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# coding: utf-8
#
# Project: X-ray image reader
# https://github.com/silx-kit/fabio
#
#
# Copyright (C) European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
"""
Authors: Henning O. Sorensen & Erik Knudsen
Center for Fundamental Research: Metal Structures in Four Dimensions
Risoe National Laboratory
Frederiksborgvej 399
DK-4000 Roskilde
email:erik.knudsen@risoe.dk
+ mods for fabio by JPW
"""
import numpy
import re
import logging
from .fabioimage import FabioImage
logger = logging.getLogger(__name__)
_DATA_TYPES = {
"signed char": numpy.int8,
"unsigned char": numpy.uint8,
"short int": numpy.int16,
"unsigned short int": numpy.uint16,
"long int": numpy.int32,
"unsigned long int": numpy.uint32,
"float IEEE": numpy.float32,
# Valid but unsupported
"Compressed": None,
# Valid but unsupported
"Other_type": None,
}
"""Mapping from Data_type content to numpy equicalent"""
class DtrekImage(FabioImage):
"""Read an image using the d*TREK format.
This format is used to process X-ray diffraction data from area detectors.
It supports processing of data from multiple detector types (imaging plates,
CCDs and pixel arrays) and from multiple vendors (Rigaku, Mar, Dectris,
Bruker and ADSC).
Rigaku providing a `specification <https://www.rigaku.com/downloads/software/free/dTREK%20Image%20Format%20v1.1.pdf>`_.
"""
DESCRIPTION = "D*trek format (Rigaku specification 1.1)"
DEFAULT_EXTENSIONS = ["img"]
_keyvalue_pattern = None
def __init__(self, *args, **kwargs):
FabioImage.__init__(self, *args, **kwargs)
if DtrekImage._keyvalue_pattern is None:
DtrekImage._keyvalue_pattern = re.compile(b"[^\n]+")
def read(self, fname, frame=None):
""" read in the file """
with self._open(fname, "rb") as infile:
try:
self._readheader(infile)
except Exception:
logger.debug("Backtrace", exc_info=True)
raise IOError("Error processing d*TREK header")
# FIXME: It would be good to read only the expected data
binary = infile.read()
# Read information of the binary data type
data_type = self.header.get("Data_type", None)
if data_type is None:
# Compatibility with old supported files
data_type = self.header.get("TYPE", None)
if data_type is not None and data_type == "unsigned_short":
pass
else:
logger.warning("Data_type key is mandatory. Fallback to unsigner integer 16-bits.")
numpy_type = numpy.uint16
else:
if data_type not in _DATA_TYPES:
raise IOError("Data_type key contains an invalid/unsupported value: %s", data_type)
numpy_type = _DATA_TYPES[data_type]
if type is None:
raise IOError("Data_type %s is not supported by fabio", data_type)
# Stored in case data reading fails
self._dtype = numpy.dtype(numpy_type)
dim = self.header.get("DIM", None)
if dim is None:
logger.warning("DIM key is mandatory. Fallback using DIM=2.")
dim = 2
else:
dim = int(dim)
shape = []
for i in range(dim):
value = int(self.header['SIZE%d' % (i + 1)])
shape.insert(0, value)
self._shape = shape
if sum(shape) == 0:
data = None
else:
# Read the data into the array
data = numpy.frombuffer(binary, numpy_type).copy()
if self.swap_needed():
try:
data.byteswap(inplace=True)
except TypeError:
# Older numpy without inplace
data = data.byteswap()
try:
data.shape = self._shape
except ValueError:
raise IOError('Size spec in d*TREK header does not match ' +
'size of image data field %s != %s' % (self._shape, data.size))
self.data = data
self._shape = None
self._dtype = None
self.resetvals()
return self
def _split_meta(self, line):
"""Split a line into key and value.
:param bytes line: A line of bytes
:rtype: Tuple[str,str]
"""
if b"=" not in line:
raise ValueError("No meta")
line = line.decode("ascii")
key, value = line.split('=')
return key.strip(), value.strip(' ;\n\r')
def _readheader(self, infile):
"""Read a d*TREK header.
After the execusion of this function, the cursor on infile will point
at the end of the header (at the start of the binary data block).
:param FileObject infile: A file object pointing at the first character
of the header.
"""
header_line = infile.readline()
assert(header_line.startswith(b"{"))
header_bytes_line = infile.readline()
key, header_bytes = self._split_meta(header_bytes_line)
assert(key == "HEADER_BYTES")
self.header[key] = header_bytes
header_bytes = int(header_bytes)
# Read the remining block
# For robustness, cause that's in fact a const
header_bytes -= len(header_line) + len(header_bytes_line)
header_block = infile.read(header_bytes)
for line in DtrekImage._keyvalue_pattern.finditer(header_block):
line = line.group(0)
if line.startswith(b'}'):
# Remining part is padding
return
try:
key, value = self._split_meta(line)
self.header[key] = value
except ValueError:
pass
# It means there was no end of block
logger.warning("The end of block '}' was not reachable. File may be corrupted.")
def write(self, fname):
"""
Write d*TREK format
"""
# From specification
HEADER_START = b"{\n"
HEADER_END = b"}\n\x0C\n"
HEADER_BYTES_TEMPLATE = "HEADER_BYTES=% 5d;\n"
# start + end + header_bytes_key + header_bytes_value + header_bytes_end
MINIMAL_HEADER_SIZE = 2 + 4 + 13 + 5 + 2
data = self.data
if data is not None:
dtrek_data_type = None
for key, value in _DATA_TYPES.items():
if data.dtype.type == value:
dtrek_data_type = key
break
if dtrek_data_type is None:
if data.dtype.kind == 'f':
dtrek_data_type = "float IEEE"
elif data.dtype.kind == 'u':
dtrek_data_type = "unsigned long int"
elif data.dtype.kind == 'i':
dtrek_data_type = "long int"
else:
raise TypeError("Unsupported data type %s", data.dtype)
new_dtype = numpy.dtype(_DATA_TYPES[dtrek_data_type])
logger.warning("Data type %s unsupported. Store it as %s.", data.dtype, new_dtype)
data = data.astype(new_dtype)
byte_order = self._get_dtrek_byte_order(default_little_endian=numpy.little_endian)
little_endian = byte_order == "little_endian"
if little_endian != numpy.little_endian:
data = data.byteswap()
# Patch header to match the data
self.header["Data_type"] = dtrek_data_type
self.header['DIM'] = str(len(data.shape))
for i, size in enumerate(reversed(data.shape)):
self.header['SIZE%d' % (i + 1)] = str(size)
self.header["BYTE_ORDER"] = byte_order
else:
# No data
self.header["Data_type"] = "long int"
self.header['DIM'] = "2"
self.header["SIZE1"] = "0"
self.header["SIZE2"] = "0"
self.header["BYTE_ORDER"] = "little_endian"
out = b""
for key in self.header:
if key == "HEADER_BYTES":
continue
line = "%s= %s;\n" % (key, self.header[key])
out += line.encode("utf-8")
# FIXME: This code do not take into account the size of "HEADER_BYTES"
if "HEADER_BYTES" in self.header:
hsize = int(self.header["HEADER_BYTES"])
pad = hsize - len(out) - MINIMAL_HEADER_SIZE
if pad < 0:
logger.warning("HEADER_BYTES have to be patched.")
minimal_hsize = hsize - pad
hsize = (minimal_hsize + 512) & ~(512 - 1)
pad = hsize - minimal_hsize
else:
minimal_hsize = len(out) + MINIMAL_HEADER_SIZE
hsize = (minimal_hsize + 512) & ~(512 - 1)
pad = hsize - minimal_hsize
header_bytes = HEADER_BYTES_TEMPLATE % hsize
out = HEADER_START + header_bytes.encode("ascii") + out + HEADER_END + (b' ' * pad)
assert len(out) % 512 == 0, "Header is not multiple of 512"
with open(fname, "wb") as outf:
outf.write(out)
if data is not None:
data.tofile(outf)
def _get_dtrek_byte_order(self, default_little_endian=None):
"""Returns the byte order value in d*TREK format."""
if "BYTE_ORDER" not in self.header:
if default_little_endian is None:
logger.warning("No byte order specified, assuming little_endian")
little_endian = True
else:
little_endian = default_little_endian
else:
byte_order = self.header["BYTE_ORDER"]
little_endian = "little" in byte_order
big_endian = "big" in byte_order
if not little_endian and not big_endian:
logger.warning("Invalid BYTE_ORDER value. Found '%s', assuming little_endian", byte_order)
little_endian = True
if little_endian:
return "little_endian"
else:
return "big_endian"
return byte_order
def swap_needed(self, check=True):
"""
Returns True if the header does not use the same endianness than the
system.
:rtype: bool
"""
byte_order = self._get_dtrek_byte_order()
little_endian = byte_order == "little_endian"
return little_endian != numpy.little_endian
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