source: sasmodels/sasmodels/generate.py @ 30b60d2

core_shell_microgelscostrafo411magnetic_modelticket-1257-vesicle-productticket_1156ticket_1265_superballticket_822_more_unit_tests
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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, or 1.0 if no volume normalization is required.
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
24    #define INVALID(v) (expr)  returns False if v.parameter is invalid
25    for some parameter or other (e.g., v.bell_radius < v.radius).  If
26    necessary, the expression can call a function.
27
28These functions are defined in a kernel module .py script and an associated
29set of .c files.  The model constructor will use them to create models with
30polydispersity across volume and orientation parameters, and provide
31scale and background parameters for each model.
32
33*Iq*, *Iqxy*, *Imagnetic* and *form_volume* should be stylized C-99
34functions written for OpenCL.  All functions need prototype declarations
35even if the are defined before they are used.  OpenCL does not support
36*#include* preprocessor directives, so instead the list of includes needs
37to be given as part of the metadata in the kernel module definition.
38The included files should be listed using a path relative to the kernel
39module, or if using "lib/file.c" if it is one of the standard includes
40provided with the sasmodels source.  The includes need to be listed in
41order so that functions are defined before they are used.
42
43Floating point values should be declared as *double*.  For single precision
44calculations, *double* will be replaced by *float*.  The single precision
45conversion will also tag floating point constants with "f" to make them
46single precision constants.  When using integral values in floating point
47expressions, they should be expressed as floating point values by including
48a decimal point.  This includes 0., 1. and 2.
49
50OpenCL has a *sincos* function which can improve performance when both
51the *sin* and *cos* values are needed for a particular argument.  Since
52this function does not exist in C99, all use of *sincos* should be
53replaced by the macro *SINCOS(value, sn, cn)* where *sn* and *cn* are
54previously declared *double* variables.  When compiled for systems without
55OpenCL, *SINCOS* will be replaced by *sin* and *cos* calls.   If *value* is
56an expression, it will appear twice in this case; whether or not it will be
57evaluated twice depends on the quality of the compiler.
58
59If the input parameters are invalid, the scattering calculator should
60return a negative number. Particularly with polydispersity, there are
61some sets of shape parameters which lead to nonsensical forms, such
62as a capped cylinder where the cap radius is smaller than the
63cylinder radius.  The polydispersity calculation will ignore these points,
64effectively chopping the parameter weight distributions at the boundary
65of the infeasible region.  The resulting scattering will be set to
66background.  This will work correctly even when polydispersity is off.
67
68*ER* and *VR* are python functions which operate on parameter vectors.
69The constructor code will generate the necessary vectors for computing
70them with the desired polydispersity.
71The kernel module must set variables defining the kernel meta data:
72
73    *id* is an implicit variable formed from the filename.  It will be
74    a valid python identifier, and will be used as the reference into
75    the html documentation, with '_' replaced by '-'.
76
77    *name* is the model name as displayed to the user.  If it is missing,
78    it will be constructed from the id.
79
80    *title* is a short description of the model, suitable for a tool tip,
81    or a one line model summary in a table of models.
82
83    *description* is an extended description of the model to be displayed
84    while the model parameters are being edited.
85
86    *parameters* is the list of parameters.  Parameters in the kernel
87    functions must appear in the same order as they appear in the
88    parameters list.  Two additional parameters, *scale* and *background*
89    are added to the beginning of the parameter list.  They will show up
90    in the documentation as model parameters, but they are never sent to
91    the kernel functions.  Note that *effect_radius* and *volfraction*
92    must occur first in structure factor calculations.
93
94    *category* is the default category for the model.  The category is
95    two level structure, with the form "group:section", indicating where
96    in the manual the model will be located.  Models are alphabetical
97    within their section.
98
99    *source* is the list of C-99 source files that must be joined to
100    create the OpenCL kernel functions.  The files defining the functions
101    need to be listed before the files which use the functions.
102
103    *ER* is a python function defining the effective radius.  If it is
104    not present, the effective radius is 0.
105
106    *VR* is a python function defining the volume ratio.  If it is not
107    present, the volume ratio is 1.
108
109    *form_volume*, *Iq*, *Iqxy*, *Imagnetic* are strings containing the
110    C source code for the body of the volume, Iq, and Iqxy functions
111    respectively.  These can also be defined in the last source file.
112
113    *Iq* and *Iqxy* also be instead be python functions defining the
114    kernel.  If they are marked as *Iq.vectorized = True* then the
115    kernel is passed the entire *q* vector at once, otherwise it is
116    passed values one *q* at a time.  The performance improvement of
117    this step is significant.
118
119    *demo* is a dictionary of parameter=value defining a set of
120    parameters to use by default when *compare* is called.  Any
121    parameter not set in *demo* gets the initial value from the
122    parameter list.  *demo* is mostly needed to set the default
123    polydispersity values for tests.
124
125A :class:`modelinfo.ModelInfo` structure is constructed from the kernel meta
126data and returned to the caller.
127
128The doc string at the start of the kernel module will be used to
129construct the model documentation web pages.  Embedded figures should
130appear in the subdirectory "img" beside the model definition, and tagged
131with the kernel module name to avoid collision with other models.  Some
132file systems are case-sensitive, so only use lower case characters for
133file names and extensions.
134
135Code follows the C99 standard with the following extensions and conditions::
136
137    M_PI_180 = pi/180
138    M_4PI_3 = 4pi/3
139    square(x) = x*x
140    cube(x) = x*x*x
141    sas_sinx_x(x) = sin(x)/x, with sin(0)/0 -> 1
142    all double precision constants must include the decimal point
143    all double declarations may be converted to half, float, or long double
144    FLOAT_SIZE is the number of bytes in the converted variables
145
146:func:`load_kernel_module` loads the model definition file and
147:func:`modelinfo.make_model_info` parses it. :func:`make_source`
148converts C-based model definitions to C source code, including the
149polydispersity integral.  :func:`model_sources` returns the list of
150source files the model depends on, and :func:`timestamp` returns
151the latest time stamp amongst the source files (so you can check if
152the model needs to be rebuilt).
153
154The function :func:`make_doc` extracts the doc string and adds the
155parameter table to the top.  *make_figure* in *sasmodels/doc/genmodel*
156creates the default figure for the model.  [These two sets of code
157should mignrate into docs.py so docs can be updated in one place].
158"""
159from __future__ import print_function
160
161# TODO: determine which functions are useful outside of generate
162#__all__ = ["model_info", "make_doc", "make_source", "convert_type"]
163
164import sys
165from os.path import abspath, dirname, join as joinpath, exists, isdir, getmtime
166import re
167import string
168from zlib import crc32
169
170import numpy as np  # type: ignore
171
172from .modelinfo import Parameter
173from .custom import load_custom_kernel_module
174
175try:
176    from typing import Tuple, Sequence, Iterator, Dict
177    from .modelinfo import ModelInfo
178except ImportError:
179    pass
180
181def get_data_path(external_dir, target_file):
182    path = abspath(dirname(__file__))
183    if exists(joinpath(path, target_file)):
184        return path
185
186    # check next to exe/zip file
187    exepath = dirname(sys.executable)
188    path = joinpath(exepath, external_dir)
189    if exists(joinpath(path, target_file)):
190        return path
191
192    # check in py2app Contents/Resources
193    path = joinpath(exepath, '..', 'Resources', external_dir)
194    if exists(joinpath(path, target_file)):
195        return abspath(path)
196
197    raise RuntimeError('Could not find '+joinpath(external_dir, target_file))
198
199EXTERNAL_DIR = 'sasmodels-data'
200DATA_PATH = get_data_path(EXTERNAL_DIR, 'kernel_template.c')
201MODEL_PATH = joinpath(DATA_PATH, 'models')
202
203F16 = np.dtype('float16')
204F32 = np.dtype('float32')
205F64 = np.dtype('float64')
206try:  # CRUFT: older numpy does not support float128
207    F128 = np.dtype('float128')
208except TypeError:
209    F128 = None
210
211# Conversion from units defined in the parameter table for each model
212# to units displayed in the sphinx documentation.
213# This section associates the unit with the macro to use to produce the LaTex
214# code.  The macro itself needs to be defined in sasmodels/doc/rst_prolog.
215#
216# NOTE: there is an RST_PROLOG at the end of this file which is NOT
217# used for the bundled documentation. Still as long as we are defining the macros
218# in two places any new addition should define the macro in both places.
219RST_UNITS = {
220    "Ang": "|Ang|",
221    "1/Ang": "|Ang^-1|",
222    "1/Ang^2": "|Ang^-2|",
223    "Ang^3": "|Ang^3|",
224    "Ang^2": "|Ang^2|",
225    "1e15/cm^3": "|1e15cm^3|",
226    "Ang^3/mol": "|Ang^3|/mol",
227    "1e-6/Ang^2": "|1e-6Ang^-2|",
228    "degrees": "degree",
229    "1/cm": "|cm^-1|",
230    "Ang/cm": "|Ang*cm^-1|",
231    "g/cm^3": "|g/cm^3|",
232    "mg/m^2": "|mg/m^2|",
233    "": "None",
234    }
235
236# Headers for the parameters tables in th sphinx documentation
237PARTABLE_HEADERS = [
238    "Parameter",
239    "Description",
240    "Units",
241    "Default value",
242    ]
243
244# Minimum width for a default value (this is shorter than the column header
245# width, so will be ignored).
246PARTABLE_VALUE_WIDTH = 10
247
248# Documentation header for the module, giving the model name, its short
249# description and its parameter table.  The remainder of the doc comes
250# from the module docstring.
251DOC_HEADER = """.. _%(id)s:
252
253%(name)s
254=======================================================
255
256%(title)s
257
258%(parameters)s
259
260%(returns)s
261
262%(docs)s
263"""
264
265
266def format_units(units):
267    # type: (str) -> str
268    """
269    Convert units into ReStructured Text format.
270    """
271    return "string" if isinstance(units, list) else RST_UNITS.get(units, units)
272
273
274def make_partable(pars):
275    # type: (List[Parameter]) -> str
276    """
277    Generate the parameter table to include in the sphinx documentation.
278    """
279    column_widths = [
280        max(len(p.name) for p in pars),
281        max(len(p.description) for p in pars),
282        max(len(format_units(p.units)) for p in pars),
283        PARTABLE_VALUE_WIDTH,
284        ]
285    column_widths = [max(w, len(h))
286                     for w, h in zip(column_widths, PARTABLE_HEADERS)]
287
288    sep = " ".join("="*w for w in column_widths)
289    lines = [
290        sep,
291        " ".join("%-*s" % (w, h)
292                 for w, h in zip(column_widths, PARTABLE_HEADERS)),
293        sep,
294        ]
295    for p in pars:
296        lines.append(" ".join([
297            "%-*s" % (column_widths[0], p.name),
298            "%-*s" % (column_widths[1], p.description),
299            "%-*s" % (column_widths[2], format_units(p.units)),
300            "%*g" % (column_widths[3], p.default),
301            ]))
302    lines.append(sep)
303    return "\n".join(lines)
304
305
306def _search(search_path, filename):
307    # type: (List[str], str) -> str
308    """
309    Find *filename* in *search_path*.
310
311    Raises ValueError if file does not exist.
312    """
313    for path in search_path:
314        target = joinpath(path, filename)
315        if exists(target):
316            return target
317    raise ValueError("%r not found in %s" % (filename, search_path))
318
319
320def model_sources(model_info):
321    # type: (ModelInfo) -> List[str]
322    """
323    Return a list of the sources file paths for the module.
324    """
325    search_path = [dirname(model_info.filename), MODEL_PATH]
326    return [_search(search_path, f) for f in model_info.source]
327
328
329def dll_timestamp(model_info):
330    # type: (ModelInfo) -> int
331    """
332    Return a timestamp for the model corresponding to the most recently
333    changed file or dependency.
334    """
335    # TODO: fails DRY; templates appear two places.
336    model_templates = [joinpath(DATA_PATH, filename)
337                       for filename in ('kernel_header.c', 'kernel_iq.c')]
338    source_files = (model_sources(model_info)
339                    + model_templates
340                    + [model_info.filename])
341    # Note: file may not exist when it is a standard model from library.zip
342    times = [getmtime(f) for f in source_files if exists(f)]
343    newest = max(times) if times else 0
344    return newest
345
346def ocl_timestamp(model_info):
347    # type: (ModelInfo) -> int
348    """
349    Return a timestamp for the model corresponding to the most recently
350    changed file or dependency.
351
352    Note that this does not look at the time stamps for the OpenCL header
353    information since that need not trigger a recompile of the DLL.
354    """
355    # TODO: fails DRY; templates appear two places.
356    model_templates = [joinpath(DATA_PATH, filename)
357                       for filename in ('kernel_header.c', 'kernel_iq.cl')]
358    source_files = (model_sources(model_info)
359                    + model_templates
360                    + [model_info.filename])
361    # Note: file may not exist when it is a standard model from library.zip
362    times = [getmtime(f) for f in source_files if exists(f)]
363    newest = max(times) if times else 0
364    return newest
365
366def tag_source(source):
367    # type: (str) -> str
368    """
369    Return a unique tag for the source code.
370    """
371    # Note: need 0xffffffff&val to force an unsigned 32-bit number
372    return "%08X"%(0xffffffff&crc32(source))
373
374def convert_type(source, dtype):
375    # type: (str, np.dtype) -> str
376    """
377    Convert code from double precision to the desired type.
378
379    Floating point constants are tagged with 'f' for single precision or 'L'
380    for long double precision.
381    """
382    source = _fix_tgmath_int(source)
383    if dtype == F16:
384        fbytes = 2
385        source = _convert_type(source, "half", "f")
386    elif dtype == F32:
387        fbytes = 4
388        source = _convert_type(source, "float", "f")
389    elif dtype == F64:
390        fbytes = 8
391        # no need to convert if it is already double
392    elif dtype == F128:
393        fbytes = 16
394        source = _convert_type(source, "long double", "L")
395    else:
396        raise ValueError("Unexpected dtype in source conversion: %s" % dtype)
397    return ("#define FLOAT_SIZE %d\n" % fbytes)+source
398
399
400def _convert_type(source, type_name, constant_flag):
401    # type: (str, str, str) -> str
402    """
403    Replace 'double' with *type_name* in *source*, tagging floating point
404    constants with *constant_flag*.
405    """
406    # Convert double keyword to float/long double/half.
407    # Accept an 'n' # parameter for vector # values, where n is 2, 4, 8 or 16.
408    # Assume complex numbers are represented as cdouble which is typedef'd
409    # to double2.
410    source = re.sub(r'(^|[^a-zA-Z0-9_]c?)double(([248]|16)?($|[^a-zA-Z0-9_]))',
411                    r'\1%s\2'%type_name, source)
412    source = _tag_float(source, constant_flag)
413    return source
414
415TGMATH_INT_RE = re.compile(r"""
416(?: # Non-capturing match; not lookbehind since pattern length is variable
417  \b              # word boundary
418   # various math functions
419  (a?(sin|cos|tan)h? | atan2
420   | erfc? | tgamma
421   | exp(2|10|m1)? | log(2|10|1p)? | pow[nr]? | sqrt | rsqrt | rootn
422   | fabs | fmax | fmin
423   )
424  \s*[(]\s*       # open parenthesis
425)
426[+-]?(0|[1-9]\d*) # integer
427(?=               # lookahead match: don't want to move from end of int
428  \s*[,)]         # comma or close parenthesis for end of argument
429)                 # end lookahead
430""", re.VERBOSE)
431def _fix_tgmath_int(source):
432    # type: (str) -> str
433    """
434    Replace f(integer) with f(integer.) for sin, cos, pow, etc.
435
436    OS X OpenCL complains that it can't resolve the type generic calls to
437    the standard math functions when they are called with integer constants,
438    but this does not happen with the Windows Intel driver for example.
439    To avoid confusion on the matrix marketplace, automatically promote
440    integers to floats if we recognize them in the source.
441
442    The specific functions we look for are:
443
444        trigonometric: sin, asin, sinh, asinh, etc., and atan2
445        exponential:   exp, exp2, exp10, expm1, log, log2, log10, logp1
446        power:         pow, pown, powr, sqrt, rsqrt, rootn
447        special:       erf, erfc, tgamma
448        float:         fabs, fmin, fmax
449
450    Note that we don't convert the second argument of dual argument
451    functions: atan2, fmax, fmin, pow, powr.  This could potentially
452    be a problem for pow(x, 2), but that case seems to work without change.
453    """
454    out = TGMATH_INT_RE.sub(r'\g<0>.', source)
455    return out
456
457
458# Floating point regular expression
459#
460# Define parts:
461#
462#    E = [eE][+-]?\d+    : Exponent
463#    P = [.]             : Decimal separator
464#    N = [1-9]\d*        : Natural number, no leading zeros
465#    Z = 0               : Zero
466#    F = \d+             : Fractional number, maybe leading zeros
467#    F? = \d*            : Optional fractional number
468#
469# We want to reject bare natural numbers and bare decimal points, so we
470# need to tediously outline the cases where we have either a fraction or
471# an exponent:
472#
473#   ( ZP | ZPF | ZE | ZPE | ZPFE | NP | NPF | NE | NPE | NPFE | PF | PFE )
474#
475#
476# We can then join cases by making parts optional.  The following are
477# some ways to do this:
478#
479#   ( (Z|N)(P|PF|E|PE|PFE) | PFE? )                   # Split on lead
480#     => ( (Z|N)(PF?|(PF?)?E) | PFE? )
481#   ( ((Z|N)PF?|PF)E? | (Z|N)E)                       # Split on point
482#   ( (ZP|ZPF|NP|NPF|PF) | (Z|ZP|ZPF|N|NP|NPF|PF)E )  # Split on E
483#     => ( ((Z|N)PF?|PF) | ((Z|N)(PF?)? | PF) E )
484FLOAT_RE = re.compile(r"""
485    (?<!\w)  # use negative lookbehind since '.' confuses \b test
486    # use split on lead to match float ( (Z|N)(PF?|(PF?)?E) | PFE? )
487    ( ( 0 | [1-9]\d* )                     # ( ( Z | N )
488      ([.]\d* | ([.]\d*)? [eE][+-]?\d+ )   #   (PF? | (PF?)? E )
489    | [.]\d+ ([eE][+-]?\d+)?               # | PF (E)?
490    )                                      # )
491    (?!\w)  # use negative lookahead since '.' confuses \b test
492    """, re.VERBOSE)
493def _tag_float(source, constant_flag):
494    # Convert floating point constants to single by adding 'f' to the end,
495    # or long double with an 'L' suffix.  OS/X complains if you don't do this.
496    out = FLOAT_RE.sub(r'\g<0>%s'%constant_flag, source)
497    #print("in",repr(source),"out",repr(out), constant_flag)
498    return out
499
500def test_tag_float():
501    """check that floating point constants are properly identified and tagged with 'f'"""
502
503    cases = """
504ZP  : 0.
505ZPF : 0.0,0.01,0.1
506Z  E: 0e+001
507ZP E: 0.E0
508ZPFE: 0.13e-031
509NP  : 1., 12.
510NPF : 1.0001, 1.1, 1.0
511N  E: 1e0, 37E-080
512NP E: 1.e0, 37.E-080
513NPFE: 845.017e+22
514 PF : .1, .0, .0100
515 PFE: .6e+9, .82E-004
516# isolated cases
5170.
5181e0
5190.13e-013
520# untouched
521struct3.e3, 03.05.67, 37
522# expressions
5233.75+-1.6e-7-27+13.2
524a3.e2 - 0.
5254*atan(1)
5264.*atan(1.)
527"""
528
529    output = """
530ZP  : 0.f
531ZPF : 0.0f,0.01f,0.1f
532Z  E: 0e+001f
533ZP E: 0.E0f
534ZPFE: 0.13e-031f
535NP  : 1.f, 12.f
536NPF : 1.0001f, 1.1f, 1.0f
537N  E: 1e0f, 37E-080f
538NP E: 1.e0f, 37.E-080f
539NPFE: 845.017e+22f
540 PF : .1f, .0f, .0100f
541 PFE: .6e+9f, .82E-004f
542# isolated cases
5430.f
5441e0f
5450.13e-013f
546# untouched
547struct3.e3, 03.05.67, 37
548# expressions
5493.75f+-1.6e-7f-27+13.2f
550a3.e2 - 0.f
5514*atan(1)
5524.f*atan(1.f)
553"""
554
555    for case_in, case_out in zip(cases.split('\n'), output.split('\n')):
556        out = _tag_float(case_in, 'f')
557        assert case_out == out, "%r => %r"%(case_in, out)
558
559
560def kernel_name(model_info, variant):
561    # type: (ModelInfo, str) -> str
562    """
563    Name of the exported kernel symbol.
564
565    *variant* is "Iq", "Iqxy" or "Imagnetic".
566    """
567    return model_info.name + "_" + variant
568
569
570def indent(s, depth):
571    # type: (str, int) -> str
572    """
573    Indent a string of text with *depth* additional spaces on each line.
574    """
575    spaces = " "*depth
576    sep = "\n" + spaces
577    return spaces + sep.join(s.split("\n"))
578
579
580_template_cache = {}  # type: Dict[str, Tuple[int, str, str]]
581def load_template(filename):
582    # type: (str) -> str
583    path = joinpath(DATA_PATH, filename)
584    mtime = getmtime(path)
585    if filename not in _template_cache or mtime > _template_cache[filename][0]:
586        with open(path) as fid:
587            _template_cache[filename] = (mtime, fid.read(), path)
588    return _template_cache[filename][1], path
589
590
591_FN_TEMPLATE = """\
592double %(name)s(%(pars)s);
593double %(name)s(%(pars)s) {
594#line %(line)d "%(filename)s"
595    %(body)s
596}
597
598"""
599def _gen_fn(name, pars, body, filename, line):
600    # type: (str, List[Parameter], str, str, int) -> str
601    """
602    Generate a function given pars and body.
603
604    Returns the following string::
605
606         double fn(double a, double b, ...);
607         double fn(double a, double b, ...) {
608             ....
609         }
610    """
611    par_decl = ', '.join(p.as_function_argument() for p in pars) if pars else 'void'
612    return _FN_TEMPLATE % {
613        'name': name, 'pars': par_decl, 'body': body,
614        'filename': filename.replace('\\', '\\\\'), 'line': line,
615    }
616
617
618def _call_pars(prefix, pars):
619    # type: (str, List[Parameter]) -> List[str]
620    """
621    Return a list of *prefix+parameter* from parameter items.
622
623    *prefix* should be "v." if v is a struct.
624    """
625    return [p.as_call_reference(prefix) for p in pars]
626
627
628# type in IQXY pattern could be single, float, double, long double, ...
629_IQXY_PATTERN = re.compile("^((inline|static) )? *([a-z ]+ )? *Iqxy *([(]|$)",
630                           flags=re.MULTILINE)
631def _have_Iqxy(sources):
632    # type: (List[str]) -> bool
633    """
634    Return true if any file defines Iqxy.
635
636    Note this is not a C parser, and so can be easily confused by
637    non-standard syntax.  Also, it will incorrectly identify the following
638    as having Iqxy::
639
640        /*
641        double Iqxy(qx, qy, ...) { ... fill this in later ... }
642        */
643
644    If you want to comment out an Iqxy function, use // on the front of the
645    line instead.
646    """
647    for path, code in sources:
648        if _IQXY_PATTERN.search(code):
649            return True
650    else:
651        return False
652
653
654def _add_source(source, code, path):
655    """
656    Add a file to the list of source code chunks, tagged with path and line.
657    """
658    path = path.replace('\\', '\\\\')
659    source.append('#line 1 "%s"' % path)
660    source.append(code)
661
662def make_source(model_info):
663    # type: (ModelInfo) -> Dict[str, str]
664    """
665    Generate the OpenCL/ctypes kernel from the module info.
666
667    Uses source files found in the given search path.  Returns None if this
668    is a pure python model, with no C source components.
669    """
670    if callable(model_info.Iq):
671        raise ValueError("can't compile python model")
672        #return None
673
674    # TODO: need something other than volume to indicate dispersion parameters
675    # No volume normalization despite having a volume parameter.
676    # Thickness is labelled a volume in order to trigger polydispersity.
677    # May want a separate dispersion flag, or perhaps a separate category for
678    # disperse, but not volume.  Volume parameters also use relative values
679    # for the distribution rather than the absolute values used by angular
680    # dispersion.  Need to be careful that necessary parameters are available
681    # for computing volume even if we allow non-disperse volume parameters.
682
683    partable = model_info.parameters
684
685    # Load templates and user code
686    kernel_header = load_template('kernel_header.c')
687    dll_code = load_template('kernel_iq.c')
688    ocl_code = load_template('kernel_iq.cl')
689    #ocl_code = load_template('kernel_iq_local.cl')
690    user_code = [(f, open(f).read()) for f in model_sources(model_info)]
691
692    # Build initial sources
693    source = []
694    _add_source(source, *kernel_header)
695    for path, code in user_code:
696        _add_source(source, code, path)
697
698    # Make parameters for q, qx, qy so that we can use them in declarations
699    q, qx, qy = [Parameter(name=v) for v in ('q', 'qx', 'qy')]
700    # Generate form_volume function, etc. from body only
701    if isinstance(model_info.form_volume, str):
702        pars = partable.form_volume_parameters
703        source.append(_gen_fn('form_volume', pars, model_info.form_volume,
704                              model_info.filename, model_info._form_volume_line))
705    if isinstance(model_info.Iq, str):
706        pars = [q] + partable.iq_parameters
707        source.append(_gen_fn('Iq', pars, model_info.Iq,
708                              model_info.filename, model_info._Iq_line))
709    if isinstance(model_info.Iqxy, str):
710        pars = [qx, qy] + partable.iqxy_parameters
711        source.append(_gen_fn('Iqxy', pars, model_info.Iqxy,
712                              model_info.filename, model_info._Iqxy_line))
713
714    # Define the parameter table
715    # TODO: plug in current line number
716    source.append('#line 542 "sasmodels/generate.py"')
717    source.append("#define PARAMETER_TABLE \\")
718    source.append("\\\n".join(p.as_definition()
719                              for p in partable.kernel_parameters))
720
721    # Define the function calls
722    if partable.form_volume_parameters:
723        refs = _call_pars("_v.", partable.form_volume_parameters)
724        call_volume = "#define CALL_VOLUME(_v) form_volume(%s)"%(",".join(refs))
725    else:
726        # Model doesn't have volume.  We could make the kernel run a little
727        # faster by not using/transferring the volume normalizations, but
728        # the ifdef's reduce readability more than is worthwhile.
729        call_volume = "#define CALL_VOLUME(v) 1.0"
730    source.append(call_volume)
731
732    refs = ["_q[_i]"] + _call_pars("_v.", partable.iq_parameters)
733    call_iq = "#define CALL_IQ(_q,_i,_v) Iq(%s)" % (",".join(refs))
734    if _have_Iqxy(user_code) or isinstance(model_info.Iqxy, str):
735        # Call 2D model
736        refs = ["_q[2*_i]", "_q[2*_i+1]"] + _call_pars("_v.", partable.iqxy_parameters)
737        call_iqxy = "#define CALL_IQ(_q,_i,_v) Iqxy(%s)" % (",".join(refs))
738    else:
739        # Call 1D model with sqrt(qx^2 + qy^2)
740        #warnings.warn("Creating Iqxy = Iq(sqrt(qx^2 + qy^2))")
741        # still defined:: refs = ["q[i]"] + _call_pars("v", iq_parameters)
742        pars_sqrt = ["sqrt(_q[2*_i]*_q[2*_i]+_q[2*_i+1]*_q[2*_i+1])"] + refs[1:]
743        call_iqxy = "#define CALL_IQ(_q,_i,_v) Iq(%s)" % (",".join(pars_sqrt))
744
745    magpars = [k-2 for k, p in enumerate(partable.call_parameters)
746               if p.type == 'sld']
747
748    # Fill in definitions for numbers of parameters
749    source.append("#define MAX_PD %s"%partable.max_pd)
750    source.append("#define NUM_PARS %d"%partable.npars)
751    source.append("#define NUM_VALUES %d" % partable.nvalues)
752    source.append("#define NUM_MAGNETIC %d" % partable.nmagnetic)
753    source.append("#define MAGNETIC_PARS %s"%",".join(str(k) for k in magpars))
754    for k, v in enumerate(magpars[:3]):
755        source.append("#define MAGNETIC_PAR%d %d"%(k+1, v))
756
757    # TODO: allow mixed python/opencl kernels?
758
759    ocl = kernels(ocl_code, call_iq, call_iqxy, model_info.name)
760    dll = kernels(dll_code, call_iq, call_iqxy, model_info.name)
761    result = {
762        'dll': '\n'.join(source+dll[0]+dll[1]+dll[2]),
763        'opencl': '\n'.join(source+ocl[0]+ocl[1]+ocl[2]),
764    }
765
766    return result
767
768
769def kernels(kernel, call_iq, call_iqxy, name):
770    # type: ([str,str], str, str, str) -> List[str]
771    code = kernel[0]
772    path = kernel[1].replace('\\', '\\\\')
773    iq = [
774        # define the Iq kernel
775        "#define KERNEL_NAME %s_Iq" % name,
776        call_iq,
777        '#line 1 "%s Iq"' % path,
778        code,
779        "#undef CALL_IQ",
780        "#undef KERNEL_NAME",
781        ]
782
783    iqxy = [
784        # define the Iqxy kernel from the same source with different #defines
785        "#define KERNEL_NAME %s_Iqxy" % name,
786        call_iqxy,
787        '#line 1 "%s Iqxy"' % path,
788        code,
789        "#undef CALL_IQ",
790        "#undef KERNEL_NAME",
791    ]
792
793    imagnetic = [
794        # define the Imagnetic kernel
795        "#define KERNEL_NAME %s_Imagnetic" % name,
796        "#define MAGNETIC 1",
797        call_iqxy,
798        '#line 1 "%s Imagnetic"' % path,
799        code,
800        "#undef MAGNETIC",
801        "#undef CALL_IQ",
802        "#undef KERNEL_NAME",
803    ]
804
805    return iq, iqxy, imagnetic
806
807
808def load_kernel_module(model_name):
809    # type: (str) -> module
810    """
811    Return the kernel module named in *model_name*.
812
813    If the name ends in *.py* then load it as a custom model using
814    :func:`sasmodels.custom.load_custom_kernel_module`, otherwise
815    load it from :mod:`sasmodels.models`.
816    """
817    if model_name.endswith('.py'):
818        kernel_module = load_custom_kernel_module(model_name)
819    else:
820        from sasmodels import models
821        __import__('sasmodels.models.'+model_name)
822        kernel_module = getattr(models, model_name, None)
823    return kernel_module
824
825
826section_marker = re.compile(r'\A(?P<first>[%s])(?P=first)*\Z'
827                            % re.escape(string.punctuation))
828def _convert_section_titles_to_boldface(lines):
829    # type: (Sequence[str]) -> Iterator[str]
830    """
831    Do the actual work of identifying and converting section headings.
832    """
833    prior = None
834    for line in lines:
835        if prior is None:
836            prior = line
837        elif section_marker.match(line):
838            if len(line) >= len(prior):
839                yield "".join(("**", prior, "**"))
840                prior = None
841            else:
842                yield prior
843                prior = line
844        else:
845            yield prior
846            prior = line
847    if prior is not None:
848        yield prior
849
850
851def convert_section_titles_to_boldface(s):
852    # type: (str) -> str
853    """
854    Use explicit bold-face rather than section headings so that the table of
855    contents is not polluted with section names from the model documentation.
856
857    Sections are identified as the title line followed by a line of punctuation
858    at least as long as the title line.
859    """
860    return "\n".join(_convert_section_titles_to_boldface(s.split('\n')))
861
862
863def make_doc(model_info):
864    # type: (ModelInfo) -> str
865    """
866    Return the documentation for the model.
867    """
868    Iq_units = "The returned value is scaled to units of |cm^-1| |sr^-1|, absolute scale."
869    Sq_units = "The returned value is a dimensionless structure factor, $S(q)$."
870    docs = model_info.docs if model_info.docs is not None else ""
871    docs = convert_section_titles_to_boldface(docs)
872    pars = make_partable(model_info.parameters.COMMON
873                         + model_info.parameters.kernel_parameters)
874    subst = dict(id=model_info.id.replace('_', '-'),
875                 name=model_info.name,
876                 title=model_info.title,
877                 parameters=pars,
878                 returns=Sq_units if model_info.structure_factor else Iq_units,
879                 docs=docs)
880    return DOC_HEADER % subst
881
882
883# TODO: need a single source for rst_prolog; it is also in doc/rst_prolog
884RST_PROLOG = r"""\
885.. |Ang| unicode:: U+212B
886.. |Ang^-1| replace:: |Ang|\ :sup:`-1`
887.. |Ang^2| replace:: |Ang|\ :sup:`2`
888.. |Ang^-2| replace:: |Ang|\ :sup:`-2`
889.. |1e-6Ang^-2| replace:: 10\ :sup:`-6`\ |Ang|\ :sup:`-2`
890.. |Ang^3| replace:: |Ang|\ :sup:`3`
891.. |Ang^-3| replace:: |Ang|\ :sup:`-3`
892.. |Ang^-4| replace:: |Ang|\ :sup:`-4`
893.. |cm^-1| replace:: cm\ :sup:`-1`
894.. |cm^2| replace:: cm\ :sup:`2`
895.. |cm^-2| replace:: cm\ :sup:`-2`
896.. |cm^3| replace:: cm\ :sup:`3`
897.. |1e15cm^3| replace:: 10\ :sup:`15`\ cm\ :sup:`3`
898.. |cm^-3| replace:: cm\ :sup:`-3`
899.. |sr^-1| replace:: sr\ :sup:`-1`
900
901.. |cdot| unicode:: U+00B7
902.. |deg| unicode:: U+00B0
903.. |g/cm^3| replace:: g\ |cdot|\ cm\ :sup:`-3`
904.. |mg/m^2| replace:: mg\ |cdot|\ m\ :sup:`-2`
905.. |fm^2| replace:: fm\ :sup:`2`
906.. |Ang*cm^-1| replace:: |Ang|\ |cdot|\ cm\ :sup:`-1`
907"""
908
909# TODO: make a better fake reference role
910RST_ROLES = """\
911.. role:: ref
912
913.. role:: numref
914
915"""
916
917def make_html(model_info):
918    """
919    Convert model docs directly to html.
920    """
921    from . import rst2html
922
923    rst = make_doc(model_info)
924    return rst2html.rst2html("".join((RST_ROLES, RST_PROLOG, rst)))
925
926def view_html(model_name):
927    from . import modelinfo
928    kernel_module = load_kernel_module(model_name)
929    info = modelinfo.make_model_info(kernel_module)
930    view_html_from_info(info)
931
932def view_html_from_info(info):
933    from . import rst2html
934    url = "file://"+dirname(info.filename)+"/"
935    rst2html.view_html(make_html(info), url=url)
936
937def demo_time():
938    # type: () -> None
939    """
940    Show how long it takes to process a model.
941    """
942    import datetime
943    from .modelinfo import make_model_info
944    from .models import cylinder
945
946    tic = datetime.datetime.now()
947    make_source(make_model_info(cylinder))
948    toc = (datetime.datetime.now() - tic).total_seconds()
949    print("time: %g"%toc)
950
951
952def main():
953    # type: () -> None
954    """
955    Program which prints the source produced by the model.
956    """
957    import sys
958    from .modelinfo import make_model_info
959
960    if len(sys.argv) <= 1:
961        print("usage: python -m sasmodels.generate modelname")
962    else:
963        name = sys.argv[1]
964        kernel_module = load_kernel_module(name)
965        model_info = make_model_info(kernel_module)
966        source = make_source(model_info)
967        print(source['dll'])
968
969
970if __name__ == "__main__":
971    main()
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