diff --git a/docs/source/userguide/notebooks/components/patchiterator.ipynb b/docs/source/userguide/notebooks/components/patchiterator.ipynb index a4ffcb15..b8d301b2 100644 --- a/docs/source/userguide/notebooks/components/patchiterator.ipynb +++ b/docs/source/userguide/notebooks/components/patchiterator.ipynb @@ -5,12 +5,15 @@ "id": "275b29fc", "metadata": {}, "source": [ - "# PatchIterator" + "# PatchIterator\n", + "\n", + "- Creating a Patch Iterator\n", + "- Creating a Patch Iterator with Mask" ] }, { "cell_type": "code", - "execution_count": 58, + "execution_count": 1, "id": "bbaaee77", "metadata": {}, "outputs": [], @@ -28,7 +31,7 @@ }, { "cell_type": "code", - "execution_count": 60, + "execution_count": 2, "id": "96ac9207", "metadata": { "tags": [] @@ -38,384 +41,5435 @@ "name": "stdout", "output_type": "stream", "text": [ - "Number of patches 352\n", + "Number of patches 900\n", "\n", - "0 (1024, 1024, 3) (1024, 1024) {'x': 30720, 'y': 1024, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "1 (1024, 1024, 3) (1024, 1024) {'x': 31744, 'y': 1024, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "2 (1024, 1024, 3) (1024, 1024) {'x': 32768, 'y': 1024, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "3 (1024, 1024, 3) (1024, 1024) {'x': 27648, 'y': 2048, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "4 (1024, 1024, 3) (1024, 1024) {'x': 28672, 'y': 2048, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "5 (1024, 1024, 3) (1024, 1024) {'x': 29696, 'y': 2048, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "6 (1024, 1024, 3) (1024, 1024) {'x': 30720, 'y': 2048, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "7 (1024, 1024, 3) (1024, 1024) {'x': 31744, 'y': 2048, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "8 (1024, 1024, 3) (1024, 1024) {'x': 32768, 'y': 2048, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "9 (1024, 1024, 3) (1024, 1024) {'x': 18432, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "10 (1024, 1024, 3) (1024, 1024) {'x': 19456, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "11 (1024, 1024, 3) (1024, 1024) {'x': 20480, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "12 (1024, 1024, 3) (1024, 1024) {'x': 21504, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "13 (1024, 1024, 3) (1024, 1024) {'x': 22528, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "14 (1024, 1024, 3) (1024, 1024) {'x': 23552, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "15 (1024, 1024, 3) (1024, 1024) {'x': 24576, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "16 (1024, 1024, 3) (1024, 1024) {'x': 25600, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "17 (1024, 1024, 3) (1024, 1024) {'x': 26624, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "18 (1024, 1024, 3) (1024, 1024) {'x': 27648, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "19 (1024, 1024, 3) (1024, 1024) {'x': 28672, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "20 (1024, 1024, 3) (1024, 1024) {'x': 29696, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "21 (1024, 1024, 3) (1024, 1024) {'x': 30720, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "22 (1024, 1024, 3) (1024, 1024) {'x': 31744, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "23 (1024, 1024, 3) (1024, 1024) {'x': 32768, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "24 (1024, 1024, 3) (1024, 1024) {'x': 14336, 'y': 4096, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "25 (1024, 1024, 3) (1024, 1024) {'x': 15360, 'y': 4096, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "26 (1024, 1024, 3) (1024, 1024) {'x': 16384, 'y': 4096, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "27 (1024, 1024, 3) (1024, 1024) {'x': 17408, 'y': 4096, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "28 (1024, 1024, 3) (1024, 1024) {'x': 18432, 'y': 4096, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "29 (1024, 1024, 3) (1024, 1024) {'x': 19456, 'y': 4096, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "30 (1024, 1024, 3) (1024, 1024) {'x': 20480, 'y': 4096, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "31 (1024, 1024, 3) (1024, 1024) {'x': 21504, 'y': 4096, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "32 (1024, 1024, 3) (1024, 1024) {'x': 22528, 'y': 4096, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "33 (1024, 1024, 3) (1024, 1024) {'x': 23552, 'y': 4096, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "34 (1024, 1024, 3) (1024, 1024) {'x': 24576, 'y': 4096, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "35 (1024, 1024, 3) (1024, 1024) {'x': 25600, 'y': 4096, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "36 (1024, 1024, 3) (1024, 1024) {'x': 26624, 'y': 4096, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "37 (1024, 1024, 3) (1024, 1024) {'x': 27648, 'y': 4096, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "38 (1024, 1024, 3) (1024, 1024) {'x': 28672, 'y': 4096, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "39 (1024, 1024, 3) (1024, 1024) {'x': 29696, 'y': 4096, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "40 (1024, 1024, 3) (1024, 1024) {'x': 30720, 'y': 4096, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "41 (1024, 1024, 3) (1024, 1024) {'x': 13312, 'y': 5120, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "42 (1024, 1024, 3) (1024, 1024) {'x': 14336, 'y': 5120, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "43 (1024, 1024, 3) (1024, 1024) {'x': 15360, 'y': 5120, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "44 (1024, 1024, 3) (1024, 1024) {'x': 16384, 'y': 5120, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "45 (1024, 1024, 3) (1024, 1024) {'x': 17408, 'y': 5120, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "46 (1024, 1024, 3) (1024, 1024) {'x': 18432, 'y': 5120, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "47 (1024, 1024, 3) (1024, 1024) {'x': 19456, 'y': 5120, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "48 (1024, 1024, 3) (1024, 1024) {'x': 20480, 'y': 5120, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "49 (1024, 1024, 3) (1024, 1024) {'x': 21504, 'y': 5120, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "50 (1024, 1024, 3) (1024, 1024) {'x': 22528, 'y': 5120, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "51 (1024, 1024, 3) (1024, 1024) {'x': 23552, 'y': 5120, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "52 (1024, 1024, 3) (1024, 1024) {'x': 24576, 'y': 5120, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "53 (1024, 1024, 3) (1024, 1024) {'x': 25600, 'y': 5120, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "54 (1024, 1024, 3) (1024, 1024) {'x': 26624, 'y': 5120, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "55 (1024, 1024, 3) (1024, 1024) {'x': 27648, 'y': 5120, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "56 (1024, 1024, 3) (1024, 1024) {'x': 28672, 'y': 5120, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "57 (1024, 1024, 3) (1024, 1024) {'x': 11264, 'y': 6144, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "58 (1024, 1024, 3) (1024, 1024) {'x': 12288, 'y': 6144, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "59 (1024, 1024, 3) (1024, 1024) {'x': 13312, 'y': 6144, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "60 (1024, 1024, 3) (1024, 1024) {'x': 14336, 'y': 6144, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "61 (1024, 1024, 3) (1024, 1024) {'x': 15360, 'y': 6144, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "62 (1024, 1024, 3) (1024, 1024) {'x': 16384, 'y': 6144, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "63 (1024, 1024, 3) (1024, 1024) {'x': 17408, 'y': 6144, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "64 (1024, 1024, 3) (1024, 1024) {'x': 18432, 'y': 6144, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "65 (1024, 1024, 3) (1024, 1024) {'x': 19456, 'y': 6144, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "66 (1024, 1024, 3) (1024, 1024) {'x': 20480, 'y': 6144, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "67 (1024, 1024, 3) (1024, 1024) {'x': 21504, 'y': 6144, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "68 (1024, 1024, 3) (1024, 1024) {'x': 22528, 'y': 6144, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "69 (1024, 1024, 3) (1024, 1024) {'x': 23552, 'y': 6144, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "70 (1024, 1024, 3) (1024, 1024) {'x': 24576, 'y': 6144, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "71 (1024, 1024, 3) (1024, 1024) {'x': 25600, 'y': 6144, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "72 (1024, 1024, 3) (1024, 1024) {'x': 26624, 'y': 6144, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "73 (1024, 1024, 3) (1024, 1024) {'x': 27648, 'y': 6144, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "74 (1024, 1024, 3) (1024, 1024) {'x': 28672, 'y': 6144, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "75 (1024, 1024, 3) (1024, 1024) {'x': 11264, 'y': 7168, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "76 (1024, 1024, 3) (1024, 1024) {'x': 12288, 'y': 7168, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "77 (1024, 1024, 3) (1024, 1024) {'x': 13312, 'y': 7168, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "78 (1024, 1024, 3) (1024, 1024) {'x': 14336, 'y': 7168, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "79 (1024, 1024, 3) (1024, 1024) {'x': 15360, 'y': 7168, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "80 (1024, 1024, 3) (1024, 1024) {'x': 16384, 'y': 7168, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "81 (1024, 1024, 3) (1024, 1024) {'x': 17408, 'y': 7168, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "82 (1024, 1024, 3) (1024, 1024) {'x': 18432, 'y': 7168, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "83 (1024, 1024, 3) (1024, 1024) {'x': 19456, 'y': 7168, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "84 (1024, 1024, 3) (1024, 1024) {'x': 20480, 'y': 7168, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "85 (1024, 1024, 3) (1024, 1024) {'x': 21504, 'y': 7168, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "86 (1024, 1024, 3) (1024, 1024) {'x': 22528, 'y': 7168, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "87 (1024, 1024, 3) (1024, 1024) {'x': 23552, 'y': 7168, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "88 (1024, 1024, 3) (1024, 1024) {'x': 24576, 'y': 7168, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "89 (1024, 1024, 3) (1024, 1024) {'x': 25600, 'y': 7168, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "90 (1024, 1024, 3) (1024, 1024) {'x': 26624, 'y': 7168, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "91 (1024, 1024, 3) (1024, 1024) {'x': 27648, 'y': 7168, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "92 (1024, 1024, 3) (1024, 1024) {'x': 28672, 'y': 7168, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "93 (1024, 1024, 3) (1024, 1024) {'x': 29696, 'y': 7168, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "94 (1024, 1024, 3) (1024, 1024) {'x': 10240, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "95 (1024, 1024, 3) (1024, 1024) {'x': 11264, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "96 (1024, 1024, 3) (1024, 1024) {'x': 12288, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "97 (1024, 1024, 3) (1024, 1024) {'x': 13312, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "98 (1024, 1024, 3) (1024, 1024) {'x': 14336, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "99 (1024, 1024, 3) (1024, 1024) {'x': 15360, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "100 (1024, 1024, 3) (1024, 1024) {'x': 16384, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "101 (1024, 1024, 3) (1024, 1024) {'x': 17408, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "102 (1024, 1024, 3) (1024, 1024) {'x': 18432, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "103 (1024, 1024, 3) (1024, 1024) {'x': 19456, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "104 (1024, 1024, 3) (1024, 1024) {'x': 20480, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "105 (1024, 1024, 3) (1024, 1024) {'x': 21504, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "106 (1024, 1024, 3) (1024, 1024) {'x': 22528, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "107 (1024, 1024, 3) (1024, 1024) {'x': 23552, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "108 (1024, 1024, 3) (1024, 1024) {'x': 24576, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "109 (1024, 1024, 3) (1024, 1024) {'x': 25600, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "110 (1024, 1024, 3) (1024, 1024) {'x': 26624, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "111 (1024, 1024, 3) (1024, 1024) {'x': 27648, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "112 (1024, 1024, 3) (1024, 1024) {'x': 28672, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "113 (1024, 1024, 3) (1024, 1024) {'x': 29696, 'y': 8192, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "114 (1024, 1024, 3) (1024, 1024) {'x': 8192, 'y': 9216, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "115 (1024, 1024, 3) (1024, 1024) {'x': 9216, 'y': 9216, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "116 (1024, 1024, 3) (1024, 1024) {'x': 10240, 'y': 9216, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "117 (1024, 1024, 3) (1024, 1024) {'x': 11264, 'y': 9216, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "118 (1024, 1024, 3) (1024, 1024) {'x': 12288, 'y': 9216, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "119 (1024, 1024, 3) (1024, 1024) {'x': 13312, 'y': 9216, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "120 (1024, 1024, 3) (1024, 1024) {'x': 14336, 'y': 9216, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "121 (1024, 1024, 3) (1024, 1024) {'x': 15360, 'y': 9216, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "122 (1024, 1024, 3) (1024, 1024) {'x': 16384, 'y': 9216, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "123 (1024, 1024, 3) (1024, 1024) {'x': 17408, 'y': 9216, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "124 (1024, 1024, 3) (1024, 1024) {'x': 18432, 'y': 9216, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "125 (1024, 1024, 3) (1024, 1024) {'x': 19456, 'y': 9216, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "126 (1024, 1024, 3) (1024, 1024) 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(1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "274 (1024, 1024, 3) (1024, 1024) {'x': 8192, 'y': 17408, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "275 (1024, 1024, 3) (1024, 1024) {'x': 9216, 'y': 17408, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "276 (1024, 1024, 3) (1024, 1024) {'x': 10240, 'y': 17408, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "277 (1024, 1024, 3) (1024, 1024) {'x': 11264, 'y': 17408, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "278 (1024, 1024, 3) (1024, 1024) {'x': 20480, 'y': 17408, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "279 (1024, 1024, 3) (1024, 1024) {'x': 21504, 'y': 17408, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "280 (1024, 1024, 3) (1024, 1024) {'x': 22528, 'y': 17408, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "281 (1024, 1024, 3) (1024, 1024) {'x': 23552, 'y': 17408, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "282 (1024, 1024, 3) (1024, 1024) {'x': 24576, 'y': 17408, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "283 (1024, 1024, 3) (1024, 1024) {'x': 25600, 'y': 17408, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "284 (1024, 1024, 3) (1024, 1024) {'x': 26624, 'y': 17408, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "285 (1024, 1024, 3) (1024, 1024) {'x': 27648, 'y': 17408, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "286 (1024, 1024, 3) (1024, 1024) {'x': 28672, 'y': 17408, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "287 (1024, 1024, 3) (1024, 1024) {'x': 5120, 'y': 18432, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "288 (1024, 1024, 3) (1024, 1024) {'x': 6144, 'y': 18432, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "289 (1024, 1024, 3) (1024, 1024) {'x': 7168, 'y': 18432, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "290 (1024, 1024, 3) (1024, 1024) {'x': 8192, 'y': 18432, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "291 (1024, 1024, 3) (1024, 1024) {'x': 9216, 'y': 18432, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "292 (1024, 1024, 3) (1024, 1024) {'x': 17408, 'y': 18432, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "293 (1024, 1024, 3) (1024, 1024) {'x': 18432, 'y': 18432, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "294 (1024, 1024, 3) (1024, 1024) {'x': 19456, 'y': 18432, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "295 (1024, 1024, 3) (1024, 1024) {'x': 20480, 'y': 18432, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "296 (1024, 1024, 3) (1024, 1024) {'x': 21504, 'y': 18432, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "297 (1024, 1024, 3) (1024, 1024) {'x': 22528, 'y': 18432, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "298 (1024, 1024, 3) (1024, 1024) {'x': 23552, 'y': 18432, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "299 (1024, 1024, 3) (1024, 1024) {'x': 24576, 'y': 18432, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "300 (1024, 1024, 3) (1024, 1024) {'x': 25600, 'y': 18432, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "301 (1024, 1024, 3) (1024, 1024) {'x': 26624, 'y': 18432, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "302 (1024, 1024, 3) (1024, 1024) {'x': 27648, 'y': 18432, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "303 (1024, 1024, 3) (1024, 1024) {'x': 28672, 'y': 18432, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "304 (1024, 1024, 3) (1024, 1024) {'x': 29696, 'y': 18432, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "305 (1024, 1024, 3) (1024, 1024) {'x': 17408, 'y': 19456, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "306 (1024, 1024, 3) (1024, 1024) {'x': 18432, 'y': 19456, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "307 (1024, 1024, 3) (1024, 1024) {'x': 19456, 'y': 19456, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "308 (1024, 1024, 3) (1024, 1024) {'x': 20480, 'y': 19456, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "309 (1024, 1024, 3) (1024, 1024) {'x': 21504, 'y': 19456, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "310 (1024, 1024, 3) (1024, 1024) {'x': 22528, 'y': 19456, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "311 (1024, 1024, 3) (1024, 1024) {'x': 23552, 'y': 19456, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "312 (1024, 1024, 3) (1024, 1024) {'x': 24576, 'y': 19456, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "313 (1024, 1024, 3) (1024, 1024) {'x': 25600, 'y': 19456, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "314 (1024, 1024, 3) (1024, 1024) {'x': 26624, 'y': 19456, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "315 (1024, 1024, 3) (1024, 1024) {'x': 27648, 'y': 19456, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "316 (1024, 1024, 3) (1024, 1024) {'x': 28672, 'y': 19456, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "317 (1024, 1024, 3) (1024, 1024) {'x': 29696, 'y': 19456, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "318 (1024, 1024, 3) (1024, 1024) {'x': 2048, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "319 (1024, 1024, 3) (1024, 1024) {'x': 3072, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "320 (1024, 1024, 3) (1024, 1024) {'x': 17408, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "321 (1024, 1024, 3) (1024, 1024) {'x': 18432, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "322 (1024, 1024, 3) (1024, 1024) {'x': 19456, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "323 (1024, 1024, 3) (1024, 1024) {'x': 20480, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "324 (1024, 1024, 3) (1024, 1024) {'x': 21504, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "325 (1024, 1024, 3) (1024, 1024) {'x': 22528, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "326 (1024, 1024, 3) (1024, 1024) {'x': 23552, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "327 (1024, 1024, 3) (1024, 1024) {'x': 24576, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "328 (1024, 1024, 3) (1024, 1024) {'x': 25600, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "329 (1024, 1024, 3) (1024, 1024) {'x': 26624, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "330 (1024, 1024, 3) (1024, 1024) {'x': 27648, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "331 (1024, 1024, 3) (1024, 1024) {'x': 28672, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "332 (1024, 1024, 3) (1024, 1024) {'x': 29696, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "333 (1024, 1024, 3) (1024, 1024) {'x': 18432, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "334 (1024, 1024, 3) (1024, 1024) {'x': 19456, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "335 (1024, 1024, 3) (1024, 1024) {'x': 20480, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "336 (1024, 1024, 3) (1024, 1024) {'x': 21504, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "337 (1024, 1024, 3) (1024, 1024) {'x': 22528, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "338 (1024, 1024, 3) (1024, 1024) {'x': 23552, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "339 (1024, 1024, 3) (1024, 1024) {'x': 24576, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "340 (1024, 1024, 3) (1024, 1024) {'x': 25600, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "341 (1024, 1024, 3) (1024, 1024) {'x': 26624, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "342 (1024, 1024, 3) (1024, 1024) {'x': 27648, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "343 (1024, 1024, 3) (1024, 1024) {'x': 28672, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "344 (1024, 1024, 3) (1024, 1024) {'x': 29696, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "345 (1024, 1024, 3) (1024, 1024) {'x': 1024, 'y': 22528, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "346 (1024, 1024, 3) (1024, 1024) {'x': 22528, 'y': 22528, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "347 (1024, 1024, 3) (1024, 1024) {'x': 23552, 'y': 22528, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "348 (1024, 1024, 3) (1024, 1024) {'x': 24576, 'y': 22528, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "349 (1024, 1024, 3) (1024, 1024) {'x': 25600, 'y': 22528, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "350 (1024, 1024, 3) (1024, 1024) {'x': 26624, 'y': 22528, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n", - "351 (1024, 1024, 3) (1024, 1024) {'x': 27648, 'y': 22528, 'tile_shape': (1024, 1024, 3), 'spacing': 0.5, 'center': False}\n" - ] - } - ], - "source": [ - "patch_configuration = PatchConfiguration(patch_shape=(1024,1024,3),\n", - " spacing=0.5,\n", - " overlap=(0,0),\n", - " offset=(0,0),\n", - " center=False)\n", - "\n", - "with create_patch_iterator(image_path='/tmp/TCGA-21-5784-01Z-00-DX1.tif',\n", - " mask_path='/tmp/TCGA-21-5784-01Z-00-DX1_tb_mask.tif',\n", - " patch_configuration=patch_configuration,\n", - " cpus=4) as patch_iterator:\n", - " \n", - " print(f\"Number of patches {len(patch_iterator)}\\n\")\n", - " for idx, (patch, mask, info) in enumerate(patch_iterator):\n", - " print(idx, patch.shape, mask.shape, info)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "5d0209a4-8936-499d-9a27-e968a1acc64b", + "Index : 0, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 0, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 1, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 1024, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 2, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 2048, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 3, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 3072, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 4, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 4096, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 5, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 5120, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 6, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 6144, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 7, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 7168, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 8, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 8192, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 9, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 9216, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 10, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 10240, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 11, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 11264, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 12, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 12288, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 13, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 13312, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 14, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 14336, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 15, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 15360, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 16, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 16384, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 17, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 17408, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 18, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 18432, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 19, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 19456, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 20, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 20480, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 21, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 21504, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 22, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 22528, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 23, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 23552, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 24, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 24576, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 25, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 25600, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 26, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 26624, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 27, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 27648, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 28, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 28672, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 29, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 29696, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 30, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 30720, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 31, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 31744, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 32, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 32768, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 33, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 33792, 'y': 0, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 34, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 34816, 'y': 0, 'tile_shape': (1024, 1024, 3), 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0, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 829, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 1024, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 830, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 2048, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 831, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 3072, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 832, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 4096, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 833, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 5120, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 834, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 6144, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 835, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 7168, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 836, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 8192, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 837, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 9216, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 838, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 10240, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 839, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 11264, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 840, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 12288, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 841, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 13312, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 842, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 14336, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 843, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 15360, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 844, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 16384, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 845, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 17408, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 846, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 18432, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 847, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 19456, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 848, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 20480, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 849, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 21504, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 850, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 22528, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 851, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 23552, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 852, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 24576, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 853, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 25600, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 854, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 26624, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 855, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 27648, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 856, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 28672, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 857, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 29696, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 858, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 30720, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 859, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 31744, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 860, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 32768, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 861, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 33792, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 862, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 34816, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 863, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 35840, 'y': 23552, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 864, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 0, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 865, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 1024, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 866, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 2048, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 867, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 3072, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 868, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 4096, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 869, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 5120, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 870, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 6144, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 871, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 7168, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 872, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 8192, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 873, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 9216, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 874, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 10240, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 875, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 11264, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 876, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 12288, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 877, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 13312, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 878, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 14336, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 879, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 15360, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 880, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 16384, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 881, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 17408, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 882, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 18432, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 883, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 19456, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 884, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 20480, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 885, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 21504, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 886, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 22528, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 887, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 23552, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 888, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 24576, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 889, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 25600, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 890, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 26624, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 891, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 27648, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 892, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 28672, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 893, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 29696, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 894, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 30720, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 895, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 31744, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 896, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 32768, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 897, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 33792, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 898, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 34816, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 899, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Info : {'x': 35840, 'y': 24576, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n" + ] + } + ], + "source": [ + "patch_configuration = PatchConfiguration(patch_shape=(1024,1024,3),\n", + " spacings=(0.5,),\n", + " overlap=(0,0),\n", + " offset=(0,0),\n", + " center=False)\n", + "\n", + "with create_patch_iterator(image_path='/tmp/TCGA-21-5784-01Z-00-DX1.tif',\n", + " patch_configuration=patch_configuration,\n", + " cpus=4,\n", + " backend='asap') as patch_iterator:\n", + " \n", + " print(f\"Number of patches {len(patch_iterator)}\\n\")\n", + " for idx, (patch, info) in enumerate(patch_iterator):\n", + " print(f\"Index : {idx}, \\n Patch shape: {patch.shape}, \\n Info : {info}\\n\")\n" + ] + }, + { + "cell_type": "markdown", + "id": "e513ab44-d65b-421c-ad09-fe91ee17b699", + "metadata": {}, + "source": [ + "## Creating a Patch Iterator with Mask" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "5d0209a4-8936-499d-9a27-e968a1acc64b", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Number of patches 352\n", + "\n", + "Index : 0, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 30720, 'y': 1024, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 1, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 31744, 'y': 1024, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 2, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 32768, 'y': 1024, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 3, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 27648, 'y': 2048, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 4, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 28672, 'y': 2048, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 5, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 29696, 'y': 2048, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 6, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 30720, 'y': 2048, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 7, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 31744, 'y': 2048, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 8, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 32768, 'y': 2048, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 9, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 18432, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 10, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 19456, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 11, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 20480, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 12, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 21504, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 13, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 22528, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 14, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 23552, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 15, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 24576, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 16, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 25600, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 17, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 26624, 'y': 3072, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': 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\n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 20480, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 324, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 21504, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 325, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 22528, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 326, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 23552, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 327, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 24576, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 328, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 25600, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 329, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 26624, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 330, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 27648, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 331, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 28672, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 332, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 29696, 'y': 20480, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 333, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 18432, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 334, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 19456, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 335, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 20480, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 336, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 21504, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 337, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 22528, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 338, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 23552, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 339, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 24576, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 340, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 25600, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 341, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 26624, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 342, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 27648, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 343, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 28672, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 344, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 29696, 'y': 21504, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 345, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 1024, 'y': 22528, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 346, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 22528, 'y': 22528, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 347, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 23552, 'y': 22528, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 348, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 24576, 'y': 22528, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 349, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 25600, 'y': 22528, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 350, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 26624, 'y': 22528, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n", + "Index : 351, \n", + " Patch shape: (1, 1, 1024, 1024, 3), \n", + " Mask shape: (1, 1, 1024, 1024), \n", + " Info : {'x': 27648, 'y': 22528, 'tile_shape': (1024, 1024, 3), 'spacings': (0.5,), 'center': False}\n", + "\n" + ] + } + ], + "source": [ + "patch_configuration = PatchConfiguration(patch_shape=(1024,1024,3),\n", + " spacings=(0.5,),\n", + " overlap=(0,0),\n", + " offset=(0,0),\n", + " center=False)\n", + "\n", + "with create_patch_iterator(image_path='/tmp/TCGA-21-5784-01Z-00-DX1.tif',\n", + " mask_path='/tmp/TCGA-21-5784-01Z-00-DX1_tb_mask.tif',\n", + " patch_configuration=patch_configuration,\n", + " cpus=4,\n", + " backend='asap') as patch_iterator:\n", + " \n", + " print(f\"Number of patches {len(patch_iterator)}\\n\")\n", + " for idx, (patch, mask, info) in enumerate(patch_iterator):\n", + " print(f\"Index : {idx}, \\n Patch shape: {patch.shape}, \\n Mask shape: {mask.shape}, \\n Info : {info}\\n\")\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "64acc38e-7aa0-4040-9c5d-90c01cbde6cc", "metadata": {}, "outputs": [], "source": [] @@ -423,7 +5477,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Python 3", "language": "python", "name": "python3" }, @@ -437,7 +5491,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.0" + "version": "3.8.10" } }, "nbformat": 4,