Tutorials¶

Step-by-step instructions on how to perform particular tasks with anonapi.

Note

These instructions use windows paths and screenshots, but all commands work the same way for linux. In addition, input files are referred to as excel files, but csv format is also accepted

Anonymize from PACS¶

How to anonymize data when you have a list of accession numbers

Requirements¶

For this tutorial you need the following:

C:\project_folder - A folder that will hold records of the jobs created. Anonymized data does not have to go into this folder.
C:\project_folder\accession_numbers.xlsx - An excel or csv input file containing a list of accession numbers that you want to anonymize. This file could be anywhere, but for convenience it is inside the project folder in this tutorial.

The path and file above are just examples. They can be anything you like.

Step 1: prepare input file¶

To start, open accession_numbers.xlsx and check the following:

The file must contain a column with header accession_number
The file may contain a column with header pseudonym. These pseudonyms will be used if found.
The file may contain any other columns and text. These will all be ignored for example, The following is a valid input file:

Some text here does not matter
The column 'project' below will also just be ignored

accession_number    pseudonym  project
1234567.12345678    studyA     some_projectA
2234567.12345678    studyB     some_projectB
3234567.12345678    studyC     some_projectB

Step 2: add input to mapping¶

Find your project folder C:\project_folder in windows explorer, shift + right-click -> Open command prompt (see opening a command prompt)
In the command line, run the following:

$ anon map init
$ anon map add-accession-numbers --input-file accession_numbers.xlsx

Now open the mapping for editing:

anon map edit

Tip

If values are not sorted into columns properly in excel, do the following:

select column A -> click menu Data -> click Text to Columns
In the menu choose delimited -> click Next
Under ‘delimiters’ check either Comma or Semicolon -> click Next

make the following edits (as shown in the image below):

project should have the correct anonymization project (usually ‘Wetenschap-Algemeen’)
destination_path should be an be a UNC path (like \\server\share) where you want your anonymized data to be written.

Step 3: create jobs¶

Make sure you have a command prompt in your project folder C:\project_folder. Then run the following:

$ anon create from-mapping

This will create all jobs defined in your mapping file and save a reference to them as a batch.

Step 4: monitor job batch¶

To see how your jobs are doing use

$ anon batch status

To print error messages for all failed jobs use

$ anon batch show-error

Other batch commands can be found here.

Anonymize from a share¶

How to anonymize data when you have data for a large number of patients on a share and want to anonymize several, but not all of these.

Step 1: prepare input file¶

To start, open the input file folders.xlsx and check the following:

The file must contain a column with header folder, containing the names of the folders you want to anonymize from \\server\share\mydata
The file may contain a column with header pseudonym. These pseudonyms will be used if found.

For example:

folder       pseudonym
patient1     anon_patientA
patient3     anon_patientB
patient5     anon_patientC

Step 2: add input to mapping¶

Find your project folder C:\project_folder in windows explorer, shift + right-click -> Open command prompt (see opening a command prompt)
In the command prompt, type anon map init and press enter. Then close the prompt again.
Now find \\server\share\mydata in windows explorer and shift + right-click -> Open command prompt there.

Note

windows command prompt will show this location as a mapped drive letter like H:\ or X:\. This is not a problem here. When setting source and destination locations later on in this tutorial, be sure to always use the \\server\share form, never the drive letter.

In the command prompt, type the following:

$ anon map add-study-folders --input-file "C:\project_folder\folders.xlsx"

This command might take some time to complete as it will scan for all DICOM files in each of the folders.

Now open the mapping for editing:

anon map edit

Tip

If values are not sorted into columns properly in excel do the following:

select column A -> click menu Data -> click Text to Columns
In the menu choose delimited -> click Next
Under ‘delimiters’ check either Comma or Semicolon -> click Next