in5_vnorm.pro 16.6 KB
 Didier Richard committed Oct 09, 2015 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 ``````FUNCTION in5_vnorm, w_in, w_van0, \$ chmin=chmin, chmax=chmax, \$ tv=tv, Ns=Ns, \$ ts=ts,\$ SMOOTH=smooth,\$ verbose=verbose ;------------------------------------------------------------------------------- ;******************************************************************************* ; ; For IN4, IN5, IN6, MIBEMOL data ; ;+ ; ;

NAME:

; vnorm ; ;

PURPOSES:

; Normalises data in w_in with vanadium in (w_van0) elastic peak integral. ; ;

ARGUMENTS:

; (all optional) ; ; chmin : lower time channel limit of integration over vanadium elastic peak ; chmax : upper time channel limit ; /verbose : more info during execution ; ;

DIMENSIONS:

; w_in=w_out(nchannels, nspectra) ; ;

COMMAND SYNTAX:

; ; w3 = vnorm(w1,w2,chmin=<min>,chmax=<max>[,/verbose]) ; - normalises data in w1 to vanadium data in w2 and store the result in w3 ; (optional arguments shown in square brackets). ; ;

EXAMPLES:

; ; w3 = vnorm(w1,w2,/verbose) ; calculation of the integration limit are automatic. ; ; w3 = vnorm(w1,w2, chmin=490,chmax=520, /SMOOTH) ; only a few case require to put the limits ; by hand. Smooth, gaussian smothe the vana ELP integral ; Absolute cross section calculation: ; ; w3 = in5_vnorm(w1,w2,tv=0.5,Ns=7.22305,ts=0.5, /verbose) ; ; Absolute cross section: ; Ns is sample number density (in 10^22 at/cm^-3) ; tv and ts are total volume [cm^3] seen by the beam that might be ; approximated by the effective sample thickness [cm] if the sample are ; flat slab and/or the the beam cross section is not known. ; ; ;

VERSION HISTORY:

; ; Written by : JR. Stewart,KH.Andersen 15/11/02 ; ; Modified by: S. Rols (for mibemol data) 4/12/03 ; J. ollivier (2006-03-21) New version with vanadium temperature correction ; for the Debye-waller factor. Add verbosity on the ; standard output. Calculation of the integral limits ; automatic. ; WARNING: D7 case removed for clarity of the code!!! ; JOR, Wed Nov 17 11:58:08 CET 2010: Absolute cross section calculation included. ; Version corrected from the error in JRS/KHA routine. ; JOR, Mon Nov 7 17:30:04 CET 2011: Add the case of 3D data (PSD). Use CMreplicate to get an ; statistically averaged over the height of the detector. ; JOR, Mon Apr 23 17:24:13 CEST 2012: Smoothing function before cmreplicate. Use the function ; FILTER_IMAGE from http://nstx.pppl.gov/ ; JOR, Fri Feb 15 19:07:51 CET 2013: Debye-Waller corrections for PSD case. ; JOR, Wed Nov 20 14:47:36 CET 2013: Add the absolute normnalisation for the PSD case. Changes have ; been made in t2e_psd for correctness of the result vnorm+t2epsd. `````` Miguel Angel Gonzalez committed Aug 02, 2019 72 73 ``````; ; JOR, Mon Oct 3 10:35:44 CEST 2016 Remove the restriction on Nb channels `````` Didier Richard committed Oct 09, 2015 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 ``````; ;- ; ;------------------------------------------------------------------------------- ;******************************************************************************* COMMON c_lamp_access, inst ; for functions that has to appear later but are unknown from here when saving ; using: save,/routines,'t2e',filename='t2e.sav' forward_function str_fit take_datp, datp take_datp, datvan, /third ; Some info along with the verbosity if keyword_set(verbose) then begin print,'VNORM: instrument is : ',strupcase(inst) print, format = '("VNORM: incident wavelength : ",F5.2," Angs")', datvan.p[21] endif ;------------------------------------------------------------------------------- ; Check workspace sizes ; ; JOR, Mon Nov 7 17:30:04 CET 2011 ; If data is 3D => single crystal data presumably. In that case, date format is ; [Phi,Z,ToF] (if data in ToF) and [hw,Phi,Z] if data in energy. ; 1st treat the simple case where data in ToF. ; ;------------------------------------------------------------------------------- isPSD = 0 size_win = SIZE(w_in) ; IF keyword_set(verbose) THEN PRINT,'SIZE(w_in)=',size_win nchannels = size_win[1] `````` Miguel Angel Gonzalez committed Aug 02, 2019 109 `````` IF size_win[0] EQ 1 THEN nspectra = 1 ; A single 1D spectrum `````` Didier Richard committed Oct 09, 2015 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 `````` IF size_win[0] EQ 2 THEN BEGIN ; 2D [ToF,phi] Debye-Scherrer usual dataset nspectra = size_win[2] nchannels = size_win[1] ENDIF IF size_win[0] EQ 3 THEN BEGIN ; 3D [Phi,z,ToF] Debye-Scherrer usual dataset isPSD = 1 nchannels= size_win[3] nPhi = size_win[1] nZ = size_win[2] nspectra = nPhi*nZ ENDIF ;------------------------------------------------------------------------------- ; External instrument cases ;------------------------------------------------------------------------------- CASE inst OF 'QENS_raw':BEGIN w_out = vnorm_qens[w_in, w_van0, chmin, chmax] GOTO, finished END 'QENS': BEGIN w_out = vnorm_qens[w_in, w_van0, chmin, chmax] GOTO, finished0 END 'DCSasc': BEGIN par = datp.p e_in = datp.e chw = FLOAT(par[14]) L2 = FLOAT(par[6]) END ELSE: BEGIN par = datp.p e_in = datp.e chw=par[18] size_err_in = SIZE(e_in) END ENDCASE ;------------------------------------------------------------------------------- ;; IF keyword_set(verbose) THEN PRINT,'SIZE(e_in) = ',size_err_in size_err_in = SIZE(e_in) IF (size_err_in[0] NE size_win[0]) OR \$ (size_err_in[1] NE size_win[1]) OR \$ (size_err_in[2] NE size_win[2]) THEN e_in = SQRT(w_in) w_van = w_van0 size_wvan = SIZE(w_van) e_van = datvan.e size_err_van = SIZE(e_van) IF (size_err_van[0] NE size_wvan[0]) OR \$ (size_err_van[1] NE size_wvan[1]) OR \$ (size_err_van[2] NE size_wvan[2]) THEN e_van = SQRT(w_van) IF (size_wvan[0] NE size_win[0]) THEN BEGIN print, 'VNORM: ERROR: Win and Vanadium data have different dimensions:' print, ' Win : ', size_win print, ' Vana : ', size_wvan GOTO, fin ENDIF `````` Miguel Angel Gonzalez committed Aug 02, 2019 175 `````` IF (size_wvan[2] NE size_win[2]) THEN BEGIN `````` Didier Richard committed Oct 09, 2015 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 `````` sstr = 'VNORM: ERROR: Win and Vanadium data are not on the same format:' print, sstr print, ' Win : ', size_win print, ' Vana : ', size_wvan GOTO, fin ENDIF ; ;------------------------------------------------------------------------------------- ; Perform normalisation: ; If chmin | chmax not defined, fit to a gaussian to find ; the integrations limits on the elastic peak. ; Then integrate as usual by a sum (thus, not a true integration, unless the ; parameters - Ns, ts, tv - are given for an absolute calculation). ;------------------------------------------------------------------------------------- IF keyword_set(verbose) THEN BEGIN IF isPSD THEN \$ PRINT,'VNORM: nchannels = ',strtrim(nchannels,2),', nPhi = ',strtrim(nPhi,2), ', nZ = ',strtrim(nZ,2) \$ ELSE \$ PRINT,'VNORM: nchannels = ',strtrim(nchannels,2),', nPhi = ',strtrim(nspectra,2) ENDIF IF ~isPSD THEN BEGIN gauss = FLTARR(4) ; The average spectra center and width in safe mode x = datvan.x y = total(w_van,2) e = total(e_van,2) ; formerly used: fitgauss, x,y,e, xmin, xmax, gauss, dgauss gauss = str_fit(y, Bkgd = 0, Xin = x) if strcmp(datvan.x_tit,'Energy Transfer (meV)',6, /FOLD_CASE) then begin print,'VNORM: warning: Vanadium is in energy!' xmin = gauss[2]-3*gauss[3] xmax = gauss[2]+3*gauss[3] ind=where(x lt xmin) & chmin=ind[n_elements(ind)-1] ind=where(x gt xmax) & chmax=ind[n_elements(0)] if keyword_set(verbose) then \$ PRINT,'VNORM: normalised to Vanadium elastic integral, energy ', \$ STRTRIM(STRING(xmin),2),' to ',STRTRIM(STRING(xmax),2) endif else begin if ~keyword_set(chmin) then chmin = fix(gauss[2]-3*gauss[3]) if ~keyword_set(chmax) then chmax = fix(gauss[2]+3*gauss[3]) if keyword_set(verbose) then \$ PRINT,'VNORM: normalised to Vanadium elastic integral, channels ', \$ STRTRIM(STRING(chmin),2),' to ',STRTRIM(STRING(chmax),2) endelse ; Sum is enough for non-absolute normalisation V = TOTAL(w_van[chmin-1:chmax-1,*],1) dV = SQRT(TOTAL(e_van[chmin-1:chmax-1,*]^2,1)) ENDIF ELSE BEGIN ; PSD case x = datvan.z ; -------- ; The average spectra center and width in safe mode y = transpose( total(w_van,1) ) gauss = str_fit(y, Bkgd = 0, Xin = x) if ~keyword_set(chmin) then chmin = fix(mean(gauss[*,2])-3*mean(gauss[*,3])) if ~keyword_set(chmax) then chmax = fix(mean(gauss[*,2])+3*mean(gauss[*,3])) if keyword_set(verbose) then \$ PRINT,'VNORM: PSD: 3D normalised to Vanadium elastic integral, channels ', \$ STRTRIM(STRING(chmin),2),' to ',STRTRIM(STRING(chmax),2) V = TOTAL(w_van[*,*,chmin-1:chmax-1],3) if keyword_set(SMOOTH) then begin ; V = smooth(V,SMOOTH,/edge_truncate) filter_image gives better result V = filter_image( V, /SMOOTH, /MEDIAN, /ALL ) if keyword_set(verbose) THEN print, 'VNORM: Smoothing ELP with boxcar of ',strtrim(smooth,2),' channels' endif dV = SQRT(TOTAL(e_van[*,*,chmin-1:chmax-1]^2,3)) ENDELSE ;------------------------------------------------------------------------------------- ; ; - Correct for the vanadium Debye-Waller factor. ; The vanadium temperature must be in vana par(11) ; ; = 0.0067*vana_temp/300.0 A^2 ) ; ;------------------------------------------------------------------------------------- ; ; Since recently, the MIBEMOL parameters are disposed the same way than the other ; ILL instruments: lambda_0 = p(21), Temp = p(11), etc. ; ; So, remove the statement: ; if strcmp(inst,'MIBEMOL',4,/fold_case) then \$ ; vana_temp = datvan.p(59) \$ ; else \$ ;------------------------------------------------------------------------------------- vana_temp = datvan.p[11] IF ~isPSD THEN BEGIN if vana_temp gt 0 then begin lambda0 = datvan.p[21] Qelast = 4.0*!PI/lambda0*sin(!PI/180.0*datvan.y/2) corr_coef = exp(-0.0067*vana_temp/300.0*Qelast*Qelast) V = V/corr_coef dV = dV/corr_coef if keyword_set(verbose) then \$ print,'VNORM: T_vana = ',strtrim(vana_temp,2),' K, Debye-Waller corrections performed.' endif else begin print, 'vnorm warning: vanadium temperature is unknown, no DW corrections performed!' endelse w_buf = FLTARR(nchannels,nspectra) e_buf = FLTARR(nchannels,nspectra) IF nspectra GT 1 THEN BEGIN V = REFORM(V,1,nspectra) dV = REFORM(dV,1,nspectra) V = (FLTARR(nchannels)+1.) # V dV = (FLTARR(nchannels)+1.) # dV ; -------------------------- ; Check for the zeroed Vana ; -------------------------- nz = WHERE(V GT 0) w_buf[nz] = w_in[nz]/V[nz] ; -------------------------- ; propagate errors ; -------------------------- e_buf[nz] = SQRT((e_in[nz]/V[nz])^2 + (w_in[nz]*dV[nz]/V[nz]^2)^2) ENDIF ELSE BEGIN ; 1 spectrum only (not 0 of course) w_buf = w_in/V ; -------------------------- ; propagate errors ; -------------------------- e_buf = SQRT((e_in/V)^2 + (w_in*dV/V^2)^2) ENDELSE ENDIF ELSE BEGIN ; isPSD: all calculations on 2D elastic vana ; --------------------------------------------------------------------- ; Try to temperature DW correction in PSD ; 1) compute the alpha = phi for each px ; 2) compute Qel for ech Alpha/px ; 3) compute the corr_coef as usual since Qel is def. for each px ; --------------------------------------------------------------------- if vana_temp gt 0 then begin ; For the DW corrections calculation phi = datp.x y = datp.y ; !!! problem for negative angles ?? phi = phi # (fltarr(1,nZ)+1.0) y = (fltarr(nPhi,1)+1.0) # y r = 400.0 ; distance IN5 detector in cm unit (as the height in y ) rcos2t = r*cos(phi*!pi/180.0) rsin2t2 = (r*sin(phi*!pi/180.0))^2 zq = sqrt(rsin2t2 + y*y) ; height -h/2 to +h/2 Alpha = atan(zq,rcos2t) ; calculate 2theta values for each px lambda0 = datvan.p[21] Qelast = 4.0*!PI/lambda0*sin(Alpha/2) corr_coef = exp(-0.0067*vana_temp/300.0*Qelast*Qelast) V = V/corr_coef dV = dV/corr_coef if keyword_set(verbose) then \$ print,'VNORM: T_vana = ',strtrim(vana_temp,2),' K, Debye-Waller corrections performed.' endif else begin print, 'vnorm warning: vanadium temperature is unknown, no DW corrections performed!' endelse ; ---------------------------------------- ; ---------------------------------------- ; replicate matrix to nchannels in 3rd dimension ; ---------------------------------------- V = cmreplicate( V,nchannels ) dV= cmreplicate( dV,nchannels ) ; -------------------------- ; Check for the zeroed Vana ; -------------------------- w_buf = FLTARR(nPhi,nZ,nchannels) e_buf = w_buf nz = WHERE(V GT 0) w_buf[nz] = w_in[nz]/V[nz] ; -------------------------- ; propagate errors ; -------------------------- e_buf[nz] = SQRT((e_in[nz]/V[nz])^2 + (w_in[nz]*dV[nz]/V[nz]^2)^2) ; if keyword_set(verbose) then \$ ; print,'VNORM: WARNING: PSD: Debye-Waller corrections not implemented.' ENDELSE ; ------------------------------------------------------------------------- ; Absolute cross section: ; Ns, Nv are number density (in 10^22 at/cm^-3) ; tv and ts are total volume [cm^3] seen by the beam that might be ; approximated by the effective sample thickness [cm] if the sample are ; flat slab and/or the the beam cross section is not known. ; vanadium: ; density = 6.11 g/cm^3 ; M = 50.9415 g/mol ; Nav = 6.022142e23 at/mol ; Sigma_i = 5.08 barns (Sears tables, 1993) ; Sigma_s = 5.10 barns (Sears tables, 1993) ; ------------------------------------------------------------------------- Sigma_s = 5.10 Sigma_i = 5.08 ; Assumes, w_buf correctly treated so far even for single crystal - 3D spectra IF( N_ELEMENTS(Ns) GT 0 ) THEN BEGIN Ns = Ns*1.E22 ; Nv = 7.197E22 Nv = 6.11/50.9415*6.022142e23 tv = FLOAT(tv) Ns = FLOAT(Ns) ts = FLOAT(ts) IF keyword_set(verbose) THEN BEGIN PRINT, 'VNORM: Absolute Normalisation performed:' PRINT, format='("VNORM: Ns = ",E10.4," at/cm^3, ts = ",F5.2," cm^3/cm")',Ns,ts PRINT, format='("VNORM: Nv = ",E10.4," at/cm^3, tv = ",F5.2," cm^3/cm")',Nv,tv ENDIF w_out = ((Nv*tv)/(Ns*ts))*w_buf*Sigma_i/(4*!pi*chw) e_out = ((Nv*tv)/(Ns*ts))*e_buf*Sigma_i/(4*!pi*chw) ENDIF ELSE BEGIN w_out = w_buf e_out = e_buf ENDELSE ; ------------------------------------------------------------------------- ; Treat the error in vanadium corrections ; ------------------------------------------------------------------------- novan = WHERE(V LE 0., n) IF n GE 1 THEN BEGIN V[novan]=1. w_out[novan] = 0. e_out[novan] = -1. ENDIF if n_elements(datp.e) eq n_elements(e_out) then begin datp.e = e_out endif else \$ print, 'VNORM: WARNING: Error_out has a different size from Error_in!' finished0: ; numor = '#'+numor numor = '#' s=' -vn('+numor+',min='+STRTRIM(STRING(chmin),2)+',max='+STRTRIM(STRING(chmax),2)+')' datp.other_tit = datp.other_tit+s give_datp, datp finished: RETURN, w_out fin: RETURN, -1 END ``````