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
|
#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# Copyright (c) 2004-2014 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"
import os
import sys
from PyMca5.PyMcaIO import MEDFile
from PyMca5.PyMcaIO import SpecFileAbstractClass
class APSMEDFileParser(object):
def __init__(self, filename, sum_all=False):
if not os.path.exists(filename):
raise IOError("File %s does not exists" % filename)
self._medFileObject = MEDFile.MEDFile(filename)
#read the data
#potentially each detector could have a different number of channels
#should I support that?
header = []
header.append('#S 1 %s Unknown command' % os.path.basename(filename))
header.append('#D %s' % self._medFileObject.mcas[0].start_time)
if sum_all:
realtime = 0
livetime = 0
cal_offset = 0
cal_slope = 0
cal_quad = 0
n = float(len(self._medFileObject.mcas))
for mca in self._medFileObject.mcas:
realtime += (mca.realtime / n)
livetime += (mca.livetime / n)
cal_offset += (cal_offset / n)
cal_slope += (cal_slope / n)
cal_quad += (cal_quad / n)
data = [self._medFileObject.get_data(sum_all=sum_all)]
# this makes no sense in any case
header.append('#@CTIME %f %f %f' % (realtime,
realtime,
livetime))
header.append('#@CALIB %f %f %f' % (cal_offset,
cal_slope,
cal_quad))
else:
data = []
for mca in self._medFileObject.mcas:
header.append('#@CTIME %f %f %f' % (mca.realtime,
mca.realtime,
mca.livetime))
header.append('#@CALIB %f %f %f' % (mca.cal_offset,
mca.cal_slope,
mca.cal_quad))
data.append(mca.data)
self.motorNames = []
motorValues = []
for item in self._medFileObject.env:
name, value = item.split("=")
self.motorNames.append(name)
motorValues.append(value)
header.append('#' + item)
#create an abstract scan object
self._scan = [APSMEDScan(data, scanheader=header,
motor_values=motorValues)]
#the methods below are called by PyMca on any SPEC file
def __getitem__(self, item):
return self._scan[item]
def scanno(self):
"""
Gives back the number of scans in the file
"""
return len(self._scan)
def list(self):
return "1:1"
def select(self, key):
"""
key is of the from s.o
scan number, scan order
"""
n = key.split(".")
return self.__getitem__(int(n[0]) - 1)
def allmotors(self):
return self.motorNames
class APSMEDScan(SpecFileAbstractClass.SpecFileAbstractScan):
def __init__(self, data, scantype='MCA',
identification="1.1", scanheader=None, labels=None,
motor_values=None):
SpecFileAbstractClass.SpecFileAbstractScan.__init__(self,
data, scantype=scantype, identification=identification,
scanheader=scanheader, labels=labels)
if motor_values is None:
motor_values = []
self.motorValues = motor_values
def allmotorpos(self):
return self.motorValues
def isAPSMEDFile(filename):
#Obviously I should put a better test than this one
if not filename.upper().endswith(".XRF"):
return False
return True
def test(filename):
if isAPSMEDFile(filename):
sf = APSMEDFileParser(filename)
else:
print("Not an APS Multi-element detector file")
print(sf[0].header('S'))
print(sf[0].header('D'))
print(sf[0].header('ID13ds'))
print(sf[0].alllabels())
print(dir(sf[0]))
print("number of mcas = %s " % sf[0].nbmca())
try:
import pylab
for i in range(sf[0].nbmca()):
pylab.plot(sf[0].mca(i + 1))
pylab.show()
except ImportError:
pass
if __name__ == "__main__":
test(sys.argv[1])
|
