update CI and merge develop

.github/workflows/publish.yml

@@ -32,10 +32,10 @@ jobs:
         sudo apt-get -qq install exiftool libgdal-dev libzbar0t64
         GDAL_VERSION=$(gdal-config --version)
         pip install "gdal==$GDAL_VERSION"
+    - name: Install package and test dependencies
+      run: pip install -e ".[test]"
     - name: Test with pytest
-      run: |
-        pip install -e .[test]
-        pytest -m "not newgdal"
+      run: pytest
     - name: Build package
       run: |
         python -m pip install build

.github/workflows/python-test.yml

@@ -37,10 +37,10 @@ jobs:
           sudo apt-get -qq install exiftool libgdal-dev libzbar0t64
           GDAL_VERSION=$(gdal-config --version)
           pip install "gdal==$GDAL_VERSION"
+      - name: Install package and test dependencies
+        run: pip install -e ".[test]"
       - name: Test with pytest
-        run: |
-          pip install -e .[test]
-          pytest -m "not newgdal" --cov=./ --cov-report=xml
+        run: pytest
       - uses: actions/upload-artifact@v6
         if: ${{ matrix.python-version == '3.12' }}
         with:

.gitignore

@@ -1,6 +1,9 @@
 # Add any directories, files, or patterns you don't want to be tracked by version control
 *.pyc
 .ipynb_checkpoints
+.coverage
+coverage.xml
+.venv/
 __pycache__
 /dist/
 /*.egg-info

.pre-commit-config.yaml

@@ -1,13 +1,13 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
       - id: check-illegal-windows-names
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.14.6
+    rev: v0.15.18
     hooks:
       # Run the linter.
       - id: ruff
@@ -17,7 +17,7 @@ repos:
       - id: ruff-format
         types_or: [ python, pyi ] # avoid jupyter
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.2
     hooks:
       - id: codespell
         additional_dependencies:

Alignment v2.ipynb

@@ -167,8 +167,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from skimage.transform import ProjectiveTransform\n",
-    "import numpy as np\n",
+    "from micasense.warp_io import load_warp_matrices\n",
     "\n",
     "if panchroCam:\n",
     "    warp_matrices_filename = cam_serial + \"_warp_matrices_SIFT.npy\"\n",
@@ -177,20 +176,13 @@
     "\n",
     "if Path(\"./\" + warp_matrices_filename).is_file():\n",
     "    print(\"Found existing warp matrices for camera\", cam_serial)\n",
-    "    load_warp_matrices = np.load(warp_matrices_filename, allow_pickle=True)\n",
-    "    loaded_warp_matrices = []\n",
-    "    for matrix in load_warp_matrices:\n",
-    "        if panchroCam:\n",
-    "            transform = ProjectiveTransform(matrix=matrix.astype(\"float64\"))\n",
-    "            loaded_warp_matrices.append(transform)\n",
-    "        else:\n",
-    "            loaded_warp_matrices.append(matrix.astype(\"float32\"))\n",
+    "    loaded = load_warp_matrices(warp_matrices_filename, as_projective=panchroCam)\n",
     "    print(\"Warp matrices successfully loaded.\")\n",
     "\n",
     "    if panchroCam:\n",
-    "        warp_matrices_SIFT = loaded_warp_matrices\n",
+    "        warp_matrices_SIFT = loaded\n",
     "    else:\n",
-    "        warp_matrices = loaded_warp_matrices\n",
+    "        warp_matrices = loaded\n",
     "else:\n",
     "    print(\"No existing warp matrices found. Create them later in the notebook.\")\n",
     "    warp_matrices_SIFT = False\n",
@@ -381,24 +373,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy\n",
-    "import skimage\n",
-    "from skimage.transform import ProjectiveTransform\n",
+    "from micasense.warp_io import save_warp_matrices\n",
     "\n",
     "if panchroCam:\n",
     "    working_wm = warp_matrices_SIFT\n",
     "else:\n",
     "    working_wm = warp_matrices\n",
     "if not Path(\"./\" + warp_matrices_filename).is_file() or regenerate:\n",
-    "    temp_matrices = []\n",
-    "    for x in working_wm:\n",
-    "        if isinstance(x, numpy.ndarray):\n",
-    "            temp_matrices.append(x)\n",
-    "        if isinstance(x, skimage.transform._geometric.ProjectiveTransform):\n",
-    "            temp_matrices.append(x.params)\n",
-    "    np.save(\n",
-    "        warp_matrices_filename, np.array(temp_matrices, dtype=object), allow_pickle=True\n",
-    "    )\n",
+    "    save_warp_matrices(warp_matrices_filename, working_wm)\n",
     "    print(\"Saved to\", Path(\"./\" + warp_matrices_filename).resolve())\n",
     "else:\n",
     "    print(\"Matrices already exist at\", Path(\"./\" + warp_matrices_filename).resolve())"

Batch Processing v2.ipynb

@@ -142,6 +142,7 @@
     "    ) > 0.005 or val == 1:  # reduces cpu usage from updating the progressbar by 10x\n",
     "        f.value = val\n",
     "\n",
+    "\n",
     "# time is not recognized and would remove the imageset as unused\n",
     "imgset = imageset.ImageSet.from_directory(imagePath, progress_callback=update_f)\n",
     "%time imgset = imageset.ImageSet.from_directory(imagePath, progress_callback=update_f)\n",
@@ -173,8 +174,8 @@
     "data, columns = imgset.as_nested_lists()\n",
     "df = pd.DataFrame.from_records(data, index=\"timestamp\", columns=columns)\n",
     "\n",
-    "# Insert your mapbox token here\n",
-    "token = \"pk.eyJ1Ijoic3RlcGhlbm1hbmd1bTIiLCJhIjoiY2xmOXdnYzF1MDFqejNvdGE0YW13aTN5ZyJ9.AG_ckhUqTBjuGC2LuWCfQQ\"\n",
+    "# Insert your Mapbox access token here (https://account.mapbox.com/access-tokens/)\n",
+    "token = \"YOUR_MAPBOX_ACCESS_TOKEN\"\n",
     "color_property = \"dls-yaw\"\n",
     "num_color_classes = 8\n",
     "\n",
@@ -218,7 +219,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from skimage.transform import ProjectiveTransform\n",
+    "from micasense.warp_io import load_warp_matrices\n",
     "\n",
     "if panchroCam:\n",
     "    warp_matrices_filename = cam_serial + \"_warp_matrices_SIFT.npy\"\n",
@@ -227,19 +228,12 @@
     "\n",
     "if Path(\"./\" + warp_matrices_filename).is_file():\n",
     "    print(\"Found existing warp matrices for camera\", cam_serial)\n",
-    "    load_warp_matrices = np.load(warp_matrices_filename, allow_pickle=True)\n",
-    "    loaded_warp_matrices = []\n",
-    "    for matrix in load_warp_matrices:\n",
-    "        if panchroCam:\n",
-    "            transform = ProjectiveTransform(matrix=matrix.astype(\"float64\"))\n",
-    "            loaded_warp_matrices.append(transform)\n",
-    "        else:\n",
-    "            loaded_warp_matrices.append(matrix.astype(\"float32\"))\n",
+    "    loaded = load_warp_matrices(warp_matrices_filename, as_projective=panchroCam)\n",
     "\n",
     "    if panchroCam:\n",
-    "        warp_matrices_SIFT = loaded_warp_matrices\n",
+    "        warp_matrices_SIFT = loaded\n",
     "    else:\n",
-    "        warp_matrices = loaded_warp_matrices\n",
+    "        warp_matrices = loaded\n",
     "    print(\"Loaded warp matrices from\", Path(\"./\" + warp_matrices_filename).resolve())\n",
     "else:\n",
     "    print(\"No warp matrices found at expected location:\", warp_matrices_filename)"
@@ -298,7 +292,7 @@
     "            if panchroCam:\n",
     "                capture.radiometric_pan_sharpened_aligned_capture(\n",
     "                    warp_matrices=warp_matrices_SIFT,\n",
-    "                    irradiance_list=capture.dls_irradiace(),\n",
+    "                    irradiance_list=capture.dls_irradiance(),\n",
     "                    img_type=img_type,\n",
     "                    write_exif=write_exif_to_individual_stacks,\n",
     "                )\n",

CHANGELOG.md

@@ -12,6 +12,23 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * repr functions to classes so that debugging is easier
 * delete old config files
 * fixed jupyter notebooks
+* `micasense.mp_config.spawn_pool()` using a per-pool spawn context (rawpy/OpenMP safe on Linux)
+* `micasense.warp_io` — `save_warp_matrices` / `load_warp_matrices` for `.npy` warp matrix I/O
+* Alignment v2, Batch Processing v2 notebooks and `batch_processing_script.py` use `warp_io`
+* pytest 9+ native `[tool.pytest]` config with coverage in CI
+
+### Changed
+
+* setup docs and README use venv/pip instead of conda; removed `micasense_conda_env.yml`
+
+### Fixed
+
+* `SIFT_align_capture`: assign reference SIFT image when reference and target bands share shape (fixes `NameError` when `ref` is a multispectral band)
+* `SIFT_align_capture`: fall back to calibrated warp matrices when SIFT match count is low (e.g. LWIR) instead of raising
+* `ImageSet.save_stacks` and `imageutils` alignment pools use spawn context (not global `set_start_method`)
+* declare `rawpy` as a runtime dependency
+* remove unused `Capture.__sift_warp_matrices`
+* `SIFT_align_capture`: remove redundant raw/undistort work and dead accumulators
 
 ## [0.1.1] - 2025-12-28