dicom-validator 0.3.4

Python DICOM tools using input from DICOM specs in docbook format

dicom-validator

dicom-validator provides the command line tool validate_iods that checks a DICOM file for missing or unexpected attributes. The check is done by comparing the contents of the DICOM file against the modules and attributes required by the DICOM standard for the SOP class of the given
dataset.

The tool gets its input from the newest version of the DICOM standard (or a specific version given as command line parameter) as provided by ACR NEMA in docbook format. pydicom is used to read and parse the DICOM files.

Additionally, the command line tool dump_dcm_info is available that displays the tag values of one or several DICOM files in a readable format. It is provided as a proof of concept of getting information directly from the DICOM standard.

Disclaimer:
No guarantees are given for the correctness of the results. This is alpha-stage software and mostly thought as a proof of concept. Also check the limitations for validate_iods described below.

Note: The original name of the package (dcm-spec-tools) has been changed to dicom-validator together with the move to the pydicom organization to reflect the fact that no other tools are planned, and that the DICOM validator is the relevant tool.

Installation

The latest version is available on pypi and can be installed via

pip install dicom-validator

Usage

dump_dcm_info [-r <revision>] [-src <spec dir>] <DICOM filename>
validate_iods [-r <revision>] [-src <spec dir>] [-v] <DICOM files or directories>

Use the --help option for each script do get usage info.

Access to the DICOM standard

Upon first start of a tool, part of the latest version of the DICOM standard in docbook format (specifically, parts 3.3, 3.4 and 3.6) are downloaded, parsed, and the needed information saved in json files. If the --src parameter is not provided, the files are downloaded to and looked up in <user home>/dicom-validator/.
These files are then used by the tools. Periodically (once a month), the tools check for a newer version of the DICOM standard and download it if found.

It is also possible to use older versions of the standard via the command line option --revision or -r, provided they are available for download (at the time of writing, standards are available since revision 2014a). A list of currently available editions can be found in /dicom-validator/editions.json after a tool has been called the first time.

validate_iods

This checks a given DICOM file, or all DICOM files recursively in a given directory, for correct tags for the related SOP class. Only the presence or
absence of the tag, and the presence of a tag value is checked, not the contained value itself (a check for correct enumerated values may be added later). This is done by looking up all required and optional modules for this SOP class, and checking the tags for these modules. Tags that are not allowed or missing in a module are listed. Parts 3 and 4 of the DICOM standard are used to collect the needed information. Conditions for type 1C and 2C modules and tags are evaluated if possible. If the evaluation fails, the respective modules and tags are considered optional.

The output for a single file may look like this:

(py3_test) c:\dev\GitHub\dicom-validator>validate_iods "c:\dev\DICOM Data\SR\test.dcm"

Processing DICOM file "c:\dev\DICOM Data\SR\test.dcm"
SOP class is "1.2.840.10008.5.1.4.1.1.88.33" (Comprehensive SR IOD)

Errors
======
Module "SR Document Content":
Tag (0040,A043) (Concept Name Code Sequence) is not allowed due to condition:
  Value Type is equal to "TEXT", "NUM", "CODE", "DATETIME", "DATE", "TIME", "UIDREF" or "PNAME"
Tag (0040,A300) (Measured Value Sequence) is missing
Tag (0040,A168) (Concept Code Sequence) is missing
Tag (0008,1199) (Referenced SOP Sequence) is missing
Tag (0070,0022) (Graphic Data) is missing
Tag (0070,0023) (Graphic Type) is missing
Tag (3006,0024) (Referenced Frame of Reference UID) is missing
Tag (0040,A130) (Temporal Range Type) is missing
Tag (0040,A138) (Referenced Time Offsets) is missing due to condition:
  Referenced Sample Positions is not present and Referenced DateTime is not present
Tag (0040,A13A) (Referenced DateTime) is missing due to condition:
  Referenced Sample Positions is not present and Referenced Time Offsets is not present

Limitations

Condition evaluation

As mentioned, if the evaluation of conditions fails, the related module or tag is considered optional, which may hide some non-conformity.
Condition evaluation may fail if:

• the needed information is not contained in the DICOM file (e.g. verbose descriptions like "if the Patient is an animal")
• the information is related to other DICOM files (e.g. referenced images)
• the parsing failed because the condition is too complicated, unexpected, or due to a bug (please write an issue if you encounter such a problem)

Retired tags

Also note that only the given standard is used to evaluate the files. If the DICOM file has been written using an older standard, it may conform to that standard, but not to the newest one. Tags that are retired in the version of the standard used for parsing are not considered at all.

Unsupported cases (support may be added in future versions)

• SOP classes not in the table in PS3.3 such as Presentation States are not handled
• functional groups in EnhancedXXX SOP classes are not handled

dcm_dump_info

This is a very simple DICOM dump tool, which uses the DICOM dictionary as read from part 6 of the standard. It prints the DICOM header of the given DICOM file, or of all DICOM files recursively in a given directory. The output looks like this:

(py3_test) c:\dev\GitHub\dicom-validator>dump_dcm_info "c:\dev\DICOM 
Data\SR\image12.dcm"

c:\dev\DICOM Data\SR\image12.dcm
(0005,0010) [Unknown]                                LO    1  [AEGIS_DICOM_2.00]
(0005,1000) [Unknown]                                UN    1  [\x00\x05 \x08\x00\x00\x00\n  RIGHT   \x00\x05\xc1X\x00\x00\x00\x06 0.09 \x00\x05...]
(0008,0008) Image Type                               CS    0  []
(0008,0016) SOP Class UID                            UI    1  [Ultrasound Image Storage (Retired)]
(0008,0018) SOP Instance UID                         UI    1  [1.2.840.113680.3.103.775.2873347909.282313.2]
(0008,0020) Study Date                               DA    1  [19950119]
(0008,0030) Study Time                               TM    1  [092854.0]
(0008,0050) Accession Number                         SH    1  [ACN000001]
(0008,0060) Modality                                 CS    1  [US]
(0008,0070) Manufacturer                             LO    1  [Acuson]
(0008,0090) Referring Physician's Name               PN    1  []
(0008,1010) Station Name                             SH    1  [QV-00775]
(0008,1030) Study Description                        LO    1  [ABDOMEN]
(0008,1050) Performing Physician's Name              PN    1  [DOE,JOHN]
(0008,1060) Name of Physician(s) Reading Study       PN    1  []
(0008,1070) Operators' Name                          PN    1  [DO]
(0008,1080) Admitting Diagnoses Description          LO    1  [RSNA'95 Data Not Delete]
(0009,0010) [Unknown]                                LO    1  [AEGIS_DICOM_2.00]
...

If you want to show only specific tags, you can use the option --show-tags:

(py3_test) c:\dev\GitHub\dicom-validator>dump_dcm_info "c:\dev\DICOM Data\SR\image12.dcm" --show-tags 0010,0010 PatientID

c:\dev\DICOM Data\SR\image12.dcm
(0010,0010) Patient's Name                           PN    1  [DOE^JANE]
(0010,0020) Patient ID                               LO    1  [ACN000001]