source: sasmodels/sasmodels/modelinfo.py @ 9ae0d2e

core_shell_microgelsmagnetic_modelticket-1257-vesicle-productticket_1156ticket_1265_superballticket_822_more_unit_tests
Last change on this file since 9ae0d2e was 9ae0d2e, checked in by Paul Kienzle <pkienzle@…>, 5 years ago

Merge branch 'master' into beta_approx

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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    return parameter
167
168
169def expand_pars(partable, pars):
170    # type: (ParameterTable, ParameterSetUser) ->  ParameterSet
171    """
172    Create demo parameter set from key-value pairs.
173
174    *pars* are the key-value pairs to use for the parameters.  Any
175    parameters not specified in *pars* are set from the *partable* defaults.
176
177    If *pars* references vector fields, such as thickness[n], then support
178    different ways of assigning the demo values, including assigning a
179    specific value (e.g., thickness3=50.0), assigning a new value to all
180    (e.g., thickness=50.0) or assigning values using list notation.
181    """
182    if pars is None:
183        result = partable.defaults
184    else:
185        lookup = dict((p.id, p) for p in partable.kernel_parameters)
186        result = partable.defaults.copy()
187        scalars = dict((name, value) for name, value in pars.items()
188                       if name not in lookup or lookup[name].length == 1)
189        vectors = dict((name, value) for name, value in pars.items()
190                       if name in lookup and lookup[name].length > 1)
191        #print("lookup", lookup)
192        #print("scalars", scalars)
193        #print("vectors", vectors)
194        if vectors:
195            for name, value in vectors.items():
196                if np.isscalar(value):
197                    # support for the form
198                    #    dict(thickness=0, thickness2=50)
199                    for k in range(1, lookup[name].length+1):
200                        key = name+str(k)
201                        if key not in scalars:
202                            scalars[key] = value
203                else:
204                    # supoprt for the form
205                    #    dict(thickness=[20,10,3])
206                    for (k, v) in enumerate(value):
207                        scalars[name+str(k+1)] = v
208        result.update(scalars)
209        #print("expanded", result)
210
211    return result
212
213def prefix_parameter(par, prefix):
214    # type: (Parameter, str) -> Parameter
215    """
216    Return a copy of the parameter with its name prefixed.
217    """
218    new_par = copy(par)
219    new_par.name = prefix + par.name
220    new_par.id = prefix + par.id
221
222def suffix_parameter(par, suffix):
223    # type: (Parameter, str) -> Parameter
224    """
225    Return a copy of the parameter with its name prefixed.
226    """
227    new_par = copy(par)
228    # If name has the form x[n], replace with x_suffix[n]
229    new_par.name = par.id + suffix + par.name[len(par.id):]
230    new_par.id = par.id + suffix
231
232class Parameter(object):
233    """
234    The available kernel parameters are defined as a list, with each parameter
235    defined as a sublist with the following elements:
236
237    *name* is the name that will be displayed to the user.  Names
238    should be lower case, with words separated by underscore.  If
239    acronyms are used, the whole acronym should be upper case. For vector
240    parameters, the name will be followed by *[len]* where *len* is an
241    integer length of the vector, or the name of the parameter which
242    controls the length.  The attribute *id* will be created from name
243    without the length.
244
245    *units* should be one of *degrees* for angles, *Ang* for lengths,
246    *1e-6/Ang^2* for SLDs.
247
248    *default value* will be the initial value for  the model when it
249    is selected, or when an initial value is not otherwise specified.
250
251    *limits = [lb, ub]* are the hard limits on the parameter value, used to
252    limit the polydispersity density function.  In the fit, the parameter limits
253    given to the fit are the limits  on the central value of the parameter.
254    If there is polydispersity, it will evaluate parameter values outside
255    the fit limits, but not outside the hard limits specified in the model.
256    If there are no limits, use +/-inf imported from numpy.
257
258    *type* indicates how the parameter will be used.  "volume" parameters
259    will be used in all functions.  "orientation" parameters are not passed,
260    but will be used to convert from *qx*, *qy* to *qa*, *qb*, *qc* in calls to
261    *Iqxy* and *Imagnetic*.  If *type* is the empty string, the parameter will
262    be used in all of *Iq*, *Iqxy* and *Imagnetic*.  "sld" parameters
263    can automatically be promoted to magnetic parameters, each of which
264    will have a magnitude and a direction, which may be different from
265    other sld parameters. The volume parameters are used for calls
266    to form_volume within the kernel (required for volume normalization)
267    and for calls to ER and VR for effective radius and volume ratio
268    respectively.
269
270    *description* is a short description of the parameter.  This will
271    be displayed in the parameter table and used as a tool tip for the
272    parameter value in the user interface.
273
274    Additional values can be set after the parameter is created:
275
276    * *length* is the length of the field if it is a vector field
277
278    * *length_control* is the parameter which sets the vector length
279
280    * *is_control* is True if the parameter is a control parameter for a vector
281
282    * *polydisperse* is true if the parameter accepts a polydispersity
283
284    * *relative_pd* is true if that polydispersity is a portion of the
285      value (so a 10% length dipsersity would use a polydispersity value
286      of 0.1) rather than absolute dispersisity (such as an angle plus or
287      minus 15 degrees).
288
289    *choices* is the option names for a drop down list of options, as for
290    example, might be used to set the value of a shape parameter.
291
292    These values are set by :func:`make_parameter_table` and
293    :func:`parse_parameter` therein.
294    """
295    def __init__(self, name, units='', default=None, limits=(-np.inf, np.inf),
296                 ptype='', description=''):
297        # type: (str, str, float, Limits, str, str) -> None
298        self.id = name.split('[')[0].strip() # type: str
299        self.name = name                     # type: str
300        self.units = units                   # type: str
301        self.default = default               # type: float
302        self.limits = limits                 # type: Limits
303        self.type = ptype                    # type: str
304        self.description = description       # type: str
305
306        # Length and length_control will be filled in once the complete
307        # parameter table is available.
308        self.length = 1                      # type: int
309        self.length_control = None           # type: Optional[str]
310        self.is_control = False              # type: bool
311
312        # TODO: need better control over whether a parameter is polydisperse
313        self.polydisperse = False            # type: bool
314        self.relative_pd = False             # type: bool
315
316        # choices are also set externally.
317        self.choices = []                    # type: List[str]
318
319    def as_definition(self):
320        # type: () -> str
321        """
322        Declare space for the variable in a parameter structure.
323
324        For example, the parameter thickness with length 3 will
325        return "double thickness[3];", with no spaces before and
326        no new line character afterward.
327        """
328        if self.length == 1:
329            return "double %s;"%self.id
330        else:
331            return "double %s[%d];"%(self.id, self.length)
332
333    def as_function_argument(self):
334        # type: () -> str
335        r"""
336        Declare the variable as a function argument.
337
338        For example, the parameter thickness with length 3 will
339        return "double \*thickness", with no spaces before and
340        no comma afterward.
341        """
342        if self.length == 1:
343            return "double %s"%self.id
344        else:
345            return "double *%s"%self.id
346
347    def as_call_reference(self, prefix=""):
348        # type: (str) -> str
349        """
350        Return *prefix* + parameter name.  For struct references, use "v."
351        as the prefix.
352        """
353        # Note: if the parameter is a struct type, then we will need to use
354        # &prefix+id.  For scalars and vectors we can just use prefix+id.
355        return prefix + self.id
356
357    def __str__(self):
358        # type: () -> str
359        return "<%s>"%self.name
360
361    def __repr__(self):
362        # type: () -> str
363        return "P<%s>"%self.name
364
365
366class ParameterTable(object):
367    """
368    ParameterTable manages the list of available parameters.
369
370    There are a couple of complications which mean that the list of parameters
371    for the kernel differs from the list of parameters that the user sees.
372
373    (1) Common parameters.  Scale and background are implicit to every model,
374    but are not passed to the kernel.
375
376    (2) Vector parameters.  Vector parameters are passed to the kernel as a
377    pointer to an array, e.g., thick[], but they are seen by the user as n
378    separate parameters thick1, thick2, ...
379
380    Therefore, the parameter table is organized by how it is expected to be
381    used. The following information is needed to set up the kernel functions:
382
383    * *kernel_parameters* is the list of parameters in the kernel parameter
384      table, with vector parameter p declared as p[].
385
386    * *iq_parameters* is the list of parameters to the Iq(q, ...) function,
387      with vector parameter p sent as p[].
388
389    * *form_volume_parameters* is the list of parameters to the form_volume(...)
390      function, with vector parameter p sent as p[].
391
392    Problem details, which sets up the polydispersity loops, requires the
393    following:
394
395    * *theta_offset* is the offset of the theta parameter in the kernel parameter
396      table, with vector parameters counted as n individual parameters
397      p1, p2, ..., or offset is -1 if there is no theta parameter.
398
399    * *max_pd* is the maximum number of polydisperse parameters, with vector
400      parameters counted as n individual parameters p1, p2, ...  Note that
401      this number is limited to sasmodels.modelinfo.MAX_PD.
402
403    * *npars* is the total number of parameters to the kernel, with vector
404      parameters counted as n individual parameters p1, p2, ...
405
406    * *call_parameters* is the complete list of parameters to the kernel,
407      including scale and background, with vector parameters recorded as
408      individual parameters p1, p2, ...
409
410    * *active_1d* is the set of names that may be polydisperse for 1d data
411
412    * *active_2d* is the set of names that may be polydisperse for 2d data
413
414    User parameters are the set of parameters visible to the user, including
415    the scale and background parameters that the kernel does not see.  User
416    parameters don't use vector notation, and instead use p1, p2, ...
417    """
418    # scale and background are implicit parameters
419    COMMON = [Parameter(*p) for p in COMMON_PARAMETERS]
420
421    def __init__(self, parameters):
422        # type: (List[Parameter]) -> None
423        self.kernel_parameters = parameters
424        self._set_vector_lengths()
425        self.npars = sum(p.length for p in self.kernel_parameters)
426        self.nmagnetic = sum(p.length for p in self.kernel_parameters
427                             if p.type == 'sld')
428        self.nvalues = 2 + self.npars
429        if self.nmagnetic:
430            self.nvalues += 3 + 3*self.nmagnetic
431        self.call_parameters = self._get_call_parameters()
432        self.defaults = self._get_defaults()
433        #self._name_table= dict((p.id, p) for p in parameters)
434
435        # Set the kernel parameters.  Assumes background and scale are the
436        # first two parameters in the parameter list, but these are not sent
437        # to the underlying kernel functions.
438        self.iq_parameters = [p for p in self.kernel_parameters
439                              if p.type not in ('orientation', 'magnetic')]
440        self.orientation_parameters = [p for p in self.kernel_parameters
441                                       if p.type == 'orientation']
442        self.form_volume_parameters = [p for p in self.kernel_parameters
443                                       if p.type == 'volume']
444
445        # Theta offset
446        offset = 0
447        for p in self.kernel_parameters:
448            if p.name == 'theta':
449                self.theta_offset = offset
450                break
451            offset += p.length
452        else:
453            self.theta_offset = -1
454
455        # number of polydisperse parameters
456        num_pd = sum(p.length for p in self.kernel_parameters if p.polydisperse)
457        # Don't use more polydisperse parameters than are available in the model
458        self.max_pd = min(num_pd, MAX_PD)
459
460        # true if has 2D parameters
461        self.has_2d = any(p.type in ('orientation', 'magnetic')
462                          for p in self.kernel_parameters)
463        self.is_asymmetric = any(p.name == 'psi' for p in self.kernel_parameters)
464        self.magnetism_index = [k for k, p in enumerate(self.call_parameters)
465                                if p.id.startswith('M0:')]
466        self.pd_1d = set(p.name for p in self.call_parameters
467                         if p.polydisperse and p.type not in ('orientation', 'magnetic'))
468        self.pd_2d = set(p.name for p in self.call_parameters if p.polydisperse)
469
470    def check_angles(self):
471        """
472        Check that orientation angles are theta, phi and possibly psi.
473        """
474        theta = phi = psi = -1
475        for k, p in enumerate(self.kernel_parameters):
476            if p.name == 'theta':
477                theta = k
478                if p.type != 'orientation':
479                    raise TypeError("theta must be an orientation parameter")
480            elif p.name == 'phi':
481                phi = k
482                if p.type != 'orientation':
483                    raise TypeError("phi must be an orientation parameter")
484            elif p.name == 'psi':
485                psi = k
486                if p.type != 'orientation':
487                    raise TypeError("psi must be an orientation parameter")
488            elif p.type == 'orientation':
489                raise TypeError("only theta, phi and psi can be orientation parameters")
490        if theta >= 0 and phi >= 0:
491            last_par = len(self.kernel_parameters) - 1
492            if phi != theta+1:
493                raise TypeError("phi must follow theta")
494            if psi >= 0 and psi != phi+1:
495                raise TypeError("psi must follow phi")
496            if (psi >= 0 and psi != last_par) or (psi < 0 and phi != last_par):
497                raise TypeError("orientation parameters must appear at the "
498                                "end of the parameter table")
499        elif theta >= 0 or phi >= 0 or psi >= 0:
500            raise TypeError("oriented shapes must have both theta and phi and maybe psi")
501
502    def __getitem__(self, key):
503        # Find the parameter definition
504        for par in self.call_parameters:
505            if par.name == key:
506                return par
507        raise KeyError("unknown parameter %r"%key)
508
509    def __contains__(self, key):
510        for par in self.call_parameters:
511            if par.name == key:
512                return True
513        return False
514
515    def _set_vector_lengths(self):
516        # type: () -> List[str]
517        """
518        Walk the list of kernel parameters, setting the length field of the
519        vector parameters from the upper limit of the reference parameter.
520
521        This needs to be done once the entire parameter table is available
522        since the reference may still be undefined when the parameter is
523        initially created.
524
525        Returns the list of control parameter names.
526
527        Note: This modifies the underlying parameter object.
528        """
529        # Sort out the length of the vector parameters such as thickness[n]
530        for p in self.kernel_parameters:
531            if p.length_control:
532                ref = self._get_ref(p)
533                ref.is_control = True
534                ref.polydisperse = False
535                low, high = ref.limits
536                if int(low) != low or int(high) != high or low < 0 or high > 20:
537                    raise ValueError("expected limits on %s to be within [0, 20]"
538                                     % ref.name)
539                p.length = int(high)
540
541    def _get_ref(self, p):
542        # type: (Parameter) -> Parameter
543        for ref in self.kernel_parameters:
544            if ref.id == p.length_control:
545                return ref
546        raise ValueError("no reference variable %r for %s"
547                         % (p.length_control, p.name))
548
549    def _get_defaults(self):
550        # type: () -> ParameterSet
551        """
552        Get a list of parameter defaults from the parameters.
553
554        Expands vector parameters into parameter id+number.
555        """
556        # Construct default values, including vector defaults
557        defaults = {}
558        for p in self.call_parameters:
559            if p.length == 1:
560                defaults[p.id] = p.default
561            else:
562                for k in range(1, p.length+1):
563                    defaults["%s%d"%(p.id, k)] = p.default
564        return defaults
565
566    def _get_call_parameters(self):
567        # type: () -> List[Parameter]
568        full_list = self.COMMON[:]
569        for p in self.kernel_parameters:
570            if p.length == 1:
571                full_list.append(p)
572            else:
573                for k in range(1, p.length+1):
574                    pk = Parameter(p.id+str(k), p.units, p.default,
575                                   p.limits, p.type, p.description)
576                    pk.polydisperse = p.polydisperse
577                    pk.relative_pd = p.relative_pd
578                    pk.choices = p.choices
579                    full_list.append(pk)
580
581        # Add the magnetic parameters to the end of the call parameter list.
582        if self.nmagnetic > 0:
583            full_list.extend([
584                Parameter('up:frac_i', '', 0., [0., 1.],
585                          'magnetic', 'fraction of spin up incident'),
586                Parameter('up:frac_f', '', 0., [0., 1.],
587                          'magnetic', 'fraction of spin up final'),
588                Parameter('up:angle', 'degrees', 0., [0., 360.],
589                          'magnetic', 'spin up angle'),
590            ])
591            slds = [p for p in full_list if p.type == 'sld']
592            for p in slds:
593                full_list.extend([
594                    Parameter('M0:'+p.id, '1e-6/Ang^2', 0., [-np.inf, np.inf],
595                              'magnetic', 'magnetic amplitude for '+p.description),
596                    Parameter('mtheta:'+p.id, 'degrees', 0., [-90., 90.],
597                              'magnetic', 'magnetic latitude for '+p.description),
598                    Parameter('mphi:'+p.id, 'degrees', 0., [-180., 180.],
599                              'magnetic', 'magnetic longitude for '+p.description),
600                ])
601        #print("call parameters", full_list)
602        return full_list
603
604    def user_parameters(self, pars, is2d=True):
605        # type: (Dict[str, float], bool) -> List[Parameter]
606        """
607        Return the list of parameters for the given data type.
608
609        Vector parameters are expanded in place.  If multiple parameters
610        share the same vector length, then the parameters will be interleaved
611        in the result.  The control parameters come first.  For example,
612        if the parameter table is ordered as::
613
614            sld_core
615            sld_shell[num_shells]
616            sld_solvent
617            thickness[num_shells]
618            num_shells
619
620        and *pars[num_shells]=2* then the returned list will be::
621
622            num_shells
623            scale
624            background
625            sld_core
626            sld_shell1
627            thickness1
628            sld_shell2
629            thickness2
630            sld_solvent
631
632        Note that shell/thickness pairs are grouped together in the result
633        even though they were not grouped in the incoming table.  The control
634        parameter is always returned first since the GUI will want to set it
635        early, and rerender the table when it is changed.
636
637        Parameters marked as sld will automatically have a set of associated
638        magnetic parameters (m0:p, mtheta:p, mphi:p), as well as polarization
639        information (up:theta, up:frac_i, up:frac_f).
640        """
641        # control parameters go first
642        control = [p for p in self.kernel_parameters if p.is_control]
643
644        # Gather entries such as name[n] into groups of the same n
645        dependent = {} # type: Dict[str, List[Parameter]]
646        dependent.update((p.id, []) for p in control)
647        for p in self.kernel_parameters:
648            if p.length_control is not None:
649                dependent[p.length_control].append(p)
650
651        # Gather entries such as name[4] into groups of the same length
652        fixed_length = {}  # type: Dict[int, List[Parameter]]
653        for p in self.kernel_parameters:
654            if p.length > 1 and p.length_control is None:
655                fixed_length.setdefault(p.length, []).append(p)
656
657        # Using the call_parameters table, we already have expanded forms
658        # for each of the vector parameters; put them in a lookup table
659        # Note: p.id and p.name are currently identical for the call parameters
660        expanded_pars = dict((p.id, p) for p in self.call_parameters)
661
662        def append_group(name):
663            """add the named parameter, and related magnetic parameters if any"""
664            result.append(expanded_pars[name])
665            if is2d:
666                for tag in 'M0:', 'mtheta:', 'mphi:':
667                    if tag+name in expanded_pars:
668                        result.append(expanded_pars[tag+name])
669
670        # Gather the user parameters in order
671        result = control + self.COMMON
672        for p in self.kernel_parameters:
673            if not is2d and p.type in ('orientation', 'magnetic'):
674                pass
675            elif p.is_control:
676                pass # already added
677            elif p.length_control is not None:
678                table = dependent.get(p.length_control, [])
679                if table:
680                    # look up length from incoming parameters
681                    table_length = int(pars.get(p.length_control, p.length))
682                    del dependent[p.length_control] # first entry seen
683                    for k in range(1, table_length+1):
684                        for entry in table:
685                            append_group(entry.id+str(k))
686                else:
687                    pass # already processed all entries
688            elif p.length > 1:
689                table = fixed_length.get(p.length, [])
690                if table:
691                    table_length = p.length
692                    del fixed_length[p.length]
693                    for k in range(1, table_length+1):
694                        for entry in table:
695                            append_group(entry.id+str(k))
696                else:
697                    pass # already processed all entries
698            else:
699                append_group(p.id)
700
701        if is2d and 'up:angle' in expanded_pars:
702            result.extend([
703                expanded_pars['up:frac_i'],
704                expanded_pars['up:frac_f'],
705                expanded_pars['up:angle'],
706            ])
707
708        return result
709
710def isstr(x):
711    # type: (Any) -> bool
712    """
713    Return True if the object is a string.
714    """
715    # TODO: 2-3 compatible tests for str, including unicode strings
716    return isinstance(x, str)
717
718
719#: Set of variables defined in the model that might contain C code
720C_SYMBOLS = ['Imagnetic', 'Iq', 'Iqxy', 'Iqac', 'Iqabc', 'form_volume', 'c_code']
721
722def _find_source_lines(model_info, kernel_module):
723    # type: (ModelInfo, ModuleType) -> None
724    """
725    Identify the location of the C source inside the model definition file.
726
727    This code runs through the source of the kernel module looking for lines
728    that contain C code (because it is a c function definition).  Clearly
729    there are all sorts of reasons why this might not work (e.g., code
730    commented out in a triple-quoted line block, code built using string
731    concatenation, code defined in the branch of an 'if' block, code imported
732    from another file), but it should work properly in the 95% case, and for
733    the remainder, getting the incorrect line number will merely be
734    inconvenient.
735    """
736    # Only need line numbers if we are creating a C module and the C symbols
737    # are defined.
738    if (callable(model_info.Iq)
739            or not any(hasattr(model_info, s) for s in C_SYMBOLS)):
740        return
741
742    # load the module source if we can
743    try:
744        source = inspect.getsource(kernel_module)
745    except IOError:
746        return
747
748    # look for symbol at the start of the line
749    for lineno, line in enumerate(source.split('\n')):
750        for name in C_SYMBOLS:
751            if line.startswith(name):
752                # Add 1 since some compilers complain about "#line 0"
753                model_info.lineno[name] = lineno + 1
754                break
755
756def make_model_info(kernel_module):
757    # type: (module) -> ModelInfo
758    """
759    Extract the model definition from the loaded kernel module.
760
761    Fill in default values for parts of the module that are not provided.
762
763    Note: vectorized Iq and Iqac/Iqabc functions will be created for python
764    models when the model is first called, not when the model is loaded.
765    """
766    if hasattr(kernel_module, "model_info"):
767        # Custom sum/multi models
768        return kernel_module.model_info
769
770    info = ModelInfo()
771    #print("make parameter table", kernel_module.parameters)
772    parameters = make_parameter_table(getattr(kernel_module, 'parameters', []))
773    demo = expand_pars(parameters, getattr(kernel_module, 'demo', None))
774    filename = abspath(kernel_module.__file__).replace('.pyc', '.py')
775    kernel_id = splitext(basename(filename))[0]
776    name = getattr(kernel_module, 'name', None)
777    if name is None:
778        name = " ".join(w.capitalize() for w in kernel_id.split('_'))
779
780    info.id = kernel_id  # string used to load the kernel
781    info.filename = filename
782    info.name = name
783    info.title = getattr(kernel_module, 'title', name+" model")
784    info.description = getattr(kernel_module, 'description', 'no description')
785    info.parameters = parameters
786    info.demo = demo
787    info.composition = None
788    info.docs = kernel_module.__doc__
789    info.category = getattr(kernel_module, 'category', None)
790    info.structure_factor = getattr(kernel_module, 'structure_factor', False)
791    # TODO: find Fq by inspection
792    info.effective_radius_type = getattr(kernel_module, 'effective_radius_type', None)
793    info.have_Fq = getattr(kernel_module, 'have_Fq', 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    info.effective_radius = getattr(kernel_module, 'effective_radius', None)
800    info.ER = None  # CRUFT
801    info.VR = None  # CRUFT
802    # TODO: check the structure of the tests
803    info.tests = getattr(kernel_module, 'tests', [])
804    info.form_volume = getattr(kernel_module, 'form_volume', None) # type: ignore
805    info.Iq = getattr(kernel_module, 'Iq', None) # type: ignore
806    info.Iqxy = getattr(kernel_module, 'Iqxy', None) # type: ignore
807    info.Iqac = getattr(kernel_module, 'Iqac', None) # type: ignore
808    info.Iqabc = getattr(kernel_module, 'Iqabc', None) # type: ignore
809    info.Imagnetic = getattr(kernel_module, 'Imagnetic', None) # type: ignore
810    info.profile = getattr(kernel_module, 'profile', None) # type: ignore
811    info.sesans = getattr(kernel_module, 'sesans', None) # type: ignore
812    # Default single and opencl to True for C models.  Python models have callable Iq.
813    info.opencl = getattr(kernel_module, 'opencl', not callable(info.Iq))
814    info.single = getattr(kernel_module, 'single', not callable(info.Iq))
815    info.random = getattr(kernel_module, 'random', None)
816
817    # multiplicity info
818    control_pars = [p.id for p in parameters.kernel_parameters if p.is_control]
819    default_control = control_pars[0] if control_pars else None
820    info.control = getattr(kernel_module, 'control', default_control)
821    info.hidden = getattr(kernel_module, 'hidden', None) # type: ignore
822
823    if callable(info.Iq) and parameters.has_2d:
824        raise ValueError("oriented python models not supported")
825
826    info.lineno = {}
827    _find_source_lines(info, kernel_module)
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    #: True if the model defines an Fq function with signature
921    #: void Fq(double q, double *F1, double *F2, ...)
922    have_Fq = False
923    #: List of C source files used to define the model.  The source files
924    #: should define the *Iq* function, and possibly *Iqac* or *Iqabc* if the
925    #: model defines orientation parameters. Files containing the most basic
926    #: functions must appear first in the list, followed by the files that
927    #: use those functions.  Form factors are indicated by providing
928    #: an :attr:`ER` function.
929    effective_radius_type = None   # type: List[str]
930    #: Returns the occupied volume and the total volume for each parameter set.
931    #: See :attr:`ER` for details on the parameters.
932    source = None           # type: List[str]
933    #: The set of tests that must pass.  The format of the tests is described
934    #: in :mod:`model_test`.
935    tests = None            # type: List[TestCondition]
936    #: Returns the effective radius of the model given its volume parameters.
937    #: The presence of *ER* indicates that the model is a form factor model
938    #: that may be used together with a structure factor to form an implicit
939    #: multiplication model.
940    #:
941    #: The parameters to the *ER* function must be marked with type *volume*.
942    #: in the parameter table.  They will appear in the same order as they
943    #: do in the table.  The values passed to *ER* will be vectors, with one
944    #: value for each polydispersity condition.  For example, if the model
945    #: is polydisperse over both length and radius, then both length and
946    #: radius will have the same number of values in the vector, with one
947    #: value for each *length X radius*.  If only *radius* is polydisperse,
948    #: then the value for *length* will be repeated once for each value of
949    #: *radius*.  The *ER* function should return one effective radius for
950    #: each parameter set.  Multiplicity parameters will be received as
951    #: arrays, with one row per polydispersity condition.
952    c_code = None
953    #: Returns the form volume for python-based models.  Form volume is needed
954    #: for volume normalization in the polydispersity integral.  If no
955    #: parameters are *volume* parameters, then form volume is not needed.
956    #: For C-based models, (with :attr:`sources` defined, or with :attr:`Iq`
957    #: defined using a string containing C code), form_volume must also be
958    #: C code, either defined as a string, or in the sources.
959    form_volume = None      # type: Union[None, str, Callable[[np.ndarray], float]]
960    #: Returns *I(q, a, b, ...)* for parameters *a*, *b*, etc. defined
961    #: by the parameter table.  *Iq* can be defined as a python function, or
962    #: as a C function.  If it is defined in C, then set *Iq* to the body of
963    #: the C function, including the return statement.  This function takes
964    #: values for *q* and each of the parameters as separate *double* values
965    #: (which may be converted to float or long double by sasmodels).  All
966    #: source code files listed in :attr:`sources` will be loaded before the
967    #: *Iq* function is defined.  If *Iq* is not present, then sources should
968    #: define *static double Iq(double q, double a, double b, ...)* which
969    #: will return *I(q, a, b, ...)*.  Multiplicity parameters are sent as
970    #: pointers to doubles.  Constants in floating point expressions should
971    #: include the decimal point. See :mod:`generate` for more details.
972    Iq = None               # type: Union[None, str, Callable[[np.ndarray], np.ndarray]]
973    #: Returns *I(qab, qc, a, b, ...)*.  The interface follows :attr:`Iq`.
974    Iqac = None             # type: Union[None, str, Callable[[np.ndarray], np.ndarray]]
975    #: Returns *I(qa, qb, qc, a, b, ...)*.  The interface follows :attr:`Iq`.
976    Iqabc = None            # type: Union[None, str, Callable[[np.ndarray], np.ndarray]]
977    #: Returns *I(qx, qy, a, b, ...)*.  The interface follows :attr:`Iq`.
978    Imagnetic = None        # type: Union[None, str, Callable[[np.ndarray], np.ndarray]]
979    #: Returns a model profile curve *x, y*.  If *profile* is defined, this
980    #: curve will appear in response to the *Show* button in SasView.  Use
981    #: :attr:`profile_axes` to set the axis labels.  Note that *y* values
982    #: will be scaled by 1e6 before plotting.
983    profile = None          # type: Optional[Callable[[np.ndarray], None]]
984    #: Axis labels for the :attr:`profile` plot.  The default is *['x', 'y']*.
985    #: Only the *x* component is used for now.
986    profile_axes = None     # type: Tuple[str, str]
987    #: Returns *sesans(z, a, b, ...)* for models which can directly compute
988    #: the SESANS correlation function.  Note: not currently implemented.
989    sesans = None           # type: Optional[Callable[[np.ndarray], np.ndarray]]
990    #: Returns a random parameter set for the model
991    random = None           # type: Optional[Callable[[], Dict[str, float]]]
992    #: Line numbers for symbols defining C code
993    lineno = None           # type: Dict[str, int]
994
995    def __init__(self):
996        # type: () -> None
997        pass
998
999    def get_hidden_parameters(self, control):
1000        """
1001        Returns the set of hidden parameters for the model.  *control* is the
1002        value of the control parameter.  Note that multiplicity models have
1003        an implicit control parameter, which is the parameter that controls
1004        the multiplicity.
1005        """
1006        if self.hidden is not None:
1007            hidden = self.hidden(control)
1008        else:
1009            controls = [p for p in self.parameters.kernel_parameters
1010                        if p.is_control]
1011            if len(controls) != 1:
1012                raise ValueError("more than one control parameter")
1013            hidden = set(p.id+str(k)
1014                         for p in self.parameters.kernel_parameters
1015                         for k in range(control+1, p.length+1)
1016                         if p.length > 1)
1017        return hidden
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