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Dicom file handler module

Posted by mysty on July 6, 2009 at 5:28pm

Hello,

a drupal project I am working on needs a dicom file handler module. Dicom is a standard for medical images, containing metadata (for more details on Dicom see here).

The project needs a module to be able to:

  • import dicom files (from upload, maybe batch?)
  • convert dicom image for display within drupal, e.g. as a jpeg
  • extract the metadata from the dicom file as CCK fields that are then searchable

.. optionally:

  • jpg image rotation
  • jpg image scaling

The resulting module would be sponsored by the project, for the author's release as open source on drupal.org

If you are interested in this please contact me on irc in channel #drupaluk or via the contact form of d.o.

Thanks!

mysty

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Comments

Sounds like a sub-class of

Posted by budda on July 6, 2009 at 5:40pm

Sounds like a sub-class of the filefield / imagefield with a custom formatter to display the additional meta data.

Looks fiddly. Good luck!

--
Ixis (UK): Drupal consultancy, Drupal hosting.

changed from the above based

Posted by mysty on July 7, 2009 at 9:21pm

changed from the above based on further information.

  • convert dicom image for display within drupal, e.g. as a PNG (as JPG is perceived as lossy by the intended audience, and therefore 'not good enough')

Also

  • release 1 of the module is not expected to include the ability to edit the meta data in the dicom file, but a future release should ideally plan for the ability to edit the meta data for 'export' (i.e. download of a single updated dicom file with the updated metadata)
  • dicom file format apparently supports multiframe images. Sounds complicated, so unless you tell me different let's assume that release 1 does not support multiframe dicom images. Though of couse mutiframe support is preferred, it will eventually be required as part of the dicome standard

Hope the above makes sense.
Please contact with any questions.
Regards,
mysty

More clarification being sought

Posted by mysty on July 7, 2009 at 11:03pm

.. trying to find out at the moment whether the project needs full resolution dicom image browser (with zoom etc) or just a 72dpi preview.

Obviously quite important so please stand by.

Answers will be provided here, along with a re-stated more clear specification, and as much as I can offer about use cases, etc.

thanks for you interest and bearing with me while I try and nail down the moving pieces as much as possible before we get going :)

mysty

OK it seems the people I've

Posted by mysty on July 15, 2009 at 11:47pm

OK it seems the people I've been trying to get clarification from are both on separate beaches! Typical ;)

So what I've proposed to them is the following:

  • "The system should be able to recognise/treat medical data (pictures) in “dicom” format (which is widely used by current medical systems). Dicom file support will include importing of dicom images for preview within the web front end, and extraction of the dicom metadata so that the metadata can be searchable within the TP front end
  • "There will be an “export” screen/facility to export .. the original dicom files."

When I say system, I mean of course the drupal site via the aforementioned dicom module.

So what is not offered is a dicom file browser.

The use case would be for a user to import a dicom file - via either a file upload (for smaller files) or from a server side directory (dicom files can be large). The dicom module would then parse the file to extract:

  • a 72dpi image preview from the dicom file - which may be high resolution, or contain multiple images. In the latter case a still image preview will be supplied, with extacted meta data indicating that there are more than one image in the original dicom file
  • the associated metadata - which would be then stored say in CCK fields so as to be searchable

So the original dicom files will not be for editing, and will be available for downloaded later.

How does that sound? Hopefully realistic and achievable :)

regards,

mysty

Oh dear, I did forget that

Posted by mysty on July 16, 2009 at 12:07am

Oh dear, I did forget that the site will be in both Greek and English so i18n interoperation (whatever that means) will be important. Unlike for example the core contact module.

Sorry that's so unclear, and trust me, I really wish it was a single language project..

Good news

Posted by mysty on April 2, 2010 at 11:15am

Using a combination of:

the following example (snipped) metadata can be extracted on the command line, so all the pieces seem to be in place, apart from the php glue to import it to the drupal DB, as described above.

-----

[ExifTool]      ExifTool Version Number         : 7.82
[File]          File Name                       : 94013143.dcm
[File]          Directory                       : .
[File]          File Size                       : 324 kB
[File]          File Modification Date/Time     : 2009:11:17 18:03:00+02:00
[File]          File Type                       : DICOM
[File]          MIME Type                       : application/dicom
[DICOM]         File Meta Info Group Length     : 178
[DICOM]         File Meta Info Version          : 0 1
[DICOM]         Media Storage SOP Class UID     : MR Image Storage
[DICOM]         Media Storage SOP Instance UID  : 1.3.12.2.1107.5.2.30.25787.2009111313343876228995174
[DICOM]         Transfer Syntax UID             : Explicit VR Little Endian
[DICOM]         Implementation Class UID        : 1.3.12.2.1107.5.2
[DICOM]         Implementation Version Name     : MR_VB15A
[DICOM]         Specific Character Set          : ISO_IR 100
[DICOM]         Image Type                      : ORIGINAL\PRIMARY\M\DIS2D
[DICOM]         Instance Creation Date          : 2009:11:13
[DICOM]         Instance Creation Time          : 13:35:15.906000
[DICOM]         SOP Class UID                   : MR Image Storage
[DICOM]         SOP Instance UID                : 1.3.12.2.1107.5.2.30.25787.2009111313343876228995174
[DICOM]         Study Date                      : 2009:11:13
[DICOM]         Series Date                     : 2009:11:13
[DICOM]         Acquisition Date                : 2009:11:13
[DICOM]         Content Date                    : 2009:11:13
[DICOM]         Study Time                      : 13:24:47.406000
[DICOM]         Series Time                     : 13:33:15.890000
[DICOM]         Acquisition Time                : 13:32:58.067500
[DICOM]         Content Time                    : 13:35:15.906000
[DICOM]         Accession Number                :
[DICOM]         Modality                        : MR
[DICOM]         Manufacturer                    : SIEMENS
[DICOM]         Institution Name                : DELETED.......
[DICOM]         Institution Address             : DELETED.......
[DICOM]         Referring Physicians Name       :
[DICOM]         Station Name                    : MRC25787
[DICOM]         Study Description               : Pelvis_AVANTO^Oncology
[DICOM]         Series Description              : VII_ep2d_diff_pelvis
[DICOM]         Performing Physicians Name      :
[DICOM]         Manufacturers Model Name        : Avanto
[DICOM]         Referenced Image Sequence       :
[DICOM]         Start Of Item                   : .P.UI.1.2.840.10008.5.1.4.1.1.4.U.UI41.3.12.2.1107.5.2.30.25787.2009111313263870384892022
[DICOM]         Start Of Item                   : .P.UI.1.2.840.10008.5.1.4.1.1.4.U.UI41.3.12.2.1107.5.2.30.25787.2009111313263293319692010
[DICOM]         Start Of Item                   : .P.UI.1.2.840.10008.5.1.4.1.1.4.U.UI41.3.12.2.1107.5.2.30.25787.2009111313264445467992034
[DICOM]         Patients Name                   : DELETED.......
[DICOM]         Patient ID                      : B 747 -  400
[DICOM]         Patients Birth Date             : DELETED.......
[DICOM]         Patients Sex                    : M
[DICOM]         Patients Age                    : 043Y
[DICOM]         Patients Weight                 : 97
[DICOM]         Scanning Sequence               : EP
[DICOM]         Sequence Variant                : SK\SP
[DICOM]         Scan Options                    : PFP\FS
[DICOM]         MR Acquisition Type             : 2D
[DICOM]         Sequence Name                   : *ep_b800t
[DICOM]         Angio Flag                      : N
[DICOM]         Slice Thickness                 : 5
*snip*

I need DICOM too

Posted by sneakyimp on September 14, 2010 at 8:50pm

I was wondering if you could share any additional information about how you put these bits together?

Write multiplayer games in AS3/PHP5 with FlashMOG:
http://flashmog.net/docs/tutorial-shooter.php

Drupal and DICOM

Posted by owen32 on November 12, 2009 at 3:16pm

- have you looked at (some how) using something like DIOwave within Drupal? (http://diowave-vs.sourceforge.net/) - I use DIOwave for other things and getting it to work throug Drupal would solve some of my problems -

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