first

.gitignore

@@ -0,0 +1 @@
+venv

Dockerfile

@@ -0,0 +1,82 @@
+FROM nvidia/cuda:12.2.2-cudnn8-devel-ubuntu22.04
+
+ENV DEBIAN_FRONTEND=noninteractive \
+    TZ=America/Los_Angeles
+
+USER root
+RUN apt-get update && apt-get install -y \
+    git \
+    make build-essential libssl-dev zlib1g-dev \
+    libbz2-dev libreadline-dev libsqlite3-dev wget curl llvm \
+    libncursesw5-dev xz-utils tk-dev libxml2-dev libxmlsec1-dev libffi-dev liblzma-dev git-lfs  \
+    cmake-curses-gui cmake libinsighttoolkit4-dev libfftw3-dev libvtk7-dev \ 
+    ffmpeg libsm6 libxext6 cmake libgl1-mesa-glx lsof \
+    orthanc orthanc-dicomweb vim \
+    nginx \
+    && rm -rf /var/lib/apt/lists/* \
+    && git lfs install
+
+# install plastimatch
+RUN git clone https://gitlab.com/plastimatch/plastimatch && cd plastimatch && mkdir build && cd build && cmake .. && make -j$(nproc) && make install
+
+WORKDIR /code
+
+COPY ./requirements.txt /code/requirements.txt
+
+# User
+RUN useradd -m -u 1000 user
+ENV HOME=/home/user \
+    PATH=/home/user/.local/bin:$PATH
+
+USER user
+
+# Pyenv
+RUN curl https://pyenv.run | bash
+ENV PATH=$HOME/.pyenv/shims:$HOME/.pyenv/bin:$PATH
+
+ARG PYTHON_VERSION=3.10.13
+# Python
+RUN pyenv install $PYTHON_VERSION && \
+    pyenv global $PYTHON_VERSION && \
+    pyenv rehash && \
+    pip install --no-cache-dir --upgrade pip setuptools wheel && \
+    pip install --no-cache-dir \
+    datasets \
+    huggingface-hub "protobuf<4" "click<8.1"
+
+RUN pip install --no-cache-dir --upgrade -r /code/requirements.txt
+
+# Set the working directory to /data if USE_PERSISTENT_DATA is set, otherwise set to $HOME/app
+WORKDIR $HOME/app
+
+ENV HOME=/home/user \
+    PATH=/home/user/.local/bin:$PATH \
+    PYTHONPATH=$HOME/app \
+    PYTHONUNBUFFERED=1 
+
+RUN monailabel apps --name radiology --download --output apps
+RUN monailabel datasets --download --name Task09_Spleen --output datasets
+
+# RUN monailabel datasets --download --name Task01_BrainTumour --output datasets
+# RUN monailabel datasets --download --name Task09_Spleen --output .
+# RUN plastimatch convert --patient-id patient1 --input Task09_Spleen/imagesTs/spleen_1.nii.gz --output-dicom dicom_output
+# monailabel start_server --app apps/radiology --studies http://127.0.0.1:8042/dicom-web --conf models deepedit
+# CMD ["monailabel", "start_server",  "--app", "apps/radiology",  "--studies", "http://0.0.0.0:8042/dicom-web", "--conf" , "models", "deepedit"]
+# CMD ["monailabel", "start_server",  "--app", "apps/radiology",  "--studies", "datasets/Task01_BrainTumour/imagesTr", "--conf" , "models", "deepedit"]
+
+# /etc/orthanc/orthanc.json -> "RemoteAccessAllowed": false, -> "RemoteAccessAllowed": true,
+# RUN sed -i 's/"RemoteAccessAllowed" : false,/"RemoteAccessAllowed" : true,/g' /etc/orthanc/orthanc.json
+USER root
+RUN mkdir -p /var/cache/orthanc /var/log/orthanc /var/lib/orthanc && \
+    chown -R user:user /var/cache/orthanc /var/log/orthanc  /usr/share/orthanc/ /var/lib/orthanc /etc/orthanc && \
+    mkdir -p /var/cache/nginx /var/log/nginx /var/lib/nginx && \
+    touch /var/run/nginx.pid && \
+    chown -R user:user /var/cache/nginx /var/log/nginx /var/lib/nginx /var/run/nginx.pid
+
+COPY --chown=user orthanc.json /etc/orthanc/orthanc.json
+COPY --chown=user nginx.conf /etc/nginx/sites-available/default
+
+USER user
+COPY --chown=user run.sh .
+CMD ["sh", "run.sh"]
+# monailabel start_server --app apps/radiology --studies datasets/Task01_BrainTumour/imagesTr --conf models deepedit

README.md

@@ -5,6 +5,7 @@ colorFrom: purple
 colorTo: purple
 sdk: docker
 pinned: false
+app_port: 8000
 ---
 
 Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference

nginx.conf

@@ -0,0 +1,51 @@
+server {
+    listen 4444 default_server;
+    server_name _;
+
+    # location / {
+    #     # Proxy pass to the app at /ohif
+    #     proxy_pass http://0.0.0.0:8000/ohif/;
+    #     proxy_http_version 1.1;
+    #     proxy_set_header Upgrade $http_upgrade;
+    #     proxy_set_header Connection 'upgrade';
+    #     proxy_set_header Host $host;
+    #     proxy_set_header X-Real-IP $remote_addr;
+    #     proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+    #     proxy_cache_bypass $http_upgrade;
+    #     proxy_read_timeout 86400;
+    #     proxy_redirect off;
+
+    #     # Handling URI
+    #     proxy_set_header X-Forwarded-Prefix "/";
+    # }
+    location / {
+        # Proxy pass to the app at /ohif
+        proxy_pass http://0.0.0.0:8000;
+        proxy_http_version 1.1;
+        proxy_set_header Upgrade $http_upgrade;
+        proxy_set_header Connection 'upgrade';
+        proxy_set_header Host $host;
+        proxy_set_header X-Real-IP $remote_addr;
+        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+        proxy_cache_bypass $http_upgrade;
+        proxy_read_timeout 86400;
+        proxy_redirect off;
+    }
+    location /orthanc {
+        # Serve backend from port 
+        proxy_pass http://0.0.0.0:8042;
+        rewrite /orthanc(.*) $1 break;
+        proxy_http_version 1.1;
+        proxy_set_header Upgrade $http_upgrade;
+        proxy_set_header Connection 'upgrade';
+        proxy_set_header Host $host;
+        proxy_set_header X-Real-IP $remote_addr;
+        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+        proxy_cache_bypass $http_upgrade;
+        proxy_read_timeout 86400;
+        proxy_redirect off;
+        proxy_request_buffering off;
+        proxy_max_temp_file_size 0;
+        client_max_body_size 0;
+    }
+}

orthanc.json

@@ -0,0 +1,438 @@
+{
+    /**
+     * General configuration of Orthanc
+     **/
+    // The logical name of this instance of Orthanc. This one is
+    // displayed in Orthanc Explorer and at the URI "/system".
+    "Name": "Orthanc",
+    // Path to the directory that holds the heavyweight files (i.e. the
+    // raw DICOM instances). Backslashes must be either escaped by
+    // doubling them, or replaced by forward slashes "/".
+    "StorageDirectory": "/var/lib/orthanc/db-v6",
+    // Path to the directory that holds the SQLite index (if unset, the
+    // value of StorageDirectory is used). This index could be stored on
+    // a RAM-drive or a SSD device for performance reasons.
+    "IndexDirectory": "/var/lib/orthanc/db-v6",
+    // Path to the directory where Orthanc stores its large temporary
+    // files. The content of this folder can be safely deleted if
+    // Orthanc once stopped. The folder must exist. The corresponding
+    // filesystem must be properly sized, given that for instance a ZIP
+    // archive of DICOM images created by a job can weight several GBs,
+    // and that there might be up to "min(JobsHistorySize,
+    // MediaArchiveSize)" archives to be stored simultaneously. If not
+    // set, Orthanc will use the default temporary folder of the
+    // operating system (such as "/tmp/" on UNIX-like systems, or
+    // "C:/Temp" on Microsoft Windows).
+    // "TemporaryDirectory" : "/tmp/Orthanc/",
+    // Enable the transparent compression of the DICOM instances
+    "StorageCompression": false,
+    // Maximum size of the storage in MB (a value of "0" indicates no
+    // limit on the storage size)
+    "MaximumStorageSize": 0,
+    // Maximum number of patients that can be stored at a given time
+    // in the storage (a value of "0" indicates no limit on the number
+    // of patients)
+    "MaximumPatientCount": 0,
+    // List of paths to the custom Lua scripts that are to be loaded
+    // into this instance of Orthanc
+    "LuaScripts": [],
+    // List of paths to the plugins that are to be loaded into this
+    // instance of Orthanc (e.g. "./libPluginTest.so" for Linux, or
+    // "./PluginTest.dll" for Windows). These paths can refer to
+    // folders, in which case they will be scanned non-recursively to
+    // find shared libraries. Backslashes must be either escaped by
+    // doubling them, or replaced by forward slashes "/".
+    "Plugins": [
+        "/usr/share/orthanc/plugins/"
+    ],
+    // Maximum number of processing jobs that are simultaneously running
+    // at any given time. A value of "0" indicates to use all the
+    // available CPU logical cores. To emulate Orthanc <= 1.3.2, set
+    // this value to "1".
+    "ConcurrentJobs": 2,
+    /**
+     * Configuration of the HTTP server
+     **/
+    // Enable the HTTP server. If this parameter is set to "false",
+    // Orthanc acts as a pure DICOM server. The REST API and Orthanc
+    // Explorer will not be available.
+    "HttpServerEnabled": true,
+    // HTTP port for the REST services and for the GUI
+    "HttpPort": 8042,
+    // When the following option is "true", if an error is encountered
+    // while calling the REST API, a JSON message describing the error
+    // is put in the HTTP answer. This feature can be disabled if the
+    // HTTP client does not properly handles such answers.
+    "HttpDescribeErrors": true,
+    // Enable HTTP compression to improve network bandwidth utilization,
+    // at the expense of more computations on the server. Orthanc
+    // supports the "gzip" and "deflate" HTTP encodings.
+    "HttpCompressionEnabled": true,
+    /**
+     * Configuration of the DICOM server
+     **/
+    // Enable the DICOM server. If this parameter is set to "false",
+    // Orthanc acts as a pure REST server. It will not be possible to
+    // receive files or to do query/retrieve through the DICOM protocol.
+    "DicomServerEnabled": true,
+    // The DICOM Application Entity Title
+    "DicomAet": "ORTHANC",
+    // Check whether the called AET corresponds to the AET of Orthanc
+    // during an incoming DICOM SCU request
+    "DicomCheckCalledAet": false,
+    // The DICOM port
+    "DicomPort": 4242,
+    // The default encoding that is assumed for DICOM files without
+    // "SpecificCharacterSet" DICOM tag, and that is used when answering
+    // C-Find requests (including worklists). The allowed values are
+    // "Ascii", "Utf8", "Latin1", "Latin2", "Latin3", "Latin4",
+    // "Latin5", "Cyrillic", "Windows1251", "Arabic", "Greek", "Hebrew",
+    // "Thai", "Japanese", "Chinese", "JapaneseKanji", "Korean", and
+    // "SimplifiedChinese".
+    "DefaultEncoding": "Latin1",
+    // The transfer syntaxes that are accepted by Orthanc C-Store SCP
+    "DeflatedTransferSyntaxAccepted": true,
+    "JpegTransferSyntaxAccepted": true,
+    "Jpeg2000TransferSyntaxAccepted": true,
+    "JpegLosslessTransferSyntaxAccepted": true,
+    "JpipTransferSyntaxAccepted": true,
+    "Mpeg2TransferSyntaxAccepted": true,
+    "RleTransferSyntaxAccepted": true,
+    // Whether Orthanc accepts to act as C-Store SCP for unknown storage
+    // SOP classes (aka. "promiscuous mode")
+    "UnknownSopClassAccepted": false,
+    // Set the timeout (in seconds) after which the DICOM associations
+    // are closed by the Orthanc SCP (server) if no further DIMSE
+    // command is received from the SCU (client).
+    "DicomScpTimeout": 30,
+    /**
+     * Security-related options for the HTTP server
+     **/
+    // Whether remote hosts can connect to the HTTP server
+    "RemoteAccessAllowed": true,
+    // Whether or not SSL is enabled
+    "SslEnabled": false,
+    // Path to the SSL certificate in the PEM format (meaningful only if
+    // SSL is enabled)
+    "SslCertificate": "certificate.pem",
+    // Whether or not the password protection is enabled (using HTTP
+    // basic access authentication). Starting with Orthanc 1.5.8, if
+    // "AuthenticationEnabled" is not explicitly set, authentication is
+    // enabled iff. remote access is allowed (i.e. the default value of
+    // "AuthenticationEnabled" equals that of "RemoteAccessAllowed").
+    "AuthenticationEnabled": false,
+    // The list of the registered users. Because Orthanc uses HTTP
+    // Basic Authentication, the passwords are stored as plain text.
+    "RegisteredUsers": {
+        // "alice" : "alicePassword"
+    },
+    /**
+     * Network topology
+     **/
+    // The list of the known DICOM modalities
+    "DicomModalities": {
+        /**
+       * Uncommenting the following line would enable Orthanc to
+       * connect to an instance of the "storescp" open-source DICOM
+       * store (shipped in the DCMTK distribution) started by the
+       * command line "storescp 2000".
+       **/
+        // "sample" : [ "STORESCP", "127.0.0.1", 2000 ]
+        "sample": [
+            "MONAILABEL",
+            "0.0.0.0",
+            104
+        ]
+        /**
+       * A fourth parameter is available to enable patches for
+       * specific PACS manufacturers. The allowed values are currently:
+       * - "Generic" (default value),
+       * - "GenericNoWildcardInDates" (to replace "*" by "" in date fields 
+       *   in outgoing C-Find requests originating from Orthanc),
+       * - "GenericNoUniversalWildcard" (to replace "*" by "" in all fields
+       *   in outgoing C-Find SCU requests originating from Orthanc),
+       * - "StoreScp" (storescp tool from DCMTK),
+       * - "ClearCanvas",
+       * - "Dcm4Chee",
+       * - "Vitrea",
+       * - "GE" (Enterprise Archive, MRI consoles and Advantage Workstation
+       *   from GE Healthcare).
+       *
+       * This parameter is case-sensitive.
+       **/
+        // "clearcanvas" : [ "CLEARCANVAS", "192.168.1.1", 104, "ClearCanvas" ]
+        /**
+       * By default, the Orthanc SCP accepts all DICOM commands (C-ECHO,
+       * C-STORE, C-FIND, C-MOVE) issued by the registered remote SCU
+       * modalities. Starting with Orthanc 1.5.0, it is possible to
+       * specify which DICOM commands are allowed, separately for each
+       * remote modality, using the syntax below. The "AllowEcho" (resp.
+       * "AllowStore") option only has an effect respectively if global
+       * option "DicomAlwaysAllowEcho" (resp. "DicomAlwaysAllowStore")
+       * is set to false.
+       **/
+        //"untrusted" : {
+        //  "AET" : "ORTHANC",
+        //  "Port" : 104,
+        //  "Host" : "127.0.0.1",
+        //  "AllowEcho" : false,
+        //  "AllowFind" : false,
+        //  "AllowMove" : false,
+        //  "AllowStore" : true
+        //}
+    },
+    // Whether to store the DICOM modalities in the Orthanc database
+    // instead of in this configuration file (new in Orthanc 1.5.0)
+    "DicomModalitiesInDatabase": false,
+    // Whether the Orthanc SCP allows incoming C-Echo requests, even
+    // from SCU modalities it does not know about (i.e. that are not
+    // listed in the "DicomModalities" option above). Orthanc 1.3.0
+    // is the only version to behave as if this argument was set to "false".
+    "DicomAlwaysAllowEcho": true,
+    // Whether the Orthanc SCP allows incoming C-Store requests, even
+    // from SCU modalities it does not know about (i.e. that are not
+    // listed in the "DicomModalities" option above)
+    "DicomAlwaysAllowStore": true,
+    // Whether Orthanc checks the IP/hostname address of the remote
+    // modality initiating a DICOM connection (as listed in the
+    // "DicomModalities" option above). If this option is set to
+    // "false", Orthanc only checks the AET of the remote modality.
+    "DicomCheckModalityHost": false,
+    // The timeout (in seconds) after which the DICOM associations are
+    // considered as closed by the Orthanc SCU (client) if the remote
+    // DICOM SCP (server) does not answer.
+    "DicomScuTimeout": 10,
+    // The list of the known Orthanc peers
+    "OrthancPeers": {
+        /**
+       * Each line gives the base URL of an Orthanc peer, possibly
+       * followed by the username/password pair (if the password
+       * protection is enabled on the peer).
+       **/
+        // "peer"  : [ "http://127.0.0.1:8043/", "alice", "alicePassword" ]
+        // "peer2" : [ "http://127.0.0.1:8044/" ]
+        /**
+       * This is another, more advanced format to define Orthanc
+       * peers. It notably allows to specify HTTP headers, a HTTPS
+       * client certificate in the PEM format (as in the "--cert" option
+       * of curl), or to enable PKCS#11 authentication for smart cards.
+       **/
+        // "peer" : {
+        //   "Url" : "http://127.0.0.1:8043/",
+        //   "Username" : "alice",
+        //   "Password" : "alicePassword",
+        //   "HttpHeaders" : { "Token" : "Hello world" },
+        //   "CertificateFile" : "client.crt",
+        //   "CertificateKeyFile" : "client.key",
+        //   "CertificateKeyPassword" : "certpass",
+        //   "Pkcs11" : false
+        // }
+    },
+    // Whether to store the Orthanc peers in the Orthanc database
+    // instead of in this configuration file (new in Orthanc 1.5.0)
+    "OrthancPeersInDatabase": false,
+    // Parameters of the HTTP proxy to be used by Orthanc. If set to the
+    // empty string, no HTTP proxy is used. For instance:
+    //   "HttpProxy" : "192.168.0.1:3128"
+    //   "HttpProxy" : "proxyUser:proxyPassword@192.168.0.1:3128"
+    "HttpProxy": "",
+    // If set to "true", debug messages from libcurl will be issued
+    // whenever Orthanc makes an outgoing HTTP request. This is notably
+    // useful to debug HTTPS-related problems.
+    "HttpVerbose": false,
+    // Set the timeout for HTTP requests issued by Orthanc (in seconds).
+    "HttpTimeout": 60,
+    // Enable the verification of the peers during HTTPS requests. This
+    // option must be set to "false" if using self-signed certificates.
+    // Pay attention that setting this option to "false" results in
+    // security risks!
+    // Reference: http://curl.haxx.se/docs/sslcerts.html
+    "HttpsVerifyPeers": true,
+    // Path to the CA (certification authority) certificates to validate
+    // peers in HTTPS requests. From curl documentation ("--cacert"
+    // option): "Tells curl to use the specified certificate file to
+    // verify the peers. The file may contain multiple CA
+    // certificates. The certificate(s) must be in PEM format." On
+    // Debian-based systems, this option can be set to
+    // "/etc/ssl/certs/ca-certificates.crt"
+    "HttpsCACertificates": "",
+    /**
+     * Advanced options
+     **/
+    // Dictionary of symbolic names for the user-defined metadata. Each
+    // entry must map an unique string to an unique number between 1024
+    // and 65535. Reserved values:
+    //  - The Orthanc whole-slide imaging plugin uses metadata 4200
+    "UserMetadata": {
+        // "Sample" : 1024
+    },
+    // Dictionary of symbolic names for the user-defined types of
+    // attached files. Each entry must map an unique string to an unique
+    // number between 1024 and 65535. Optionally, a second argument can
+    // provided to specify a MIME content type for the attachment.
+    "UserContentType": {
+        // "sample" : 1024
+        // "sample2" : [ 1025, "application/pdf" ]
+    },
+    // Number of seconds without receiving any instance before a
+    // patient, a study or a series is considered as stable.
+    "StableAge": 60,
+    // By default, Orthanc compares AET (Application Entity Titles) in a
+    // case-insensitive way. Setting this option to "true" will enable
+    // case-sensitive matching.
+    "StrictAetComparison": false,
+    // When the following option is "true", the MD5 of the DICOM files
+    // will be computed and stored in the Orthanc database. This
+    // information can be used to detect disk corruption, at the price
+    // of a small performance overhead.
+    "StoreMD5ForAttachments": true,
+    // The maximum number of results for a single C-FIND request at the
+    // Patient, Study or Series level. Setting this option to "0" means
+    // no limit.
+    "LimitFindResults": 0,
+    // The maximum number of results for a single C-FIND request at the
+    // Instance level. Setting this option to "0" means no limit.
+    "LimitFindInstances": 0,
+    // The maximum number of active jobs in the Orthanc scheduler. When
+    // this limit is reached, the addition of new jobs is blocked until
+    // some job finishes.
+    "LimitJobs": 10,
+    // If this option is set to "true" (default behavior until Orthanc
+    // 1.3.2), Orthanc will log the resources that are exported to other
+    // DICOM modalities or Orthanc peers, inside the URI
+    // "/exports". Setting this option to "false" is useful to prevent
+    // the index to grow indefinitely in auto-routing tasks (this is the
+    // default behavior since Orthanc 1.4.0).
+    "LogExportedResources": false,
+    // Enable or disable HTTP Keep-Alive (persistent HTTP
+    // connections). Setting this option to "true" prevents Orthanc
+    // issue #32 ("HttpServer does not support multiple HTTP requests in
+    // the same TCP stream"), but can possibly slow down HTTP clients
+    // that do not support persistent connections. The default behavior
+    // used to be "false" in Orthanc <= 1.5.1. Setting this option to
+    // "false" is also recommended if Orthanc is compiled against
+    // Mongoose.
+    "KeepAlive": true,
+    // Enable or disable Nagle's algorithm. Only taken into
+    // consideration if Orthanc is compiled to use CivetWeb. Experiments
+    // show that best performance can be obtained by setting both
+    // "KeepAlive" and "TcpNoDelay" to "true". Beware however of
+    // caveats: https://eklitzke.org/the-caveats-of-tcp-nodelay
+    "TcpNoDelay": true,
+    // Number of threads that are used by the embedded HTTP server.
+    "HttpThreadsCount": 50,
+    // If this option is set to "false", Orthanc will run in index-only
+    // mode. The DICOM files will not be stored on the drive. Note that
+    // this option might prevent the upgrade to newer versions of Orthanc.
+    "StoreDicom": true,
+    // DICOM associations initiated by Lua scripts are kept open as long
+    // as new DICOM commands are issued. This option sets the number of
+    // seconds of inactivity to wait before automatically closing a
+    // DICOM association used by Lua. If set to 0, the connection is
+    // closed immediately.
+    "DicomAssociationCloseDelay": 5,
+    // Maximum number of query/retrieve DICOM requests that are
+    // maintained by Orthanc. The least recently used requests get
+    // deleted as new requests are issued.
+    "QueryRetrieveSize": 100,
+    // When handling a C-Find SCP request, setting this flag to "true"
+    // will enable case-sensitive match for PN value representation
+    // (such as PatientName). By default, the search is
+    // case-insensitive, which does not follow the DICOM standard.
+    "CaseSensitivePN": false,
+    // Configure PKCS#11 to use hardware security modules (HSM) and
+    // smart cards when carrying on HTTPS client authentication.
+    /**
+       "Pkcs11" : {
+         "Module" : "/usr/local/lib/libbeidpkcs11.so",
+         "Module" : "C:/Windows/System32/beidpkcs11.dll",
+         "Pin" : "1234",
+         "Verbose" : true
+       }
+     **/
+    // If set to "false", Orthanc will not load its default dictionary
+    // of private tags. This might be necessary if you cannot import a
+    // DICOM file encoded using the Implicit VR Endian transfer syntax,
+    // and containing private tags: Such an import error might stem from
+    // a bad dictionary. You can still list your private tags of
+    // interest in the "Dictionary" configuration option below.
+    "LoadPrivateDictionary": true,
+    // Locale to be used by Orthanc. Currently, only used if comparing
+    // strings in a case-insensitive way. It should be safe to keep this
+    // value undefined, which lets Orthanc autodetect the suitable locale.
+    // "Locale" : "en_US.UTF-8",
+    // Register a new tag in the dictionary of DICOM tags that are known
+    // to Orthanc. Each line must contain the tag (formatted as 2
+    // hexadecimal numbers), the value representation (2 upcase
+    // characters), a nickname for the tag, possibly the minimum
+    // multiplicity (> 0 with defaults to 1), possibly the maximum
+    // multiplicity (0 means arbitrary multiplicity, defaults to 1), and
+    // possibly the Private Creator (for private tags).
+    "Dictionary": {
+        // "0014,1020" : [ "DA", "ValidationExpiryDate", 1, 1 ]
+        // "00e1,10c2" : [ "UI", "PET-CT Multi Modality Name", 1, 1, "ELSCINT1" ]
+        // "7053,1003" : [ "ST", "Original Image Filename", 1, 1, "Philips PET Private Group" ]
+        // "2001,5f" : [ "SQ", "StackSequence", 1, 1, "Philips Imaging DD 001" ]
+    },
+    // Whether to run DICOM C-Move operations synchronously. If set to
+    // "false" (asynchronous mode), each incoming C-Move request results
+    // in the creation of a new background job. Up to Orthanc 1.3.2, the
+    // implicit behavior was to use synchronous C-Move ("true"). Between
+    // Orthanc 1.4.0 and 1.4.2, the default behavior was set to
+    // asynchronous C-Move ("false"). Since Orthanc 1.5.0, the default
+    // behavior is back to synchronous C-Move ("true", which ensures
+    // backward compatibility with Orthanc <= 1.3.2).
+    "SynchronousCMove": true,
+    // Maximum number of completed jobs that are kept in memory. A
+    // processing job is considered as complete once it is tagged as
+    // "Success" or "Failure". Since Orthanc 1.5.0, a value of "0"
+    // indicates to keep no job in memory (i.e. jobs are removed from
+    // the history as soon as they are completed), which prevents the
+    // use of some features of Orthanc (typically, synchronous mode in
+    // REST API) and should be avoided for non-developers.
+    "JobsHistorySize": 10,
+    // Whether to save the jobs into the Orthanc database. If this
+    // option is set to "true", the pending/running/completed jobs are
+    // automatically reloaded from the database if Orthanc is stopped
+    // then restarted (except if the "--no-jobs" command-line argument
+    // is specified). This option should be set to "false" if multiple
+    // Orthanc servers are using the same database (e.g. if PostgreSQL
+    // or MariaDB/MySQL is used).
+    "SaveJobs": true,
+    // Specifies how Orthanc reacts when it receives a DICOM instance
+    // whose SOPInstanceUID is already stored. If set to "true", the new
+    // instance replaces the old one. If set to "false", the new
+    // instance is discarded and the old one is kept. Up to Orthanc
+    // 1.4.1, the implicit behavior corresponded to "false".
+    "OverwriteInstances": false,
+    // Maximum number of ZIP/media archives that are maintained by
+    // Orthanc, as a response to the asynchronous creation of archives.
+    // The least recently used archives get deleted as new archives are
+    // generated. This option was introduced in Orthanc 1.5.0, and has
+    // no effect on the synchronous generation of archives.
+    "MediaArchiveSize": 1,
+    // Performance setting to specify how Orthanc accesses the storage
+    // area during C-FIND. Three modes are available: (1) "Always"
+    // allows Orthanc to read the storage area as soon as it needs an
+    // information that is not present in its database (slowest mode),
+    // (2) "Never" prevents Orthanc from accessing the storage area, and
+    // makes it uses exclusively its database (fastest mode), and (3)
+    // "Answers" allows Orthanc to read the storage area to generate its
+    // answers, but not to filter the DICOM resources (balance between
+    // the two modes). By default, the mode is "Always", which
+    // corresponds to the behavior of Orthanc <= 1.5.0.
+    "StorageAccessOnFind": "Always",
+    // Whether Orthanc monitors its metrics (new in Orthanc 1.5.4). If
+    // set to "true", the metrics can be retrieved at
+    // "/tools/metrics-prometheus" formetted using the Prometheus
+    // text-based exposition format.
+    "MetricsEnabled": true,
+    // Whether calls to URI "/tools/execute-script" is enabled. Starting
+    // with Orthanc 1.5.8, this URI is disabled by default for security.
+    "ExecuteLuaEnabled": false,
+    // Set the timeout for HTTP requests, in seconds. This corresponds
+    // to option "request_timeout_ms" of Mongoose/Civetweb. It will set
+    // the socket options "SO_RCVTIMEO" and "SO_SNDTIMEO" to the
+    // specified value.
+    "HttpRequestTimeout": 30
+}

requirements.txt

@@ -0,0 +1 @@
+monailabel

run.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+
+# Start the orthanc service
+# nginx &
+Orthanc &
+
+for i in ls datasets/Task09_Spleen/imagesTs/*.nii.gz; do plastimatch convert --patient-id patient1 --input $i --output-dicom test; done && \
+
+python -m pynetdicom storescu 127.0.0.1 4242 test -aet MONAILABEL -r   && \
+# # Start the monailabel service
+monailabel start_server --app apps/radiology --studies http://127.0.0.1:8042/dicom-web --conf models deepedit 
+# monailabel start_server --app apps/radiology --studies datasets/Task09_Spleen/imagesTr --conf models deepedit