| 1 | """ |
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| 2 | SESANS reader |
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| 3 | """ |
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| 4 | |
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| 5 | import numpy |
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| 6 | import os |
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| 7 | from sas.dataloader.data_info import SESANSData1D |
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| 8 | |
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| 9 | # Check whether we have a converter available |
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| 10 | has_converter = True |
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| 11 | try: |
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| 12 | from sas.data_util.nxsunit import Converter |
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| 13 | except: |
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| 14 | has_converter = False |
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| 15 | _ZERO = 1e-16 |
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| 16 | |
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| 17 | class Reader: |
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| 18 | """ |
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| 19 | Class to load sesans files (6 columns). |
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| 20 | """ |
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| 21 | ## File type |
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| 22 | type_name = "SESANS" |
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| 23 | |
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| 24 | ## Wildcards |
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| 25 | type = ["SESANS files (*.ses)|*.ses", |
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| 26 | "SESANS files (*..sesans)|*.sesans"] |
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| 27 | ## List of allowed extensions |
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| 28 | ext = ['.ses', '.SES', '.sesans', '.SESANS'] |
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| 29 | |
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| 30 | ## Flag to bypass extension check |
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| 31 | allow_all = True |
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| 32 | |
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| 33 | def read(self, path): |
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| 34 | |
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| 35 | # print "reader triggered" |
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| 36 | |
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| 37 | """ |
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| 38 | Load data file |
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| 39 | |
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| 40 | :param path: file path |
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| 41 | |
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| 42 | :return: SESANSData1D object, or None |
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| 43 | |
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| 44 | :raise RuntimeError: when the file can't be opened |
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| 45 | :raise ValueError: when the length of the data vectors are inconsistent |
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| 46 | """ |
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| 47 | if os.path.isfile(path): |
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| 48 | basename = os.path.basename(path) |
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| 49 | _, extension = os.path.splitext(basename) |
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| 50 | if self.allow_all or extension.lower() in self.ext: |
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| 51 | try: |
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| 52 | # Read in binary mode since GRASP frequently has no-ascii |
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| 53 | # characters that brakes the open operation |
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| 54 | input_f = open(path,'rb') |
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| 55 | except: |
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| 56 | raise RuntimeError, "sesans_reader: cannot open %s" % path |
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| 57 | buff = input_f.read() |
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| 58 | # print buff |
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| 59 | lines = buff.splitlines() |
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| 60 | # print lines |
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| 61 | #Jae could not find python universal line spliter: |
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| 62 | #keep the below for now |
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| 63 | # some ascii data has \r line separator, |
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| 64 | # try it when the data is on only one long line |
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| 65 | # if len(lines) < 2 : |
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| 66 | # lines = buff.split('\r') |
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| 67 | |
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| 68 | x = numpy.zeros(0) |
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| 69 | y = numpy.zeros(0) |
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| 70 | dy = numpy.zeros(0) |
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| 71 | lam = numpy.zeros(0) |
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| 72 | dlam = numpy.zeros(0) |
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| 73 | dx = numpy.zeros(0) |
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| 74 | |
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| 75 | #temp. space to sort data |
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| 76 | tx = numpy.zeros(0) |
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| 77 | ty = numpy.zeros(0) |
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| 78 | tdy = numpy.zeros(0) |
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| 79 | tlam = numpy.zeros(0) |
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| 80 | tdlam = numpy.zeros(0) |
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| 81 | tdx = numpy.zeros(0) |
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| 82 | # print "all good" |
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| 83 | output = SESANSData1D(x=x, y=y, lam=lam, dy=dy, dx=dx, dlam=dlam) |
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| 84 | # print output |
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| 85 | self.filename = output.filename = basename |
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| 86 | |
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| 87 | |
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| 88 | data_conv_z = None |
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| 89 | data_conv_P = None |
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| 90 | # print "passing" |
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| 91 | if has_converter == True and output.x_unit != 'A': |
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| 92 | data_conv_z = Converter('nm') |
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| 93 | # Test it |
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| 94 | data_conv_z(1.0, output.x_unit) |
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| 95 | # print data_conv_z |
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| 96 | # print data_conv_z(1.0, output.x_unit) |
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| 97 | if has_converter == True and output.y_unit != ' ': |
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| 98 | data_conv_P = Converter('a.u.') |
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| 99 | # Test it |
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| 100 | data_conv_P(1.0, output.y_unit) |
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| 101 | # print data_conv_P |
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| 102 | # print data_conv_P(1.0, output.y_unit) |
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| 103 | # The first good line of data will define whether |
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| 104 | # we have 2-column or 3-column ascii |
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| 105 | # print output.x_unit |
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| 106 | # print output.y_unit |
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| 107 | |
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| 108 | # print "past output" |
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| 109 | |
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| 110 | # has_error_dx = None |
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| 111 | # has_error_dy = None |
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| 112 | |
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| 113 | # #Initialize counters for data lines and header lines. |
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| 114 | # is_data = False # Has more than 5 lines |
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| 115 | # # More than "5" lines of data is considered as actual |
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| 116 | # # data unless that is the only data |
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| 117 | # mum_data_lines = 5 |
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| 118 | # # To count # of current data candidate lines |
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| 119 | # i = -1 |
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| 120 | # # To count total # of previous data candidate lines |
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| 121 | # i1 = -1 |
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| 122 | # # To count # of header lines |
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| 123 | # j = -1 |
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| 124 | # # Helps to count # of header lines |
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| 125 | # j1 = -1 |
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| 126 | # #minimum required number of columns of data; ( <= 4). |
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| 127 | # lentoks = 2 |
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| 128 | paramnames=[] |
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| 129 | paramvals=[] |
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| 130 | zvals=[] |
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| 131 | dzvals=[] |
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| 132 | lamvals=[] |
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| 133 | dlamvals=[] |
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| 134 | Pvals=[] |
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| 135 | dPvals=[] |
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| 136 | # print x |
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| 137 | # print zvals |
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| 138 | for line in lines: |
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| 139 | # Initial try for CSV (split on ,) |
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| 140 | # print line |
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| 141 | line=line.strip() |
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| 142 | # print line |
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| 143 | toks = line.split('\t') |
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| 144 | # print toks |
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| 145 | if len(toks)==2: |
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| 146 | paramnames.append(toks[0]) |
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| 147 | # print paramnames |
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| 148 | paramvals.append(toks[1]) |
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| 149 | # print paramvals |
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| 150 | if len(toks)>5: |
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| 151 | zvals.append(toks[0]) |
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| 152 | dzvals.append(toks[1]) |
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| 153 | lamvals.append(toks[2]) |
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| 154 | dlamvals.append(toks[3]) |
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| 155 | Pvals.append(toks[4]) |
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| 156 | dPvals.append(toks[5]) |
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| 157 | else: |
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| 158 | continue |
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| 159 | # print varheaders |
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| 160 | # print paramnames |
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| 161 | # print paramvals |
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| 162 | # print zvals |
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| 163 | # print len(zvals) |
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| 164 | |
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| 165 | x=[] |
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| 166 | y=[] |
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| 167 | lam=[] |
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| 168 | dx=[] |
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| 169 | dy=[] |
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| 170 | dlam=[] |
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| 171 | varheader=[zvals[0],dzvals[0],lamvals[0],dlamvals[0],Pvals[0],dPvals[0]] |
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| 172 | # print varheader |
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| 173 | valrange=range(len(zvals)-1) |
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| 174 | # print valrange |
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| 175 | for i in valrange: |
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| 176 | x.append(float(zvals[i+1])) |
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| 177 | y.append(float(Pvals[i+1])) |
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| 178 | lam.append(float(lamvals[i+1])) |
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| 179 | dy.append(float(dPvals[i+1])) |
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| 180 | dx.append(float(dzvals[i+1])) |
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| 181 | dlam.append(float(dlamvals[i+1])) |
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| 182 | |
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| 183 | x,y,lam,dy,dx,dlam = [ |
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| 184 | numpy.asarray(v, 'double') |
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| 185 | for v in (x,y,lam,dy,dx,dlam) |
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| 186 | ] |
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| 187 | |
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| 188 | # print x |
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| 189 | # print y |
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| 190 | # print dx |
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| 191 | # print dy |
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| 192 | # print len(x) |
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| 193 | # print len(y) |
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| 194 | # print len(dx) |
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| 195 | # print len(dy) |
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| 196 | |
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| 197 | |
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| 198 | input_f.close() |
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| 199 | # Sanity check |
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| 200 | # if has_error_dy == True and not len(y) == len(dy): |
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| 201 | # msg = "sesans_reader: y and dy have different length" |
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| 202 | # raise RuntimeError, msg |
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| 203 | # if has_error_dx == True and not len(x) == len(dx): |
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| 204 | # msg = "sesans_reader: y and dy have different length" |
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| 205 | # raise RuntimeError, msg |
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| 206 | # # If the data length is zero, consider this as |
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| 207 | # # though we were not able to read the file. |
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| 208 | # if len(x) == 0: |
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| 209 | # raise RuntimeError, "sesans_reader: could not load file" |
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| 210 | # print "alive" |
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| 211 | #Let's re-order the data to make cal. |
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| 212 | # curve look better some cases |
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| 213 | # ind = numpy.lexsort((ty, tx)) |
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| 214 | # for i in ind: |
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| 215 | # x[i] = tx[ind[i]] |
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| 216 | # y[i] = ty[ind[i]] |
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| 217 | # if has_error_dy == True: |
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| 218 | # dy[i] = tdy[ind[i]] |
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| 219 | # if has_error_dx == True: |
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| 220 | # dx[i] = tdx[ind[i]] |
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| 221 | # Zeros in dx, dy |
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| 222 | # if has_error_dx: |
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| 223 | # dx[dx == 0] = _ZERO |
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| 224 | # if has_error_dy: |
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| 225 | # dy[dy == 0] = _ZERO |
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| 226 | #Data |
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| 227 | output.x = x #[x != 0] |
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| 228 | # print output.x |
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| 229 | output.y = y #[x != 0] |
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| 230 | # print output.y |
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| 231 | # output.dy = dy[x != 0] if has_error_dy == True\ |
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| 232 | # else numpy.zeros(len(output.y)) |
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| 233 | # output.dx = dx[x != 0] if has_error_dx == True\ |
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| 234 | # else numpy.zeros(len(output.x)) |
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| 235 | output.dy = dy |
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| 236 | output.dx = dx |
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| 237 | output.lam = lam |
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| 238 | output.dlam = dlam |
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| 239 | |
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| 240 | |
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| 241 | # print "still alive" |
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| 242 | # if data_conv_z is not None: |
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| 243 | # output.xaxis("\\rm{z}", output.x_unit) |
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| 244 | # else: |
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| 245 | # output.xaxis("\\rm{z}", 'nm') |
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| 246 | # if data_conv_P is not None: |
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| 247 | # output.yaxis("\\rm{P/P0}", output.y_unit) |
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| 248 | # else: |
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| 249 | # output.yaxis("\\rm{P/P0}", "a.u.") |
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| 250 | output.xaxis("\\rm{z}", 'A') |
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| 251 | output.yaxis("\\rm{P/P0}", " ") |
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| 252 | # Store loading process information |
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| 253 | output.meta_data['loader'] = self.type_name |
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| 254 | output.sample.thickness = float(paramvals[6]) |
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| 255 | output.sample.name = paramvals[1] |
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| 256 | output.sample.ID = paramvals[0] |
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| 257 | output.sample.zacceptance=float(paramvals[7]) |
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| 258 | # print output |
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| 259 | |
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| 260 | # print "sesans_reader end" |
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| 261 | |
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| 262 | if len(output.x) < 1: |
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| 263 | raise RuntimeError, "%s is empty" % path |
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| 264 | # print output |
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| 265 | |
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| 266 | return output |
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| 267 | |
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| 268 | else: |
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| 269 | raise RuntimeError, "%s is not a file" % path |
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| 270 | return None |
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