = 4 * i +1
configuration[conf[j]]["code"] = conf[j + 1]
configuration[conf[j]]["cons1"] = conf[j + 2]
configuration[conf[j]]["cons2"] = conf[j + 3]
}
configuration[0] = "0"
}
return(configuration)
}'
#%UU% (specfitdevicename,configuration)
#%MDESC%
# Configure the keys of the associative array configuration recognized
# by the device server.
def specfitserversetconstraints(specfitdevice,parameters) '{
local i
local n
local key, key0
local key1, key2
local conf[]
local temp[]
local errors
i = 0
key0 = "0"
for (key in parameters) {
if ((key != "0") && (key != 0)){
n=split(key,temp,"\034")
key1=temp[0]
key2=temp[1]
if (key1 != key0){
key0=key1
conf[i] = key0
i++
conf[i] = sprintf("%s",parameters[key0]["code"])
i++
conf[i] = sprintf("%.6g",parameters[key0]["cons1"])
i++
conf[i] = sprintf("%.6g",parameters[key0]["cons2"])
i++
}
}
}
errors=esrf_io(specfitdevice,"SpecfitSetConstraints",conf)
if (errors == -1){
print "Error setting constraints"
}
return(errors)
}'
#%MACROS%
#%IMACROS%
#%AUTHOR% V.A.Sole - BLISS Group - ESRF - Copyright 2003
#%TOC%
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