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sct_propseg: Labels and centerline are now output with correct header if -rescale is used #1926

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merged 6 commits into from
Jul 17, 2018
Merged

sct_propseg: Labels and centerline are now output with correct header if -rescale is used #1926

merged 6 commits into from
Jul 17, 2018

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jcohenadad
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@jcohenadad jcohenadad commented Jul 12, 2018 •
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Description of the Change

This PR fixes a few issues associated with the recently-introduced -rescale flag:

  • The output centerline is now scaled back to the original data header
  • The manual labels (if used) are now output and rescaled appropriately
  • If -init-centerline or -init-mask is used along with -rescale, the input labels are rescaled.

Fixes #1925

@jcohenadad jcohenadad requested a review from zougloub July 12, 2018 20:48
@jcohenadad jcohenadad added this to the v3.2.3 milestone Jul 12, 2018
@jcohenadad jcohenadad self-assigned this Jul 12, 2018
@jcohenadad jcohenadad added enhancement category: improves performance/results of an existing feature sct_propseg context: labels Jul 12, 2018
zougloub
zougloub approved these changes Jul 15, 2018
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Added some suggestions but the code looks fine.

scripts/sct_propseg.py Outdated
if use_viewer:
fname_labels_viewer_new = os.path.join(folder_output, os.path.basename(sct.add_suffix(fname_data,
"_labels_viewer")))
shutil.copy(fname_labels_viewer, fname_labels_viewer_new)
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Actually we added a sct.copy(), you could use it.

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And we also have sct.mv() which can replace the os.rename() above.

@jcohenadad jcohenadad merged commit 070207d into master Jul 17, 2018
@jcohenadad jcohenadad deleted the jca/1925-propseg-rescale-output branch July 17, 2018 16:27
@jcohenadad jcohenadad changed the title Labels and centerline are now output with correct header sct_propseg: Labels and centerline are now output with correct header Jul 21, 2018
@jcohenadad jcohenadad changed the title sct_propseg: Labels and centerline are now output with correct header sct_propseg: Labels and centerline are now output with correct header if -rescale is used Jul 21, 2018
jcohenadad added a commit that referenced this pull request Dec 18, 2019
@jcohenadad
Labels and centerline are now output with correct header (#1926)
541733e 
* labels and centerline are now output with correct header (fixes #1925)

* Fixed issue when manual labels are input and rescale is used

* replaced os.rename by sct.mv and shutil.copy by sct.copy


Former-commit-id: 070207d
@joshuacwnewton joshuacwnewton mentioned this pull request Jan 19, 2023
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@zougloub zougloub zougloub approved these changes

@benjamindeleener benjamindeleener Awaiting requested review from benjamindeleener

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enhancement category: improves performance/results of an existing feature sct_propseg context:
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if -rescale is used, the output centerline should be scaled back to the original data header
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@jcohenadad @zougloub