source: sasmodels/sasmodels/modelinfo.py @ 01c8d9e

core_shell_microgelsmagnetic_modelticket-1257-vesicle-productticket_1156ticket_1265_superballticket_822_more_unit_tests
Last change on this file since 01c8d9e was 01c8d9e, checked in by Suczewski <ges3@…>, 13 months ago

beta approximation, first pass

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1"""
2Model Info and Parameter Tables
3===============================
4
5Defines :class:`ModelInfo` and :class:`ParameterTable` and the routines for
6manipulating them.  In particular, :func:`make_model_info` converts a kernel
7module into the model info block as seen by the rest of the sasmodels library.
8"""
9from __future__ import print_function
10
11from copy import copy
12from os.path import abspath, basename, splitext
13import inspect
14
15import numpy as np  # type: ignore
16
17# Optional typing
18# pylint: disable=unused-import
19try:
20    from typing import Tuple, List, Union, Dict, Optional, Any, Callable, Sequence, Set
21    from types import ModuleType
22except ImportError:
23    pass
24else:
25    Limits = Tuple[float, float]
26    #LimitsOrChoice = Union[Limits, Tuple[Sequence[str]]]
27    ParameterDef = Tuple[str, str, float, Limits, str, str]
28    ParameterSetUser = Dict[str, Union[float, List[float]]]
29    ParameterSet = Dict[str, float]
30    TestInput = Union[str, float, List[float], Tuple[float, float], List[Tuple[float, float]]]
31    TestValue = Union[float, List[float]]
32    TestCondition = Tuple[ParameterSetUser, TestInput, TestValue]
33# pylint: enable=unused-import
34
35# If MAX_PD changes, need to change the loop macros in kernel_iq.c
36MAX_PD = 5 #: Maximum number of simultaneously polydisperse parameters
37
38# assumptions about common parameters exist throughout the code, such as:
39# (1) kernel functions Iq, Iqxy, Iqac, Iqabc, form_volume, ... don't see them
40# (2) kernel drivers assume scale is par[0] and background is par[1]
41# (3) mixture models drop the background on components and replace the scale
42#     with a scale that varies from [-inf, inf]
43# (4) product models drop the background and reassign scale
44# and maybe other places.
45# Note that scale and background cannot be coordinated parameters whose value
46# depends on the some polydisperse parameter with the current implementation
47COMMON_PARAMETERS = [
48    ("scale", "", 1, (0.0, np.inf), "", "Source intensity"),
49    ("background", "1/cm", 1e-3, (-np.inf, np.inf), "", "Source background"),
50]
51assert (len(COMMON_PARAMETERS) == 2
52        and COMMON_PARAMETERS[0][0] == "scale"
53        and COMMON_PARAMETERS[1][0] == "background"), "don't change common parameters"
54
55
56def make_parameter_table(pars):
57    # type: (List[ParameterDef]) -> ParameterTable
58    """
59    Construct a parameter table from a list of parameter definitions.
60
61    This is used by the module processor to convert the parameter block into
62    the parameter table seen in the :class:`ModelInfo` for the module.
63    """
64    processed = []
65    for p in pars:
66        if not isinstance(p, (list, tuple)) or len(p) != 6:
67            raise ValueError("Parameter should be [name, units, default, limits, type, desc], but got %r"
68                             %str(p))
69        processed.append(parse_parameter(*p))
70    partable = ParameterTable(processed)
71    partable.check_angles()
72    return partable
73
74def parse_parameter(name, units='', default=np.NaN,
75                    user_limits=None, ptype='', description=''):
76    # type: (str, str, float, Sequence[Any], str, str) -> Parameter
77    """
78    Parse an individual parameter from the parameter definition block.
79
80    This does type and value checking on the definition, leading
81    to early failure in the model loading process and easier debugging.
82    """
83    # Parameter is a user facing class.  Do robust type checking.
84    if not isstr(name):
85        raise ValueError("expected string for parameter name %r"%name)
86    if not isstr(units):
87        raise ValueError("expected units to be a string for %s"%name)
88
89    # Process limits as [float, float] or [[str, str, ...]]
90    choices = []  # type: List[str]
91    if user_limits is None:
92        limits = (-np.inf, np.inf)
93    elif not isinstance(user_limits, (tuple, list)):
94        raise ValueError("invalid limits for %s"%name)
95    else:
96        # if limits is [[str,...]], then this is a choice list field,
97        # and limits are 1 to length of string list
98        if isinstance(user_limits[0], (tuple, list)):
99            choices = user_limits[0]
100            limits = (0., len(choices)-1.)
101            if not all(isstr(k) for k in choices):
102                raise ValueError("choices must be strings for %s"%name)
103        else:
104            try:
105                low, high = user_limits
106                limits = (float(low), float(high))
107            except Exception:
108                raise ValueError("invalid limits for %s: %r"%(name, user_limits))
109            if low >= high:
110                raise ValueError("require lower limit < upper limit")
111
112    # Process default value as float, making sure it is in range
113    if not isinstance(default, (int, float)):
114        raise ValueError("expected default %r to be a number for %s"
115                         % (default, name))
116    if default < limits[0] or default > limits[1]:
117        raise ValueError("default value %r not in range for %s"
118                         % (default, name))
119
120    # Check for valid parameter type
121    if ptype not in ("volume", "orientation", "sld", "magnetic", ""):
122        raise ValueError("unexpected type %r for %s" % (ptype, name))
123
124    # Check for valid parameter description
125    if not isstr(description):
126        raise ValueError("expected description to be a string")
127
128    # Parameter id for name[n] does not include [n]
129    if "[" in name:
130        if not name.endswith(']'):
131            raise ValueError("Expected name[len] for vector parameter %s"%name)
132        pid, ref = name[:-1].split('[', 1)
133        ref = ref.strip()
134    else:
135        pid, ref = name, None
136
137    # automatically identify sld types
138    if ptype == '' and (pid.startswith('sld') or pid.endswith('sld')):
139        ptype = 'sld'
140
141    # Check if using a vector definition, name[k], as the parameter name
142    if ref:
143        if ref == '':
144            raise ValueError("Need to specify vector length for %s"%name)
145        try:
146            length = int(ref)
147            control = None
148        except ValueError:
149            length = None
150            control = ref
151    else:
152        length = 1
153        control = None
154
155    # Build the parameter
156    parameter = Parameter(name=name, units=units, default=default,
157                          limits=limits, ptype=ptype, description=description)
158
159    # TODO: need better control over whether a parameter is polydisperse
160    parameter.polydisperse = ptype in ('orientation', 'volume')
161    parameter.relative_pd = ptype == 'volume'
162    parameter.choices = choices
163    parameter.length = length
164    parameter.length_control = control
165    return parameter
166
167
168def expand_pars(partable, pars):
169    # type: (ParameterTable, ParameterSetUser) ->  ParameterSet
170    """
171    Create demo parameter set from key-value pairs.
172
173    *pars* are the key-value pairs to use for the parameters.  Any
174    parameters not specified in *pars* are set from the *partable* defaults.
175
176    If *pars* references vector fields, such as thickness[n], then support
177    different ways of assigning the demo values, including assigning a
178    specific value (e.g., thickness3=50.0), assigning a new value to all
179    (e.g., thickness=50.0) or assigning values using list notation.
180    """
181    if pars is None:
182        result = partable.defaults
183    else:
184        lookup = dict((p.id, p) for p in partable.kernel_parameters)
185        result = partable.defaults.copy()
186        scalars = dict((name, value) for name, value in pars.items()
187                       if name not in lookup or lookup[name].length == 1)
188        vectors = dict((name, value) for name, value in pars.items()
189                       if name in lookup and lookup[name].length > 1)
190        #print("lookup", lookup)
191        #print("scalars", scalars)
192        #print("vectors", vectors)
193        if vectors:
194            for name, value in vectors.items():
195                if np.isscalar(value):
196                    # support for the form
197                    #    dict(thickness=0, thickness2=50)
198                    for k in range(1, lookup[name].length+1):
199                        key = name+str(k)
200                        if key not in scalars:
201                            scalars[key] = value
202                else:
203                    # supoprt for the form
204                    #    dict(thickness=[20,10,3])
205                    for (k, v) in enumerate(value):
206                        scalars[name+str(k+1)] = v
207        result.update(scalars)
208        #print("expanded", result)
209
210    return result
211
212def prefix_parameter(par, prefix):
213    # type: (Parameter, str) -> Parameter
214    """
215    Return a copy of the parameter with its name prefixed.
216    """
217    new_par = copy(par)
218    new_par.name = prefix + par.name
219    new_par.id = prefix + par.id
220
221def suffix_parameter(par, suffix):
222    # type: (Parameter, str) -> Parameter
223    """
224    Return a copy of the parameter with its name prefixed.
225    """
226    new_par = copy(par)
227    # If name has the form x[n], replace with x_suffix[n]
228    new_par.name = par.id + suffix + par.name[len(par.id):]
229    new_par.id = par.id + suffix
230
231class Parameter(object):
232    """
233    The available kernel parameters are defined as a list, with each parameter
234    defined as a sublist with the following elements:
235
236    *name* is the name that will be displayed to the user.  Names
237    should be lower case, with words separated by underscore.  If
238    acronyms are used, the whole acronym should be upper case. For vector
239    parameters, the name will be followed by *[len]* where *len* is an
240    integer length of the vector, or the name of the parameter which
241    controls the length.  The attribute *id* will be created from name
242    without the length.
243
244    *units* should be one of *degrees* for angles, *Ang* for lengths,
245    *1e-6/Ang^2* for SLDs.
246
247    *default value* will be the initial value for  the model when it
248    is selected, or when an initial value is not otherwise specified.
249
250    *limits = [lb, ub]* are the hard limits on the parameter value, used to
251    limit the polydispersity density function.  In the fit, the parameter limits
252    given to the fit are the limits  on the central value of the parameter.
253    If there is polydispersity, it will evaluate parameter values outside
254    the fit limits, but not outside the hard limits specified in the model.
255    If there are no limits, use +/-inf imported from numpy.
256
257    *type* indicates how the parameter will be used.  "volume" parameters
258    will be used in all functions.  "orientation" parameters are not passed,
259    but will be used to convert from *qx*, *qy* to *qa*, *qb*, *qc* in calls to
260    *Iqxy* and *Imagnetic*.  If *type* is the empty string, the parameter will
261    be used in all of *Iq*, *Iqxy* and *Imagnetic*.  "sld" parameters
262    can automatically be promoted to magnetic parameters, each of which
263    will have a magnitude and a direction, which may be different from
264    other sld parameters. The volume parameters are used for calls
265    to form_volume within the kernel (required for volume normalization)
266    and for calls to ER and VR for effective radius and volume ratio
267    respectively.
268
269    *description* is a short description of the parameter.  This will
270    be displayed in the parameter table and used as a tool tip for the
271    parameter value in the user interface.
272
273    Additional values can be set after the parameter is created:
274
275    * *length* is the length of the field if it is a vector field
276
277    * *length_control* is the parameter which sets the vector length
278
279    * *is_control* is True if the parameter is a control parameter for a vector
280
281    * *polydisperse* is true if the parameter accepts a polydispersity
282
283    * *relative_pd* is true if that polydispersity is a portion of the
284      value (so a 10% length dipsersity would use a polydispersity value
285      of 0.1) rather than absolute dispersisity (such as an angle plus or
286      minus 15 degrees).
287
288    *choices* is the option names for a drop down list of options, as for
289    example, might be used to set the value of a shape parameter.
290
291    These values are set by :func:`make_parameter_table` and
292    :func:`parse_parameter` therein.
293    """
294    def __init__(self, name, units='', default=None, limits=(-np.inf, np.inf),
295                 ptype='', description=''):
296        # type: (str, str, float, Limits, str, str) -> None
297        self.id = name.split('[')[0].strip() # type: str
298        self.name = name                     # type: str
299        self.units = units                   # type: str
300        self.default = default               # type: float
301        self.limits = limits                 # type: Limits
302        self.type = ptype                    # type: str
303        self.description = description       # type: str
304
305        # Length and length_control will be filled in once the complete
306        # parameter table is available.
307        self.length = 1                      # type: int
308        self.length_control = None           # type: Optional[str]
309        self.is_control = False              # type: bool
310
311        # TODO: need better control over whether a parameter is polydisperse
312        self.polydisperse = False            # type: bool
313        self.relative_pd = False             # type: bool
314
315        # choices are also set externally.
316        self.choices = []                    # type: List[str]
317
318    def as_definition(self):
319        # type: () -> str
320        """
321        Declare space for the variable in a parameter structure.
322
323        For example, the parameter thickness with length 3 will
324        return "double thickness[3];", with no spaces before and
325        no new line character afterward.
326        """
327        if self.length == 1:
328            return "double %s;"%self.id
329        else:
330            return "double %s[%d];"%(self.id, self.length)
331
332    def as_function_argument(self):
333        # type: () -> str
334        r"""
335        Declare the variable as a function argument.
336
337        For example, the parameter thickness with length 3 will
338        return "double \*thickness", with no spaces before and
339        no comma afterward.
340        """
341        if self.length == 1:
342            return "double %s"%self.id
343        else:
344            return "double *%s"%self.id
345
346    def as_call_reference(self, prefix=""):
347        # type: (str) -> str
348        """
349        Return *prefix* + parameter name.  For struct references, use "v."
350        as the prefix.
351        """
352        # Note: if the parameter is a struct type, then we will need to use
353        # &prefix+id.  For scalars and vectors we can just use prefix+id.
354        return prefix + self.id
355
356    def __str__(self):
357        # type: () -> str
358        return "<%s>"%self.name
359
360    def __repr__(self):
361        # type: () -> str
362        return "P<%s>"%self.name
363
364
365class ParameterTable(object):
366    """
367    ParameterTable manages the list of available parameters.
368
369    There are a couple of complications which mean that the list of parameters
370    for the kernel differs from the list of parameters that the user sees.
371
372    (1) Common parameters.  Scale and background are implicit to every model,
373    but are not passed to the kernel.
374
375    (2) Vector parameters.  Vector parameters are passed to the kernel as a
376    pointer to an array, e.g., thick[], but they are seen by the user as n
377    separate parameters thick1, thick2, ...
378
379    Therefore, the parameter table is organized by how it is expected to be
380    used. The following information is needed to set up the kernel functions:
381
382    * *kernel_parameters* is the list of parameters in the kernel parameter
383      table, with vector parameter p declared as p[].
384
385    * *iq_parameters* is the list of parameters to the Iq(q, ...) function,
386      with vector parameter p sent as p[].
387
388    * *form_volume_parameters* is the list of parameters to the form_volume(...)
389      function, with vector parameter p sent as p[].
390
391    Problem details, which sets up the polydispersity loops, requires the
392    following:
393
394    * *theta_offset* is the offset of the theta parameter in the kernel parameter
395      table, with vector parameters counted as n individual parameters
396      p1, p2, ..., or offset is -1 if there is no theta parameter.
397
398    * *max_pd* is the maximum number of polydisperse parameters, with vector
399      parameters counted as n individual parameters p1, p2, ...  Note that
400      this number is limited to sasmodels.modelinfo.MAX_PD.
401
402    * *npars* is the total number of parameters to the kernel, with vector
403      parameters counted as n individual parameters p1, p2, ...
404
405    * *call_parameters* is the complete list of parameters to the kernel,
406      including scale and background, with vector parameters recorded as
407      individual parameters p1, p2, ...
408
409    * *active_1d* is the set of names that may be polydisperse for 1d data
410
411    * *active_2d* is the set of names that may be polydisperse for 2d data
412
413    User parameters are the set of parameters visible to the user, including
414    the scale and background parameters that the kernel does not see.  User
415    parameters don't use vector notation, and instead use p1, p2, ...
416    """
417    # scale and background are implicit parameters
418    COMMON = [Parameter(*p) for p in COMMON_PARAMETERS]
419    def __init__(self, parameters):
420        # type: (List[Parameter]) -> None
421        self.kernel_parameters = parameters
422        self._set_vector_lengths()
423        self.npars = sum(p.length for p in self.kernel_parameters)
424        self.nmagnetic = sum(p.length for p in self.kernel_parameters
425                             if p.type == 'sld')
426        self.nvalues = 2 + self.npars
427        if self.nmagnetic:
428            self.nvalues += 3 + 3*self.nmagnetic
429        self.call_parameters = self._get_call_parameters()
430        self.defaults = self._get_defaults()
431        #self._name_table= dict((p.id, p) for p in parameters)
432
433        # Set the kernel parameters.  Assumes background and scale are the
434        # first two parameters in the parameter list, but these are not sent
435        # to the underlying kernel functions.
436        self.iq_parameters = [p for p in self.kernel_parameters
437                              if p.type not in ('orientation', 'magnetic')]
438        self.orientation_parameters = [p for p in self.kernel_parameters
439                                       if p.type == 'orientation']
440        self.form_volume_parameters = [p for p in self.kernel_parameters
441                                       if p.type == 'volume']
442        # Theta offset
443        offset = 0
444        for p in self.kernel_parameters:
445            if p.name == 'theta':
446                self.theta_offset = offset
447                break
448            offset += p.length
449        else:
450            self.theta_offset = -1
451
452        # number of polydisperse parameters
453        num_pd = sum(p.length for p in self.kernel_parameters if p.polydisperse)
454        # Don't use more polydisperse parameters than are available in the model
455        self.max_pd = min(num_pd, MAX_PD)
456
457        # true if has 2D parameters
458        self.has_2d = any(p.type in ('orientation', 'magnetic')
459                          for p in self.kernel_parameters)
460        self.is_asymmetric = any(p.name == 'psi' for p in self.kernel_parameters)
461        self.magnetism_index = [k for k, p in enumerate(self.call_parameters)
462                                if p.id.startswith('M0:')]
463        self.pd_1d = set(p.name for p in self.call_parameters
464                         if p.polydisperse and p.type not in ('orientation', 'magnetic'))
465        self.pd_2d = set(p.name for p in self.call_parameters if p.polydisperse)
466
467    def check_angles(self):
468        """
469        Check that orientation angles are theta, phi and possibly psi.
470        """
471        theta = phi = psi = -1
472        for k, p in enumerate(self.kernel_parameters):
473            if p.name == 'theta':
474                theta = k
475                if p.type != 'orientation':
476                    raise TypeError("theta must be an orientation parameter")
477            elif p.name == 'phi':
478                phi = k
479                if p.type != 'orientation':
480                    raise TypeError("phi must be an orientation parameter")
481            elif p.name == 'psi':
482                psi = k
483                if p.type != 'orientation':
484                    raise TypeError("psi must be an orientation parameter")
485            elif p.type == 'orientation':
486                raise TypeError("only theta, phi and psi can be orientation parameters")
487        if theta >= 0 and phi >= 0:
488            last_par = len(self.kernel_parameters) - 1
489            if phi != theta+1:
490                raise TypeError("phi must follow theta")
491            if psi >= 0 and psi != phi+1:
492                raise TypeError("psi must follow phi")
493            if (psi >= 0 and psi != last_par) or (psi < 0 and phi != last_par):
494                raise TypeError("orientation parameters must appear at the "
495                                "end of the parameter table")
496        elif theta >= 0 or phi >= 0 or psi >= 0:
497            raise TypeError("oriented shapes must have both theta and phi and maybe psi")
498
499    def __getitem__(self, key):
500        # Find the parameter definition
501        for par in self.call_parameters:
502            if par.name == key:
503                return par
504        raise KeyError("unknown parameter %r"%key)
505
506    def __contains__(self, key):
507        for par in self.call_parameters:
508            if par.name == key:
509                return True
510        return False
511
512    def _set_vector_lengths(self):
513        # type: () -> List[str]
514        """
515        Walk the list of kernel parameters, setting the length field of the
516        vector parameters from the upper limit of the reference parameter.
517
518        This needs to be done once the entire parameter table is available
519        since the reference may still be undefined when the parameter is
520        initially created.
521
522        Returns the list of control parameter names.
523
524        Note: This modifies the underlying parameter object.
525        """
526        # Sort out the length of the vector parameters such as thickness[n]
527        for p in self.kernel_parameters:
528            if p.length_control:
529                ref = self._get_ref(p)
530                ref.is_control = True
531                ref.polydisperse = False
532                low, high = ref.limits
533                if int(low) != low or int(high) != high or low < 0 or high > 20:
534                    raise ValueError("expected limits on %s to be within [0, 20]"
535                                     % ref.name)
536                p.length = int(high)
537
538    def _get_ref(self, p):
539        # type: (Parameter) -> Parameter
540        for ref in self.kernel_parameters:
541            if ref.id == p.length_control:
542                return ref
543        raise ValueError("no reference variable %r for %s"
544                         % (p.length_control, p.name))
545
546    def _get_defaults(self):
547        # type: () -> ParameterSet
548        """
549        Get a list of parameter defaults from the parameters.
550
551        Expands vector parameters into parameter id+number.
552        """
553        # Construct default values, including vector defaults
554        defaults = {}
555        for p in self.call_parameters:
556            if p.length == 1:
557                defaults[p.id] = p.default
558            else:
559                for k in range(1, p.length+1):
560                    defaults["%s%d"%(p.id, k)] = p.default
561        return defaults
562
563    def _get_call_parameters(self):
564        # type: () -> List[Parameter]
565        full_list = self.COMMON[:]
566        for p in self.kernel_parameters:
567            if p.length == 1:
568                full_list.append(p)
569            else:
570                for k in range(1, p.length+1):
571                    pk = Parameter(p.id+str(k), p.units, p.default,
572                                   p.limits, p.type, p.description)
573                    pk.polydisperse = p.polydisperse
574                    pk.relative_pd = p.relative_pd
575                    pk.choices = p.choices
576                    full_list.append(pk)
577
578        # Add the magnetic parameters to the end of the call parameter list.
579        if self.nmagnetic > 0:
580            full_list.extend([
581                Parameter('up:frac_i', '', 0., [0., 1.],
582                          'magnetic', 'fraction of spin up incident'),
583                Parameter('up:frac_f', '', 0., [0., 1.],
584                          'magnetic', 'fraction of spin up final'),
585                Parameter('up:angle', 'degress', 0., [0., 360.],
586                          'magnetic', 'spin up angle'),
587            ])
588            slds = [p for p in full_list if p.type == 'sld']
589            for p in slds:
590                full_list.extend([
591                    Parameter('M0:'+p.id, '1e-6/Ang^2', 0., [-np.inf, np.inf],
592                              'magnetic', 'magnetic amplitude for '+p.description),
593                    Parameter('mtheta:'+p.id, 'degrees', 0., [-90., 90.],
594                              'magnetic', 'magnetic latitude for '+p.description),
595                    Parameter('mphi:'+p.id, 'degrees', 0., [-180., 180.],
596                              'magnetic', 'magnetic longitude for '+p.description),
597                ])
598        #print("call parameters", full_list)
599        return full_list
600
601    def user_parameters(self, pars, is2d=True):
602        # type: (Dict[str, float], bool) -> List[Parameter]
603        """
604        Return the list of parameters for the given data type.
605
606        Vector parameters are expanded in place.  If multiple parameters
607        share the same vector length, then the parameters will be interleaved
608        in the result.  The control parameters come first.  For example,
609        if the parameter table is ordered as::
610
611            sld_core
612            sld_shell[num_shells]
613            sld_solvent
614            thickness[num_shells]
615            num_shells
616
617        and *pars[num_shells]=2* then the returned list will be::
618
619            num_shells
620            scale
621            background
622            sld_core
623            sld_shell1
624            thickness1
625            sld_shell2
626            thickness2
627            sld_solvent
628
629        Note that shell/thickness pairs are grouped together in the result
630        even though they were not grouped in the incoming table.  The control
631        parameter is always returned first since the GUI will want to set it
632        early, and rerender the table when it is changed.
633
634        Parameters marked as sld will automatically have a set of associated
635        magnetic parameters (m0:p, mtheta:p, mphi:p), as well as polarization
636        information (up:theta, up:frac_i, up:frac_f).
637        """
638        # control parameters go first
639        control = [p for p in self.kernel_parameters if p.is_control]
640
641        # Gather entries such as name[n] into groups of the same n
642        dependent = {} # type: Dict[str, List[Parameter]]
643        dependent.update((p.id, []) for p in control)
644        for p in self.kernel_parameters:
645            if p.length_control is not None:
646                dependent[p.length_control].append(p)
647
648        # Gather entries such as name[4] into groups of the same length
649        fixed_length = {}  # type: Dict[int, List[Parameter]]
650        for p in self.kernel_parameters:
651            if p.length > 1 and p.length_control is None:
652                fixed_length.setdefault(p.length, []).append(p)
653
654        # Using the call_parameters table, we already have expanded forms
655        # for each of the vector parameters; put them in a lookup table
656        # Note: p.id and p.name are currently identical for the call parameters
657        expanded_pars = dict((p.id, p) for p in self.call_parameters)
658
659        def append_group(name):
660            """add the named parameter, and related magnetic parameters if any"""
661            result.append(expanded_pars[name])
662            if is2d:
663                for tag in 'M0:', 'mtheta:', 'mphi:':
664                    if tag+name in expanded_pars:
665                        result.append(expanded_pars[tag+name])
666
667        # Gather the user parameters in order
668        result = control + self.COMMON
669        for p in self.kernel_parameters:
670            if not is2d and p.type in ('orientation', 'magnetic'):
671                pass
672            elif p.is_control:
673                pass # already added
674            elif p.length_control is not None:
675                table = dependent.get(p.length_control, [])
676                if table:
677                    # look up length from incoming parameters
678                    table_length = int(pars.get(p.length_control, p.length))
679                    del dependent[p.length_control] # first entry seen
680                    for k in range(1, table_length+1):
681                        for entry in table:
682                            append_group(entry.id+str(k))
683                else:
684                    pass # already processed all entries
685            elif p.length > 1:
686                table = fixed_length.get(p.length, [])
687                if table:
688                    table_length = p.length
689                    del fixed_length[p.length]
690                    for k in range(1, table_length+1):
691                        for entry in table:
692                            append_group(entry.id+str(k))
693                else:
694                    pass # already processed all entries
695            else:
696                append_group(p.id)
697
698        if is2d and 'up:angle' in expanded_pars:
699            result.extend([
700                expanded_pars['up:frac_i'],
701                expanded_pars['up:frac_f'],
702                expanded_pars['up:angle'],
703            ])
704
705        return result
706
707def isstr(x):
708    # type: (Any) -> bool
709    """
710    Return True if the object is a string.
711    """
712    # TODO: 2-3 compatible tests for str, including unicode strings
713    return isinstance(x, str)
714
715
716#: Set of variables defined in the model that might contain C code
717C_SYMBOLS = ['Imagnetic', 'Iq', 'Iqxy', 'Iqac', 'Iqabc', 'form_volume', 'c_code']
718
719def _find_source_lines(model_info, kernel_module):
720    # type: (ModelInfo, ModuleType) -> None
721    """
722    Identify the location of the C source inside the model definition file.
723
724    This code runs through the source of the kernel module looking for lines
725    that contain C code (because it is a c function definition).  Clearly
726    there are all sorts of reasons why this might not work (e.g., code
727    commented out in a triple-quoted line block, code built using string
728    concatenation, code defined in the branch of an 'if' block, code imported
729    from another file), but it should work properly in the 95% case, and for
730    the remainder, getting the incorrect line number will merely be
731    inconvenient.
732    """
733    # Only need line numbers if we are creating a C module and the C symbols
734    # are defined.
735    if (callable(model_info.Iq)
736            or not any(hasattr(model_info, s) for s in C_SYMBOLS)):
737        return
738
739    # load the module source if we can
740    try:
741        source = inspect.getsource(kernel_module)
742    except IOError:
743        return
744
745    # look for symbol at the start of the line
746    for lineno, line in enumerate(source.split('\n')):
747        for name in C_SYMBOLS:
748            if line.startswith(name):
749                # Add 1 since some compilers complain about "#line 0"
750                model_info.lineno[name] = lineno + 1
751                break
752
753def make_model_info(kernel_module):
754    # type: (module) -> ModelInfo
755    """
756    Extract the model definition from the loaded kernel module.
757
758    Fill in default values for parts of the module that are not provided.
759
760    Note: vectorized Iq and Iqac/Iqabc functions will be created for python
761    models when the model is first called, not when the model is loaded.
762    """
763    if hasattr(kernel_module, "model_info"):
764        # Custom sum/multi models
765        return kernel_module.model_info
766
767    info = ModelInfo()
768    #print("make parameter table", kernel_module.parameters)
769    parameters = make_parameter_table(getattr(kernel_module, 'parameters', []))
770    demo = expand_pars(parameters, getattr(kernel_module, 'demo', None))
771    filename = abspath(kernel_module.__file__).replace('.pyc', '.py')
772    kernel_id = splitext(basename(filename))[0]
773    name = getattr(kernel_module, 'name', None)
774    if name is None:
775        name = " ".join(w.capitalize() for w in kernel_id.split('_'))
776
777    info.id = kernel_id  # string used to load the kernel
778    info.filename = filename
779    info.name = name
780    info.title = getattr(kernel_module, 'title', name+" model")
781    info.description = getattr(kernel_module, 'description', 'no description')
782    info.parameters = parameters
783    info.demo = demo
784    info.composition = None
785    info.docs = kernel_module.__doc__
786    info.category = getattr(kernel_module, 'category', None)
787    info.structure_factor = getattr(kernel_module, 'structure_factor', False)
788    info.profile_axes = getattr(kernel_module, 'profile_axes', ['x', 'y'])
789    info.source = getattr(kernel_module, 'source', [])
790    info.c_code = getattr(kernel_module, 'c_code', None)
791    # TODO: check the structure of the tests
792    info.tests = getattr(kernel_module, 'tests', [])
793    info.ER = getattr(kernel_module, 'ER', None) # type: ignore
794    info.VR = getattr(kernel_module, 'VR', None) # type: ignore
795    info.form_volume = getattr(kernel_module, 'form_volume', None) # type: ignore
796    info.Iq = getattr(kernel_module, 'Iq', None) # type: ignore
797    info.Iqxy = getattr(kernel_module, 'Iqxy', None) # type: ignore
798    info.Iqac = getattr(kernel_module, 'Iqac', None) # type: ignore
799    info.Iqabc = getattr(kernel_module, 'Iqabc', None) # type: ignore
800    info.Imagnetic = getattr(kernel_module, 'Imagnetic', None) # type: ignore
801    info.profile = getattr(kernel_module, 'profile', None) # type: ignore
802    info.sesans = getattr(kernel_module, 'sesans', None) # type: ignore
803    # Default single and opencl to True for C models.  Python models have callable Iq.
804    info.opencl = getattr(kernel_module, 'opencl', not callable(info.Iq))
805    info.single = getattr(kernel_module, 'single', not callable(info.Iq))
806    info.random = getattr(kernel_module, 'random', None)
807
808    # multiplicity info
809    control_pars = [p.id for p in parameters.kernel_parameters if p.is_control]
810    default_control = control_pars[0] if control_pars else None
811    info.control = getattr(kernel_module, 'control', default_control)
812    info.hidden = getattr(kernel_module, 'hidden', None) # type: ignore
813
814    if callable(info.Iq) and parameters.has_2d:
815        raise ValueError("oriented python models not supported")
816
817    info.lineno = {}
818    _find_source_lines(info, kernel_module)
819    return info
820
821class ModelInfo(object):
822    """
823    Interpret the model definition file, categorizing the parameters.
824
825    The module can be loaded with a normal python import statement if you
826    know which module you need, or with __import__('sasmodels.model.'+name)
827    if the name is in a string.
828
829    The structure should be mostly static, other than the delayed definition
830    of *Iq*, *Iqac* and *Iqabc* if they need to be defined.
831    """
832    #: Full path to the file defining the kernel, if any.
833    filename = None         # type: Optional[str]
834    #: Id of the kernel used to load it from the filesystem.
835    id = None               # type: str
836    #: Display name of the model, which defaults to the model id but with
837    #: capitalization of the parts so for example core_shell defaults to
838    #: "Core Shell".
839    name = None             # type: str
840    #: Short description of the model.
841    title = None            # type: str
842    #: Long description of the model.
843    description = None      # type: str
844    #: Model parameter table. Parameters are defined using a list of parameter
845    #: definitions, each of which is contains parameter name, units,
846    #: default value, limits, type and description.  See :class:`Parameter`
847    #: for details on the individual parameters.  The parameters are gathered
848    #: into a :class:`ParameterTable`, which provides various views into the
849    #: parameter list.
850    parameters = None       # type: ParameterTable
851    #: Demo parameters as a *parameter:value* map used as the default values
852    #: for :mod:`compare`.  Any parameters not set in *demo* will use the
853    #: defaults from the parameter table.  That means no polydispersity, and
854    #: in the case of multiplicity models, a minimal model with no interesting
855    #: scattering.
856    demo = None             # type: Dict[str, float]
857    #: Composition is None if this is an independent model, or it is a
858    #: tuple with comoposition type ('product' or 'misture') and a list of
859    #: :class:`ModelInfo` blocks for the composed objects.  This allows us
860    #: to rebuild a complete mixture or product model from the info block.
861    #: *composition* is not given in the model definition file, but instead
862    #: arises when the model is constructed using names such as
863    #: *sphere*hardsphere* or *cylinder+sphere*.
864    composition = None      # type: Optional[Tuple[str, List[ModelInfo]]]
865    #: Name of the control parameter for a variant model such as :ref:`rpa`.
866    #: The *control* parameter should appear in the parameter table, with
867    #: limits defined as *[CASES]*, for case names such as
868    #: *CASES = ["diblock copolymer", "triblock copolymer", ...]*.
869    #: This should give *limits=[[case1, case2, ...]]*, but the
870    #: model loader translates this to *limits=[0, len(CASES)-1]*, and adds
871    #: *choices=CASES* to the :class:`Parameter` definition. Note that
872    #: models can use a list of cases as a parameter without it being a
873    #: control parameter.  Either way, the parameter is sent to the model
874    #: evaluator as *float(choice_num)*, where choices are numbered from 0.
875    #: See also :attr:`hidden`.
876    control = None          # type: str
877    #: Different variants require different parameters.  In order to show
878    #: just the parameters needed for the variant selected by :attr:`control`,
879    #: you should provide a function *hidden(control) -> set(['a', 'b', ...])*
880    #: indicating which parameters need to be hidden.  For multiplicity
881    #: models, you need to use the complete name of the parameter, including
882    #: its number.  So for example, if variant "a" uses only *sld1* and *sld2*,
883    #: then *sld3*, *sld4* and *sld5* of multiplicity parameter *sld[5]*
884    #: should be in the hidden set.
885    hidden = None           # type: Optional[Callable[[int], Set[str]]]
886    #: Doc string from the top of the model file.  This should be formatted
887    #: using ReStructuredText format, with latex markup in ".. math"
888    #: environments, or in dollar signs.  This will be automatically
889    #: extracted to a .rst file by :func:`generate.make_docs`, then
890    #: converted to HTML or PDF by Sphinx.
891    docs = None             # type: str
892    #: Location of the model description in the documentation.  This takes the
893    #: form of "section" or "section:subsection".  So for example,
894    #: :ref:`porod` uses *category="shape-independent"* so it is in the
895    #: :ref:`shape-independent` section whereas
896    #: :ref:`capped-cylinder` uses: *category="shape:cylinder"*, which puts
897    #: it in the :ref:`shape-cylinder` section.
898    category = None         # type: Optional[str]
899    #: True if the model can be computed accurately with single precision.
900    #: This is True by default, but models such as :ref:`bcc-paracrystal` set
901    #: it to False because they require double precision calculations.
902    single = None           # type: bool
903    #: True if the model can be run as an opencl model.  If for some reason
904    #: the model cannot be run in opencl (e.g., because the model passes
905    #: functions by reference), then set this to false.
906    opencl = None           # type: bool
907    #: True if the model is a structure factor used to model the interaction
908    #: between form factor models.  This will default to False if it is not
909    #: provided in the file.
910    structure_factor = None # type: bool
911    #: List of C source files used to define the model.  The source files
912    #: should define the *Iq* function, and possibly *Iqac* or *Iqabc* if the
913    #: model defines orientation parameters. Files containing the most basic
914    #: functions must appear first in the list, followed by the files that
915    #: use those functions.  Form factors are indicated by providing
916    #: an :attr:`ER` function.
917    source = None           # type: List[str]
918    #: The set of tests that must pass.  The format of the tests is described
919    #: in :mod:`model_test`.
920    tests = None            # type: List[TestCondition]
921    #: Returns the effective radius of the model given its volume parameters.
922    #: The presence of *ER* indicates that the model is a form factor model
923    #: that may be used together with a structure factor to form an implicit
924    #: multiplication model.
925    #:
926    #: The parameters to the *ER* function must be marked with type *volume*.
927    #: in the parameter table.  They will appear in the same order as they
928    #: do in the table.  The values passed to *ER* will be vectors, with one
929    #: value for each polydispersity condition.  For example, if the model
930    #: is polydisperse over both length and radius, then both length and
931    #: radius will have the same number of values in the vector, with one
932    #: value for each *length X radius*.  If only *radius* is polydisperse,
933    #: then the value for *length* will be repeated once for each value of
934    #: *radius*.  The *ER* function should return one effective radius for
935    #: each parameter set.  Multiplicity parameters will be received as
936    #: arrays, with one row per polydispersity condition.
937    ER = None               # type: Optional[Callable[[np.ndarray], np.ndarray]]
938    #: Returns the occupied volume and the total volume for each parameter set.
939    #: See :attr:`ER` for details on the parameters.
940    VR = None               # type: Optional[Callable[[np.ndarray], Tuple[np.ndarray, np.ndarray]]]
941    #: Arbitrary C code containing supporting functions, etc., to be inserted
942    #: after everything in source.  This can include Iq and Iqxy functions with
943    #: the full function signature, including all parameters.
944    c_code = None
945    #: Returns the form volume for python-based models.  Form volume is needed
946    #: for volume normalization in the polydispersity integral.  If no
947    #: parameters are *volume* parameters, then form volume is not needed.
948    #: For C-based models, (with :attr:`sources` defined, or with :attr:`Iq`
949    #: defined using a string containing C code), form_volume must also be
950    #: C code, either defined as a string, or in the sources.
951    form_volume = None      # type: Union[None, str, Callable[[np.ndarray], float]]
952    #: Returns *I(q, a, b, ...)* for parameters *a*, *b*, etc. defined
953    #: by the parameter table.  *Iq* can be defined as a python function, or
954    #: as a C function.  If it is defined in C, then set *Iq* to the body of
955    #: the C function, including the return statement.  This function takes
956    #: values for *q* and each of the parameters as separate *double* values
957    #: (which may be converted to float or long double by sasmodels).  All
958    #: source code files listed in :attr:`sources` will be loaded before the
959    #: *Iq* function is defined.  If *Iq* is not present, then sources should
960    #: define *static double Iq(double q, double a, double b, ...)* which
961    #: will return *I(q, a, b, ...)*.  Multiplicity parameters are sent as
962    #: pointers to doubles.  Constants in floating point expressions should
963    #: include the decimal point. See :mod:`generate` for more details.
964    Iq = None               # type: Union[None, str, Callable[[np.ndarray], np.ndarray]]
965    #: Returns *I(qab, qc, a, b, ...)*.  The interface follows :attr:`Iq`.
966    Iqac = None             # type: Union[None, str, Callable[[np.ndarray], np.ndarray]]
967    #: Returns *I(qa, qb, qc, a, b, ...)*.  The interface follows :attr:`Iq`.
968    Iqabc = None            # type: Union[None, str, Callable[[np.ndarray], np.ndarray]]
969    #: Returns *I(qx, qy, a, b, ...)*.  The interface follows :attr:`Iq`.
970    Imagnetic = None        # type: Union[None, str, Callable[[np.ndarray], np.ndarray]]
971    #: Returns a model profile curve *x, y*.  If *profile* is defined, this
972    #: curve will appear in response to the *Show* button in SasView.  Use
973    #: :attr:`profile_axes` to set the axis labels.  Note that *y* values
974    #: will be scaled by 1e6 before plotting.
975    profile = None          # type: Optional[Callable[[np.ndarray], None]]
976    #: Axis labels for the :attr:`profile` plot.  The default is *['x', 'y']*.
977    #: Only the *x* component is used for now.
978    profile_axes = None     # type: Tuple[str, str]
979    #: Returns *sesans(z, a, b, ...)* for models which can directly compute
980    #: the SESANS correlation function.  Note: not currently implemented.
981    sesans = None           # type: Optional[Callable[[np.ndarray], np.ndarray]]
982    #: Returns a random parameter set for the model
983    random = None           # type: Optional[Callable[[], Dict[str, float]]]
984    #: Line numbers for symbols defining C code
985    lineno = None           # type: Dict[str, int]
986
987    def __init__(self):
988        # type: () -> None
989        pass
990
991    def get_hidden_parameters(self, control):
992        """
993        Returns the set of hidden parameters for the model.  *control* is the
994        value of the control parameter.  Note that multiplicity models have
995        an implicit control parameter, which is the parameter that controls
996        the multiplicity.
997        """
998        if self.hidden is not None:
999            hidden = self.hidden(control)
1000        else:
1001            controls = [p for p in self.parameters.kernel_parameters
1002                        if p.is_control]
1003            if len(controls) != 1:
1004                raise ValueError("more than one control parameter")
1005            hidden = set(p.id+str(k)
1006                         for p in self.parameters.kernel_parameters
1007                         for k in range(control+1, p.length+1)
1008                         if p.length > 1)
1009        return hidden
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