The program runs on any computer with Java 7 or better.
To run the program, either double-click the Anonymizer.jar file or
launch a command window, navigate to the Anonymizer directory,
and type:
java -jar CovidClient.jar
If the program reports errors that are not obvious from the text shown in the Results pane, you may get additional information by running the program in a command window.
If an out-of-memory error occurs, you may assign more memory to
the program by running it in a command window with the command:
java -Xmx768m -jar Anonymizer.jar
The Q/R SCU Tab
The Q/R SCU tab provides control of a DICOM Query/Retrieve SCU for finding and importing images via the DICOM protocol from a PACS Q/R SCP. It also lists the AE Title used by the SCU for the query. These parameters may be obtained from the PACS administrator when the PACS is configured to accept connections from the program.
Text boxes are supplied for the PatientName, PatientID, and StudyDate search fields. At least one search field must contain text for a query to be initiated. A blank field is considered a match for anything. The Clear button erases the fields.
When specifying a query, the ? character matches any individual character, and the * character matches any sequence of characters. A StudyDate must be specified in full, for example 20190315, and wild card characters are not allowed.
BACKGROUND: A PACS is configured with Application Entity Titles (AE Titles, or AETs) for all of the external Service Class Providers (SCPs) and Service Class Users (SCUs) with which it interacts. The PACS knows the SCPs and SCUs by their AETs, which it uses to search its internal tables for the IP addresses and ports of the computers on which they are running. The Anonymizer program contains a DICOM Query/Retrieve SCU and a DICOM Storage SCP. When the Anonymizer program retrieves images from the PACS, the Q/R SCU tells the PACS to send to the AET of the Storage SCP. The PACS uses the IP and port information that it associates with the AET it is given, so if your computer's IP address has changed, or if you have changed the SCP's port, the transfer will fail. For this reason, if the computer running the Anonymizer program has a dynamic IP address, you must configure the PACS to use a domain name for the computer so the PACS will be able to get the IP address from a DNS.
The Storage SCP Tab
The Storage SCP tab provides control of a DICOM Storage SCP for receiving images via the DICOM protocol from modalities, workstations, and PACS.
The header displays the IP address of the SCP and provides a text box allowing the port to be specified. It also provides a button for starting and stopping the SCP. The Autostart checkbox, if checked, causes the program to start the SCP automatically when the program starts. Events are logged in the main panel of the tab as images are processed. The Clear button erases the panel.
Processing of images is automatic. The processing is the same as that done when images are imported manually using the Directory tab.
The Directory Tab
The Directory tab has a left and right pane. The left pane provides navigation through the files on the computer. The right pane displays the results of actions. At the bottom of the right pane, there are buttons to initiate the functions provided by the program.
The pulldown menu in the upper right of the Directory pane allows selection of the file system root that will be displayed in the directory tree.
The directory tree does not track changes in the directory structure that occur behind the program's back. You can refresh the directory tree by clicking the root of the tree or clicking the Refresh button in the header of the left pane.
The button in the lower right of the Directory pane displays a dialog that allows selection of the file extensions that are displayed in the directory tree. If the list of extensions includes an asterisk, all files are displayed. There is a special notation, "[dcm]", that selects files whose names contain only numerals and periods. This can be used, for example, to select images on DICOM CDs or files that were named by their SOPInstanceUIDs.
The Import button starts the import and deidentification process. Which files are processed depends on whether a file or a directory is selected in the Directory pane and on whether the Include subdirectories checkbox is selected:
Events that occur during the anonymization process are logged in the Results pane.
Images are stored in file structures for each date of processing. The file structures are stored in a parent directory. By default, the parent directory is called Submissions, and it is located in the directory containing the program. To change the parent directory, click the Set Storage Directory button, navigate to the desired directory, and click Save. The currently selected output directory is shown in the header of the right pane. Clicking that text repositions the directory tree in the left pane to point to the submisssions directory.
The Viewer Tab
The Viewer tab displays the currently selected DICOM image. If the image file contains multiple frames, the Next Frame and Previous Frame buttons sequence through the frames. Frame sequencing is also provided through the mouse wheel.
Zoom, pan, and window width and level functions are provided through icons in the upper right of the window.
The window width and level can also be set manually by typing values into the provided text boxes. When entering text in the window width and level boxes, the values do not take effect until the Enter key is pressed.
The Save As JPEG button saves the image, reduced to the width specified in a popup dialog.
The Elements Tab
The Elements tab displays the element contents of the selected DICOM image.
The Filter Tab
To be accepted for import and processing, a file must be a DICOM image. It must also match a filter script as described in http://mircwiki.rsna.org/index.php?title=The_CTP_DICOM_Filter.
The Filter tab provides an editing window for creating or modifying the filter script. Any text changes in the window are immediately active, but they are not saved until the Save button is clicked. The Refresh button discards any unsaved changes and reloads the filter text from the last saved version.
The Script Tab
The DICOM deidentification process is driven by a script file called "dicom-anonymizer.script" located in the directory containing the program. A default version is included in the installation.
The Script tab displays the DICOM anonymizer scripts. You can edit the scripts and click the Save Changes button. Changes are not effective until the scripts are saved. If you make a change and decide you made an error before saving, click the Reset button and the scripts will be refreshed from the last saved version.
The DICOM anonymizer script functions are documented in http://mircwiki.rsna.org/index.php?title=The_CTP_DICOM_Anonymizer.
Before beginning to import and process images, the first item in the script should be updated to reflect the site identifier (SITEID). Unless special deidentification rules are required by the project, no other parts of the script need be modified.
The Submission Tab
The Submission tab provides an interface for creating metadata files summarizing the contents of a submission directory created during the import and deidentification process. The Select Submission button displays a file chooser allowing a submission directory to be selected. Selection of a directory displays a form that allows information to be entered on the patients, studies, series included in the submission. Clicking the Save Metadata saves the metadata XML file.
The Index Tab
The Index tab provides an interface for searching the index of files that have been anonymized and stored in the directory tree of submissions. The index is persistent, so it contains information on every patient processed by the program. To find the original PatientName and PatientID for a study subject, enter the anonymized PatientName in the search field and type the Enter key or click the Search button. The search field is not case sensitive.
To list the entire index, click the List button. When in the List pane, the Save button saves the index in a spreadsheet file, including study information.
The Log Tab
The Log tab lists events logged by various components in the program. The log may be useful in initial setup, as the configuration is tested before production use.