Changes in src/sas/sascalc/dataloader/readers/sesans_reader.py [0ac6e11:9a5097c] in sasview
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src/sas/sascalc/dataloader/readers/sesans_reader.py
r0ac6e11 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 import logging9 8 import numpy as np 10 9 import os … … 19 18 _ZERO = 1e-16 20 19 21 22 20 class Reader: 23 21 """ 24 22 Class to load sesans files (6 columns). 25 23 """ 26 # File type24 ## File type 27 25 type_name = "SESANS" 28 29 # Wildcards26 27 ## Wildcards 30 28 type = ["SESANS files (*.ses)|*.ses", 31 29 "SESANS files (*..sesans)|*.sesans"] 32 # List of allowed extensions30 ## List of allowed extensions 33 31 ext = ['.ses', '.SES', '.sesans', '.SESANS'] 34 35 # Flag to bypass extension check32 33 ## Flag to bypass extension check 36 34 allow_all = True 37 35 38 36 def read(self, path): 37 38 # print "reader triggered" 39 39 40 """ 40 41 Load data file 41 42 42 43 :param path: file path 43 44 44 45 :return: SESANSData1D object, or None 45 46 46 47 :raise RuntimeError: when the file can't be opened 47 48 :raise ValueError: when the length of the data vectors are inconsistent … … 50 51 basename = os.path.basename(path) 51 52 _, extension = os.path.splitext(basename) 52 if not (self.allow_all or extension.lower() in self.ext): 53 raise RuntimeError("{} 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 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() 164 raise RuntimeError, "%s is not a file" % path 165 return None 68 166 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 dx = data[:, headers.index("SpinEchoLength_error")] 74 lam = data[:, headers.index("Wavelength")] 75 dlam = data[:, headers.index("Wavelength_error")] 76 y = data[:, headers.index("Depolarisation")] 77 dy = data[:, headers.index("Depolarisation_error")] 78 79 lam_unit = self._unit_fetch("Wavelength") 80 x, x_unit = self._unit_conversion(x, "A", self._unit_fetch("SpinEchoLength")) 81 dx, dx_unit = self._unit_conversion( 82 dx, lam_unit, 83 self._unit_fetch("SpinEchoLength")) 84 dlam, dlam_unit = self._unit_conversion( 85 dlam, lam_unit, 86 self._unit_fetch("Wavelength")) 87 y_unit = self._unit_fetch("Depolarisation") 88 89 output = Data1D(x=x, y=y, lam=lam, dy=dy, dx=dx, dlam=dlam, 90 isSesans=True) 91 92 output.y_unit = y_unit 93 output.x_unit = x_unit 94 output.source.wavelength_unit = lam_unit 95 output.source.wavelength = lam 96 self.filename = output.filename = basename 97 output.xaxis(r"\rm{z}", x_unit) 98 # Adjust label to ln P/(lam^2 t), remove lam column refs 99 output.yaxis(r"\rm{ln(P)/(t \lambda^2)}", y_unit) 100 # Store loading process information 101 output.meta_data['loader'] = self.type_name 102 output.sample.name = params["Sample"] 103 output.sample.ID = params["DataFileTitle"] 104 output.sample.thickness = float( 105 self._unit_conversion( 106 params["Thickness"], "cm", self._unit_fetch("Thickness"))[0]) 107 108 output.sample.zacceptance = ( 109 float(params["Theta_zmax"]), 110 self._unit_fetch("Theta_zmax")) 111 112 output.sample.yacceptance = ( 113 float(params["Theta_ymax"]), 114 self._unit_fetch("Theta_ymax")) 115 return output 116 117 @staticmethod 118 def _unit_conversion(value, value_unit, default_unit): 119 """ 120 Performs unit conversion on a measurement. 121 122 :param value: The magnitude of the measurement 123 :param value_unit: a string containing the final desired unit 124 :param default_unit: a string containing the units of the original measurement 125 :return: The magnitude of the measurement in the new units 126 """ 127 # (float, string, string) -> float 128 if has_converter and value_unit != default_unit: 167 def _unit_conversion(self, value, value_unit, default_unit): 168 if has_converter == True and value_unit != default_unit: 129 169 data_conv_q = Converter(value_unit) 130 170 value = data_conv_q(value, units=default_unit) … … 133 173 new_unit = value_unit 134 174 return value, new_unit 135 136 def _unit_fetch(self, unit):137 return self.params[unit+"_unit"]
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