pyisyntax 0.1.1__tar.gz → 0.1.2__tar.gz

{pyisyntax-0.1.1/pyisyntax.egg-info → pyisyntax-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyisyntax
-Version: 0.1.1
+Version: 0.1.2
 Summary: Python bindings for libisyntax
 Author-email: Aiden Nibali <dismaldenizen@gmail.com>
 License: MIT
@@ -23,6 +23,12 @@ Requires-Dist: typing_extensions; extra == "dev"
 A Python library for working with pathology images in the iSyntax file format,
 powered by [libisyntax](https://github.com/amspath/libisyntax).
 
+## Installation
+
+```console
+$ pip install pyisyntax
+```
+
 ## Usage
 
 Read and display a region of the WSI via

{pyisyntax-0.1.1 → pyisyntax-0.1.2}/README.md

@@ -3,6 +3,12 @@
 A Python library for working with pathology images in the iSyntax file format,
 powered by [libisyntax](https://github.com/amspath/libisyntax).
 
+## Installation
+
+```console
+$ pip install pyisyntax
+```
+
 ## Usage
 
 Read and display a region of the WSI via

{pyisyntax-0.1.1 → pyisyntax-0.1.2}/isyntax/lowlevel/io_management.py

@@ -3,7 +3,7 @@ from dataclasses import dataclass
 from io import BufferedIOBase, RawIOBase
 from typing import Generic, NewType, TypeVar
 
-from _pyisyntax import ffi, lib
+from isyntax._pyisyntax import ffi, lib
 
 VoidPtr = NewType("VoidPtr", object)
 T = TypeVar("T")

{pyisyntax-0.1.1 → pyisyntax-0.1.2}/isyntax/lowlevel/libisyntax.py

@@ -3,8 +3,7 @@ from enum import IntEnum
 from pathlib import Path
 from typing import TYPE_CHECKING, NewType
 
-from _pyisyntax import ffi, lib
-
+from isyntax._pyisyntax import ffi, lib
 from isyntax.lowlevel.io_management import init_python_io_hooks, register_io
 
 if TYPE_CHECKING:
@@ -108,12 +107,16 @@ def get_tile_height(isyntax: ISyntaxPtr) -> int:
     return lib.libisyntax_get_tile_height(isyntax)
 
 
-def get_wsi_image_index(isyntax: ISyntaxPtr) -> int:
-    return lib.libisyntax_get_wsi_image_index(isyntax)
+def get_wsi_image(isyntax: ISyntaxPtr) -> ISyntaxImagePtr:
+    return lib.libisyntax_get_wsi_image(isyntax)
+
+
+def get_label_image(isyntax: ISyntaxPtr) -> ISyntaxImagePtr:
+    return lib.libisyntax_get_label_image(isyntax)
 
 
-def get_image(isyntax: ISyntaxPtr, wsi_image_index: int) -> ISyntaxImagePtr:
-    return lib.libisyntax_get_image(isyntax, wsi_image_index)
+def get_macro_image(isyntax: ISyntaxPtr) -> ISyntaxImagePtr:
+    return lib.libisyntax_get_macro_image(isyntax)
 
 
 def image_get_level_count(wsi_image: ISyntaxImagePtr) -> int:

{pyisyntax-0.1.1 → pyisyntax-0.1.2}/isyntax/wrapper.py

@@ -78,18 +78,19 @@ class ISyntaxImage:
 
 
 class ISyntax:
-    def __init__(self, f: RawIOBase | BufferedIOBase, n_bytes: int) -> None:
+    def __init__(self, f: RawIOBase | BufferedIOBase, n_bytes: int, cache_size: int = 2000) -> None:
         self.io_handle = register_io(f, n_bytes)
         self.ptr = libisyntax.open_from_registered_handle(self.io_handle, is_init_allocators=False)
         self.closed = False
+        self._cache_size = cache_size
         self._cache = None
 
     @classmethod
-    def open(cls: type["ISyntax"], filename: str | Path) -> "ISyntax":
+    def open(cls: type["ISyntax"], filename: str | Path, cache_size: int = 2000) -> "ISyntax":
         filename = Path(filename)
         f = filename.open("rb")
         n_bytes = os.fstat(f.fileno()).st_size
-        return cls(f, n_bytes)
+        return cls(f, n_bytes, cache_size)
 
     def close(self) -> None:
         if self.closed:
@@ -105,20 +106,13 @@ class ISyntax:
     def tile_height(self) -> int:
         return libisyntax.get_tile_height(self.ptr)
 
-    @property
-    def wsi_index(self) -> int:
-        return libisyntax.get_wsi_image_index(self.ptr)
-
-    def get_image(self, image_index: int) -> ISyntaxImage:
-        return ISyntaxImage(libisyntax.get_image(self.ptr, image_index))
-
     @property
     def wsi(self) -> ISyntaxImage:
-        return self.get_image(self.wsi_index)
+        return ISyntaxImage(libisyntax.get_wsi_image(self.ptr))
 
     def get_cache(self) -> ISyntaxCache:
         if self._cache is None:
-            self._cache = ISyntaxCache(cache_size=2000)
+            self._cache = ISyntaxCache(cache_size=self._cache_size)
             self._cache.inject(self)
         return self._cache
 
@@ -180,14 +174,14 @@ class ISyntax:
         except libisyntax.LibISyntaxFatalError:
             return None
 
-    def read_icc_profile(self, image_index: int) -> memoryview | None:
+    def read_icc_profile(self) -> memoryview | None:
         """Reads the ICC color profile for an image.
 
         Returns:
             The ICC color profile, or None if it can't be read.
         """
         try:
-            return libisyntax.read_icc_profile(self.ptr, self.get_image(image_index).ptr)
+            return libisyntax.read_icc_profile(self.ptr, self.wsi.ptr)
         except libisyntax.LibISyntaxFatalError:
             return None
 

{pyisyntax-0.1.1 → pyisyntax-0.1.2}/isyntax_build/builder.py

@@ -43,7 +43,7 @@ def create_ffibuilder() -> FFI:
         libraries = []
 
     ffibuilder.set_source(
-        "_pyisyntax",
+        "isyntax._pyisyntax",
         resources.read_text(isyntax_build, "pyisyntax.c"),
         sources=paths_to_strings(
             libisyntax_src/"libisyntax.c",

{pyisyntax-0.1.1 → pyisyntax-0.1.2}/isyntax_build/vendor/libisyntax/src/examples/isyntax_example.c

@@ -15,9 +15,7 @@
 #define LOG_VAR(fmt, var) printf("%s: %s=" fmt "\n", __FUNCTION__, #var, var)
 
 void print_isyntax_levels(isyntax_t* isyntax) {
-    int wsi_image_idx = libisyntax_get_wsi_image_index(isyntax);
-    LOG_VAR("%d", wsi_image_idx);
-    const isyntax_image_t* wsi_image = libisyntax_get_image(isyntax, wsi_image_idx);
+    const isyntax_image_t* wsi_image = libisyntax_get_wsi_image(isyntax);
 
     for (int i = 0; i < libisyntax_image_get_level_count(wsi_image); ++i) {
         const isyntax_level_t* level = libisyntax_image_get_level(wsi_image, i);

{pyisyntax-0.1.1 → pyisyntax-0.1.2}/isyntax_build/vendor/libisyntax/src/examples/isyntax_to_tiff.c

@@ -1,7 +1,7 @@
 /*
   BSD 2-Clause License
 
-  Copyright (c) 2019-2023, Pieter Valkema, Alexandr Virodov, Jonas Teuwen
+  Copyright (c) 2019-2024, Pieter Valkema, Alexandr Virodov, Jonas Teuwen
 
   Redistribution and use in source and binary forms, with or without
   modification, are permitted provided that the following conditions are met:
@@ -445,7 +445,7 @@ int main(int argc, char **argv) {
         return -1;
     }
 
-    const isyntax_image_t *image = libisyntax_get_image(isyntax, 0);
+    const isyntax_image_t *image = libisyntax_get_wsi_image(isyntax);
 
     // Check if the page we selected actually exists.
     int32_t level_count = libisyntax_image_get_level_count(image);

{pyisyntax-0.1.1 → pyisyntax-0.1.2}/isyntax_build/vendor/libisyntax/src/isyntax/isyntax.c

@@ -3327,6 +3327,17 @@ bool isyntax_open(isyntax_t* isyntax, const char* filename, bool init_allocators
 				isyntax->is_block_allocator_owned = false;
 			}
 
+			// Initialize dummy blocks with 'background' coefficients, to use for filling in margins at the edges (in case the neighboring codeblock doesn't exist)
+			if (!isyntax->black_dummy_coeff) {
+				isyntax->black_dummy_coeff = (icoeff_t*)calloc(1, isyntax->block_width * isyntax->block_height * sizeof(icoeff_t));
+			}
+			if (!isyntax->white_dummy_coeff) {
+				isyntax->white_dummy_coeff = (icoeff_t*)malloc(isyntax->block_width * isyntax->block_height * sizeof(icoeff_t));
+				for (i32 i = 0; i < isyntax->block_width * isyntax->block_height; ++i) {
+					isyntax->white_dummy_coeff[i] = 255;
+				}
+			}
+
 			success = true;
 
 			free(read_buffer);

{pyisyntax-0.1.1 → pyisyntax-0.1.2}/isyntax_build/vendor/libisyntax/src/isyntax/isyntax_reader.c

@@ -128,7 +128,7 @@ static void isyntax_openslide_load_tile_coefficients_ll_or_h(isyntax_cache_t* ca
 
         isyntax_hulsken_decompress(codeblock_data, codeblock->block_size,
                                    isyntax->block_width, isyntax->block_height,
-                                   codeblock->coefficient, 1,
+                                   codeblock->coefficient, wsi->compressor_version,
                                    is_ll ? tile->color_channels[color].coeff_ll : tile->color_channels[color].coeff_h);
         free(codeblock_data);
     }

{pyisyntax-0.1.1 → pyisyntax-0.1.2}/isyntax_build/vendor/libisyntax/src/isyntax/isyntax_streamer.c

@@ -51,19 +51,6 @@ static void submit_tile_completed(isyntax_streamer_t* streamer, void* tile_pixel
 
 }
 
-static void isyntax_init_dummy_codeblocks(isyntax_t* isyntax) {
-	// Blocks with 'background' coefficients, to use for filling in margins at the edges (in case the neighboring codeblock doesn't exist)
-	if (!isyntax->black_dummy_coeff) {
-		isyntax->black_dummy_coeff = (icoeff_t*)calloc(1, isyntax->block_width * isyntax->block_height * sizeof(icoeff_t));
-	}
-	if (!isyntax->white_dummy_coeff) {
-		isyntax->white_dummy_coeff = (icoeff_t*)malloc(isyntax->block_width * isyntax->block_height * sizeof(icoeff_t));
-		for (i32 i = 0; i < isyntax->block_width * isyntax->block_height; ++i) {
-			isyntax->white_dummy_coeff[i] = 255;
-		}
-	}
-}
-
 static i32 isyntax_load_all_tiles_in_level(isyntax_streamer_t* streamer, i32 scale) {
 	i32 tiles_loaded = 0;
 	i32 tile_index = 0;
@@ -125,8 +112,6 @@ static void isyntax_do_first_load(isyntax_streamer_t* streamer) {
 	i32 tiles_loaded = 0;
 	isyntax->total_rgb_transform_time = 0.0f;
 
-	isyntax_init_dummy_codeblocks(isyntax);
-
 	i32 scale = wsi->max_scale;
 	isyntax_level_t* current_level = wsi->levels + scale;
 	i32 codeblocks_per_color = isyntax_get_chunk_codeblocks_per_color_for_level(scale, true); // most often 1 + 4 + 16 (for scale n, n-1, n-2) + 1 (LL block)

{pyisyntax-0.1.1 → pyisyntax-0.1.2}/isyntax_build/vendor/libisyntax/src/libisyntax.c

@@ -1,7 +1,7 @@
 /*
   BSD 2-Clause License
 
-  Copyright (c) 2019-2023, Pieter Valkema
+  Copyright (c) 2019-2024, Pieter Valkema
 
   Redistribution and use in source and binary forms, with or without
   modification, are permitted provided that the following conditions are met:
@@ -42,7 +42,7 @@
 
 #define CHECK_LIBISYNTAX_OK(_libisyntax_call) do { \
     isyntax_error_t result = _libisyntax_call;     \
-    assert(result == LIBISYNTAX_OK);               \
+    ASSERT(result == LIBISYNTAX_OK);               \
 } while(0);
 
 static platform_thread_info_t thread_infos[MAX_THREAD_COUNT];
@@ -249,12 +249,16 @@ int32_t libisyntax_get_tile_height(const isyntax_t* isyntax) {
     return isyntax->tile_height;
 }
 
-int32_t libisyntax_get_wsi_image_index(const isyntax_t* isyntax) {
-    return isyntax->wsi_image_index;
+const isyntax_image_t* libisyntax_get_wsi_image(const isyntax_t* isyntax) {
+    return isyntax->images + isyntax->wsi_image_index;
 }
 
-const isyntax_image_t* libisyntax_get_image(const isyntax_t* isyntax, int32_t wsi_image_index) {
-    return &isyntax->images[wsi_image_index];
+const isyntax_image_t* libisyntax_get_label_image(const isyntax_t* isyntax) {
+	return isyntax->images + isyntax->label_image_index;
+}
+
+const isyntax_image_t* libisyntax_get_macro_image(const isyntax_t* isyntax) {
+	return isyntax->images + isyntax->label_image_index;
 }
 
 int32_t libisyntax_image_get_level_count(const isyntax_image_t* image) {

{pyisyntax-0.1.1 → pyisyntax-0.1.2}/isyntax_build/vendor/libisyntax/src/libisyntax.h

@@ -47,8 +47,9 @@ void            libisyntax_close(isyntax_t* isyntax);
 //== Getters API ==
 int32_t                libisyntax_get_tile_width(const isyntax_t* isyntax);
 int32_t                libisyntax_get_tile_height(const isyntax_t* isyntax);
-int32_t                libisyntax_get_wsi_image_index(const isyntax_t* isyntax);
-const isyntax_image_t* libisyntax_get_image(const isyntax_t* isyntax, int32_t wsi_image_index);
+const isyntax_image_t* libisyntax_get_wsi_image(const isyntax_t* isyntax);
+const isyntax_image_t* libisyntax_get_label_image(const isyntax_t* isyntax);
+const isyntax_image_t* libisyntax_get_macro_image(const isyntax_t* isyntax);
 int32_t                libisyntax_image_get_level_count(const isyntax_image_t* image);
 const isyntax_level_t* libisyntax_image_get_level(const isyntax_image_t* image, int32_t index);
 

{pyisyntax-0.1.1 → pyisyntax-0.1.2/pyisyntax.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyisyntax
-Version: 0.1.1
+Version: 0.1.2
 Summary: Python bindings for libisyntax
 Author-email: Aiden Nibali <dismaldenizen@gmail.com>
 License: MIT
@@ -23,6 +23,12 @@ Requires-Dist: typing_extensions; extra == "dev"
 A Python library for working with pathology images in the iSyntax file format,
 powered by [libisyntax](https://github.com/amspath/libisyntax).
 
+## Installation
+
+```console
+$ pip install pyisyntax
+```
+
 ## Usage
 
 Read and display a region of the WSI via

pyisyntax-0.1.2/pyisyntax.egg-info/top_level.txt

@@ -0,0 +1 @@
+isyntax

{pyisyntax-0.1.1 → pyisyntax-0.1.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pyisyntax"
-version = "0.1.1"
+version = "0.1.2"
 description = "Python bindings for libisyntax"
 readme = { content-type = "text/markdown", file = "README.md" }
 authors = [{ name = "Aiden Nibali", email = "dismaldenizen@gmail.com" }]
@@ -72,7 +72,7 @@ env_list = lint, type, py{310,311,312}
 deps =
   pytest
   pytest-mock
-commands = pytest {posargs:tests}
+commands = pytest --import-mode=importlib {posargs:tests}
 
 [testenv:lint]
 skip_install = true

{pyisyntax-0.1.1 → pyisyntax-0.1.2}/tests/test_lowlevel.py

@@ -23,7 +23,7 @@ def isyntax(sample_isyntax_file: Path) -> Iterator[ISyntaxPtr]:
 
 @pytest.fixture()
 def wsi_image(isyntax: ISyntaxPtr) -> ISyntaxImagePtr:
-    return libisyntax.get_image(isyntax, 0)
+    return libisyntax.get_wsi_image(isyntax)
 
 
 @pytest.fixture()
@@ -59,10 +59,6 @@ def test_libisyntax_get_tile_height(isyntax: ISyntaxPtr) -> None:
     assert libisyntax.get_tile_height(isyntax) == expected
 
 
-def test_libisyntax_get_wsi_image_index(isyntax: ISyntaxPtr) -> None:
-    assert libisyntax.get_wsi_image_index(isyntax) == 0
-
-
 def test_libisyntax_image_get_level_count(wsi_image: ISyntaxImagePtr) -> None:
     expected = 8
     assert libisyntax.image_get_level_count(wsi_image) == expected
@@ -159,7 +155,7 @@ def test_libisyntax_read_macro_image_jpeg(isyntax: ISyntaxPtr, mocker: MockerFix
 
 def test_libisyntax_read_icc_profile(isyntax: ISyntaxPtr, mocker: MockerFixture) -> None:
     free_spy = mocker.spy(libisyntax, "free")
-    wsi_image = libisyntax.get_image(isyntax, 0)
+    wsi_image = libisyntax.get_wsi_image(isyntax)
     buf = libisyntax.read_icc_profile(isyntax, wsi_image)
     version_major = buf[8]
     version_minor = buf[9] >> 4

{pyisyntax-0.1.1 → pyisyntax-0.1.2}/tests/test_wrapper.py

@@ -22,10 +22,6 @@ class TestISyntax:
         expected = 256
         assert isyntax.tile_height == expected
 
-    def test_wsi_index(self, isyntax: ISyntax) -> None:
-        expected = 0
-        assert isyntax.wsi_index == expected
-
     def test_level_count(self, isyntax: ISyntax) -> None:
         expected = 8
         assert isyntax.level_count == expected

pyisyntax-0.1.1/pyisyntax.egg-info/top_level.txt

@@ -1,2 +0,0 @@
-_pyisyntax
-isyntax