source: sasmodels/sasmodels/generate.py @ eafc9fa

core_shell_microgelscostrafo411magnetic_modelrelease_v0.94release_v0.95ticket-1257-vesicle-productticket_1156ticket_1265_superballticket_822_more_unit_tests
Last change on this file since eafc9fa was eafc9fa, checked in by Paul Kienzle <pkienzle@…>, 8 years ago

refactor kernel wrappers to simplify q input handling

  • Property mode set to 100644
File size: 26.9 KB
Line 
1"""
2SAS model constructor.
3
4Small angle scattering models are defined by a set of kernel functions:
5
6    *Iq(q, p1, p2, ...)* returns the scattering at q for a form with
7    particular dimensions averaged over all orientations.
8
9    *Iqxy(qx, qy, p1, p2, ...)* returns the scattering at qx, qy for a form
10    with particular dimensions for a single orientation.
11
12    *Imagnetic(qx, qy, result[], p1, p2, ...)* returns the scattering for the
13    polarized neutron spin states (up-up, up-down, down-up, down-down) for
14    a form with particular dimensions for a single orientation.
15
16    *form_volume(p1, p2, ...)* returns the volume of the form with particular
17    dimension.
18
19    *ER(p1, p2, ...)* returns the effective radius of the form with
20    particular dimensions.
21
22    *VR(p1, p2, ...)* returns the volume ratio for core-shell style forms.
23
24These functions are defined in a kernel module .py script and an associated
25set of .c files.  The model constructor will use them to create models with
26polydispersity across volume and orientation parameters, and provide
27scale and background parameters for each model.
28
29*Iq*, *Iqxy*, *Imagnetic* and *form_volume* should be stylized C-99
30functions written for OpenCL.  All functions need prototype declarations
31even if the are defined before they are used.  OpenCL does not support
32*#include* preprocessor directives, so instead the list of includes needs
33to be given as part of the metadata in the kernel module definition.
34The included files should be listed using a path relative to the kernel
35module, or if using "lib/file.c" if it is one of the standard includes
36provided with the sasmodels source.  The includes need to be listed in
37order so that functions are defined before they are used.
38
39Floating point values should be declared as *double*.  For single precision
40calculations, *double* will be replaced by *float*.  The single precision
41conversion will also tag floating point constants with "f" to make them
42single precision constants.  When using integral values in floating point
43expressions, they should be expressed as floating point values by including
44a decimal point.  This includes 0., 1. and 2.
45
46OpenCL has a *sincos* function which can improve performance when both
47the *sin* and *cos* values are needed for a particular argument.  Since
48this function does not exist in C99, all use of *sincos* should be
49replaced by the macro *SINCOS(value, sn, cn)* where *sn* and *cn* are
50previously declared *double* variables.  When compiled for systems without
51OpenCL, *SINCOS* will be replaced by *sin* and *cos* calls.   If *value* is
52an expression, it will appear twice in this case; whether or not it will be
53evaluated twice depends on the quality of the compiler.
54
55If the input parameters are invalid, the scattering calculator should
56return a negative number. Particularly with polydispersity, there are
57some sets of shape parameters which lead to nonsensical forms, such
58as a capped cylinder where the cap radius is smaller than the
59cylinder radius.  The polydispersity calculation will ignore these points,
60effectively chopping the parameter weight distributions at the boundary
61of the infeasible region.  The resulting scattering will be set to
62background.  This will work correctly even when polydispersity is off.
63
64*ER* and *VR* are python functions which operate on parameter vectors.
65The constructor code will generate the necessary vectors for computing
66them with the desired polydispersity.
67
68The available kernel parameters are defined as a list, with each parameter
69defined as a sublist with the following elements:
70
71    *name* is the name that will be used in the call to the kernel
72    function and the name that will be displayed to the user.  Names
73    should be lower case, with words separated by underscore.  If
74    acronyms are used, the whole acronym should be upper case.
75
76    *units* should be one of *degrees* for angles, *Ang* for lengths,
77    *1e-6/Ang^2* for SLDs.
78
79    *default value* will be the initial value for  the model when it
80    is selected, or when an initial value is not otherwise specified.
81
82    [*lb*, *ub*] are the hard limits on the parameter value, used to limit
83    the polydispersity density function.  In the fit, the parameter limits
84    given to the fit are the limits  on the central value of the parameter.
85    If there is polydispersity, it will evaluate parameter values outside
86    the fit limits, but not outside the hard limits specified in the model.
87    If there are no limits, use +/-inf imported from numpy.
88
89    *type* indicates how the parameter will be used.  "volume" parameters
90    will be used in all functions.  "orientation" parameters will be used
91    in *Iqxy* and *Imagnetic*.  "magnetic* parameters will be used in
92    *Imagnetic* only.  If *type* is the empty string, the parameter will
93    be used in all of *Iq*, *Iqxy* and *Imagnetic*.
94
95    *description* is a short description of the parameter.  This will
96    be displayed in the parameter table and used as a tool tip for the
97    parameter value in the user interface.
98
99The kernel module must set variables defining the kernel meta data:
100
101    *id* is an implicit variable formed from the filename.  It will be
102    a valid python identifier, and will be used as the reference into
103    the html documentation, with '_' replaced by '-'.
104
105    *name* is the model name as displayed to the user.  If it is missing,
106    it will be constructed from the id.
107
108    *title* is a short description of the model, suitable for a tool tip,
109    or a one line model summary in a table of models.
110
111    *description* is an extended description of the model to be displayed
112    while the model parameters are being edited.
113
114    *parameters* is the list of parameters.  Parameters in the kernel
115    functions must appear in the same order as they appear in the
116    parameters list.  Two additional parameters, *scale* and *background*
117    are added to the beginning of the parameter list.  They will show up
118    in the documentation as model parameters, but they are never sent to
119    the kernel functions.
120
121    *category* is the default category for the model.  Models in the
122    *structure-factor* category do not have *scale* and *background*
123    added.
124
125    *source* is the list of C-99 source files that must be joined to
126    create the OpenCL kernel functions.  The files defining the functions
127    need to be listed before the files which use the functions.
128
129    *ER* is a python function defining the effective radius.  If it is
130    not present, the effective radius is 0.
131
132    *VR* is a python function defining the volume ratio.  If it is not
133    present, the volume ratio is 1.
134
135    *form_volume*, *Iq*, *Iqxy*, *Imagnetic* are strings containing the
136    C source code for the body of the volume, Iq, and Iqxy functions
137    respectively.  These can also be defined in the last source file.
138
139    *Iq* and *Iqxy* also be instead be python functions defining the
140    kernel.  If they are marked as *Iq.vectorized = True* then the
141    kernel is passed the entire *q* vector at once, otherwise it is
142    passed values one *q* at a time.  The performance improvement of
143    this step is significant.
144
145    *demo* is a dictionary of parameter=value defining a set of
146    parameters to use by default when *compare* is called.  Any
147    parameter not set in *demo* gets the initial value from the
148    parameter list.  *demo* is mostly needed to set the default
149    polydispersity values for tests.
150
151    *oldname* is the name of the model in sasview before sasmodels
152    was split into its own package, and *oldpars* is a dictionary
153    of *parameter: old_parameter* pairs defining the new names for
154    the parameters.  This is used by *compare* to check the values
155    of the new model against the values of the old model before
156    you are ready to add the new model to sasmodels.
157
158
159An *info* dictionary is constructed from the kernel meta data and
160returned to the caller.
161
162The model evaluator, function call sequence consists of q inputs and the return vector,
163followed by the loop value/weight vector, followed by the values for
164the non-polydisperse parameters, followed by the lengths of the
165polydispersity loops.  To construct the call for 1D models, the
166categories *fixed-1d* and *pd-1d* list the names of the parameters
167of the non-polydisperse and the polydisperse parameters respectively.
168Similarly, *fixed-2d* and *pd-2d* provide parameter names for 2D models.
169The *pd-rel* category is a set of those parameters which give
170polydispersitiy as a portion of the value (so a 10% length dispersity
171would use a polydispersity value of 0.1) rather than absolute
172dispersity such as an angle plus or minus 15 degrees.
173
174The *volume* category lists the volume parameters in order for calls
175to volume within the kernel (used for volume normalization) and for
176calls to ER and VR for effective radius and volume ratio respectively.
177
178The *orientation* and *magnetic* categories list the orientation and
179magnetic parameters.  These are used by the sasview interface.  The
180blank category is for parameters such as scale which don't have any
181other marking.
182
183The doc string at the start of the kernel module will be used to
184construct the model documentation web pages.  Embedded figures should
185appear in the subdirectory "img" beside the model definition, and tagged
186with the kernel module name to avoid collision with other models.  Some
187file systems are case-sensitive, so only use lower case characters for
188file names and extensions.
189
190
191The function :func:`make` loads the metadata from the module and returns
192the kernel source.  The function :func:`doc` extracts the doc string
193and adds the parameter table to the top.  The function :func:`sources`
194returns a list of files required by the model.
195"""
196from __future__ import print_function
197
198# TODO: identify model files which have changed since loading and reload them.
199
200import sys
201from os.path import abspath, dirname, join as joinpath, exists, basename, \
202    splitext
203import re
204import string
205
206import numpy as np
207
208__all__ = ["make", "doc", "sources", "convert_type"]
209
210C_KERNEL_TEMPLATE_PATH = joinpath(dirname(__file__), 'kernel_template.c')
211
212F16 = np.dtype('float16')
213F32 = np.dtype('float32')
214F64 = np.dtype('float64')
215try:  # CRUFT: older numpy does not support float128
216    F128 = np.dtype('float128')
217except TypeError:
218    F128 = None
219
220# Scale and background, which are parameters common to every form factor
221COMMON_PARAMETERS = [
222    ["scale", "", 1, [0, np.inf], "", "Source intensity"],
223    ["background", "1/cm", 0, [0, np.inf], "", "Source background"],
224    ]
225
226# Conversion from units defined in the parameter table for each model
227# to units displayed in the sphinx documentation.
228RST_UNITS = {
229    "Ang": "|Ang|",
230    "1/Ang": "|Ang^-1|",
231    "1/Ang^2": "|Ang^-2|",
232    "1e-6/Ang^2": "|1e-6Ang^-2|",
233    "degrees": "degree",
234    "1/cm": "|cm^-1|",
235    "": "None",
236    }
237
238# Headers for the parameters tables in th sphinx documentation
239PARTABLE_HEADERS = [
240    "Parameter",
241    "Description",
242    "Units",
243    "Default value",
244    ]
245
246# Minimum width for a default value (this is shorter than the column header
247# width, so will be ignored).
248PARTABLE_VALUE_WIDTH = 10
249
250# Documentation header for the module, giving the model name, its short
251# description and its parameter table.  The remainder of the doc comes
252# from the module docstring.
253DOC_HEADER = """.. _%(id)s:
254
255%(name)s
256=======================================================
257
258%(title)s
259
260%(parameters)s
261
262%(returns)s
263
264%(docs)s
265"""
266
267def format_units(units):
268    """
269    Convert units into ReStructured Text format.
270    """
271    return "string" if isinstance(units, list) else RST_UNITS.get(units, units)
272
273def make_partable(pars):
274    """
275    Generate the parameter table to include in the sphinx documentation.
276    """
277    column_widths = [
278        max(len(p[0]) for p in pars),
279        max(len(p[-1]) for p in pars),
280        max(len(format_units(p[1])) for p in pars),
281        PARTABLE_VALUE_WIDTH,
282        ]
283    column_widths = [max(w, len(h))
284                     for w, h in zip(column_widths, PARTABLE_HEADERS)]
285
286    sep = " ".join("="*w for w in column_widths)
287    lines = [
288        sep,
289        " ".join("%-*s" % (w, h)
290                 for w, h in zip(column_widths, PARTABLE_HEADERS)),
291        sep,
292        ]
293    for p in pars:
294        lines.append(" ".join([
295            "%-*s" % (column_widths[0], p[0]),
296            "%-*s" % (column_widths[1], p[-1]),
297            "%-*s" % (column_widths[2], format_units(p[1])),
298            "%*g" % (column_widths[3], p[2]),
299            ]))
300    lines.append(sep)
301    return "\n".join(lines)
302
303def _search(search_path, filename):
304    """
305    Find *filename* in *search_path*.
306
307    Raises ValueError if file does not exist.
308    """
309    for path in search_path:
310        target = joinpath(path, filename)
311        if exists(target):
312            return target
313    raise ValueError("%r not found in %s" % (filename, search_path))
314
315def model_sources(info):
316    """
317    Return a list of the sources file paths for the module.
318    """
319    search_path = [dirname(info['filename']),
320                   abspath(joinpath(dirname(__file__), 'models'))]
321    return [_search(search_path, f) for f in info['source']]
322
323# Pragmas for enable OpenCL features.  Be sure to protect them so that they
324# still compile even if OpenCL is not present.
325_F16_PRAGMA = """\
326#if defined(__OPENCL_VERSION__) && !defined(cl_khr_fp16)
327#  pragma OPENCL EXTENSION cl_khr_fp16: enable
328#endif
329"""
330
331_F64_PRAGMA = """\
332#if defined(__OPENCL_VERSION__) && !defined(cl_khr_fp64)
333#  pragma OPENCL EXTENSION cl_khr_fp64: enable
334#endif
335"""
336
337def convert_type(source, dtype):
338    """
339    Convert code from double precision to the desired type.
340
341    Floating point constants are tagged with 'f' for single precision or 'L'
342    for long double precision.
343    """
344    if dtype == F16:
345        source = _F16_PRAGMA + _convert_type(source, "half", "f")
346    elif dtype == F32:
347        source = _convert_type(source, "float", "f")
348    elif dtype == F64:
349        source = _F64_PRAGMA + source  # Source is already double
350    elif dtype == F128:
351        source = _convert_type(source, "long double", "L")
352    else:
353        raise ValueError("Unexpected dtype in source conversion: %s"%dtype)
354    return source
355
356
357def _convert_type(source, type_name, constant_flag):
358    """
359    Replace 'double' with *type_name* in *source*, tagging floating point
360    constants with *constant_flag*.
361    """
362    # Convert double keyword to float/long double/half.
363    # Accept an 'n' # parameter for vector # values, where n is 2, 4, 8 or 16.
364    # Assume complex numbers are represented as cdouble which is typedef'd
365    # to double2.
366    source = re.sub(r'(^|[^a-zA-Z0-9_]c?)double(([248]|16)?($|[^a-zA-Z0-9_]))',
367                    r'\1%s\2'%type_name, source)
368    # Convert floating point constants to single by adding 'f' to the end,
369    # or long double with an 'L' suffix.  OS/X complains if you don't do this.
370    source = re.sub(r'[^a-zA-Z_](\d*[.]\d+|\d+[.]\d*)([eE][+-]?\d+)?',
371                    r'\g<0>%s'%constant_flag, source)
372    return source
373
374
375def kernel_name(info, is_2d):
376    """
377    Name of the exported kernel symbol.
378    """
379    return info['name'] + "_" + ("Iqxy" if is_2d else "Iq")
380
381
382def categorize_parameters(pars):
383    """
384    Build parameter categories out of the the parameter definitions.
385
386    Returns a dictionary of categories.
387    """
388    partype = {
389        'volume': [], 'orientation': [], 'magnetic': [], '': [],
390        'fixed-1d': [], 'fixed-2d': [], 'pd-1d': [], 'pd-2d': [],
391        'pd-rel': set(),
392    }
393
394    for p in pars:
395        name, ptype = p[0], p[4]
396        if ptype == 'volume':
397            partype['pd-1d'].append(name)
398            partype['pd-2d'].append(name)
399            partype['pd-rel'].add(name)
400        elif ptype == 'magnetic':
401            partype['fixed-2d'].append(name)
402        elif ptype == 'orientation':
403            partype['pd-2d'].append(name)
404        elif ptype == '':
405            partype['fixed-1d'].append(name)
406            partype['fixed-2d'].append(name)
407        else:
408            raise ValueError("unknown parameter type %r" % ptype)
409        partype[ptype].append(name)
410
411    return partype
412
413def indent(s, depth):
414    """
415    Indent a string of text with *depth* additional spaces on each line.
416    """
417    spaces = " "*depth
418    sep = "\n" + spaces
419    return spaces + sep.join(s.split("\n"))
420
421
422LOOP_OPEN = """\
423for (int %(name)s_i=0; %(name)s_i < N%(name)s; %(name)s_i++) {
424  const double %(name)s = loops[2*(%(name)s_i%(offset)s)];
425  const double %(name)s_w = loops[2*(%(name)s_i%(offset)s)+1];\
426"""
427def build_polydispersity_loops(pd_pars):
428    """
429    Build polydispersity loops
430
431    Returns loop opening and loop closing
432    """
433    depth = 4
434    offset = ""
435    loop_head = []
436    loop_end = []
437    for name in pd_pars:
438        subst = {'name': name, 'offset': offset}
439        loop_head.append(indent(LOOP_OPEN % subst, depth))
440        loop_end.insert(0, (" "*depth) + "}")
441        offset += '+N' + name
442        depth += 2
443    return "\n".join(loop_head), "\n".join(loop_end)
444
445C_KERNEL_TEMPLATE = None
446def make_model(info):
447    """
448    Generate the code for the kernel defined by info, using source files
449    found in the given search path.
450    """
451    # TODO: need something other than volume to indicate dispersion parameters
452    # No volume normalization despite having a volume parameter.
453    # Thickness is labelled a volume in order to trigger polydispersity.
454    # May want a separate dispersion flag, or perhaps a separate category for
455    # disperse, but not volume.  Volume parameters also use relative values
456    # for the distribution rather than the absolute values used by angular
457    # dispersion.  Need to be careful that necessary parameters are available
458    # for computing volume even if we allow non-disperse volume parameters.
459
460    # Load template
461    global C_KERNEL_TEMPLATE
462    if C_KERNEL_TEMPLATE is None:
463        with open(C_KERNEL_TEMPLATE_PATH) as fid:
464            C_KERNEL_TEMPLATE = fid.read()
465
466    # Load additional sources
467    source = [open(f).read() for f in model_sources(info)]
468
469    # Prepare defines
470    defines = []
471    partype = info['partype']
472    pd_1d = partype['pd-1d']
473    pd_2d = partype['pd-2d']
474    fixed_1d = partype['fixed-1d']
475    fixed_2d = partype['fixed-1d']
476
477    iq_parameters = [p[0]
478                     for p in info['parameters'][2:] # skip scale, background
479                     if p[0] in set(fixed_1d + pd_1d)]
480    iqxy_parameters = [p[0]
481                       for p in info['parameters'][2:] # skip scale, background
482                       if p[0] in set(fixed_2d + pd_2d)]
483    volume_parameters = [p[0]
484                         for p in info['parameters']
485                         if p[4] == 'volume']
486
487    # Fill in defintions for volume parameters
488    if volume_parameters:
489        defines.append(('VOLUME_PARAMETERS',
490                        ','.join(volume_parameters)))
491        defines.append(('VOLUME_WEIGHT_PRODUCT',
492                        '*'.join(p + '_w' for p in volume_parameters)))
493
494    # Generate form_volume function from body only
495    if info['form_volume'] is not None:
496        if volume_parameters:
497            vol_par_decl = ', '.join('double ' + p for p in volume_parameters)
498        else:
499            vol_par_decl = 'void'
500        defines.append(('VOLUME_PARAMETER_DECLARATIONS',
501                        vol_par_decl))
502        fn = """\
503double form_volume(VOLUME_PARAMETER_DECLARATIONS);
504double form_volume(VOLUME_PARAMETER_DECLARATIONS) {
505    %(body)s
506}
507""" % {'body':info['form_volume']}
508        source.append(fn)
509
510    # Fill in definitions for Iq parameters
511    defines.append(('IQ_KERNEL_NAME', info['name'] + '_Iq'))
512    defines.append(('IQ_PARAMETERS', ', '.join(iq_parameters)))
513    if fixed_1d:
514        defines.append(('IQ_FIXED_PARAMETER_DECLARATIONS',
515                        ', \\\n    '.join('const double %s' % p for p in fixed_1d)))
516    if pd_1d:
517        defines.append(('IQ_WEIGHT_PRODUCT',
518                        '*'.join(p + '_w' for p in pd_1d)))
519        defines.append(('IQ_DISPERSION_LENGTH_DECLARATIONS',
520                        ', \\\n    '.join('const int N%s' % p for p in pd_1d)))
521        defines.append(('IQ_DISPERSION_LENGTH_SUM',
522                        '+'.join('N' + p for p in pd_1d)))
523        open_loops, close_loops = build_polydispersity_loops(pd_1d)
524        defines.append(('IQ_OPEN_LOOPS',
525                        open_loops.replace('\n', ' \\\n')))
526        defines.append(('IQ_CLOSE_LOOPS',
527                        close_loops.replace('\n', ' \\\n')))
528    if info['Iq'] is not None:
529        defines.append(('IQ_PARAMETER_DECLARATIONS',
530                        ', '.join('double ' + p for p in iq_parameters)))
531        fn = """\
532double Iq(double q, IQ_PARAMETER_DECLARATIONS);
533double Iq(double q, IQ_PARAMETER_DECLARATIONS) {
534    %(body)s
535}
536""" % {'body':info['Iq']}
537        source.append(fn)
538
539    # Fill in definitions for Iqxy parameters
540    defines.append(('IQXY_KERNEL_NAME', info['name'] + '_Iqxy'))
541    defines.append(('IQXY_PARAMETERS', ', '.join(iqxy_parameters)))
542    if fixed_2d:
543        defines.append(('IQXY_FIXED_PARAMETER_DECLARATIONS',
544                        ', \\\n    '.join('const double %s' % p for p in fixed_2d)))
545    if pd_2d:
546        defines.append(('IQXY_WEIGHT_PRODUCT',
547                        '*'.join(p + '_w' for p in pd_2d)))
548        defines.append(('IQXY_DISPERSION_LENGTH_DECLARATIONS',
549                        ', \\\n    '.join('const int N%s' % p for p in pd_2d)))
550        defines.append(('IQXY_DISPERSION_LENGTH_SUM',
551                        '+'.join('N' + p for p in pd_2d)))
552        open_loops, close_loops = build_polydispersity_loops(pd_2d)
553        defines.append(('IQXY_OPEN_LOOPS',
554                        open_loops.replace('\n', ' \\\n')))
555        defines.append(('IQXY_CLOSE_LOOPS',
556                        close_loops.replace('\n', ' \\\n')))
557    if info['Iqxy'] is not None:
558        defines.append(('IQXY_PARAMETER_DECLARATIONS',
559                        ', '.join('double ' + p for p in iqxy_parameters)))
560        fn = """\
561double Iqxy(double qx, double qy, IQXY_PARAMETER_DECLARATIONS);
562double Iqxy(double qx, double qy, IQXY_PARAMETER_DECLARATIONS) {
563    %(body)s
564}
565""" % {'body':info['Iqxy']}
566        source.append(fn)
567
568    # Need to know if we have a theta parameter for Iqxy; it is not there
569    # for the magnetic sphere model, for example, which has a magnetic
570    # orientation but no shape orientation.
571    if 'theta' in pd_2d:
572        defines.append(('IQXY_HAS_THETA', '1'))
573
574    #for d in defines: print(d)
575    defines = '\n'.join('#define %s %s' % (k, v) for k, v in defines)
576    sources = '\n\n'.join(source)
577    return C_KERNEL_TEMPLATE % {
578        'DEFINES': defines,
579        'SOURCES': sources,
580        }
581
582def make_info(kernel_module):
583    """
584    Interpret the model definition file, categorizing the parameters.
585    """
586    #print(kernelfile)
587    category = getattr(kernel_module, 'category', None)
588    parameters = COMMON_PARAMETERS + kernel_module.parameters
589    # Default the demo parameters to the starting values for the individual
590    # parameters if an explicit demo parameter set has not been specified.
591    demo_parameters = getattr(kernel_module, 'demo', None)
592    if demo_parameters is None:
593        demo_parameters = dict((p[0], p[2]) for p in parameters)
594    filename = abspath(kernel_module.__file__)
595    kernel_id = splitext(basename(filename))[0]
596    name = getattr(kernel_module, 'name', None)
597    if name is None:
598        name = " ".join(w.capitalize() for w in kernel_id.split('_'))
599    info = dict(
600        id=kernel_id,  # string used to load the kernel
601        filename=abspath(kernel_module.__file__),
602        name=name,
603        title=kernel_module.title,
604        description=kernel_module.description,
605        category=category,
606        parameters=parameters,
607        demo=demo_parameters,
608        source=getattr(kernel_module, 'source', []),
609        oldname=kernel_module.oldname,
610        oldpars=kernel_module.oldpars,
611        )
612    # Fill in attributes which default to None
613    info.update((k, getattr(kernel_module, k, None))
614                for k in ('ER', 'VR', 'form_volume', 'Iq', 'Iqxy'))
615    # Fill in the derived attributes
616    info['limits'] = dict((p[0], p[3]) for p in info['parameters'])
617    info['partype'] = categorize_parameters(info['parameters'])
618    info['defaults'] = dict((p[0], p[2]) for p in info['parameters'])
619    return info
620
621def make(kernel_module):
622    """
623    Build an OpenCL/ctypes function from the definition in *kernel_module*.
624
625    The module can be loaded with a normal python import statement if you
626    know which module you need, or with __import__('sasmodels.model.'+name)
627    if the name is in a string.
628    """
629    info = make_info(kernel_module)
630    # Assume if one part of the kernel is python then all parts are.
631    source = make_model(info) if not callable(info['Iq']) else None
632    return source, info
633
634section_marker = re.compile(r'\A(?P<first>[%s])(?P=first)*\Z'
635                            %re.escape(string.punctuation))
636def _convert_section_titles_to_boldface(lines):
637    """
638    Do the actual work of identifying and converting section headings.
639    """
640    prior = None
641    for line in lines:
642        if prior is None:
643            prior = line
644        elif section_marker.match(line):
645            if len(line) >= len(prior):
646                yield "".join(("**", prior, "**"))
647                prior = None
648            else:
649                yield prior
650                prior = line
651        else:
652            yield prior
653            prior = line
654    if prior is not None:
655        yield prior
656
657def convert_section_titles_to_boldface(s):
658    """
659    Use explicit bold-face rather than section headings so that the table of
660    contents is not polluted with section names from the model documentation.
661
662    Sections are identified as the title line followed by a line of punctuation
663    at least as long as the title line.
664    """
665    return "\n".join(_convert_section_titles_to_boldface(s.split('\n')))
666
667def doc(kernel_module):
668    """
669    Return the documentation for the model.
670    """
671    Iq_units = "The returned value is scaled to units of |cm^-1| |sr^-1|, absolute scale."
672    Sq_units = "The returned value is a dimensionless structure factor, $S(q)$."
673    info = make_info(kernel_module)
674    is_Sq = ("structure-factor" in info['category'])
675    #docs = kernel_module.__doc__
676    docs = convert_section_titles_to_boldface(kernel_module.__doc__)
677    subst = dict(id=info['id'].replace('_', '-'),
678                 name=info['name'],
679                 title=info['title'],
680                 parameters=make_partable(info['parameters']),
681                 returns=Sq_units if is_Sq else Iq_units,
682                 docs=docs)
683    return DOC_HEADER % subst
684
685
686
687def demo_time():
688    """
689    Show how long it takes to process a model.
690    """
691    from .models import cylinder
692    import datetime
693    tic = datetime.datetime.now()
694    make(cylinder)
695    toc = (datetime.datetime.now() - tic).total_seconds()
696    print("time: %g"%toc)
697
698def main():
699    """
700    Program which prints the source produced by the model.
701    """
702    if len(sys.argv) <= 1:
703        print("usage: python -m sasmodels.generate modelname")
704    else:
705        name = sys.argv[1]
706        import sasmodels.models
707        __import__('sasmodels.models.' + name)
708        model = getattr(sasmodels.models, name)
709        source, _ = make(model)
710        print(source)
711
712if __name__ == "__main__":
713    main()
Note: See TracBrowser for help on using the repository browser.