Changeset 24c382a in sasview
- Timestamp:
- Apr 6, 2017 9:20:42 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:
- 4c7aa9c
- Parents:
- cc47336 (diff), ec8886e (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. - Files:
-
- 3 added
- 6 edited
Legend:
- Unmodified
- Added
- Removed
-
src/sas/sascalc/dataloader/data_info.py
r747334d rc44baf97 353 353 details = None 354 354 ## SESANS zacceptance 355 zacceptance = None356 yacceptance = None355 zacceptance = (0,"") 356 yacceptance = (0,"") 357 357 358 358 def __init__(self): -
src/sas/sasgui/guiframe/media/data_formats_help.rst
r98c44f3 r76c4469 86 86 87 87 - Spin echo length (z, in Angstroms) 88 - depolarization (:math:`log(P/P_0)/(lambda^2 * thickness)`, in Angstrom ^-1 cm^-1)88 - depolarization (:math:`log(P/P_0)/(lambda^2 * thickness)`, in Angstrom :sup:`-1` cm :sup:`-1`\ ) 89 89 - depolarization error in the same unit) (measurement error) 90 90 - Spin echo length error (:math:`\Delta`\ z, in Angstroms) (experimental resolution) -
src/sas/sasgui/plottools/LineModel.py
rdd5bf63 rec8886e 8 8 function should disappear in a future iteration (see notes in fitDialog) 9 9 10 -PDB July 10, 2016 10 PDB July 10, 2016 11 11 12 """ 12 13 … … 70 71 runXY is when the if statement is true. I however cannot see what that 71 72 function is for. It needs to be documented here or removed. 72 -PDB 7/10/1673 PDB 7/10/16 73 74 74 75 :param x: simple value … … 92 93 but the only difference between this and run is when the if 93 94 statement is true. I however cannot see what that function 94 is for. It needs to be documented here or removed. -PDB 7/10/1695 is for. It needs to be documented here or removed. PDB 7/10/16 95 96 96 97 :param x: simple value -
sasview/test/sesans_data/sphere2micron.ses
r2a2b43a rd3bce8c 1 DataFileTitle "Polystyrene of Markus Strobl, Full Sine, ++ only " 2 Sample "Polystyrene 2 um in 53% H2O, 47% D2O " 3 Settings "D1=D2=20x8 mm,Ds = 16x10 mm (WxH), GF1 =scanning, GF2 = 2.5 A. 2 um polystyrene in 53% H2O, 47% D2O; 8.55% contrast " 4 Operator CPD 5 Date do 10 jul 2014 16:37:30 6 ScanType sine one element scan 7 Thickness [cm] 2.00E-01 8 Q_zmax [\A^-1] 0.05 9 Q_ymax [\A^-1] 0.05 10 11 spin echo length [A] Depolarisation [A-2 cm-1] error depol [A-2 cm-1] error SEL [A] wavelength [A] error wavelength [A] polarisation error pol 12 391.56 0.0041929 0.0036894 19.578 2.11 0.1055 1.0037 0.0032974 13 1564 -0.0046571 0.0038185 78.2 2.11 0.1055 0.99586 0.003386 14 2735.6 -0.017007 0.0038132 136.78 2.11 0.1055 0.98497 0.0033444 15 3907.9 -0.033462 0.0035068 195.39 2.11 0.1055 0.97064 0.0030309 16 5080.2 -0.047483 0.0038208 254.01 2.11 0.1055 0.9586 0.0032613 17 6251.8 -0.070375 0.00376 312.59 2.11 0.1055 0.93926 0.0031446 18 7423.2 -0.092217 0.0037927 371.16 2.11 0.1055 0.92117 0.0031108 19 8595.5 -0.10238 0.004006 429.77 2.11 0.1055 0.91287 0.0032562 20 9767.7 -0.12672 0.0038534 488.39 2.11 0.1055 0.8933 0.0030651 21 10940 -0.1374 0.004243 546.98 2.11 0.1055 0.88484 0.003343 22 12112 -0.16072 0.0045837 605.58 2.11 0.1055 0.86666 0.0035372 23 13284 -0.16623 0.0045613 664.2 2.11 0.1055 0.86242 0.0035027 24 14456 -0.18468 0.0044918 722.79 2.11 0.1055 0.84837 0.0033931 25 15628 -0.19143 0.0048967 781.38 2.11 0.1055 0.84328 0.0036768 26 16800 -0.20029 0.0045421 840.02 2.11 0.1055 0.83666 0.0033837 27 17971 -0.19798 0.0046642 898.56 2.11 0.1055 0.83838 0.0034819 28 19143 -0.21442 0.0047052 957.17 2.11 0.1055 0.82619 0.0034614 29 20316 -0.20885 0.0044931 1015.8 2.11 0.1055 0.8303 0.0033218 30 21488 -0.21393 0.0049186 1074.4 2.11 0.1055 0.82655 0.00362 31 22660 -0.20685 0.004423 1133 2.11 0.1055 0.83179 0.0032758 32 23832 -0.20802 0.0046979 1191.6 2.11 0.1055 0.83092 0.0034758 33 25003 -0.19848 0.0045953 1250.2 2.11 0.1055 0.838 0.0034289 34 26175 -0.21117 0.0044567 1308.8 2.11 0.1055 0.82859 0.0032881 35 27347 -0.21283 0.004137 1367.4 2.11 0.1055 0.82736 0.0030477 36 28520 -0.2042 0.0044587 1426 2.11 0.1055 0.83375 0.0033101 37 29692 -0.2112 0.0042852 1484.6 2.11 0.1055 0.82857 0.0031615 38 30864 -0.20319 0.0043483 1543.2 2.11 0.1055 0.8345 0.003231 39 32036 -0.20752 0.0044297 1601.8 2.11 0.1055 0.83129 0.0032788 40 33207 -0.20654 0.0043188 1660.4 2.11 0.1055 0.83201 0.0031995 41 34380 -0.20126 0.0046375 1719 2.11 0.1055 0.83593 0.0034518 42 35551 -0.20924 0.0042871 1777.6 2.11 0.1055 0.83001 0.0031684 43 36724 -0.21323 0.0045471 1836.2 2.11 0.1055 0.82707 0.0033487 44 37895 -0.21324 0.0045354 1894.7 2.11 0.1055 0.82706 0.00334 45 39067 -0.19905 0.0044141 1953.4 2.11 0.1055 0.83758 0.003292 46 40239 -0.1991 0.0047441 2012 2.11 0.1055 0.83754 0.003538 47 41411 -0.20359 0.0050136 2070.5 2.11 0.1055 0.8342 0.003724 48 42583 -0.21032 0.0049474 2129.1 2.11 0.1055 0.82922 0.0036529 49 43755 -0.20689 0.0048203 2187.8 2.11 0.1055 0.83176 0.00357 50 44927 -0.21075 0.0052337 2246.4 2.11 0.1055 0.8289 0.0038628 51 46099 -0.19956 0.0047827 2304.9 2.11 0.1055 0.8372 0.0035653 1 FileFormatVersion 1.0 2 DataFileTitle Polystyrene of Markus Strobl, Full Sine, ++ only 3 Sample Polystyrene 2 um in 53% H2O, 47% D2O 4 Settings D1=D2=20x8 mm,Ds = 16x10 mm (WxH), GF1 =scanning, GF2 = 2.5 A. 2 um polystyrene in 53% H2O, 47% D2O; 8.55% contrast 5 Operator CPD 6 Date do 10 jul 2014 16:37:30 7 ScanType sine one element scan 8 Thickness 2.00E-01 9 Thickness_unit cm 10 Theta_zmax 0.0168 11 Theta_zmax_unit radians 12 Theta_ymax 0.0168 13 Theta_ymax_unit radians 14 Orientation Z 15 SpinEchoLength_unit A 16 Depolarisation_unit A-2 cm-1 17 Wavelength_unit A 18 19 BEGIN_DATA 20 SpinEchoLength Depolarisation Depolarisation_error SpinEchoLength_error Wavelength Wavelength_error Polarisation Polarisation_error 21 391.56 0.0041929 0.0036894 19.578 2.11 0.1055 1.0037 0.0032974 22 1564 -0.0046571 0.0038185 78.2 2.11 0.1055 0.99586 0.003386 23 2735.6 -0.017007 0.0038132 136.78 2.11 0.1055 0.98497 0.0033444 24 3907.9 -0.033462 0.0035068 195.39 2.11 0.1055 0.97064 0.0030309 25 5080.2 -0.047483 0.0038208 254.01 2.11 0.1055 0.9586 0.0032613 26 6251.8 -0.070375 0.00376 312.59 2.11 0.1055 0.93926 0.0031446 27 7423.2 -0.092217 0.0037927 371.16 2.11 0.1055 0.92117 0.0031108 28 8595.5 -0.10238 0.004006 429.77 2.11 0.1055 0.91287 0.0032562 29 9767.7 -0.12672 0.0038534 488.39 2.11 0.1055 0.8933 0.0030651 30 10940 -0.1374 0.004243 546.98 2.11 0.1055 0.88484 0.003343 31 12112 -0.16072 0.0045837 605.58 2.11 0.1055 0.86666 0.0035372 32 13284 -0.16623 0.0045613 664.2 2.11 0.1055 0.86242 0.0035027 33 14456 -0.18468 0.0044918 722.79 2.11 0.1055 0.84837 0.0033931 34 15628 -0.19143 0.0048967 781.38 2.11 0.1055 0.84328 0.0036768 35 16800 -0.20029 0.0045421 840.02 2.11 0.1055 0.83666 0.0033837 36 17971 -0.19798 0.0046642 898.56 2.11 0.1055 0.83838 0.0034819 37 19143 -0.21442 0.0047052 957.17 2.11 0.1055 0.82619 0.0034614 38 20316 -0.20885 0.0044931 1015.8 2.11 0.1055 0.8303 0.0033218 39 21488 -0.21393 0.0049186 1074.4 2.11 0.1055 0.82655 0.00362 40 22660 -0.20685 0.004423 1133 2.11 0.1055 0.83179 0.0032758 41 23832 -0.20802 0.0046979 1191.6 2.11 0.1055 0.83092 0.0034758 42 25003 -0.19848 0.0045953 1250.2 2.11 0.1055 0.838 0.0034289 43 26175 -0.21117 0.0044567 1308.8 2.11 0.1055 0.82859 0.0032881 44 27347 -0.21283 0.004137 1367.4 2.11 0.1055 0.82736 0.0030477 45 28520 -0.2042 0.0044587 1426 2.11 0.1055 0.83375 0.0033101 46 29692 -0.2112 0.0042852 1484.6 2.11 0.1055 0.82857 0.0031615 47 30864 -0.20319 0.0043483 1543.2 2.11 0.1055 0.8345 0.003231 48 32036 -0.20752 0.0044297 1601.8 2.11 0.1055 0.83129 0.0032788 49 33207 -0.20654 0.0043188 1660.4 2.11 0.1055 0.83201 0.0031995 50 34380 -0.20126 0.0046375 1719 2.11 0.1055 0.83593 0.0034518 51 35551 -0.20924 0.0042871 1777.6 2.11 0.1055 0.83001 0.0031684 52 36724 -0.21323 0.0045471 1836.2 2.11 0.1055 0.82707 0.0033487 53 37895 -0.21324 0.0045354 1894.7 2.11 0.1055 0.82706 0.00334 54 39067 -0.19905 0.0044141 1953.4 2.11 0.1055 0.83758 0.003292 55 40239 -0.1991 0.0047441 2012 2.11 0.1055 0.83754 0.003538 56 41411 -0.20359 0.0050136 2070.5 2.11 0.1055 0.8342 0.003724 57 42583 -0.21032 0.0049474 2129.1 2.11 0.1055 0.82922 0.0036529 58 43755 -0.20689 0.0048203 2187.8 2.11 0.1055 0.83176 0.00357 59 44927 -0.21075 0.0052337 2246.4 2.11 0.1055 0.8289 0.0038628 60 46099 -0.19956 0.0047827 2304.9 2.11 0.1055 0.8372 0.0035653 -
src/sas/sascalc/data_util/qsmearing.py
r9a5097c rd01b55c 67 67 if _found_sesans == True: 68 68 #Pre-compute the Hankel matrix (H) 69 qmax, qunits = data.sample.zacceptance70 69 SElength = Converter(data._xunit)(data.x, "A") 71 zaccept = Converter(qunits)(qmax, "1/A"), 70 71 theta_max = Converter("radians")(data.sample.zacceptance)[0] 72 q_max = 2 * np.pi / np.max(data.source.wavelength) * np.sin(theta_max) 73 zaccept = Converter("1/A")(q_max, "1/" + data.source.wavelength_unit), 74 72 75 Rmax = 10000000 73 hankel = SesansTransform(data.x, SElength, zaccept, Rmax)76 hankel = SesansTransform(data.x, SElength, data.source.wavelength, zaccept, Rmax) 74 77 # Then return the actual transform, as if it were a smearing function 75 78 return PySmear(hankel, model, offset=0) -
src/sas/sascalc/dataloader/readers/sesans_reader.py
r9a5097c r857cc58 1 1 """ 2 2 SESANS reader (based on ASCII reader) 3 3 4 4 Reader for .ses or .sesans file format 5 6 Jurrian Bakker 5 6 Jurrian Bakker 7 7 """ 8 import logging 8 9 import numpy as np 9 10 import os … … 18 19 _ZERO = 1e-16 19 20 21 20 22 class Reader: 21 23 """ 22 24 Class to load sesans files (6 columns). 23 25 """ 24 # #File type26 # File type 25 27 type_name = "SESANS" 26 27 # #Wildcards28 29 # Wildcards 28 30 type = ["SESANS files (*.ses)|*.ses", 29 31 "SESANS files (*..sesans)|*.sesans"] 30 # #List of allowed extensions32 # List of allowed extensions 31 33 ext = ['.ses', '.SES', '.sesans', '.SESANS'] 32 33 # #Flag to bypass extension check34 35 # Flag to bypass extension check 34 36 allow_all = True 35 37 36 38 def read(self, path): 37 38 # print "reader triggered"39 40 39 """ 41 40 Load data file 42 41 43 42 :param path: file path 44 43 45 44 :return: SESANSData1D object, or None 46 45 47 46 :raise RuntimeError: when the file can't be opened 48 47 :raise ValueError: when the length of the data vectors are inconsistent … … 51 50 basename = os.path.basename(path) 52 51 _, extension = os.path.splitext(basename) 53 if self.allow_all or extension.lower() in self.ext: 54 try: 55 # Read in binary mode since GRASP frequently has no-ascii 56 # characters that brakes the open operation 57 input_f = open(path,'rb') 58 except: 59 raise RuntimeError, "sesans_reader: cannot open %s" % path 60 buff = input_f.read() 61 lines = buff.splitlines() 62 x = np.zeros(0) 63 y = np.zeros(0) 64 dy = np.zeros(0) 65 lam = np.zeros(0) 66 dlam = np.zeros(0) 67 dx = np.zeros(0) 68 69 #temp. space to sort data 70 tx = np.zeros(0) 71 ty = np.zeros(0) 72 tdy = np.zeros(0) 73 tlam = np.zeros(0) 74 tdlam = np.zeros(0) 75 tdx = np.zeros(0) 76 output = Data1D(x=x, y=y, lam=lam, dy=dy, dx=dx, dlam=dlam, isSesans=True) 77 self.filename = output.filename = basename 52 if not (self.allow_all or extension.lower() in self.ext): 53 raise RuntimeError("{} has an unrecognized file extension".format(path)) 54 else: 55 raise RunetimeError("{} is not a file".format(path)) 56 with open(path, 'r') as input_f: 57 # Read in binary mode since GRASP frequently has no-ascii 58 # characters that brakes the open operation 59 line = input_f.readline() 60 params = {} 61 while not line.startswith("BEGIN_DATA"): 62 terms = line.split() 63 if len(terms) >= 2: 64 params[terms[0]] = " ".join(terms[1:]) 65 line = input_f.readline() 66 self.params = params 67 headers = input_f.readline().split() 78 68 79 paramnames=[] 80 paramvals=[] 81 zvals=[] 82 dzvals=[] 83 lamvals=[] 84 dlamvals=[] 85 Pvals=[] 86 dPvals=[] 69 data = np.loadtxt(input_f) 70 if data.size < 1: 71 raise RuntimeError("{} is empty".format(path)) 72 x = data[:, headers.index("SpinEchoLength")] 73 if "SpinEchoLength_error" in headers: 74 dx = data[:, headers.index("SpinEchoLength_error")] 75 else: 76 dx = x*0.05 77 lam = data[:, headers.index("Wavelength")] 78 if "Wavelength_error" in headers: 79 dlam = data[:, headers.index("Wavelength_error")] 80 else: 81 dlam = lam*0.05 82 y = data[:, headers.index("Depolarisation")] 83 dy = data[:, headers.index("Depolarisation_error")] 87 84 88 for line in lines: 89 # Initial try for CSV (split on ,) 90 line=line.strip() 91 toks = line.split('\t') 92 if len(toks)==2: 93 paramnames.append(toks[0]) 94 paramvals.append(toks[1]) 95 if len(toks)>5: 96 zvals.append(toks[0]) 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]) 102 else: 103 continue 85 lam_unit = self._unit_fetch("Wavelength") 86 x, x_unit = self._unit_conversion(x, "A", self._unit_fetch("SpinEchoLength")) 87 dx, dx_unit = self._unit_conversion( 88 dx, lam_unit, 89 self._unit_fetch("SpinEchoLength")) 90 dlam, dlam_unit = self._unit_conversion( 91 dlam, lam_unit, 92 self._unit_fetch("Wavelength")) 93 y_unit = self._unit_fetch("Depolarisation") 104 94 105 x=[] 106 y=[] 107 lam=[] 108 dx=[] 109 dy=[] 110 dlam=[] 111 lam_header = lamvals[0].split() 112 data_conv_z = None 113 default_z_unit = "A" 114 data_conv_P = None 115 default_p_unit = " " # Adjust unit for axis (L^-3) 116 lam_unit = lam_header[1].replace("[","").replace("]","") 117 if lam_unit == 'AA': 118 lam_unit = 'A' 119 varheader=[zvals[0],dzvals[0],lamvals[0],dlamvals[0],Pvals[0],dPvals[0]] 120 valrange=range(1, len(zvals)) 121 for i in valrange: 122 x.append(float(zvals[i])) 123 y.append(float(Pvals[i])) 124 lam.append(float(lamvals[i])) 125 dy.append(float(dPvals[i])) 126 dx.append(float(dzvals[i])) 127 dlam.append(float(dlamvals[i])) 95 output = Data1D(x=x, y=y, lam=lam, dy=dy, dx=dx, dlam=dlam, 96 isSesans=True) 128 97 129 x,y,lam,dy,dx,dlam = [ 130 np.asarray(v, 'double') 131 for v in (x,y,lam,dy,dx,dlam) 132 ] 98 output.y_unit = y_unit 99 output.x_unit = x_unit 100 output.source.wavelength_unit = lam_unit 101 output.source.wavelength = lam 102 self.filename = output.filename = basename 103 output.xaxis(r"\rm{z}", x_unit) 104 # Adjust label to ln P/(lam^2 t), remove lam column refs 105 output.yaxis(r"\rm{ln(P)/(t \lambda^2)}", y_unit) 106 # Store loading process information 107 output.meta_data['loader'] = self.type_name 108 output.sample.name = params["Sample"] 109 output.sample.ID = params["DataFileTitle"] 110 output.sample.thickness = self._unit_conversion( 111 float(params["Thickness"]), "cm", 112 self._unit_fetch("Thickness"))[0] 133 113 134 input_f.close() 114 output.sample.zacceptance = ( 115 float(params["Theta_zmax"]), 116 self._unit_fetch("Theta_zmax")) 135 117 136 output.x, output.x_unit = self._unit_conversion(x, lam_unit, default_z_unit) 137 output.y = y 138 output.y_unit = r'\AA^{-2} cm^{-1}' # output y_unit added 139 output.dx, output.dx_unit = self._unit_conversion(dx, lam_unit, default_z_unit) 140 output.dy = dy 141 output.lam, output.lam_unit = self._unit_conversion(lam, lam_unit, default_z_unit) 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 118 output.sample.yacceptance = ( 119 float(params["Theta_ymax"]), 120 self._unit_fetch("Theta_ymax")) 121 return output 146 122 147 # Store loading process information 148 output.meta_data['loader'] = self.type_name 149 #output.sample.thickness = float(paramvals[6]) 150 output.sample.name = paramvals[1] 151 output.sample.ID = paramvals[0] 152 zaccept_unit_split = paramnames[7].split("[") 153 zaccept_unit = zaccept_unit_split[1].replace("]","") 154 if zaccept_unit.strip() == r'\AA^-1' or zaccept_unit.strip() == r'\A^-1': 155 zaccept_unit = "1/A" 156 output.sample.zacceptance=(float(paramvals[7]),zaccept_unit) 157 output.vars = varheader 123 @staticmethod 124 def _unit_conversion(value, value_unit, default_unit): 125 """ 126 Performs unit conversion on a measurement. 158 127 159 if len(output.x) < 1: 160 raise RuntimeError, "%s is empty" % path 161 return output 162 163 else: 164 raise RuntimeError, "%s is not a file" % path 165 return None 166 167 def _unit_conversion(self, value, value_unit, default_unit): 168 if has_converter == True and value_unit != default_unit: 169 data_conv_q = Converter(value_unit) 170 value = data_conv_q(value, units=default_unit) 128 :param value: The magnitude of the measurement 129 :param value_unit: a string containing the final desired unit 130 :param default_unit: a string containing the units of the original measurement 131 :return: The magnitude of the measurement in the new units 132 """ 133 # (float, string, string) -> float 134 if has_converter and value_unit != default_unit: 135 data_conv_q = Converter(default_unit) 136 value = data_conv_q(value, units=value_unit) 171 137 new_unit = default_unit 172 138 else: 173 139 new_unit = value_unit 174 140 return value, new_unit 141 142 def _unit_fetch(self, unit): 143 return self.params[unit+"_unit"]
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