1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
|
#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# Copyright (c) 2004-2015 European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
#############################################################################*/
__author__ = "V.A. Sole - ESRF Data Analysis"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__doc__="""
Minimalistic support to read and write JCAMP-DX files.
The first three lines of a JCAMP-DX file have to be:
##TITLE=
##JCAMP-DX= JCAMP version number $$ Optional comment about the writing software
##DATA TYPE=
The next two lines were considered mandatory in Applied Spectroscopy 42 (1998) 151-162.
##ORIGIN=
##OWNER=
Then came several optional lines
##XUNITS=
##YUNITS=
##XFACTOR=
##YFACTOR=
##FIRSTX=
##LASTX=
##NPOINTS=
##FIRSTY=
##XYDATA=(X++(Y..Y))
data block
##END=
"""
import os
import sys
import re
import numpy
patternKey=re.compile(r'^[#][#]\s*(?P<name>[^=]+)=(?P<value>.*)$')
#patternNumber = re.compile(r'([+-]?\d+\.?\d*)')
patternNumber = re.compile(r'[+-]?[0-9]+\.?[0-9]*(?:[eE][+-]?[0-9]+)?')
DEBUG = 0
if DEBUG:
text = '1.23 +2 456-7.98+5 10+3.4E+01 98-7.6E-2+3'
print("RESULT:")
print(re.findall(patternNumber, text))
print("EXPECTED:")
print(['1.23', '+2', '456', '-7.98', '+5', '10', '+3.4E+01', '98', '-7.6E-2', '+3'])
class BufferedFile(object):
def __init__(self, filename):
f = open(filename, 'r')
self.__buffer = f.read()
f.close()
self.__buffer = self.__buffer.replace("\r", "\n")
self.__buffer = self.__buffer.replace("\n\n", "\n")
self.__buffer = self.__buffer.split("\n")
self.__currentLine = 0
def readline(self):
if self.__currentLine >= len(self.__buffer):
return ""
line = self.__buffer[self.__currentLine]
self.__currentLine += 1
return line
def close(self):
self.__buffer = [""]
self.__currentLine = 0
return
class JcampReader(object):
def __init__(self, filename):
if not os.path.exists(filename):
raise IOError("File %s does not exists")
_fileObject = BufferedFile(filename)
# only one measurement per file
ddict = {}
header = []
# test we are actually using a JCAMP-DX file
testKeys = ["TITLE", "JCAMP-DX", "DATA TYPE"]
for i, key in enumerate(testKeys):
line = _fileObject.readline()
info = re.findall(patternKey, line)
if len(info):
actualKey = key.replace(" ","")
if info[0][0].replace(" ", "").upper().startswith(actualKey):
header.append(line)
ddict[key] = info[0][1]
else:
raise IOError("This does not look as a JCAMP-DX file")
line = _fileObject.readline()
while not line.startswith("##XYDATA"):
header.append(line)
line = _fileObject.readline()
key, value = re.findall(patternKey, line)[0]
ddict["XYDATA"] = value.upper()
header.append(line)
# we are at the data block
data = []
line = _fileObject.readline()
while not line.startswith("##END"):
data.append(line)
line = _fileObject.readline()
_fileObject.close()
self._header = header
self.info = self.parseHeader()
self.data = self.parseData(data)
def parseHeader(self, keyList=None):
if keyList is None:
keyList = ["TITLE", "JCAMP-DX", "DATA TYPE",
"ORIGIN", "OWNER",
"XUNITS", "YUNITS",
"XFACTOR", "YFACTOR",
"FIRSTX", "LASTX", "DELTAX", "NPOINTS",
"FIRSTY",
"XYDATA"]
ddict = {}
for line in self._header:
for key in keyList:
info = re.findall(patternKey, line)
if len(info):
actualKey = key.replace(" ","")
if info[0][0].replace(" ", "").upper().startswith(actualKey):
ddict[key] = info[0][1]
return ddict
def parseData(self, dataLines):
if self.info['XYDATA'].upper().strip() not in ["(X++(Y..Y))", "(XY..XY)"]:
raise IOError("Format <%s> not supported yet" % self.info['XYDATA'])
if self.info['XYDATA'].upper().strip() == "(X++(Y..Y))":
xValues = []
yValues = []
nValues = []
for line in dataLines:
values = [float(x) for x in re.findall(patternNumber, line)]
xValues.append(values[0])
yValues += values[1:]
nValues.append(len(values) - 1)
# the y values are all there, but the x values are not
lastX = float(self.info["LASTX"])
try:
# try to apply the formula given in the article
# the problem is that DELTAX is not mandatory
firstX = float(self.info["FIRSTX"])
deltaX = float(self.info["DELTAX"])
nPoints = int(self.info.get("NPOINTS", 0))
if nPoints != len(yValues):
print("Number of points does not match number of values")
nPoints = len(yValues)
# this formula is given in the article
x = firstX + numpy.arange(nPoints) * \
((lastX - firstX) / (nPoints - 1.0))
except KeyError:
xValues.append(lastX)
x = numpy.zeros((len(yValues),), dtype=numpy.float)
start = 0
nDataLines = len(nValues)
for i in range(nDataLines):
n = nValues[i]
end = start + n
if i == (nDataLines - 1):
endpoint = True
else:
endpoint = False
x[start:end] = numpy.linspace(xValues[i],
xValues[i+1],
n, endpoint=endpoint)
start = end
else:
# XY, XY, ...
values = []
for line in dataLines:
values += [float(x) for x in re.findall(patternNumber, line)]
values = numpy.array(values)
x = values[0::2]
yValues = values[1::2]
xFactor = float(self.info.get("XFACTOR", 1.0))
yFactor = float(self.info.get("YFACTOR", 1.0))
return x * xFactor, numpy.array(yValues) * yFactor
def isJcampFile(filename):
try:
testKeys = ["TITLE", "JCAMP-DX", "DATA TYPE"]
# if read mode is 'rb' python 3 does not work
fid = open(filename, mode='r')
for i, key in enumerate(testKeys):
line = fid.readline()
info = re.findall(patternKey, line)
if len(info):
actualKey = key.replace(" ","")
if info[0][0].replace(" ", "").upper().startswith(actualKey):
continue
else:
return False
return True
except:
return False
if __name__ == "__main__":
filename = None
if len(sys.argv) > 1:
filename = sys.argv[1]
print("is JCAMP-DX File?", isJcampFile(filename))
instance = JcampReader(filename)
print(instance.info)
x, y = instance.data
try:
import matplotlib.pylab as plt
plt.figure(0)
plt.plot(x, y)
plt.xlabel(instance.info.get('XUNITS', 'X'))
plt.ylabel(instance.info.get('YUNITS', 'Y'))
plt.show()
except:
pass
|
