[5ceb7d0] | 1 | """ |
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| 2 | SAS model constructor. |
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| 3 | |
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| 4 | Small angle scattering models are defined by a set of kernel functions: |
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| 5 | |
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| 6 | *Iq(q, p1, p2, ...)* returns the scattering at q for a form with |
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| 7 | particular dimensions averaged over all orientations. |
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| 8 | |
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| 9 | *Iqxy(qx, qy, p1, p2, ...)* returns the scattering at qx, qy for a form |
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| 10 | with particular dimensions for a single orientation. |
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| 11 | |
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| 12 | *Imagnetic(qx, qy, result[], p1, p2, ...)* returns the scattering for the |
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| 13 | polarized neutron spin states (up-up, up-down, down-up, down-down) for |
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| 14 | a form with particular dimensions for a single orientation. |
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| 15 | |
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| 16 | *form_volume(p1, p2, ...)* returns the volume of the form with particular |
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| 17 | dimension. |
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| 18 | |
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| 19 | *ER(p1, p2, ...)* returns the effective radius of the form with |
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| 20 | particular dimensions. |
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| 21 | |
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| 22 | *VR(p1, p2, ...)* returns the volume ratio for core-shell style forms. |
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| 23 | |
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| 24 | These functions are defined in a kernel module .py script and an associated |
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| 25 | set of .c files. The model constructor will use them to create models with |
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| 26 | polydispersity across volume and orientation parameters, and provide |
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| 27 | scale and background parameters for each model. |
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| 28 | |
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| 29 | *Iq*, *Iqxy*, *Imagnetic* and *form_volume* should be stylized C-99 |
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| 30 | functions written for OpenCL. All functions need prototype declarations |
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| 31 | even if the are defined before they are used. OpenCL does not support |
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| 32 | *#include* preprocessor directives, so instead the list of includes needs |
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| 33 | to be given as part of the metadata in the kernel module definition. |
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| 34 | The included files should be listed using a path relative to the kernel |
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| 35 | module, or if using "lib/file.c" if it is one of the standard includes |
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| 36 | provided with the sasmodels source. The includes need to be listed in |
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| 37 | order so that functions are defined before they are used. |
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| 38 | |
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| 39 | Floating point values should be declared as *double*. For single precision |
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| 40 | calculations, *double* will be replaced by *float*. The single precision |
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| 41 | conversion will also tag floating point constants with "f" to make them |
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| 42 | single precision constants. When using integral values in floating point |
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| 43 | expressions, they should be expressed as floating point values by including |
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| 44 | a decimal point. This includes 0., 1. and 2. |
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| 45 | |
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| 46 | OpenCL has a *sincos* function which can improve performance when both |
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| 47 | the *sin* and *cos* values are needed for a particular argument. Since |
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| 48 | this function does not exist in C99, all use of *sincos* should be |
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| 49 | replaced by the macro *SINCOS(value, sn, cn)* where *sn* and *cn* are |
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| 50 | previously declared *double* variables. When compiled for systems without |
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| 51 | OpenCL, *SINCOS* will be replaced by *sin* and *cos* calls. If *value* is |
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| 52 | an expression, it will appear twice in this case; whether or not it will be |
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| 53 | evaluated twice depends on the quality of the compiler. |
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| 54 | |
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| 55 | If the input parameters are invalid, the scattering calculator should |
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| 56 | return a negative number. Particularly with polydispersity, there are |
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| 57 | some sets of shape parameters which lead to nonsensical forms, such |
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| 58 | as a capped cylinder where the cap radius is smaller than the |
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| 59 | cylinder radius. The polydispersity calculation will ignore these points, |
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| 60 | effectively chopping the parameter weight distributions at the boundary |
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| 61 | of the infeasible region. The resulting scattering will be set to |
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| 62 | background. This will work correctly even when polydispersity is off. |
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| 63 | |
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| 64 | *ER* and *VR* are python functions which operate on parameter vectors. |
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| 65 | The constructor code will generate the necessary vectors for computing |
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| 66 | them with the desired polydispersity. |
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| 67 | |
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| 68 | The available kernel parameters are defined as a list, with each parameter |
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| 69 | defined as a sublist with the following elements: |
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| 70 | |
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| 71 | *name* is the name that will be used in the call to the kernel |
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| 72 | function and the name that will be displayed to the user. Names |
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| 73 | should be lower case, with words separated by underscore. If |
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| 74 | acronyms are used, the whole acronym should be upper case. |
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| 75 | |
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| 76 | *units* should be one of *degrees* for angles, *Ang* for lengths, |
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| 77 | *1e-6/Ang^2* for SLDs. |
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| 78 | |
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| 79 | *default value* will be the initial value for the model when it |
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| 80 | is selected, or when an initial value is not otherwise specified. |
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| 81 | |
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[fcd7bbd] | 82 | *limits = [lb, ub]* are the hard limits on the parameter value, used to |
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| 83 | limit the polydispersity density function. In the fit, the parameter limits |
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[5ceb7d0] | 84 | given to the fit are the limits on the central value of the parameter. |
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| 85 | If there is polydispersity, it will evaluate parameter values outside |
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| 86 | the fit limits, but not outside the hard limits specified in the model. |
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| 87 | If there are no limits, use +/-inf imported from numpy. |
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| 88 | |
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| 89 | *type* indicates how the parameter will be used. "volume" parameters |
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| 90 | will be used in all functions. "orientation" parameters will be used |
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| 91 | in *Iqxy* and *Imagnetic*. "magnetic* parameters will be used in |
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| 92 | *Imagnetic* only. If *type* is the empty string, the parameter will |
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[78d3341] | 93 | be used in all of *Iq*, *Iqxy* and *Imagnetic*. "sld" parameters |
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| 94 | can automatically be promoted to magnetic parameters, each of which |
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| 95 | will have a magnitude and a direction, which may be different from |
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| 96 | other sld parameters. |
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[5ceb7d0] | 97 | |
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| 98 | *description* is a short description of the parameter. This will |
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| 99 | be displayed in the parameter table and used as a tool tip for the |
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| 100 | parameter value in the user interface. |
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| 101 | |
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| 102 | The kernel module must set variables defining the kernel meta data: |
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| 103 | |
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| 104 | *id* is an implicit variable formed from the filename. It will be |
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| 105 | a valid python identifier, and will be used as the reference into |
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| 106 | the html documentation, with '_' replaced by '-'. |
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| 107 | |
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| 108 | *name* is the model name as displayed to the user. If it is missing, |
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| 109 | it will be constructed from the id. |
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| 110 | |
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| 111 | *title* is a short description of the model, suitable for a tool tip, |
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| 112 | or a one line model summary in a table of models. |
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| 113 | |
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| 114 | *description* is an extended description of the model to be displayed |
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| 115 | while the model parameters are being edited. |
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| 116 | |
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| 117 | *parameters* is the list of parameters. Parameters in the kernel |
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| 118 | functions must appear in the same order as they appear in the |
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| 119 | parameters list. Two additional parameters, *scale* and *background* |
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| 120 | are added to the beginning of the parameter list. They will show up |
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| 121 | in the documentation as model parameters, but they are never sent to |
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[17bbadd] | 122 | the kernel functions. Note that *effect_radius* and *volfraction* |
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| 123 | must occur first in structure factor calculations. |
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[5ceb7d0] | 124 | |
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[17bbadd] | 125 | *category* is the default category for the model. The category is |
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| 126 | two level structure, with the form "group:section", indicating where |
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| 127 | in the manual the model will be located. Models are alphabetical |
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| 128 | within their section. |
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[5ceb7d0] | 129 | |
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| 130 | *source* is the list of C-99 source files that must be joined to |
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| 131 | create the OpenCL kernel functions. The files defining the functions |
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| 132 | need to be listed before the files which use the functions. |
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| 133 | |
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| 134 | *ER* is a python function defining the effective radius. If it is |
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| 135 | not present, the effective radius is 0. |
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| 136 | |
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| 137 | *VR* is a python function defining the volume ratio. If it is not |
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| 138 | present, the volume ratio is 1. |
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| 139 | |
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| 140 | *form_volume*, *Iq*, *Iqxy*, *Imagnetic* are strings containing the |
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| 141 | C source code for the body of the volume, Iq, and Iqxy functions |
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| 142 | respectively. These can also be defined in the last source file. |
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| 143 | |
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| 144 | *Iq* and *Iqxy* also be instead be python functions defining the |
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| 145 | kernel. If they are marked as *Iq.vectorized = True* then the |
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| 146 | kernel is passed the entire *q* vector at once, otherwise it is |
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| 147 | passed values one *q* at a time. The performance improvement of |
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| 148 | this step is significant. |
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| 149 | |
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| 150 | *demo* is a dictionary of parameter=value defining a set of |
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| 151 | parameters to use by default when *compare* is called. Any |
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| 152 | parameter not set in *demo* gets the initial value from the |
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| 153 | parameter list. *demo* is mostly needed to set the default |
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| 154 | polydispersity values for tests. |
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| 155 | |
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[17bbadd] | 156 | An *model_info* dictionary is constructed from the kernel meta data and |
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[5ceb7d0] | 157 | returned to the caller. |
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| 158 | |
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| 159 | The model evaluator, function call sequence consists of q inputs and the return vector, |
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| 160 | followed by the loop value/weight vector, followed by the values for |
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| 161 | the non-polydisperse parameters, followed by the lengths of the |
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| 162 | polydispersity loops. To construct the call for 1D models, the |
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| 163 | categories *fixed-1d* and *pd-1d* list the names of the parameters |
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| 164 | of the non-polydisperse and the polydisperse parameters respectively. |
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| 165 | Similarly, *fixed-2d* and *pd-2d* provide parameter names for 2D models. |
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| 166 | The *pd-rel* category is a set of those parameters which give |
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| 167 | polydispersitiy as a portion of the value (so a 10% length dispersity |
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| 168 | would use a polydispersity value of 0.1) rather than absolute |
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| 169 | dispersity such as an angle plus or minus 15 degrees. |
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| 170 | |
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| 171 | The *volume* category lists the volume parameters in order for calls |
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| 172 | to volume within the kernel (used for volume normalization) and for |
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| 173 | calls to ER and VR for effective radius and volume ratio respectively. |
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| 174 | |
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| 175 | The *orientation* and *magnetic* categories list the orientation and |
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| 176 | magnetic parameters. These are used by the sasview interface. The |
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| 177 | blank category is for parameters such as scale which don't have any |
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| 178 | other marking. |
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| 179 | |
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| 180 | The doc string at the start of the kernel module will be used to |
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| 181 | construct the model documentation web pages. Embedded figures should |
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| 182 | appear in the subdirectory "img" beside the model definition, and tagged |
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| 183 | with the kernel module name to avoid collision with other models. Some |
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| 184 | file systems are case-sensitive, so only use lower case characters for |
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| 185 | file names and extensions. |
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| 186 | |
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| 187 | |
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| 188 | The function :func:`make` loads the metadata from the module and returns |
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[17bbadd] | 189 | the kernel source. The function :func:`make_doc` extracts the doc string |
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[5ceb7d0] | 190 | and adds the parameter table to the top. The function :func:`model_sources` |
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| 191 | returns a list of files required by the model. |
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| 192 | |
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| 193 | Code follows the C99 standard with the following extensions and conditions:: |
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| 194 | |
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| 195 | M_PI_180 = pi/180 |
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| 196 | M_4PI_3 = 4pi/3 |
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| 197 | square(x) = x*x |
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| 198 | cube(x) = x*x*x |
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| 199 | sinc(x) = sin(x)/x, with sin(0)/0 -> 1 |
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| 200 | all double precision constants must include the decimal point |
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| 201 | all double declarations may be converted to half, float, or long double |
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| 202 | FLOAT_SIZE is the number of bytes in the converted variables |
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| 203 | """ |
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| 204 | from __future__ import print_function |
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| 205 | |
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[4d76711] | 206 | #TODO: identify model files which have changed since loading and reload them. |
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| 207 | #TODO: determine which functions are useful outside of generate |
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| 208 | #__all__ = ["model_info", "make_doc", "make_source", "convert_type"] |
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[5ceb7d0] | 209 | |
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| 210 | import sys |
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| 211 | from os.path import abspath, dirname, join as joinpath, exists, basename, \ |
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| 212 | splitext |
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| 213 | import re |
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| 214 | import string |
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[78d3341] | 215 | import warnings |
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[fcd7bbd] | 216 | from collections import namedtuple |
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[5ceb7d0] | 217 | |
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| 218 | import numpy as np |
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| 219 | |
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[4d76711] | 220 | from .custom import load_custom_kernel_module |
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| 221 | |
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[fcd7bbd] | 222 | PARAMETER_FIELDS = ['name', 'units', 'default', 'limits', 'type', 'description'] |
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| 223 | Parameter = namedtuple('Parameter', PARAMETER_FIELDS) |
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| 224 | |
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[5ceb7d0] | 225 | C_KERNEL_TEMPLATE_PATH = joinpath(dirname(__file__), 'kernel_template.c') |
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| 226 | |
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| 227 | F16 = np.dtype('float16') |
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| 228 | F32 = np.dtype('float32') |
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| 229 | F64 = np.dtype('float64') |
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| 230 | try: # CRUFT: older numpy does not support float128 |
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| 231 | F128 = np.dtype('float128') |
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| 232 | except TypeError: |
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| 233 | F128 = None |
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| 234 | |
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| 235 | # Scale and background, which are parameters common to every form factor |
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| 236 | COMMON_PARAMETERS = [ |
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| 237 | ["scale", "", 1, [0, np.inf], "", "Source intensity"], |
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[b8e5e21] | 238 | ["background", "1/cm", 1e-3, [0, np.inf], "", "Source background"], |
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[5ceb7d0] | 239 | ] |
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| 240 | |
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| 241 | # Conversion from units defined in the parameter table for each model |
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| 242 | # to units displayed in the sphinx documentation. |
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| 243 | RST_UNITS = { |
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| 244 | "Ang": "|Ang|", |
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| 245 | "1/Ang": "|Ang^-1|", |
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| 246 | "1/Ang^2": "|Ang^-2|", |
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| 247 | "1e-6/Ang^2": "|1e-6Ang^-2|", |
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| 248 | "degrees": "degree", |
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| 249 | "1/cm": "|cm^-1|", |
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| 250 | "Ang/cm": "|Ang*cm^-1|", |
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| 251 | "g/cm3": "|g/cm^3|", |
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| 252 | "mg/m2": "|mg/m^2|", |
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| 253 | "": "None", |
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| 254 | } |
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| 255 | |
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| 256 | # Headers for the parameters tables in th sphinx documentation |
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| 257 | PARTABLE_HEADERS = [ |
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| 258 | "Parameter", |
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| 259 | "Description", |
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| 260 | "Units", |
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| 261 | "Default value", |
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| 262 | ] |
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| 263 | |
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| 264 | # Minimum width for a default value (this is shorter than the column header |
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| 265 | # width, so will be ignored). |
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| 266 | PARTABLE_VALUE_WIDTH = 10 |
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| 267 | |
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| 268 | # Documentation header for the module, giving the model name, its short |
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| 269 | # description and its parameter table. The remainder of the doc comes |
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| 270 | # from the module docstring. |
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| 271 | DOC_HEADER = """.. _%(id)s: |
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| 272 | |
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| 273 | %(name)s |
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| 274 | ======================================================= |
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| 275 | |
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| 276 | %(title)s |
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| 277 | |
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| 278 | %(parameters)s |
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| 279 | |
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| 280 | %(returns)s |
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| 281 | |
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| 282 | %(docs)s |
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| 283 | """ |
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| 284 | |
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| 285 | def format_units(units): |
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| 286 | """ |
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| 287 | Convert units into ReStructured Text format. |
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| 288 | """ |
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| 289 | return "string" if isinstance(units, list) else RST_UNITS.get(units, units) |
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| 290 | |
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| 291 | def make_partable(pars): |
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| 292 | """ |
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| 293 | Generate the parameter table to include in the sphinx documentation. |
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| 294 | """ |
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| 295 | column_widths = [ |
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[fcd7bbd] | 296 | max(len(p.name) for p in pars), |
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| 297 | max(len(p.description) for p in pars), |
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| 298 | max(len(format_units(p.units)) for p in pars), |
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[5ceb7d0] | 299 | PARTABLE_VALUE_WIDTH, |
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| 300 | ] |
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| 301 | column_widths = [max(w, len(h)) |
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| 302 | for w, h in zip(column_widths, PARTABLE_HEADERS)] |
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| 303 | |
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| 304 | sep = " ".join("="*w for w in column_widths) |
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| 305 | lines = [ |
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| 306 | sep, |
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| 307 | " ".join("%-*s" % (w, h) |
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| 308 | for w, h in zip(column_widths, PARTABLE_HEADERS)), |
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| 309 | sep, |
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| 310 | ] |
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| 311 | for p in pars: |
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| 312 | lines.append(" ".join([ |
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[fcd7bbd] | 313 | "%-*s" % (column_widths[0], p.name), |
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| 314 | "%-*s" % (column_widths[1], p.description), |
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| 315 | "%-*s" % (column_widths[2], format_units(p.units)), |
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| 316 | "%*g" % (column_widths[3], p.default), |
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[5ceb7d0] | 317 | ])) |
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| 318 | lines.append(sep) |
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| 319 | return "\n".join(lines) |
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| 320 | |
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| 321 | def _search(search_path, filename): |
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| 322 | """ |
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| 323 | Find *filename* in *search_path*. |
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| 324 | |
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| 325 | Raises ValueError if file does not exist. |
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| 326 | """ |
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| 327 | for path in search_path: |
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| 328 | target = joinpath(path, filename) |
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| 329 | if exists(target): |
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| 330 | return target |
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| 331 | raise ValueError("%r not found in %s" % (filename, search_path)) |
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| 332 | |
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[17bbadd] | 333 | def model_sources(model_info): |
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[5ceb7d0] | 334 | """ |
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| 335 | Return a list of the sources file paths for the module. |
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| 336 | """ |
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[17bbadd] | 337 | search_path = [dirname(model_info['filename']), |
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[5ceb7d0] | 338 | abspath(joinpath(dirname(__file__), 'models'))] |
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[17bbadd] | 339 | return [_search(search_path, f) for f in model_info['source']] |
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[5ceb7d0] | 340 | |
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| 341 | # Pragmas for enable OpenCL features. Be sure to protect them so that they |
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| 342 | # still compile even if OpenCL is not present. |
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| 343 | _F16_PRAGMA = """\ |
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[9ef9dd9] | 344 | #if defined(__OPENCL_VERSION__) // && !defined(cl_khr_fp16) |
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[5ceb7d0] | 345 | # pragma OPENCL EXTENSION cl_khr_fp16: enable |
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| 346 | #endif |
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| 347 | """ |
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| 348 | |
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| 349 | _F64_PRAGMA = """\ |
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[9ef9dd9] | 350 | #if defined(__OPENCL_VERSION__) // && !defined(cl_khr_fp64) |
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[5ceb7d0] | 351 | # pragma OPENCL EXTENSION cl_khr_fp64: enable |
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| 352 | #endif |
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| 353 | """ |
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| 354 | |
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| 355 | def convert_type(source, dtype): |
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| 356 | """ |
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| 357 | Convert code from double precision to the desired type. |
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| 358 | |
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| 359 | Floating point constants are tagged with 'f' for single precision or 'L' |
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| 360 | for long double precision. |
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| 361 | """ |
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| 362 | if dtype == F16: |
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| 363 | fbytes = 2 |
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| 364 | source = _F16_PRAGMA + _convert_type(source, "half", "f") |
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| 365 | elif dtype == F32: |
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| 366 | fbytes = 4 |
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| 367 | source = _convert_type(source, "float", "f") |
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| 368 | elif dtype == F64: |
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| 369 | fbytes = 8 |
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| 370 | source = _F64_PRAGMA + source # Source is already double |
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| 371 | elif dtype == F128: |
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| 372 | fbytes = 16 |
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| 373 | source = _convert_type(source, "long double", "L") |
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| 374 | else: |
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| 375 | raise ValueError("Unexpected dtype in source conversion: %s"%dtype) |
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| 376 | return ("#define FLOAT_SIZE %d\n"%fbytes)+source |
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| 377 | |
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| 378 | |
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| 379 | def _convert_type(source, type_name, constant_flag): |
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| 380 | """ |
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| 381 | Replace 'double' with *type_name* in *source*, tagging floating point |
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| 382 | constants with *constant_flag*. |
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| 383 | """ |
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| 384 | # Convert double keyword to float/long double/half. |
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| 385 | # Accept an 'n' # parameter for vector # values, where n is 2, 4, 8 or 16. |
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| 386 | # Assume complex numbers are represented as cdouble which is typedef'd |
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| 387 | # to double2. |
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| 388 | source = re.sub(r'(^|[^a-zA-Z0-9_]c?)double(([248]|16)?($|[^a-zA-Z0-9_]))', |
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| 389 | r'\1%s\2'%type_name, source) |
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| 390 | # Convert floating point constants to single by adding 'f' to the end, |
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| 391 | # or long double with an 'L' suffix. OS/X complains if you don't do this. |
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| 392 | source = re.sub(r'[^a-zA-Z_](\d*[.]\d+|\d+[.]\d*)([eE][+-]?\d+)?', |
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| 393 | r'\g<0>%s'%constant_flag, source) |
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| 394 | return source |
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| 395 | |
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| 396 | |
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[17bbadd] | 397 | def kernel_name(model_info, is_2d): |
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[5ceb7d0] | 398 | """ |
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| 399 | Name of the exported kernel symbol. |
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| 400 | """ |
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[17bbadd] | 401 | return model_info['name'] + "_" + ("Iqxy" if is_2d else "Iq") |
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[5ceb7d0] | 402 | |
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| 403 | |
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| 404 | def indent(s, depth): |
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| 405 | """ |
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| 406 | Indent a string of text with *depth* additional spaces on each line. |
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| 407 | """ |
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| 408 | spaces = " "*depth |
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| 409 | sep = "\n" + spaces |
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| 410 | return spaces + sep.join(s.split("\n")) |
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| 411 | |
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| 412 | |
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| 413 | LOOP_OPEN = """\ |
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| 414 | for (int %(name)s_i=0; %(name)s_i < N%(name)s; %(name)s_i++) { |
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| 415 | const double %(name)s = loops[2*(%(name)s_i%(offset)s)]; |
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| 416 | const double %(name)s_w = loops[2*(%(name)s_i%(offset)s)+1];\ |
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| 417 | """ |
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| 418 | def build_polydispersity_loops(pd_pars): |
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| 419 | """ |
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| 420 | Build polydispersity loops |
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| 421 | |
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| 422 | Returns loop opening and loop closing |
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| 423 | """ |
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| 424 | depth = 4 |
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| 425 | offset = "" |
---|
| 426 | loop_head = [] |
---|
| 427 | loop_end = [] |
---|
| 428 | for name in pd_pars: |
---|
| 429 | subst = {'name': name, 'offset': offset} |
---|
| 430 | loop_head.append(indent(LOOP_OPEN % subst, depth)) |
---|
| 431 | loop_end.insert(0, (" "*depth) + "}") |
---|
| 432 | offset += '+N' + name |
---|
| 433 | depth += 2 |
---|
| 434 | return "\n".join(loop_head), "\n".join(loop_end) |
---|
| 435 | |
---|
| 436 | C_KERNEL_TEMPLATE = None |
---|
[17bbadd] | 437 | def make_source(model_info): |
---|
[5ceb7d0] | 438 | """ |
---|
[17bbadd] | 439 | Generate the OpenCL/ctypes kernel from the module info. |
---|
| 440 | |
---|
| 441 | Uses source files found in the given search path. |
---|
[5ceb7d0] | 442 | """ |
---|
[17bbadd] | 443 | if callable(model_info['Iq']): |
---|
| 444 | return None |
---|
| 445 | |
---|
[5ceb7d0] | 446 | # TODO: need something other than volume to indicate dispersion parameters |
---|
| 447 | # No volume normalization despite having a volume parameter. |
---|
| 448 | # Thickness is labelled a volume in order to trigger polydispersity. |
---|
| 449 | # May want a separate dispersion flag, or perhaps a separate category for |
---|
| 450 | # disperse, but not volume. Volume parameters also use relative values |
---|
| 451 | # for the distribution rather than the absolute values used by angular |
---|
| 452 | # dispersion. Need to be careful that necessary parameters are available |
---|
| 453 | # for computing volume even if we allow non-disperse volume parameters. |
---|
| 454 | |
---|
| 455 | # Load template |
---|
| 456 | global C_KERNEL_TEMPLATE |
---|
| 457 | if C_KERNEL_TEMPLATE is None: |
---|
| 458 | with open(C_KERNEL_TEMPLATE_PATH) as fid: |
---|
| 459 | C_KERNEL_TEMPLATE = fid.read() |
---|
| 460 | |
---|
| 461 | # Load additional sources |
---|
[17bbadd] | 462 | source = [open(f).read() for f in model_sources(model_info)] |
---|
[5ceb7d0] | 463 | |
---|
| 464 | # Prepare defines |
---|
| 465 | defines = [] |
---|
[17bbadd] | 466 | partype = model_info['partype'] |
---|
[5ceb7d0] | 467 | pd_1d = partype['pd-1d'] |
---|
| 468 | pd_2d = partype['pd-2d'] |
---|
| 469 | fixed_1d = partype['fixed-1d'] |
---|
| 470 | fixed_2d = partype['fixed-1d'] |
---|
| 471 | |
---|
[fcd7bbd] | 472 | iq_parameters = [p.name |
---|
[17bbadd] | 473 | for p in model_info['parameters'][2:] # skip scale, background |
---|
[fcd7bbd] | 474 | if p.name in set(fixed_1d + pd_1d)] |
---|
| 475 | iqxy_parameters = [p.name |
---|
[17bbadd] | 476 | for p in model_info['parameters'][2:] # skip scale, background |
---|
[fcd7bbd] | 477 | if p.name in set(fixed_2d + pd_2d)] |
---|
| 478 | volume_parameters = [p.name |
---|
[17bbadd] | 479 | for p in model_info['parameters'] |
---|
[fcd7bbd] | 480 | if p.type == 'volume'] |
---|
[5ceb7d0] | 481 | |
---|
| 482 | # Fill in defintions for volume parameters |
---|
| 483 | if volume_parameters: |
---|
| 484 | defines.append(('VOLUME_PARAMETERS', |
---|
| 485 | ','.join(volume_parameters))) |
---|
| 486 | defines.append(('VOLUME_WEIGHT_PRODUCT', |
---|
| 487 | '*'.join(p + '_w' for p in volume_parameters))) |
---|
| 488 | |
---|
| 489 | # Generate form_volume function from body only |
---|
[17bbadd] | 490 | if model_info['form_volume'] is not None: |
---|
[5ceb7d0] | 491 | if volume_parameters: |
---|
| 492 | vol_par_decl = ', '.join('double ' + p for p in volume_parameters) |
---|
| 493 | else: |
---|
| 494 | vol_par_decl = 'void' |
---|
| 495 | defines.append(('VOLUME_PARAMETER_DECLARATIONS', |
---|
| 496 | vol_par_decl)) |
---|
| 497 | fn = """\ |
---|
| 498 | double form_volume(VOLUME_PARAMETER_DECLARATIONS); |
---|
| 499 | double form_volume(VOLUME_PARAMETER_DECLARATIONS) { |
---|
| 500 | %(body)s |
---|
| 501 | } |
---|
[17bbadd] | 502 | """ % {'body':model_info['form_volume']} |
---|
[5ceb7d0] | 503 | source.append(fn) |
---|
| 504 | |
---|
| 505 | # Fill in definitions for Iq parameters |
---|
[17bbadd] | 506 | defines.append(('IQ_KERNEL_NAME', model_info['name'] + '_Iq')) |
---|
[5ceb7d0] | 507 | defines.append(('IQ_PARAMETERS', ', '.join(iq_parameters))) |
---|
| 508 | if fixed_1d: |
---|
| 509 | defines.append(('IQ_FIXED_PARAMETER_DECLARATIONS', |
---|
| 510 | ', \\\n '.join('const double %s' % p for p in fixed_1d))) |
---|
| 511 | if pd_1d: |
---|
| 512 | defines.append(('IQ_WEIGHT_PRODUCT', |
---|
| 513 | '*'.join(p + '_w' for p in pd_1d))) |
---|
| 514 | defines.append(('IQ_DISPERSION_LENGTH_DECLARATIONS', |
---|
| 515 | ', \\\n '.join('const int N%s' % p for p in pd_1d))) |
---|
| 516 | defines.append(('IQ_DISPERSION_LENGTH_SUM', |
---|
| 517 | '+'.join('N' + p for p in pd_1d))) |
---|
| 518 | open_loops, close_loops = build_polydispersity_loops(pd_1d) |
---|
| 519 | defines.append(('IQ_OPEN_LOOPS', |
---|
| 520 | open_loops.replace('\n', ' \\\n'))) |
---|
| 521 | defines.append(('IQ_CLOSE_LOOPS', |
---|
| 522 | close_loops.replace('\n', ' \\\n'))) |
---|
[17bbadd] | 523 | if model_info['Iq'] is not None: |
---|
[5ceb7d0] | 524 | defines.append(('IQ_PARAMETER_DECLARATIONS', |
---|
| 525 | ', '.join('double ' + p for p in iq_parameters))) |
---|
| 526 | fn = """\ |
---|
| 527 | double Iq(double q, IQ_PARAMETER_DECLARATIONS); |
---|
| 528 | double Iq(double q, IQ_PARAMETER_DECLARATIONS) { |
---|
| 529 | %(body)s |
---|
| 530 | } |
---|
[17bbadd] | 531 | """ % {'body':model_info['Iq']} |
---|
[5ceb7d0] | 532 | source.append(fn) |
---|
| 533 | |
---|
| 534 | # Fill in definitions for Iqxy parameters |
---|
[17bbadd] | 535 | defines.append(('IQXY_KERNEL_NAME', model_info['name'] + '_Iqxy')) |
---|
[5ceb7d0] | 536 | defines.append(('IQXY_PARAMETERS', ', '.join(iqxy_parameters))) |
---|
| 537 | if fixed_2d: |
---|
| 538 | defines.append(('IQXY_FIXED_PARAMETER_DECLARATIONS', |
---|
| 539 | ', \\\n '.join('const double %s' % p for p in fixed_2d))) |
---|
| 540 | if pd_2d: |
---|
| 541 | defines.append(('IQXY_WEIGHT_PRODUCT', |
---|
| 542 | '*'.join(p + '_w' for p in pd_2d))) |
---|
| 543 | defines.append(('IQXY_DISPERSION_LENGTH_DECLARATIONS', |
---|
| 544 | ', \\\n '.join('const int N%s' % p for p in pd_2d))) |
---|
| 545 | defines.append(('IQXY_DISPERSION_LENGTH_SUM', |
---|
| 546 | '+'.join('N' + p for p in pd_2d))) |
---|
| 547 | open_loops, close_loops = build_polydispersity_loops(pd_2d) |
---|
| 548 | defines.append(('IQXY_OPEN_LOOPS', |
---|
| 549 | open_loops.replace('\n', ' \\\n'))) |
---|
| 550 | defines.append(('IQXY_CLOSE_LOOPS', |
---|
| 551 | close_loops.replace('\n', ' \\\n'))) |
---|
[17bbadd] | 552 | if model_info['Iqxy'] is not None: |
---|
[5ceb7d0] | 553 | defines.append(('IQXY_PARAMETER_DECLARATIONS', |
---|
| 554 | ', '.join('double ' + p for p in iqxy_parameters))) |
---|
| 555 | fn = """\ |
---|
| 556 | double Iqxy(double qx, double qy, IQXY_PARAMETER_DECLARATIONS); |
---|
| 557 | double Iqxy(double qx, double qy, IQXY_PARAMETER_DECLARATIONS) { |
---|
| 558 | %(body)s |
---|
| 559 | } |
---|
[17bbadd] | 560 | """ % {'body':model_info['Iqxy']} |
---|
[5ceb7d0] | 561 | source.append(fn) |
---|
| 562 | |
---|
| 563 | # Need to know if we have a theta parameter for Iqxy; it is not there |
---|
| 564 | # for the magnetic sphere model, for example, which has a magnetic |
---|
| 565 | # orientation but no shape orientation. |
---|
| 566 | if 'theta' in pd_2d: |
---|
| 567 | defines.append(('IQXY_HAS_THETA', '1')) |
---|
| 568 | |
---|
| 569 | #for d in defines: print(d) |
---|
| 570 | defines = '\n'.join('#define %s %s' % (k, v) for k, v in defines) |
---|
| 571 | sources = '\n\n'.join(source) |
---|
| 572 | return C_KERNEL_TEMPLATE % { |
---|
| 573 | 'DEFINES': defines, |
---|
| 574 | 'SOURCES': sources, |
---|
| 575 | } |
---|
| 576 | |
---|
[17bbadd] | 577 | def categorize_parameters(pars): |
---|
[5ceb7d0] | 578 | """ |
---|
[17bbadd] | 579 | Build parameter categories out of the the parameter definitions. |
---|
| 580 | |
---|
| 581 | Returns a dictionary of categories. |
---|
| 582 | |
---|
| 583 | Note: these categories are subject to change, depending on the needs of |
---|
| 584 | the UI and the needs of the kernel calling function. |
---|
| 585 | |
---|
| 586 | The categories are as follows: |
---|
| 587 | |
---|
| 588 | * *volume* list of volume parameter names |
---|
| 589 | * *orientation* list of orientation parameters |
---|
| 590 | * *magnetic* list of magnetic parameters |
---|
| 591 | * *<empty string>* list of parameters that have no type info |
---|
| 592 | |
---|
| 593 | Each parameter is in one and only one category. |
---|
| 594 | |
---|
| 595 | The following derived categories are created: |
---|
| 596 | |
---|
| 597 | * *fixed-1d* list of non-polydisperse parameters for 1D models |
---|
| 598 | * *pd-1d* list of polydisperse parameters for 1D models |
---|
| 599 | * *fixed-2d* list of non-polydisperse parameters for 2D models |
---|
| 600 | * *pd-d2* list of polydisperse parameters for 2D models |
---|
[5ceb7d0] | 601 | """ |
---|
[17bbadd] | 602 | partype = { |
---|
[78d3341] | 603 | 'volume': [], 'orientation': [], 'magnetic': [], 'sld': [], '': [], |
---|
[17bbadd] | 604 | 'fixed-1d': [], 'fixed-2d': [], 'pd-1d': [], 'pd-2d': [], |
---|
| 605 | 'pd-rel': set(), |
---|
| 606 | } |
---|
| 607 | |
---|
| 608 | for p in pars: |
---|
[fcd7bbd] | 609 | if p.type == 'volume': |
---|
| 610 | partype['pd-1d'].append(p.name) |
---|
| 611 | partype['pd-2d'].append(p.name) |
---|
| 612 | partype['pd-rel'].add(p.name) |
---|
| 613 | elif p.type == 'magnetic': |
---|
| 614 | partype['fixed-2d'].append(p.name) |
---|
| 615 | elif p.type == 'orientation': |
---|
| 616 | partype['pd-2d'].append(p.name) |
---|
[78d3341] | 617 | elif p.type in ('', 'sld'): |
---|
[fcd7bbd] | 618 | partype['fixed-1d'].append(p.name) |
---|
| 619 | partype['fixed-2d'].append(p.name) |
---|
[17bbadd] | 620 | else: |
---|
[fcd7bbd] | 621 | raise ValueError("unknown parameter type %r" % p.type) |
---|
| 622 | partype[p.type].append(p.name) |
---|
[17bbadd] | 623 | |
---|
| 624 | return partype |
---|
| 625 | |
---|
| 626 | def process_parameters(model_info): |
---|
| 627 | """ |
---|
| 628 | Process parameter block, precalculating parameter details. |
---|
| 629 | """ |
---|
[fcd7bbd] | 630 | # convert parameters into named tuples |
---|
[78d3341] | 631 | for p in model_info['parameters']: |
---|
| 632 | if p[4] == '' and (p[0].startswith('sld') or p[0].endswith('sld')): |
---|
| 633 | p[4] = 'sld' |
---|
| 634 | # TODO: make sure all models explicitly label their sld parameters |
---|
| 635 | #raise ValueError("%s.%s needs to be explicitly set to type 'sld'" %(model_info['id'], p[0])) |
---|
| 636 | |
---|
[fcd7bbd] | 637 | pars = [Parameter(*p) for p in model_info['parameters']] |
---|
[17bbadd] | 638 | # Fill in the derived attributes |
---|
[fcd7bbd] | 639 | model_info['parameters'] = pars |
---|
| 640 | partype = categorize_parameters(pars) |
---|
| 641 | model_info['limits'] = dict((p.name, p.limits) for p in pars) |
---|
[b8e5e21] | 642 | model_info['partype'] = partype |
---|
[fcd7bbd] | 643 | model_info['defaults'] = dict((p.name, p.default) for p in pars) |
---|
[17bbadd] | 644 | if model_info.get('demo', None) is None: |
---|
| 645 | model_info['demo'] = model_info['defaults'] |
---|
[b8e5e21] | 646 | model_info['has_2d'] = partype['orientation'] or partype['magnetic'] |
---|
[17bbadd] | 647 | |
---|
[4d76711] | 648 | |
---|
| 649 | def load_kernel_module(model_name): |
---|
| 650 | if model_name.endswith('.py'): |
---|
| 651 | kernel_module = load_custom_kernel_module(model_name) |
---|
| 652 | else: |
---|
| 653 | from sasmodels import models |
---|
| 654 | __import__('sasmodels.models.'+model_name) |
---|
| 655 | kernel_module = getattr(models, model_name, None) |
---|
| 656 | return kernel_module |
---|
| 657 | |
---|
| 658 | |
---|
[17bbadd] | 659 | def make_model_info(kernel_module): |
---|
| 660 | """ |
---|
| 661 | Interpret the model definition file, categorizing the parameters. |
---|
| 662 | |
---|
| 663 | The module can be loaded with a normal python import statement if you |
---|
| 664 | know which module you need, or with __import__('sasmodels.model.'+name) |
---|
| 665 | if the name is in a string. |
---|
| 666 | |
---|
| 667 | The *model_info* structure contains the following fields: |
---|
| 668 | |
---|
| 669 | * *id* is the id of the kernel |
---|
| 670 | * *name* is the display name of the kernel |
---|
[fcd7bbd] | 671 | * *filename* is the full path to the module defining the file (if any) |
---|
[17bbadd] | 672 | * *title* is a short description of the kernel |
---|
| 673 | * *description* is a long description of the kernel (this doesn't seem |
---|
| 674 | very useful since the Help button on the model page brings you directly |
---|
| 675 | to the documentation page) |
---|
| 676 | * *docs* is the docstring from the module. Use :func:`make_doc` to |
---|
| 677 | * *category* specifies the model location in the docs |
---|
| 678 | * *parameters* is the model parameter table |
---|
| 679 | * *single* is True if the model allows single precision |
---|
[b8e5e21] | 680 | * *structure_factor* is True if the model is useable in a product |
---|
| 681 | * *variant_info* contains the information required to select between |
---|
| 682 | model variants (e.g., the list of cases) or is None if there are no |
---|
| 683 | model variants |
---|
[17bbadd] | 684 | * *defaults* is the *{parameter: value}* table built from the parameter |
---|
| 685 | description table. |
---|
| 686 | * *limits* is the *{parameter: [min, max]}* table built from the |
---|
| 687 | parameter description table. |
---|
| 688 | * *partypes* categorizes the model parameters. See |
---|
| 689 | :func:`categorize_parameters` for details. |
---|
| 690 | * *demo* contains the *{parameter: value}* map used in compare (and maybe |
---|
| 691 | for the demo plot, if plots aren't set up to use the default values). |
---|
| 692 | If *demo* is not given in the file, then the default values will be used. |
---|
| 693 | * *tests* is a set of tests that must pass |
---|
| 694 | * *source* is the list of library files to include in the C model build |
---|
[2f0c07d] | 695 | * *Iq*, *Iqxy*, *form_volume*, *ER*, *VR* and *sesans* are python functions |
---|
[17bbadd] | 696 | implementing the kernel for the module, or None if they are not |
---|
| 697 | defined in python |
---|
| 698 | * *composition* is None if the model is independent, otherwise it is a |
---|
| 699 | tuple with composition type ('product' or 'mixture') and a list of |
---|
| 700 | *model_info* blocks for the composition objects. This allows us to |
---|
| 701 | build complete product and mixture models from just the info. |
---|
[2f0c07d] | 702 | |
---|
[17bbadd] | 703 | """ |
---|
| 704 | # TODO: maybe turn model_info into a class ModelDefinition |
---|
[5ceb7d0] | 705 | parameters = COMMON_PARAMETERS + kernel_module.parameters |
---|
| 706 | filename = abspath(kernel_module.__file__) |
---|
| 707 | kernel_id = splitext(basename(filename))[0] |
---|
| 708 | name = getattr(kernel_module, 'name', None) |
---|
| 709 | if name is None: |
---|
| 710 | name = " ".join(w.capitalize() for w in kernel_id.split('_')) |
---|
[17bbadd] | 711 | model_info = dict( |
---|
[5ceb7d0] | 712 | id=kernel_id, # string used to load the kernel |
---|
| 713 | filename=abspath(kernel_module.__file__), |
---|
| 714 | name=name, |
---|
| 715 | title=kernel_module.title, |
---|
| 716 | description=kernel_module.description, |
---|
| 717 | parameters=parameters, |
---|
[17bbadd] | 718 | composition=None, |
---|
[b8e5e21] | 719 | docs=kernel_module.__doc__, |
---|
| 720 | category=getattr(kernel_module, 'category', None), |
---|
| 721 | single=getattr(kernel_module, 'single', True), |
---|
| 722 | structure_factor=getattr(kernel_module, 'structure_factor', False), |
---|
| 723 | variant_info=getattr(kernel_module, 'invariant_info', None), |
---|
| 724 | demo=getattr(kernel_module, 'demo', None), |
---|
[5ceb7d0] | 725 | source=getattr(kernel_module, 'source', []), |
---|
[17bbadd] | 726 | tests=getattr(kernel_module, 'tests', []), |
---|
[5ceb7d0] | 727 | ) |
---|
[17bbadd] | 728 | process_parameters(model_info) |
---|
[2f0c07d] | 729 | # Check for optional functions |
---|
| 730 | functions = "ER VR form_volume Iq Iqxy shape sesans".split() |
---|
| 731 | model_info.update((k, getattr(kernel_module, k, None)) for k in functions) |
---|
[17bbadd] | 732 | return model_info |
---|
[5ceb7d0] | 733 | |
---|
| 734 | section_marker = re.compile(r'\A(?P<first>[%s])(?P=first)*\Z' |
---|
| 735 | %re.escape(string.punctuation)) |
---|
| 736 | def _convert_section_titles_to_boldface(lines): |
---|
| 737 | """ |
---|
| 738 | Do the actual work of identifying and converting section headings. |
---|
| 739 | """ |
---|
| 740 | prior = None |
---|
| 741 | for line in lines: |
---|
| 742 | if prior is None: |
---|
| 743 | prior = line |
---|
| 744 | elif section_marker.match(line): |
---|
| 745 | if len(line) >= len(prior): |
---|
| 746 | yield "".join(("**", prior, "**")) |
---|
| 747 | prior = None |
---|
| 748 | else: |
---|
| 749 | yield prior |
---|
| 750 | prior = line |
---|
| 751 | else: |
---|
| 752 | yield prior |
---|
| 753 | prior = line |
---|
| 754 | if prior is not None: |
---|
| 755 | yield prior |
---|
| 756 | |
---|
| 757 | def convert_section_titles_to_boldface(s): |
---|
| 758 | """ |
---|
| 759 | Use explicit bold-face rather than section headings so that the table of |
---|
| 760 | contents is not polluted with section names from the model documentation. |
---|
| 761 | |
---|
| 762 | Sections are identified as the title line followed by a line of punctuation |
---|
| 763 | at least as long as the title line. |
---|
| 764 | """ |
---|
| 765 | return "\n".join(_convert_section_titles_to_boldface(s.split('\n'))) |
---|
| 766 | |
---|
[17bbadd] | 767 | def make_doc(model_info): |
---|
[5ceb7d0] | 768 | """ |
---|
| 769 | Return the documentation for the model. |
---|
| 770 | """ |
---|
| 771 | Iq_units = "The returned value is scaled to units of |cm^-1| |sr^-1|, absolute scale." |
---|
| 772 | Sq_units = "The returned value is a dimensionless structure factor, $S(q)$." |
---|
[17bbadd] | 773 | docs = convert_section_titles_to_boldface(model_info['docs']) |
---|
| 774 | subst = dict(id=model_info['id'].replace('_', '-'), |
---|
| 775 | name=model_info['name'], |
---|
| 776 | title=model_info['title'], |
---|
| 777 | parameters=make_partable(model_info['parameters']), |
---|
[91c5fdc] | 778 | returns=Sq_units if model_info['structure_factor'] else Iq_units, |
---|
[5ceb7d0] | 779 | docs=docs) |
---|
| 780 | return DOC_HEADER % subst |
---|
| 781 | |
---|
| 782 | |
---|
| 783 | def demo_time(): |
---|
| 784 | """ |
---|
| 785 | Show how long it takes to process a model. |
---|
| 786 | """ |
---|
| 787 | from .models import cylinder |
---|
| 788 | import datetime |
---|
| 789 | tic = datetime.datetime.now() |
---|
[17bbadd] | 790 | make_source(make_model_info(cylinder)) |
---|
[5ceb7d0] | 791 | toc = (datetime.datetime.now() - tic).total_seconds() |
---|
| 792 | print("time: %g"%toc) |
---|
| 793 | |
---|
| 794 | def main(): |
---|
| 795 | """ |
---|
| 796 | Program which prints the source produced by the model. |
---|
| 797 | """ |
---|
| 798 | if len(sys.argv) <= 1: |
---|
| 799 | print("usage: python -m sasmodels.generate modelname") |
---|
| 800 | else: |
---|
| 801 | name = sys.argv[1] |
---|
[4d76711] | 802 | kernel_module = load_kernel_module(name) |
---|
| 803 | model_info = make_model_info(kernel_module) |
---|
[17bbadd] | 804 | source = make_source(model_info) |
---|
[5ceb7d0] | 805 | print(source) |
---|
| 806 | |
---|
| 807 | if __name__ == "__main__": |
---|
| 808 | main() |
---|