fix alignment notebook coordinate systems names

Author: Ubuntu

notebooks/examples/alignment_using_landmarks.ipynb

@@ -86,15 +86,12 @@
        "│     └── 'transcripts': DataFrame with shape: (<Delayed>, 8) (3D points)\n",
        "├── Shapes\n",
        "│     ├── 'cell_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
-       "│     ├── 'cell_circles': GeoDataFrame shape: (167780, 2) (2D shapes)\n",
-       "│     └── 'xenium_landmarks': GeoDataFrame shape: (3, 2) (2D shapes)\n",
+       "│     └── 'cell_circles': GeoDataFrame shape: (167780, 2) (2D shapes)\n",
        "└── Tables\n",
        "      └── 'table': AnnData (167780, 313)\n",
        "with coordinate systems:\n",
-       "    ▸ 'aligned', with elements:\n",
-       "        morphology_focus (Images)\n",
        "    ▸ 'global', with elements:\n",
-       "        morphology_focus (Images), morphology_mip (Images), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), xenium_landmarks (Shapes)"
+       "        morphology_focus (Images), morphology_mip (Images), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes)"
       ]
      },
      "execution_count": 2,
@@ -142,19 +139,16 @@
        "│     ├── 'CytAssist_FFPE_Human_Breast_Cancer_hires_image': DataArray[cyx] (3, 2000, 1809)\n",
        "│     └── 'CytAssist_FFPE_Human_Breast_Cancer_lowres_image': DataArray[cyx] (3, 600, 543)\n",
        "├── Shapes\n",
-       "│     ├── 'CytAssist_FFPE_Human_Breast_Cancer': GeoDataFrame shape: (4992, 2) (2D shapes)\n",
-       "│     └── 'visium_landmarks': GeoDataFrame shape: (3, 2) (2D shapes)\n",
+       "│     └── 'CytAssist_FFPE_Human_Breast_Cancer': GeoDataFrame shape: (4992, 2) (2D shapes)\n",
        "└── Tables\n",
        "      └── 'table': AnnData (4992, 18085)\n",
        "with coordinate systems:\n",
-       "    ▸ 'aligned', with elements:\n",
-       "        CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer_hires_image (Images), CytAssist_FFPE_Human_Breast_Cancer_lowres_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes), visium_landmarks (Shapes)\n",
-       "    ▸ 'downscaled_hires', with elements:\n",
+       "    ▸ 'CytAssist_FFPE_Human_Breast_Cancer', with elements:\n",
+       "        CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer_hires_image (Images), CytAssist_FFPE_Human_Breast_Cancer_lowres_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
+       "    ▸ 'CytAssist_FFPE_Human_Breast_Cancer_downscaled_hires', with elements:\n",
        "        CytAssist_FFPE_Human_Breast_Cancer_hires_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
-       "    ▸ 'downscaled_lowres', with elements:\n",
-       "        CytAssist_FFPE_Human_Breast_Cancer_lowres_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
-       "    ▸ 'global', with elements:\n",
-       "        CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer_hires_image (Images), CytAssist_FFPE_Human_Breast_Cancer_lowres_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes), visium_landmarks (Shapes)"
+       "    ▸ 'CytAssist_FFPE_Human_Breast_Cancer_downscaled_lowres', with elements:\n",
+       "        CytAssist_FFPE_Human_Breast_Cancer_lowres_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)"
       ]
      },
      "execution_count": 3,
@@ -282,12 +276,14 @@
    "outputs": [],
    "source": [
     "from spatialdata.models import ShapesModel\n",
+    "from spatialdata.transformations import Identity\n",
     "\n",
     "visium_landmarks = ShapesModel.parse(\n",
-    "    np.array([[10556.699, 7829.764], [13959.155, 13522.025], [10621.200, 17392.116]]), geometry=0, radius=500\n",
+    "    np.array([[10556.699, 7829.764], [13959.155, 13522.025], [10621.200, 17392.116]]), geometry=0, radius=500, transformations={'CytAssist_FFPE_Human_Breast_Cancer': Identity()}\n",
     ")\n",
     "visium_sdata[\"visium_landmarks\"] = visium_landmarks\n",
     "\n",
+    "# for Xenium data, the data is aligned to the 'global' coordinate system as with can see with print(xenium_sdata), so there is no need to specify transformations in .parse()\n",
     "xenium_landmarks = ShapesModel.parse(\n",
     "    np.array([[9438.385, 13933.017], [24847.866, 5948.002], [34082.584, 15234.235]]), geometry=0, radius=500\n",
     ")\n",
@@ -389,7 +385,7 @@
     "    reference_element=xenium_sdata[\"morphology_focus\"],\n",
     "    moving_element=visium_sdata[\"CytAssist_FFPE_Human_Breast_Cancer_full_image\"],\n",
     "    reference_coordinate_system=\"global\",\n",
-    "    moving_coordinate_system=\"global\",\n",
+    "    moving_coordinate_system=\"CytAssist_FFPE_Human_Breast_Cancer\",\n",
     "    new_coordinate_system=\"aligned\",\n",
     ")\n",
     "affine"
@@ -571,7 +567,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.10.0"
   },
   "vscode": {
    "interpreter": {