Add level-weighted module

.gitignore

@@ -10,6 +10,9 @@ build/
 .eggs/
 *.egg
 
+# Version file
+_version.py
+
 # Installer logs
 pip-log.txt
 pip-delete-this-directory.txt

notebooks/Test pnanolocz-lib.ipynb

@@ -17,7 +17,6 @@
    "source": [
     "data_path = r\"C:/Users/ggjh246/OneDrive - University of Leeds/Code/playNano_testdata/save-2025.05.20-12.57.06.187.h5-jpk\"\n",
     "from playnano.io.loader import load_afm_stack\n",
-    "\n",
     "afm_stack = load_afm_stack(data_path, channel = \"height_trace\")"
    ]
   },
@@ -41,7 +40,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pnanolocz_lib import level, level_auto\n",
+    "from pnanolocz_lib import level_auto, level, level_weighted\n",
     "\n",
     "frames = afm_stack.n_frames\n",
     "frame_ind = range(0, frames)\n",
@@ -68,7 +67,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "auto_leveled = level_auto.apply_level_auto(afm_stack.data, \"iterative 1nm high\")"
+    "auto_leveled = level_auto.apply_level_auto(afm_stack.data, \"multi-plane-otsu\")"
    ]
   },
   {
@@ -89,7 +88,6 @@
    "outputs": [],
    "source": [
     "from pnanolocz_lib.thresholder import thresholder\n",
-    "\n",
     "mask_hist = thresholder(plane_levelled, 'histogram', limits = (0.2, 100),invert = False)"
    ]
   },
@@ -109,6 +107,18 @@
    "id": "9",
    "metadata": {},
    "outputs": [],
+   "source": [
+    "from pnanolocz_lib.level_weighted import apply_level_weighted\n",
+    "lev_weight = apply_level_weighted(plane_levelled, 1, 1, \"smed_line\", mask=mask_hist)\n",
+    "plt.imshow(lev_weight[5], cmap=\"afmhot\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "10",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "masked_line_levelled = level.apply_level(plane_levelled, 1, 0, \"line\", mask_hist)\n",
     "plt.imshow(masked_line_levelled[5], cmap=\"afmhot\")"
@@ -117,7 +127,15 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "11",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -128,7 +146,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -139,17 +157,17 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
-    "mask_hist2 =thresholder(maksed_line_levelled, 'histogram', limits= (0.5,100), invert=False)"
+    "mask_hist2 =thresholder(maksed_linemed_levelled, 'histogram', limits= (0.5,100), invert=False)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -160,7 +178,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -171,15 +189,15 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": []
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -189,7 +207,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "19",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -199,7 +217,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -209,7 +227,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "19",
+   "id": "21",
    "metadata": {},
    "outputs": [],
    "source": []

pyproject.toml

@@ -71,7 +71,6 @@ classifiers = [
   "Topic :: Scientific/Engineering :: Image Processing",
 ]
 
-
 [project.optional-dependencies]
 dev = [
     "pytest>=7.0",
@@ -82,6 +81,7 @@ dev = [
     "black",
     "codespell>=2.3.0",
     "mypy==1.11.1",
+    "nbstripout",
 ]
 
 [project.urls]
@@ -93,6 +93,9 @@ package-dir = { "" = "src" }
 [tool.setuptools.packages.find]
 where = ["src"]
 
+[tool.setuptools_scm]
+write_to = "src/pnanolocz_lib/_version.py"
+
 [tool.black]
 line-length = 88
 target-version = ["py310"]
@@ -138,7 +141,7 @@ ignore = ["D100", "D104", "D203", "D212", "D401"]
 convention = "numpy"
 
 [tool.codespell]
-skip = "*.egg-info,*.png,*.jpg,*.jpeg,*.gif,*.bmp,*.svg,*.ico,*.pdf,*.zip,*.gz,*.bz2,*.xz,*.7z,*.mp3,*.wav,*.mp4,*.mov,*.tif,*.tiff,*.ipynb,docs/_build/*,build/*,dist/*"
+skip = "*.egg-info,*.png,*.jpg,*.jpeg,*.gif,*.bmp,*.svg,*.ico,*.pdf,*.zip,*.gz,*.bz2,*.xz,*.7z,*.mp3,*.wav,*.mp4,*.mov,*.tif,*.tiff,*.ipynb,docs/_build/*,build/*,dist/*,*.html,*.css,*.js"
 ignore-words-list = "tabel,crate"
 check-filenames = false
 check-hidden = false
@@ -156,12 +159,18 @@ namespace_packages = false
 
 # Your existing strictness
 strict = true
-warn_unused_ignores = true
+warn_unused_ignores = false
 disallow_untyped_defs = true
 exclude = '^tests/'
 
 [[tool.mypy.overrides]]
-module = ["scipy.*", "skimage.*", "ruptures", "sknw"]
+module = [
+    "scipy.*",
+    "skimage.*",
+    "ruptures",
+    "sknw",
+    "numpy.*"
+]
 ignore_missing_imports = true
 
 [tool.pytest.ini_options]

src/pnanolocz_lib/__init__.py

@@ -3,6 +3,9 @@
 from importlib.metadata import PackageNotFoundError, version
 
 try:
-    __version__ = version("pnanolocz_lib")
-except PackageNotFoundError:
-    __version__ = "0.0.0"
+    from ._version import version as __version__  # type: ignore[import-not-found]
+except Exception:
+    try:
+        __version__ = version("pnanolocz_lib")
+    except PackageNotFoundError:
+        __version__ = "0.0.0"