Fix data types in panel detection

.github/workflows/gh-pages.yml

@@ -19,7 +19,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v7
         with:
           lfs: true
       - uses: actions/setup-python@v6
@@ -36,8 +36,8 @@ jobs:
       - name: Install dependencies
         run: pip install -e .[docs]
       - name: Build GitHub Pages site
-        run: scripts/build_gh_pages.sh
-      - uses: actions/upload-pages-artifact@v3
+        run: EXECUTE=1 scripts/build_gh_pages.sh
+      - uses: actions/upload-pages-artifact@v5
         with:
           path: _site
 
@@ -49,4 +49,4 @@ jobs:
       url: ${{ steps.deployment.outputs.page_url }}
     steps:
       - id: deployment
-        uses: actions/deploy-pages@v4
+        uses: actions/deploy-pages@v5

.github/workflows/pr-agent.yml

@@ -13,7 +13,7 @@ jobs:
       contents: write
     steps:
       - name: PR Agent action step
-        uses: the-pr-agent/pr-agent@v0.36.1
+        uses: the-pr-agent/pr-agent@v0.38.0
         env:
           OPENAI_KEY: ${{ secrets.OPENAI_KEY }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/publish.yml

@@ -8,7 +8,7 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v7
       - uses: actions/setup-python@v6
         with:
           python-version: "3.12"
@@ -18,7 +18,7 @@ jobs:
     needs: [lint]
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v7
       with:
         lfs: true
     - uses: actions/setup-python@v6
@@ -41,7 +41,7 @@ jobs:
         python -m pip install build
         python -m build
     - name: Store the distribution packages
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: python-package-distributions
         path: dist/
@@ -57,7 +57,7 @@ jobs:
       id-token: write  # IMPORTANT: mandatory for trusted publishing
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v7
+      uses: actions/download-artifact@v8
       with:
         name: python-package-distributions
         path: dist/

.github/workflows/python-test.yml

@@ -11,7 +11,7 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v7
       - uses: actions/setup-python@v6
         with:
           python-version: "3.12"
@@ -25,7 +25,7 @@ jobs:
       matrix:
         python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v7
         with:
           lfs: true
       - uses: actions/setup-python@v6
@@ -41,7 +41,7 @@ jobs:
         run: pip install -e ".[test]"
       - name: Test with pytest
         run: pytest
-      - uses: actions/upload-artifact@v6
+      - uses: actions/upload-artifact@v7
         if: ${{ matrix.python-version == '3.12' }}
         with:
           name: coverage-report

.gitignore

@@ -8,3 +8,5 @@ __pycache__
 /dist/
 /*.egg-info
 /_site/
+.idea
+docs/*.html

Alignment v2.ipynb

@@ -697,17 +697,17 @@
     "# Compute and display a histogram\n",
     "# ndvi_hist_min = np.min(ndvi)\n",
     "# ndvi_hist_max = np.max(ndvi)\n",
-    "ndvi_hist_min = np.min(np.percentile(ndvi, 0.5))\n",
-    "ndvi_hist_max = np.max(np.percentile(ndvi, 99.5))\n",
-    "fig, axis = plt.subplots(1, 1, figsize=(10, 4))\n",
+    "ndvi_hist_min = np.min(np.percentile(ndvi.compressed(), 0.5))\n",
+    "ndvi_hist_max = np.max(np.percentile(ndvi.compressed(), 99.5))\n",
+    "fig, axis = plt.subplots(1, 1, figsize=(10,4))\n",
     "axis.hist(ndvi.ravel(), bins=512, range=(ndvi_hist_min, ndvi_hist_max))\n",
     "plt.title(\"NDVI Histogram\")\n",
     "plt.show()\n",
     "\n",
     "min_display_ndvi = 0.45  # further mask soil by removing low-ndvi values\n",
     "# min_display_ndvi = np.percentile(ndvi.flatten(),  5.0)  # modify with these percentilse to adjust contrast\n",
     "max_display_ndvi = np.percentile(\n",
-    "    ndvi.flatten(), 99.5\n",
+    "    ndvi.compressed(), 99.5\n",
     ")  # for many images, 0.5 and 99.5 are good values\n",
     "masked_ndvi = np.ma.masked_where(ndvi < min_display_ndvi, ndvi)\n",
     "\n",
@@ -752,15 +752,15 @@
     "masked_ndre = np.ma.masked_where(ndvi < min_display_ndvi, ndre)\n",
     "\n",
     "# Compute a histogram\n",
-    "ndre_hist_min = np.min(np.percentile(masked_ndre, 0.5))\n",
-    "ndre_hist_max = np.max(np.percentile(masked_ndre, 99.5))\n",
-    "fig, axis = plt.subplots(1, 1, figsize=(10, 4))\n",
+    "ndre_hist_min = np.min(np.percentile(masked_ndre.compressed(), 0.5))\n",
+    "ndre_hist_max = np.max(np.percentile(masked_ndre.compressed(), 99.5))\n",
+    "fig, axis = plt.subplots(1, 1, figsize=(10,4))\n",
     "axis.hist(masked_ndre.ravel(), bins=512, range=(ndre_hist_min, ndre_hist_max))\n",
     "plt.title(\"NDRE Histogram (filtered to only plants)\")\n",
     "plt.show()\n",
     "\n",
-    "min_display_ndre = np.percentile(masked_ndre, 5)\n",
-    "max_display_ndre = np.percentile(masked_ndre, 99.5)\n",
+    "min_display_ndre = np.percentile(masked_ndre.compressed(), 5)\n",
+    "max_display_ndre = np.percentile(masked_ndre.compressed(), 99.5)\n",
     "\n",
     "fig, axis = plotutils.plot_overlay_withcolorbar(\n",
     "    gamma_corr_rgb,\n",

Alignment-10Band.ipynb

@@ -403,9 +403,9 @@
     "plt.show()\n",
     "\n",
     "min_display_ndvi = 0.45  # further mask soil by removing low-ndvi values\n",
-    "# min_display_ndvi = np.percentile(ndvi.flatten(),  5.0)  # modify with these percentilse to adjust contrast\n",
+    "# min_display_ndvi = np.percentile(ndvi.compressed(),  5.0)  # modify with these percentilse to adjust contrast\n",
     "max_display_ndvi = np.percentile(\n",
-    "    ndvi.flatten(), 99.5\n",
+    "    ndvi.compressed(), 99.5\n",
     ")  # for many images, 0.5 and 99.5 are good values\n",
     "masked_ndvi = np.ma.masked_where(ndvi < min_display_ndvi, ndvi)\n",
     "\n",
@@ -456,8 +456,8 @@
     "plt.title(\"NDRE Histogram (filtered to only plants)\")\n",
     "plt.show()\n",
     "\n",
-    "min_display_ndre = np.percentile(masked_ndre, 5)\n",
-    "max_display_ndre = np.percentile(masked_ndre, 99.5)\n",
+    "min_display_ndre = np.percentile(masked_ndre.compressed(), 5)\n",
+    "max_display_ndre = np.percentile(masked_ndre.compressed(), 99.5)\n",
     "\n",
     "fig, axis = plotutils.plot_overlay_withcolorbar(\n",
     "    gamma_corr_rgb,\n",

Alignment-RigRelatives.ipynb

@@ -372,9 +372,9 @@
     "plt.show()\n",
     "\n",
     "min_display_ndvi = 0.45  # further mask soil by removing low-ndvi values\n",
-    "# min_display_ndvi = np.percentile(ndvi.flatten(),  5.0)  # modify with these percentilse to adjust contrast\n",
+    "# min_display_ndvi = np.percentile(ndvi.compressed(),  5.0)  # modify with these percentilse to adjust contrast\n",
     "max_display_ndvi = np.percentile(\n",
-    "    ndvi.flatten(), 99.5\n",
+    "    ndvi.compressed(), 99.5\n",
     ")  # for many images, 0.5 and 99.5 are good values\n",
     "masked_ndvi = np.ma.masked_where(ndvi < min_display_ndvi, ndvi)\n",
     "\n",
@@ -426,8 +426,8 @@
     "plt.title(\"NDRE Histogram (filtered to only plants)\")\n",
     "plt.show()\n",
     "\n",
-    "min_display_ndre = np.percentile(masked_ndre, 5)\n",
-    "max_display_ndre = np.percentile(masked_ndre, 99.5)\n",
+    "min_display_ndre = np.percentile(masked_ndre.compressed(), 5)\n",
+    "max_display_ndre = np.percentile(masked_ndre.compressed(), 99.5)\n",
     "\n",
     "fig, axis = plotutils.plot_overlay_withcolorbar(\n",
     "    gamma_corr_rgb,\n",

Alignment.ipynb

@@ -422,9 +422,9 @@
     "plt.show()\n",
     "\n",
     "min_display_ndvi = 0.45  # further mask soil by removing low-ndvi values\n",
-    "# min_display_ndvi = np.percentile(ndvi.flatten(),  5.0)  # modify with these percentilse to adjust contrast\n",
+    "# min_display_ndvi = np.percentile(ndvi.compressed(),  5.0)  # modify with these percentilse to adjust contrast\n",
     "max_display_ndvi = np.percentile(\n",
-    "    ndvi.flatten(), 99.5\n",
+    "    ndvi.compressed(), 99.5\n",
     ")  # for many images, 0.5 and 99.5 are good values\n",
     "masked_ndvi = np.ma.masked_where(ndvi < min_display_ndvi, ndvi)\n",
     "\n",
@@ -475,8 +475,8 @@
     "plt.title(\"NDRE Histogram (filtered to only plants)\")\n",
     "plt.show()\n",
     "\n",
-    "min_display_ndre = np.percentile(masked_ndre, 5)\n",
-    "max_display_ndre = np.percentile(masked_ndre, 99.5)\n",
+    "min_display_ndre = np.percentile(masked_ndre.compressed(), 5)\n",
+    "max_display_ndre = np.percentile(masked_ndre.compressed(), 99.5)\n",
     "\n",
     "fig, axis = plotutils.plot_overlay_withcolorbar(\n",
     "    gamma_corr_rgb,\n",