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import sys
import operator
import functools
import cython
from libc.stdlib cimport malloc, free
from cython cimport view
from libc.stdint cimport uint8_t
import itertools
if sys.version_info[0] == 2:
from itertools import izip_longest as zip_longest
elif sys.version_info[0] == 3:
from itertools import zip_longest
cimport zfpy
import numpy as np
cimport numpy as np
# export #define's
HEADER_MAGIC = ZFP_HEADER_MAGIC
HEADER_META = ZFP_HEADER_META
HEADER_MODE = ZFP_HEADER_MODE
HEADER_FULL = ZFP_HEADER_FULL
# export enums
type_none = zfp_type_none
type_int32 = zfp_type_int32
type_int64 = zfp_type_int64
type_float = zfp_type_float
type_double = zfp_type_double
mode_null = zfp_mode_null
mode_expert = zfp_mode_expert
mode_fixed_rate = zfp_mode_fixed_rate
mode_fixed_precision = zfp_mode_fixed_precision
mode_fixed_accuracy = zfp_mode_fixed_accuracy
cpdef dtype_to_ztype(dtype):
if dtype == np.int32:
return zfp_type_int32
elif dtype == np.int64:
return zfp_type_int64
elif dtype == np.float32:
return zfp_type_float
elif dtype == np.float64:
return zfp_type_double
else:
raise TypeError("Unknown dtype: {}".format(dtype))
cpdef dtype_to_format(dtype):
# format characters detailed here:
# https://docs.python.org/3/library/array.html
if dtype == np.int32:
return 'i' # signed int
elif dtype == np.int64:
return 'q' # signed long long
elif dtype == np.float32:
return 'f' # float
elif dtype == np.float64:
return 'd' # double
else:
raise TypeError("Unknown dtype: {}".format(dtype))
zfp_to_dtype_map = {
zfp_type_int32: np.int32,
zfp_type_int64: np.int64,
zfp_type_float: np.float32,
zfp_type_double: np.float64,
}
cpdef ztype_to_dtype(zfp_type ztype):
try:
return zfp_to_dtype_map[ztype]
except KeyError:
raise ValueError("Unsupported zfp_type {}".format(ztype))
zfp_mode_map = {
zfp_mode_null: "null",
zfp_mode_expert: "expert",
zfp_mode_reversible: "reversible",
zfp_mode_fixed_accuracy: "tolerance",
zfp_mode_fixed_precision: "precision",
zfp_mode_fixed_rate: "rate",
}
cpdef zmode_to_str(zfp_mode zmode):
try:
return zfp_mode_map[zmode]
except KeyError:
raise ValueError("Unsupported zfp_mode {}".format(zmode))
cdef zfp_field* _init_field(np.ndarray arr) except NULL:
shape = arr.shape
cdef int ndim = arr.ndim
cdef zfp_type ztype = dtype_to_ztype(arr.dtype)
cdef zfp_field* field
cdef void* pointer = arr.data
strides = [int(x) / arr.itemsize for x in arr.strides[:ndim]]
if ndim == 1:
field = zfp_field_1d(pointer, ztype, shape[0])
zfp_field_set_stride_1d(field, strides[0])
elif ndim == 2:
field = zfp_field_2d(pointer, ztype, shape[1], shape[0])
zfp_field_set_stride_2d(field, strides[1], strides[0])
elif ndim == 3:
field = zfp_field_3d(pointer, ztype, shape[2], shape[1], shape[0])
zfp_field_set_stride_3d(field, strides[2], strides[1], strides[0])
elif ndim == 4:
field = zfp_field_4d(pointer, ztype, shape[3], shape[2], shape[1], shape[0])
zfp_field_set_stride_4d(field, strides[3], strides[2], strides[1], strides[0])
else:
raise RuntimeError("Greater than 4 dimensions not supported")
return field
cdef gen_padded_int_list(orig_array, pad=0, length=4):
return [int(x) for x in
itertools.islice(
itertools.chain(
orig_array,
itertools.repeat(pad)
),
length
)
]
@cython.final
cdef class Memory:
cdef void* data
def __cinit__(self, size_t size):
self.data = malloc(size)
if self.data == NULL:
raise MemoryError()
cdef void* __enter__(self):
return self.data
def __exit__(self, exc_type, exc_value, exc_tb):
free(self.data)
cpdef bytes compress_numpy(
np.ndarray arr,
double tolerance = -1,
double rate = -1,
int precision = -1,
write_header=True
):
# Input validation
if arr is None:
raise TypeError("Input array cannot be None")
num_params_set = sum([1 for x in [tolerance, rate, precision] if x >= 0])
if num_params_set > 1:
raise ValueError("Only one of tolerance, rate, or precision can be set")
# Setup zfp structs to begin compression
cdef zfp_field* field = _init_field(arr)
cdef zfp_stream* stream = zfp_stream_open(NULL)
cdef zfp_type ztype = zfp_type_none
cdef int ndim = arr.ndim
_set_compression_mode(stream, ztype, ndim, tolerance, rate, precision)
# Allocate space based on the maximum size potentially required by zfp to
# store the compressed array
cdef bytes compress_str = None
cdef size_t maxsize = zfp_stream_maximum_size(stream, field)
try:
with Memory(maxsize) as data:
bstream = stream_open(data, maxsize)
zfp_stream_set_bit_stream(stream, bstream)
zfp_stream_rewind(stream)
# write the full header so we can reconstruct the numpy array on
# decompression
if write_header and zfp_write_header(stream, field, HEADER_FULL) == 0:
raise RuntimeError("Failed to write header to stream")
with nogil:
compressed_size = zfp_compress(stream, field)
if compressed_size == 0:
raise RuntimeError("Failed to write to stream")
# copy the compressed data into a perfectly sized bytes object
compress_str = (<char *>data)[:compressed_size]
finally:
zfp_field_free(field)
zfp_stream_close(stream)
stream_close(bstream)
return compress_str
cdef view.array _decompress_with_view(
zfp_field* field,
zfp_stream* stream,
):
cdef zfp_type ztype = field[0]._type
dtype = ztype_to_dtype(ztype)
format_type = dtype_to_format(dtype)
shape = (field[0].nw, field[0].nz, field[0].ny, field[0].nx)
shape = tuple([x for x in shape if x > 0])
cdef view.array decomp_arr = view.array(
shape,
itemsize=np.dtype(dtype).itemsize,
format=format_type,
allocate_buffer=True
)
cdef void* pointer = <void *> decomp_arr.data
with nogil:
zfp_field_set_pointer(field, pointer)
ret = zfp_decompress(stream, field)
if ret == 0:
raise RuntimeError("error during zfp decompression")
return decomp_arr
cdef _decompress_with_user_array(
zfp_field* field,
zfp_stream* stream,
void* out,
):
with nogil:
zfp_field_set_pointer(field, out)
ret = zfp_decompress(stream, field)
if ret == 0:
raise RuntimeError("error during zfp decompression")
cdef _set_compression_mode(
zfp_stream *stream,
zfp_type ztype,
int ndim,
double tolerance = -1,
double rate = -1,
int precision = -1,
):
if tolerance >= 0:
zfp_stream_set_accuracy(stream, tolerance)
elif rate >= 0:
zfp_stream_set_rate(stream, rate, ztype, ndim, 0)
elif precision >= 0:
zfp_stream_set_precision(stream, precision)
else:
zfp_stream_set_reversible(stream)
cdef _validate_4d_list(in_list, list_name):
# Validate that the input list is either a valid list for strides or shape
# Specifically, check it is a list and the length is > 0 and <= 4
# Throws a TypeError or ValueError if invalid
try:
if len(in_list) > 4:
raise ValueError(
"User-provided {} has too many dimensions "
"(up to 4 supported)"
)
elif len(in_list) <= 0:
raise ValueError(
"User-provided {} needs at least one dimension"
)
except TypeError:
raise TypeError(
"User-provided {} is not an iterable"
)
cpdef np.ndarray _decompress(
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 const void* comp_data_pointer = <const void*>&compressed_data[0]
cdef zfp_field* field = zfp_field_alloc()
cdef bitstream* bstream = stream_open(
<void *>comp_data_pointer,
len(compressed_data)
)
cdef zfp_stream* stream = zfp_stream_open(bstream)
cdef np.ndarray output
try:
zfp_stream_rewind(stream)
zshape = gen_padded_int_list(reversed(shape), pad=0, length=4)
# set the shape, type, and compression mode
# strides are set further down
field[0].nx, field[0].ny, field[0].nz, field[0].nw = zshape
zfp_field_set_type(field, ztype)
ndim = sum([1 for x in zshape if x > 0])
_set_compression_mode(stream, ztype, ndim, tolerance, rate, precision)
# pad the shape with zeros to reach len == 4
# strides = gen_padded_int_list(reversed(strides), pad=0, length=4)
# field[0].sx, field[0].sy, field[0].sz, field[0].sw = strides
if out is None:
output = np.asarray(_decompress_with_view(field, stream))
else:
dtype = zfpy.ztype_to_dtype(ztype)
if isinstance(out, np.ndarray):
output = out
# check that numpy and user-provided types match
if out.dtype != dtype:
raise ValueError(
"Out ndarray has dtype {} but decompression is using "
"{}. Use out=ndarray.data to avoid this check.".format(
out.dtype,
dtype
)
)
# check that numpy and user-provided shape match
numpy_shape = out.shape
user_shape = [x for x in shape if x > 0]
if not all(
[x == y for x, y in
zip_longest(numpy_shape, user_shape)
]
):
raise ValueError(
"Out ndarray has shape {} but decompression is using "
"{}. Use out=ndarray.data to avoid this check.".format(
numpy_shape,
user_shape
)
)
else:
output = np.frombuffer(out, dtype=dtype)
output = output.reshape(shape)
_decompress_with_user_array(field, stream, <void *>output.data)
finally:
zfp_field_free(field)
zfp_stream_close(stream)
stream_close(bstream)
return output
cpdef np.ndarray decompress_numpy(
const uint8_t[::1] compressed_data,
):
if compressed_data is None:
raise TypeError("compressed_data cannot be None")
cdef const void* comp_data_pointer = <const void *>&compressed_data[0]
cdef zfp_field* field = zfp_field_alloc()
cdef bitstream* bstream = stream_open(
<void *>comp_data_pointer,
len(compressed_data)
)
cdef zfp_stream* stream = zfp_stream_open(bstream)
cdef np.ndarray output
try:
if zfp_read_header(stream, field, HEADER_FULL) == 0:
raise ValueError("Failed to read required zfp header")
output = np.asarray(_decompress_with_view(field, stream))
finally:
zfp_field_free(field)
zfp_stream_close(stream)
stream_close(bstream)
return output
cpdef dict header(const uint8_t[::1] compressed_data):
"""Return stream header information in a python dict."""
if compressed_data is None:
raise TypeError("compressed_data cannot be None")
cdef const void* comp_data_pointer = <const void *>&compressed_data[0]
cdef zfp_field* field = zfp_field_alloc()
cdef bitstream* bstream = stream_open(
<void *>comp_data_pointer,
len(compressed_data)
)
cdef zfp_stream* stream = zfp_stream_open(bstream)
cdef zfp_mode mode
cdef unsigned int minbits = 0
cdef unsigned int maxbits = 0
cdef unsigned int maxprec = 0
cdef int minexp = 0
try:
if zfp_read_header(stream, field, HEADER_FULL) == 0:
raise ValueError("Failed to read required zfp header")
mode = zfp_stream_compression_mode(stream)
ndim = 0
for dim in [field.nx, field.ny, field.nz, field.nw]:
ndim += int(dim > 0)
zfp_stream_params(stream, &minbits, &maxbits, &maxprec, &minexp)
return {
"nx": int(field.nx),
"ny": int(field.ny),
"nz": int(field.nz),
"nw": int(field.nw),
"type": ztype_to_dtype(field._type),
"mode": zmode_to_str(mode),
"config": {
"mode": int(mode),
"tolerance": float(zfp_stream_accuracy(stream)),
"rate": float(zfp_stream_rate(stream, ndim)),
"precision": int(zfp_stream_precision(stream)),
"expert": {
"minbits": int(minbits),
"maxbits": int(minbits),
"maxprec": int(maxprec),
"minexp": int(minexp),
},
},
}
finally:
zfp_field_free(field)
zfp_stream_close(stream)
stream_close(bstream)
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