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64 | 64 | }, |
65 | 65 | { |
66 | 66 | "cell_type": "code", |
67 | | - "execution_count": 1, |
| 67 | + "execution_count": null, |
68 | 68 | "metadata": { |
69 | 69 | "colab": { |
70 | 70 | "base_uri": "https://localhost:8080/" |
71 | 71 | }, |
72 | 72 | "id": "Y9weWEaezOmg", |
73 | 73 | "outputId": "e5b6dc7e-67c2-44c2-b25b-5e8e45e7023c" |
74 | 74 | }, |
75 | | - "outputs": [ |
76 | | - { |
77 | | - "name": "stdout", |
78 | | - "output_type": "stream", |
79 | | - "text": [ |
80 | | - "Collecting idc-index\n", |
81 | | - " Downloading idc_index-0.9.2-py3-none-any.whl.metadata (7.9 kB)\n", |
82 | | - "Collecting wsidicom\n", |
83 | | - " Downloading wsidicom-0.27.1-py3-none-any.whl.metadata (25 kB)\n", |
84 | | - "Collecting openslide-python\n", |
85 | | - " Downloading openslide_python-1.4.2-cp311-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (4.9 kB)\n", |
86 | | - "Collecting openslide-bin\n", |
87 | | - " Downloading openslide_bin-4.0.0.8-py3-none-manylinux_2_28_x86_64.whl.metadata (4.5 kB)\n", |
88 | | - "Requirement already satisfied: click in /usr/local/lib/python3.12/dist-packages (from idc-index) (8.2.1)\n", |
89 | | - "Collecting duckdb<=1.2.1,>=0.10.0 (from idc-index)\n", |
90 | | - " Downloading duckdb-1.2.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (966 bytes)\n", |
91 | | - "Collecting idc-index-data==21.0.0 (from idc-index)\n", |
92 | | - " Downloading idc_index_data-21.0.0-py3-none-any.whl.metadata (5.5 kB)\n", |
93 | | - "Requirement already satisfied: packaging in /usr/local/lib/python3.12/dist-packages (from idc-index) (25.0)\n", |
94 | | - "Requirement already satisfied: pandas<=2.2.4 in /usr/local/lib/python3.12/dist-packages (from idc-index) (2.2.2)\n", |
95 | | - "Requirement already satisfied: platformdirs in /usr/local/lib/python3.12/dist-packages (from idc-index) (4.4.0)\n", |
96 | | - "Requirement already satisfied: psutil in /usr/local/lib/python3.12/dist-packages (from idc-index) (5.9.5)\n", |
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98 | | - "Requirement already satisfied: requests in /usr/local/lib/python3.12/dist-packages (from idc-index) (2.32.4)\n", |
99 | | - "Collecting s5cmd (from idc-index)\n", |
100 | | - " Downloading s5cmd-0.2.0-py3-none-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.7 kB)\n", |
101 | | - "Collecting sphinx-click (from idc-index)\n", |
102 | | - " Downloading sphinx_click-6.0.0-py3-none-any.whl.metadata (3.4 kB)\n", |
103 | | - "Requirement already satisfied: tqdm in /usr/local/lib/python3.12/dist-packages (from idc-index) (4.67.1)\n", |
104 | | - "Requirement already satisfied: Pillow>=9.1.1 in /usr/local/lib/python3.12/dist-packages (from wsidicom) (11.3.0)\n", |
105 | | - "Collecting dicomweb-client<0.60.0,>=0.59.2 (from wsidicom)\n", |
106 | | - " Downloading dicomweb_client-0.59.3-py3-none-any.whl.metadata (4.5 kB)\n", |
107 | | - "Collecting fsspec<2025.0.0,>=2024.2.0 (from wsidicom)\n", |
108 | | - " Downloading fsspec-2024.12.0-py3-none-any.whl.metadata (11 kB)\n", |
109 | | - "Collecting marshmallow<4.0.0,>=3.20.1 (from wsidicom)\n", |
110 | | - " Downloading marshmallow-3.26.1-py3-none-any.whl.metadata (7.3 kB)\n", |
111 | | - "Requirement already satisfied: numpy>=1.22.0 in /usr/local/lib/python3.12/dist-packages (from wsidicom) (2.0.2)\n", |
112 | | - "Collecting pydicom>=3.0.0 (from wsidicom)\n", |
113 | | - " Downloading pydicom-3.0.1-py3-none-any.whl.metadata (9.4 kB)\n", |
114 | | - "Collecting universal-pathlib<0.3.0,>=0.2.1 (from wsidicom)\n", |
115 | | - " Downloading universal_pathlib-0.2.6-py3-none-any.whl.metadata (25 kB)\n", |
116 | | - "Collecting retrying>=1.3.3 (from dicomweb-client<0.60.0,>=0.59.2->wsidicom)\n", |
117 | | - " Downloading retrying-1.4.2-py3-none-any.whl.metadata (5.5 kB)\n", |
118 | | - "Requirement already satisfied: python-dateutil>=2.8.2 in /usr/local/lib/python3.12/dist-packages (from pandas<=2.2.4->idc-index) (2.9.0.post0)\n", |
119 | | - "Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.12/dist-packages (from pandas<=2.2.4->idc-index) (2025.2)\n", |
120 | | - "Requirement already satisfied: tzdata>=2022.7 in /usr/local/lib/python3.12/dist-packages (from pandas<=2.2.4->idc-index) (2025.2)\n", |
121 | | - "Requirement already satisfied: charset_normalizer<4,>=2 in /usr/local/lib/python3.12/dist-packages (from requests->idc-index) (3.4.3)\n", |
122 | | - "Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.12/dist-packages (from requests->idc-index) (3.10)\n", |
123 | | - "Requirement already satisfied: urllib3<3,>=1.21.1 in /usr/local/lib/python3.12/dist-packages (from requests->idc-index) (2.5.0)\n", |
124 | | - "Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.12/dist-packages (from requests->idc-index) (2025.8.3)\n", |
125 | | - "Requirement already satisfied: sphinx>=4.0 in /usr/local/lib/python3.12/dist-packages (from sphinx-click->idc-index) (8.2.3)\n", |
126 | | - "Requirement already satisfied: docutils in /usr/local/lib/python3.12/dist-packages (from sphinx-click->idc-index) (0.21.2)\n", |
127 | | - "Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.12/dist-packages (from python-dateutil>=2.8.2->pandas<=2.2.4->idc-index) (1.17.0)\n", |
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135 | | - "Requirement already satisfied: Pygments>=2.17 in /usr/local/lib/python3.12/dist-packages (from sphinx>=4.0->sphinx-click->idc-index) (2.19.2)\n", |
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142 | | - "Downloading idc_index-0.9.2-py3-none-any.whl (27 kB)\n", |
143 | | - "Downloading idc_index_data-21.0.0-py3-none-any.whl (80.6 MB)\n", |
144 | | - "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m80.6/80.6 MB\u001b[0m \u001b[31m10.2 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", |
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152 | | - "\u001b[?25hDownloading duckdb-1.2.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (20.2 MB)\n", |
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162 | | - "\u001b[?25hDownloading s5cmd-0.2.0-py3-none-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.7 MB)\n", |
163 | | - "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m4.7/4.7 MB\u001b[0m \u001b[31m33.8 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", |
164 | | - "\u001b[?25hDownloading sphinx_click-6.0.0-py3-none-any.whl (9.9 kB)\n", |
165 | | - "Downloading retrying-1.4.2-py3-none-any.whl (10 kB)\n", |
166 | | - "Installing collected packages: s5cmd, retrying, pydicom, openslide-python, openslide-bin, marshmallow, idc-index-data, fsspec, duckdb, universal-pathlib, dicomweb-client, wsidicom, sphinx-click, idc-index\n", |
167 | | - " Attempting uninstall: fsspec\n", |
168 | | - " Found existing installation: fsspec 2025.3.0\n", |
169 | | - " Uninstalling fsspec-2025.3.0:\n", |
170 | | - " Successfully uninstalled fsspec-2025.3.0\n", |
171 | | - " Attempting uninstall: duckdb\n", |
172 | | - " Found existing installation: duckdb 1.3.2\n", |
173 | | - " Uninstalling duckdb-1.3.2:\n", |
174 | | - " Successfully uninstalled duckdb-1.3.2\n", |
175 | | - "\u001b[31mERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.\n", |
176 | | - "gcsfs 2025.3.0 requires fsspec==2025.3.0, but you have fsspec 2024.12.0 which is incompatible.\u001b[0m\u001b[31m\n", |
177 | | - "\u001b[0mSuccessfully installed dicomweb-client-0.59.3 duckdb-1.2.1 fsspec-2024.12.0 idc-index-0.9.2 idc-index-data-21.0.0 marshmallow-3.26.1 openslide-bin-4.0.0.8 openslide-python-1.4.2 pydicom-3.0.1 retrying-1.4.2 s5cmd-0.2.0 sphinx-click-6.0.0 universal-pathlib-0.2.6 wsidicom-0.27.1\n" |
178 | | - ] |
179 | | - } |
180 | | - ], |
| 75 | + "outputs": [], |
181 | 76 | "source": [ |
182 | 77 | "!pip3 install --upgrade idc-index wsidicom openslide-python openslide-bin" |
183 | 78 | ] |
|
193 | 88 | }, |
194 | 89 | { |
195 | 90 | "cell_type": "code", |
196 | | - "execution_count": 2, |
| 91 | + "execution_count": null, |
197 | 92 | "metadata": { |
198 | 93 | "colab": { |
199 | 94 | "base_uri": "https://localhost:8080/" |
200 | 95 | }, |
201 | 96 | "id": "vd-PJ23N2GRT", |
202 | 97 | "outputId": "c3ca9bb8-474e-46a3-b1a7-1753d96ff3c4" |
203 | 98 | }, |
204 | | - "outputs": [ |
205 | | - { |
206 | | - "name": "stdout", |
207 | | - "output_type": "stream", |
208 | | - "text": [ |
209 | | - "Cloning into 'IDC-Tutorials'...\n", |
210 | | - "remote: Enumerating objects: 2629, done.\u001b[K\n", |
211 | | - "remote: Counting objects: 100% (519/519), done.\u001b[K\n", |
212 | | - "remote: Compressing objects: 100% (190/190), done.\u001b[K\n", |
213 | | - "remote: Total 2629 (delta 427), reused 329 (delta 329), pack-reused 2110 (from 1)\u001b[K\n", |
214 | | - "Receiving objects: 100% (2629/2629), 148.64 MiB | 27.46 MiB/s, done.\n", |
215 | | - "Resolving deltas: 100% (1597/1597), done.\n", |
216 | | - "Updating files: 100% (106/106), done.\n" |
217 | | - ] |
218 | | - } |
219 | | - ], |
| 99 | + "outputs": [], |
220 | 100 | "source": [ |
221 | 101 | "!git clone https://github.com/ImagingDataCommons/IDC-Tutorials.git" |
222 | 102 | ] |
|
232 | 112 | }, |
233 | 113 | { |
234 | 114 | "cell_type": "code", |
235 | | - "execution_count": 3, |
| 115 | + "execution_count": null, |
236 | 116 | "metadata": { |
237 | 117 | "colab": { |
238 | 118 | "base_uri": "https://localhost:8080/" |
|
244 | 124 | "outputId": "f4086cd0-5288-4edd-a845-8b361fb47662", |
245 | 125 | "tags": [] |
246 | 126 | }, |
247 | | - "outputs": [ |
248 | | - { |
249 | | - "name": "stderr", |
250 | | - "output_type": "stream", |
251 | | - "text": [ |
252 | | - "WARNING:pydicom:get_frame_offsets is deprecated and will be removed in v4.0\n" |
253 | | - ] |
254 | | - } |
255 | | - ], |
| 127 | + "outputs": [], |
256 | 128 | "source": [ |
257 | 129 | "import os\n", |
258 | 130 | "import numpy as np\n", |
|
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