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
|
#!/usr/bin/env python
#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# Copyright (c) 2004-2020 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 sys
import os
import numpy
import types
import logging
_logger = logging.getLogger(__name__)
#the file format is based on XML
import xml.etree.ElementTree as ElementTree
from PyMca5.PyMcaCore import DataObject
from PyMca5.PyMcaIO import ArtaxFileParser
from PyMca5.PyMcaIO import SpecFileStack
#SOURCE_TYPE = "EdfFileStack"
SOURCE_TYPE ="SpecFileStack"
myFloat = ArtaxFileParser.myFloat
class RTXMap(DataObject.DataObject):
'''
Class to read ARTAX .rtx files
'''
def __init__(self, filename):
'''
Parameters:
-----------
filename : str
Name of the .rtx file.
'''
if not os.path.exists(filename):
raise IOError("File %s does not exists" % filename)
if 0:
# this works but it is very slow
DataObject.DataObject.__init__(self)
stack = SpecFileStack.SpecFileStack(filename)
self.data = stack.data
self.info = stack.info
return
sf = ArtaxFileParser.ArtaxFileParser(filename)
# get some Artax map specific information
tScanInfo = sf.artaxTScanInfo
# the rest is specfile like
nScans = sf.scanno()
scan = sf[0]
calib0 = scan.header("@CALIB")
ctime = scan.header("@CTIME")
positioners = None
motorNames = sf.allmotors()
# assuming dictionaries are ordered
if len(motorNames):
positioners = {}
for mne in motorNames:
positioners[mne] = numpy.zeros((nScans,),
dtype=numpy.float32)
if ctime:
liveTime = numpy.zeros((nScans,), dtype=numpy.float32)
spectrum = sf[0].mca(1)
data = numpy.zeros((1, nScans, len(spectrum)),
dtype=numpy.float32)
for i in range(nScans):
scan = sf[i]
if ctime:
ctime = scan.header("@CTIME")[0]
liveTime[i] = myFloat(ctime.split()[-2])
if positioners:
motorPos = scan.allmotorpos()
for mneIdx in range(len(motorNames)):
mne = motorNames[mneIdx]
positioners[mne][i] = motorPos[mneIdx]
data[0, i] = scan.mca(1)
DataObject.DataObject.__init__(self)
self.data = data
if positioners:
self.info["positioners"] = positioners
if ctime:
self.info["McaLiveTime"] = liveTime
self.info["McaCalib"] = [myFloat(x) for x in calib0[0].split()[1:]]
self.info["SourceName"] = os.path.abspath(filename)
if tScanInfo.get("Mapping", False):
_logger.info("Regular Artax Map")
else:
_logger.info("Non-regular Artax Map")
# we are supposed to have a regular map
# let's figure out the shape?
if tScanInfo["XFirst"] == tScanInfo["XLast"] and \
tScanInfo["YFirst"] != tScanInfo["YLast"] and \
tScanInfo["ZFirst"] != tScanInfo["ZLast"]:
_logger.info("YZ scan if Y and Z are finite")
meshType = "YZ"
elif tScanInfo["XFirst"] != tScanInfo["XLast"] and \
tScanInfo["YFirst"] != tScanInfo["YLast"] and \
tScanInfo["ZFirst"] == tScanInfo["ZLast"]:
_logger.info("XY scan if X and Y are finite")
meshType = "XY"
elif tScanInfo["XFirst"] != tScanInfo["XLast"] and \
tScanInfo["YFirst"] == tScanInfo["YLast"] and \
tScanInfo["ZFirst"] != tScanInfo["ZLast"]:
_logger.info("XZ scan if X and Z are finite")
meshType = "XZ"
elif tScanInfo["XFirst"] != tScanInfo["XLast"] and \
tScanInfo["YFirst"] != tScanInfo["YLast"] and \
numpy.isnan(tScanInfo["ZFirst"]) and \
numpy.isnan(tScanInfo["ZLast"]):
_logger.info("XY scan if X and Y are finite")
meshType = "XY"
else:
meshType = None
if meshType:
for axis in meshType:
key=axis+"First"
if not numpy.isfinite(tScanInfo[key]):
meshType = None
break
if meshType == "XY":
_logger.info("XY scan")
x = positioners["x"]
y = positioners["y"]
xFirst = tScanInfo["XFirst"]
xLast = tScanInfo["XLast"]
yFirst = tScanInfo["YFirst"]
yLast = tScanInfo["YLast"]
elif meshType == "XZ":
_logger.info("XZ scan")
x = positioners["x"]
y = positioners["z"]
xFirst = tScanInfo["XFirst"]
xLast = tScanInfo["XLast"]
yFirst = tScanInfo["ZFirst"]
yLast = tScanInfo["ZLast"]
elif meshType == "YZ":
_logger.info("YZ scan")
x = positioners["y"]
y = positioners["z"]
xFirst = tScanInfo["YFirst"]
xLast = tScanInfo["YLast"]
yFirst = tScanInfo["ZFirst"]
yLast = tScanInfo["ZLast"]
else:
return
if len(x) == 1 or len(y) == 1:
return
reasonableDeltaX = numpy.abs(x.max() - x.min()) / (1.0 + len(x))
reasonableDeltaY = numpy.abs(y.max() - y.min()) / (1.0 + len(y))
if numpy.abs(x[1] - x[0]) > reasonableDeltaX:
x0 = x[0]
i = 1
while (i < len(x)) and (numpy.abs(x[i] - x[0]) > reasonableDeltaX):
i += 1
nColumns = i
else:
x0 = x[0]
i = 0
while (i < len(x)) and (numpy.abs(x[i] - x[0]) < reasonableDeltaX):
i += 1
nColumns = i
# the scan can be in zig-zag
# it is safer to rely on the scatter view
if nScans % nColumns == 0:
nRows = nScans // nColumns
self.data.shape = nRows, nColumns, -1
self.info["xScale"] = [xFirst, (xLast - xFirst) / nColumns]
self.info["yScale"] = [yFirst, (yLast - yFirst) / nRows]
def isRTXMap(filename):
try:
if filename[-3:].lower() not in ["rtx", "spx"]:
return False
with open(filename, 'rb') as f:
# expected to read an xml file
someChar = f.read(20).decode()
if "<" in someChar and "xml version" in someChar:
return True
except:
pass
return False
def test(filename):
print("isRTXMap? = ", isRTXMap(filename))
a = RTXMap(filename)
print("info = ", a.info)
print("Data shape = ", a.data.shape)
if __name__ == "__main__":
test(sys.argv[1])
|
