dcm-spec-tools 0.3.1

Python DICOM tools using input from DICOM specs in docbook format

dcm-spec-tools

dcm-spec-tools is planned to be a collection of simple pure python command line tools which get the input from the DICOM standard in docbook format as provided by ACR NEMA.

Currently available tools:

• validate_iods checks DICOM files for correct attributes for the given SOP class.
• dump_dcm_info outputs the DICOM tag IDs and values of a given DICOM file.

Note that this is still in an early stage of development.

pydicom is used to read/parse DICOM files.

Installation

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

pip install dcm-spec-tools

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 DICOM standard

Upon first start of a tool, part of the latest version of the DICOM standard in docbook format is downloaded, parsed, and the needed information saved in json files. 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 Periodically (once a month), the tools check for a newer version of the DICOM standard and download it if found.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 a command line option, provided they are still available for download (at the time of writing, standards are available since 2014a).

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\dcm-spec-tools>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  [KLOFAS,EDWARD]
(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\dcm-spec-tools>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  [NAPPER^MARGRET]
(0010,0020) Patient ID                               LO    1  [ACN000001]

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. 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
• the related tags are retired and not listed in the current standard

The output for a single file may look like this:

(py3_test) c:\dev\GitHub\dcm-spec-tools>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

Note: No guarantees are given for the correctness of the results. This is pre-alpha software and mostly thought as a proof of concept.