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# coding: utf-8
#
# Project: X-ray image reader
# https://github.com/silx-kit/fabio
#
# Copyright (C) 2015 European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# 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.
"""New Cython version of cf_iomodule.c for preparing the migration to Python3"""
__authors__ = ["Jerome Kieffer"]
__contact__ = "jerome.kieffer@esrf.eu"
__license__ = "MIT"
__copyright__ = "2013, European Synchrotron Radiation Facility, Grenoble, France"
import cython
cimport numpy as cnumpy
import numpy
import os
import tempfile
import logging
logger = logging.getLogger(__name__)
from libc.string cimport memcpy
from libc.stdio cimport fopen, FILE
CF_H = 1
CF_INIT_ROWS = 8192
CF_INIT_COLS = 32
CF_HEADER_ITEM = 128
CF_GZ_COMP = 1
CF_BIN = 2
cdef extern from "columnfile.h":
struct cf_data:
int ncols, nrows
unsigned int nralloc
double **data
char **clabels
void * cf_read_ascii(void *fp, void *dest, unsigned int FLAGS)nogil
void * cf_read_bin(void *fp, void *dest, unsigned int FLAGS)nogil
int cf_write(char *fname, void *cf_handle, unsigned int FLAGS)nogil
int cf_write_bin(void *fp, void *cf_handle)nogil
int cf_write_ascii(void *fp, void *cf_handle,unsigned int FLAGS)nogil
void cf_free( cf_data *cf_handle)nogil
def read(py_file, mode="a"):
"""
Call the c-columnfile reading interface.
The mode keyword argument is either:
"a" for ascii (the default)
"b" for binary
"""
cdef cf_data *cf__
cdef unsigned int flags = 0, fd
# perhaps not const
cdef int i
cdef FILE *file
# Here is a big issue !!! and I got an even worse solution !
# file = PyFile_AsFile(py_file)
(fd, fname) = tempfile.mkstemp()
os.fdopen(fd, mode="wb").write(py_file.read())
os.close(fd)
file = fopen(fname, "r")
if "z" in mode:
flags |= CF_GZ_COMP
if "b" in mode:
cf__ = <cf_data *> cf_read_bin(file, NULL, flags)
elif "a" in mode:
cf__ = <cf_data *> cf_read_ascii(file, NULL, flags)
else:
logger.error("Unrecognized mode for columnfile %s (assuming ascii)", mode)
cf__ = <cf_data *> cf_read_ascii(file, NULL, flags)
# check for failure to read
if (cf__ == NULL):
return None, None
dims = (cf__.nrows, cf__.ncols)
# since data may be non-contigous we can't simply create a numpy-array from
# cf__->data, as Numpy's memory model prohibits it
# i.e. py_data=(PyArrayObject*)PyArray_SimpleNewFromData(2, dims, NPY_DOUBLE, (void*)(&(cf__->data[0][0])))
# won't work
cdef cnumpy.float64_t[:, ::1] py_data = numpy.empty(dims, dtype=numpy.float64)
for i in range(cf__.nrows):
memcpy(&py_data[i, 0], cf__.data[i], cf__.ncols * sizeof(double))
clabels = []
for i in range(cf__.ncols):
clabels.append(str(cf__.clabels[i]))
cf_free(cf__)
return numpy.asarray(py_data), clabels
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