source: sasmodels/sasmodels/modelinfo.py @ bd547d0

core_shell_microgelsmagnetic_modelticket-1257-vesicle-productticket_1156ticket_1265_superballticket_822_more_unit_tests
Last change on this file since bd547d0 was bd547d0, checked in by Paul Kienzle <pkienzle@…>, 13 months ago

restrict magnetic parameters to visible shells. Refs #1188

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Line 
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
47DEFAULT_BACKGROUND = 1e-3
48COMMON_PARAMETERS = [
49    ("scale", "", 1, (0.0, np.inf), "", "Source intensity"),
50    ("background", "1/cm", DEFAULT_BACKGROUND, (-np.inf, np.inf), "", "Source background"),
51]
52assert (len(COMMON_PARAMETERS) == 2
53        and COMMON_PARAMETERS[0][0] == "scale"
54        and COMMON_PARAMETERS[1][0] == "background"), "don't change common parameters"
55
56
57def make_parameter_table(pars):
58    # type: (List[ParameterDef]) -> ParameterTable
59    """
60    Construct a parameter table from a list of parameter definitions.
61
62    This is used by the module processor to convert the parameter block into
63    the parameter table seen in the :class:`ModelInfo` for the module.
64    """
65    processed = []
66    for p in pars:
67        if not isinstance(p, (list, tuple)) or len(p) != 6:
68            raise ValueError("Parameter should be [name, units, default, limits, type, desc], but got %r"
69                             %str(p))
70        processed.append(parse_parameter(*p))
71    partable = ParameterTable(processed)
72    partable.check_angles()
73    return partable
74
75def parse_parameter(name, units='', default=np.NaN,
76                    user_limits=None, ptype='', description=''):
77    # type: (str, str, float, Sequence[Any], str, str) -> Parameter
78    """
79    Parse an individual parameter from the parameter definition block.
80
81    This does type and value checking on the definition, leading
82    to early failure in the model loading process and easier debugging.
83    """
84    # Parameter is a user facing class.  Do robust type checking.
85    if not isstr(name):
86        raise ValueError("expected string for parameter name %r"%name)
87    if not isstr(units):
88        raise ValueError("expected units to be a string for %s"%name)
89
90    # Process limits as [float, float] or [[str, str, ...]]
91    choices = []  # type: List[str]
92    if user_limits is None:
93        limits = (-np.inf, np.inf)
94    elif not isinstance(user_limits, (tuple, list)):
95        raise ValueError("invalid limits for %s"%name)
96    else:
97        # if limits is [[str,...]], then this is a choice list field,
98        # and limits are 1 to length of string list
99        if isinstance(user_limits[0], (tuple, list)):
100            choices = user_limits[0]
101            limits = (0., len(choices)-1.)
102            if not all(isstr(k) for k in choices):
103                raise ValueError("choices must be strings for %s"%name)
104        else:
105            try:
106                low, high = user_limits
107                limits = (float(low), float(high))
108            except Exception:
109                raise ValueError("invalid limits for %s: %r"%(name, user_limits))
110            if low >= high:
111                raise ValueError("require lower limit < upper limit")
112
113    # Process default value as float, making sure it is in range
114    if not isinstance(default, (int, float)):
115        raise ValueError("expected default %r to be a number for %s"
116                         % (default, name))
117    if default < limits[0] or default > limits[1]:
118        raise ValueError("default value %r not in range for %s"
119                         % (default, name))
120
121    # Check for valid parameter type
122    if ptype not in ("volume", "orientation", "sld", "magnetic", ""):
123        raise ValueError("unexpected type %r for %s" % (ptype, name))
124
125    # Check for valid parameter description
126    if not isstr(description):
127        raise ValueError("expected description to be a string")
128
129    # Parameter id for name[n] does not include [n]
130    if "[" in name:
131        if not name.endswith(']'):
132            raise ValueError("Expected name[len] for vector parameter %s"%name)
133        pid, ref = name[:-1].split('[', 1)
134        ref = ref.strip()
135    else:
136        pid, ref = name, None
137
138    # automatically identify sld types
139    if ptype == '' and (pid.startswith('sld') or pid.endswith('sld')):
140        ptype = 'sld'
141
142    # Check if using a vector definition, name[k], as the parameter name
143    if ref:
144        if ref == '':
145            raise ValueError("Need to specify vector length for %s"%name)
146        try:
147            length = int(ref)
148            control = None
149        except ValueError:
150            length = None
151            control = ref
152    else:
153        length = 1
154        control = None
155
156    # Build the parameter
157    parameter = Parameter(name=name, units=units, default=default,
158                          limits=limits, ptype=ptype, description=description)
159
160    # TODO: need better control over whether a parameter is polydisperse
161    parameter.polydisperse = ptype in ('orientation', 'volume')
162    parameter.relative_pd = ptype == 'volume'
163    parameter.choices = choices
164    parameter.length = length
165    parameter.length_control = control
166
167    return parameter
168
169
170def expand_pars(partable, pars):
171    # type: (ParameterTable, ParameterSetUser) ->  ParameterSet
172    """
173    Create demo parameter set from key-value pairs.
174
175    *pars* are the key-value pairs to use for the parameters.  Any
176    parameters not specified in *pars* are set from the *partable* defaults.
177
178    If *pars* references vector fields, such as thickness[n], then support
179    different ways of assigning the demo values, including assigning a
180    specific value (e.g., thickness3=50.0), assigning a new value to all
181    (e.g., thickness=50.0) or assigning values using list notation.
182    """
183    if pars is None:
184        result = partable.defaults
185    else:
186        lookup = dict((p.id, p) for p in partable.kernel_parameters)
187        result = partable.defaults.copy()
188        scalars = dict((name, value) for name, value in pars.items()
189                       if name not in lookup or lookup[name].length == 1)
190        vectors = dict((name, value) for name, value in pars.items()
191                       if name in lookup and lookup[name].length > 1)
192        #print("lookup", lookup)
193        #print("scalars", scalars)
194        #print("vectors", vectors)
195        if vectors:
196            for name, value in vectors.items():
197                if np.isscalar(value):
198                    # support for the form
199                    #    dict(thickness=0, thickness2=50)
200                    for k in range(1, lookup[name].length+1):
201                        key = name+str(k)
202                        if key not in scalars:
203                            scalars[key] = value
204                else:
205                    # supoprt for the form
206                    #    dict(thickness=[20,10,3])
207                    for (k, v) in enumerate(value):
208                        scalars[name+str(k+1)] = v
209        result.update(scalars)
210        #print("expanded", result)
211
212    return result
213
214def prefix_parameter(par, prefix):
215    # type: (Parameter, str) -> Parameter
216    """
217    Return a copy of the parameter with its name prefixed.
218    """
219    new_par = copy(par)
220    new_par.name = prefix + par.name
221    new_par.id = prefix + par.id
222
223def suffix_parameter(par, suffix):
224    # type: (Parameter, str) -> Parameter
225    """
226    Return a copy of the parameter with its name prefixed.
227    """
228    new_par = copy(par)
229    # If name has the form x[n], replace with x_suffix[n]
230    new_par.name = par.id + suffix + par.name[len(par.id):]
231    new_par.id = par.id + suffix
232
233class Parameter(object):
234    """
235    The available kernel parameters are defined as a list, with each parameter
236    defined as a sublist with the following elements:
237
238    *name* is the name that will be displayed to the user.  Names
239    should be lower case, with words separated by underscore.  If
240    acronyms are used, the whole acronym should be upper case. For vector
241    parameters, the name will be followed by *[len]* where *len* is an
242    integer length of the vector, or the name of the parameter which
243    controls the length.  The attribute *id* will be created from name
244    without the length.
245
246    *units* should be one of *degrees* for angles, *Ang* for lengths,
247    *1e-6/Ang^2* for SLDs.
248
249    *default value* will be the initial value for  the model when it
250    is selected, or when an initial value is not otherwise specified.
251
252    *limits = [lb, ub]* are the hard limits on the parameter value, used to
253    limit the polydispersity density function.  In the fit, the parameter limits
254    given to the fit are the limits  on the central value of the parameter.
255    If there is polydispersity, it will evaluate parameter values outside
256    the fit limits, but not outside the hard limits specified in the model.
257    If there are no limits, use +/-inf imported from numpy.
258
259    *type* indicates how the parameter will be used.  "volume" parameters
260    will be used in all functions.  "orientation" parameters are not passed,
261    but will be used to convert from *qx*, *qy* to *qa*, *qb*, *qc* in calls to
262    *Iqxy* and *Imagnetic*.  If *type* is the empty string, the parameter will
263    be used in all of *Iq*, *Iqxy* and *Imagnetic*.  "sld" parameters
264    can automatically be promoted to magnetic parameters, each of which
265    will have a magnitude and a direction, which may be different from
266    other sld parameters. The volume parameters are used for calls
267    to form_volume within the kernel (required for volume normalization)
268    and for calls to ER and VR for effective radius and volume ratio
269    respectively.
270
271    *description* is a short description of the parameter.  This will
272    be displayed in the parameter table and used as a tool tip for the
273    parameter value in the user interface.
274
275    Additional values can be set after the parameter is created:
276
277    * *length* is the length of the field if it is a vector field
278
279    * *length_control* is the parameter which sets the vector length
280
281    * *is_control* is True if the parameter is a control parameter for a vector
282
283    * *polydisperse* is true if the parameter accepts a polydispersity
284
285    * *relative_pd* is true if that polydispersity is a portion of the
286      value (so a 10% length dipsersity would use a polydispersity value
287      of 0.1) rather than absolute dispersisity (such as an angle plus or
288      minus 15 degrees).
289
290    *choices* is the option names for a drop down list of options, as for
291    example, might be used to set the value of a shape parameter.
292
293    These values are set by :func:`make_parameter_table` and
294    :func:`parse_parameter` therein.
295    """
296    def __init__(self, name, units='', default=None, limits=(-np.inf, np.inf),
297                 ptype='', description=''):
298        # type: (str, str, float, Limits, str, str) -> None
299        self.id = name.split('[')[0].strip() # type: str
300        self.name = name                     # type: str
301        self.units = units                   # type: str
302        self.default = default               # type: float
303        self.limits = limits                 # type: Limits
304        self.type = ptype                    # type: str
305        self.description = description       # type: str
306
307        # Length and length_control will be filled in once the complete
308        # parameter table is available.
309        self.length = 1                      # type: int
310        self.length_control = None           # type: Optional[str]
311        self.is_control = False              # type: bool
312
313        # TODO: need better control over whether a parameter is polydisperse
314        self.polydisperse = False            # type: bool
315        self.relative_pd = False             # type: bool
316
317        # choices are also set externally.
318        self.choices = []                    # type: List[str]
319
320    def as_definition(self):
321        # type: () -> str
322        """
323        Declare space for the variable in a parameter structure.
324
325        For example, the parameter thickness with length 3 will
326        return "double thickness[3];", with no spaces before and
327        no new line character afterward.
328        """
329        if self.length == 1:
330            return "double %s;"%self.id
331        else:
332            return "double %s[%d];"%(self.id, self.length)
333
334    def as_function_argument(self):
335        # type: () -> str
336        r"""
337        Declare the variable as a function argument.
338
339        For example, the parameter thickness with length 3 will
340        return "double \*thickness", with no spaces before and
341        no comma afterward.
342        """
343        if self.length == 1:
344            return "double %s"%self.id
345        else:
346            return "double *%s"%self.id
347
348    def as_call_reference(self, prefix=""):
349        # type: (str) -> str
350        """
351        Return *prefix* + parameter name.  For struct references, use "v."
352        as the prefix.
353        """
354        # Note: if the parameter is a struct type, then we will need to use
355        # &prefix+id.  For scalars and vectors we can just use prefix+id.
356        return prefix + self.id
357
358    def __str__(self):
359        # type: () -> str
360        return "<%s>"%self.name
361
362    def __repr__(self):
363        # type: () -> str
364        return "P<%s>"%self.name
365
366
367class ParameterTable(object):
368    """
369    ParameterTable manages the list of available parameters.
370
371    There are a couple of complications which mean that the list of parameters
372    for the kernel differs from the list of parameters that the user sees.
373
374    (1) Common parameters.  Scale and background are implicit to every model,
375    but are not passed to the kernel.
376
377    (2) Vector parameters.  Vector parameters are passed to the kernel as a
378    pointer to an array, e.g., thick[], but they are seen by the user as n
379    separate parameters thick1, thick2, ...
380
381    Therefore, the parameter table is organized by how it is expected to be
382    used. The following information is needed to set up the kernel functions:
383
384    * *kernel_parameters* is the list of parameters in the kernel parameter
385      table, with vector parameter p declared as p[].
386
387    * *iq_parameters* is the list of parameters to the Iq(q, ...) function,
388      with vector parameter p sent as p[].
389
390    * *form_volume_parameters* is the list of parameters to the form_volume(...)
391      function, with vector parameter p sent as p[].
392
393    Problem details, which sets up the polydispersity loops, requires the
394    following:
395
396    * *theta_offset* is the offset of the theta parameter in the kernel parameter
397      table, with vector parameters counted as n individual parameters
398      p1, p2, ..., or offset is -1 if there is no theta parameter.
399
400    * *max_pd* is the maximum number of polydisperse parameters, with vector
401      parameters counted as n individual parameters p1, p2, ...  Note that
402      this number is limited to sasmodels.modelinfo.MAX_PD.
403
404    * *npars* is the total number of parameters to the kernel, with vector
405      parameters counted as n individual parameters p1, p2, ...
406
407    * *call_parameters* is the complete list of parameters to the kernel,
408      including scale and background, with vector parameters recorded as
409      individual parameters p1, p2, ...
410
411    * *active_1d* is the set of names that may be polydisperse for 1d data
412
413    * *active_2d* is the set of names that may be polydisperse for 2d data
414
415    User parameters are the set of parameters visible to the user, including
416    the scale and background parameters that the kernel does not see.  User
417    parameters don't use vector notation, and instead use p1, p2, ...
418    """
419    # scale and background are implicit parameters
420    COMMON = [Parameter(*p) for p in COMMON_PARAMETERS]
421
422    def __init__(self, parameters):
423        # type: (List[Parameter]) -> None
424        self.kernel_parameters = parameters
425        self._set_vector_lengths()
426
427        self.npars = sum(p.length for p in self.kernel_parameters)
428        self.nmagnetic = sum(p.length for p in self.kernel_parameters
429                             if p.type == 'sld')
430        self.nvalues = 2 + self.npars
431        if self.nmagnetic:
432            self.nvalues += 3 + 3*self.nmagnetic
433
434        self.call_parameters = self._get_call_parameters()
435        self.defaults = self._get_defaults()
436        #self._name_table= dict((p.id, p) for p in parameters)
437
438        # Set the kernel parameters.  Assumes background and scale are the
439        # first two parameters in the parameter list, but these are not sent
440        # to the underlying kernel functions.
441        self.iq_parameters = [p for p in self.kernel_parameters
442                              if p.type not in ('orientation', 'magnetic')]
443        self.orientation_parameters = [p for p in self.kernel_parameters
444                                       if p.type == 'orientation']
445        self.form_volume_parameters = [p for p in self.kernel_parameters
446                                       if p.type == 'volume']
447
448        # Theta offset
449        offset = 0
450        for p in self.kernel_parameters:
451            if p.name == 'theta':
452                self.theta_offset = offset
453                break
454            offset += p.length
455        else:
456            self.theta_offset = -1
457
458        # number of polydisperse parameters
459        num_pd = sum(p.length for p in self.kernel_parameters if p.polydisperse)
460        # Don't use more polydisperse parameters than are available in the model
461        self.max_pd = min(num_pd, MAX_PD)
462
463        # true if has 2D parameters
464        self.has_2d = any(p.type in ('orientation', 'magnetic')
465                          for p in self.kernel_parameters)
466        self.is_asymmetric = any(p.name == 'psi' for p in self.kernel_parameters)
467        self.magnetism_index = [k for k, p in enumerate(self.call_parameters)
468                                if p.id.endswith('_M0')]
469
470        self.pd_1d = set(p.name for p in self.call_parameters
471                         if p.polydisperse and p.type not in ('orientation', 'magnetic'))
472        self.pd_2d = set(p.name for p in self.call_parameters if p.polydisperse)
473
474    def check_angles(self):
475        """
476        Check that orientation angles are theta, phi and possibly psi.
477        """
478        theta = phi = psi = -1
479        for k, p in enumerate(self.kernel_parameters):
480            if p.name == 'theta':
481                theta = k
482                if p.type != 'orientation':
483                    raise TypeError("theta must be an orientation parameter")
484            elif p.name == 'phi':
485                phi = k
486                if p.type != 'orientation':
487                    raise TypeError("phi must be an orientation parameter")
488            elif p.name == 'psi':
489                psi = k
490                if p.type != 'orientation':
491                    raise TypeError("psi must be an orientation parameter")
492            elif p.type == 'orientation':
493                raise TypeError("only theta, phi and psi can be orientation parameters")
494        if theta >= 0 and phi >= 0:
495            last_par = len(self.kernel_parameters) - 1
496            if phi != theta+1:
497                raise TypeError("phi must follow theta")
498            if psi >= 0 and psi != phi+1:
499                raise TypeError("psi must follow phi")
500            if (psi >= 0 and psi != last_par) or (psi < 0 and phi != last_par):
501                raise TypeError("orientation parameters must appear at the "
502                                "end of the parameter table")
503        elif theta >= 0 or phi >= 0 or psi >= 0:
504            raise TypeError("oriented shapes must have both theta and phi and maybe psi")
505
506    def __getitem__(self, key):
507        # Find the parameter definition
508        for par in self.call_parameters:
509            if par.name == key:
510                return par
511        raise KeyError("unknown parameter %r"%key)
512
513    def __contains__(self, key):
514        for par in self.call_parameters:
515            if par.name == key:
516                return True
517        return False
518
519    def _set_vector_lengths(self):
520        # type: () -> List[str]
521        """
522        Walk the list of kernel parameters, setting the length field of the
523        vector parameters from the upper limit of the reference parameter.
524
525        This needs to be done once the entire parameter table is available
526        since the reference may still be undefined when the parameter is
527        initially created.
528
529        Returns the list of control parameter names.
530
531        Note: This modifies the underlying parameter object.
532        """
533        # Sort out the length of the vector parameters such as thickness[n]
534        for p in self.kernel_parameters:
535            if p.length_control:
536                ref = self._get_ref(p)
537                ref.is_control = True
538                ref.polydisperse = False
539                low, high = ref.limits
540                if int(low) != low or int(high) != high or low < 0 or high > 20:
541                    raise ValueError("expected limits on %s to be within [0, 20]"
542                                     % ref.name)
543                p.length = int(high)
544
545    def _get_ref(self, p):
546        # type: (Parameter) -> Parameter
547        for ref in self.kernel_parameters:
548            if ref.id == p.length_control:
549                return ref
550        raise ValueError("no reference variable %r for %s"
551                         % (p.length_control, p.name))
552
553    def _get_defaults(self):
554        # type: () -> ParameterSet
555        """
556        Get a list of parameter defaults from the parameters.
557
558        Expands vector parameters into parameter id+number.
559        """
560        # Construct default values, including vector defaults
561        defaults = {}
562        for p in self.call_parameters:
563            if p.length == 1:
564                defaults[p.id] = p.default
565            else:
566                for k in range(1, p.length+1):
567                    defaults["%s%d"%(p.id, k)] = p.default
568        return defaults
569
570    def _get_call_parameters(self):
571        # type: () -> List[Parameter]
572        full_list = self.COMMON[:]
573        for p in self.kernel_parameters:
574            if p.length == 1:
575                full_list.append(p)
576            else:
577                for k in range(1, p.length+1):
578                    pk = Parameter(p.id+str(k), p.units, p.default,
579                                   p.limits, p.type, p.description)
580                    pk.polydisperse = p.polydisperse
581                    pk.relative_pd = p.relative_pd
582                    pk.choices = p.choices
583                    full_list.append(pk)
584
585        # Add the magnetic parameters to the end of the call parameter list.
586        if self.nmagnetic > 0:
587            full_list.extend([
588                Parameter('up_frac_i', '', 0., [0., 1.],
589                          'magnetic', 'fraction of spin up incident'),
590                Parameter('up_frac_f', '', 0., [0., 1.],
591                          'magnetic', 'fraction of spin up final'),
592                Parameter('up_angle', 'degrees', 0., [0., 360.],
593                          'magnetic', 'spin up angle'),
594            ])
595            slds = [p for p in full_list if p.type == 'sld']
596            for p in slds:
597                full_list.extend([
598                    Parameter(p.id+'_M0', '1e-6/Ang^2', 0., [-np.inf, np.inf],
599                              'magnetic', 'magnetic amplitude for '+p.description),
600                    Parameter(p.id+'_mtheta', 'degrees', 0., [-90., 90.],
601                              'magnetic', 'magnetic latitude for '+p.description),
602                    Parameter(p.id+'_mphi', 'degrees', 0., [-180., 180.],
603                              'magnetic', 'magnetic longitude for '+p.description),
604                ])
605        #print("call parameters", full_list)
606        return full_list
607
608    def user_parameters(self, pars, is2d=True):
609        # type: (Dict[str, float], bool) -> List[Parameter]
610        """
611        Return the list of parameters for the given data type.
612
613        Vector parameters are expanded in place.  If multiple parameters
614        share the same vector length, then the parameters will be interleaved
615        in the result.  The control parameters come first.  For example,
616        if the parameter table is ordered as::
617
618            sld_core
619            sld_shell[num_shells]
620            sld_solvent
621            thickness[num_shells]
622            num_shells
623
624        and *pars[num_shells]=2* then the returned list will be::
625
626            num_shells
627            scale
628            background
629            sld_core
630            sld_shell1
631            thickness1
632            sld_shell2
633            thickness2
634            sld_solvent
635
636        Note that shell/thickness pairs are grouped together in the result
637        even though they were not grouped in the incoming table.  The control
638        parameter is always returned first since the GUI will want to set it
639        early, and rerender the table when it is changed.
640
641        Parameters marked as sld will automatically have a set of associated
642        magnetic parameters (p_M0, p_mtheta, p_mphi), as well as polarization
643        information (up_theta, up_frac_i, up_frac_f).
644        """
645        # control parameters go first
646        control = [p for p in self.kernel_parameters if p.is_control]
647
648        # Gather entries such as name[n] into groups of the same n
649        dependent = {} # type: Dict[str, List[Parameter]]
650        dependent.update((p.id, []) for p in control)
651        for p in self.kernel_parameters:
652            if p.length_control is not None:
653                dependent[p.length_control].append(p)
654
655        # Gather entries such as name[4] into groups of the same length
656        fixed_length = {}  # type: Dict[int, List[Parameter]]
657        for p in self.kernel_parameters:
658            if p.length > 1 and p.length_control is None:
659                fixed_length.setdefault(p.length, []).append(p)
660
661        # Using the call_parameters table, we already have expanded forms
662        # for each of the vector parameters; put them in a lookup table
663        # Note: p.id and p.name are currently identical for the call parameters
664        expanded_pars = dict((p.id, p) for p in self.call_parameters)
665
666        def append_group(name):
667            """add the named parameter, and related magnetic parameters if any"""
668            result.append(expanded_pars[name])
669            if is2d:
670                for tag in '_M0', '_mtheta', '_mphi':
671                    if name+tag in expanded_pars:
672                        result.append(expanded_pars[name+tag])
673
674        # Gather the user parameters in order
675        result = control + self.COMMON
676        for p in self.kernel_parameters:
677            if not is2d and p.type in ('orientation', 'magnetic'):
678                pass
679            elif p.is_control:
680                pass # already added
681            elif p.length_control is not None:
682                table = dependent.get(p.length_control, [])
683                if table:
684                    # look up length from incoming parameters
685                    table_length = int(pars.get(p.length_control, p.length))
686                    del dependent[p.length_control] # first entry seen
687                    for k in range(1, table_length+1):
688                        for entry in table:
689                            append_group(entry.id+str(k))
690                else:
691                    pass # already processed all entries
692            elif p.length > 1:
693                table = fixed_length.get(p.length, [])
694                if table:
695                    table_length = p.length
696                    del fixed_length[p.length]
697                    for k in range(1, table_length+1):
698                        for entry in table:
699                            append_group(entry.id+str(k))
700                else:
701                    pass # already processed all entries
702            else:
703                append_group(p.id)
704
705        if is2d and 'up_angle' in expanded_pars:
706            result.extend([
707                expanded_pars['up_frac_i'],
708                expanded_pars['up_frac_f'],
709                expanded_pars['up_angle'],
710            ])
711
712        return result
713
714def isstr(x):
715    # type: (Any) -> bool
716    """
717    Return True if the object is a string.
718    """
719    # TODO: 2-3 compatible tests for str, including unicode strings
720    return isinstance(x, str)
721
722
723#: Set of variables defined in the model that might contain C code
724C_SYMBOLS = ['Imagnetic', 'Iq', 'Iqxy', 'Iqac', 'Iqabc', 'form_volume', 'c_code']
725
726def _find_source_lines(model_info, kernel_module):
727    # type: (ModelInfo, ModuleType) -> None
728    """
729    Identify the location of the C source inside the model definition file.
730
731    This code runs through the source of the kernel module looking for lines
732    that contain C code (because it is a c function definition).  Clearly
733    there are all sorts of reasons why this might not work (e.g., code
734    commented out in a triple-quoted line block, code built using string
735    concatenation, code defined in the branch of an 'if' block, code imported
736    from another file), but it should work properly in the 95% case, and for
737    the remainder, getting the incorrect line number will merely be
738    inconvenient.
739    """
740    # Only need line numbers if we are creating a C module and the C symbols
741    # are defined.
742    if (callable(model_info.Iq)
743            or not any(hasattr(model_info, s) for s in C_SYMBOLS)):
744        return
745
746    # load the module source if we can
747    try:
748        source = inspect.getsource(kernel_module)
749    except IOError:
750        return
751
752    # look for symbol at the start of the line
753    for lineno, line in enumerate(source.split('\n')):
754        for name in C_SYMBOLS:
755            if line.startswith(name):
756                # Add 1 since some compilers complain about "#line 0"
757                model_info.lineno[name] = lineno + 1
758                break
759
760def make_model_info(kernel_module):
761    # type: (module) -> ModelInfo
762    """
763    Extract the model definition from the loaded kernel module.
764
765    Fill in default values for parts of the module that are not provided.
766
767    Note: vectorized Iq and Iqac/Iqabc functions will be created for python
768    models when the model is first called, not when the model is loaded.
769    """
770    if hasattr(kernel_module, "model_info"):
771        # Custom sum/multi models
772        return kernel_module.model_info
773    info = ModelInfo()
774    #print("make parameter table", kernel_module.parameters)
775    parameters = make_parameter_table(getattr(kernel_module, 'parameters', []))
776    demo = expand_pars(parameters, getattr(kernel_module, 'demo', None))
777    filename = abspath(kernel_module.__file__).replace('.pyc', '.py')
778    kernel_id = splitext(basename(filename))[0]
779    name = getattr(kernel_module, 'name', None)
780    if name is None:
781        name = " ".join(w.capitalize() for w in kernel_id.split('_'))
782
783    info.id = kernel_id  # string used to load the kernel
784    info.filename = filename
785    info.name = name
786    info.title = getattr(kernel_module, 'title', name+" model")
787    info.description = getattr(kernel_module, 'description', 'no description')
788    info.parameters = parameters
789    info.demo = demo
790    info.composition = None
791    info.docs = kernel_module.__doc__
792    info.category = getattr(kernel_module, 'category', None)
793    info.structure_factor = getattr(kernel_module, 'structure_factor', False)
794    info.profile_axes = getattr(kernel_module, 'profile_axes', ['x', 'y'])
795    # Note: custom.load_custom_kernel_module assumes the C sources are defined
796    # by this attribute.
797    info.source = getattr(kernel_module, 'source', [])
798    info.c_code = getattr(kernel_module, 'c_code', None)
799    # TODO: check the structure of the tests
800    info.tests = getattr(kernel_module, 'tests', [])
801    info.ER = getattr(kernel_module, 'ER', None) # type: ignore
802    info.VR = getattr(kernel_module, 'VR', None) # type: ignore
803    info.form_volume = getattr(kernel_module, 'form_volume', None) # type: ignore
804    info.Iq = getattr(kernel_module, 'Iq', None) # type: ignore
805    info.Iqxy = getattr(kernel_module, 'Iqxy', None) # type: ignore
806    info.Iqac = getattr(kernel_module, 'Iqac', None) # type: ignore
807    info.Iqabc = getattr(kernel_module, 'Iqabc', None) # type: ignore
808    info.Imagnetic = getattr(kernel_module, 'Imagnetic', None) # type: ignore
809    info.profile = getattr(kernel_module, 'profile', None) # type: ignore
810    info.sesans = getattr(kernel_module, 'sesans', None) # type: ignore
811    # Default single and opencl to True for C models.  Python models have callable Iq.
812    info.opencl = getattr(kernel_module, 'opencl', not callable(info.Iq))
813    info.single = getattr(kernel_module, 'single', not callable(info.Iq))
814    info.random = getattr(kernel_module, 'random', None)
815
816    # multiplicity info
817    control_pars = [p.id for p in parameters.kernel_parameters if p.is_control]
818    default_control = control_pars[0] if control_pars else None
819    info.control = getattr(kernel_module, 'control', default_control)
820    info.hidden = getattr(kernel_module, 'hidden', None) # type: ignore
821
822    if callable(info.Iq) and parameters.has_2d:
823        raise ValueError("oriented python models not supported")
824
825    info.lineno = {}
826    _find_source_lines(info, kernel_module)
827
828    return info
829
830class ModelInfo(object):
831    """
832    Interpret the model definition file, categorizing the parameters.
833
834    The module can be loaded with a normal python import statement if you
835    know which module you need, or with __import__('sasmodels.model.'+name)
836    if the name is in a string.
837
838    The structure should be mostly static, other than the delayed definition
839    of *Iq*, *Iqac* and *Iqabc* if they need to be defined.
840    """
841    #: Full path to the file defining the kernel, if any.
842    filename = None         # type: Optional[str]
843    #: Id of the kernel used to load it from the filesystem.
844    id = None               # type: str
845    #: Display name of the model, which defaults to the model id but with
846    #: capitalization of the parts so for example core_shell defaults to
847    #: "Core Shell".
848    name = None             # type: str
849    #: Short description of the model.
850    title = None            # type: str
851    #: Long description of the model.
852    description = None      # type: str
853    #: Model parameter table. Parameters are defined using a list of parameter
854    #: definitions, each of which is contains parameter name, units,
855    #: default value, limits, type and description.  See :class:`Parameter`
856    #: for details on the individual parameters.  The parameters are gathered
857    #: into a :class:`ParameterTable`, which provides various views into the
858    #: parameter list.
859    parameters = None       # type: ParameterTable
860    #: Demo parameters as a *parameter:value* map used as the default values
861    #: for :mod:`compare`.  Any parameters not set in *demo* will use the
862    #: defaults from the parameter table.  That means no polydispersity, and
863    #: in the case of multiplicity models, a minimal model with no interesting
864    #: scattering.
865    demo = None             # type: Dict[str, float]
866    #: Composition is None if this is an independent model, or it is a
867    #: tuple with comoposition type ('product' or 'misture') and a list of
868    #: :class:`ModelInfo` blocks for the composed objects.  This allows us
869    #: to rebuild a complete mixture or product model from the info block.
870    #: *composition* is not given in the model definition file, but instead
871    #: arises when the model is constructed using names such as
872    #: *sphere*hardsphere* or *cylinder+sphere*.
873    composition = None      # type: Optional[Tuple[str, List[ModelInfo]]]
874    #: Name of the control parameter for a variant model such as :ref:`rpa`.
875    #: The *control* parameter should appear in the parameter table, with
876    #: limits defined as *[CASES]*, for case names such as
877    #: *CASES = ["diblock copolymer", "triblock copolymer", ...]*.
878    #: This should give *limits=[[case1, case2, ...]]*, but the
879    #: model loader translates this to *limits=[0, len(CASES)-1]*, and adds
880    #: *choices=CASES* to the :class:`Parameter` definition. Note that
881    #: models can use a list of cases as a parameter without it being a
882    #: control parameter.  Either way, the parameter is sent to the model
883    #: evaluator as *float(choice_num)*, where choices are numbered from 0.
884    #: See also :attr:`hidden`.
885    control = None          # type: str
886    #: Different variants require different parameters.  In order to show
887    #: just the parameters needed for the variant selected by :attr:`control`,
888    #: you should provide a function *hidden(control) -> set(['a', 'b', ...])*
889    #: indicating which parameters need to be hidden.  For multiplicity
890    #: models, you need to use the complete name of the parameter, including
891    #: its number.  So for example, if variant "a" uses only *sld1* and *sld2*,
892    #: then *sld3*, *sld4* and *sld5* of multiplicity parameter *sld[5]*
893    #: should be in the hidden set.
894    hidden = None           # type: Optional[Callable[[int], Set[str]]]
895    #: Doc string from the top of the model file.  This should be formatted
896    #: using ReStructuredText format, with latex markup in ".. math"
897    #: environments, or in dollar signs.  This will be automatically
898    #: extracted to a .rst file by :func:`generate.make_docs`, then
899    #: converted to HTML or PDF by Sphinx.
900    docs = None             # type: str
901    #: Location of the model description in the documentation.  This takes the
902    #: form of "section" or "section:subsection".  So for example,
903    #: :ref:`porod` uses *category="shape-independent"* so it is in the
904    #: :ref:`shape-independent` section whereas
905    #: :ref:`capped-cylinder` uses: *category="shape:cylinder"*, which puts
906    #: it in the :ref:`shape-cylinder` section.
907    category = None         # type: Optional[str]
908    #: True if the model can be computed accurately with single precision.
909    #: This is True by default, but models such as :ref:`bcc-paracrystal` set
910    #: it to False because they require double precision calculations.
911    single = None           # type: bool
912    #: True if the model can be run as an opencl model.  If for some reason
913    #: the model cannot be run in opencl (e.g., because the model passes
914    #: functions by reference), then set this to false.
915    opencl = None           # type: bool
916    #: True if the model is a structure factor used to model the interaction
917    #: between form factor models.  This will default to False if it is not
918    #: provided in the file.
919    structure_factor = None # type: bool
920    #: List of C source files used to define the model.  The source files
921    #: should define the *Iq* function, and possibly *Iqac* or *Iqabc* if the
922    #: model defines orientation parameters. Files containing the most basic
923    #: functions must appear first in the list, followed by the files that
924    #: use those functions.  Form factors are indicated by providing
925    #: an :attr:`ER` function.
926    source = None           # type: List[str]
927    #: The set of tests that must pass.  The format of the tests is described
928    #: in :mod:`model_test`.
929    tests = None            # type: List[TestCondition]
930    #: Returns the effective radius of the model given its volume parameters.
931    #: The presence of *ER* indicates that the model is a form factor model
932    #: that may be used together with a structure factor to form an implicit
933    #: multiplication model.
934    #:
935    #: The parameters to the *ER* function must be marked with type *volume*.
936    #: in the parameter table.  They will appear in the same order as they
937    #: do in the table.  The values passed to *ER* will be vectors, with one
938    #: value for each polydispersity condition.  For example, if the model
939    #: is polydisperse over both length and radius, then both length and
940    #: radius will have the same number of values in the vector, with one
941    #: value for each *length X radius*.  If only *radius* is polydisperse,
942    #: then the value for *length* will be repeated once for each value of
943    #: *radius*.  The *ER* function should return one effective radius for
944    #: each parameter set.  Multiplicity parameters will be received as
945    #: arrays, with one row per polydispersity condition.
946    ER = None               # type: Optional[Callable[[np.ndarray], np.ndarray]]
947    #: Returns the occupied volume and the total volume for each parameter set.
948    #: See :attr:`ER` for details on the parameters.
949    VR = None               # type: Optional[Callable[[np.ndarray], Tuple[np.ndarray, np.ndarray]]]
950    #: Arbitrary C code containing supporting functions, etc., to be inserted
951    #: after everything in source.  This can include Iq and Iqxy functions with
952    #: the full function signature, including all parameters.
953    c_code = None
954    #: Returns the form volume for python-based models.  Form volume is needed
955    #: for volume normalization in the polydispersity integral.  If no
956    #: parameters are *volume* parameters, then form volume is not needed.
957    #: For C-based models, (with :attr:`sources` defined, or with :attr:`Iq`
958    #: defined using a string containing C code), form_volume must also be
959    #: C code, either defined as a string, or in the sources.
960    form_volume = None      # type: Union[None, str, Callable[[np.ndarray], float]]
961    #: Returns *I(q, a, b, ...)* for parameters *a*, *b*, etc. defined
962    #: by the parameter table.  *Iq* can be defined as a python function, or
963    #: as a C function.  If it is defined in C, then set *Iq* to the body of
964    #: the C function, including the return statement.  This function takes
965    #: values for *q* and each of the parameters as separate *double* values
966    #: (which may be converted to float or long double by sasmodels).  All
967    #: source code files listed in :attr:`sources` will be loaded before the
968    #: *Iq* function is defined.  If *Iq* is not present, then sources should
969    #: define *static double Iq(double q, double a, double b, ...)* which
970    #: will return *I(q, a, b, ...)*.  Multiplicity parameters are sent as
971    #: pointers to doubles.  Constants in floating point expressions should
972    #: include the decimal point. See :mod:`generate` for more details.
973    Iq = None               # type: Union[None, str, Callable[[np.ndarray], np.ndarray]]
974    #: Returns *I(qab, qc, a, b, ...)*.  The interface follows :attr:`Iq`.
975    Iqac = None             # type: Union[None, str, Callable[[np.ndarray], np.ndarray]]
976    #: Returns *I(qa, qb, qc, a, b, ...)*.  The interface follows :attr:`Iq`.
977    Iqabc = None            # type: Union[None, str, Callable[[np.ndarray], np.ndarray]]
978    #: Returns *I(qx, qy, a, b, ...)*.  The interface follows :attr:`Iq`.
979    Imagnetic = None        # type: Union[None, str, Callable[[np.ndarray], np.ndarray]]
980    #: Returns a model profile curve *x, y*.  If *profile* is defined, this
981    #: curve will appear in response to the *Show* button in SasView.  Use
982    #: :attr:`profile_axes` to set the axis labels.  Note that *y* values
983    #: will be scaled by 1e6 before plotting.
984    profile = None          # type: Optional[Callable[[np.ndarray], None]]
985    #: Axis labels for the :attr:`profile` plot.  The default is *['x', 'y']*.
986    #: Only the *x* component is used for now.
987    profile_axes = None     # type: Tuple[str, str]
988    #: Returns *sesans(z, a, b, ...)* for models which can directly compute
989    #: the SESANS correlation function.  Note: not currently implemented.
990    sesans = None           # type: Optional[Callable[[np.ndarray], np.ndarray]]
991    #: Returns a random parameter set for the model
992    random = None           # type: Optional[Callable[[], Dict[str, float]]]
993    #: Line numbers for symbols defining C code
994    lineno = None           # type: Dict[str, int]
995
996    def __init__(self):
997        # type: () -> None
998        pass
999
1000    def get_hidden_parameters(self, control):
1001        """
1002        Returns the set of hidden parameters for the model.  *control* is the
1003        value of the control parameter.  Note that multiplicity models have
1004        an implicit control parameter, which is the parameter that controls
1005        the multiplicity.
1006        """
1007        if self.hidden is not None:
1008            hidden = self.hidden(control)
1009        else:
1010            controls = [p for p in self.parameters.kernel_parameters
1011                        if p.is_control]
1012            if len(controls) != 1:
1013                raise ValueError("more than one control parameter")
1014            hidden = set(p.id+str(k)
1015                         for p in self.parameters.kernel_parameters
1016                         for k in range(control+1, p.length+1)
1017                         if p.length > 1)
1018            for p in self.parameters.kernel_parameters:
1019                if p.length > 1 and p.type == "sld":
1020                    for k in range(control+1, p.length+1):
1021                        base = p.id+str(k)
1022                        hidden.update((base+"_M0", base+"_mtheta", base+"_mphi"))
1023        return hidden
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