healthcare-api-dicom-fuse

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healthcare-api-dicom-fuse

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FUSE plugin for the Google Cloud Healthcare DICOM API

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// repository documentation

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# DICOMFuse

DICOMFuse is a file system that integrates with the
[Cloud Healthcare API](https://cloud.google.com/healthcare/). DICOMFuse lets you
anonymize (using an anonymization tool), read, upload, and delete images in
[DICOM stores](https://cloud.google.com/healthcare/docs/how-tos/dicom). \
DICOMFuse is cross-platform application written in Java. You can use it in
Linux, Windows or macOS.

## Prerequisites

### Applications

Before running DICOMFuse, ensure that you've installed the following
applications:

*   Java SE Runtime Environment 8.
*   [WinFsp](https://github.com/billziss-gh/winfsp) for using FUSE in Windows 
    (Windows 7x64, Windows 10x64).
*   [OSXFuse](https://osxfuse.github.io/) for using FUSE in macOS (macOS 10.14
    Mojave).
*   [libfuse](https://github.com/libfuse/libfuse) for using FUSE in Linux, install 
    libfuse - `sudo apt install libfuse2`

> FUSE has been supported in Linux kernel since 2.6.14 version.

### Credentials

DICOMFuse will use 
[application default credentials](https://cloud.google.com/docs/authentication/production)
to authenticate access to the Cloud Healthcare API. The identity must have the 
permissions within the 
[Healthcare DICOM Editor role](https://cloud.google.com/healthcare/docs/concepts/access-control#roles).  
Alternatively, you can specify a service account key via the `--keyFile` flag.
The easiest way to set up credentials is to use your user credentials with the 
[gcloud tool](https://cloud.google.com/sdk/gcloud/):

`gcloud auth application-default login`

## Running DICOMFuse

To run DICOMFuse:

1.  Download the latest JAR from the releases tab.
2.  To start DICOMFuse, open a terminal in the DICOMFuse folder and input:  
    `java -jar healthcare-api-dicom-fuse-X.Y.Z.jar [options]`  
    In Windows - `java -Dfile.encoding=UTF8 -jar healthcare-api-dicom-fuse-X.Y.Z.jar [options]`
3.  To stop DICOMFuse, press CTRL+C.

> ERROR and INFO logs present in the terminal. During launching DICOMFuse, logs 
> folder will be created next to the DICOMFuse JAR, where DEBUG, INFO and ERROR logs
> will be saved.

### Mount options

You can specify the following mount options when you start DICOMFuse:

```
* --datasetAddr, -a
    Web address to the Dataset.
    Example: https://healthcare.googleapis.com/v1beta1/projects/PROJECT/locations/LOCATION/datasets/DATASET
* --mountPath, -p
    Path to mount the Dataset.
    Example on Linux: /home/user/fuse-mount-folder
    Example on macOS: /Users/user/fuse-mount-folder
    Example on Windows: J:\
  --cacheTime, -t
    Each value in this option is measured in seconds.
    To optimize DICOMFuse, the following resources are cached: DICOM store folders, Study folders, Series folders,
    list of Instances (first parameter in option), and opened Instances files (second parameter).
    Opened Instance files are cached to the temporary folder in the user space on disk.
    Other objects are cached to RAM. Cached files will be deleted if you close DICOMFuse or if the cached
    files become out of date. If you delete or upload an Instance file locally, the cache will
    be invalidated, and updated if you open a folder again.
    Default: 60,300
  --cacheSize, -s
    Maximum cache size in megabytes for cached instances. The maximum file size that can be
    downloaded/uploaded is cacheSize / 4
    Default: 10000
  --enableDeletion, -d
    Some programs can delete files and deletion can also be done manually. Sometimes accidental deletions can occur.
    If you don't want to delete files, you can set `--enableDeletion=false`
    Default: true
  --keyFile, -k
    Path to the account service key
  --extraMountOptions
    You can add additional mount options for libfuse, WinFsp or OSXFuse.
    Example: --extraMountOptions allow_other,option2=VALUE,etc  Note: since DICOMFuse is specific 
    for correct behavior in different operating systems, some mount options were included initially. 
    See: https://github.com/GoogleCloudPlatform/healthcare-api-dicom-fuse/blob/develop/src/main/java/com/google/dicomwebfuse/MountOptions.java
    Default: []
  --help, -h
    Print help
```

> Note: * are required options. \
> The current implementation supports 15,000 results in folders.

## Description

### Data [model](https://cloud.google.com/healthcare/docs/concepts/projects-datasets-data-stores)

*   Dataset: mounted folder.
*   DICOM Store: subfolder of dataset.
*   DICOM Study: subfolder of store.
*   DICOM Series: subfolder of Study.
*   DICOM Instance: a file within Series.

### Operations supported

You can use a graphical interface on an OS or commands in the terminal to
navigate through folders.

#### Operations supported in graphical interface:

*   Upload a file in the DICOM Store folder (drag and drop).
*   Upload a file in the Series folder (drag and drop).
*   Delete a *.dcm file in the Series folder.
*   Overwrite existing file.
*   Create DICOM Store folder. If you try to create a folder at a 
    different level, you will get the error:  
    _Error creating directory path_to_the_directory: Operation not permitted_
*   Rename empty DICOM Store (previous DICOM Store will be deleted and a new one will be created. 
    Only supported for empty DICOM Stores, otherwise an error will be returned).
*   Replace operation (drag and drop) is not supported.

> Note: to get better performance, you must upload files to DICOM Store folder, and
> files must have **.dcm** or another extension.

#### Operations supported in the terminal:

*   cd - change a directory. Supported navigate to unpresented results in folders 
    if they exist on the server.
*   ls - list the objects existing in a folder.
*   cp - copy **only instances files** (not folders) to another DICOM store or
    to a local computer.
*   rm - delete instances files.
*   Create DICOM Store folder. If you try to create a folder at a different level, 
    you will get the error:  
    _mkdir: cannot create directory ‘new_folder’: Operation not permitted_
*   mv - rename empty DICOM Store (previous DICOM Store will be deleted and a new one will be 
    created. Only supported for empty DICOM Stores, otherwise an error will be returned).

Any reading use cases can be used, such as de-identification or manual editing
of the (binary) DICOM object.

### Caching objects

To optimize DICOMFuse, the following resources are cached: DICOM store folders,
Study folders, Series folders, list of Instances (first parameter in option),
and opened Instances files (second parameter). Opened Instance files are cached
to the temporary folder in the user space on disk. Other objects are cached to
RAM. Cached files will be deleted if you close DICOMFuse or if the cached files
become out of date.

*   If you delete or upload an Instance, the cache will be invalidated, and 
    updated if you open a folder again.
*   Before opening an Instance, the size of it is 0 bytes. If you open the
    Instance, it will be downloaded from the server and you will see the
    Instance size. If you read the Instance again, it will be reading from the
    local cache, not from the server. After repeated requests, if the cacheTime
    of the Instance is out of date, the Instance will be downloaded from the
    server again.
*   If you create a request (e.g. cd command in a Dataset folder) and the object
    does not exist in the local cache, the request will be sent to the server
    and object will be cached if object exist on the server.

## Packaging

1.  **git clone https://github.com/GoogleCloudPlatform/healthcare-api-dicom-fuse.git**
2.  **mvn package** in the healthcare-api-dicom-fuse folder in the terminal (for 
    packaging to jar).

There is a **healthcare-api-dicom-fuse-X.Y.Z.jar** file in the **healthcare-api-dicom-fuse/target** folder.

## License

This application is licensed under Apache License, Version 2.0. Full license
text is available in LICENSE.

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