revert to full_image

Author: melonora

notebooks/examples/technology_visium_hd.ipynb

@@ -190,7 +190,9 @@
    "source": [
     "from spatialdata import get_extent\n",
     "\n",
-    "data_extent = get_extent(sdata[\"Visium_HD_Mouse_Small_Intestine_full_image\"], coordinate_system=\"global\")\n",
+    "data_extent = get_extent(\n",
+    "    sdata[\"Visium_HD_Mouse_Small_Intestine_full_image\"], coordinate_system=\"Visium_HD_Mouse_Small_Intestine\"\n",
+    ")\n",
     "data_extent"
    ]
   },
@@ -208,7 +210,7 @@
     "    min_coordinate=[data_extent[\"x\"][0], data_extent[\"y\"][0]],\n",
     "    max_coordinate=[data_extent[\"x\"][1], data_extent[\"y\"][1]],\n",
     "    axes=(\"x\", \"y\"),\n",
-    "    target_coordinate_system=\"global\",\n",
+    "    target_coordinate_system=\"Visium_HD_Mouse_Small_Intestine\",\n",
     ")\n",
     "sdata[\"queried_cytassist\"] = queried_cytassist"
    ]
@@ -254,10 +256,10 @@
     "\n",
     "\n",
     "crop0(sdata).pl.render_images(\"Visium_HD_Mouse_Small_Intestine_full_image\").pl.show(\n",
-    "    ax=axes[0], title=\"Full image\", coordinate_systems=\"global\"\n",
+    "    ax=axes[0], title=\"Full image\", coordinate_systems=\"Visium_HD_Mouse_Small_Intestine\"\n",
     ")\n",
     "crop0(sdata).pl.render_images(\"queried_cytassist\").pl.show(\n",
-    "    ax=axes[1], title=\"CytAssit image\", coordinate_systems=\"global\"\n",
+    "    ax=axes[1], title=\"CytAssit image\", coordinate_systems=\"Visium_HD_Mouse_Small_Intestine\"\n",
     ")"
    ]
   },
@@ -601,7 +603,7 @@
     "gene_name = \"AA986860\"\n",
     "\n",
     "for bin_size in [16, 8]:\n",
-    "    sdata_small.pl.render_images(\"Visium_HD_Mouse_Small_Intestine_hires_image\").pl.render_shapes(\n",
+    "    sdata_small.pl.render_images(\"Visium_HD_Mouse_Small_Intestine_full_image\").pl.render_shapes(\n",
     "        f\"Visium_HD_Mouse_Small_Intestine_square_{bin_size:03}um\", color=gene_name, cmap=new_cmap\n",
     "    ).pl.show(coordinate_systems=\"Visium_HD_Mouse_Small_Intestine\", title=f\"bin_size={bin_size}µm\", figsize=(10, 10))"
    ]
@@ -641,7 +643,7 @@
     "    )\n",
     "\n",
     "\n",
-    "crop1(sdata_small).pl.render_images(\"Visium_HD_Mouse_Small_Intestine_hires_image\").pl.render_shapes(\n",
+    "crop1(sdata_small).pl.render_images(\"Visium_HD_Mouse_Small_Intestine_full_image\").pl.render_shapes(\n",
     "    \"Visium_HD_Mouse_Small_Intestine_square_002um\", color=gene_name, cmap=new_cmap, method=\"matplotlib\"\n",
     ").pl.show(coordinate_systems=\"Visium_HD_Mouse_Small_Intestine\", title=\"bin_size=2µm\", figsize=(10, 10))"
    ]
@@ -772,7 +774,7 @@
    "outputs": [],
    "source": [
     "%%time\n",
-    "crop1(sdata).pl.render_images(\"Visium_HD_Mouse_Small_Intestine_hires_image\").pl.render_shapes(\n",
+    "crop0(sdata).pl.render_images(\"Visium_HD_Mouse_Small_Intestine_full_image\").pl.render_shapes(\n",
     "    \"Visium_HD_Mouse_Small_Intestine_square_016um\", color=\"Cluster\"\n",
     ").pl.show(coordinate_systems=\"Visium_HD_Mouse_Small_Intestine\", title=\"bin_size=016µm\", figsize=(10, 10))"
    ]