- Timestamp:
- Apr 5, 2017 11:21:10 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:
- 610af69
- Parents:
- bfd34a7 (diff), 98c44f3 (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:
-
- 2 edited
-
sasgui/guiframe/media/data_formats_help.rst (modified) (3 diffs)
-
sascalc/dataloader/readers/sesans_reader.py (modified) (4 diffs)
Legend:
- Unmodified
- Added
- Removed
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src/sas/sasgui/guiframe/media/data_formats_help.rst
r48b8f6d r98c44f3 4 4 .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. 5 5 .. WG Bouwman, DUT, added during CodeCamp-V in Oct 2016 the SESANS data format 6 .. WG Bouwman, DUT, updated during CodeCamp-VI in Apr 2017 the SESANS data format 6 7 7 8 .. _Formats: … … 82 83 The file format has a list of name-value pairs at the top of the file which detail the general experimental parameters necessary for fitting and analyzing data. This list should contain all the information necessary for the file to be 'portable' between users. 83 84 84 Following the header is a 6column list of instrument experimental variables:85 Following the header is a 8 (only the first 4 are really needed) column list of instrument experimental variables: 85 86 86 87 - Spin echo length (z, in Angstroms) 88 - depolarization (:math:`log(P/P_0)/(lambda^2 * thickness)`, in Angstrom^-1 cm^-1) 89 - depolarization error in the same unit) (measurement error) 87 90 - Spin echo length error (:math:`\Delta`\ z, in Angstroms) (experimental resolution) 88 - Neutron wavelength (:math:`\lambda`, in Angstroms) (essential for ToF instruments)91 - Neutron wavelength (:math:`\lambda`, in Angstroms) 89 92 - Neutron wavelength error (:math:`\Delta \lambda`, in Angstroms) 90 93 - Normalized polarization (:math:`P/P_0`, unitless) … … 93 96 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 94 97 95 .. note:: This help document was last changed by Steve King, 07Oct201698 .. note:: This help document was last changed by Wim Bouwman, 05Apr2017 -
src/sas/sascalc/dataloader/readers/sesans_reader.py
r9a5097c r2b310602 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 20 21 class Reader: 21 22 """ 22 23 Class to load sesans files (6 columns). 23 24 """ 24 # #File type25 # File type 25 26 type_name = "SESANS" 26 27 # #Wildcards27 28 # Wildcards 28 29 type = ["SESANS files (*.ses)|*.ses", 29 30 "SESANS files (*..sesans)|*.sesans"] 30 # #List of allowed extensions31 # List of allowed extensions 31 32 ext = ['.ses', '.SES', '.sesans', '.SESANS'] 32 33 # #Flag to bypass extension check33 34 # Flag to bypass extension check 34 35 allow_all = True 35 36 36 37 def read(self, path): 37 38 # print "reader triggered"39 40 38 """ 41 39 Load data file 42 40 43 41 :param path: file path 44 42 45 43 :return: SESANSData1D object, or None 46 44 47 45 :raise RuntimeError: when the file can't be opened 48 46 :raise ValueError: when the length of the data vectors are inconsistent … … 51 49 basename = os.path.basename(path) 52 50 _, 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 51 if not (self.allow_all or extension.lower() in self.ext): 52 raise RuntimeError("{} has an unrecognized file extension".format(path)) 53 else: 54 raise RunetimeError("{} is not a file".format(path)) 55 with open(path, 'r') as input_f: 56 # Read in binary mode since GRASP frequently has no-ascii 57 # characters that brakes the open operation 58 line = input_f.readline() 59 params = {} 60 while not line.startswith("BEGIN_DATA"): 61 terms = line.split() 62 if len(terms) >= 2: 63 params[terms[0]] = " ".join(terms[1:]) 64 line = input_f.readline() 65 self.params = params 66 headers = input_f.readline().split() 78 67 79 paramnames=[] 80 paramvals=[] 81 zvals=[] 82 dzvals=[] 83 lamvals=[] 84 dlamvals=[] 85 Pvals=[] 86 dPvals=[] 68 data = np.loadtxt(input_f) 69 if data.size < 1: 70 raise RuntimeError("{} is empty".format(path)) 71 x = data[:, headers.index("SpinEchoLength")] 72 dx = data[:, headers.index("SpinEchoLength_error")] 73 lam = data[:, headers.index("Wavelength")] 74 dlam = data[:, headers.index("Wavelength_error")] 75 y = data[:, headers.index("Depolarisation")] 76 dy = data[:, headers.index("Depolarisation_error")] 87 77 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 78 lam_unit = self._unit_fetch("Wavelength") 79 x, x_unit = self._unit_conversion(x, "A", self._unit_fetch("SpinEchoLength")) 80 dx, dx_unit = self._unit_conversion( 81 dx, lam_unit, 82 self._unit_fetch("SpinEchoLength")) 83 dlam, dlam_unit = self._unit_conversion( 84 dlam, lam_unit, 85 self._unit_fetch("Wavelength")) 86 y_unit = self._unit_fetch("Depolarisation") 104 87 105 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])) 88 output = Data1D(x=x, y=y, lam=lam, dy=dy, dx=dx, dlam=dlam, 89 isSesans=True) 128 90 129 x,y,lam,dy,dx,dlam = [ 130 np.asarray(v, 'double') 131 for v in (x,y,lam,dy,dx,dlam) 132 ] 91 output.y_unit = y_unit 92 output.x_unit = x_unit 93 self.filename = output.filename = basename 94 output.xaxis(r"\rm{z}", x_unit) 95 # Adjust label to ln P/(lam^2 t), remove lam column refs 96 output.yaxis(r"\rm{ln(P)/(t \lambda^2)}", y_unit) 97 # Store loading process information 98 output.meta_data['loader'] = self.type_name 99 output.sample.name = params["Sample"] 100 output.sample.ID = params["DataFileTitle"] 101 output.sample.thickness = float( 102 self._unit_conversion( 103 params["Thickness"], "cm", self._unit_fetch("Thickness"))[0]) 133 104 134 input_f.close() 105 output.sample.zacceptance = ( 106 float(params["Theta_zmax"]), 107 self._unit_fetch("Theta_zmax")) 135 108 136 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 109 output.sample.yacceptance = ( 110 float(params["Theta_ymax"]), 111 self._unit_fetch("Theta_ymax")) 112 return output 146 113 147 # 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 114 @staticmethod 115 def _unit_conversion(value, value_unit, default_unit): 116 """ 117 Performs unit conversion on a measurement. 158 118 159 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: 119 :param value: The magnitude of the measurement 120 :param value_unit: a string containing the final desired unit 121 :param default_unit: a string containing the units of the original measurement 122 :return: The magnitude of the measurement in the new units 123 """ 124 # (float, string, string) -> float 125 if has_converter and value_unit != default_unit: 169 126 data_conv_q = Converter(value_unit) 170 127 value = data_conv_q(value, units=default_unit) … … 173 130 new_unit = value_unit 174 131 return value, new_unit 132 133 def _unit_fetch(self, unit): 134 return self.params[unit+"_unit"]
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