Changeset 2f17d40 in sasview for src/sas/sascalc/dataloader
- Timestamp:
- May 16, 2017 8:16:20 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:
- 81b1f4d
- Parents:
- 658dd57 (diff), 8e9536f (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. - git-author:
- Adam Washington <rprospero@…> (05/16/17 08:16:20)
- git-committer:
- GitHub <noreply@…> (05/16/17 08:16:20)
- Location:
- src/sas/sascalc/dataloader
- Files:
-
- 5 edited
-
readers/sesans_reader.py (modified) (3 diffs)
-
data_info.py (modified) (1 diff)
-
readers/IgorReader.py (modified) (1 diff)
-
readers/associations.py (modified) (2 diffs)
-
readers/red2d_reader.py (modified) (2 diffs)
Legend:
- Unmodified
- Added
- Removed
-
src/sas/sascalc/dataloader/readers/sesans_reader.py
r9a5097c r149b8f6 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( 53 "{} has an unrecognized file extension".format(path)) 54 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 78 65 79 paramnames=[] 80 paramvals=[] 81 zvals=[] 82 dzvals=[] 83 lamvals=[] 84 dlamvals=[] 85 Pvals=[] 86 dPvals=[] 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") 87 70 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 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.") 104 82 105 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])) 83 headers = input_f.readline().split() 128 84 129 x,y,lam,dy,dx,dlam = [130 np.asarray(v, 'double')131 for v in (x,y,lam,dy,dx,dlam)132 ]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") 133 89 134 input_f.close()90 data = np.loadtxt(input_f) 135 91 136 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 92 if data.shape[1] != len(headers): 93 raise RuntimeError( 94 "File has {} headers, but {} columns".format( 95 len(headers), 96 data.shape[1])) 146 97 147 # 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 98 if not data.size: 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")] 158 112 159 if len(output.x) < 1: 160 raise RuntimeError, "%s is empty" % path 161 return output 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") 162 124 163 else: 164 raise RuntimeError, "%s is not a file" % path 165 return None 125 output = Data1D(x=x, y=y, lam=lam, dy=dy, dx=dx, dlam=dlam, 126 isSesans=True) 166 127 167 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 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) 171 173 new_unit = default_unit 172 174 else: 173 175 new_unit = value_unit 174 176 return value, new_unit 177 178 def _unit_fetch(self, unit): 179 return self.params[unit+"_unit"] -
src/sas/sascalc/dataloader/data_info.py
r7432acb ra1b8fee 16 16 ###################################################################### 17 17 18 from __future__ import print_function 18 19 19 20 #TODO: Keep track of data manipulation in the 'process' data structure. -
src/sas/sascalc/dataloader/readers/IgorReader.py
r959eb01 ra1b8fee 12 12 #copyright 2008, University of Tennessee 13 13 ############################################################################# 14 from __future__ import print_function 15 14 16 import os 15 17 -
src/sas/sascalc/dataloader/readers/associations.py
r959eb01 ra1b8fee 14 14 #copyright 2009, University of Tennessee 15 15 ############################################################################# 16 from __future__ import print_function 17 16 18 import os 17 19 import sys … … 71 73 logger.error(msg) 72 74 else: 73 print "Could not find reader association settings\n %s [%s]" % (__file__, os.getcwd())75 print("Could not find reader association settings\n %s [%s]" % (__file__, os.getcwd())) 74 76 75 77 -
src/sas/sascalc/dataloader/readers/red2d_reader.py
r959eb01 ra1b8fee 9 9 #copyright 2008, University of Tennessee 10 10 ###################################################################### 11 from __future__ import print_function 12 11 13 import os 12 14 import numpy as np … … 82 84 detector = Detector() 83 85 if len(output.detector) > 0: 84 print str(output.detector[0])86 print(str(output.detector[0])) 85 87 output.detector.append(detector) 86 88
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