Changes in / [5d1e040:5b2b04d] in sasview
- Files:
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- 9 deleted
- 3 edited
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sasview/test/sesans_data/sphere2micron.ses (modified) (1 diff)
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sasview/test/sesans_data/sphere_isis.ses (deleted)
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src/sas/sascalc/data_util/qsmearing.py (modified) (1 diff)
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src/sas/sascalc/dataloader/readers/sesans_reader.py (modified) (3 diffs)
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test/sasdataloader/test/sesans_examples/next_gen.ses (deleted)
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test/sasdataloader/test/sesans_examples/no_spin_echo_unit.ses (deleted)
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test/sasdataloader/test/sesans_examples/no_wavelength.ses (deleted)
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test/sasdataloader/test/sesans_examples/sesans_no_data.ses (deleted)
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test/sasdataloader/test/sesans_examples/sphere2micron.ses (deleted)
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test/sasdataloader/test/sesans_examples/sphere_isis.ses (deleted)
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test/sasdataloader/test/sesans_examples/too_many_headers.ses (deleted)
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test/sasdataloader/test/utest_sesans.py (deleted)
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sasview/test/sesans_data/sphere2micron.ses
rd3bce8c r2a2b43a 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 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 -
src/sas/sascalc/data_util/qsmearing.py
re962d85 r9a5097c 65 65 raise ValueError('one or more of your dx values are negative, please check the data file!') 66 66 67 if _found_sesans: 68 # Pre-compute the Hankel matrix (H) 67 if _found_sesans == True: 68 #Pre-compute the Hankel matrix (H) 69 qmax, qunits = data.sample.zacceptance 69 70 SElength = Converter(data._xunit)(data.x, "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 71 zaccept = Converter(qunits)(qmax, "1/A"), 75 72 Rmax = 10000000 76 hankel = SesansTransform(data.x, SElength, 77 data.source.wavelength, 78 zaccept, Rmax) 73 hankel = SesansTransform(data.x, SElength, zaccept, Rmax) 79 74 # Then return the actual transform, as if it were a smearing function 80 75 return PySmear(hankel, model, offset=0) -
src/sas/sascalc/dataloader/readers/sesans_reader.py
rf6c2555 r9a5097c 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 8 import numpy as np … … 18 18 _ZERO = 1e-16 19 19 20 21 20 class Reader: 22 21 """ 23 22 Class to load sesans files (6 columns). 24 23 """ 25 # File type24 ## File type 26 25 type_name = "SESANS" 27 28 # Wildcards26 27 ## Wildcards 29 28 type = ["SESANS files (*.ses)|*.ses", 30 29 "SESANS files (*..sesans)|*.sesans"] 31 # List of allowed extensions30 ## List of allowed extensions 32 31 ext = ['.ses', '.SES', '.sesans', '.SESANS'] 33 34 # Flag to bypass extension check32 33 ## Flag to bypass extension check 35 34 allow_all = True 36 35 37 36 def read(self, path): 37 38 # print "reader triggered" 39 38 40 """ 39 41 Load data file 40 42 41 43 :param path: file path 42 44 43 45 :return: SESANSData1D object, or None 44 46 45 47 :raise RuntimeError: when the file can't be opened 46 48 :raise ValueError: when the length of the data vectors are inconsistent … … 49 51 basename = os.path.basename(path) 50 52 _, extension = os.path.splitext(basename) 51 if not (self.allow_all or extension.lower() in self.ext): 52 raise RuntimeError( 53 "{} has an unrecognized file extension".format(path)) 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 78 79 paramnames=[] 80 paramvals=[] 81 zvals=[] 82 dzvals=[] 83 lamvals=[] 84 dlamvals=[] 85 Pvals=[] 86 dPvals=[] 87 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 104 105 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])) 128 129 x,y,lam,dy,dx,dlam = [ 130 np.asarray(v, 'double') 131 for v in (x,y,lam,dy,dx,dlam) 132 ] 133 134 input_f.close() 135 136 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 146 147 # 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 158 159 if len(output.x) < 1: 160 raise RuntimeError, "%s is empty" % path 161 return output 162 54 163 else: 55 raise RuntimeError("{} is not a file".format(path)) 56 with open(path, 'r') as input_f: 57 line = input_f.readline() 58 params = {} 59 while not line.startswith("BEGIN_DATA"): 60 terms = line.split() 61 if len(terms) >= 2: 62 params[terms[0]] = " ".join(terms[1:]) 63 line = input_f.readline() 64 self.params = params 164 raise RuntimeError, "%s is not a file" % path 165 return None 65 166 66 if "FileFormatVersion" not in self.params: 67 raise RuntimeError("SES file missing FileFormatVersion") 68 if float(self.params["FileFormatVersion"]) >= 2.0: 69 raise RuntimeError("SASView only supports SES version 1") 70 71 if "SpinEchoLength_unit" not in self.params: 72 raise RuntimeError("SpinEchoLength has no units") 73 if "Wavelength_unit" not in self.params: 74 raise RuntimeError("Wavelength has no units") 75 if params["SpinEchoLength_unit"] != params["Wavelength_unit"]: 76 raise RuntimeError("The spin echo data has rudely used " 77 "different units for the spin echo length " 78 "and the wavelength. While sasview could " 79 "handle this instance, it is a violation " 80 "of the file format and will not be " 81 "handled by other software.") 82 83 headers = input_f.readline().split() 84 85 self._insist_header(headers, "SpinEchoLength") 86 self._insist_header(headers, "Depolarisation") 87 self._insist_header(headers, "Depolarisation_error") 88 self._insist_header(headers, "Wavelength") 89 90 data = np.loadtxt(input_f) 91 92 if data.shape[1] != len(headers): 93 raise RuntimeError( 94 "File has {} headers, but {} columns".format( 95 len(headers), 96 data.shape[1])) 97 98 if data.size < 1: 99 raise RuntimeError("{} is empty".format(path)) 100 x = data[:, headers.index("SpinEchoLength")] 101 if "SpinEchoLength_error" in headers: 102 dx = data[:, headers.index("SpinEchoLength_error")] 103 else: 104 dx = x*0.05 105 lam = data[:, headers.index("Wavelength")] 106 if "Wavelength_error" in headers: 107 dlam = data[:, headers.index("Wavelength_error")] 108 else: 109 dlam = lam*0.05 110 y = data[:, headers.index("Depolarisation")] 111 dy = data[:, headers.index("Depolarisation_error")] 112 113 lam_unit = self._unit_fetch("Wavelength") 114 x, x_unit = self._unit_conversion(x, "A", 115 self._unit_fetch( 116 "SpinEchoLength")) 117 dx, dx_unit = self._unit_conversion( 118 dx, lam_unit, 119 self._unit_fetch("SpinEchoLength")) 120 dlam, dlam_unit = self._unit_conversion( 121 dlam, lam_unit, 122 self._unit_fetch("Wavelength")) 123 y_unit = self._unit_fetch("Depolarisation") 124 125 output = Data1D(x=x, y=y, lam=lam, dy=dy, dx=dx, dlam=dlam, 126 isSesans=True) 127 128 output.y_unit = y_unit 129 output.x_unit = x_unit 130 output.source.wavelength_unit = lam_unit 131 output.source.wavelength = lam 132 self.filename = output.filename = basename 133 output.xaxis(r"\rm{z}", x_unit) 134 # Adjust label to ln P/(lam^2 t), remove lam column refs 135 output.yaxis(r"\rm{ln(P)/(t \lambda^2)}", y_unit) 136 # Store loading process information 137 output.meta_data['loader'] = self.type_name 138 output.sample.name = params["Sample"] 139 output.sample.ID = params["DataFileTitle"] 140 output.sample.thickness = self._unit_conversion( 141 float(params["Thickness"]), "cm", 142 self._unit_fetch("Thickness"))[0] 143 144 output.sample.zacceptance = ( 145 float(params["Theta_zmax"]), 146 self._unit_fetch("Theta_zmax")) 147 148 output.sample.yacceptance = ( 149 float(params["Theta_ymax"]), 150 self._unit_fetch("Theta_ymax")) 151 return output 152 153 @staticmethod 154 def _insist_header(headers, name): 155 if name not in headers: 156 raise RuntimeError( 157 "Missing {} column in spin echo data".format(name)) 158 159 @staticmethod 160 def _unit_conversion(value, value_unit, default_unit): 161 """ 162 Performs unit conversion on a measurement. 163 164 :param value: The magnitude of the measurement 165 :param value_unit: a string containing the final desired unit 166 :param default_unit: string with the units of the original measurement 167 :return: The magnitude of the measurement in the new units 168 """ 169 # (float, string, string) -> float 170 if has_converter and value_unit != default_unit: 171 data_conv_q = Converter(default_unit) 172 value = data_conv_q(value, units=value_unit) 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) 173 171 new_unit = default_unit 174 172 else: 175 173 new_unit = value_unit 176 174 return value, new_unit 177 178 def _unit_fetch(self, unit):179 return self.params[unit+"_unit"]
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