diff --git a/examples/integrations/itk/SelectROI.ipynb b/examples/integrations/itk/SelectROI.ipynb index 766c5167..b6beb01b 100644 --- a/examples/integrations/itk/SelectROI.ipynb +++ b/examples/integrations/itk/SelectROI.ipynb @@ -32,12 +32,12 @@ "# Install dependencies for this example\n", "import sys\n", "\n", - "!{sys.executable} -m pip install -q pooch tqdm \"itk-io>=5.3.0\" \"itkwidgets[all]>=1.0a40\"" + "!{sys.executable} -m pip install -q pooch tqdm \"itk-io>=5.3.0\" \"itkwidgets[all]>=1.0a41\" rich" ] }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 1, "metadata": { "tags": [] }, @@ -47,12 +47,13 @@ "import pooch\n", "from ngff_zarr import ngff_image_to_itk_image\n", "from itkwidgets import view\n", - "import zarr" + "import zarr\n", + "from rich import print" ] }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 2, "metadata": { "tags": [] }, @@ -66,7 +67,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 3, "metadata": { "tags": [] }, @@ -77,7 +78,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 4, "metadata": { "tags": [] }, @@ -86,11 +87,11 @@ "data": { "text/html": [ "\n", - " \n", + " \n", " \n", @@ -106,7 +107,7 @@ { "data": { "application/javascript": [ - "window.connectPlugin && window.connectPlugin(\"36aff9cb-6524-4587-8126-ab3615cdeb6f\")" + "window.connectPlugin && window.connectPlugin(\"948b285c-c11c-4f71-81d8-e11c7fced0e8\")" ], "text/plain": [ "" @@ -118,7 +119,7 @@ { "data": { "text/html": [ - "
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" ], "text/plain": [ "" @@ -157,7 +158,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 5, "metadata": { "tags": [ "skip-execution" @@ -171,7 +172,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 6, "metadata": { "tags": [ "skip-execution" @@ -184,7 +185,7 @@ "0" ] }, - "execution_count": 7, + "execution_count": 6, "metadata": {}, "output_type": "execute_result" } @@ -202,7 +203,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 7, "metadata": { "tags": [ "skip-execution" @@ -225,7 +226,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 8, "metadata": { "tags": [ "skip-execution" @@ -233,12 +234,30 @@ }, "outputs": [ { - "name": "stdout", - "output_type": "stream", - "text": [ - "Slices for loaded scale: (slice(0, 250, None), slice(0, 350, None), slice(122, 170, None))\n", - "Slices with default parameter: (slice(0, 250, None), slice(0, 350, None), slice(122, 170, None))\n" - ] + "data": { + "text/html": [ + "
Slices for loaded scale:       (slice(0, 250, None), slice(0, 350, None), slice(131, 186, None))\n",
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Slices with default parameter: (slice(0, 250, None), slice(0, 350, None), slice(131, 186, None))\n",
+       "
\n" + ], + "text/plain": [ + "Slices with default parameter: \u001b[1m(\u001b[0m\u001b[1;35mslice\u001b[0m\u001b[1m(\u001b[0m\u001b[1;36m0\u001b[0m, \u001b[1;36m250\u001b[0m, \u001b[3;35mNone\u001b[0m\u001b[1m)\u001b[0m, \u001b[1;35mslice\u001b[0m\u001b[1m(\u001b[0m\u001b[1;36m0\u001b[0m, \u001b[1;36m350\u001b[0m, \u001b[3;35mNone\u001b[0m\u001b[1m)\u001b[0m, \u001b[1;35mslice\u001b[0m\u001b[1m(\u001b[0m\u001b[1;36m131\u001b[0m, \u001b[1;36m186\u001b[0m, \u001b[3;35mNone\u001b[0m\u001b[1m)\u001b[0m\u001b[1m)\u001b[0m\n" + ] + }, + "metadata": {}, + "output_type": "display_data" } ], "source": [ @@ -256,7 +275,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 9, "metadata": { "tags": [ "skip-execution" @@ -270,7 +289,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 10, "metadata": { "tags": [ "skip-execution" @@ -279,23 +298,31 @@ "outputs": [ { "data": { + "text/html": [ + "
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+       "    {'x': 29.12353376902817, 'y': -6.971699953079224, 'z': -6.971699953079224},\n",
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+       "]\n",
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NgffImage(\n",
+       "    data=dask.array<getitem, shape=(250, 350, 55), dtype=int16, chunksize=(128, 128, 55), chunktype=numpy.ndarray>,\n",
+       "    dims=['z', 'y', 'x'],\n",
+       "    scale={'z': 0.2734, 'y': 0.2734, 'x': 0.2734},\n",
+       "    translation={'x': 29.12353376902817, 'y': -6.971699953079224, 'z': -6.971699953079224},\n",
+       "    name='Image',\n",
+       "    axes_units={'z': None, 'y': None, 'x': None},\n",
+       "    computed_callbacks=[]\n",
+       ")\n",
+       "
\n" + ], "text/plain": [ - "NgffImage(data=dask.array, dims=['z', 'y', 'x'], scale={'z': 0.2734, 'y': 0.2734, 'x': 0.2734}, translation={'x': 26.70976023219073, 'y': -6.971699714660643, 'z': -6.971699953079224}, name='Image', axes_units={'z': None, 'y': None, 'x': None}, computed_callbacks=[])" + "\u001b[1;35mNgffImage\u001b[0m\u001b[1m(\u001b[0m\n", + " \u001b[33mdata\u001b[0m=\u001b[35mdask\u001b[0m.array\u001b[1m<\u001b[0m\u001b[1;95mgetitem\u001b[0m\u001b[39m, \u001b[0m\u001b[33mshape\u001b[0m\u001b[39m=\u001b[0m\u001b[1;39m(\u001b[0m\u001b[1;36m250\u001b[0m\u001b[39m, \u001b[0m\u001b[1;36m350\u001b[0m\u001b[39m, \u001b[0m\u001b[1;36m55\u001b[0m\u001b[1;39m)\u001b[0m\u001b[39m, \u001b[0m\u001b[33mdtype\u001b[0m\u001b[39m=\u001b[0m\u001b[35mint16\u001b[0m\u001b[39m, \u001b[0m\u001b[33mchunksize\u001b[0m\u001b[39m=\u001b[0m\u001b[1;39m(\u001b[0m\u001b[1;36m128\u001b[0m\u001b[39m, \u001b[0m\u001b[1;36m128\u001b[0m\u001b[39m, \u001b[0m\u001b[1;36m55\u001b[0m\u001b[1;39m)\u001b[0m\u001b[39m, \u001b[0m\u001b[33mchunktype\u001b[0m\u001b[39m=\u001b[0m\u001b[35mnumpy\u001b[0m\u001b[39m.ndarray\u001b[0m\u001b[1m>\u001b[0m,\n", + " \u001b[33mdims\u001b[0m=\u001b[1m[\u001b[0m\u001b[32m'z'\u001b[0m, \u001b[32m'y'\u001b[0m, \u001b[32m'x'\u001b[0m\u001b[1m]\u001b[0m,\n", + " \u001b[33mscale\u001b[0m=\u001b[1m{\u001b[0m\u001b[32m'z'\u001b[0m: \u001b[1;36m0.2734\u001b[0m, \u001b[32m'y'\u001b[0m: \u001b[1;36m0.2734\u001b[0m, \u001b[32m'x'\u001b[0m: \u001b[1;36m0.2734\u001b[0m\u001b[1m}\u001b[0m,\n", + " \u001b[33mtranslation\u001b[0m=\u001b[1m{\u001b[0m\u001b[32m'x'\u001b[0m: \u001b[1;36m29.12353376902817\u001b[0m, \u001b[32m'y'\u001b[0m: \u001b[1;36m-6.971699953079224\u001b[0m, \u001b[32m'z'\u001b[0m: \u001b[1;36m-6.971699953079224\u001b[0m\u001b[1m}\u001b[0m,\n", + " \u001b[33mname\u001b[0m=\u001b[32m'Image'\u001b[0m,\n", + " \u001b[33maxes_units\u001b[0m=\u001b[1m{\u001b[0m\u001b[32m'z'\u001b[0m: \u001b[3;35mNone\u001b[0m, \u001b[32m'y'\u001b[0m: \u001b[3;35mNone\u001b[0m, \u001b[32m'x'\u001b[0m: \u001b[3;35mNone\u001b[0m\u001b[1m}\u001b[0m,\n", + " \u001b[33mcomputed_callbacks\u001b[0m=\u001b[1m[\u001b[0m\u001b[1m]\u001b[0m\n", + "\u001b[1m)\u001b[0m\n" ] }, - "execution_count": 13, "metadata": {}, - "output_type": "execute_result" + "output_type": "display_data" } ], "source": [ - "roi_image" + "print(roi_image)" ] }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 13, "metadata": { "tags": [ "skip-execution" @@ -348,7 +394,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 14, "metadata": { "tags": [ "skip-execution" @@ -357,17 +403,124 @@ "outputs": [ { "data": { + "text/html": [ + "
Multiscales(\n",
+       "    images=[\n",
+       "        NgffImage(\n",
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+       "chunktype=numpy.ndarray>,\n",
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+       "            name='Image',\n",
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+       "        ),\n",
+       "        NgffImage(\n",
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+       "chunktype=numpy.ndarray>,\n",
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+       "            name='Image',\n",
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+       "            computed_callbacks=[]\n",
+       "        )\n",
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+       "            Axis(name='y', type='space', unit=None),\n",
+       "            Axis(name='x', type='space', unit=None)\n",
+       "        ],\n",
+       "        datasets=[\n",
+       "            Dataset(\n",
+       "                path='scale0/image',\n",
+       "                coordinateTransformations=[\n",
+       "                    Scale(scale=[0.2734, 0.2734, 0.2734], type='scale'),\n",
+       "                    Translation(translation=[-6.835, -6.835, -6.835], type='translation')\n",
+       "                ]\n",
+       "            ),\n",
+       "            Dataset(\n",
+       "                path='scale1/image',\n",
+       "                coordinateTransformations=[\n",
+       "                    Scale(scale=[0.2734, 0.5468, 0.5468], type='scale'),\n",
+       "                    Translation(translation=[-6.835, -6.6983, -6.6983], type='translation')\n",
+       "                ]\n",
+       "            )\n",
+       "        ],\n",
+       "        coordinateTransformations=None,\n",
+       "        name='image',\n",
+       "        version='0.4'\n",
+       "    ),\n",
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+       "    method=None,\n",
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+       ")\n",
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coordinateTransformations=[Scale(scale=[0.2734, 0.5468, 0.2734], type='scale'), Translation(translation=[-6.971699953079224, -6.8349997146606425, 26.70976023219073], type='translation')])], coordinateTransformations=None, name='Image', version='0.4'), scale_factors=[{'x': 1, 'y': 2, 'z': 1}], method=, chunks={'z': 128, 'y': 128, 'x': 128})" + "\u001b[1;35mMultiscales\u001b[0m\u001b[1m(\u001b[0m\n", + " \u001b[33mimages\u001b[0m=\u001b[1m[\u001b[0m\n", + " \u001b[1;35mNgffImage\u001b[0m\u001b[1m(\u001b[0m\n", + " \u001b[33mdata\u001b[0m=\u001b[35mdask\u001b[0m.array\u001b[1m<\u001b[0m\u001b[1;95mgetitem\u001b[0m\u001b[39m, \u001b[0m\u001b[33mshape\u001b[0m\u001b[39m=\u001b[0m\u001b[1;39m(\u001b[0m\u001b[1;36m250\u001b[0m\u001b[39m, \u001b[0m\u001b[1;36m350\u001b[0m\u001b[39m, \u001b[0m\u001b[1;36m55\u001b[0m\u001b[1;39m)\u001b[0m\u001b[39m, \u001b[0m\u001b[33mdtype\u001b[0m\u001b[39m=\u001b[0m\u001b[35mint16\u001b[0m\u001b[39m, \u001b[0m\u001b[33mchunksize\u001b[0m\u001b[39m=\u001b[0m\u001b[1;39m(\u001b[0m\u001b[1;36m128\u001b[0m\u001b[39m, \u001b[0m\u001b[1;36m128\u001b[0m\u001b[39m, \u001b[0m\u001b[1;36m55\u001b[0m\u001b[1;39m)\u001b[0m\u001b[39m, \u001b[0m\n", + "\u001b[33mchunktype\u001b[0m\u001b[39m=\u001b[0m\u001b[35mnumpy\u001b[0m\u001b[39m.ndarray>,\u001b[0m\n", + "\u001b[39m \u001b[0m\u001b[33mdims\u001b[0m\u001b[39m=\u001b[0m\u001b[1;39m[\u001b[0m\u001b[32m'z'\u001b[0m\u001b[39m, \u001b[0m\u001b[32m'y'\u001b[0m\u001b[39m, \u001b[0m\u001b[32m'x'\u001b[0m\u001b[1;39m]\u001b[0m\u001b[39m,\u001b[0m\n", + "\u001b[39m \u001b[0m\u001b[33mscale\u001b[0m\u001b[39m=\u001b[0m\u001b[1;39m{\u001b[0m\u001b[32m'z'\u001b[0m\u001b[39m: \u001b[0m\u001b[1;36m0.2734\u001b[0m\u001b[39m, \u001b[0m\u001b[32m'y'\u001b[0m\u001b[39m: \u001b[0m\u001b[1;36m0.2734\u001b[0m\u001b[39m, \u001b[0m\u001b[32m'x'\u001b[0m\u001b[39m: \u001b[0m\u001b[1;36m0.2734\u001b[0m\u001b[1;39m}\u001b[0m\u001b[39m,\u001b[0m\n", + "\u001b[39m \u001b[0m\u001b[33mtranslation\u001b[0m\u001b[39m=\u001b[0m\u001b[1;39m{\u001b[0m\u001b[32m'x'\u001b[0m\u001b[39m: \u001b[0m\u001b[1;36m29.12353376902817\u001b[0m\u001b[39m, \u001b[0m\u001b[32m'y'\u001b[0m\u001b[39m: \u001b[0m\u001b[1;36m-6.971699953079224\u001b[0m\u001b[39m, \u001b[0m\u001b[32m'z'\u001b[0m\u001b[39m: \u001b[0m\u001b[1;36m-6.971699953079224\u001b[0m\u001b[1;39m}\u001b[0m\u001b[39m,\u001b[0m\n", + "\u001b[39m \u001b[0m\u001b[33mname\u001b[0m\u001b[39m=\u001b[0m\u001b[32m'Image'\u001b[0m\u001b[39m,\u001b[0m\n", + "\u001b[39m \u001b[0m\u001b[33maxes_units\u001b[0m\u001b[39m=\u001b[0m\u001b[1;39m{\u001b[0m\u001b[32m'z'\u001b[0m\u001b[39m: \u001b[0m\u001b[3;35mNone\u001b[0m\u001b[39m, \u001b[0m\u001b[32m'y'\u001b[0m\u001b[39m: \u001b[0m\u001b[3;35mNone\u001b[0m\u001b[39m, \u001b[0m\u001b[32m'x'\u001b[0m\u001b[39m: \u001b[0m\u001b[3;35mNone\u001b[0m\u001b[1;39m}\u001b[0m\u001b[39m,\u001b[0m\n", + "\u001b[39m \u001b[0m\u001b[33mcomputed_callbacks\u001b[0m\u001b[39m=\u001b[0m\u001b[1;39m[\u001b[0m\u001b[1;39m]\u001b[0m\n", + "\u001b[39m \u001b[0m\u001b[1;39m)\u001b[0m\u001b[39m,\u001b[0m\n", + "\u001b[39m \u001b[0m\u001b[1;35mNgffImage\u001b[0m\u001b[1;39m(\u001b[0m\n", + "\u001b[39m \u001b[0m\u001b[33mdata\u001b[0m\u001b[39m=\u001b[0m\u001b[35mdask\u001b[0m\u001b[39m.array\u001b[0m,\n", + " \u001b[33mdims\u001b[0m=\u001b[1m[\u001b[0m\u001b[32m'z'\u001b[0m, \u001b[32m'y'\u001b[0m, \u001b[32m'x'\u001b[0m\u001b[1m]\u001b[0m,\n", + " \u001b[33mscale\u001b[0m=\u001b[1m{\u001b[0m\u001b[32m'z'\u001b[0m: \u001b[1;36m0.2734\u001b[0m, \u001b[32m'y'\u001b[0m: \u001b[1;36m0.5468\u001b[0m, \u001b[32m'x'\u001b[0m: \u001b[1;36m0.5468\u001b[0m\u001b[1m}\u001b[0m,\n", + " \u001b[33mtranslation\u001b[0m=\u001b[1m{\u001b[0m\u001b[32m'x'\u001b[0m: \u001b[1;36m29.12353376902817\u001b[0m, \u001b[32m'y'\u001b[0m: \u001b[1;36m-6.971699953079224\u001b[0m, \u001b[32m'z'\u001b[0m: \u001b[1;36m-6.971699953079224\u001b[0m\u001b[1m}\u001b[0m,\n", + " \u001b[33mname\u001b[0m=\u001b[32m'Image'\u001b[0m,\n", + " \u001b[33maxes_units\u001b[0m=\u001b[1m{\u001b[0m\u001b[32m'z'\u001b[0m: \u001b[3;35mNone\u001b[0m, \u001b[32m'y'\u001b[0m: \u001b[3;35mNone\u001b[0m, \u001b[32m'x'\u001b[0m: \u001b[3;35mNone\u001b[0m\u001b[1m}\u001b[0m,\n", + " \u001b[33mcomputed_callbacks\u001b[0m=\u001b[1m[\u001b[0m\u001b[1m]\u001b[0m\n", + " \u001b[1m)\u001b[0m\n", + " \u001b[1m]\u001b[0m,\n", + " \u001b[33mmetadata\u001b[0m=\u001b[1;35mMetadata\u001b[0m\u001b[1m(\u001b[0m\n", + " \u001b[33maxes\u001b[0m=\u001b[1m[\u001b[0m\n", + " \u001b[1;35mAxis\u001b[0m\u001b[1m(\u001b[0m\u001b[33mname\u001b[0m=\u001b[32m'z'\u001b[0m, \u001b[33mtype\u001b[0m=\u001b[32m'space'\u001b[0m, \u001b[33munit\u001b[0m=\u001b[3;35mNone\u001b[0m\u001b[1m)\u001b[0m,\n", + " \u001b[1;35mAxis\u001b[0m\u001b[1m(\u001b[0m\u001b[33mname\u001b[0m=\u001b[32m'y'\u001b[0m, \u001b[33mtype\u001b[0m=\u001b[32m'space'\u001b[0m, \u001b[33munit\u001b[0m=\u001b[3;35mNone\u001b[0m\u001b[1m)\u001b[0m,\n", + " \u001b[1;35mAxis\u001b[0m\u001b[1m(\u001b[0m\u001b[33mname\u001b[0m=\u001b[32m'x'\u001b[0m, \u001b[33mtype\u001b[0m=\u001b[32m'space'\u001b[0m, \u001b[33munit\u001b[0m=\u001b[3;35mNone\u001b[0m\u001b[1m)\u001b[0m\n", + " \u001b[1m]\u001b[0m,\n", + " \u001b[33mdatasets\u001b[0m=\u001b[1m[\u001b[0m\n", + " \u001b[1;35mDataset\u001b[0m\u001b[1m(\u001b[0m\n", + " \u001b[33mpath\u001b[0m=\u001b[32m'scale0/image'\u001b[0m,\n", + " \u001b[33mcoordinateTransformations\u001b[0m=\u001b[1m[\u001b[0m\n", + " \u001b[1;35mScale\u001b[0m\u001b[1m(\u001b[0m\u001b[33mscale\u001b[0m=\u001b[1m[\u001b[0m\u001b[1;36m0.2734\u001b[0m, \u001b[1;36m0.2734\u001b[0m, \u001b[1;36m0.2734\u001b[0m\u001b[1m]\u001b[0m, \u001b[33mtype\u001b[0m=\u001b[32m'scale'\u001b[0m\u001b[1m)\u001b[0m,\n", + " \u001b[1;35mTranslation\u001b[0m\u001b[1m(\u001b[0m\u001b[33mtranslation\u001b[0m=\u001b[1m[\u001b[0m\u001b[1;36m-6.835\u001b[0m, \u001b[1;36m-6.835\u001b[0m, \u001b[1;36m-6.835\u001b[0m\u001b[1m]\u001b[0m, \u001b[33mtype\u001b[0m=\u001b[32m'translation'\u001b[0m\u001b[1m)\u001b[0m\n", + " \u001b[1m]\u001b[0m\n", + " \u001b[1m)\u001b[0m,\n", + " \u001b[1;35mDataset\u001b[0m\u001b[1m(\u001b[0m\n", + " \u001b[33mpath\u001b[0m=\u001b[32m'scale1/image'\u001b[0m,\n", + " \u001b[33mcoordinateTransformations\u001b[0m=\u001b[1m[\u001b[0m\n", + " \u001b[1;35mScale\u001b[0m\u001b[1m(\u001b[0m\u001b[33mscale\u001b[0m=\u001b[1m[\u001b[0m\u001b[1;36m0.2734\u001b[0m, \u001b[1;36m0.5468\u001b[0m, \u001b[1;36m0.5468\u001b[0m\u001b[1m]\u001b[0m, \u001b[33mtype\u001b[0m=\u001b[32m'scale'\u001b[0m\u001b[1m)\u001b[0m,\n", + " \u001b[1;35mTranslation\u001b[0m\u001b[1m(\u001b[0m\u001b[33mtranslation\u001b[0m=\u001b[1m[\u001b[0m\u001b[1;36m-6.835\u001b[0m, \u001b[1;36m-6.6983\u001b[0m, \u001b[1;36m-6.6983\u001b[0m\u001b[1m]\u001b[0m, \u001b[33mtype\u001b[0m=\u001b[32m'translation'\u001b[0m\u001b[1m)\u001b[0m\n", + " \u001b[1m]\u001b[0m\n", + " \u001b[1m)\u001b[0m\n", + " \u001b[1m]\u001b[0m,\n", + " \u001b[33mcoordinateTransformations\u001b[0m=\u001b[3;35mNone\u001b[0m,\n", + " \u001b[33mname\u001b[0m=\u001b[32m'image'\u001b[0m,\n", + " \u001b[33mversion\u001b[0m=\u001b[32m'0.4'\u001b[0m\n", + " \u001b[1m)\u001b[0m,\n", + " \u001b[33mscale_factors\u001b[0m=\u001b[3;35mNone\u001b[0m,\n", + " \u001b[33mmethod\u001b[0m=\u001b[3;35mNone\u001b[0m,\n", + " \u001b[33mchunks\u001b[0m=\u001b[3;35mNone\u001b[0m\n", + "\u001b[1m)\u001b[0m\n" ] }, - "execution_count": 15, "metadata": {}, - "output_type": "execute_result" + "output_type": "display_data" } ], "source": [ - "roi_multiscales" + "print(roi_multiscales)" ] }, { @@ -532,7 +685,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.18" + "version": "3.10.13" } }, "nbformat": 4,