loading DICOM images

[James Kerns]

Hello! First of all let me thank those of you who built the guidata/guiqwt
project. I'm an amateur programmer converting from Matlab to Python and
it's nice to have high-level GUI tools available. As a total noob of Python
I'm not qualified to say whether or not something is bug, but I did want to
see about an error I'm getting using the *guiqwt.io._imread_dcm* function.

I use Python(x,y) and my version of guiqwt is 2.3.1 and pydicom is 0.9.8-2
(the versions bundled with the most recent release of Pythonxy).

The *guiqwt.io.imread* function is said to be able to read in DICOM
files/images, but I get errors whenever I try to do so (there and when I
also call *io._imread_dcm*). Apparently the syntax of pydicom has changed
in it's main read function from "ReadFile" to "read_file". I've worked
around this by adding an if statement to check if the extension is dicom
and then explicitly calling dicom.read_file instead, but figured I'd 1)
maybe report a bug (yay!) or 2) be told my simple mistake and keep my code
clean and tight.

As is indicated in the *_imread_dcm* notes: "The following is necessary
until pydicom numpy support is improved: (after that, a simple: 'arr =
dcm.PixelArray' will work the same)". It would seem this has been done
because the dicom method *pixel_array* does indeed work, returning a numpy
array.

Like I said, I can easily work around this, but I'd rather leave it to the
experts if indeed it can be fixed.

Cheers,
James

[Pierre Raybaut]

Hi James,


Thanks a lot for the feedback and for your interest in guidata/guiqwt.


We’ll look into it and update those DICOM support features.


Cheers,

-Pierre






De : James Kerns
Envoyé : samedi 16 novembre 2013 13:22
À : guidata_guiqwt-/***@public.gmane.org





Hello! First of all let me thank those of you who built the guidata/guiqwt project. I'm an amateur programmer converting from Matlab to Python and it's nice to have high-level GUI tools available. As a total noob of Python I'm not qualified to say whether or not something is bug, but I did want to see about an error I'm getting using the guiqwt.io._imread_dcm function.



I use Python(x,y) and my version of guiqwt is 2.3.1 and pydicom is 0.9.8-2 (the versions bundled with the most recent release of Pythonxy).




The guiqwt.io.imread function is said to be able to read in DICOM files/images, but I get errors whenever I try to do so (there and when I also call io._imread_dcm). Apparently the syntax of pydicom has changed in it's main read function from "ReadFile" to "read_file". I've worked around this by adding an if statement to check if the extension is dicom and then explicitly calling dicom.read_file instead, but figured I'd 1) maybe report a bug (yay!) or 2) be told my simple mistake and keep my code clean and tight.




As is indicated in the _imread_dcm notes: "The following is necessary until pydicom numpy support is improved: (after that, a simple: 'arr = dcm.PixelArray' will work the same)". It would seem this has been done because the dicom method pixel_array does indeed work, returning a numpy array.




Like I said, I can easily work around this, but I'd rather leave it to the experts if indeed it can be fixed.




Cheers,

James