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--- |
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license: apache-2.0 |
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--- |
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# Dataset Summary |
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Healthy CT data for abdominal organs (liver, pancreas and kidney) are filtered out from public dataset. |
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# Downloading Instructions |
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#### 1- Install the Hugging Face library: |
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```bash |
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pip install -U "huggingface_hub[cli]" |
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``` |
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#### 2- Download the dataset: |
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```bash |
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mkdir HealthyCT |
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cd HealthyCT |
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huggingface-cli download qicq1c/HealthyCT --repo-type dataset --local-dir . --cache-dir ./cache |
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``` |
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<details> |
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<summary style="margin-left: 25px;">[Optional] Resume downloading</summary> |
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<div style="margin-left: 25px;"> |
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In case you had a previous interrupted download, resume it by adding “--resume-download” to the download command: |
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```bash |
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huggingface-cli download qicq1c/HealthyCT --repo-type dataset --local-dir . --cache-dir ./cache --resume-download |
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``` |
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</div> |
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</details> |
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#### 3- Extract files: the dataset is formatted as a multi-part zip file. Use the first part (AbdomenAtlasMini.zip.001) to extract the dataset. With the GUI, |
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just right-click on the file and select "Extract Here". With the command-line, we suggest using 7zip (faster, see below). |
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If it is not available, you can concatenate the files and unzip (slower): |
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```bash |
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cat healthy_ct.zip* > HealthyCT.zip |
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unzip -o -q HealthyCT.zip |
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``` |
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<details> |
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<summary style="margin-left: 25px;">[Optional] 7zip</summary> |
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<div style="margin-left: 25px;"> |
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With 7zip, just run: |
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```bash |
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7z x healthy_ct.zip.001 |
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``` |
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Installing 7zip (optional): |
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For Debian/Ubuntu: |
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```bash |
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sudo apt update |
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sudo apt install p7zip-full |
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``` |
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For Fedora: |
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```bash |
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sudo dnf install p7zip |
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``` |
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For CentOS/RHEL: |
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```bash |
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sudo yum install p7zip |
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``` |
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</div> |
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</details> |
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--- |
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# Uploading Instructions |
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#### 0- Install 7zip |
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For Debian/Ubuntu: |
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```bash |
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sudo apt update |
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sudo apt install p7zip-full |
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``` |
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<details> |
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<summary style="margin-left: 25px;">[Optional] Other operating systems</summary> |
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<div style="margin-left: 25px;"> |
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For Fedora: |
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```bash |
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sudo dnf install p7zip |
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``` |
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For CentOS/RHEL: |
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```bash |
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sudo yum install p7zip |
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``` |
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For MacOS: |
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```bash |
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brew update |
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brew install p7zip |
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``` |
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If you do not have brew installed, another possible solution is: |
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```bash |
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sudo port install p7zip |
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``` |
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</div> |
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</details> |
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#### 1- Compress the folder for uploading |
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To compress the folder you want to upload into multi-part zip file with parts of 5GB (-v5g), take "AbdomenAtlas1.0" as an example: |
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Note: if AbdomenAtlas1.0ZipFolder and AbdomenAtlas1.0 share the same parent directory, please use the relative path for AbdomenAtlas1.0ZipFolder. Otherwise, please use the absolute path for AbdomenAtlas1.0ZipFolder. |
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```bash |
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mkdir /path/to/the/HealthyCT_ZipFolder |
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cd /path/to/the/HealthyCT |
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cd .. |
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7z -v5g a /path/to/the/HealthyCT_ZipFolder/healthy_ct.zip HealthyCT/ |
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``` |
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After zipping, the structure of the compressed folder (e.g., AbdomenAtlas1.0ZipFolder) will be: |
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``` |
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HealthyCT_ZipFolder |
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├── healthy_ct.zip.001 |
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├── healthy_ct.zip.002 |
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├── healthy_ct.zip.003 |
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├── ... |
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``` |
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#### 2- Upload to Hugging Face |
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Create a repository at Hugging Face (e.g., a repository named AbdomenAtlas1.0) |
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Install huggingface_hub from the PyPi registry |
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```bash |
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pip install --upgrade huggingface_hub |
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``` |
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Upload the compressed folder (e.g., AbdomenAtlas1.0ZipFolder) to this repository |
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```bash |
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python uploading_files_to_hugging_face.py --folder_directory /path/to/the/HealthyCT_ZipFolder --repository qicq1c/HealthyCT --repository_type dataset |
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``` |
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