- Timestamp:
- Mar 31, 2017 5:20:15 AM (8 years ago)
- Branches:
- master, ESS_GUI, ESS_GUI_Docs, ESS_GUI_batch_fitting, ESS_GUI_bumps_abstraction, ESS_GUI_iss1116, ESS_GUI_iss879, ESS_GUI_iss959, ESS_GUI_opencl, ESS_GUI_ordering, ESS_GUI_sync_sascalc, costrafo411, magnetic_scatt, release-4.2.2, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, ticket885, unittest-saveload
- Children:
- 7b15990
- Parents:
- 1a8e13f0 (diff), 7cbbacd (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. - Location:
- src/sas
- Files:
-
- 26 edited
Legend:
- Unmodified
- Added
- Removed
-
TabularUnified src/sas/sascalc/calculator/slit_length_calculator.py ¶
rb699768 rbfba720 16 16 # y data 17 17 self.y = None 18 # default slit length18 # default slit length 19 19 self.slit_length = 0.0 20 20 … … 42 42 """ 43 43 # None data do nothing 44 if self.y == None or self.x ==None:44 if self.y is None or self.x is None: 45 45 return 46 46 # set local variable … … 54 54 y_sum = 0.0 55 55 y_max = 0.0 56 ind = 0 .056 ind = 0 57 57 58 58 # sum 10 or more y values until getting max_y, … … 70 70 # defaults 71 71 y_half_d = 0.0 72 ind = 0 .072 ind = 0 73 73 # find indices where it crosses y = y_half. 74 74 while True: … … 81 81 82 82 # y value and ind just before passed the spot of the half height 83 y_half_u = y[ind -1]83 y_half_u = y[ind - 1] 84 84 85 85 # get corresponding x values 86 86 x_half_d = x[ind] 87 x_half_u = x[ind -1]87 x_half_u = x[ind - 1] 88 88 89 89 # calculate x at y = y_half using linear interpolation … … 91 91 x_half = (x_half_d + x_half_u)/2.0 92 92 else: 93 x_half = ( x_half_u * (y_half - y_half_d) \94 + x_half_d * (y_half_u - y_half)) \95 / (y_half_u - y_half_d)93 x_half = ((x_half_u * (y_half - y_half_d) 94 + x_half_d * (y_half_u - y_half)) 95 / (y_half_u - y_half_d)) 96 96 97 97 # Our slit length is half width, so just give half beam value -
TabularUnified src/sas/sascalc/data_util/qsmearing.py ¶
rd3911e3 r775e0b7 14 14 import sys 15 15 16 import numpy as np # type: ignore 17 from numpy import pi, exp # type:ignore 18 16 19 from sasmodels.resolution import Slit1D, Pinhole1D 20 from sasmodels.sesans import SesansTransform 17 21 from sasmodels.resolution2d import Pinhole2D 22 from .nxsunit import Converter 18 23 19 24 def smear_selection(data, model = None): … … 36 41 # Sanity check. If we are not dealing with a SAS Data1D 37 42 # object, just return None 43 # This checks for 2D data (does not throw exception because fail is common) 38 44 if data.__class__.__name__ not in ['Data1D', 'Theory1D']: 39 45 if data == None: … … 41 47 elif data.dqx_data == None or data.dqy_data == None: 42 48 return None 43 return PySmear2D(data , model)44 49 return PySmear2D(data) 50 # This checks for 1D data with smearing info in the data itself (again, fail is likely; no exceptions) 45 51 if not hasattr(data, "dx") and not hasattr(data, "dxl")\ 46 52 and not hasattr(data, "dxw"): … … 48 54 49 55 # Look for resolution smearing data 56 # This is the code that checks for SESANS data; it looks for the file loader 57 # TODO: change other sanity checks to check for file loader instead of data structure? 58 _found_sesans = False 59 #if data.dx is not None and data.meta_data['loader']=='SESANS': 60 if data.dx is not None and data.isSesans: 61 #if data.dx[0] > 0.0: 62 if numpy.size(data.dx[data.dx <= 0]) == 0: 63 _found_sesans = True 64 # if data.dx[0] <= 0.0: 65 if numpy.size(data.dx[data.dx <= 0]) > 0: 66 raise ValueError('one or more of your dx values are negative, please check the data file!') 67 68 if _found_sesans == True: 69 #Pre-compute the Hankel matrix (H) 70 qmax, qunits = data.sample.zacceptance 71 SElength = Converter(data._xunit)(data.x, "A") 72 zaccept = Converter(qunits)(qmax, "1/A"), 73 Rmax = 10000000 74 hankel = SesansTransform(data.x, SElength, zaccept, Rmax) 75 # Then return the actual transform, as if it were a smearing function 76 return PySmear(hankel, model, offset=0) 77 50 78 _found_resolution = False 51 79 if data.dx is not None and len(data.dx) == len(data.x): … … 89 117 Wrapper for pure python sasmodels resolution functions. 90 118 """ 91 def __init__(self, resolution, model ):119 def __init__(self, resolution, model, offset=None): 92 120 self.model = model 93 121 self.resolution = resolution 94 self.offset = numpy.searchsorted(self.resolution.q_calc, self.resolution.q[0]) 122 if offset is None: 123 offset = numpy.searchsorted(self.resolution.q_calc, self.resolution.q[0]) 124 self.offset = offset 95 125 96 126 def apply(self, iq_in, first_bin=0, last_bin=None): -
TabularUnified src/sas/sascalc/dataloader/data_info.py ¶
r345e7e4 r2ffe241 25 25 import numpy 26 26 import 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 mutually36 # exclusive with the presence of Qdev (dx)37 x = None38 y = None39 lam = None40 dx = None41 dy = None42 dlam = None43 ## Slit smearing length44 dxl = None45 ## Slit smearing width46 dxw = None47 48 # Units49 _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 unit69 """70 self._xaxis = label71 self._xunit = unit72 73 def yaxis(self, label, unit):74 """75 set the y axis label and unit76 """77 self._yaxis = label78 self._yunit = unit79 80 27 81 28 class plottable_1D(object): … … 93 40 ## Slit smearing width 94 41 dxw = None 42 ## SESANS specific params (wavelengths for spin echo length calculation) 43 lam = None 44 dlam = None 95 45 96 46 # Units … … 100 50 _yunit = '' 101 51 102 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): 103 53 self.x = numpy.asarray(x) 104 54 self.y = numpy.asarray(y) … … 111 61 if dxw is not None: 112 62 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) 113 67 114 68 def xaxis(self, label, unit): … … 398 352 ## Details 399 353 details = None 354 ## SESANS zacceptance 355 zacceptance = None 400 356 401 357 def __init__(self): … … 535 491 ## Loading errors 536 492 errors = None 493 ## SESANS data check 494 isSesans = None 495 537 496 538 497 def __init__(self): … … 567 526 ## Loading errors 568 527 self.errors = [] 528 ## SESANS data check 529 self.isSesans = False 569 530 570 531 def append_empty_process(self): … … 586 547 _str += "Title: %s\n" % self.title 587 548 _str += "Run: %s\n" % str(self.run) 549 _str += "SESANS: %s\n" % str(self.isSesans) 588 550 _str += "Instrument: %s\n" % str(self.instrument) 589 551 _str += "%s\n" % str(self.sample) … … 736 698 return self._perform_union(other) 737 699 738 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): 700 class 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): 746 705 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') 748 717 749 718 def __str__(self): … … 759 728 return _str 760 729 761 def clone_without_data(self, length=0, clone=None):762 """763 Clone the current object, without copying the data (which764 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 initialized768 :param clone: if provided, the data will be copied to clone769 """770 from copy import deepcopy771 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.title779 clone.run = self.run780 clone.filename = self.filename781 clone.instrument = self.instrument782 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 clone793 794 class Data1D(plottable_1D, DataInfo):795 """796 1D data class797 """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 printout808 """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 _str816 817 730 def is_slit_smeared(self): 818 731 """ … … 843 756 y = numpy.zeros(length) 844 757 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) 846 761 847 762 clone.title = self.title … … 1018 933 ## Vector of Q-values at the center of each bin in y 1019 934 y_bins = None 935 ## No 2D SESANS data as of yet. Always set it to False 936 isSesans = False 1020 937 1021 938 def __init__(self, data=None, err_data=None, qx_data=None, 1022 939 qy_data=None, q_data=None, mask=None, 1023 940 dqx_data=None, dqy_data=None): 1024 self.y_bins = []1025 self.x_bins = []1026 941 DataInfo.__init__(self) 1027 942 plottable_2D.__init__(self, data, err_data, qx_data, 1028 943 qy_data, q_data, mask, dqx_data, dqy_data) 944 self.y_bins = [] 945 self.x_bins = [] 946 1029 947 if len(self.detector) > 0: 1030 948 raise RuntimeError, "Data2D: Detector bank already filled at init" … … 1265 1183 final_dataset.xmin = data.xmin 1266 1184 final_dataset.ymin = data.ymin 1185 final_dataset.isSesans = datainfo.isSesans 1267 1186 final_dataset.title = datainfo.title 1268 1187 final_dataset.run = datainfo.run -
TabularUnified src/sas/sascalc/dataloader/readers/cansas_constants.py ¶
r250fec92 rad4632c 133 133 "variable" : None, 134 134 "children" : {"Idata" : SASDATA_IDATA, 135 "Sesans": {"storeas": "content"}, 136 "zacceptance": {"storeas": "float"}, 135 137 "<any>" : ANY 136 138 } -
TabularUnified src/sas/sascalc/dataloader/readers/cansas_reader.py ¶
rbcabf4e r8434365 261 261 # I and Q - 1D data 262 262 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) 264 269 self.current_dataset.y = np.append(self.current_dataset.y, data_point) 265 270 elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D): 266 271 self.current_dataset.dy = np.append(self.current_dataset.dy, data_point) 267 272 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) 269 279 self.current_dataset.x = np.append(self.current_dataset.x, data_point) 270 280 elif tagname == 'Qdev': … … 278 288 elif tagname == 'Shadowfactor': 279 289 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) 280 294 281 295 # I and Qx, Qy - 2D data … … 916 930 self._write_data(datainfo, entry_node) 917 931 # Transmission Spectrum Info 918 self._write_trans_spectrum(datainfo, entry_node) 932 # TODO: fix the writer to linearize all data, including T_spectrum 933 # self._write_trans_spectrum(datainfo, entry_node) 919 934 # Sample info 920 935 self._write_sample_info(datainfo, entry_node) … … 1020 1035 node.append(point) 1021 1036 self.write_node(point, "Q", datainfo.x[i], 1022 {'unit': datainfo. x_unit})1037 {'unit': datainfo._xaxis + " | " + datainfo._xunit}) 1023 1038 if len(datainfo.y) >= i: 1024 1039 self.write_node(point, "I", datainfo.y[i], 1025 {'unit': datainfo. y_unit})1040 {'unit': datainfo._yaxis + " | " + datainfo._yunit}) 1026 1041 if datainfo.dy is not None and len(datainfo.dy) > i: 1027 1042 self.write_node(point, "Idev", datainfo.dy[i], 1028 {'unit': datainfo. y_unit})1043 {'unit': datainfo._yaxis + " | " + datainfo._yunit}) 1029 1044 if datainfo.dx is not None and len(datainfo.dx) > i: 1030 1045 self.write_node(point, "Qdev", datainfo.dx[i], 1031 {'unit': datainfo. x_unit})1046 {'unit': datainfo._xaxis + " | " + datainfo._xunit}) 1032 1047 if datainfo.dxw is not None and len(datainfo.dxw) > i: 1033 1048 self.write_node(point, "dQw", datainfo.dxw[i], 1034 {'unit': datainfo. x_unit})1049 {'unit': datainfo._xaxis + " | " + datainfo._xunit}) 1035 1050 if datainfo.dxl is not None and len(datainfo.dxl) > i: 1036 1051 self.write_node(point, "dQl", datainfo.dxl[i], 1037 {'unit': datainfo.x_unit}) 1052 {'unit': datainfo._xaxis + " | " + datainfo._xunit}) 1053 if datainfo.isSesans: 1054 sesans = self.create_element("Sesans") 1055 sesans.text = str(datainfo.isSesans) 1056 node.append(sesans) 1057 self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0], 1058 {'unit': datainfo.sample.zacceptance[1]}) 1059 1038 1060 1039 1061 def _write_data_2d(self, datainfo, entry_node): -
TabularUnified src/sas/sascalc/dataloader/readers/cansas_reader_HDF5.py ¶
rbbd0f37 rc94280c 9 9 import sys 10 10 11 from sas.sascalc.dataloader.data_info import plottable_1D, plottable_2D, Data1D, Data2D, DataInfo, Process, Aperture 12 from sas.sascalc.dataloader.data_info import Collimation, TransmissionSpectrum, Detector 11 from sas.sascalc.dataloader.data_info import plottable_1D, plottable_2D,\ 12 Data1D, Data2D, DataInfo, Process, Aperture, Collimation, \ 13 TransmissionSpectrum, Detector 13 14 from sas.sascalc.dataloader.data_info import combine_data_info_with_plottable 14 15 15 16 16 17 17 class Reader(): 18 18 """ 19 A class for reading in CanSAS v2.0 data files. The existing iteration opens Mantid generated HDF5 formatted files 20 with file extension .h5/.H5. Any number of data sets may be present within the file and any dimensionality of data 21 may be used. Currently 1D and 2D SAS data sets are supported, but future implementations will include 1D and 2D 22 SESANS data. 23 24 Any number of SASdata sets may be present in a SASentry and the data within can be either 1D I(Q) or 2D I(Qx, Qy). 19 A class for reading in CanSAS v2.0 data files. The existing iteration opens 20 Mantid generated HDF5 formatted files with file extension .h5/.H5. Any 21 number of data sets may be present within the file and any dimensionality 22 of data may be used. Currently 1D and 2D SAS data sets are supported, but 23 future implementations will include 1D and 2D SESANS data. 24 25 Any number of SASdata sets may be present in a SASentry and the data within 26 can be either 1D I(Q) or 2D I(Qx, Qy). 25 27 26 28 Also supports reading NXcanSAS formatted HDF5 files … … 30 32 """ 31 33 32 # #CanSAS version34 # CanSAS version 33 35 cansas_version = 2.0 34 # #Logged warnings or messages36 # Logged warnings or messages 35 37 logging = None 36 # #List of errors for the current data set38 # List of errors for the current data set 37 39 errors = None 38 # #Raw file contents to be processed40 # Raw file contents to be processed 39 41 raw_data = None 40 # #Data info currently being read in42 # Data info currently being read in 41 43 current_datainfo = None 42 # #SASdata set currently being read in44 # SASdata set currently being read in 43 45 current_dataset = None 44 # #List of plottable1D objects that should be linked to the current_datainfo46 # List of plottable1D objects that should be linked to the current_datainfo 45 47 data1d = None 46 # #List of plottable2D objects that should be linked to the current_datainfo48 # List of plottable2D objects that should be linked to the current_datainfo 47 49 data2d = None 48 # #Data type name50 # Data type name 49 51 type_name = "CanSAS 2.0" 50 # #Wildcards52 # Wildcards 51 53 type = ["CanSAS 2.0 HDF5 Files (*.h5)|*.h5"] 52 # #List of allowed extensions54 # List of allowed extensions 53 55 ext = ['.h5', '.H5'] 54 # #Flag to bypass extension check55 allow_all = False56 # #List of files to return56 # Flag to bypass extension check 57 allow_all = True 58 # List of files to return 57 59 output = None 58 60 … … 64 66 :return: List of Data1D/2D objects and/or a list of errors. 65 67 """ 66 # # Reinitialize the classwhen loading a new data file to reset all class variables68 # Reinitialize when loading a new data file to reset all class variables 67 69 self.reset_class_variables() 68 # #Check that the file exists70 # Check that the file exists 69 71 if os.path.isfile(filename): 70 72 basename = os.path.basename(filename) … … 72 74 # If the file type is not allowed, return empty list 73 75 if extension in self.ext or self.allow_all: 74 # #Load the data file76 # Load the data file 75 77 self.raw_data = h5py.File(filename, 'r') 76 # #Read in all child elements of top level SASroot78 # Read in all child elements of top level SASroot 77 79 self.read_children(self.raw_data, []) 78 # #Add the last data set to the list of outputs80 # Add the last data set to the list of outputs 79 81 self.add_data_set() 80 # #Close the data file82 # Close the data file 81 83 self.raw_data.close() 82 # #Return data set(s)84 # Return data set(s) 83 85 return self.output 84 86 … … 110 112 """ 111 113 112 # #Loop through each element of the parent and process accordingly114 # Loop through each element of the parent and process accordingly 113 115 for key in data.keys(): 114 # #Get all information for the current key116 # Get all information for the current key 115 117 value = data.get(key) 116 118 if value.attrs.get(u'canSAS_class') is not None: … … 126 128 self.parent_class = class_name 127 129 parent_list.append(key) 128 ## If this is a new sasentry, store the current data sets and create a fresh Data1D/2D object 130 # If a new sasentry, store the current data sets and create 131 # a fresh Data1D/2D object 129 132 if class_prog.match(u'SASentry'): 130 133 self.add_data_set(key) 131 134 elif class_prog.match(u'SASdata'): 132 135 self._initialize_new_data_set(parent_list) 133 # #Recursion step to access data within the group136 # Recursion step to access data within the group 134 137 self.read_children(value, parent_list) 135 138 self.add_intermediate() … … 137 140 138 141 elif isinstance(value, h5py.Dataset): 139 # #If this is a dataset, store the data appropriately142 # If this is a dataset, store the data appropriately 140 143 data_set = data[key][:] 141 144 unit = self._get_unit(value) 142 145 143 # #I and Q Data146 # I and Q Data 144 147 if key == u'I': 145 if type(self.current_dataset) is plottable_2D:148 if isinstance(self.current_dataset, plottable_2D): 146 149 self.current_dataset.data = data_set 147 150 self.current_dataset.zaxis("Intensity", unit) … … 151 154 continue 152 155 elif key == u'Idev': 153 if type(self.current_dataset) is plottable_2D:156 if isinstance(self.current_dataset, plottable_2D): 154 157 self.current_dataset.err_data = data_set.flatten() 155 158 else: … … 158 161 elif key == u'Q': 159 162 self.current_dataset.xaxis("Q", unit) 160 if type(self.current_dataset) is plottable_2D:163 if isinstance(self.current_dataset, plottable_2D): 161 164 self.current_dataset.q = data_set.flatten() 162 165 else: … … 166 169 self.current_dataset.dx = data_set.flatten() 167 170 continue 171 elif key == u'dQw': 172 self.current_dataset.dxw = data_set.flatten() 173 continue 174 elif key == u'dQl': 175 self.current_dataset.dxl = data_set.flatten() 176 continue 168 177 elif key == u'Qy': 169 178 self.current_dataset.yaxis("Q_y", unit) … … 183 192 self.current_dataset.mask = data_set.flatten() 184 193 continue 194 # Transmission Spectrum 195 elif (key == u'T' 196 and self.parent_class == u'SAStransmission_spectrum'): 197 self.trans_spectrum.transmission = data_set.flatten() 198 continue 199 elif (key == u'Tdev' 200 and self.parent_class == u'SAStransmission_spectrum'): 201 self.trans_spectrum.transmission_deviation = \ 202 data_set.flatten() 203 continue 204 elif (key == u'lambda' 205 and self.parent_class == u'SAStransmission_spectrum'): 206 self.trans_spectrum.wavelength = data_set.flatten() 207 continue 185 208 186 209 for data_point in data_set: 187 # #Top Level Meta Data210 # Top Level Meta Data 188 211 if key == u'definition': 189 212 self.current_datainfo.meta_data['reader'] = data_point … … 201 224 self.current_datainfo.notes.append(data_point) 202 225 203 ## Sample Information 204 elif key == u'Title' and self.parent_class == u'SASsample': # CanSAS 2.0 format 226 # Sample Information 227 # CanSAS 2.0 format 228 elif key == u'Title' and self.parent_class == u'SASsample': 205 229 self.current_datainfo.sample.name = data_point 206 elif key == u'ID' and self.parent_class == u'SASsample': # NXcanSAS format 230 # NXcanSAS format 231 elif key == u'name' and self.parent_class == u'SASsample': 207 232 self.current_datainfo.sample.name = data_point 208 elif key == u'thickness' and self.parent_class == u'SASsample': 233 # NXcanSAS format 234 elif key == u'ID' and self.parent_class == u'SASsample': 235 self.current_datainfo.sample.name = data_point 236 elif (key == u'thickness' 237 and self.parent_class == u'SASsample'): 209 238 self.current_datainfo.sample.thickness = data_point 210 elif key == u'temperature' and self.parent_class == u'SASsample': 239 elif (key == u'temperature' 240 and self.parent_class == u'SASsample'): 211 241 self.current_datainfo.sample.temperature = data_point 212 elif key == u'transmission' and self.parent_class == u'SASsample': 242 elif (key == u'transmission' 243 and self.parent_class == u'SASsample'): 213 244 self.current_datainfo.sample.transmission = data_point 214 elif key == u'x_position' and self.parent_class == u'SASsample': 245 elif (key == u'x_position' 246 and self.parent_class == u'SASsample'): 215 247 self.current_datainfo.sample.position.x = data_point 216 elif key == u'y_position' and self.parent_class == u'SASsample': 248 elif (key == u'y_position' 249 and self.parent_class == u'SASsample'): 217 250 self.current_datainfo.sample.position.y = data_point 218 elif key == u'p olar_angle' and self.parent_class == u'SASsample':251 elif key == u'pitch' and self.parent_class == u'SASsample': 219 252 self.current_datainfo.sample.orientation.x = data_point 220 elif key == u'azimuthal_angle' and self.parent_class == u'SASsample': 253 elif key == u'yaw' and self.parent_class == u'SASsample': 254 self.current_datainfo.sample.orientation.y = data_point 255 elif key == u'roll' and self.parent_class == u'SASsample': 221 256 self.current_datainfo.sample.orientation.z = data_point 222 elif key == u'details' and self.parent_class == u'SASsample': 257 elif (key == u'details' 258 and self.parent_class == u'SASsample'): 223 259 self.current_datainfo.sample.details.append(data_point) 224 260 225 ## Instrumental Information 226 elif key == u'name' and self.parent_class == u'SASinstrument': 261 # Instrumental Information 262 elif (key == u'name' 263 and self.parent_class == u'SASinstrument'): 227 264 self.current_datainfo.instrument = data_point 228 265 elif key == u'name' and self.parent_class == u'SASdetector': … … 231 268 self.detector.distance = float(data_point) 232 269 self.detector.distance_unit = unit 233 elif key == u'slit_length' and self.parent_class == u'SASdetector': 270 elif (key == u'slit_length' 271 and self.parent_class == u'SASdetector'): 234 272 self.detector.slit_length = float(data_point) 235 273 self.detector.slit_length_unit = unit 236 elif key == u'x_position' and self.parent_class == u'SASdetector': 274 elif (key == u'x_position' 275 and self.parent_class == u'SASdetector'): 237 276 self.detector.offset.x = float(data_point) 238 277 self.detector.offset_unit = unit 239 elif key == u'y_position' and self.parent_class == u'SASdetector': 278 elif (key == u'y_position' 279 and self.parent_class == u'SASdetector'): 240 280 self.detector.offset.y = float(data_point) 241 281 self.detector.offset_unit = unit 242 elif key == u'polar_angle' and self.parent_class == u'SASdetector': 282 elif (key == u'pitch' 283 and self.parent_class == u'SASdetector'): 243 284 self.detector.orientation.x = float(data_point) 244 285 self.detector.orientation_unit = unit 245 elif key == u' azimuthal_angle' and self.parent_class == u'SASdetector':286 elif key == u'roll' and self.parent_class == u'SASdetector': 246 287 self.detector.orientation.z = float(data_point) 247 288 self.detector.orientation_unit = unit 248 elif key == u'beam_center_x' and self.parent_class == u'SASdetector': 289 elif key == u'yaw' and self.parent_class == u'SASdetector': 290 self.detector.orientation.y = float(data_point) 291 self.detector.orientation_unit = unit 292 elif (key == u'beam_center_x' 293 and self.parent_class == u'SASdetector'): 249 294 self.detector.beam_center.x = float(data_point) 250 295 self.detector.beam_center_unit = unit 251 elif key == u'beam_center_y' and self.parent_class == u'SASdetector': 296 elif (key == u'beam_center_y' 297 and self.parent_class == u'SASdetector'): 252 298 self.detector.beam_center.y = float(data_point) 253 299 self.detector.beam_center_unit = unit 254 elif key == u'x_pixel_size' and self.parent_class == u'SASdetector': 300 elif (key == u'x_pixel_size' 301 and self.parent_class == u'SASdetector'): 255 302 self.detector.pixel_size.x = float(data_point) 256 303 self.detector.pixel_size_unit = unit 257 elif key == u'y_pixel_size' and self.parent_class == u'SASdetector': 304 elif (key == u'y_pixel_size' 305 and self.parent_class == u'SASdetector'): 258 306 self.detector.pixel_size.y = float(data_point) 259 307 self.detector.pixel_size_unit = unit 260 elif key == u'SSD' and self.parent_class == u'SAScollimation': 308 elif (key == u'distance' 309 and self.parent_class == u'SAScollimation'): 261 310 self.collimation.length = data_point 262 311 self.collimation.length_unit = unit 263 elif key == u'name' and self.parent_class == u'SAScollimation': 312 elif (key == u'name' 313 and self.parent_class == u'SAScollimation'): 264 314 self.collimation.name = data_point 265 266 ## Process Information 267 elif key == u'name' and self.parent_class == u'SASprocess': 315 elif (key == u'shape' 316 and self.parent_class == u'SASaperture'): 317 self.aperture.shape = data_point 318 elif (key == u'x_gap' 319 and self.parent_class == u'SASaperture'): 320 self.aperture.size.x = data_point 321 elif (key == u'y_gap' 322 and self.parent_class == u'SASaperture'): 323 self.aperture.size.y = data_point 324 325 # Process Information 326 elif (key == u'Title' 327 and self.parent_class == u'SASprocess'): # CanSAS 2.0 268 328 self.process.name = data_point 269 elif key == u'Title' and self.parent_class == u'SASprocess': # CanSAS 2.0 format 329 elif (key == u'name' 330 and self.parent_class == u'SASprocess'): # NXcanSAS 270 331 self.process.name = data_point 271 elif key == u'name' and self.parent_class == u'SASprocess': # NXcanSAS format 272 self.process.name = data_point 273 elif key == u'description' and self.parent_class == u'SASprocess': 332 elif (key == u'description' 333 and self.parent_class == u'SASprocess'): 274 334 self.process.description = data_point 275 335 elif key == u'date' and self.parent_class == u'SASprocess': 276 336 self.process.date = data_point 337 elif key == u'term' and self.parent_class == u'SASprocess': 338 self.process.term = data_point 277 339 elif self.parent_class == u'SASprocess': 278 340 self.process.notes.append(data_point) 279 341 280 ## Transmission Spectrum 281 elif key == u'T' and self.parent_class == u'SAStransmission_spectrum': 282 self.trans_spectrum.transmission.append(data_point) 283 elif key == u'Tdev' and self.parent_class == u'SAStransmission_spectrum': 284 self.trans_spectrum.transmission_deviation.append(data_point) 285 elif key == u'lambda' and self.parent_class == u'SAStransmission_spectrum': 286 self.trans_spectrum.wavelength.append(data_point) 287 288 ## Source 289 elif key == u'wavelength' and self.parent_class == u'SASdata': 342 # Source 343 elif (key == u'wavelength' 344 and self.parent_class == u'SASdata'): 290 345 self.current_datainfo.source.wavelength = data_point 291 346 self.current_datainfo.source.wavelength_unit = unit 292 elif key == u'incident_wavelength' and self.parent_class == u'SASsource': 347 elif (key == u'incident_wavelength' 348 and self.parent_class == 'SASsource'): 293 349 self.current_datainfo.source.wavelength = data_point 294 350 self.current_datainfo.source.wavelength_unit = unit 295 elif key == u'wavelength_max' and self.parent_class == u'SASsource': 351 elif (key == u'wavelength_max' 352 and self.parent_class == u'SASsource'): 296 353 self.current_datainfo.source.wavelength_max = data_point 297 354 self.current_datainfo.source.wavelength_max_unit = unit 298 elif key == u'wavelength_min' and self.parent_class == u'SASsource': 355 elif (key == u'wavelength_min' 356 and self.parent_class == u'SASsource'): 299 357 self.current_datainfo.source.wavelength_min = data_point 300 358 self.current_datainfo.source.wavelength_min_unit = unit 301 elif key == u'wavelength_spread' and self.parent_class == u'SASsource': 302 self.current_datainfo.source.wavelength_spread = data_point 303 self.current_datainfo.source.wavelength_spread_unit = unit 304 elif key == u'beam_size_x' and self.parent_class == u'SASsource': 359 elif (key == u'incident_wavelength_spread' 360 and self.parent_class == u'SASsource'): 361 self.current_datainfo.source.wavelength_spread = \ 362 data_point 363 self.current_datainfo.source.wavelength_spread_unit = \ 364 unit 365 elif (key == u'beam_size_x' 366 and self.parent_class == u'SASsource'): 305 367 self.current_datainfo.source.beam_size.x = data_point 306 368 self.current_datainfo.source.beam_size_unit = unit 307 elif key == u'beam_size_y' and self.parent_class == u'SASsource': 369 elif (key == u'beam_size_y' 370 and self.parent_class == u'SASsource'): 308 371 self.current_datainfo.source.beam_size.y = data_point 309 372 self.current_datainfo.source.beam_size_unit = unit 310 elif key == u'beam_shape' and self.parent_class == u'SASsource': 373 elif (key == u'beam_shape' 374 and self.parent_class == u'SASsource'): 311 375 self.current_datainfo.source.beam_shape = data_point 312 elif key == u'radiation' and self.parent_class == u'SASsource': 376 elif (key == u'radiation' 377 and self.parent_class == u'SASsource'): 313 378 self.current_datainfo.source.radiation = data_point 314 elif key == u'transmission' and self.parent_class == u'SASdata': 379 elif (key == u'transmission' 380 and self.parent_class == u'SASdata'): 315 381 self.current_datainfo.sample.transmission = data_point 316 382 317 # #Everything else goes in meta_data383 # Everything else goes in meta_data 318 384 else: 319 new_key = self._create_unique_key(self.current_datainfo.meta_data, key) 385 new_key = self._create_unique_key( 386 self.current_datainfo.meta_data, key) 320 387 self.current_datainfo.meta_data[new_key] = data_point 321 388 322 389 else: 323 # #I don't know if this reachable code390 # I don't know if this reachable code 324 391 self.errors.add("ShouldNeverHappenException") 325 392 326 393 def add_intermediate(self): 327 394 """ 328 This method stores any intermediate objects within the final data set after fully reading the set. 329 330 :param parent: The NXclass name for the h5py Group object that just finished being processed 395 This method stores any intermediate objects within the final data set 396 after fully reading the set. 397 398 :param parent: The NXclass name for the h5py Group object that just 399 finished being processed 331 400 """ 332 401 … … 347 416 self.aperture = Aperture() 348 417 elif self.parent_class == u'SASdata': 349 if type(self.current_dataset) is plottable_2D:418 if isinstance(self.current_dataset, plottable_2D): 350 419 self.data2d.append(self.current_dataset) 351 elif type(self.current_dataset) is plottable_1D:420 elif isinstance(self.current_dataset, plottable_1D): 352 421 self.data1d.append(self.current_dataset) 353 422 354 423 def final_data_cleanup(self): 355 424 """ 356 Does some final cleanup and formatting on self.current_datainfo and all data1D and data2D objects and then 357 combines the data and info into Data1D and Data2D objects 358 """ 359 360 ## Type cast data arrays to float64 425 Does some final cleanup and formatting on self.current_datainfo and 426 all data1D and data2D objects and then combines the data and info into 427 Data1D and Data2D objects 428 """ 429 430 # Type cast data arrays to float64 361 431 if len(self.current_datainfo.trans_spectrum) > 0: 362 432 spectrum_list = [] … … 364 434 spectrum.transmission = np.delete(spectrum.transmission, [0]) 365 435 spectrum.transmission = spectrum.transmission.astype(np.float64) 366 spectrum.transmission_deviation = np.delete(spectrum.transmission_deviation, [0]) 367 spectrum.transmission_deviation = spectrum.transmission_deviation.astype(np.float64) 436 spectrum.transmission_deviation = np.delete( 437 spectrum.transmission_deviation, [0]) 438 spectrum.transmission_deviation = \ 439 spectrum.transmission_deviation.astype(np.float64) 368 440 spectrum.wavelength = np.delete(spectrum.wavelength, [0]) 369 441 spectrum.wavelength = spectrum.wavelength.astype(np.float64) … … 372 444 self.current_datainfo.trans_spectrum = spectrum_list 373 445 374 # #Append errors to dataset and reset class errors446 # Append errors to dataset and reset class errors 375 447 self.current_datainfo.errors = self.errors 376 448 self.errors.clear() 377 449 378 # #Combine all plottables with datainfo and append each to output379 # #Type cast data arrays to float64 and find min/max as appropriate450 # Combine all plottables with datainfo and append each to output 451 # Type cast data arrays to float64 and find min/max as appropriate 380 452 for dataset in self.data2d: 381 453 dataset.data = dataset.data.astype(np.float64) … … 397 469 zeros = np.ones(dataset.data.size, dtype=bool) 398 470 try: 399 for i in range 471 for i in range(0, dataset.mask.size - 1): 400 472 zeros[i] = dataset.mask[i] 401 473 except: 402 474 self.errors.add(sys.exc_value) 403 475 dataset.mask = zeros 404 # #Calculate the actual Q matrix476 # Calculate the actual Q matrix 405 477 try: 406 478 if dataset.q_data.size <= 1: 407 dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data + dataset.qy_data * dataset.qy_data) 479 dataset.q_data = np.sqrt(dataset.qx_data 480 * dataset.qx_data 481 + dataset.qy_data 482 * dataset.qy_data) 408 483 except: 409 484 dataset.q_data = None … … 415 490 dataset.data = dataset.data.flatten() 416 491 417 final_dataset = combine_data_info_with_plottable(dataset, self.current_datainfo) 492 final_dataset = combine_data_info_with_plottable( 493 dataset, self.current_datainfo) 418 494 self.output.append(final_dataset) 419 495 … … 435 511 if dataset.dy is not None: 436 512 dataset.dy = dataset.dy.astype(np.float64) 437 final_dataset = combine_data_info_with_plottable(dataset, self.current_datainfo) 513 final_dataset = combine_data_info_with_plottable( 514 dataset, self.current_datainfo) 438 515 self.output.append(final_dataset) 439 516 440 517 def add_data_set(self, key=""): 441 518 """ 442 Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a 443 private method to generate a new data set. 519 Adds the current_dataset to the list of outputs after preforming final 520 processing on the data and then calls a private method to generate a 521 new data set. 444 522 445 523 :param key: NeXus group name for current tree level … … 453 531 454 532 455 def _initialize_new_data_set(self, parent_list = None): 456 """ 457 A private class method to generate a new 1D or 2D data object based on the type of data within the set. 458 Outside methods should call add_data_set() to be sure any existing data is stored properly. 533 def _initialize_new_data_set(self, parent_list=None): 534 """ 535 A private class method to generate a new 1D or 2D data object based on 536 the type of data within the set. Outside methods should call 537 add_data_set() to be sure any existing data is stored properly. 459 538 460 539 :param parent_list: List of names of parent elements … … 473 552 def _find_intermediate(self, parent_list, basename=""): 474 553 """ 475 A private class used to find an entry by either using a direct key or knowing the approximate basename. 476 477 :param parent_list: List of parents to the current level in the HDF5 file 554 A private class used to find an entry by either using a direct key or 555 knowing the approximate basename. 556 557 :param parent_list: List of parents nodes in the HDF5 file 478 558 :param basename: Approximate name of an entry to search for 479 559 :return: … … 486 566 top = top.get(parent) 487 567 for key in top.keys(): 488 if (key_prog.match(key)):568 if key_prog.match(key): 489 569 entry = True 490 570 break … … 516 596 """ 517 597 unit = value.attrs.get(u'units') 518 if unit ==None:598 if unit is None: 519 599 unit = value.attrs.get(u'unit') 520 # #Convert the unit formats600 # Convert the unit formats 521 601 if unit == "1/A": 522 602 unit = "A^{-1}" -
TabularUnified src/sas/sascalc/dataloader/readers/sesans_reader.py ¶
r345e7e4 r7caf3e5 8 8 import numpy 9 9 import os 10 from sas.sascalc.dataloader.data_info import SESANSData1D10 from sas.sascalc.dataloader.data_info import Data1D 11 11 12 12 # Check whether we have a converter available … … 59 59 raise RuntimeError, "sesans_reader: cannot open %s" % path 60 60 buff = input_f.read() 61 # print buff62 61 lines = buff.splitlines() 63 # print lines64 #Jae could not find python universal line spliter:65 #keep the below for now66 # some ascii data has \r line separator,67 # try it when the data is on only one long line68 # if len(lines) < 2 :69 # lines = buff.split('\r')70 71 62 x = numpy.zeros(0) 72 63 y = numpy.zeros(0) … … 83 74 tdlam = numpy.zeros(0) 84 75 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) 88 77 self.filename = output.filename = basename 89 78 90 # #Initialize counters for data lines and header lines.91 # is_data = False # Has more than 5 lines92 # # More than "5" lines of data is considered as actual93 # # data unless that is the only data94 # mum_data_lines = 595 # # To count # of current data candidate lines96 # i = -197 # # To count total # of previous data candidate lines98 # i1 = -199 # # To count # of header lines100 # j = -1101 # # Helps to count # of header lines102 # j1 = -1103 # #minimum required number of columns of data; ( <= 4).104 # lentoks = 2105 79 paramnames=[] 106 80 paramvals=[] … … 111 85 Pvals=[] 112 86 dPvals=[] 113 # print x 114 # print zvals 87 115 88 for line in lines: 116 89 # Initial try for CSV (split on ,) … … 122 95 if len(toks)>5: 123 96 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]) 129 102 else: 130 103 continue … … 140 113 default_z_unit = "A" 141 114 data_conv_P = None 142 default_p_unit = " " 115 default_p_unit = " " # Adjust unit for axis (L^-3) 143 116 lam_unit = lam_header[1].replace("[","").replace("]","") 117 if lam_unit == 'AA': 118 lam_unit = 'A' 144 119 varheader=[zvals[0],dzvals[0],lamvals[0],dlamvals[0],Pvals[0],dPvals[0]] 145 120 valrange=range(1, len(zvals)) … … 161 136 output.x, output.x_unit = self._unit_conversion(x, lam_unit, default_z_unit) 162 137 output.y = y 138 output.y_unit = r'\AA^{-2} cm^{-1}' # output y_unit added 163 139 output.dx, output.dx_unit = self._unit_conversion(dx, lam_unit, default_z_unit) 164 140 output.dy = dy 165 141 output.lam, output.lam_unit = self._unit_conversion(lam, lam_unit, default_z_unit) 166 142 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 167 146 168 output.xaxis("\rm{z}", output.x_unit)169 output.yaxis("\\rm{P/P0}", output.y_unit)170 147 # Store loading process information 171 148 output.meta_data['loader'] = self.type_name 172 output.sample.thickness = float(paramvals[6])149 #output.sample.thickness = float(paramvals[6]) 173 150 output.sample.name = paramvals[1] 174 151 output.sample.ID = paramvals[0] 175 152 zaccept_unit_split = paramnames[7].split("[") 176 153 zaccept_unit = zaccept_unit_split[1].replace("]","") 177 if zaccept_unit.strip() == '\AA^-1':154 if zaccept_unit.strip() == r'\AA^-1' or zaccept_unit.strip() == r'\A^-1': 178 155 zaccept_unit = "1/A" 179 156 output.sample.zacceptance=(float(paramvals[7]),zaccept_unit) 180 output.vars =varheader157 output.vars = varheader 181 158 182 159 if len(output.x) < 1: -
TabularUnified src/sas/sascalc/fit/AbstractFitEngine.py ¶
rd3911e3 ra9f579c 131 131 a way to get residuals from data. 132 132 """ 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): 134 134 """ 135 135 :param smearer: is an object of class QSmearer or SlitSmearer … … 152 152 153 153 """ 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) 155 155 self.num_points = len(x) 156 156 self.sas_data = data -
TabularUnified src/sas/sascalc/fit/BumpsFitting.py ¶
r345e7e4 r1a30720 352 352 except Exception as exc: 353 353 best, fbest = None, numpy.NaN 354 errors = [str(exc), traceback. traceback.format_exc()]354 errors = [str(exc), traceback.format_exc()] 355 355 finally: 356 356 mapper.stop_mapper(fitdriver.mapper) -
TabularUnified src/sas/sasgui/guiframe/CategoryInstaller.py ¶
r212bfc2 rddbac66 123 123 compile it and install 124 124 :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. 126 127 """ 127 128 _model_dict = { model.name: model for model in model_list} -
TabularUnified src/sas/sasgui/guiframe/acknowledgebox.py ¶
rc1fdf84 r74c8cd0 11 11 import wx.richtext 12 12 import wx.lib.hyperlink 13 from wx.lib.expando import ExpandoTextCtrl 13 14 import random 14 15 import os.path … … 36 37 Shows the current method for acknowledging SasView in 37 38 scholarly publications. 38 39 39 """ 40 40 … … 44 44 wx.Dialog.__init__(self, *args, **kwds) 45 45 46 self.ack = wx.TextCtrl(self, style=wx.TE_LEFT|wx.TE_MULTILINE|wx.TE_BESTWRAP|wx.TE_READONLY|wx.TE_NO_VSCROLL)46 self.ack = ExpandoTextCtrl(self, style=wx.TE_LEFT|wx.TE_MULTILINE|wx.TE_BESTWRAP|wx.TE_READONLY|wx.TE_NO_VSCROLL) 47 47 self.ack.SetValue(config._acknowledgement_publications) 48 self.ack.SetMinSize((-1, 55)) 48 #self.ack.SetMinSize((-1, 55)) 49 self.citation = ExpandoTextCtrl(self, style=wx.TE_LEFT|wx.TE_MULTILINE|wx.TE_BESTWRAP|wx.TE_READONLY|wx.TE_NO_VSCROLL) 50 self.citation.SetValue(config._acknowledgement_citation) 49 51 self.preamble = wx.StaticText(self, -1, config._acknowledgement_preamble) 50 52 items = [config._acknowledgement_preamble_bullet1, … … 52 54 config._acknowledgement_preamble_bullet3, 53 55 config._acknowledgement_preamble_bullet4] 54 self.list1 = wx.StaticText(self, -1, " \t(1) " + items[0])55 self.list2 = wx.StaticText(self, -1, " \t(2) " + items[1])56 self.list3 = wx.StaticText(self, -1, " \t(3) " + items[2])57 self.list4 = wx.StaticText(self, -1, " \t(4) " + items[3])56 self.list1 = wx.StaticText(self, -1, "(1) " + items[0]) 57 self.list2 = wx.StaticText(self, -1, "(2) " + items[1]) 58 self.list3 = wx.StaticText(self, -1, "(3) " + items[2]) 59 self.list4 = wx.StaticText(self, -1, "(4) " + items[3]) 58 60 self.static_line = wx.StaticLine(self, 0) 59 61 self.__set_properties() … … 69 71 self.SetTitle("Acknowledging SasView") 70 72 #Increased size of box from (525, 225), SMK, 04/10/16 71 self.Set Size((600, 300))73 self.SetClientSize((600, 320)) 72 74 # end wxGlade 73 75 … … 81 83 sizer_titles.Add(self.preamble, 0, wx.ALL|wx.EXPAND, 5) 82 84 sizer_titles.Add(self.list1, 0, wx.ALL|wx.EXPAND, 5) 85 sizer_titles.Add(self.ack, 0, wx.ALL|wx.EXPAND, 5) 83 86 sizer_titles.Add(self.list2, 0, wx.ALL|wx.EXPAND, 5) 87 sizer_titles.Add(self.citation, 0, wx.ALL|wx.EXPAND, 5) 84 88 sizer_titles.Add(self.list3, 0, wx.ALL|wx.EXPAND, 5) 89 #sizer_titles.Add(self.static_line, 0, wx.ALL|wx.EXPAND, 0) 85 90 sizer_titles.Add(self.list4, 0, wx.ALL|wx.EXPAND, 5) 86 sizer_titles.Add(self.static_line, 0, wx.ALL|wx.EXPAND, 0)87 sizer_titles.Add(self.ack, 0, wx.ALL|wx.EXPAND, 5)88 91 sizer_main.Add(sizer_titles, -1, wx.ALL|wx.EXPAND, 5) 89 92 self.SetAutoLayout(True) … … 91 94 self.Layout() 92 95 self.Centre() 96 #self.SetClientSize(sizer_main.GetSize()) 93 97 # end wxGlade 94 98 -
TabularUnified src/sas/sasgui/guiframe/config.py ¶
rd85c194 rf9d1f60 1 1 """ 2 Application settings2 Application settings 3 3 """ 4 import time 4 5 import os 5 import time6 6 from sas.sasgui.guiframe.gui_style import GUIFRAME 7 import sas.sasview 8 import logging 9 7 10 # Version of the application 8 __appname__ = " DummyView"9 __version__ = '0.0.0'10 __build__ = '1'11 __appname__ = "SasView" 12 __version__ = sas.sasview.__version__ 13 __build__ = sas.sasview.__build__ 11 14 __download_page__ = 'https://github.com/SasView/sasview/releases' 12 15 __update_URL__ = 'http://www.sasview.org/latestversion.json' 13 16 14 15 17 # Debug message flag 16 __EVT_DEBUG__ = True18 __EVT_DEBUG__ = False 17 19 18 20 # Flag for automated testing … … 29 31 _acknowledgement_preamble =\ 30 32 '''To ensure the long term support and development of this software please''' +\ 31 ''' remember to do the following.'''33 ''' remember to:''' 32 34 _acknowledgement_preamble_bullet1 =\ 33 '''Acknowledge its use in your publications as suggested below'''35 '''Acknowledge its use in your publications as :''' 34 36 _acknowledgement_preamble_bullet2 =\ 35 '''Reference the following website: http://www.sasview.org'''37 '''Reference SasView as:''' 36 38 _acknowledgement_preamble_bullet3 =\ 37 39 '''Reference the model you used if appropriate (see documentation for refs)''' … … 39 41 '''Send us your reference for our records: developers@sasview.org''' 40 42 _acknowledgement_publications = \ 41 '''This work benefited from the use of the SasView application, originally 42 developed under NSF award DMR-0520547. 43 '''This work benefited from the use of the SasView application, originally developed under NSF Award DMR-0520547. SasView also contains code developed with funding from the EU Horizon 2020 programme under the SINE2020 project Grant No 654000.''' 44 _acknowledgement_citation = \ 45 '''M. Doucet et al. SasView Version 4.1, Zenodo, 10.5281/zenodo.438138''' 46 47 _acknowledgement = \ 48 '''This work was originally developed as part of the DANSE project funded by the US NSF under Award DMR-0520547,\n but is currently maintained by a collaboration between UTK, UMD, NIST, ORNL, ISIS, ESS, ILL, ANSTO and TU Delft and the scattering community.\n\n SasView also contains code developed with funding from the EU Horizon 2020 programme under the SINE2020 project (Grant No 654000).\nA list of individual contributors can be found at: https://github.com/orgs/SasView/people 43 49 ''' 44 _acknowledgement = \45 '''This work originally developed as part of the DANSE project funded by the NSF46 under grant DMR-0520547, and currently maintained by NIST, UMD, ORNL, ISIS, ESS47 and ILL.48 50 49 '''50 51 _homepage = "http://www.sasview.org" 51 _download = "http://sourceforge.net/projects/sasview/files/"52 _download = __download_page__ 52 53 _authors = [] 53 54 _paper = "http://sourceforge.net/p/sasview/tickets/" 54 55 _license = "mailto:help@sasview.org" 55 _nsf_logo = "images/nsf_logo.png" 56 _danse_logo = "images/danse_logo.png" 57 _inst_logo = "images/utlogo.gif" 58 _nist_logo = "images/nist_logo.png" 59 _umd_logo = "images/umd_logo.png" 60 _sns_logo = "images/sns_logo.png" 61 _isis_logo = "images/isis_logo.png" 62 _ess_logo = "images/ess_logo.png" 63 _ill_logo = "images/ill_logo.png" 56 57 58 icon_path = os.path.abspath(os.path.join(os.path.dirname(__file__), "images")) 59 logging.info("icon path: %s" % icon_path) 60 media_path = os.path.abspath(os.path.join(os.path.dirname(__file__), "media")) 61 test_path = os.path.abspath(os.path.join(os.path.dirname(__file__), "test")) 62 63 _nist_logo = os.path.join(icon_path, "nist_logo.png") 64 _umd_logo = os.path.join(icon_path, "umd_logo.png") 65 _sns_logo = os.path.join(icon_path, "sns_logo.png") 66 _ornl_logo = os.path.join(icon_path, "ornl_logo.png") 67 _isis_logo = os.path.join(icon_path, "isis_logo.png") 68 _ess_logo = os.path.join(icon_path, "ess_logo.png") 69 _ill_logo = os.path.join(icon_path, "ill_logo.png") 70 _ansto_logo = os.path.join(icon_path, "ansto_logo.png") 71 _tudelft_logo = os.path.join(icon_path, "tudelft_logo.png") 72 _nsf_logo = os.path.join(icon_path, "nsf_logo.png") 73 _danse_logo = os.path.join(icon_path, "danse_logo.png") 74 _inst_logo = os.path.join(icon_path, "utlogo.gif") 64 75 _nist_url = "http://www.nist.gov/" 65 76 _umd_url = "http://www.umd.edu/" 66 77 _sns_url = "http://neutrons.ornl.gov/" 78 _ornl_url = "http://neutrons.ornl.gov/" 67 79 _nsf_url = "http://www.nsf.gov" 68 _danse_url = "http://www.cacr.caltech.edu/projects/danse/release/index.html"69 _inst_url = "http://www.utk.edu"70 80 _isis_url = "http://www.isis.stfc.ac.uk/" 71 81 _ess_url = "http://ess-scandinavia.eu/" 72 82 _ill_url = "http://www.ill.eu/" 73 _corner_image = "images/angles_flat.png" 74 _welcome_image = "images/SVwelcome.png" 75 _copyright = "(c) 2008, University of Tennessee" 76 #edit the lists below of file state your plugin can read 77 #for sasview this how you can edit these lists 78 #PLUGIN_STATE_EXTENSIONS = ['.prv','.fitv', '.inv'] 79 #APPLICATION_STATE_EXTENSION = '.svs' 80 #PLUGINS_WLIST = ['P(r) files (*.prv)|*.prv', 81 # 'Fitting files (*.fitv)|*.fitv', 82 # 'Invariant files (*.inv)|*.inv'] 83 #APPLICATION_WLIST = 'SasView files (*.svs)|*.svs' 84 APPLICATION_WLIST = '' 85 APPLICATION_STATE_EXTENSION = None 86 PLUGINS_WLIST = [] 87 PLUGIN_STATE_EXTENSIONS = [] 88 SPLASH_SCREEN_PATH = "images/danse_logo.png" 89 DEFAULT_STYLE = GUIFRAME.SINGLE_APPLICATION 90 SPLASH_SCREEN_WIDTH = 500 91 SPLASH_SCREEN_HEIGHT = 300 92 WELCOME_PANEL_ON = False 93 TUTORIAL_PATH = None 94 SS_MAX_DISPLAY_TIME = 1500 95 PLOPANEL_WIDTH = 350 96 PLOPANEL_HEIGTH = 350 97 GUIFRAME_WIDTH = 1000 98 GUIFRAME_HEIGHT = 800 99 CONTROL_WIDTH = -1 100 CONTROL_HEIGHT = -1 101 SetupIconFile_win = os.path.join("images", "ball.ico") 102 SetupIconFile_mac = os.path.join("images", "ball.icns") 103 DefaultGroupName = "DANSE" 104 OutputBaseFilename = "setupGuiFrame" 83 _ansto_url = "http://www.ansto.gov.au/" 84 _tudelft_url = "http://www.tnw.tudelft.nl/en/cooperation/facilities/reactor-instituut-delft/" 85 _danse_url = "http://www.cacr.caltech.edu/projects/danse/release/index.html" 86 _inst_url = "http://www.utk.edu" 87 _corner_image = os.path.join(icon_path, "angles_flat.png") 88 _welcome_image = os.path.join(icon_path, "SVwelcome.png") 89 _copyright = "(c) 2009 - 2017, UTK, UMD, NIST, ORNL, ISIS, ESS, ILL, ANSTO and TU Delft" 90 marketplace_url = "http://marketplace.sasview.org/" 91 92 #edit the list of file state your plugin can read 93 APPLICATION_WLIST = 'SasView files (*.svs)|*.svs' 94 APPLICATION_STATE_EXTENSION = '.svs' 95 GUIFRAME_WIDTH = 1150 96 GUIFRAME_HEIGHT = 840 97 PLUGIN_STATE_EXTENSIONS = ['.fitv', '.inv', '.prv', '.crf'] 98 PLUGINS_WLIST = ['Fitting files (*.fitv)|*.fitv', 99 'Invariant files (*.inv)|*.inv', 100 'P(r) files (*.prv)|*.prv', 101 'Corfunc files (*.crf)|*.crf'] 102 PLOPANEL_WIDTH = 415 103 PLOPANEL_HEIGTH = 370 105 104 DATAPANEL_WIDTH = 235 106 105 DATAPANEL_HEIGHT = 700 106 SPLASH_SCREEN_PATH = os.path.join(icon_path, "SVwelcome_mini.png") 107 TUTORIAL_PATH = os.path.join(media_path, "Tutorial.pdf") 108 DEFAULT_STYLE = GUIFRAME.MULTIPLE_APPLICATIONS|GUIFRAME.MANAGER_ON\ 109 |GUIFRAME.CALCULATOR_ON|GUIFRAME.TOOLBAR_ON 110 SPLASH_SCREEN_WIDTH = 512 111 SPLASH_SCREEN_HEIGHT = 366 112 SS_MAX_DISPLAY_TIME = 2000 113 WELCOME_PANEL_ON = True 114 WELCOME_PANEL_SHOW = False 115 CLEANUP_PLOT = False 116 # OPEN and SAVE project menu 117 OPEN_SAVE_PROJECT_MENU = True 118 #VIEW MENU 119 VIEW_MENU = True 120 #EDIT MENU 121 EDIT_MENU = True 122 123 SetupIconFile_win = os.path.join(icon_path, "ball.ico") 124 SetupIconFile_mac = os.path.join(icon_path, "ball.icns") 125 DefaultGroupName = "." 126 OutputBaseFilename = "setupSasView" 127 107 128 FIXED_PANEL = True 108 129 DATALOADER_SHOW = True … … 113 134 # set a default perspective 114 135 DEFAULT_PERSPECTIVE = 'None' 115 # OPEN and SAVE project menu 116 OPEN_SAVE_PROJECT_MENU = True 117 CLEANUP_PLOT = False 118 # OPEN and SAVE project menu 119 OPEN_SAVE_PROJECT_MENU = False 120 #VIEW MENU 121 VIEW_MENU = False 122 #EDIT MENU 123 EDIT_MENU = False 124 import wx.lib.newevent 125 (StatusBarEvent, EVT_STATUS) = wx.lib.newevent.NewEvent() 136 137 # Time out for updating sasview 138 UPDATE_TIMEOUT = 2 139 140 #OpenCL option 141 SAS_OPENCL = None 126 142 127 143 def printEVT(message): 128 """129 :TODO - need method documentation130 """131 144 if __EVT_DEBUG__: 145 """ 146 :TODO - Need method doc string 147 """ 132 148 print "%g: %s" % (time.clock(), message) 133 149 134 150 if __EVT_DEBUG_2_FILE__: 135 151 out = open(__EVT_DEBUG_FILENAME__, 'a') 136 152 out.write("%10g: %s\n" % (time.clock(), message)) 137 153 out.close() 138 -
TabularUnified src/sas/sasgui/guiframe/dataFitting.py ¶
r345e7e4 r68adf86 17 17 """ 18 18 """ 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): 20 21 """ 21 22 """ … … 24 25 if y is None: 25 26 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 28 31 self.id = None 29 32 self.list_group_id = [] … … 32 35 self.path = None 33 36 self.xtransform = None 37 if self.isSesans: 38 self.xtransform = "x" 34 39 self.ytransform = None 40 if self.isSesans: 41 self.ytransform = "y" 35 42 self.title = "" 36 43 self.scale = None … … 68 75 # First, check the data compatibility 69 76 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) 71 78 result.clone_without_data(length=len(self.x), clone=self) 72 79 result.copy_from_datainfo(data1d=self) … … 115 122 # First, check the data compatibility 116 123 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) 118 125 tot_length = len(self.x) + len(other.x) 119 126 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) 120 131 if self.dy == None or other.dy is None: 121 132 result.dy = None … … 141 152 result.y = numpy.append(self.y, other.y) 142 153 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] 143 159 if result.dy != None: 144 160 result.dy = numpy.append(self.dy, other.dy) … … 260 276 # First, check the data compatibility 261 277 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=[]) 263 279 tot_length = len(self.x)+len(other.x) 264 280 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) 265 285 if self.dy == None or other.dy is None: 266 286 result.dy = None … … 285 305 result.y = numpy.append(self.y, other.y) 286 306 result.y = result.y[ind] 307 result.lam = numpy.append(self.lam, other.lam) 308 result.lam = result.lam[ind] 287 309 if result.dy != None: 288 310 result.dy = numpy.append(self.dy, other.dy) -
TabularUnified src/sas/sasgui/guiframe/data_manager.py ¶
r345e7e4 r2ffe241 61 61 62 62 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 67 73 new_plot.copy_from_datainfo(data) 68 74 data.clone_without_data(clone=new_plot) -
TabularUnified src/sas/sasgui/guiframe/data_panel.py ¶
rc8e1996 ra45a298 66 66 IS_MAC = True 67 67 68 STYLE_FLAG = wx.RAISED_BORDER | CT.TR_HAS_BUTTONS | CT.TR_HIDE_ROOT |\69 wx.WANTS_CHARS | CT.TR_HAS_VARIABLE_ROW_HEIGHT 68 STYLE_FLAG = (wx.RAISED_BORDER | CT.TR_HAS_BUTTONS | 69 wx.WANTS_CHARS | CT.TR_HAS_VARIABLE_ROW_HEIGHT) 70 70 71 71 … … 74 74 Check list control to be used for Data Panel 75 75 """ 76 def __init__(self, parent, *args, **kwds):76 def __init__(self, parent, root, *args, **kwds): 77 77 # agwstyle is introduced in wx.2.8.11 but is not working for mac 78 78 if IS_MAC and wx_version < 812: … … 97 97 del kwds['style'] 98 98 CT.CustomTreeCtrl.__init__(self, parent, *args, **kwds) 99 self.root = self.AddRoot( "Available Data")99 self.root = self.AddRoot(root) 100 100 101 101 def OnCompareItems(self, item1, item2): … … 520 520 Add a listcrtl in the panel 521 521 """ 522 tree_ctrl_label = wx.StaticText(self, -1, "Data") 523 tree_ctrl_label.SetForegroundColour('blue') 524 self.tree_ctrl = DataTreeCtrl(parent=self, style=wx.SUNKEN_BORDER) 522 # Add splitter 523 w, h = self.parent.GetSize() 524 splitter = wx.SplitterWindow(self) 525 splitter.SetMinimumPaneSize(50) 526 splitter.SetSashGravity(1.0) 527 528 file_sizer = wx.BoxSizer(wx.VERTICAL) 529 file_sizer.SetMinSize(wx.Size(w/13, h*2/5)) 530 theory_sizer = wx.BoxSizer(wx.VERTICAL) 531 theory_sizer.SetMinSize(wx.Size(w/13, h*2/5)) 532 533 self.tree_ctrl = DataTreeCtrl(parent=splitter, 534 style=wx.SUNKEN_BORDER, 535 root="Available Data") 536 525 537 self.tree_ctrl.Bind(CT.EVT_TREE_ITEM_CHECKING, self.on_check_item) 526 538 self.tree_ctrl.Bind(CT.EVT_TREE_ITEM_MENU, self.on_right_click_data) … … 557 569 wx.EVT_MENU(self, self.editmask_id, self.on_edit_data) 558 570 559 tree_ctrl_theory_label = wx.StaticText(self, -1, "Theory") 560 tree_ctrl_theory_label.SetForegroundColour('blue') 561 self.tree_ctrl_theory = DataTreeCtrl(parent=self, 562 style=wx.SUNKEN_BORDER) 571 self.tree_ctrl_theory = DataTreeCtrl(parent=splitter, 572 style=wx.SUNKEN_BORDER, 573 root="Available Theory") 563 574 self.tree_ctrl_theory.Bind(CT.EVT_TREE_ITEM_CHECKING, 564 575 self.on_check_item) 565 576 self.tree_ctrl_theory.Bind(CT.EVT_TREE_ITEM_MENU, 566 577 self.on_right_click_theory) 567 self.sizer1.Add(tree_ctrl_label, 0, wx.LEFT, 10) 568 self.sizer1.Add(self.tree_ctrl, 1, wx.EXPAND | wx.ALL, 10) 569 self.sizer1.Add(tree_ctrl_theory_label, 0, wx.LEFT, 10) 570 self.sizer1.Add(self.tree_ctrl_theory, 1, wx.EXPAND | wx.ALL, 10) 578 splitter.SplitHorizontally(self.tree_ctrl, self.tree_ctrl_theory) 579 self.sizer1.Add(splitter, 1, wx.EXPAND | wx.ALL, 10) 571 580 572 581 def on_right_click_theory(self, event): … … 722 731 if self.tree_ctrl.root: 723 732 self.tree_ctrl.SortChildren(self.tree_ctrl.root) 733 # Expand root if # of data sets > 0 734 if self.tree_ctrl.GetCount() > 0: 735 self.tree_ctrl.root.Expand() 724 736 self.enable_remove() 725 737 self.enable_import() … … 760 772 state_id=state_id, 761 773 theory_list=theory_list) 774 if self.tree_ctrl_theory.GetCount() > 0: 775 self.tree_ctrl_theory.root.Expand() 762 776 763 777 def append_theory_helper(self, tree, root, state_id, theory_list): -
TabularUnified src/sas/sasgui/perspectives/calculator/model_editor.py ¶
ra08b89b rddbac66 5 5 function of y (usually the intensity). It also provides a drop down of 6 6 standard available math functions. Finally a full python editor panel for 7 complete customizati n is provided.8 9 :TODO the writi ong of the file and name checking (and maybe some other10 fun tions?) should be moved to a computational module which could be called11 fro pm a python script. Basically one just needs to pass the name,7 complete customization is provided. 8 9 :TODO the writing of the file and name checking (and maybe some other 10 functions?) should be moved to a computational module which could be called 11 from a python script. Basically one just needs to pass the name, 12 12 description text and function text (or in the case of the composite editor 13 13 the names of the first and second model and the operator to be used). … … 61 61 """ 62 62 Dialog for easy custom composite models. Provides a wx.Dialog panel 63 to choose two existing models (including pre-existing custom models which63 to choose two existing models (including pre-existing Plugin Models which 64 64 may themselves be composite models) as well as an operation on those models 65 65 (add or multiply) the resulting model will add a scale parameter for summed … … 380 380 color = 'blue' 381 381 except: 382 msg = "Easy Custom Sum/Multipy: Error occurred..."382 msg = "Easy Sum/Multipy Plugin: Error occurred..." 383 383 info = 'Error' 384 384 color = 'red' … … 501 501 self.factor = factor 502 502 self._operator = operator 503 self.explanation = " CustomModel = %s %s (model1 %s model2)\n" % \503 self.explanation = " Plugin Model = %s %s (model1 %s model2)\n" % \ 504 504 (self.factor, f_oper, self._operator) 505 505 self.explanationctr.SetLabel(self.explanation) … … 617 617 class EditorPanel(wx.ScrolledWindow): 618 618 """ 619 Custom model function editor619 Simple Plugin Model function editor 620 620 """ 621 621 def __init__(self, parent, base, path, title, *args, **kwds): … … 652 652 self.msg_sizer = None 653 653 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" 655 657 self.function_tcl = None 656 658 self.math_combo = None … … 991 993 else: 992 994 self._notes = result 993 msg = "Successful! Please look for %s in CustomizedModels."%name995 msg = "Successful! Please look for %s in Plugin Models."%name 994 996 msg += " " + self._notes 995 997 info = 'Info' … … 1138 1140 def on_help(self, event): 1139 1141 """ 1140 Bring up the CustomModel Editor Documentation whenever1142 Bring up the New Plugin Model Editor Documentation whenever 1141 1143 the HELP button is clicked. 1142 1144 … … 1190 1192 #self.Destroy() 1191 1193 1192 ## Templates for custommodels1194 ## Templates for plugin models 1193 1195 1194 1196 CUSTOM_TEMPLATE = """ -
TabularUnified src/sas/sasgui/perspectives/calculator/pyconsole.py ¶
rd472e86 rddbac66 302 302 success = show_model_output(self, fname) 303 303 304 # Update custommodel list in fitpage combobox304 # Update plugin model list in fitpage combobox 305 305 if success and self._manager != None and self.panel != None: 306 306 self._manager.set_edit_menu_helper(self.parent) -
TabularUnified src/sas/sasgui/perspectives/fitting/basepage.py ¶
r1a8e13f0 r5156918 53 53 ON_MAC = True 54 54 55 CUSTOM_MODEL = 'Plugin Models' 56 55 57 class BasicPage(ScrolledPanel, PanelBase): 56 58 """ 57 This class provide general structure of fitpanel page59 This class provide general structure of the fitpanel page 58 60 """ 59 61 # Internal name for the AUI manager … … 118 120 self.dxw = None 119 121 # pinhole smear 120 self.dx_min = None 121 self.dx_max = None 122 self.dx_percent = None 122 123 # smear attrbs 123 124 self.enable_smearer = None … … 677 678 def _copy_info(self, flag): 678 679 """ 679 Send event d pemding on flag680 681 : Param flag: flag that distinguish event680 Send event depending on flag 681 682 : Param flag: flag that distinguishes the event 682 683 """ 683 684 # messages depending on the flag … … 847 848 self.state.pinhole_smearer = \ 848 849 copy.deepcopy(self.pinhole_smearer.GetValue()) 849 self.state.dx_max = copy.deepcopy(self.dx_max) 850 self.state.dx_min = copy.deepcopy(self.dx_min) 850 self.state.dx_percent = copy.deepcopy(self.dx_percent) 851 851 self.state.dxl = copy.deepcopy(self.dxl) 852 852 self.state.dxw = copy.deepcopy(self.dxw) … … 1119 1119 :precondition: the page is already drawn or created 1120 1120 1121 :postcondition: the state of the underlying data change as well as the1121 :postcondition: the state of the underlying data changes as well as the 1122 1122 state of the graphic interface 1123 1123 """ … … 1167 1167 self._show_combox(None) 1168 1168 from models import PLUGIN_NAME_BASE 1169 if self.categorybox.GetValue() == 'Customized Models'\1169 if self.categorybox.GetValue() == CUSTOM_MODEL \ 1170 1170 and PLUGIN_NAME_BASE not in state.formfactorcombobox: 1171 1171 state.formfactorcombobox = \ … … 1245 1245 # we have two more options for smearing 1246 1246 if self.pinhole_smearer.GetValue(): 1247 self.dx_min = state.dx_min 1248 self.dx_max = state.dx_max 1249 if self.dx_min is not None: 1250 self.smear_pinhole_min.SetValue(str(self.dx_min)) 1251 if self.dx_max is not None: 1252 self.smear_pinhole_max.SetValue(str(self.dx_max)) 1247 self.dx_percent = state.dx_percent 1248 if self.dx_percent is not None: 1249 if state.dx_old: 1250 self.dx_percent = 100 * (self.dx_percent / self.data.x[0]) 1251 self.smear_pinhole_percent.SetValue("%.2f" % self.dx_percent) 1253 1252 self.onPinholeSmear(event=None) 1254 1253 elif self.slit_smearer.GetValue(): … … 1335 1334 def _selectDlg(self): 1336 1335 """ 1337 open a dialog file to select ed the customized dispersity1336 open a dialog file to select the customized polydispersity function 1338 1337 """ 1339 1338 if self.parent is not None: … … 1747 1746 def _set_multfactor_combobox(self, multiplicity=10): 1748 1747 """ 1749 Set comboBox for mu itfactor of CoreMultiShellModel1748 Set comboBox for multitfactor of CoreMultiShellModel 1750 1749 :param multiplicit: no. of multi-functionality 1751 1750 """ … … 1785 1784 Fill panel's combo box according to the type of model selected 1786 1785 """ 1787 custom_model = 'Customized Models' 1786 1788 1787 mod_cat = self.categorybox.GetStringSelection() 1789 1788 self.structurebox.SetSelection(0) … … 1794 1793 m_list = [] 1795 1794 try: 1796 if mod_cat == custom_model:1795 if mod_cat == CUSTOM_MODEL: 1797 1796 for model in self.model_list_box[mod_cat]: 1798 1797 m_list.append(self.model_dict[model.name]) … … 3430 3429 fills out the category list box 3431 3430 """ 3432 uncat_str = ' CustomizedModels'3431 uncat_str = 'Plugin Models' 3433 3432 self._read_category_info() 3434 3433 … … 3459 3458 self.model_box.Clear() 3460 3459 3461 if category == ' CustomizedModels':3460 if category == 'Plugin Models': 3462 3461 for model in self.model_list_box[category]: 3463 3462 str_m = str(model).split(".")[0] -
TabularUnified src/sas/sasgui/perspectives/fitting/fitpage.py ¶
r1a8e13f0 r5156918 29 29 _BOX_WIDTH = 76 30 30 _DATA_BOX_WIDTH = 300 31 SMEAR_SIZE_L = 0.0032 31 SMEAR_SIZE_H = 0.00 33 32 CUSTOM_MODEL = 'Plugin Models' 34 33 35 34 class FitPage(BasicPage): … … 164 163 On_select_data 165 164 """ 166 if event is None and self.dataSource.GetCount() > 0: 167 data = self.dataSource.GetClientData(0) 168 self.set_data(data) 169 elif self.dataSource.GetCount() > 0: 170 pos = self.dataSource.GetSelection() 165 if self.dataSource.GetCount() > 0: 166 pos = self.dataSource.GetSelection() if event is not None else 0 171 167 data = self.dataSource.GetClientData(pos) 172 168 self.set_data(data) … … 213 209 "Please enter only the value of interest to customize smearing..." 214 210 smear_message_new_psmear = \ 215 "Please enter both; the dQ will be generated by interpolation..."211 "Please enter a fixed percentage to be applied to all Q values..." 216 212 smear_message_2d_x_title = "<dQp>[1/A]:" 217 213 smear_message_2d_y_title = "<dQs>[1/A]:" 218 smear_message_pinhole_min_title = "dQ_low[1/A]:" 219 smear_message_pinhole_max_title = "dQ_high[1/A]:" 214 smear_message_pinhole_percent_title = "dQ[%]:" 220 215 smear_message_slit_height_title = "Slit height[1/A]:" 221 216 smear_message_slit_width_title = "Slit width[1/A]:" … … 256 251 self.Bind(wx.EVT_RADIOBUTTON, self.onWeighting, 257 252 id=self.dI_idata.GetId()) 258 self.dI_ didata.SetValue(True)253 self.dI_noweight.SetValue(True) 259 254 # add 4 types of weighting to the sizer 260 255 sizer_weighting.Add(self.dI_noweight, 0, wx.LEFT, 10) … … 266 261 sizer_weighting.Add(self.dI_idata) 267 262 sizer_weighting.Add((10, 10)) 268 self.dI_noweight.Enable( False)263 self.dI_noweight.Enable(True) 269 264 self.dI_didata.Enable(False) 270 265 self.dI_sqrdata.Enable(False) … … 310 305 311 306 # textcntrl for custom resolution 312 self.smear_pinhole_max = ModelTextCtrl(self, wx.ID_ANY, 313 size=(_BOX_WIDTH - 25, 20), 314 style=wx.TE_PROCESS_ENTER, 315 text_enter_callback=self.onPinholeSmear) 316 self.smear_pinhole_min = ModelTextCtrl(self, wx.ID_ANY, 317 size=(_BOX_WIDTH - 25, 20), 318 style=wx.TE_PROCESS_ENTER, 319 text_enter_callback=self.onPinholeSmear) 307 self.smear_pinhole_percent = ModelTextCtrl(self, wx.ID_ANY, 308 size=(_BOX_WIDTH - 25, 20), 309 style=wx.TE_PROCESS_ENTER, 310 text_enter_callback= 311 self.onPinholeSmear) 320 312 self.smear_slit_height = ModelTextCtrl(self, wx.ID_ANY, 321 313 size=(_BOX_WIDTH - 25, 20), … … 336 328 337 329 # set default values for smear 338 self.smear_pinhole_max.SetValue(str(self.dx_max)) 339 self.smear_pinhole_min.SetValue(str(self.dx_min)) 330 self.smear_pinhole_percent.SetValue(str(self.dx_percent)) 340 331 self.smear_slit_height.SetValue(str(self.dxl)) 341 332 self.smear_slit_width.SetValue(str(self.dxw)) … … 362 353 self.Bind(wx.EVT_RADIOBUTTON, self.onSlitSmear, 363 354 id=self.slit_smearer.GetId()) 364 self. enable_smearer.SetValue(True)355 self.disable_smearer.SetValue(True) 365 356 366 357 sizer_smearer.Add(self.disable_smearer, 0, wx.LEFT, 10) … … 429 420 self.smear_description_2d_y.SetToolTipString( 430 421 " dQs(perpendicular) in q_phi direction.") 431 self.smear_description_pin_min = wx.StaticText(self, wx.ID_ANY, 432 smear_message_pinhole_min_title, style=wx.ALIGN_LEFT) 433 self.smear_description_pin_max = wx.StaticText(self, wx.ID_ANY, 434 smear_message_pinhole_max_title, style=wx.ALIGN_LEFT) 422 self.smear_description_pin_percent = wx.StaticText(self, wx.ID_ANY, 423 smear_message_pinhole_percent_title, 424 style=wx.ALIGN_LEFT) 435 425 self.smear_description_slit_height = wx.StaticText(self, wx.ID_ANY, 436 426 smear_message_slit_height_title, style=wx.ALIGN_LEFT) … … 456 446 self.sizer_new_smear.Add((15, -1)) 457 447 self.sizer_new_smear.Add(self.smear_description_2d_x, 0, wx.CENTER, 10) 458 self.sizer_new_smear.Add(self.smear_description_pin_min,459 0, wx.CENTER, 10)460 448 self.sizer_new_smear.Add(self.smear_description_slit_height, 461 449 0, wx.CENTER, 10) 462 450 463 self.sizer_new_smear.Add(self.smear_pinhole_min, 0, wx.CENTER, 10)464 451 self.sizer_new_smear.Add(self.smear_slit_height, 0, wx.CENTER, 10) 465 452 self.sizer_new_smear.Add(self.smear_data_left, 0, wx.CENTER, 10) … … 467 454 self.sizer_new_smear.Add(self.smear_description_2d_y, 468 455 0, wx.CENTER, 10) 469 self.sizer_new_smear.Add(self.smear_description_pin_ max,456 self.sizer_new_smear.Add(self.smear_description_pin_percent, 470 457 0, wx.CENTER, 10) 471 458 self.sizer_new_smear.Add(self.smear_description_slit_width, 472 459 0, wx.CENTER, 10) 473 460 474 self.sizer_new_smear.Add(self.smear_pinhole_ max, 0, wx.CENTER, 10)461 self.sizer_new_smear.Add(self.smear_pinhole_percent, 0, wx.CENTER, 10) 475 462 self.sizer_new_smear.Add(self.smear_slit_width, 0, wx.CENTER, 10) 476 463 self.sizer_new_smear.Add(self.smear_data_right, 0, wx.CENTER, 10) … … 1249 1236 wx.PostEvent(self.parent, new_event) 1250 1237 # update list of plugins if new plugin is available 1251 custom_model = 'Customized Models'1238 custom_model = CUSTOM_MODEL 1252 1239 mod_cat = self.categorybox.GetStringSelection() 1253 1240 if mod_cat == custom_model: … … 1271 1258 if copy_flag: 1272 1259 self.get_paste_params(copy_flag) 1273 1260 wx.CallAfter(self._onDraw, None) 1274 1261 1275 1262 else: … … 1584 1571 if self.dxw is None: 1585 1572 self.dxw = "" 1586 if self.dx_min is None: 1587 self.dx_min = SMEAR_SIZE_L 1588 if self.dx_max is None: 1589 self.dx_max = SMEAR_SIZE_H 1573 if self.dx_percent is None: 1574 self.dx_percent = SMEAR_SIZE_H 1590 1575 1591 1576 def _get_smear_info(self): … … 1627 1612 elif data.dxl is not None or data.dxw is not None: 1628 1613 self.smear_type = "Slit" 1629 if data.dxl is not None and n ot numpy.all(data.dxl, 0):1614 if data.dxl is not None and numpy.all(data.dxl, 0): 1630 1615 self.dq_l = data.dxl[0] 1631 if data.dxw is not None and n ot numpy.all(data.dxw, 0):1616 if data.dxw is not None and numpy.all(data.dxw, 0): 1632 1617 self.dq_r = data.dxw[0] 1633 1618 # return self.smear_type,self.dq_l,self.dq_r … … 1649 1634 self.smear_description_2d_y.Show(True) 1650 1635 if self.pinhole_smearer.GetValue(): 1651 self.smear_pinhole_min.Show(True) 1652 self.smear_pinhole_max.Show(True) 1636 self.smear_pinhole_percent.Show(True) 1653 1637 # smear from data 1654 1638 elif self.enable_smearer.GetValue(): … … 1661 1645 self.smear_description_slit_width.Show(True) 1662 1646 elif self.smear_type == 'Pinhole': 1663 self.smear_description_pin_min.Show(True) 1664 self.smear_description_pin_max.Show(True) 1647 self.smear_description_pin_percent.Show(True) 1665 1648 self.smear_description_smear_type.Show(True) 1666 1649 self.smear_description_type.Show(True) … … 1671 1654 if self.smear_type == 'Pinhole': 1672 1655 self.smear_message_new_p.Show(True) 1673 self.smear_description_pin_min.Show(True) 1674 self.smear_description_pin_max.Show(True) 1675 1676 self.smear_pinhole_min.Show(True) 1677 self.smear_pinhole_max.Show(True) 1656 self.smear_description_pin_percent.Show(True) 1657 1658 self.smear_pinhole_percent.Show(True) 1678 1659 # custom slit smear 1679 1660 elif self.slit_smearer.GetValue(): … … 1700 1681 self.smear_data_left.Hide() 1701 1682 self.smear_data_right.Hide() 1702 self.smear_description_pin_min.Hide() 1703 self.smear_pinhole_min.Hide() 1704 self.smear_description_pin_max.Hide() 1705 self.smear_pinhole_max.Hide() 1683 self.smear_description_pin_percent.Hide() 1684 self.smear_pinhole_percent.Hide() 1706 1685 self.smear_description_slit_height.Hide() 1707 1686 self.smear_slit_height.Hide() … … 1927 1906 1928 1907 # more disables for 2D 1908 di_flag = False 1909 dq_flag = False 1929 1910 if self.data.__class__.__name__ == "Data2D" or \ 1930 1911 self.enable2D: … … 1932 1913 self.pinhole_smearer.Enable(True) 1933 1914 self.default_mask = copy.deepcopy(self.data.mask) 1934 if self.data.err_data is None or\ 1935 numpy.all(err == 1 for err in self.data.err_data) or \ 1936 not numpy.any(self.data.err_data): 1937 self.dI_didata.Enable(False) 1938 self.dI_noweight.SetValue(True) 1939 self.weightbt_string = self.dI_noweight.GetLabelText() 1940 else: 1941 self.dI_didata.Enable(True) 1942 self.dI_didata.SetValue(True) 1943 self.weightbt_string = self.dI_didata.GetLabelText() 1915 if self.data.err_data is not None \ 1916 and numpy.any(self.data.err_data): 1917 di_flag = True 1918 if self.data.dqx_data is not None \ 1919 and numpy.any(self.data.dqx_data): 1920 dq_flag = True 1944 1921 else: 1945 1922 self.slit_smearer.Enable(True) 1946 1923 self.pinhole_smearer.Enable(True) 1947 1948 if self.data.dy is None or\ 1949 numpy.all(self.data.dy == 1) or\ 1950 not numpy.any(self.data.dy): 1951 self.dI_didata.Enable(False) 1952 self.dI_noweight.SetValue(True) 1953 self.weightbt_string = self.dI_noweight.GetLabelText() 1954 else: 1955 self.dI_didata.Enable(True) 1956 self.dI_didata.SetValue(True) 1957 self.weightbt_string = self.dI_didata.GetLabelText() 1924 if self.data.dy is not None and numpy.any(self.data.dy): 1925 di_flag = True 1926 if self.data.dx is not None and numpy.any(self.data.dx): 1927 dq_flag = True 1928 elif self.data.dxl is not None and numpy.any(self.data.dxl): 1929 dq_flag = True 1930 1931 if dq_flag: 1932 self.enable_smearer.Enable(True) 1933 self.enable_smearer.SetValue(True) 1934 self.disable_smearer.SetValue(False) 1935 else: 1936 self.enable_smearer.Disable() 1937 self.disable_smearer.Enable(True) 1938 self.disable_smearer.SetValue(True) 1939 1940 if di_flag: 1941 self.dI_didata.Enable(True) 1942 self.dI_didata.SetValue(True) 1943 self.weightbt_string = self.dI_didata.GetLabelText() 1944 else: 1945 self.dI_didata.Enable(False) 1946 self.dI_noweight.SetValue(True) 1947 self.weightbt_string = self.dI_noweight.GetLabelText() 1948 1958 1949 # Enable weighting radio buttons 1959 1950 self.dI_noweight.Enable(True) … … 1997 1988 self.EditMask_title.Disable() 1998 1989 1990 self.on_smear_helper() 1999 1991 self.on_set_focus(None) 2000 1992 self.Refresh() … … 2228 2220 # event case of radio button 2229 2221 if tcrtl.GetValue(): 2230 self.dx_min = 0.0 2231 self.dx_max = 0.0 2222 self.dx_percent = 0.0 2232 2223 is_new_pinhole = True 2233 2224 else: … … 2266 2257 """ 2267 2258 # get the values 2268 pin_min = self.smear_pinhole_min.GetValue() 2269 pin_max = self.smear_pinhole_max.GetValue() 2270 2271 # Check changes in slit width 2259 pin_percent = self.smear_pinhole_percent.GetValue() 2260 2261 # Check changes in slit heigth 2272 2262 try: 2273 dx_ min = float(pin_min)2263 dx_percent = float(pin_percent) 2274 2264 except: 2275 2265 return True 2276 if self.dx_min != dx_min: 2277 return True 2278 2279 # Check changes in slit heigth 2280 try: 2281 dx_max = float(pin_max) 2282 except: 2283 return True 2284 if self.dx_max != dx_max: 2266 if self.dx_percent != dx_percent: 2285 2267 return True 2286 2268 return False … … 2308 2290 msg = None 2309 2291 2310 get_pin_min = self.smear_pinhole_min 2311 get_pin_max = self.smear_pinhole_max 2312 2313 if not check_float(get_pin_min): 2314 get_pin_min.SetBackgroundColour("pink") 2315 msg = "Model Error:wrong value entered!!!" 2316 elif not check_float(get_pin_max): 2317 get_pin_max.SetBackgroundColour("pink") 2292 get_pin_percent = self.smear_pinhole_percent 2293 2294 if not check_float(get_pin_percent): 2295 get_pin_percent.SetBackgroundColour("pink") 2318 2296 msg = "Model Error:wrong value entered!!!" 2319 2297 else: 2320 2298 if len_data < 2: 2321 2299 len_data = 2 2322 self.dx_min = float(get_pin_min.GetValue()) 2323 self.dx_max = float(get_pin_max.GetValue()) 2324 if self.dx_min < 0: 2325 get_pin_min.SetBackgroundColour("pink") 2300 self.dx_percent = float(get_pin_percent.GetValue()) 2301 if self.dx_percent < 0: 2302 get_pin_percent.SetBackgroundColour("pink") 2326 2303 msg = "Model Error:This value can not be negative!!!" 2327 elif self.dx_max < 0: 2328 get_pin_max.SetBackgroundColour("pink") 2329 msg = "Model Error:This value can not be negative!!!" 2330 elif self.dx_min is not None and self.dx_max is not None: 2304 elif self.dx_percent is not None: 2305 percent = self.dx_percent/100 2331 2306 if self._is_2D(): 2332 data.dqx_data[data.dqx_data == 0] = self.dx_min 2333 data.dqy_data[data.dqy_data == 0] = self.dx_max 2334 elif self.dx_min == self.dx_max: 2335 data.dx[data.dx == 0] = self.dx_min 2307 data.dqx_data[data.dqx_data == 0] = percent * data.qx_data 2308 data.dqy_data[data.dqy_data == 0] = percent * data.qy_data 2336 2309 else: 2337 step = (self.dx_max - self.dx_min) / (len_data - 1) 2338 data.dx = numpy.arange(self.dx_min, 2339 self.dx_max + step / 1.1, 2340 step) 2341 elif self.dx_min is not None: 2342 if self._is_2D(): 2343 data.dqx_data[data.dqx_data == 0] = self.dx_min 2344 else: 2345 data.dx[data.dx == 0] = self.dx_min 2346 elif self.dx_max is not None: 2347 if self._is_2D(): 2348 data.dqy_data[data.dqy_data == 0] = self.dx_max 2349 else: 2350 data.dx[data.dx == 0] = self.dx_max 2310 data.dx = percent * data.x 2351 2311 self.current_smearer = smear_selection(data, self.model) 2352 2312 # 2D need to set accuracy … … 2358 2318 wx.PostEvent(self._manager.parent, StatusEvent(status=msg)) 2359 2319 else: 2360 get_pin_min.SetBackgroundColour("white") 2361 get_pin_max.SetBackgroundColour("white") 2320 get_pin_percent.SetBackgroundColour("white") 2362 2321 # set smearing value whether or not the data contain the smearing info 2363 2322 -
TabularUnified src/sas/sasgui/perspectives/fitting/fitting.py ¶
r1a8e13f0 r5156918 225 225 226 226 self.id_edit = wx.NewId() 227 editmodel_help = "Edit customized model sample file"228 227 self.menu1.AppendMenu(self.id_edit, "Plugin Model Operations", 229 self.edit_model_menu , editmodel_help)228 self.edit_model_menu) 230 229 #create menubar items 231 230 return [(self.menu1, self.sub_menu)] … … 260 259 self.update_custom_combo() 261 260 if os.path.isfile(p_path): 262 msg = "Sorry! Could not beable to delete the default "263 msg += " custommodel... \n"261 msg = "Sorry! unable to delete the default " 262 msg += "plugin model... \n" 264 263 msg += "Please manually remove the files (.py, .pyc) " 265 264 msg += "in the 'plugin_models' folder \n" … … 274 273 if item.GetLabel() == label: 275 274 self.edit_menu.DeleteItem(item) 276 msg = "The custommodel, %s, has been deleted." % label275 msg = "The plugin model, %s, has been deleted." % label 277 276 evt = StatusEvent(status=msg, type='stop', info='info') 278 277 wx.PostEvent(self.parent, evt) … … 331 330 temp = self.fit_panel.reset_pmodel_list() 332 331 if temp: 333 # Set the new custommodel list for all fit pages332 # Set the new plugin model list for all fit pages 334 333 for uid, page in self.fit_panel.opened_pages.iteritems(): 335 334 if hasattr(page, "formfactorbox"): … … 1746 1745 data_id="Data " + data.name + " unsmeared", 1747 1746 dy=unsmeared_error) 1748 1749 if sq_model is not None and pq_model is not None: 1750 self.create_theory_1D(x, sq_model, page_id, model, data, state, 1751 data_description=model.name + " S(q)", 1752 data_id=str(page_id) + " " + data.name + " S(q)") 1753 self.create_theory_1D(x, pq_model, page_id, model, data, state, 1754 data_description=model.name + " P(q)", 1755 data_id=str(page_id) + " " + data.name + " P(q)") 1756 1747 # Comment this out until we can get P*S models with correctly populated parameters 1748 #if sq_model is not None and pq_model is not None: 1749 # self.create_theory_1D(x, sq_model, page_id, model, data, state, 1750 # data_description=model.name + " S(q)", 1751 # data_id=str(page_id) + " " + data.name + " S(q)") 1752 # self.create_theory_1D(x, pq_model, page_id, model, data, state, 1753 # data_description=model.name + " P(q)", 1754 # data_id=str(page_id) + " " + data.name + " P(q)") 1757 1755 1758 1756 current_pg = self.fit_panel.get_page_by_id(page_id) … … 1955 1953 ## then kill itself but cannot. Paul Kienzle came up with 1956 1954 ## this fix to prevent threads from stepping on each other 1957 ## which was causing a simple custom model to crash Sasview. 1955 ## which was causing a simple custom plugin model to crash 1956 ##Sasview. 1958 1957 ## We still don't know why the fit sometimes lauched a second 1959 1958 ## thread -- something which should also be investigated. -
TabularUnified src/sas/sasgui/perspectives/fitting/media/fitting_help.rst ¶
r26c8be3 r5295cf5 34 34 * in *Single* fit mode - individual data sets are fitted independently one-by-one 35 35 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) 37 39 38 40 * 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!) … … 43 45 ----------------- 44 46 45 By default, the models in SasView are grouped into five categories 46 47 * *Shapes* - models describing 'objects' (spheres, cylinders, etc) 47 The 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) 48 56 * *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) 51 58 * *Structure Factor* - S(Q) models 59 * *Plugin Models* - User-created (custom/non-library) Python models 52 60 53 61 Use the *Category* drop-down menu to chose a category of model, then select … … 84 92 .. image:: cat_fig0.bmp 85 93 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.94 The categorization of all models except the user supplied Plugin Models can be 95 reassigned, added to, and removed using *Category Manager*. Models can also be 96 hidden from view in the drop-down menus. 89 97 90 98 .. image:: cat_fig1.bmp … … 93 101 ^^^^^^^^^^^^^^^^^ 94 102 95 To change category, highlight a model in the list by left-clicking on its entry and96 then click the *Modify* button. Use the *Change Category* panel that appears to make 97 t he required changes.103 To change category, highlight a model in the list by left-clicking on its entry 104 and then click the *Modify* button. Use the *Change Category* panel that appears 105 to make the required changes. 98 106 99 107 .. image:: cat_fig2.bmp … … 106 114 ^^^^^^^^^^^^^^^^^^^^^ 107 115 108 Use the *Enable All / Disable All* buttons and the check boxes beside each model to109 select the models to show/hide. To apply the selection, click *Ok*. Otherwise click 110 *Cancel*.116 Use the *Enable All / Disable All* buttons and the check boxes beside each model 117 to select the models to show/hide. To apply the selection, click *Ok*. Otherwise 118 click *Cancel*. 111 119 112 120 *NB: It may be necessary to change to a different category and then back again* … … 118 126 --------------- 119 127 120 For a complete list of all the library models available in SasView, see the `Model Documentation <../../../index.html>`_ . 128 For a complete list of all the library models available in SasView, see 129 the `Model Documentation <../../../index.html>`_ . 121 130 122 131 It is also possible to add your own models. … … 131 140 There are essentially three ways to generate new fitting models for SasView: 132 141 133 * 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!) 136 149 137 150 Please read the guidance on :ref:`Writing_a_Plugin` before proceeding. … … 163 176 ^^^^^^^^^^^^^^^^ 164 177 165 Relatively straightforward models can be programmed directly from the SasView GUI166 using the *New Plugin Model Function*.178 Relatively straightforward models can be programmed directly from the SasView 179 GUI using the *New Plugin Model Function*. 167 180 168 181 .. image:: new_model.bmp … … 175 188 *checked*\ . 176 189 177 Also note that the 'Fit Parameters' have been split into two sections: those which178 can be polydisperse (shape and orientation parameters) and those which are not 179 (eg, scattering length densities).190 Also note that the 'Fit Parameters' have been split into two sections: those 191 which can be polydisperse (shape and orientation parameters) and those which are 192 not (eg, scattering length densities). 180 193 181 194 A model file generated by this option can be viewed and further modified using … … 187 200 .. image:: sum_model.bmp 188 201 189 This option creates a custom model of the form::190 191 Custom Model = scale_factor \* {(scale_1 \* model_1) \+ (scale_2 \* model_2)} \+ background202 This option creates a custom Plugin Model of the form:: 203 204 Plugin Model = scale_factor * {(scale_1 * model_1) +/- (scale_2 * model_2)} + background 192 205 193 206 or:: 194 207 195 Custom Model = scale_factor \* model_1 \* model_2 \+ background208 Plugin Model = scale_factor * model_1 /* model_2 + background 196 209 197 210 In the *Easy Sum/Multi Editor* give the new model a function name and brief … … 232 245 Simply highlight the plugin model to be removed. The operation is final!!! 233 246 234 *NB: Plugin models shipped with SasView cannot be removed in this way.*247 *NB: Models shipped with SasView cannot be removed in this way.* 235 248 236 249 Load Plugin Models 237 250 ^^^^^^^^^^^^^^^^^^ 238 251 239 This option loads (or re-loads) all models present in the *~\\.sasview\\plugin_models* folder. 252 This option loads (or re-loads) all models present in the 253 *~\\.sasview\\plugin_models* folder. 240 254 241 255 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ … … 400 414 :ref:`Assessing_Fit_Quality`. 401 415 402 *NB: If you need to use a custom ized 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 417 available first (see* :ref:`Adding_your_own_models` *).* 404 418 405 419 Method … … 484 498 If multiple data sets are in one file, load just that file. *Unselect All Data*, then 485 499 select 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 custom ized model, you must ensure that model is available*489 *first (see* :ref:`Adding_your_own_models` *).*500 above under :ref:`Single_Fit_Mode`. 501 502 *NB: If you need to use a custom Plugin Model, you must ensure that model is 503 available first (see* :ref:`Adding_your_own_models` *).* 490 504 491 505 Method -
TabularUnified src/sas/sasgui/perspectives/fitting/media/plugin.rst ¶
rca6cbc1c r984f3fc 27 27 28 28 the next time SasView is started it will compile the plugin and add 29 it to the list of * CustomizedModels* in a FitPage.29 it to the list of *Plugin Models* in a FitPage. 30 30 31 31 SasView models can be of three types: … … 364 364 - the limits will show up as the default limits for the fit making it easy, 365 365 for example, to force the radius to always be greater than zero. 366 367 - these are hard limits defining the valid range of parameter values; 368 polydisperity distributions will be truncated at the limits. 366 369 367 370 - **"type"** can be one of: "", "sld", "volume", or "orientation". -
TabularUnified src/sas/sasgui/perspectives/fitting/model_thread.py ¶
rc1681ea rc1c9929 177 177 unsmeared_output = numpy.zeros((len(self.data.x))) 178 178 unsmeared_output[first_bin:last_bin+1] = self.model.evalDistribution(mask) 179 self.smearer.model = self.model 179 180 output = self.smearer(unsmeared_output, first_bin, last_bin) 180 181 -
TabularUnified src/sas/sasgui/perspectives/fitting/models.py ¶
r0de74af r11b094f 325 325 self.plugins.append(plug) 326 326 self.model_dictionary[name] = plug 327 self.model_combobox.set_list(" CustomizedModels", self.plugins)327 self.model_combobox.set_list("Plugin Models", self.plugins) 328 328 return self.model_combobox.get_list() 329 329 else: … … 346 346 self.model_dictionary[name] = plug 347 347 348 self.model_combobox.reset_list(" CustomizedModels", self.plugins)348 self.model_combobox.reset_list("Plugin Models", self.plugins) 349 349 return self.model_combobox.get_list() 350 350 … … 389 389 # self.shape_indep_list) 390 390 self.model_combobox.set_list("Structure Factors", self.struct_list) 391 self.model_combobox.set_list(" CustomizedModels", self.plugins)391 self.model_combobox.set_list("Plugin Models", self.plugins) 392 392 self.model_combobox.set_list("P(Q)*S(Q)", self.multiplication_factor) 393 393 self.model_combobox.set_list("multiplication", -
TabularUnified src/sas/sasgui/perspectives/fitting/pagestate.py ¶
r6d2b50b r27109e5 33 33 from sas.sascalc.dataloader.data_info import Data2D, Collimation, Detector 34 34 from sas.sascalc.dataloader.data_info import Process, Aperture 35 35 36 # Information to read/write state as xml 36 37 FITTING_NODE_NAME = 'fitting_plug_in' 37 38 CANSAS_NS = "cansas1d/1.0" 39 40 CUSTOM_MODEL = 'Plugin Models' 41 CUSTOM_MODEL_OLD = 'Customized Models' 38 42 39 43 LIST_OF_DATA_ATTRIBUTES = [["is_data", "is_data", "bool"], … … 70 74 ["dq_l", "dq_l", "float"], 71 75 ["dq_r", "dq_r", "float"], 72 ["dx_max", "dx_max", "float"], 73 ["dx_min", "dx_min", "float"], 76 ["dx_percent", "dx_percent", "float"], 74 77 ["dxl", "dxl", "float"], 75 78 ["dxw", "dxw", "float"]] … … 211 214 self.dq_l = None 212 215 self.dq_r = None 213 self.dx_ max= None214 self.dx_ min = None216 self.dx_percent = None 217 self.dx_old = False 215 218 self.dxl = None 216 219 self.dxw = None … … 339 342 obj.dq_l = copy.deepcopy(self.dq_l) 340 343 obj.dq_r = copy.deepcopy(self.dq_r) 341 obj.dx_ max = copy.deepcopy(self.dx_max)342 obj.dx_ min = copy.deepcopy(self.dx_min)344 obj.dx_percent = copy.deepcopy(self.dx_percent) 345 obj.dx_old = copy.deepcopy(self.dx_old) 343 346 obj.dxl = copy.deepcopy(self.dxl) 344 347 obj.dxw = copy.deepcopy(self.dxw) … … 366 369 :return: None 367 370 """ 371 if self.categorycombobox == CUSTOM_MODEL_OLD: 372 self.categorycombobox = CUSTOM_MODEL 368 373 if self.formfactorcombobox == '': 369 374 FIRST_FORM = { … … 378 383 'Sphere' : 'adsorbed_layer', 379 384 'Structure Factor' : 'hardsphere', 380 'Customized Models': ''385 CUSTOM_MODEL : '' 381 386 } 382 387 if self.categorycombobox == '': … … 556 561 rep += "dq_l : %s\n" % self.dq_l 557 562 rep += "dq_r : %s\n" % self.dq_r 558 rep += "dx_max : %s\n" % str(self.dx_max) 559 rep += "dx_min : %s\n" % str(self.dx_min) 563 rep += "dx_percent : %s\n" % str(self.dx_percent) 560 564 rep += "dxl : %s\n" % str(self.dxl) 561 565 rep += "dxw : %s\n" % str(self.dxw) … … 815 819 816 820 attr = newdoc.createAttribute("version") 817 import sasview821 from sas import sasview 818 822 attr.nodeValue = sasview.__version__ 819 823 # attr.nodeValue = '1.0' … … 1042 1046 setattr(self, item[0], parse_entry_helper(node, item)) 1043 1047 1048 dx_old_node = get_content('ns:%s' % 'dx_min', entry) 1044 1049 for item in LIST_OF_STATE_ATTRIBUTES: 1045 node = get_content('ns:%s' % item[0], entry) 1046 setattr(self, item[0], parse_entry_helper(node, item)) 1050 if item[0] == "dx_percent" and dx_old_node is not None: 1051 dxmin = ["dx_min", "dx_min", "float"] 1052 setattr(self, item[0], parse_entry_helper(dx_old_node, 1053 dxmin)) 1054 self.dx_old = True 1055 else: 1056 node = get_content('ns:%s' % item[0], entry) 1057 setattr(self, item[0], parse_entry_helper(node, item)) 1047 1058 1048 1059 for item in LIST_OF_STATE_PARAMETERS: -
TabularUnified src/sas/sasgui/plottools/plottables.py ¶
r345e7e4 ra9f579c 1023 1023 """ 1024 1024 1025 def __init__(self, x, y, dx=None, dy=None ):1025 def __init__(self, x, y, dx=None, dy=None, lam=None, dlam=None): 1026 1026 """ 1027 1027 Draw points specified by x[i],y[i] in the current color/symbol. … … 1037 1037 self.x = x 1038 1038 self.y = y 1039 self.lam = lam 1039 1040 self.dx = dx 1040 1041 self.dy = dy 1042 self.dlam = dlam 1041 1043 self.source = None 1042 1044 self.detector = None
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