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obi arrays that don't work because of cython bug passing wrong pointers

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This commit is contained in:
Celine Mercier
2015-11-03 14:22:00 +01:00
parent ecb9d97adb
commit 456551ffeb
25 changed files with 1669 additions and 128 deletions
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2
python/obitools3/obidms/_obidms.cfiles
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@ -12,3 +12,5 @@
../../../src/obitypes.c
../../../src/private_at_functions.h
../../../src/private_at_functions.c
../../../src/obiarray.h
../../../src/obiarray.c

3
python/obitools3/obidms/_obidms.pxd
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@ -23,7 +23,8 @@ cdef class OBIDMS:
OBIType_t data_type=*,
size_t nb_lines=*,
size_t nb_elements_per_line=*,
list elements_names=*)
list elements_names=*,
str array_name=*)
cdef class OBIDMS_column:

44
python/obitools3/obidms/_obidms.pyx
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@ -42,10 +42,10 @@ from ._obidmscolumn_char cimport OBIDMS_column_char, \
OBIDMS_column_char_multi_elts, \
OBIDMS_column_char_multi_elts_writable
# from ._obidmscolumn_idx cimport OBIDMS_column_idx, \
# OBIDMS_column_idx_writable, \
# OBIDMS_column_idx_multi_elts, \
# OBIDMS_column_idx_multi_elts_writable
from ._obidmscolumn_str cimport OBIDMS_column_str, \
OBIDMS_column_str_writable, \
OBIDMS_column_str_multi_elts, \
OBIDMS_column_str_multi_elts_writable
cdef class OBIDMS :
@ -119,7 +119,8 @@ cdef class OBIDMS :
OBIType_t data_type= <OBIType_t> 0,
size_t nb_lines=0,
size_t nb_elements_per_line=0,
list elements_names=None):
list elements_names=None,
str array_name="default_obiarray"):
# Declarations
cdef OBIDMS_column column
@ -202,17 +203,17 @@ cdef class OBIDMS :
subclass = OBIDMS_column_char
else :
subclass = OBIDMS_column_char_multi_elts
# elif data_type == 5 :
# if (create or clone) :
# if nb_elements_per_line == 1 :
# subclass = OBIDMS_column_idx_writable
# else :
# subclass = OBIDMS_column_idx_multi_elts_writable
# else :
# if nb_elements_per_line == 1 :
# subclass = OBIDMS_column_idx
# else :
# subclass = OBIDMS_column_idx_multi_elts
elif data_type == 5 :
if (create or clone) :
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_str_writable
else :
subclass = OBIDMS_column_str_multi_elts_writable
else :
if nb_elements_per_line == 1 :
subclass = OBIDMS_column_str
else :
subclass = OBIDMS_column_str_multi_elts
else :
raise Exception("Problem with the data type")
@ -220,7 +221,7 @@ cdef class OBIDMS :
create, clone, clone_data,
version_number, data_type,
nb_lines, nb_elements_per_line,
elements_names)
elements_names, array_name)
return column
@ -238,11 +239,13 @@ cdef class OBIDMS_column :
OBIType_t type,
size_t nb_lines,
size_t nb_elements_per_line,
list elements_names):
list elements_names,
str array_name):
# Declarations
cdef bytes column_name_b
cdef bytes dms_name_b
cdef bytes array_name_b
cdef bytes elements_names_b
# Fill structure
@ -255,6 +258,7 @@ cdef class OBIDMS_column :
# Format the character strings to send them to C functions
column_name_b = str2bytes(column_name)
dms_name_b = str2bytes(self.dms.dms_name)
array_name_b = str2bytes(array_name)
# Create, clone or open column
if create :
@ -262,7 +266,9 @@ cdef class OBIDMS_column :
elements_names_b = column_name_b
else :
elements_names_b = str2bytes(";".join(elements_names))
self.pointer = obi_create_column(self.dms.pointer, column_name_b, type, nb_lines, nb_elements_per_line, elements_names_b)
self.pointer = obi_create_column(self.dms.pointer, column_name_b, type,
nb_lines, nb_elements_per_line,
elements_names_b, array_name_b)
else :
if clone :
self.pointer = obi_clone_column(self.dms.pointer, column_name_b, version_number, clone_data)

2
python/obitools3/obidms/_obidmscolumn_bool.cfiles
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@ -14,3 +14,5 @@
../../../src/obitypes.c
../../../src/private_at_functions.h
../../../src/private_at_functions.c
../../../src/obiarray.h
../../../src/obiarray.c

2
python/obitools3/obidms/_obidmscolumn_char.cfiles
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@ -14,3 +14,5 @@
../../../src/obitypes.c
../../../src/private_at_functions.h
../../../src/private_at_functions.c
../../../src/obiarray.h
../../../src/obiarray.c

2
python/obitools3/obidms/_obidmscolumn_float.cfiles
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@ -14,3 +14,5 @@
../../../src/obitypes.c
../../../src/private_at_functions.h
../../../src/private_at_functions.c
../../../src/obiarray.h
../../../src/obiarray.c

2
python/obitools3/obidms/_obidmscolumn_int.cfiles
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@ -14,3 +14,5 @@
../../../src/obitypes.c
../../../src/private_at_functions.h
../../../src/private_at_functions.c
../../../src/obiarray.h
../../../src/obiarray.c

6
python/obitools3/obidms/_obidmscolumn_idx.cfiles → python/obitools3/obidms/_obidmscolumn_str.cfiles
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@ -1,5 +1,5 @@
../../../src/obidmscolumn_idx.c
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_str.c
../../../src/obidmscolumn_str.h
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
@ -14,3 +14,5 @@
../../../src/obitypes.c
../../../src/private_at_functions.h
../../../src/private_at_functions.c
../../../src/obiarray.h
../../../src/obiarray.c

13
python/obitools3/obidms/_obidmscolumn_idx.pxd → python/obitools3/obidms/_obidmscolumn_str.pxd
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@ -1,25 +1,24 @@
#cython: language_level=3
from .capi.obitypes cimport obiidx_t
from ._obidms cimport OBIDMS_column
cdef class OBIDMS_column_idx(OBIDMS_column):
cdef class OBIDMS_column_str(OBIDMS_column):
cpdef object get_line(self, size_t line_nb)
cpdef set_line(self, size_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_idx_writable(OBIDMS_column_idx):
cdef class OBIDMS_column_str_writable(OBIDMS_column_str):
cpdef set_line(self, size_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_idx_multi_elts(OBIDMS_column_idx):
cdef class OBIDMS_column_str_multi_elts(OBIDMS_column_str):
cpdef object get_item(self, size_t line_nb, str element_name)
cpdef object get_line(self, size_t line_nb)
cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value)
cpdef set_item(self, size_t line_nb, str element_name, str value)
cpdef set_line(self, size_t line_nb, object values)
cdef class OBIDMS_column_idx_multi_elts_writable(OBIDMS_column_idx_multi_elts):
cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value)
cdef class OBIDMS_column_str_multi_elts_writable(OBIDMS_column_str_multi_elts):
cpdef set_item(self, size_t line_nb, str element_name, str value)
cpdef set_line(self, size_t line_nb, object values)
cpdef close(self)

66
python/obitools3/obidms/_obidmscolumn_idx.pyx → python/obitools3/obidms/_obidmscolumn_str.pyx
View File

@ -2,30 +2,46 @@
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_obiidx_with_elt_name, \
obi_column_get_obiidx_with_elt_idx, \
obi_column_set_obiidx_with_elt_name, \
obi_column_set_obiidx_with_elt_idx
obi_column_get_obistr_with_elt_name, \
obi_column_get_obistr_with_elt_idx, \
obi_column_set_obistr_with_elt_name, \
obi_column_set_obistr_with_elt_idx
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIIdx_NA
from .capi.obitypes cimport OBIIdx_NA, const_char_p
from obitools3.utils cimport str2bytes
from libc.string cimport strlen
from obitools3.utils cimport str2bytes, bytes2str
from cpython.int cimport PyInt_FromSsize_t
cdef class OBIDMS_column_idx(OBIDMS_column):
cdef class OBIDMS_column_str(OBIDMS_column):
cpdef object get_line(self, size_t line_nb):
cdef obiidx_t value
cdef const_char_p cvalue
cdef bytes value
cdef object result
value = obi_column_get_obiidx_with_elt_idx(self.pointer, line_nb, 0)
cvalue = obi_column_get_obistr_with_elt_idx(self.pointer, line_nb, 0)
print('test 1')
print(hex(<int> cvalue))
print(strlen(cvalue))
print("test")
value = <bytes> cvalue
print(value)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIIdx_NA :
result = None
else :
result = PyInt_FromSsize_t(value)
print(value)
result = bytes2str(value)
return result
cpdef set_line(self, size_t line_nb, object value):
@ -36,10 +52,10 @@ cdef class OBIDMS_column_idx(OBIDMS_column):
raise Exception("Problem closing a column")
cdef class OBIDMS_column_idx_writable(OBIDMS_column_idx):
cdef class OBIDMS_column_str_writable(OBIDMS_column_str):
cpdef set_line(self, size_t line_nb, object value):
if obi_column_set_obiidx_with_elt_idx(self.pointer, line_nb, 0, <obiidx_t> value) < 0:
if obi_column_set_obistr_with_elt_idx(self.pointer, line_nb, 0, str2bytes(value)) < 0:
raise Exception("Problem setting a value in a column")
cpdef close(self):
@ -47,55 +63,55 @@ cdef class OBIDMS_column_idx_writable(OBIDMS_column_idx):
raise Exception("Problem closing a column")
cdef class OBIDMS_column_idx_multi_elts(OBIDMS_column_idx):
cdef class OBIDMS_column_str_multi_elts(OBIDMS_column_str):
cpdef object get_item(self, size_t line_nb, str element_name):
cdef obiidx_t value
cdef bytes value
cdef object result
value = obi_column_get_obiidx_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
value = obi_column_get_obistr_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIIdx_NA :
result = None
else :
result = PyInt_FromSsize_t(value)
result = bytes2str(value)
return result
cpdef object get_line(self, size_t line_nb) :
cdef obiidx_t value
cdef bytes value
cdef object result
cdef size_t i
cdef bint all_NA
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_column_get_obiidx_with_elt_idx(self.pointer, line_nb, i)
value = obi_column_get_obistr_with_elt_idx(self.pointer, line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
result[self.elements_names[i]] = PyInt_FromSsize_t(value)
result[self.elements_names[i]] = bytes2str(value)
if all_NA and (value != OBIIdx_NA) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value):
cpdef set_item(self, size_t line_nb, str element_name, str value):
raise Exception("Column is read-only")
cpdef set_line(self, size_t line_nb, object values):
raise Exception("Column is read-only")
cdef class OBIDMS_column_idx_multi_elts_writable(OBIDMS_column_idx_multi_elts):
cdef class OBIDMS_column_str_multi_elts_writable(OBIDMS_column_str_multi_elts):
cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value):
if obi_column_set_obiidx_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
cpdef set_item(self, size_t line_nb, str element_name, str value):
if obi_column_set_obistr_with_elt_name(self.pointer, line_nb, str2bytes(element_name), str2bytes(value)) < 0:
raise Exception("Problem setting a value in a column")
cpdef set_line(self, size_t line_nb, object values):
cdef obiidx_t value
cdef str value
for element_name in values :
value = <obiidx_t> values[element_name]
value = values[element_name]
self.set_item(line_nb, element_name, value)
cpdef close(self):

27
python/obitools3/obidms/capi/obidmscolumn.pxd
View File

@ -8,7 +8,6 @@ from ..capi.obitypes cimport const_char_p, \
obibool_t, \
obichar_t, \
obifloat_t, \
obiidx_t, \
time_t
@ -26,6 +25,7 @@ cdef extern from "obidmscolumn.h" nogil:
obiversion_t version
obiversion_t cloned_from
const_char_p name
const_char_p array_name
const_char_p comments
ctypedef OBIDMS_column_header_t* OBIDMS_column_header_p
@ -40,7 +40,8 @@ cdef extern from "obidmscolumn.h" nogil:
OBIType_t type,
size_t nb_lines,
size_t nb_elements_per_line,
const_char_p elements_names)
const_char_p elements_names,
const_char_p array_name)
OBIDMS_column_p obi_open_column(OBIDMS_p dms,
const_char_p column_name,
@ -146,23 +147,23 @@ cdef extern from "obidmscolumn_float.h" nogil:
size_t line_nb,
size_t element_idx)
cdef extern from "obidmscolumn_idx.h" nogil:
cdef extern from "obidmscolumn_str.h" nogil:
int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column,
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
const_char_p element_name,
obiidx_t value)
char* value)
int obi_column_set_obiidx_with_elt_idx(OBIDMS_column_p column,
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column,
size_t line_nb,
size_t element_idx,
obiidx_t value)
char* value)
obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
const_char_p element_name)
const_char_p obi_column_get_obistr_with_elt_name(OBIDMS_column_p column,
size_t line_nb,
const_char_p element_name)
obiidx_t obi_column_get_obiidx_with_elt_idx(OBIDMS_column_p column,
size_t line_nb,
size_t element_idx)
const_char_p obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column,
size_t line_nb,
size_t element_idx)