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replace bytes of compressed stream with uint8_t #106

Merged
merged 21 commits into from
Oct 1, 2020
Merged

replace bytes of compressed stream with uint8_t #106

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2361be0
replace bytes of compressed stream to uint8_t
halehawk Sep 17, 2020
3479dd7
Update python/zfpy.pyx
halehawk Sep 17, 2020
b737a9b
Update python/zfpy.pyx
halehawk Sep 17, 2020
14131c3
add const to char*
halehawk Sep 17, 2020
470b0f5
Merge branch 'develop' of https://github.com/halehawk/zfp into develop
halehawk Sep 17, 2020
ebd227e
remove const for test
halehawk Sep 18, 2020
d87759c
add <char*> in stream_open
halehawk Sep 18, 2020
01a5a97
change to void *
halehawk Sep 18, 2020
0a730b8
check cython version in zfpy.pyx
halehawk Sep 19, 2020
c1e444e
add cython version check in travis.sh
halehawk Sep 19, 2020
07022fd
enable cython3 upgrade on xenial
halehawk Sep 19, 2020
0f74a36
change cython3 in .travis.yml
halehawk Sep 19, 2020
b3bc658
use pip3 instead pip
halehawk Sep 19, 2020
219f0ce
remove upgrade pip
halehawk Sep 19, 2020
b4c96fb
change back to pip
halehawk Sep 19, 2020
1a65860
upgrade pip first
halehawk Sep 19, 2020
f084835
change cython3 to cython
halehawk Sep 19, 2020
bd0e413
remove apt-get cython3
halehawk Sep 19, 2020
0583611
remove print cython version
halehawk Sep 20, 2020
fdde60b
change to void, add tests similar to ensure_ndarray
halehawk Sep 26, 2020
f1709a4
changed uint8_t and memoryview test
halehawk Oct 1, 2020
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29 changes: 15 additions & 14 deletions .travis.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,8 +14,8 @@ matrix:
- g++-6
- gfortran-6
- libpython3.5-dev
- cython3
- python3-numpy
- python3-pip
env: CC='gcc-6' CXX='g++-6' FC='gfortran-6' FORTRAN_STANDARD='2003' PYTHON_VERSION='3.5' COVERAGE='ON'

- os: linux
Expand All @@ -29,8 +29,8 @@ matrix:
- g++-7
- gfortran-6
- libpython3.5-dev
- cython3
- python3-numpy
- python3-pip
env: CC='clang-3.6' CXX='clang++-3.6' FC='gfortran-6' FORTRAN_STANDARD='2003' PYTHON_VERSION='3.5'

- os: linux
Expand All @@ -46,8 +46,8 @@ matrix:
- g++-7
- gfortran-6
- libpython3.5-dev
- cython3
- python3-numpy
- python3-pip
env: CC='clang-4.0' CXX='clang++-4.0' FC='gfortran-6' FORTRAN_STANDARD='2003' PYTHON_VERSION='3.5'

- os: linux
Expand All @@ -61,8 +61,8 @@ matrix:
- g++-4.4
- gfortran-4.4
- libpython3.5-dev
- cython3
- python3-numpy
- python3-pip
env: CC='gcc-4.4' CXX='g++-4.4' FC='gfortran-4.4' FORTRAN_STANDARD='2003' PYTHON_VERSION='3.5'

- os: linux
Expand All @@ -76,8 +76,8 @@ matrix:
- g++-4.7
- gfortran-4.7
- libpython3.5-dev
- cython3
- python3-numpy
- python3-pip
env: CC='gcc-4.7' CXX='g++-4.7' FC='gfortran-4.7' FORTRAN_STANDARD='2003' PYTHON_VERSION='3.5'

- os: linux
Expand All @@ -91,8 +91,8 @@ matrix:
- g++-4.8
- gfortran-4.8
- libpython3.5-dev
- cython3
- python3-numpy
- python3-pip
env: CC='gcc-4.8' CXX='g++-4.8' FC='gfortran-4.8' FORTRAN_STANDARD='2003' PYTHON_VERSION='3.5'

- os: linux
Expand All @@ -106,8 +106,8 @@ matrix:
- g++-4.9
- gfortran-4.9
- libpython3.5-dev
- cython3
- python3-numpy
- python3-pip
env: CC='gcc-4.9' CXX='g++-4.9' FC='gfortran-4.9' FORTRAN_STANDARD='2003' PYTHON_VERSION='3.5'

- os: linux
Expand Down Expand Up @@ -135,7 +135,6 @@ matrix:
- g++-6
- gfortran-6
- libpython2.7
- python-pip
env: CC='gcc-6' CXX='g++-6' FC='gfortran-6' FORTRAN_STANDARD='2003' PYTHON_VERSION='2.7'

- os: linux
Expand All @@ -149,8 +148,8 @@ matrix:
- g++-6
- gfortran-6
- libpython3.5-dev
- cython3
- python3-numpy
- python3-pip
env: CC='gcc-6' CXX='g++-6' FC='gfortran-6' FORTRAN_STANDARD='2003' PYTHON_VERSION='3.5' C_STANDARD='90'

- os: linux
Expand All @@ -164,8 +163,8 @@ matrix:
- g++-6
- gfortran-6
- libpython3.5-dev
- cython3
- python3-numpy
- python3-pip
env: CC='gcc-6' CXX='g++-6' FC='gfortran-6' FORTRAN_STANDARD='2003' PYTHON_VERSION='3.5' C_STANDARD='11'

- os: linux
Expand All @@ -179,8 +178,8 @@ matrix:
- g++-6
- gfortran-6
- libpython3.5-dev
- cython3
- python3-numpy
- python3-pip
env: CC='gcc-6' CXX='g++-6' FC='gfortran-6' FORTRAN_STANDARD='2003' PYTHON_VERSION='3.5' CXX_STANDARD='11'

- os: linux
Expand All @@ -194,8 +193,8 @@ matrix:
- g++-6
- gfortran-6
- libpython3.5
- cython3
- python3-numpy
- python3-pip
env: CC='gcc-6' CXX='g++-6' FC='gfortran-6' FORTRAN_STANDARD='2003' PYTHON_VERSION='3.5' CXX_STANDARD='14'

- os: linux
Expand All @@ -209,8 +208,8 @@ matrix:
- g++-6
- gfortran-6
- libpython3.5
- cython3
- python3-numpy
- python3-pip
env: CC='gcc-6' CXX='g++-6' FC='gfortran-6' FORTRAN_STANDARD='2008' PYTHON_VERSION='3.5'

- os: linux
Expand All @@ -224,8 +223,8 @@ matrix:
- g++-7
- gfortran-7
- libpython3.5
- cython3
- python3-numpy
- python3-pip
env: CC='gcc-7' CXX='g++-7' FC='gfortran-7' FORTRAN_STANDARD='2008' PYTHON_VERSION='3.5'

- os: osx
Expand Down Expand Up @@ -284,6 +283,8 @@ script:
if [ "$TRAVIS_OS_NAME" = "linux" ] && [ "$PYTHON_VERSION" = "3.5" ]; then
export PYTHON_INCLUDE_DIR=/usr/include/python3.5m;
export PYTHON_LIBRARY=/usr/lib/x86_64-linux-gnu/libpython3.5m.so;
sudo $PYTHON_EXECUTABLE -m pip install --upgrade pip;
sudo $PYTHON_EXECUTABLE -m pip install --upgrade cython;
fi
- |
if [ "$TRAVIS_OS_NAME" = "linux" ] && [ "$DISTRIB_CODENAME" = "trusty" ] && [ "$PYTHON_VERSION" = "2.7" ]; then
Expand Down
14 changes: 7 additions & 7 deletions python/zfpy.pyx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ import cython
from libc.stdlib cimport malloc, free
from cython cimport view
from cpython cimport array
from libc.stdint cimport uint8_t
import array

import itertools
Expand Down Expand Up @@ -245,25 +246,24 @@ cdef _validate_4d_list(in_list, list_name):
)

cpdef np.ndarray _decompress(
bytes compressed_data,
const uint8_t[::1] compressed_data,
zfp_type ztype,
shape,
out=None,
double tolerance = -1,
double rate = -1,
int precision = -1,
):

if compressed_data is None:
raise TypeError("compressed_data cannot be None")
if compressed_data is out:
raise ValueError("Cannot decompress in-place")
_validate_4d_list(shape, "shape")

cdef char* comp_data_pointer = compressed_data
cdef const void* comp_data_pointer = <const void*>&compressed_data[0]
cdef zfp_field* field = zfp_field_alloc()
cdef bitstream* bstream = stream_open(
comp_data_pointer,
<void *>comp_data_pointer,
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Is this second cast from const void* to void* necessary, or can comp_data_pointer be declared as void*?

len(compressed_data)
)
cdef zfp_stream* stream = zfp_stream_open(bstream)
Expand Down Expand Up @@ -329,15 +329,15 @@ cpdef np.ndarray _decompress(
return output

cpdef np.ndarray decompress_numpy(
bytes compressed_data,
const uint8_t[::1] compressed_data,
):
if compressed_data is None:
raise TypeError("compressed_data cannot be None")

cdef char* comp_data_pointer = compressed_data
cdef const void* comp_data_pointer = <const void *>&compressed_data[0]
cdef zfp_field* field = zfp_field_alloc()
cdef bitstream* bstream = stream_open(
comp_data_pointer,
<void *>comp_data_pointer,
len(compressed_data)
)
cdef zfp_stream* stream = zfp_stream_open(bstream)
Expand Down
15 changes: 12 additions & 3 deletions tests/python/test_numpy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,12 +59,16 @@ def test_advanced_decompression_checksum(self):
compress_param_num
),
}
compressed_array = zfpy.compress_numpy(
compressed_array_t = zfpy.compress_numpy(
random_array,
write_header=False,
**compression_kwargs
)

if isinstance(compressed_array_t, np.ndarray):
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I'm not sure I understand the intent here. compressed_array_t is by definition a bytes object, so this conditional should always be false.

Wouldn't the appropriate test be to ensure that we can pass both a bytes object and an ndarray to zfpy.decompress_numpy? What other array-like objects are we trying to support here?

Minor nit: As a C/C++ programmer, I think compressed_array_t is a confusing name as the _t suffix makes it look like a type.

compressed_array = compressed_array_t
else:
mem = memoryview(compressed_array_t)
compressed_array = np.array(mem, copy=False)
# Decompression using the "advanced" interface which enforces no header,
# and the user must provide all the metadata
decompressed_array = np.empty_like(random_array)
Expand Down Expand Up @@ -177,11 +181,16 @@ def test_utils(self):
# Decompression using the "public" interface
# requires a header, so re-compress with the header
# included in the stream
compressed_array = zfpy.compress_numpy(
compressed_array_t = zfpy.compress_numpy(
random_array,
write_header=True,
**compression_kwargs
)
if isinstance(compressed_array_t, np.ndarray):
compressed_array = compressed_array_t
else:
mem = memoryview(compressed_array_t)
compressed_array = np.array(mem, copy=False)
decompressed_array = zfpy.decompress_numpy(
compressed_array,
)
Expand Down