Generated by Cython 0.16.beta0 on Fri Apr 20 09:46:40 2012
Raw output: mar345_IO.c
1: """
/* "mar345_IO.pyx":1 * """ #<<<<<<<<<<<<<<* New Cython version of mar345_io for preparing the migration to Python3 * */ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_1))<0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
2: New Cython version of mar345_io for preparing the migration to Python3
3:
4: Compressor & decompressor for "pack" algorithm by JPA, binding to CCP4 libraries
5:
6: Warning: decompressor is just a cython porting of mar345_io, but in cython so (soon) python3 compliant.
7:
8: Future: make those algorithm actually generate strings not go via files;
9: it will allow a broader use of the algorithm.
10:
11: """
12:
13: __authors__ = ["Jerome Kieffer", "Gael Goret"]
/* "mar345_IO.pyx":13 * """ * * __authors__ = ["Jerome Kieffer", "Gael Goret"] #<<<<<<<<<<<<<<* __contact__ = "jerome.kieffer@esrf.eu" * __license__ = "LGPLv3+" */ __pyx_t_1 = PyList_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 13; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_INCREF(((PyObject *)__pyx_kp_s_26)); PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_26)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_26)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_27)); PyList_SET_ITEM(__pyx_t_1, 1, ((PyObject *)__pyx_kp_s_27)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_27)); if (PyObject_SetAttr(__pyx_m, __pyx_n_s____authors__, ((PyObject *)__pyx_t_1))<0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 13; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
14: __contact__ = "jerome.kieffer@esrf.eu"
/* "mar345_IO.pyx":14 * * __authors__ = ["Jerome Kieffer", "Gael Goret"] * __contact__ = "jerome.kieffer@esrf.eu" #<<<<<<<<<<<<<<* __license__ = "LGPLv3+" * __copyright__ = "2012, European Synchrotron Radiation Facility, Grenoble, France" */ if (PyObject_SetAttr(__pyx_m, __pyx_n_s____contact__, ((PyObject *)__pyx_kp_s_28))<0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
15: __license__ = "LGPLv3+"
/* "mar345_IO.pyx":15 * __authors__ = ["Jerome Kieffer", "Gael Goret"] * __contact__ = "jerome.kieffer@esrf.eu" * __license__ = "LGPLv3+" #<<<<<<<<<<<<<<* __copyright__ = "2012, European Synchrotron Radiation Facility, Grenoble, France" * */ if (PyObject_SetAttr(__pyx_m, __pyx_n_s____license__, ((PyObject *)__pyx_kp_s_29))<0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
16: __copyright__ = "2012, European Synchrotron Radiation Facility, Grenoble, France"
/* "mar345_IO.pyx":16 * __contact__ = "jerome.kieffer@esrf.eu" * __license__ = "LGPLv3+" * __copyright__ = "2012, European Synchrotron Radiation Facility, Grenoble, France" #<<<<<<<<<<<<<<* * import cython */ if (PyObject_SetAttr(__pyx_m, __pyx_n_s____copyright__, ((PyObject *)__pyx_kp_s_30))<0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 16; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
17:
18: import cython
19: cimport numpy
20: import numpy
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21: import os,tempfile
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22:
23: #cdef extern from "pack_c.h":
24: # void pack_wordimage_c(short int*, int , int , char*) nogil
25: # void unpack_word(FILE *packfile, int x, int y, short int *img) nogil
26:
27: cdef extern from "ccp4_pack.h":
28: void* mar345_read_data_string(char *instream, int ocount, int dim1, int dim2) nogil
29: void pack_wordimage_c(short int*, int , int , char*) nogil
30:
31: @cython.boundscheck(False)
32: def compress_pck(numpy.ndarray inputArray not None):
/* "mar345_IO.pyx":32 * * @cython.boundscheck(False) * def compress_pck(numpy.ndarray inputArray not None): #<<<<<<<<<<<<<<* """ * @param inputArray: numpy array as input */ static PyObject *__pyx_pf_9mar345_IO_compress_pck(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_inputArray) { CYTHON_UNUSED long __pyx_v_size; int __pyx_v_dim0; int __pyx_v_dim1; int __pyx_v_fd; char *__pyx_v_name; PyArrayObject *__pyx_v_data = 0; short *__pyx_v_cdata; PyObject *__pyx_v_fname = NULL; PyObject *__pyx_v_f = NULL; PyObject *__pyx_v_output = NULL; __Pyx_LocalBuf_ND __pyx_pybuffernd_data; __Pyx_Buffer __pyx_pybuffer_data; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("compress_pck", 0); __pyx_pybuffer_data.pybuffer.buf = NULL; __pyx_pybuffer_data.refcount = 0; __pyx_pybuffernd_data.data = NULL; __pyx_pybuffernd_data.rcbuffer = &__pyx_pybuffer_data; /* "mar345_IO.pyx":32 * * @cython.boundscheck(False) * def compress_pck(numpy.ndarray inputArray not None): #<<<<<<<<<<<<<<* """ * @param inputArray: numpy array as input */ __pyx_k_tuple_31 = PyTuple_New(14); if (unlikely(!__pyx_k_tuple_31)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_31); __Pyx_INCREF(((PyObject *)__pyx_n_s__inputArray)); PyTuple_SET_ITEM(__pyx_k_tuple_31, 0, ((PyObject *)__pyx_n_s__inputArray)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__inputArray)); __Pyx_INCREF(((PyObject *)__pyx_n_s__size)); PyTuple_SET_ITEM(__pyx_k_tuple_31, 1, ((PyObject *)__pyx_n_s__size)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__size)); __Pyx_INCREF(((PyObject *)__pyx_n_s__dim0)); PyTuple_SET_ITEM(__pyx_k_tuple_31, 2, ((PyObject *)__pyx_n_s__dim0)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__dim0)); __Pyx_INCREF(((PyObject *)__pyx_n_s__dim1)); PyTuple_SET_ITEM(__pyx_k_tuple_31, 3, ((PyObject *)__pyx_n_s__dim1)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__dim1)); __Pyx_INCREF(((PyObject *)__pyx_n_s__i)); PyTuple_SET_ITEM(__pyx_k_tuple_31, 4, ((PyObject *)__pyx_n_s__i)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__i)); __Pyx_INCREF(((PyObject *)__pyx_n_s__j)); PyTuple_SET_ITEM(__pyx_k_tuple_31, 5, ((PyObject *)__pyx_n_s__j)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__j)); __Pyx_INCREF(((PyObject *)__pyx_n_s__fd)); PyTuple_SET_ITEM(__pyx_k_tuple_31, 6, ((PyObject *)__pyx_n_s__fd)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fd)); __Pyx_INCREF(((PyObject *)__pyx_n_s__ret)); PyTuple_SET_ITEM(__pyx_k_tuple_31, 7, ((PyObject *)__pyx_n_s__ret)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ret)); __Pyx_INCREF(((PyObject *)__pyx_n_s__name)); PyTuple_SET_ITEM(__pyx_k_tuple_31, 8, ((PyObject *)__pyx_n_s__name)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__name)); __Pyx_INCREF(((PyObject *)__pyx_n_s__data)); PyTuple_SET_ITEM(__pyx_k_tuple_31, 9, ((PyObject *)__pyx_n_s__data)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__data)); __Pyx_INCREF(((PyObject *)__pyx_n_s__cdata)); PyTuple_SET_ITEM(__pyx_k_tuple_31, 10, ((PyObject *)__pyx_n_s__cdata)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__cdata)); __Pyx_INCREF(((PyObject *)__pyx_n_s__fname)); PyTuple_SET_ITEM(__pyx_k_tuple_31, 11, ((PyObject *)__pyx_n_s__fname)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fname)); __Pyx_INCREF(((PyObject *)__pyx_n_s__f)); PyTuple_SET_ITEM(__pyx_k_tuple_31, 12, ((PyObject *)__pyx_n_s__f)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__f)); __Pyx_INCREF(((PyObject *)__pyx_n_s__output)); PyTuple_SET_ITEM(__pyx_k_tuple_31, 13, ((PyObject *)__pyx_n_s__output)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__output)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_31)); /* "mar345_IO.pyx":32 * * @cython.boundscheck(False) * def compress_pck(numpy.ndarray inputArray not None): #<<<<<<<<<<<<<<* """ * @param inputArray: numpy array as input */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_9mar345_IO_1compress_pck, NULL, __pyx_n_s__mar345_IO); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetAttr(__pyx_m, __pyx_n_s__compress_pck, __pyx_t_1)<0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_k_codeobj_32 = (PyObject*)__Pyx_PyCode_New(1, 0, 14, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_31, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_33, __pyx_n_s__compress_pck, 32, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_32)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
33: """
34: @param inputArray: numpy array as input
35: @param filename: file to write data to
36: """
37: cdef long size = inputArray.size
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38: cdef int dim0, dim1, i, j, fd, ret
39: cdef char* name
40: assert inputArray.ndim == 2, "shape is 2D"
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41: dim0 = inputArray.shape[0]
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42: dim1 = inputArray.shape[1]
/* "mar345_IO.pyx":42 * assert inputArray.ndim == 2, "shape is 2D" * dim0 = inputArray.shape[0] * dim1 = inputArray.shape[1] #<<<<<<<<<<<<<<* cdef numpy.ndarray[numpy.uint16_t, ndim = 1] data = numpy.ascontiguousarray(inputArray.astype(numpy.uint16).ravel(), dtype=numpy.uint16) * cdef short int * cdata */ __pyx_v_dim1 = (__pyx_v_inputArray->dimensions[1]);
43: cdef numpy.ndarray[numpy.uint16_t, ndim = 1] data = numpy.ascontiguousarray(inputArray.astype(numpy.uint16).ravel(), dtype=numpy.uint16)
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44: cdef short int * cdata
45: cdata = < short int *> data.data
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51: f.seek(0)
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52: output = f.read()
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53: os.close(fd)
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54: os.remove(name)
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goto __pyx_L5;
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96: else:
97: chigh = < int > overflowPix
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