Added an option for keypoints transformation #2533

lrouhier · 2019-11-21T21:31:11Z

This PR aims to add the -label flag to the sct_apply_transfo script. This flag can be used when applying a warping field to images containing point-like labels (e.g., discs label).
It performs the following :

Change interpolation to 'nearest neighbor'
Dilate labels on the image
Apply the warping field to the dilated image
Apply cubic_to_point function to retrieve point-like labels on the transformed image.

Fixes #2519

…n to perform because the input file contains point like label. It seems fonctionnal but is still a work in progress. The transformed file overwrite the first created one. the option is here activated by default but an accepted argument

…ts. removing extra lines as well

…n question about where to save the actual straight file before using cubic to points.

…mage (before applying cubic to point)

…ate the dilatation and nearest neighbors interpolation.

jcohenadad · 2019-11-21T21:42:55Z

scripts/sct_apply_transfo.py

@@ -19,10 +19,12 @@
 import sys, io, os, time, functools
 import argparse

+


only single line separation
see: https://github.com/neuropoly/spinalcordtoolbox/wiki/example_script

jcohenadad · 2019-11-21T21:43:05Z

scripts/sct_apply_transfo.py

 from spinalcordtoolbox.utils import Metavar, SmartFormatter
 from spinalcordtoolbox.image import Image
 from spinalcordtoolbox.cropping import ImageCropper

+


single line

jcohenadad · 2019-11-21T21:43:26Z

scripts/sct_apply_transfo.py

@@ -120,7 +128,7 @@ def get_parser():


 class Transform:
-    def __init__(self, input_filename, fname_dest, list_warp, list_warpinv=[], output_filename='', verbose=0, crop=0,
+    def __init__(self, input_filename, fname_dest, list_warp, list_warpinv=[], output_filename='', verbose=0, crop=0,label=0,


space after comma-- PEP8

jcohenadad · 2019-11-21T21:43:43Z

scripts/sct_apply_transfo.py

@@ -132,7 +140,8 @@ def __init__(self, input_filename, fname_dest, list_warp, list_warpinv=[], outpu
        self.verbose = verbose
        self.remove_temp_files = remove_temp_files
        self.debug = debug
-
+        self.label=label


space between =.
PEP8

jcohenadad · 2019-11-21T21:44:10Z

scripts/sct_apply_transfo.py

@@ -142,6 +151,9 @@ def apply(self):
        verbose = self.verbose
        remove_temp_files = self.remove_temp_files
        crop_reference = self.crop  # if = 1, put 0 everywhere around warping field, if = 2, real crop
+        label=self.label


space. Please apply PEP8 for all your modifs (there are other formatting issues below)

jcohenadad · 2019-11-21T22:32:36Z

scripts/sct_apply_transfo.py

+                tmp_src=os.path.join(path_tmp, "dilated_data.nii")
+                tmp_out=os.path.join(path_tmp, "dilated_data_reg.nii")
+
+                sct.run(['isct_antsApplyTransforms',


duplicated code (see below)

jcohenadad · 2019-11-22T18:16:35Z

@lrouhier after giving it some thoughts, how about adding a possible value label to the flag -x, instead of creating a new boolean flag -label? It would save some lines of code, and make it explicit that "label" is very much related to the interpolation (and cannot be used with any other interpolation method)

lrouhier · 2019-11-22T20:19:01Z

Maybe it will be clearer! It does not change much in the code for me and i think it's easier for the user. Any thoughts on how to explain it in the help?

for now I wrote : Interpolation method. the 'label' interpolation method is designed to improve results on keypoints label file (e.g., disc label files) by dilating the original label and retrieving key points after the transformation. (line 102-103)

jcohenadad · 2019-11-22T20:25:01Z

i would go with:

Interpolation method. the 'label' method is to be used if you would like to apply a transformation on a file that has single-voxel labels (classical interpolation methods won't work, as resampled labels might disappear or their values be altered). The function will dilate each label, apply the transformation using nearest neighbour interpolation, and then take the center-of-mass of each "blob" and output a single voxel per blob.

…t used.

- Added verbose - Added ImplementationError for dim=4 case

jcohenadad

Great contribution! 👍

jcohenadad · 2019-11-28T02:45:55Z

Let's merge #2522 before this one

* First implementation of a -label option that specify certain operation to perform because the input file contains point like label. It seems fonctionnal but is still a work in progress. The transformed file overwrite the first created one. the option is here activated by default but an accepted argument * forget to change a parameter. which causes it to not label every points. removing extra lines as well * refactoring with precisting sct function. everything look smooth. open question about where to save the actual straight file before using cubic to points. * force the nearest neighbors interpolation when using the -label flag. * added creation of tmp folder to stor dilated and straighten dilated image (before applying cubic to point) * Added the removal of temporary files (if not stated otherwise) * removing lines. PEP-8 normalization * remove extra lines * refactor parser. the -label flag does not need any argument and activate the dilatation and nearest neighbors interpolation. * PEP-8 formatting * remove duplicated code * put -label flag as an interpolation option. * changing help discription for -x flag * removing extra lines * rmoving extra line and defining label in the case that the flag is not used. * sct_apply_transfo: Updated usage * sct_apply_transfo: Minor refactoring - Added verbose - Added ImplementationError for dim=4 case Former-commit-id: f89d6cb

lrouhier and others added 9 commits November 20, 2019 14:48

forget to change a parameter. which causes it to not label every poin…

2a5a4aa

…ts. removing extra lines as well

refactoring with precisting sct function. everything look smooth. ope…

c6d85ad

…n question about where to save the actual straight file before using cubic to points.

force the nearest neighbors interpolation when using the -label flag.

4fb5c09

added creation of tmp folder to stor dilated and straighten dilated i…

a8c7b0a

…mage (before applying cubic to point)

Added the removal of temporary files (if not stated otherwise)

c1e2ea6

removing lines. PEP-8 normalization

dd68bd5

remove extra lines

deb57dd

refactor parser. the -label flag does not need any argument and activ…

2f39ad6

…ate the dilatation and nearest neighbors interpolation.

lrouhier changed the title ~~adding an option for keypoints transformation in sct_apply_transfo~~ adding an option for keypoints transformation in sct_apply_transfo (fix #2519) Nov 21, 2019

jcohenadad changed the title ~~adding an option for keypoints transformation in sct_apply_transfo (fix #2519)~~ Added an option for keypoints transformation in sct_apply_transfo Nov 21, 2019

jcohenadad self-requested a review November 21, 2019 21:40

jcohenadad reviewed Nov 21, 2019

View reviewed changes

lrouhier added 2 commits November 22, 2019 10:46

PEP-8 formatting

443878a

remove duplicated code

c612af0

put -label flag as an interpolation option.

43a2e6b

lrouhier added 3 commits November 22, 2019 15:42

changing help discription for -x flag

d55ab64

removing extra lines

c377895

rmoving extra line and defining label in the case that the flag is no…

9d8bc78

…t used.

jcohenadad added feature category: new functionality sct_apply_transfo context: labels Nov 26, 2019

jcohenadad changed the title ~~Added an option for keypoints transformation in sct_apply_transfo~~ Added an option for keypoints transformation Nov 26, 2019

jcohenadad added this to the 4.1.1 milestone Nov 26, 2019

lrouhier and others added 4 commits November 26, 2019 13:15

Merge branch 'master' into lrouhier/2519-xlabel-option

2dce3d5

Merge branch 'master' into lrouhier/2519-xlabel-option

1914e36

sct_apply_transfo: Updated usage

8a91a9d

sct_apply_transfo: Minor refactoring

d50a66e

- Added verbose - Added ImplementationError for dim=4 case

jcohenadad approved these changes Nov 28, 2019

View reviewed changes

Merge branch 'master' into lrouhier/2519-xlabel-option

f7d3e57

jcohenadad merged commit f89d6cb into master Nov 28, 2019

jcohenadad deleted the lrouhier/2519-xlabel-option branch November 28, 2019 14:29

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Added an option for keypoints transformation #2533

Added an option for keypoints transformation #2533

lrouhier commented Nov 21, 2019 •

edited by jcohenadad

jcohenadad Nov 21, 2019

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jcohenadad commented Nov 28, 2019

		@@ -19,10 +19,12 @@
		import sys, io, os, time, functools
		import argparse

Added an option for keypoints transformation #2533

Added an option for keypoints transformation #2533

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lrouhier commented Nov 21, 2019 • edited by jcohenadad

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lrouhier commented Nov 21, 2019 •

edited by jcohenadad