Collection

Scenario

You wish to collect and structure data from your own PACS or a partners' PACS. This assumes that you have have installed pacsanini and are familiar with pacsanini configuration files.

Given the configuration file setup, the collection process will then go as follows:

1. Find the DICOM resources that are stored in the target PACS
2. Request the DICOM resources and:
   • Parse the resources' DICOM tags
   • Write the collected DICOM files to disk

Environment Setup

The idea behind the configuration file is that you are able to store all of your settings in one place and re-use those same settings during the entire collection process.

For the purposes of this guide, let's assume that we will be using the following configuration file (saved under pacsaniniconf.yaml):

YAML

move:
    start_time: 20:00
    end_time: 08:00
    query_level: STUDY
net:
    local_node:
        aetitle: mytitle
        port: 11112
    called_node:
        aetitle: theirtitle
        ip: 127.0.0.1
        port: 11112
find:
    query_level: STUDY
    search_fields:
        - StudyInstanceUID
        - PatientID
    start_date: "20200101"
    end_date: "20201212"
    modality: CT
storage:
    resources: my/resources.csv
    directory: my/dicom/dir
    sort_by: PATIENT
tags:
    - tag_name: PatientName
      callback: str
    - tag_name: StudyDate
      tag_alias: study_date
      callback: pacsanini.convert:str2datetime
    - tag_name: Laterality
      default_val: U
      callback: str
    - tag_name: StudyInstanceUID
    - tag_name: SOPInstanceUID

JSON

{
    "move": {
        "start_time": "20:00",
        "end_time": "08:00",
        "query_level": "STUDY"
    },
    "net": {
        "local_node": {
            "aetitle": "mytitle",
            "port": 11112
        },
        "called_node": {
            "aetitle": "theirtitle",
            "ip": "127.0.0.1",
            "port": 11112
        }
    },
    "find": {
        "query_level": "STUDY",
        "search_fields": ["StudyInstanceUID", "PatientID"],
        "start_date": "20200101",
        "end_date": "20201212",
        "modality": "CT"
    },
    "storage": {
        "resources": "my/resources.csv",
        "directory": "my/dicom/dir",
        "sort_by": "PATIENT"
    },
    "tags": [
        {
            "tag_name": "PatientName",
            "callback": "str"
        },
        {
            "tag_name": "StudyDate",
            "tag_alias": "study_date",
            "callback": "pacsanini.convert:str2datetime"
        },
        {
            "tag_name": "Laterality",
            "default_val": "U",
            "callback": "str"
        },
        {
            "tag_name": "StudyInstanceUID"
        },
        {
            "tag_name": "SOPInstanceUID"
        }
    ]
}

Collecting Resources

To collect resources, simply run the following commands in a terminal:

pacsanini find -f pacsaniniconf.yaml
pacsanini move -f pacsaniniconf.yaml

With these two commands, you have just been able to:

1. Find all the computed tomography (CT) resources stored on the PACS between the first of January 2021 and the 12th of December 2021 (pacsanini find -f pacsaniniconf.yaml); and
2. Request the found resources from the PACS and store them on disk (pacsanini move -f pacsaniniconf.yaml).