update notebooks

fractal-analytics-platform · Oct 9, 2024 · 95bc9a4 · 95bc9a4
1 parent 44d05fc
commit 95bc9a4
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Showing 3 changed files with 16 additions and 9 deletions.
diff --git a/docs/notebooks/basic_usage.ipynb b/docs/notebooks/basic_usage.ipynb
@@ -145,7 +145,7 @@
     "roi_table = ngff_image.table.get_table(\"FOV_ROI_table\")\n",
     "\n",
     "print(f\"{roi_table.list_field_indexes=}\")\n",
-    "print(f\"{roi_table.get_roi(\"FOV_1\")=}\")\n",
+    "print(f\"{roi_table.get_roi('FOV_1')=}\")\n",
     "\n",
     "roi_table.table"
    ]
@@ -175,6 +175,13 @@
     "print(f\"{new_ngff_image.num_levels=}\")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -199,7 +206,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.7"
+   "version": "3.11.10"
   }
  },
  "nbformat": 4,

diff --git a/docs/notebooks/image.ipynb b/docs/notebooks/image.ipynb
@@ -330,7 +330,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.7"
+   "version": "3.11.10"
   }
  },
  "nbformat": 4,

diff --git a/docs/notebooks/processing.ipynb b/docs/notebooks/processing.ipynb
@@ -90,7 +90,7 @@
     "# - calculate the MIP\n",
     "# - set the data in the MIP image\n",
     "for roi in roi_table.list_rois:\n",
-    "    print(f\" - Processing ROI {roi.infos.get(\"field_index\")}\")\n",
+    "    print(f\" - Processing ROI {roi.infos.get('field_index')}\")\n",
     "    patch = source_image.get_array_from_roi(roi)\n",
     "    mip_patch = patch.max(axis=1, keepdims=True)\n",
     "    mip_image.set_array_from_roi(patch=mip_patch, roi=roi)\n",
@@ -162,7 +162,7 @@
     "\n",
     "roi_list = []\n",
     "for roi in roi_table.list_rois:\n",
-    "    print(f\" - Processing ROI {roi.infos.get(\"field_index\")}\")\n",
+    "    print(f\" - Processing ROI {roi.infos.get('field_index')}\")\n",
     "    roi.z_length = 1 # In the MIP image, the z dimension is 1\n",
     "    roi_list.append(roi)\n",
     "\n",
@@ -243,7 +243,7 @@
     "print(\"Source image loaded with shape:\", source_image.shape)\n",
     "\n",
     "# Get a ROI table\n",
-    "roi_table = mip_ngff.table.get(\"FOV_ROI_table\")\n",
+    "roi_table = mip_ngff.table.get_table(\"FOV_ROI_table\")\n",
     "print(\"ROI table loaded with\", len(roi_table.list_rois), \"ROIs\")\n",
     "\n",
     "# Find the DAPI channel\n",
@@ -255,8 +255,8 @@
     "# - set the data in segmentation image\n",
     "max_label = 0\n",
     "for roi in roi_table.list_rois:\n",
-    "    print(f\" - Processing ROI {roi.infos.get(\"field_index\")}\")\n",
-    "    patch = source_image.array_from_roi(roi, c=dapi_idx)\n",
+    "    print(f\" - Processing ROI {roi.infos.get('field_index')}\")\n",
+    "    patch = source_image.get_array_from_roi(roi, c=dapi_idx)\n",
     "    segmentation = otsu_threshold_segmentation(patch, max_label)\n",
     "\n",
     "    # Add the max label of the previous segmentation to avoid overlapping labels\n",
@@ -303,7 +303,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.7"
+   "version": "3.11.10"
   }
  },
  "nbformat": 4,