[CCPPETMR/SIRF] Fix PET interactive scripts (#374)
Edoardo Pasca
closes #370
fix functionality of pet interactive examples
renamed files to clarify the order they should be run
uses iterno instead of iter
uses sliceno instead of slice
You can view, comment on, or merge this pull request online at:
https://github.com/CCPPETMR/SIRF/pull/374
Commit Summary
- closes #370
File Changes
- R examples/Python/PET/interactive/01-display_and_projection.py (6)
- R examples/Python/PET/interactive/02-image_creation_and_projection.py (0)
- R examples/Python/PET/interactive/03-basic_reconstruction.py (11)
- M examples/Python/PET/interactive/reconstruction.py (40)
Patch Links:
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Edoardo Pasca
Still standing issue: running the whole script in spyder doesn't run the whole script.
Running the script cell-by-cell works.
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Edoardo Pasca
any comments?
evgueni-ovtchinnikov
@evgueni-ovtchinnikov commented on this pull request.
i understand you commented out help() to be able to run the whole script?
i would rather put a warning somewhere at the beginning "comment out help() to run the whole script"
(after all, these scripts were designed to run interactively one chunk at a time)
minor remark: our style conventions require slice_num rather than sliceno (cf. our developers guide)
Kris Thielemans
@KrisThielemans requested changes on this pull request.
I have the same comments as @evgueni-ovtchinnikov
- rename
slicenotoslice_numetc - why remove
help?
In examples/Python/PET/interactive/01-display_and_projection.py:
> @@ -198,5 +198,5 @@ def make_cylindrical_FOV(image):
#%% close all plots
plt.close('all')
-
+print ("here")
delete
In examples/Python/PET/interactive/03-basic_reconstruction.py:
> @@ -69,13 +69,14 @@
#%% display of image
reconstructed_array=reconstructed_image.as_array()
-slice=reconstructed_array.shape[0]//3;
-show_2D_array('reconstructed image after 5 sub-iterations',reconstructed_array[slice,:,:,]);
+# slice=reconstructed_array.shape[0]//3;
+sliceno = 9
I'd prefer to have it in terms of the shape somehow, but fine to leave if that's too hard
Kris Thielemans
one other thing: you didn't update the README...
Edoardo Pasca
@paskino commented on this pull request.
In examples/Python/PET/interactive/03-basic_reconstruction.py:
> @@ -69,13 +69,14 @@
#%% display of image
reconstructed_array=reconstructed_image.as_array()
-slice=reconstructed_array.shape[0]//3;
-show_2D_array('reconstructed image after 5 sub-iterations',reconstructed_array[slice,:,:,]);
+# slice=reconstructed_array.shape[0]//3;
+sliceno = 9
I have the same comments as @evgueni-ovtchinnikov
- rename
slicenotoslice_numetc
OK
- why remove
help?
I removed help thinking that it may fix the problem that that was the reason spyder wouldn't run the whole script correctly. As that is not the case I'll put it back. However, the problem of spyder reaching the end without running correctly still remains.
Edoardo Pasca
According to the README the scripts should be run cell-by-cell.
Edoardo Pasca
Merged #374 into master.