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#
# openslide-python - Python bindings for the OpenSlide library
#
# Copyright (c) 2010-2013 Carnegie Mellon University
# Copyright (c) 2016-2024 Benjamin Gilbert
#
# This library is free software; you can redistribute it and/or modify it
# under the terms of version 2.1 of the GNU Lesser General Public License
# as published by the Free Software Foundation.
#
# This library is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
# License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with this library; if not, write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
"""
Low-level interface to the OpenSlide library.
Most users should use the openslide.OpenSlide class rather than this
module.
This module provides nearly direct equivalents to the OpenSlide C API.
(As an implementation detail, conversion of premultiplied image data
returned by OpenSlide into a non-premultiplied PIL.Image happens here
rather than in the high-level interface.)
"""
from __future__ import annotations
from ctypes import (
CDLL,
POINTER,
_Pointer,
byref,
c_char,
c_char_p,
c_double,
c_int32,
c_int64,
c_size_t,
c_uint32,
c_void_p,
cdll,
)
from itertools import count
import os
import platform
from typing import TYPE_CHECKING, Any, Callable, Protocol, TypeVar, cast
from PIL import Image
from . import _convert
if TYPE_CHECKING:
# Python 3.10+
from typing import ParamSpec, TypeAlias
from _convert import _Buffer
def _load_library() -> CDLL:
try:
import openslide_bin
return openslide_bin.libopenslide1
except (AttributeError, ModuleNotFoundError):
pass
def try_load(names: list[str]) -> CDLL:
try:
return cdll.LoadLibrary(names[0])
except OSError:
remaining = names[1:]
if remaining:
# handle recursively so implicit exception chaining captures
# all the failures
return try_load(remaining)
else:
raise
if platform.system() == 'Windows':
try:
return try_load(['libopenslide-1.dll', 'libopenslide-0.dll'])
except FileNotFoundError as exc:
raise ModuleNotFoundError(
"Couldn't locate OpenSlide DLL. "
"Try `pip install openslide-bin`, "
"or if you're using an OpenSlide binary package, "
"ensure you've called os.add_dll_directory(). "
"https://openslide.org/api/python/#installing"
) from exc
elif platform.system() == 'Darwin':
try:
return try_load(['libopenslide.1.dylib', 'libopenslide.0.dylib'])
except OSError as exc:
# MacPorts doesn't add itself to the dyld search path, but
# does add itself to the find_library() search path
# (DEFAULT_LIBRARY_FALLBACK in ctypes.macholib.dyld).
import ctypes.util
lib = ctypes.util.find_library('openslide')
if lib is None:
raise ModuleNotFoundError(
"Couldn't locate OpenSlide dylib. "
"Try `pip install openslide-bin`. "
"https://openslide.org/api/python/#installing"
) from exc
return cdll.LoadLibrary(lib)
else:
try:
return try_load(['libopenslide.so.1', 'libopenslide.so.0'])
except OSError as exc:
raise ModuleNotFoundError(
"Couldn't locate OpenSlide shared library. "
"Try `pip install openslide-bin`. "
"https://openslide.org/api/python/#installing"
) from exc
_lib = _load_library()
class OpenSlideError(Exception):
"""An error produced by the OpenSlide library.
Import this from openslide rather than from openslide.lowlevel.
"""
class OpenSlideVersionError(OpenSlideError):
"""This version of OpenSlide does not support the requested functionality.
Import this from openslide rather than from openslide.lowlevel.
"""
def __init__(self, minimum_version: str):
super().__init__(f'OpenSlide >= {minimum_version} required')
self.minimum_version = minimum_version
class OpenSlideUnsupportedFormatError(OpenSlideError):
"""OpenSlide does not support the requested file.
Import this from openslide rather than from openslide.lowlevel.
"""
class _OpenSlide:
"""Wrapper class to make sure we correctly pass an OpenSlide handle."""
def __init__(self, ptr: c_void_p):
self._as_parameter_ = ptr
self._valid = True
# Retain a reference to close() to avoid GC problems during
# interpreter shutdown
self._close = close
def __del__(self) -> None:
if self._valid:
self._close(self)
def invalidate(self) -> None:
self._valid = False
@classmethod
def from_param(cls, obj: _OpenSlide) -> _OpenSlide:
if obj.__class__ != cls:
raise ValueError("Not an OpenSlide reference")
if not obj._as_parameter_:
raise ValueError("Passing undefined slide object")
if not obj._valid:
raise ValueError("Passing closed slide object")
return obj
class _OpenSlideCache:
"""Wrapper class to make sure we correctly pass an OpenSlide cache."""
def __init__(self, ptr: c_void_p):
self._as_parameter_ = ptr
# Retain a reference to cache_release() to avoid GC problems during
# interpreter shutdown
self._cache_release = cache_release
def __del__(self) -> None:
self._cache_release(self)
@classmethod
def from_param(cls, obj: _OpenSlideCache) -> _OpenSlideCache:
if obj.__class__ != cls:
raise ValueError("Not an OpenSlide cache reference")
if not obj._as_parameter_:
raise ValueError("Passing undefined cache object")
return obj
if TYPE_CHECKING:
# Python 3.10+
Filename: TypeAlias = str | bytes | os.PathLike[Any]
class _filename_p:
"""Wrapper class to convert filename arguments to bytes."""
@classmethod
def from_param(cls, obj: Filename) -> bytes:
# fspath and fsencode raise TypeError on unexpected types
if platform.system() == 'Windows':
# OpenSlide 4.0.0+ requires UTF-8 on Windows
obj = os.fspath(obj)
if isinstance(obj, str):
return obj.encode('UTF-8')
else:
return obj
else:
return os.fsencode(obj)
class _utf8_p:
"""Wrapper class to convert string arguments to bytes."""
@classmethod
def from_param(cls, obj: str | bytes) -> bytes:
if isinstance(obj, bytes):
return obj
elif isinstance(obj, str):
return obj.encode('UTF-8')
else:
raise TypeError('Incorrect type')
class _size_t:
"""Wrapper class to convert size_t arguments to c_size_t."""
@classmethod
def from_param(cls, obj: int) -> c_size_t:
if not isinstance(obj, int):
raise TypeError('Incorrect type')
if obj < 0:
raise ValueError('Value out of range')
return c_size_t(obj)
def _load_image(buf: _Buffer, size: tuple[int, int]) -> Image.Image:
'''buf must be a mutable buffer.'''
_convert.argb2rgba(buf)
return Image.frombuffer('RGBA', size, buf, 'raw', 'RGBA', 0, 1)
# check for errors opening an image file and wrap the resulting handle
def _check_open(result: int | None, _func: Any, _args: Any) -> _OpenSlide:
if result is None:
raise OpenSlideUnsupportedFormatError("Unsupported or missing image file")
slide = _OpenSlide(c_void_p(result))
err = get_error(slide)
if err is not None:
raise OpenSlideError(err)
return slide
# prevent further operations on slide handle after it is closed
def _check_close(_result: Any, _func: Any, args: tuple[_OpenSlide]) -> None:
args[0].invalidate()
# wrap the handle returned when creating a cache
def _check_cache_create(result: int, _func: Any, _args: Any) -> _OpenSlideCache:
return _OpenSlideCache(c_void_p(result))
# Convert returned byte array, if present, into a string
def _check_string(result: Any, func: _CTypesFunc[..., Any], _args: Any) -> Any:
if func.restype is c_char_p and result is not None:
return result.decode('UTF-8', 'replace')
else:
return result
# check if the library got into an error state after each library call
def _check_error(result: Any, func: Any, args: tuple[Any, ...]) -> Any:
assert isinstance(args[0], _OpenSlide)
err = get_error(args[0])
if err is not None:
raise OpenSlideError(err)
return _check_string(result, func, args)
# Convert returned NULL-terminated char** into a list of strings
def _check_name_list(result: _Pointer[c_char_p], func: Any, args: Any) -> list[str]:
_check_error(result, func, args)
names = []
for i in count():
name = result[i]
if not name:
break
names.append(name.decode('UTF-8', 'replace'))
return names
class _FunctionUnavailable:
'''Standin for a missing optional function. Fails when called.'''
def __init__(self, minimum_version: str):
self._minimum_version = minimum_version
# allow checking for availability without calling the function
self.available = False
def __call__(self, *_args: Any) -> Any:
raise OpenSlideVersionError(self._minimum_version)
# gate runtime code that requires ParamSpec, Python 3.10+
if TYPE_CHECKING:
_P = ParamSpec('_P')
_T = TypeVar('_T', covariant=True)
class _Func(Protocol[_P, _T]):
available: bool
def __call__(self, *args: _P.args) -> _T: ...
class _CTypesFunc(_Func[_P, _T]):
restype: type | None
argtypes: list[type]
errcheck: _ErrCheck
_ErrCheck: TypeAlias = (
Callable[[Any, _CTypesFunc[..., Any], tuple[Any, ...]], Any] | None
)
# resolve and return an OpenSlide function with the specified properties
def _func(
name: str,
restype: type | None,
argtypes: list[type],
errcheck: _ErrCheck = _check_error,
minimum_version: str | None = None,
) -> _Func[_P, _T]:
try:
func: _CTypesFunc[_P, _T] = getattr(_lib, name)
except AttributeError:
if minimum_version is None:
raise
else:
return _FunctionUnavailable(minimum_version)
func.argtypes = argtypes
func.restype = restype
if errcheck is not None:
func.errcheck = errcheck
func.available = True
return func
def _wraps_funcs(
wrapped: list[_Func[..., Any]]
) -> Callable[[Callable[_P, _T]], _Func[_P, _T]]:
def decorator(fn: Callable[_P, _T]) -> _Func[_P, _T]:
if TYPE_CHECKING:
# requires ParamSpec, Python 3.10+
f = cast(_Func[_P, _T], fn)
else:
f = fn
f.available = True
for w in wrapped:
f.available = f.available and w.available
return f
return decorator
try:
detect_vendor: _Func[[Filename], str] = _func(
'openslide_detect_vendor', c_char_p, [_filename_p], _check_string
)
except AttributeError:
raise OpenSlideVersionError('3.4.0')
open: _Func[[Filename], _OpenSlide] = _func(
'openslide_open', c_void_p, [_filename_p], _check_open
)
close: _Func[[_OpenSlide], None] = _func(
'openslide_close', None, [_OpenSlide], _check_close
)
get_level_count: _Func[[_OpenSlide], int] = _func(
'openslide_get_level_count', c_int32, [_OpenSlide]
)
_get_level_dimensions: _Func[
[_OpenSlide, int, _Pointer[c_int64], _Pointer[c_int64]], None
] = _func(
'openslide_get_level_dimensions',
None,
[_OpenSlide, c_int32, POINTER(c_int64), POINTER(c_int64)],
)
@_wraps_funcs([_get_level_dimensions])
def get_level_dimensions(slide: _OpenSlide, level: int) -> tuple[int, int]:
w, h = c_int64(), c_int64()
_get_level_dimensions(slide, level, byref(w), byref(h))
return w.value, h.value
get_level_downsample: _Func[[_OpenSlide, int], float] = _func(
'openslide_get_level_downsample', c_double, [_OpenSlide, c_int32]
)
get_best_level_for_downsample: _Func[[_OpenSlide, float], int] = _func(
'openslide_get_best_level_for_downsample', c_int32, [_OpenSlide, c_double]
)
_read_region: _Func[[_OpenSlide, _Pointer[c_uint32], int, int, int, int, int], None] = (
_func(
'openslide_read_region',
None,
[_OpenSlide, POINTER(c_uint32), c_int64, c_int64, c_int32, c_int64, c_int64],
)
)
@_wraps_funcs([_read_region])
def read_region(
slide: _OpenSlide, x: int, y: int, level: int, w: int, h: int
) -> Image.Image:
if w < 0 or h < 0:
# OpenSlide would catch this, but not before we tried to allocate
# a negative-size buffer
raise OpenSlideError(
"negative width (%d) or negative height (%d) not allowed" % (w, h)
)
if w == 0 or h == 0:
# Image.frombuffer() would raise an exception
return Image.new('RGBA', (w, h))
buf = (w * h * c_uint32)()
_read_region(slide, buf, x, y, level, w, h)
return _load_image(buf, (w, h))
get_icc_profile_size: _Func[[_OpenSlide], int] = _func(
'openslide_get_icc_profile_size',
c_int64,
[_OpenSlide],
minimum_version='4.0.0',
)
_read_icc_profile: _Func[[_OpenSlide, _Pointer[c_char]], None] = _func(
'openslide_read_icc_profile',
None,
[_OpenSlide, POINTER(c_char)],
minimum_version='4.0.0',
)
@_wraps_funcs([get_icc_profile_size, _read_icc_profile])
def read_icc_profile(slide: _OpenSlide) -> bytes | None:
size = get_icc_profile_size(slide)
if size == 0:
return None
buf = (size * c_char)()
_read_icc_profile(slide, buf)
return buf.raw
get_error: _Func[[_OpenSlide], str] = _func(
'openslide_get_error', c_char_p, [_OpenSlide], _check_string
)
get_property_names: _Func[[_OpenSlide], list[str]] = _func(
'openslide_get_property_names', POINTER(c_char_p), [_OpenSlide], _check_name_list
)
get_property_value: _Func[[_OpenSlide, str | bytes], str] = _func(
'openslide_get_property_value', c_char_p, [_OpenSlide, _utf8_p]
)
get_associated_image_names: _Func[[_OpenSlide], list[str]] = _func(
'openslide_get_associated_image_names',
POINTER(c_char_p),
[_OpenSlide],
_check_name_list,
)
_get_associated_image_dimensions: _Func[
[_OpenSlide, str | bytes, _Pointer[c_int64], _Pointer[c_int64]], None
] = _func(
'openslide_get_associated_image_dimensions',
None,
[_OpenSlide, _utf8_p, POINTER(c_int64), POINTER(c_int64)],
)
@_wraps_funcs([_get_associated_image_dimensions])
def get_associated_image_dimensions(
slide: _OpenSlide, name: str | bytes
) -> tuple[int, int]:
w, h = c_int64(), c_int64()
_get_associated_image_dimensions(slide, name, byref(w), byref(h))
return w.value, h.value
_read_associated_image: _Func[[_OpenSlide, str | bytes, _Pointer[c_uint32]], None] = (
_func(
'openslide_read_associated_image',
None,
[_OpenSlide, _utf8_p, POINTER(c_uint32)],
)
)
@_wraps_funcs([get_associated_image_dimensions, _read_associated_image])
def read_associated_image(slide: _OpenSlide, name: str | bytes) -> Image.Image:
w, h = get_associated_image_dimensions(slide, name)
buf = (w * h * c_uint32)()
_read_associated_image(slide, name, buf)
return _load_image(buf, (w, h))
get_associated_image_icc_profile_size: _Func[[_OpenSlide, str | bytes], int] = _func(
'openslide_get_associated_image_icc_profile_size',
c_int64,
[_OpenSlide, _utf8_p],
minimum_version='4.0.0',
)
_read_associated_image_icc_profile: _Func[
[_OpenSlide, str | bytes, _Pointer[c_char]], None
] = _func(
'openslide_read_associated_image_icc_profile',
None,
[_OpenSlide, _utf8_p, POINTER(c_char)],
minimum_version='4.0.0',
)
@_wraps_funcs(
[get_associated_image_icc_profile_size, _read_associated_image_icc_profile]
)
def read_associated_image_icc_profile(
slide: _OpenSlide, name: str | bytes
) -> bytes | None:
size = get_associated_image_icc_profile_size(slide, name)
if size == 0:
return None
buf = (size * c_char)()
_read_associated_image_icc_profile(slide, name, buf)
return buf.raw
get_version: _Func[[], str] = _func(
'openslide_get_version', c_char_p, [], _check_string
)
cache_create: _Func[[int], _OpenSlideCache] = _func(
'openslide_cache_create',
c_void_p,
[_size_t],
_check_cache_create,
minimum_version='4.0.0',
)
set_cache: _Func[[_OpenSlide, _OpenSlideCache], None] = _func(
'openslide_set_cache',
None,
[_OpenSlide, _OpenSlideCache],
minimum_version='4.0.0',
)
cache_release: _Func[[_OpenSlideCache], None] = _func(
'openslide_cache_release', None, [_OpenSlideCache], None, minimum_version='4.0.0'
)
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