1 | #pragma rtGlobals=1 // Use modern global access method. |
---|
2 | #pragma IgorVersion=6.0 |
---|
3 | |
---|
4 | //////////////////////////////////////////////////// |
---|
5 | // |
---|
6 | // A template for writing your own scattering functions |
---|
7 | // |
---|
8 | // FIVE things to do: |
---|
9 | // 1) identify the equation and the free variables before coding |
---|
10 | // |
---|
11 | // --then you may start coding --- |
---|
12 | // |
---|
13 | // 2) change coef_MyModel to have the coefficients (defined in w[]) |
---|
14 | // in the exact order you have specified |
---|
15 | // - this change is one line, search for "CH#1" |
---|
16 | // 3) change parameters_MyModel to has parameter names, that match |
---|
17 | // the coefficients - this line follows the coefficients of step 1 |
---|
18 | // - this is "CH#2" |
---|
19 | // 4) change the function MyModel() to calculate what you want |
---|
20 | // w[N] must contain all the fitting parameters - search for "CH#3" |
---|
21 | // 5) repeat steps 2 and 3 (copy/paste) changing the RHS of the same |
---|
22 | // lines in the macro for the smeared model calculation |
---|
23 | // - search for "CH#4", and the following line |
---|
24 | // |
---|
25 | // - then, all you need to do is (re)plot the macro from the Macros menu |
---|
26 | // |
---|
27 | // As-is, the model calculates a form factor for a uniform sphere |
---|
28 | // |
---|
29 | // v 2.00 -- 01 MAY 2006 SRK |
---|
30 | // v 2.1 -- Jul 2007 SRK |
---|
31 | // converted to use structures, AAO, like the rest of the package |
---|
32 | // |
---|
33 | //////////////////////////////////////////////////// |
---|
34 | |
---|
35 | //this macro sets up all the necessary parameters and waves that are |
---|
36 | //needed to calculate the model function. |
---|
37 | // |
---|
38 | Macro PlotMyModel(num,qmin,qmax) |
---|
39 | Variable num=200, qmin=0.001, qmax=0.7 |
---|
40 | Prompt num "Enter number of data points for model: " |
---|
41 | Prompt qmin "Enter minimum q-value (^-1) for model: " |
---|
42 | Prompt qmax "Enter maximum q-value (^-1) for model: " |
---|
43 | // |
---|
44 | Make/O/D/n=(num) xwave_MyModel, ywave_MyModel |
---|
45 | xwave_MyModel = alog(log(qmin) + x*((log(qmax)-log(qmin))/num)) |
---|
46 | Make/O/D coef_MyModel = {0.01,60,6e-6,0.01} //CH#1 |
---|
47 | make/o/t parameters_MyModel = {"scale","Radius (A)","contrast (-2)","bkgd (cm-1)"} //CH#2 |
---|
48 | Edit parameters_MyModel, coef_MyModel |
---|
49 | |
---|
50 | Variable/G root:g_MyModel |
---|
51 | g_MyModel := MyModel(coef_MyModel, ywave_MyModel, xwave_MyModel) |
---|
52 | Display ywave_MyModel vs xwave_MyModel |
---|
53 | ModifyGraph marker=29, msize=2, mode=4 |
---|
54 | ModifyGraph log=1,grid=1,mirror=2 |
---|
55 | Label bottom "q (\\S-1\\M) " |
---|
56 | Label left "I(q) (cm\\S-1\\M)" |
---|
57 | AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2) |
---|
58 | |
---|
59 | AddModelToStrings("MyModel","coef_MyModel","MyModel") |
---|
60 | // |
---|
61 | End |
---|
62 | |
---|
63 | // |
---|
64 | //this macro sets up all the necessary parameters and waves that are |
---|
65 | //needed to calculate the smeared model function. |
---|
66 | // |
---|
67 | //no input parameters are necessary, it MUST use the experimental q-values |
---|
68 | // from the experimental data read in from an AVE/QSIG data file |
---|
69 | //////////////////////////////////////////////////// |
---|
70 | // - sets up a dependency to a wrapper, not the actual SmearedModelFunction |
---|
71 | Macro PlotSmearedMyModel(str) |
---|
72 | String str |
---|
73 | Prompt str,"Pick the data folder containing the resolution you want",popup,getAList(4) |
---|
74 | |
---|
75 | // if any of the resolution waves are missing => abort |
---|
76 | if(ResolutionWavesMissingDF(str)) //updated to NOT use global strings (in GaussUtils) |
---|
77 | Abort |
---|
78 | endif |
---|
79 | |
---|
80 | SetDataFolder $("root:"+str) |
---|
81 | |
---|
82 | // Setup parameter table for model function |
---|
83 | Make/O/D smear_coef_MyModel = {0.01,60,6e-6,0.0} //CH#4 change this line and the following line |
---|
84 | make/o/t smear_parameters_MyModel = {"scale","Radius (A)","contrast (-2)","bkgd (cm-1)"} |
---|
85 | Edit smear_parameters_MyModel,smear_coef_MyModel //display parameters in a table |
---|
86 | |
---|
87 | // output smeared intensity wave, dimensions are identical to experimental QSIG values |
---|
88 | // make extra copy of experimental q-values for easy plotting |
---|
89 | Duplicate/O $(str+"_q") smeared_MyModel,smeared_qvals |
---|
90 | SetScale d,0,0,"1/cm",smeared_MyModel |
---|
91 | |
---|
92 | Variable/G gs_MyModel=0 |
---|
93 | gs_MyModel := fSmearedMyModel(smear_coef_MyModel,smeared_MyModel,smeared_qvals) //this wrapper fills the STRUCT |
---|
94 | |
---|
95 | Display smeared_MyModel vs smeared_qvals |
---|
96 | ModifyGraph log=1,marker=29,msize=2,mode=4 |
---|
97 | Label bottom "q (\\S-1\\M)" |
---|
98 | Label left "I(q) (cm\\S-1\\M)" |
---|
99 | AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2) |
---|
100 | |
---|
101 | SetDataFolder root: |
---|
102 | AddModelToStrings("SmearedMyModel","smear_coef_MyModel","MyModel") |
---|
103 | End |
---|
104 | |
---|
105 | |
---|
106 | // nothing to change here |
---|
107 | // |
---|
108 | //AAO version, uses XOP if available |
---|
109 | // simply calls the original single point calculation with |
---|
110 | // a wave assignment (this will behave nicely if given point ranges) |
---|
111 | Function MyModel(cw,yw,xw) : FitFunc |
---|
112 | Wave cw,yw,xw |
---|
113 | |
---|
114 | #if exists("MyModelX") |
---|
115 | yw = MyModelX(cw,xw) |
---|
116 | #else |
---|
117 | yw = fMyModel(cw,xw) |
---|
118 | #endif |
---|
119 | return(0) |
---|
120 | End |
---|
121 | |
---|
122 | |
---|
123 | //CH#3 |
---|
124 | // you should write your function to calculate the intensity |
---|
125 | // for a single q-value (that's the input parameter x) |
---|
126 | // based on the wave (array) of parameters that you send it (w) |
---|
127 | // |
---|
128 | // unsmeared model calculation |
---|
129 | // |
---|
130 | Function fMyModel(w,x) : FitFunc |
---|
131 | Wave w |
---|
132 | Variable x |
---|
133 | |
---|
134 | // Input (fitting) variables are: |
---|
135 | //[0] scale |
---|
136 | //[1] radius () |
---|
137 | //[2] delrho (-2) |
---|
138 | //[3] background (cm-1) |
---|
139 | |
---|
140 | Variable scale,radius,delrho,bkg,qval |
---|
141 | scale = w[0] |
---|
142 | radius = w[1] |
---|
143 | delrho = w[2] |
---|
144 | bkg = w[3] |
---|
145 | |
---|
146 | qval = x //rename the input q-value, purely for readability |
---|
147 | |
---|
148 | // calculates scale * f^2/Vol where f=Vol*3*delrho*((sin(qr)-qrcos(qr))/qr^3 |
---|
149 | // and is rescaled to give [=] cm^-1 |
---|
150 | |
---|
151 | Variable bes,f,vol,f2 |
---|
152 | // |
---|
153 | //handle q==0 separately to avoid divide-by-zero in the Bessel func |
---|
154 | If(qval==0) |
---|
155 | f = 4/3*pi*radius^3*delrho*delrho*scale*1e8 + bkg |
---|
156 | return(f) |
---|
157 | Endif |
---|
158 | |
---|
159 | bes = 3*(sin(qval*radius)-qval*radius*cos(qval*radius))/qval^3/radius^3 |
---|
160 | vol = 4*pi/3*radius^3 |
---|
161 | f = vol*bes*delrho // [=] |
---|
162 | // normalize to single particle volume and convert to 1/cm |
---|
163 | f2 = f * f / vol * 1e8 // [=] 1/cm |
---|
164 | |
---|
165 | return (scale*f2+bkg) // Scale, then add in the background |
---|
166 | |
---|
167 | End |
---|
168 | |
---|
169 | //CH#4 |
---|
170 | /////////////////////////////////////////////////////////////// |
---|
171 | // smeared model calculation |
---|
172 | // |
---|
173 | // you don't need to do anything with this function, as long as |
---|
174 | // your MyModel works correctly, you get the resolution-smeared |
---|
175 | // version for free. |
---|
176 | // |
---|
177 | // this is all there is to the smeared model calculation! |
---|
178 | Function SmearedMyModel(s) : FitFunc |
---|
179 | Struct ResSmearAAOStruct &s |
---|
180 | |
---|
181 | // the name of your unsmeared model (AAO) is the first argument |
---|
182 | Smear_Model_20(MyModel,s.coefW,s.xW,s.yW,s.resW) |
---|
183 | |
---|
184 | return(0) |
---|
185 | End |
---|
186 | |
---|
187 | |
---|
188 | /////////////////////////////////////////////////////////////// |
---|
189 | |
---|
190 | |
---|
191 | // nothing to change here |
---|
192 | // |
---|
193 | //wrapper to calculate the smeared model as an AAO-Struct |
---|
194 | // fills the struct and calls the ususal function with the STRUCT parameter |
---|
195 | // |
---|
196 | // used only for the dependency, not for fitting |
---|
197 | // |
---|
198 | Function fSmearedMyModel(coefW,yW,xW) |
---|
199 | Wave coefW,yW,xW |
---|
200 | |
---|
201 | String str = getWavesDataFolder(yW,0) |
---|
202 | String DF="root:"+str+":" |
---|
203 | |
---|
204 | WAVE resW = $(DF+str+"_res") |
---|
205 | |
---|
206 | STRUCT ResSmearAAOStruct fs |
---|
207 | WAVE fs.coefW = coefW |
---|
208 | WAVE fs.yW = yW |
---|
209 | WAVE fs.xW = xW |
---|
210 | WAVE fs.resW = resW |
---|
211 | |
---|
212 | Variable err |
---|
213 | err = SmearedMyModel(fs) |
---|
214 | |
---|
215 | return (0) |
---|
216 | End |
---|