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#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# Copyright (c) 2019 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 struct
import numpy
__doc__ = """
Reads IR maps from Perkin Elmer files.
The files are structured in a set of blocks.
The most relevant ones are:
5100 - Data
5101 - Coordinates
"""
def _parse5100(fid):
# 5100
blockNameLength = struct.unpack('<H', fid.read(2))[0]
#print("blockNameLength = ", blockNameLength)
blockName = fid.read(blockNameLength)
if hasattr(blockName, "decode"):
blockName = blockName.decode("utf-8")
#print("blockName = ", blockName)
fmt = '<ddd'
size = struct.calcsize(fmt)
xDelta, yDelta, zDelta = struct.unpack(fmt, fid.read(size))
fmt = '<dd'
size = struct.calcsize(fmt)
zStart, zEnd = struct.unpack(fmt, fid.read(size))
dataMin, dataMax = struct.unpack(fmt, fid.read(size))
fmt = '<ddd'
size = struct.calcsize(fmt)
x0, y0, z0 = struct.unpack(fmt, fid.read(size))
fmt = '<iii'
size = struct.calcsize(fmt)
xLen, yLen, zLen = struct.unpack(fmt, fid.read(size))
# get the labels
for i in range(4):
length = struct.unpack('<h', fid.read(2))[0]
text = fid.read(length)
if hasattr(text, "decode"):
text = text.decode("utf-8")
if i == 0:
xLabel = text
elif i == 1:
yLabel = text
elif i == 3:
zLabel = text
else:
wLabel = text
#print("text%d = %s" % (i,text))
return {"xStart": x0,
"yStart": y0,
"zStart": z0,
"xDelta": xDelta,
"yDelta": yDelta,
"zDelta": zDelta,
"xLength": xLen,
"yLength": yLen,
"zLength": zLen,
"labels": (xLabel, yLabel, zLabel, wLabel),
"xLabel": xLabel,
"yLabel": yLabel,
"zLabel": zLabel,
"dataMin": dataMin,
"dataMax": dataMax}
def parseFile(filename):
fid = open(filename, mode='rb')
# should we read the whole file into memory?
signature = fid.read(4)
if signature not in ["PEPE", b"PEPE"]:
raise IOError("This does not look like a PE Fsm file")
comment = fid.read(40)
if hasattr(comment, "decode"):
comment = comment.decode("utf-8")
if hasattr(comment, "strip"):
comment = comment.strip("\0")
# read 6 bytes indicating block ID and block size
blockHeader = fid.read(6)
idx = 0
while len(blockHeader) == 6:
blockId, blockSize = struct.unpack('<Hi', blockHeader)
if blockId == 5100:
info = _parse5100(fid)
nRows = info["yLength"]
nColumns = info["xLength"]
data = None
elif blockId == 5105:
blockContent = fid.read(blockSize)
# data are stored as 32 bit floats
if data is None:
tmpData = numpy.frombuffer(blockContent,
dtype=numpy.float32)
nChannels = tmpData.shape[0]
data = numpy.zeros((nRows * nColumns, nChannels),
dtype=numpy.float32)
data[idx] = tmpData
else:
data[idx] = numpy.frombuffer(blockContent,
dtype=numpy.float32)
idx += 1
else:
blockContent = fid.read(blockSize)
if len(blockContent) < blockSize:
raise IOError("Cannot read block %d" % blockId)
blockHeader = fid.read(6)
info["Title"] = comment
data.shape = nRows, nColumns, nChannels
return info, data
def isFsmFile(filename):
isSupported = False
try:
if not hasattr(filename, "seek"):
fid = open(filename, mode='rb')
owner = True
else:
fid =filename
current = fid.tell()
fid.seek(0)
signature = fid.read(4)
if signature in ["PEPE", b"PEPE"]:
isSupported = True
except:
isSupported = False
if owner:
fid.close()
else:
fid.seek(current)
return isSupported
if __name__ == "__main__":
import sys
filename = None
if len(sys.argv) > 1:
filename = sys.argv[1]
print("is PE fms File?", isFsmFile(filename))
info, data = parseFile(filename)
print(info)
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