Changeset 46f798f in sasview for src/sas


Ignore:
Timestamp:
Feb 28, 2017 12:05:36 PM (8 years ago)
Author:
GitHub <noreply@…>
Children:
13043af, 0d64713
Parents:
587ce8c (diff), c221349 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.
git-author:
Jeff Krzywon <krzywon@…> (02/28/17 12:05:36)
git-committer:
GitHub <noreply@…> (02/28/17 12:05:36)
Message:

Merge pull request #31 from SasView?/sesans41

Sesans integration into sasview.

Location:
src/sas
Files:
19 edited

Legend:

Unmodified
Added
Removed

  • src/sas/sascalc/data_util/qsmearing.py

    rd3911e3 r2ffe241  
    1313import logging 
    1414import sys 
    15  
     15import numpy as np  # type: ignore 
     16from numpy import pi, exp # type:ignore 
    1617from sasmodels.resolution import Slit1D, Pinhole1D 
     18from sasmodels.sesans import SesansTransform 
    1719from sasmodels.resolution2d import Pinhole2D 
     20from src.sas.sascalc.data_util.nxsunit import Converter 
    1821 
    1922def smear_selection(data, model = None): 
    … …  
    3639    # Sanity check. If we are not dealing with a SAS Data1D 
    3740    # object, just return None 
     41    # This checks for 2D data (does not throw exception because fail is common) 
    3842    if  data.__class__.__name__ not in ['Data1D', 'Theory1D']: 
    3943        if data == None: 
    … …  
    4145        elif data.dqx_data == None or data.dqy_data == None: 
    4246            return None 
    43         return PySmear2D(data, model) 
    44  
     47        return PySmear2D(data) 
     48    # This checks for 1D data with smearing info in the data itself (again, fail is likely; no exceptions) 
    4549    if  not hasattr(data, "dx") and not hasattr(data, "dxl")\ 
    4650         and not hasattr(data, "dxw"): 
    … …  
    4852 
    4953    # Look for resolution smearing data 
     54    # This is the code that checks for SESANS data; it looks for the file loader 
     55    # TODO: change other sanity checks to check for file loader instead of data structure? 
     56    _found_sesans = False 
     57    #if data.dx is not None and data.meta_data['loader']=='SESANS': 
     58    if data.dx is not None and data.isSesans: 
     59        #if data.dx[0] > 0.0: 
     60        if numpy.size(data.dx[data.dx <= 0]) == 0: 
     61            _found_sesans = True 
     62        # if data.dx[0] <= 0.0: 
     63        if numpy.size(data.dx[data.dx <= 0]) > 0: 
     64            raise ValueError('one or more of your dx values are negative, please check the data file!') 
     65 
     66    if _found_sesans == True: 
     67        #Pre-compute the Hankel matrix (H) 
     68        qmax, qunits = data.sample.zacceptance 
     69        SElength = Converter(data._xunit)(data.x, "A") 
     70        zaccept = Converter(qunits)(qmax, "1/A"), 
     71        Rmax = 10000000 
     72        hankel = SesansTransform(data.x, SElength, zaccept, Rmax) 
     73        # Then return the actual transform, as if it were a smearing function 
     74        return PySmear(hankel, model, offset=0) 
     75 
    5076    _found_resolution = False 
    5177    if data.dx is not None and len(data.dx) == len(data.x): 
    … …  
    89115    Wrapper for pure python sasmodels resolution functions. 
    90116    """ 
    91     def __init__(self, resolution, model): 
     117    def __init__(self, resolution, model, offset=None): 
    92118        self.model = model 
    93119        self.resolution = resolution 
    94         self.offset = numpy.searchsorted(self.resolution.q_calc, self.resolution.q[0]) 
     120        if offset is None: 
     121            offset = numpy.searchsorted(self.resolution.q_calc, self.resolution.q[0]) 
     122        self.offset = offset 
    95123 
    96124    def apply(self, iq_in, first_bin=0, last_bin=None): 

  • src/sas/sascalc/dataloader/data_info.py

    r345e7e4 r2ffe241  
    2525import numpy 
    2626import math 
    27  
    28 class plottable_sesans1D(object): 
    29     """ 
    30     SESANS is a place holder for 1D SESANS plottables. 
    31  
    32     #TODO: This was directly copied from the plottables_1D. Modified Somewhat. 
    33     #Class has been updated. 
    34     """ 
    35     # The presence of these should be mutually 
    36     # exclusive with the presence of Qdev (dx) 
    37     x = None 
    38     y = None 
    39     lam = None 
    40     dx = None 
    41     dy = None 
    42     dlam = None 
    43     ## Slit smearing length 
    44     dxl = None 
    45     ## Slit smearing width 
    46     dxw = None 
    47  
    48     # Units 
    49     _xaxis = '' 
    50     _xunit = '' 
    51     _yaxis = '' 
    52     _yunit = '' 
    53  
    54     def __init__(self, x, y, lam, dx=None, dy=None, dlam=None): 
    55 #        print "SESANS plottable working" 
    56         self.x = numpy.asarray(x) 
    57         self.y = numpy.asarray(y) 
    58         self.lam = numpy.asarray(lam) 
    59         if dx is not None: 
    60             self.dx = numpy.asarray(dx) 
    61         if dy is not None: 
    62             self.dy = numpy.asarray(dy) 
    63         if dlam is not None: 
    64             self.dlam = numpy.asarray(dlam) 
    65  
    66     def xaxis(self, label, unit): 
    67         """ 
    68         set the x axis label and unit 
    69         """ 
    70         self._xaxis = label 
    71         self._xunit = unit 
    72  
    73     def yaxis(self, label, unit): 
    74         """ 
    75         set the y axis label and unit 
    76         """ 
    77         self._yaxis = label 
    78         self._yunit = unit 
    79  
    8027 
    8128class plottable_1D(object): 
    … …  
    9340    ## Slit smearing width 
    9441    dxw = None 
     42    ## SESANS specific params (wavelengths for spin echo length calculation) 
     43    lam = None 
     44    dlam = None 
    9545 
    9646    # Units 
    … …  
    10050    _yunit = '' 
    10151 
    102     def __init__(self, x, y, dx=None, dy=None, dxl=None, dxw=None): 
     52    def __init__(self, x, y, dx=None, dy=None, dxl=None, dxw=None, lam=None, dlam=None): 
    10353        self.x = numpy.asarray(x) 
    10454        self.y = numpy.asarray(y) 
    … …  
    11161        if dxw is not None: 
    11262            self.dxw = numpy.asarray(dxw) 
     63        if lam is not None: 
     64            self.lam = numpy.asarray(lam) 
     65        if dlam is not None: 
     66            self.dlam = numpy.asarray(dlam) 
    11367 
    11468    def xaxis(self, label, unit): 
    … …  
    398352    ## Details 
    399353    details = None 
     354    ## SESANS zacceptance 
     355    zacceptance = None 
    400356 
    401357    def __init__(self): 
    … …  
    535491    ## Loading errors 
    536492    errors = None 
     493    ## SESANS data check 
     494    isSesans = None 
     495 
    537496 
    538497    def __init__(self): 
    … …  
    567526        ## Loading errors 
    568527        self.errors = [] 
     528        ## SESANS data check 
     529        self.isSesans = False 
    569530 
    570531    def append_empty_process(self): 
    … …  
    586547        _str += "Title:           %s\n" % self.title 
    587548        _str += "Run:             %s\n" % str(self.run) 
     549        _str += "SESANS:          %s\n" % str(self.isSesans) 
    588550        _str += "Instrument:      %s\n" % str(self.instrument) 
    589551        _str += "%s\n" % str(self.sample) 
    … …  
    736698        return self._perform_union(other) 
    737699 
    738 class SESANSData1D(plottable_sesans1D, DataInfo): 
    739     """ 
    740     SESANS 1D data class 
    741     """ 
    742     x_unit = 'nm' 
    743     y_unit = 'pol' 
    744  
    745     def __init__(self, x=None, y=None, lam=None, dx=None, dy=None, dlam=None): 
     700class Data1D(plottable_1D, DataInfo): 
     701    """ 
     702    1D data class 
     703    """ 
     704    def __init__(self, x=None, y=None, dx=None, dy=None, lam=None, dlam=None, isSesans=None): 
    746705        DataInfo.__init__(self) 
    747         plottable_sesans1D.__init__(self, x, y, lam, dx, dy, dlam) 
     706        plottable_1D.__init__(self, x, y, dx, dy,None, None, lam, dlam) 
     707        self.isSesans = isSesans 
     708        try: 
     709            if self.isSesans: # the data is SESANS 
     710                self.x_unit = 'A' 
     711                self.y_unit = 'pol' 
     712            elif not self.isSesans: # the data is SANS 
     713                self.x_unit = '1/A' 
     714                self.y_unit = '1/cm' 
     715        except: # the data is not recognized/supported, and the user is notified 
     716            raise(TypeError, 'data not recognized, check documentation for supported 1D data formats') 
    748717 
    749718    def __str__(self): 
    … …  
    759728        return _str 
    760729 
    761     def clone_without_data(self, length=0, clone=None): 
    762         """ 
    763         Clone the current object, without copying the data (which 
    764         will be filled out by a subsequent operation). 
    765         The data arrays will be initialized to zero. 
    766  
    767         :param length: length of the data array to be initialized 
    768         :param clone: if provided, the data will be copied to clone 
    769         """ 
    770         from copy import deepcopy 
    771         if clone is None or not issubclass(clone.__class__, Data1D): 
    772             x = numpy.zeros(length) 
    773             dx = numpy.zeros(length) 
    774             y = numpy.zeros(length) 
    775             dy = numpy.zeros(length) 
    776             clone = Data1D(x, y, dx=dx, dy=dy) 
    777  
    778         clone.title = self.title 
    779         clone.run = self.run 
    780         clone.filename = self.filename 
    781         clone.instrument = self.instrument 
    782         clone.notes = deepcopy(self.notes) 
    783         clone.process = deepcopy(self.process) 
    784         clone.detector = deepcopy(self.detector) 
    785         clone.sample = deepcopy(self.sample) 
    786         clone.source = deepcopy(self.source) 
    787         clone.collimation = deepcopy(self.collimation) 
    788         clone.trans_spectrum = deepcopy(self.trans_spectrum) 
    789         clone.meta_data = deepcopy(self.meta_data) 
    790         clone.errors = deepcopy(self.errors) 
    791  
    792         return clone 
    793  
    794 class Data1D(plottable_1D, DataInfo): 
    795     """ 
    796     1D data class 
    797     """ 
    798     x_unit = '1/A' 
    799     y_unit = '1/cm' 
    800  
    801     def __init__(self, x, y, dx=None, dy=None): 
    802         DataInfo.__init__(self) 
    803         plottable_1D.__init__(self, x, y, dx, dy) 
    804  
    805     def __str__(self): 
    806         """ 
    807         Nice printout 
    808         """ 
    809         _str = "%s\n" % DataInfo.__str__(self) 
    810         _str += "Data:\n" 
    811         _str += "   Type:         %s\n" % self.__class__.__name__ 
    812         _str += "   X-axis:       %s\t[%s]\n" % (self._xaxis, self._xunit) 
    813         _str += "   Y-axis:       %s\t[%s]\n" % (self._yaxis, self._yunit) 
    814         _str += "   Length:       %g\n" % len(self.x) 
    815         return _str 
    816  
    817730    def is_slit_smeared(self): 
    818731        """ 
    … …  
    843756            y = numpy.zeros(length) 
    844757            dy = numpy.zeros(length) 
    845             clone = Data1D(x, y, dx=dx, dy=dy) 
     758            lam = numpy.zeros(length) 
     759            dlam = numpy.zeros(length) 
     760            clone = Data1D(x, y, lam=lam, dx=dx, dy=dy, dlam=dlam) 
    846761 
    847762        clone.title = self.title 
    … …  
    1018933    ## Vector of Q-values at the center of each bin in y 
    1019934    y_bins = None 
     935    ## No 2D SESANS data as of yet. Always set it to False 
     936    isSesans = False 
    1020937 
    1021938    def __init__(self, data=None, err_data=None, qx_data=None, 
    1022939                 qy_data=None, q_data=None, mask=None, 
    1023940                 dqx_data=None, dqy_data=None): 
    1024         self.y_bins = [] 
    1025         self.x_bins = [] 
    1026941        DataInfo.__init__(self) 
    1027942        plottable_2D.__init__(self, data, err_data, qx_data, 
    1028943                              qy_data, q_data, mask, dqx_data, dqy_data) 
     944        self.y_bins = [] 
     945        self.x_bins = [] 
     946 
    1029947        if len(self.detector) > 0: 
    1030948            raise RuntimeError, "Data2D: Detector bank already filled at init" 
    … …  
    12651183    final_dataset.xmin = data.xmin 
    12661184    final_dataset.ymin = data.ymin 
     1185    final_dataset.isSesans = datainfo.isSesans 
    12671186    final_dataset.title = datainfo.title 
    12681187    final_dataset.run = datainfo.run 

  • src/sas/sascalc/dataloader/readers/cansas_constants.py

    r250fec92 rad4632c  
    133133               "variable" : None, 
    134134               "children" : {"Idata" : SASDATA_IDATA, 
     135                             "Sesans": {"storeas": "content"}, 
     136                             "zacceptance": {"storeas": "float"}, 
    135137                             "<any>" : ANY 
    136138                            } 

  • src/sas/sascalc/dataloader/readers/cansas_reader.py

    rbcabf4e rc221349  
    261261                # I and Q - 1D data 
    262262                elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D): 
    263                     self.current_dataset.yaxis("Intensity", unit) 
     263                    unit_list = unit.split("|") 
     264                    if len(unit_list) > 1: 
     265                        self.current_dataset.yaxis(unit_list[0].strip(), 
     266                                                   unit_list[1].strip()) 
     267                    else: 
     268                        self.current_dataset.yaxis("Intensity", unit) 
    264269                    self.current_dataset.y = np.append(self.current_dataset.y, data_point) 
    265270                elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D): 
    266271                    self.current_dataset.dy = np.append(self.current_dataset.dy, data_point) 
    267272                elif tagname == 'Q': 
    268                     self.current_dataset.xaxis("Q", unit) 
     273                    unit_list = unit.split("|") 
     274                    if len(unit_list) > 1: 
     275                        self.current_dataset.xaxis(unit_list[0].strip(), 
     276                                                   unit_list[1].strip()) 
     277                    else: 
     278                        self.current_dataset.xaxis("Q", unit) 
    269279                    self.current_dataset.x = np.append(self.current_dataset.x, data_point) 
    270280                elif tagname == 'Qdev': 
    … …  
    278288                elif tagname == 'Shadowfactor': 
    279289                    pass 
     290                elif tagname == 'Sesans': 
     291                    self.current_datainfo.isSesans = bool(data_point) 
     292                elif tagname == 'zacceptance': 
     293                    self.current_datainfo.sample.zacceptance = (data_point, unit) 
    280294 
    281295                # I and Qx, Qy - 2D data 
    … …  
    10201034            node.append(point) 
    10211035            self.write_node(point, "Q", datainfo.x[i], 
    1022                             {'unit': datainfo.x_unit}) 
     1036                            {'unit': datainfo._xaxis + " | " + datainfo._xunit}) 
    10231037            if len(datainfo.y) >= i: 
    10241038                self.write_node(point, "I", datainfo.y[i], 
    1025                                 {'unit': datainfo.y_unit}) 
     1039                                {'unit': datainfo._yaxis + " | " + datainfo._yunit}) 
    10261040            if datainfo.dy is not None and len(datainfo.dy) > i: 
    10271041                self.write_node(point, "Idev", datainfo.dy[i], 
    1028                                 {'unit': datainfo.y_unit}) 
     1042                                {'unit': datainfo._yaxis + " | " + datainfo._yunit}) 
    10291043            if datainfo.dx is not None and len(datainfo.dx) > i: 
    10301044                self.write_node(point, "Qdev", datainfo.dx[i], 
    1031                                 {'unit': datainfo.x_unit}) 
     1045                                {'unit': datainfo._xaxis + " | " + datainfo._xunit}) 
    10321046            if datainfo.dxw is not None and len(datainfo.dxw) > i: 
    10331047                self.write_node(point, "dQw", datainfo.dxw[i], 
    1034                                 {'unit': datainfo.x_unit}) 
     1048                                {'unit': datainfo._xaxis + " | " + datainfo._xunit}) 
    10351049            if datainfo.dxl is not None and len(datainfo.dxl) > i: 
    10361050                self.write_node(point, "dQl", datainfo.dxl[i], 
    1037                                 {'unit': datainfo.x_unit}) 
     1051                                {'unit': datainfo._xaxis + " | " + datainfo._xunit}) 
     1052        if datainfo.isSesans: 
     1053            sesans = self.create_element("Sesans") 
     1054            sesans.text = str(datainfo.isSesans) 
     1055            node.append(sesans) 
     1056            self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0], 
     1057                             {'unit': datainfo.sample.zacceptance[1]}) 
     1058 
    10381059 
    10391060    def _write_data_2d(self, datainfo, entry_node): 

  • src/sas/sascalc/dataloader/readers/sesans_reader.py

    r9525358 r7caf3e5  
    88import numpy 
    99import os 
    10 from sas.sascalc.dataloader.data_info import SESANSData1D 
     10from sas.sascalc.dataloader.data_info import Data1D 
    1111 
    1212# Check whether we have a converter available 
    … …  
    5959                    raise  RuntimeError, "sesans_reader: cannot open %s" % path 
    6060                buff = input_f.read() 
    61 #                print buff 
    6261                lines = buff.splitlines() 
    63 #                print lines 
    64                 #Jae could not find python universal line spliter: 
    65                 #keep the below for now 
    66                 # some ascii data has \r line separator, 
    67                 # try it when the data is on only one long line 
    68 #                if len(lines) < 2 : 
    69 #                    lines = buff.split('\r') 
    70                   
    7162                x  = numpy.zeros(0) 
    7263                y  = numpy.zeros(0) 
    … …  
    8374                tdlam = numpy.zeros(0) 
    8475                tdx = numpy.zeros(0) 
    85 #                print "all good" 
    86                 output = SESANSData1D(x=x, y=y, lam=lam, dy=dy, dx=dx, dlam=dlam) 
    87 #                print output                 
     76                output = Data1D(x=x, y=y, lam=lam, dy=dy, dx=dx, dlam=dlam, isSesans=True) 
    8877                self.filename = output.filename = basename 
    8978 
    90 #                #Initialize counters for data lines and header lines. 
    91 #                is_data = False  # Has more than 5 lines 
    92 #                # More than "5" lines of data is considered as actual 
    93 #                # data unless that is the only data 
    94 #                mum_data_lines = 5 
    95 #                # To count # of current data candidate lines 
    96 #                i = -1 
    97 #                # To count total # of previous data candidate lines 
    98 #                i1 = -1 
    99 #                # To count # of header lines 
    100 #                j = -1 
    101 #                # Helps to count # of header lines 
    102 #                j1 = -1 
    103 #                #minimum required number of columns of data; ( <= 4). 
    104 #                lentoks = 2 
    10579                paramnames=[] 
    10680                paramvals=[] 
    … …  
    11185                Pvals=[] 
    11286                dPvals=[] 
    113 #                print x 
    114 #                print zvals 
     87 
    11588                for line in lines: 
    11689                    # Initial try for CSV (split on ,) 
    … …  
    12295                    if len(toks)>5: 
    12396                        zvals.append(toks[0]) 
    124                         dzvals.append(toks[1]) 
    125                         lamvals.append(toks[2]) 
    126                         dlamvals.append(toks[3]) 
    127                         Pvals.append(toks[4]) 
    128                         dPvals.append(toks[5]) 
     97                        dzvals.append(toks[3]) 
     98                        lamvals.append(toks[4]) 
     99                        dlamvals.append(toks[5]) 
     100                        Pvals.append(toks[1]) 
     101                        dPvals.append(toks[2]) 
    129102                    else: 
    130103                        continue 
    … …  
    140113                default_z_unit = "A" 
    141114                data_conv_P = None 
    142                 default_p_unit = " " 
     115                default_p_unit = " " # Adjust unit for axis (L^-3) 
    143116                lam_unit = lam_header[1].replace("[","").replace("]","") 
     117                if lam_unit == 'AA': 
     118                    lam_unit = 'A' 
    144119                varheader=[zvals[0],dzvals[0],lamvals[0],dlamvals[0],Pvals[0],dPvals[0]] 
    145120                valrange=range(1, len(zvals)) 
    … …  
    161136                output.x, output.x_unit = self._unit_conversion(x, lam_unit, default_z_unit) 
    162137                output.y = y 
     138                output.y_unit = r'\AA^{-2} cm^{-1}'  # output y_unit added 
    163139                output.dx, output.dx_unit = self._unit_conversion(dx, lam_unit, default_z_unit) 
    164140                output.dy = dy 
    165141                output.lam, output.lam_unit = self._unit_conversion(lam, lam_unit, default_z_unit) 
    166142                output.dlam, output.dlam_unit = self._unit_conversion(dlam, lam_unit, default_z_unit) 
     143                 
     144                output.xaxis(r"\rm{z}", output.x_unit) 
     145                output.yaxis(r"\rm{ln(P)/(t \lambda^2)}", output.y_unit)  # Adjust label to ln P/(lam^2 t), remove lam column refs 
    167146 
    168                 output.xaxis(r"\rm{z}", output.x_unit) 
    169                 output.yaxis(r"\rm{P/P0}", output.y_unit) 
    170147                # Store loading process information 
    171148                output.meta_data['loader'] = self.type_name 
    172                 output.sample.thickness = float(paramvals[6]) 
     149                #output.sample.thickness = float(paramvals[6]) 
    173150                output.sample.name = paramvals[1] 
    174151                output.sample.ID = paramvals[0] 
    175152                zaccept_unit_split = paramnames[7].split("[") 
    176153                zaccept_unit = zaccept_unit_split[1].replace("]","") 
    177                 if zaccept_unit.strip() == r'\AA^-1': 
     154                if zaccept_unit.strip() == r'\AA^-1' or zaccept_unit.strip() == r'\A^-1': 
    178155                    zaccept_unit = "1/A" 
    179156                output.sample.zacceptance=(float(paramvals[7]),zaccept_unit) 
    180                 output.vars=varheader 
     157                output.vars = varheader 
    181158 
    182159                if len(output.x) < 1: 

  • src/sas/sascalc/fit/AbstractFitEngine.py

    rd3911e3 ra9f579c  
    131131        a way to get residuals from data. 
    132132    """ 
    133     def __init__(self, x, y, dx=None, dy=None, smearer=None, data=None): 
     133    def __init__(self, x, y, dx=None, dy=None, smearer=None, data=None, lam=None, dlam=None): 
    134134        """ 
    135135            :param smearer: is an object of class QSmearer or SlitSmearer 
    … …  
    152152                 
    153153        """ 
    154         Data1D.__init__(self, x=x, y=y, dx=dx, dy=dy) 
     154        Data1D.__init__(self, x=x, y=y, dx=dx, dy=dy, lam=lam, dlam=dlam) 
    155155        self.num_points = len(x) 
    156156        self.sas_data = data 

  • src/sas/sasgui/guiframe/dataFitting.py

    r345e7e4 r68adf86  
    1717    """ 
    1818    """ 
    19     def __init__(self, x=None, y=None, dx=None, dy=None): 
     19 
     20    def __init__(self, x=None, y=None, dx=None, dy=None, lam=None, dlam=None, isSesans=False): 
    2021        """ 
    2122        """ 
    … …  
    2425        if y is None: 
    2526            y = [] 
    26         PlotData1D.__init__(self, x, y, dx, dy) 
    27         LoadData1D.__init__(self, x, y, dx, dy) 
     27        self.isSesans = isSesans 
     28        PlotData1D.__init__(self, x, y, dx, dy, lam, dlam) 
     29        LoadData1D.__init__(self, x, y, dx, dy, lam, dlam, isSesans) 
     30 
    2831        self.id = None 
    2932        self.list_group_id = [] 
    … …  
    3235        self.path = None 
    3336        self.xtransform = None 
     37        if self.isSesans: 
     38            self.xtransform = "x" 
    3439        self.ytransform = None 
     40        if self.isSesans: 
     41            self.ytransform = "y" 
    3542        self.title = "" 
    3643        self.scale = None 
    … …  
    6875        # First, check the data compatibility 
    6976        dy, dy_other = self._validity_check(other) 
    70         result = Data1D(x=[], y=[], dx=None, dy=None) 
     77        result = Data1D(x=[], y=[], lam=[], dx=None, dy=None, dlam=None) 
    7178        result.clone_without_data(length=len(self.x), clone=self) 
    7279        result.copy_from_datainfo(data1d=self) 
    … …  
    115122        # First, check the data compatibility 
    116123        self._validity_check_union(other) 
    117         result = Data1D(x=[], y=[], dx=None, dy=None) 
     124        result = Data1D(x=[], y=[], lam=[], dx=None, dy=None, dlam=None) 
    118125        tot_length = len(self.x) + len(other.x) 
    119126        result = self.clone_without_data(length=tot_length, clone=result) 
     127        if self.dlam == None or other.dlam is None: 
     128            result.dlam = None 
     129        else: 
     130            result.dlam = numpy.zeros(tot_length) 
    120131        if self.dy == None or other.dy is None: 
    121132            result.dy = None 
    … …  
    141152        result.y = numpy.append(self.y, other.y) 
    142153        result.y = result.y[ind] 
     154        result.lam = numpy.append(self.lam, other.lam) 
     155        result.lam = result.lam[ind] 
     156        if result.dlam != None: 
     157            result.dlam = numpy.append(self.dlam, other.dlam) 
     158            result.dlam = result.dlam[ind] 
    143159        if result.dy != None: 
    144160            result.dy = numpy.append(self.dy, other.dy) 
    … …  
    260276        # First, check the data compatibility 
    261277        self._validity_check_union(other) 
    262         result = Data1D(x=[], y=[], dx=None, dy=None) 
     278        result = Data1D(x=[], y=[], lam=[], dx=None, dy=None, dlam=[]) 
    263279        tot_length = len(self.x)+len(other.x) 
    264280        result.clone_without_data(length=tot_length, clone=self) 
     281        if self.dlam == None or other.dlam is None: 
     282            result.dlam = None 
     283        else: 
     284            result.dlam = numpy.zeros(tot_length) 
    265285        if self.dy == None or other.dy is None: 
    266286            result.dy = None 
    … …  
    285305        result.y = numpy.append(self.y, other.y) 
    286306        result.y = result.y[ind] 
     307        result.lam = numpy.append(self.lam, other.lam) 
     308        result.lam = result.lam[ind] 
    287309        if result.dy != None: 
    288310            result.dy = numpy.append(self.dy, other.dy) 

  • src/sas/sasgui/guiframe/data_manager.py

    r345e7e4 r2ffe241  
    6161         
    6262        if issubclass(Data2D, data.__class__): 
    63             new_plot = Data2D(image=None, err_image=None)  
    64         else:  
    65             new_plot = Data1D(x=[], y=[], dx=None, dy=None) 
    66             
     63            new_plot = Data2D(image=None, err_image=None) # For now, isSesans for 2D data is always false 
     64        else: 
     65            new_plot = Data1D(x=[], y=[], dx=None, dy=None, lam=None, dlam=None, isSesans=data.isSesans) 
     66 
     67 
     68        #elif data.meta_data['loader'] == 'SESANS': 
     69        #    new_plot = Data1D(x=[], y=[], dx=None, dy=None, lam=None, dlam=None, isSesans=True) 
     70        #else: 
     71        #    new_plot = Data1D(x=[], y=[], dx=None, dy=None, lam=None, dlam=None) #SESANS check??? 
     72 
    6773        new_plot.copy_from_datainfo(data) 
    6874        data.clone_without_data(clone=new_plot) 

  • src/sas/sasgui/plottools/plottables.py

    r345e7e4 ra9f579c  
    10231023    """ 
    10241024 
    1025     def __init__(self, x, y, dx=None, dy=None): 
     1025    def __init__(self, x, y, dx=None, dy=None, lam=None, dlam=None): 
    10261026        """ 
    10271027        Draw points specified by x[i],y[i] in the current color/symbol. 
    … …  
    10371037        self.x = x 
    10381038        self.y = y 
     1039        self.lam = lam 
    10391040        self.dx = dx 
    10401041        self.dy = dy 
     1042        self.dlam = dlam 
    10411043        self.source = None 
    10421044        self.detector = None 

  • src/sas/sasgui/guiframe/CategoryInstaller.py

    r212bfc2 rddbac66  
    123123        compile it and install 
    124124        :param homefile: Override the default home directory 
    125         :param model_list: List of model names except customized models 
     125        :param model_list: List of model names except those in Plugin Models 
     126               which are user supplied. 
    126127        """ 
    127128        _model_dict = { model.name: model for model in model_list} 

  • src/sas/sasgui/perspectives/calculator/model_editor.py

    ra08b89b rddbac66  
    55function of y (usually the intensity).  It also provides a drop down of 
    66standard available math functions.  Finally a full python editor panel for 
    7 complete customizatin is provided. 
    8  
    9 :TODO the writiong of the file and name checking (and maybe some other 
    10 funtions?) should be moved to a computational module which could be called 
    11 fropm a python script.  Basically one just needs to pass the name, 
     7complete customization is provided. 
     8 
     9:TODO the writing of the file and name checking (and maybe some other 
     10functions?) should be moved to a computational module which could be called 
     11from a python script.  Basically one just needs to pass the name, 
    1212description text and function text (or in the case of the composite editor 
    1313the names of the first and second model and the operator to be used). 
    … …  
    6161    """ 
    6262    Dialog for easy custom composite models.  Provides a wx.Dialog panel 
    63     to choose two existing models (including pre-existing custom models which 
     63    to choose two existing models (including pre-existing Plugin Models which 
    6464    may themselves be composite models) as well as an operation on those models 
    6565    (add or multiply) the resulting model will add a scale parameter for summed 
    … …  
    380380            color = 'blue' 
    381381        except: 
    382             msg = "Easy Custom Sum/Multipy: Error occurred..." 
     382            msg = "Easy Sum/Multipy Plugin: Error occurred..." 
    383383            info = 'Error' 
    384384            color = 'red' 
    … …  
    501501        self.factor = factor 
    502502        self._operator = operator 
    503         self.explanation = "  Custom Model = %s %s (model1 %s model2)\n" % \ 
     503        self.explanation = "  Plugin Model = %s %s (model1 %s model2)\n" % \ 
    504504                           (self.factor, f_oper, self._operator) 
    505505        self.explanationctr.SetLabel(self.explanation) 
    … …  
    617617class EditorPanel(wx.ScrolledWindow): 
    618618    """ 
    619     Custom model function editor 
     619    Simple Plugin Model function editor 
    620620    """ 
    621621    def __init__(self, parent, base, path, title, *args, **kwds): 
    … …  
    652652        self.msg_sizer = None 
    653653        self.warning = "" 
    654         self._description = "New Custom Model" 
     654        #This does not seem to be used anywhere so commenting out for now 
     655        #    -- PDB 2/26/17  
     656        #self._description = "New Plugin Model" 
    655657        self.function_tcl = None 
    656658        self.math_combo = None 
    … …  
    991993        else: 
    992994            self._notes = result 
    993             msg = "Successful! Please look for %s in Customized Models."%name 
     995            msg = "Successful! Please look for %s in Plugin Models."%name 
    994996            msg += "  " + self._notes 
    995997            info = 'Info' 
    … …  
    11381140    def on_help(self, event): 
    11391141        """ 
    1140         Bring up the Custom Model Editor Documentation whenever 
     1142        Bring up the New Plugin Model Editor Documentation whenever 
    11411143        the HELP button is clicked. 
    11421144 
    … …  
    11901192        #self.Destroy() 
    11911193 
    1192 ## Templates for custom models 
     1194## Templates for plugin models 
    11931195 
    11941196CUSTOM_TEMPLATE = """ 

  • src/sas/sasgui/perspectives/calculator/pyconsole.py

    rd472e86 rddbac66  
    302302        success = show_model_output(self, fname) 
    303303 
    304         # Update custom model list in fitpage combobox 
     304        # Update plugin model list in fitpage combobox 
    305305        if success and self._manager != None and self.panel != None: 
    306306            self._manager.set_edit_menu_helper(self.parent) 

  • src/sas/sasgui/perspectives/fitting/basepage.py

    ra6fccd7 r7a5aedd  
    5353    ON_MAC = True 
    5454 
     55CUSTOM_MODEL = 'Plugin Models' 
     56 
    5557class BasicPage(ScrolledPanel, PanelBase): 
    5658    """ 
    57     This class provide general structure of fitpanel page 
     59    This class provide general structure of the fitpanel page 
    5860    """ 
    5961    # Internal name for the AUI manager 
    … …  
    677679    def _copy_info(self, flag): 
    678680        """ 
    679         Send event dpemding on flag 
    680  
    681         : Param flag: flag that distinguish event 
     681        Send event depending on flag 
     682 
     683        : Param flag: flag that distinguishes the event 
    682684        """ 
    683685        # messages depending on the flag 
    … …  
    11191121        :precondition: the page is already drawn or created 
    11201122 
    1121         :postcondition: the state of the underlying data change as well as the 
     1123        :postcondition: the state of the underlying data changes as well as the 
    11221124            state of the graphic interface 
    11231125        """ 
    … …  
    11671169        self._show_combox(None) 
    11681170        from models import PLUGIN_NAME_BASE 
    1169         if self.categorybox.GetValue() == 'Customized Models' \ 
     1171        if self.categorybox.GetValue() == CUSTOM_MODEL \ 
    11701172                and PLUGIN_NAME_BASE not in state.formfactorcombobox: 
    11711173            state.formfactorcombobox = \ 
    … …  
    13351337    def _selectDlg(self): 
    13361338        """ 
    1337         open a dialog file to selected the customized dispersity 
     1339        open a dialog file to select the customized polydispersity function 
    13381340        """ 
    13391341        if self.parent is not None: 
    … …  
    17601762    def _set_multfactor_combobox(self, multiplicity=10): 
    17611763        """ 
    1762         Set comboBox for muitfactor of CoreMultiShellModel 
     1764        Set comboBox for multitfactor of CoreMultiShellModel 
    17631765        :param multiplicit: no. of multi-functionality 
    17641766        """ 
    … …  
    17981800        Fill panel's combo box according to the type of model selected 
    17991801        """ 
    1800         custom_model = 'Customized Models' 
     1802 
    18011803        mod_cat = self.categorybox.GetStringSelection() 
    18021804        self.structurebox.SetSelection(0) 
    … …  
    18071809        m_list = [] 
    18081810        try: 
    1809             if mod_cat == custom_model: 
     1811            if mod_cat == CUSTOM_MODEL: 
    18101812                for model in self.model_list_box[mod_cat]: 
    18111813                    m_list.append(self.model_dict[model.name]) 
    … …  
    34533455        fills out the category list box 
    34543456        """ 
    3455         uncat_str = 'Customized Models' 
     3457        uncat_str = 'Plugin Models' 
    34563458        self._read_category_info() 
    34573459 
    … …  
    34823484        self.model_box.Clear() 
    34833485 
    3484         if category == 'Customized Models': 
     3486        if category == 'Plugin Models': 
    34853487            for model in self.model_list_box[category]: 
    34863488                str_m = str(model).split(".")[0] 

  • src/sas/sasgui/perspectives/fitting/fitpage.py

    r3d55219 ref2cdb3  
    3131SMEAR_SIZE_L = 0.00 
    3232SMEAR_SIZE_H = 0.00 
    33  
     33CUSTOM_MODEL = 'Plugin Models' 
    3434 
    3535class FitPage(BasicPage): 
    … …  
    12491249            wx.PostEvent(self.parent, new_event) 
    12501250            # update list of plugins if new plugin is available 
    1251             custom_model = 'Customized Models' 
     1251            custom_model = CUSTOM_MODEL 
    12521252            mod_cat = self.categorybox.GetStringSelection() 
    12531253            if mod_cat == custom_model: 

  • src/sas/sasgui/perspectives/fitting/fitting.py

    r73cbeec rddbac66  
    225225 
    226226        self.id_edit = wx.NewId() 
    227         editmodel_help = "Edit customized model sample file" 
    228227        self.menu1.AppendMenu(self.id_edit, "Plugin Model Operations", 
    229                               self.edit_model_menu, editmodel_help) 
     228                              self.edit_model_menu) 
    230229        #create  menubar items 
    231230        return [(self.menu1, self.sub_menu)] 
    … …  
    260259            self.update_custom_combo() 
    261260            if os.path.isfile(p_path): 
    262                 msg = "Sorry! Could not be able to delete the default " 
    263                 msg += "custom model... \n" 
     261                msg = "Sorry! unable to delete the default " 
     262                msg += "plugin model... \n" 
    264263                msg += "Please manually remove the files (.py, .pyc) " 
    265264                msg += "in the 'plugin_models' folder \n" 
    … …  
    274273                    if item.GetLabel() == label: 
    275274                        self.edit_menu.DeleteItem(item) 
    276                         msg = "The custom model, %s, has been deleted." % label 
     275                        msg = "The plugin model, %s, has been deleted." % label 
    277276                        evt = StatusEvent(status=msg, type='stop', info='info') 
    278277                        wx.PostEvent(self.parent, evt) 
    … …  
    331330            temp = self.fit_panel.reset_pmodel_list() 
    332331            if temp: 
    333                 # Set the new custom model list for all fit pages 
     332                # Set the new plugin model list for all fit pages 
    334333                for uid, page in self.fit_panel.opened_pages.iteritems(): 
    335334                    if hasattr(page, "formfactorbox"): 
    … …  
    19651964                ## then kill itself but cannot.  Paul Kienzle came up with 
    19661965                ## this fix to prevent threads from stepping on each other 
    1967                 ## which was causing a simple custom model to crash Sasview. 
     1966                ## which was causing a simple custom plugin model to crash 
     1967                ##Sasview. 
    19681968                ## We still don't know why the fit sometimes lauched a second 
    19691969                ## thread -- something which should also be investigated. 

  • src/sas/sasgui/perspectives/fitting/media/fitting_help.rst

    r26c8be3 r5295cf5  
    3434*  in *Single* fit mode - individual data sets are fitted independently one-by-one 
    3535 
    36 *  in *Simultaneous* fit mode - multiple data sets are fitted simultaneously to the *same* model with/without constrained parameters (this might be useful, for example, if you have measured the same sample at different contrasts) 
     36*  in *Simultaneous* fit mode - multiple data sets are fitted simultaneously to 
     37   the *same* model with/without constrained parameters (this might be useful, 
     38   for example, if you have measured the same sample at different contrasts) 
    3739 
    3840*  in *Batch* fit mode - multiple data sets are fitted sequentially to the *same* model (this might be useful, for example, if you have performed a kinetic or time-resolved experiment and have *lots* of data sets!) 
    … …  
    4345----------------- 
    4446 
    45 By default, the models in SasView are grouped into five categories 
    46  
    47 *  *Shapes* - models describing 'objects' (spheres, cylinders, etc) 
     47The models in SasView are grouped into categories. By default these consist of: 
     48 
     49*  *Cylinder* - cylindrical shapes (disc, right cylinder, cylinder with endcaps 
     50   etc) 
     51*  *Ellipsoid* - ellipsoidal shapes (oblate,prolate, core shell, etc) 
     52*  *Parellelepiped* - as the name implies 
     53*  *Sphere* - sheroidal shapes (sphere, core multishell, vesicle, etc) 
     54*  *Lamellae* - lamellar shapes (lamellar, core shell lamellar, stacked 
     55   lamellar, etc) 
    4856*  *Shape-Independent* - models describing structure in terms of density correlation functions, fractals, peaks, power laws, etc 
    49 *  *Customized Models* - SasView- or User-created (non-library) Python models 
    50 *  *Uncategorised* - other models (for reflectivity, etc) 
     57*  *Paracrystal* - semi ordered structures (bcc, fcc, etc) 
    5158*  *Structure Factor* - S(Q) models 
     59*  *Plugin Models* - User-created (custom/non-library) Python models 
    5260 
    5361Use the *Category* drop-down menu to chose a category of model, then select 
    … …  
    8492.. image:: cat_fig0.bmp 
    8593 
    86 The categorization of all models except the customized models can be reassigned, 
    87 added to, and removed using *Category Manager*. Models can also be hidden from view 
    88 in the drop-down menus. 
     94The categorization of all models except the user supplied Plugin Models can be 
     95reassigned, added to, and removed using *Category Manager*. Models can also be 
     96hidden from view in the drop-down menus. 
    8997 
    9098.. image:: cat_fig1.bmp 
    … …  
    93101^^^^^^^^^^^^^^^^^ 
    94102 
    95 To change category, highlight a model in the list by left-clicking on its entry and 
    96 then click the *Modify* button. Use the *Change Category* panel that appears to make 
    97 the required changes. 
     103To change category, highlight a model in the list by left-clicking on its entry 
     104and then click the *Modify* button. Use the *Change Category* panel that appears 
     105to make the required changes. 
    98106 
    99107.. image:: cat_fig2.bmp 
    … …  
    106114^^^^^^^^^^^^^^^^^^^^^ 
    107115 
    108 Use the *Enable All / Disable All* buttons and the check boxes beside each model to 
    109 select the models to show/hide. To apply the selection, click *Ok*. Otherwise click 
    110 *Cancel*. 
     116Use the *Enable All / Disable All* buttons and the check boxes beside each model 
     117to select the models to show/hide. To apply the selection, click *Ok*. Otherwise 
     118click *Cancel*. 
    111119 
    112120*NB: It may be necessary to change to a different category and then back again* 
    … …  
    118126--------------- 
    119127 
    120 For a complete list of all the library models available in SasView, see the `Model Documentation <../../../index.html>`_ . 
     128For a complete list of all the library models available in SasView, see 
     129the `Model Documentation <../../../index.html>`_ . 
    121130 
    122131It is also possible to add your own models. 
    … …  
    131140There are essentially three ways to generate new fitting models for SasView: 
    132141 
    133 * Using the SasView :ref:`New_Plugin_Model` helper dialog (best for beginners and/or relatively simple models) 
    134 * By copying/editing an existing model (this can include models generated by the *New Plugin Model* dialog) in the :ref:`Python_shell` or :ref:`Advanced_Plugin_Editor` (suitable for all use cases) 
    135 * By writing a model from scratch outside of SasView (only recommended for code monkeys!) 
     142*  Using the SasView :ref:`New_Plugin_Model` helper dialog (best for beginners 
     143   and/or relatively simple models) 
     144*  By copying/editing an existing model (this can include models generated by 
     145   the New Plugin Model* dialog) in the :ref:`Python_shell` or  
     146   :ref:`Advanced_Plugin_Editor` (suitable for all use cases) 
     147*  By writing a model from scratch outside of SasView (only recommended for code 
     148   monkeys!) 
    136149 
    137150Please read the guidance on :ref:`Writing_a_Plugin` before proceeding. 
    … …  
    163176^^^^^^^^^^^^^^^^ 
    164177 
    165 Relatively straightforward models can be programmed directly from the SasView GUI  
    166 using the *New Plugin Model Function*. 
     178Relatively straightforward models can be programmed directly from the SasView 
     179GUI using the *New Plugin Model Function*. 
    167180 
    168181.. image:: new_model.bmp 
    … …  
    175188*checked*\ . 
    176189 
    177 Also note that the 'Fit Parameters' have been split into two sections: those which  
    178 can be polydisperse (shape and orientation parameters) and those which are not 
    179 (eg, scattering length densities). 
     190Also note that the 'Fit Parameters' have been split into two sections: those 
     191which can be polydisperse (shape and orientation parameters) and those which are 
     192not (eg, scattering length densities). 
    180193 
    181194A model file generated by this option can be viewed and further modified using 
    … …  
    187200.. image:: sum_model.bmp 
    188201 
    189 This option creates a custom model of the form:: 
    190  
    191      Custom Model = scale_factor \* {(scale_1 \* model_1) \+ (scale_2 \* model_2)} \+ background 
     202This option creates a custom Plugin Model of the form:: 
     203 
     204     Plugin Model = scale_factor * {(scale_1 * model_1) +/- (scale_2 * model_2)} + background 
    192205 
    193206or:: 
    194207 
    195      Custom Model = scale_factor \* model_1 \* model_2 \+ background 
     208     Plugin Model = scale_factor * model_1 /* model_2 + background 
    196209 
    197210In the *Easy Sum/Multi Editor* give the new model a function name and brief 
    … …  
    232245Simply highlight the plugin model to be removed. The operation is final!!! 
    233246 
    234 *NB: Plugin models shipped with SasView cannot be removed in this way.* 
     247*NB: Models shipped with SasView cannot be removed in this way.* 
    235248 
    236249Load Plugin Models 
    237250^^^^^^^^^^^^^^^^^^ 
    238251 
    239 This option loads (or re-loads) all models present in the *~\\.sasview\\plugin_models* folder. 
     252This option loads (or re-loads) all models present in the 
     253*~\\.sasview\\plugin_models* folder. 
    240254 
    241255.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    … …  
    400414:ref:`Assessing_Fit_Quality`. 
    401415 
    402 *NB: If you need to use a customized model, you must ensure that model is available* 
    403 *first (see* :ref:`Adding_your_own_models` *).* 
     416*NB: If you need to use a custom Plugin Model, you must ensure that model is 
     417available first (see* :ref:`Adding_your_own_models` *).* 
    404418 
    405419Method 
    … …  
    484498If multiple data sets are in one file, load just that file. *Unselect All Data*, then 
    485499select a single initial data set to be fitted. Fit that selected data set as described 
    486 above under :ref:`Single_Fit_Mode` . 
    487  
    488 *NB: If you need to use a customized model, you must ensure that model is available* 
    489 *first (see* :ref:`Adding_your_own_models` *).* 
     500above under :ref:`Single_Fit_Mode`. 
     501 
     502*NB: If you need to use a custom Plugin Model, you must ensure that model is 
     503available first (see* :ref:`Adding_your_own_models` *).* 
    490504 
    491505Method 

  • src/sas/sasgui/perspectives/fitting/media/plugin.rst

    rca6cbc1c r5295cf5  
    2727 
    2828the next time SasView is started it will compile the plugin and add 
    29 it to the list of *Customized Models* in a FitPage. 
     29it to the list of *Plugin Models* in a FitPage. 
    3030 
    3131SasView models can be of three types: 

  • src/sas/sasgui/perspectives/fitting/models.py

    r0de74af r11b094f  
    325325                    self.plugins.append(plug) 
    326326                    self.model_dictionary[name] = plug 
    327             self.model_combobox.set_list("Customized Models", self.plugins) 
     327            self.model_combobox.set_list("Plugin Models", self.plugins) 
    328328            return self.model_combobox.get_list() 
    329329        else: 
    … …  
    346346            self.model_dictionary[name] = plug 
    347347 
    348         self.model_combobox.reset_list("Customized Models", self.plugins) 
     348        self.model_combobox.reset_list("Plugin Models", self.plugins) 
    349349        return self.model_combobox.get_list() 
    350350 
    … …  
    389389#                                     self.shape_indep_list) 
    390390        self.model_combobox.set_list("Structure Factors", self.struct_list) 
    391         self.model_combobox.set_list("Customized Models", self.plugins) 
     391        self.model_combobox.set_list("Plugin Models", self.plugins) 
    392392        self.model_combobox.set_list("P(Q)*S(Q)", self.multiplication_factor) 
    393393        self.model_combobox.set_list("multiplication", 

  • src/sas/sasgui/perspectives/fitting/pagestate.py

    r6d2b50b r71601312  
    3333from sas.sascalc.dataloader.data_info import Data2D, Collimation, Detector 
    3434from sas.sascalc.dataloader.data_info import Process, Aperture 
     35 
    3536# Information to read/write state as xml 
    3637FITTING_NODE_NAME = 'fitting_plug_in' 
    3738CANSAS_NS = "cansas1d/1.0" 
     39 
     40CUSTOM_MODEL = 'Plugin Models' 
     41CUSTOM_MODEL_OLD = 'Customized Models' 
    3842 
    3943LIST_OF_DATA_ATTRIBUTES = [["is_data", "is_data", "bool"], 
    … …  
    366370        :return: None 
    367371        """ 
     372        if self.categorycombobox == CUSTOM_MODEL_OLD: 
     373            self.categorycombobox = CUSTOM_MODEL 
    368374        if self.formfactorcombobox == '': 
    369375            FIRST_FORM = { 
    … …  
    378384                'Sphere' : 'adsorbed_layer', 
    379385                'Structure Factor' : 'hardsphere', 
    380                 'Customized Models' : '' 
     386                CUSTOM_MODEL : '' 
    381387            } 
    382388            if self.categorycombobox == '': 
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