Now possible to add existing label from an external file in the create-viewer option #2520

lrouhier · 2019-11-11T17:45:53Z

The goal of this PR is to create an option to see previously existing labels when using the -create-viewer option in sct_label_utils. The user could then add some missing labels or modify the existing one within the GUI.
DONE :

Create a -ilabel option allowing to enter the existing label files and extract the existing label coordinates and value
Modify the existing SagittalController in gui/sagittal.py to create the existing points on the GUI when showing the image.
When the user fails to enter enough label. example: sct_label_utils -i t2.nii.gz -ilabel labels.nii.gz -create-viewer 1,2 will create the GUI with all pre-existing labels as discussed in this PR.
Modify the code to project the existing point onto the mid_saggital plane.

…at each opening.WIP

…e value or error.

jcohenadad · 2019-11-11T17:54:26Z

spinalcordtoolbox/gui/sagittal.py

@@ -20,8 +20,12 @@


 class SagittalController(base.BaseController):
- def __init__(self, image, params, init_values=None):
+ def __init__(self, image, params, init_values=None,previous_point=None):


could you please add a space after "," (PEP8)

p.s. the same comment applies to all your other edits in this PR

Yes will do.

jcohenadad · 2019-11-11T17:57:15Z

scripts/sct_label_utils.py

@@ -69,6 +69,14 @@ def __init__(self, fname_label, fname_output=None, fname_ref=None, cross_radius=
 self.fname_output = fname_output
 else:
 self.fname_output = fname_output
+
+ if isinstance(fname_previous, list):


why the need for this if? how about simply enforcing fname_previous to be a file name (could be verified by the parser)

I think you are right it will be enough. I just modeled it after the fname_output to begin with.

…he mid_slice (if not modified)

…mprove on the version.

…bugging ellemnt previously created

jcohenadad · 2019-11-12T16:36:42Z

scripts/sct_label_utils.py

+ points=np.append(previous_points[i], np.array([previous_lab.data[previous_points[i][0], previous_points[i][1], previous_points[i][2]]]), axis=-1)
+ points=np.reshape(points, (1, 4))
+ previous_label=np.append(previous_label, points, axis=0)
+


no need for these extra lines

lrouhier · 2019-11-20T14:39:09Z

update on the decision: when the user fails to enter all the labels already existing in the -ilabel argument files, it will just show the ones he asked for.
Existing points are projected onto the mid-sagittal plane as this is what shows up in the GUI, it is easier for the user to correct the label.

jcohenadad · 2019-11-20T22:37:32Z

update on the decision: when the user fails to enter all the labels already existing in the -ilabel argument files, it will just show the ones he asked for.

sounds good (if i understand correctly)

Existing points are projected onto the mid-sagittal plane as this is what shows up in the GUI, it is easier for the user to correct the label.

that's the part i don't understand: if the gui only show the labels he asked for, how can he correct for the one he didn't ask for?

lrouhier · 2019-11-20T23:28:52Z

the -ilabel flag launch an algorithm that retrieves the existing coordinates. The retrieved coordinates are then passed as input for the GUI which considers them the same way it does selected points. The checklist on the right allows the modification of the coordinates of each label (retrieved from another file or clicked on). The user can correct the labels he did ask for if one is misplaced.

The drawback is that the points that are not asked for won’t be part of the new label image (for now). I was thinking that it was more coherent to just save what the user sees

jcohenadad · 2019-11-20T23:42:01Z

the -ilabel flag launch an algorithm that retrieves the existing coordinates. The retrieved coordinates are then passed as input for the GUI which considers them the same way it does selected points. The checklist on the right allows the modification of the coordinates of each label (retrieved from another file or clicked on). The user can correct the labels he did ask for if one is misplaced.

The drawback is that the points that are not asked for won’t be part of the new label image (for now). I was thinking that it was more coherent to just save what the user sees

sorry i still don't understand-- let's me write a scenario to clarify:

users runs: sct_label_utils -i bla -create-viewer 3,4,5,6 -ilabel FILE_WITH_LABELS_2-3-4
GUI shows:
- on the left (not on the right): the list: 2,3,4,5,6
- on the image: points: 2,3,4
User can select/unselect whatever he wants. He can correct labels 2,3,4 if he wants
When clicking on save, labels 2,3,4,5,6 are saved

is that what you suggested?

if not, please explain with a step-by-step scenario for clarity-- thanks

lrouhier · 2019-11-20T23:55:45Z

Not entirely. the scenario is the following:

user run sct_label_utils -i bla -create-viewer 3,4,5,6 -ilabel FILE_WITH_LABELS_2-3-4
GUI shows :
- on the left : 3,4,5,6
- on the image : points 3,4 (common points between what is already defined and what he asked for)
he can select what he wants and correct 3,4 if he wants to.
when clicking, on save labels 3,4,5,6 are saved

jcohenadad · 2019-11-21T00:03:02Z

Not entirely. the scenario is the following:

user run sct_label_utils -i bla -create-viewer 3,4,5,6 -ilabel FILE_WITH_LABELS_2-3-4

GUI shows :

on the left : 3,4,5,6

on the image : points 3,4 (common points between what is already defined and what he asked for)

he can select what he wants and correct 3,4 if he wants to.

when clicking, on save labels 3,4,5,6 are saved

ok got it! how about adding 5,6 on the right, to give the user the possibility to correct for them? what are the cons?

lrouhier · 2019-11-21T00:22:24Z

ok got it! how about adding 5,6 on the right, to give the user the possibility to correct for them? what are the cons?

Do you mean 2? ( I assumed FILE_WITH_LABELS_2-3-4 contained only label 2, 3 and 4 ).
The user can already add 5,6 on the image (they are not defined yet).

jcohenadad · 2019-11-21T00:23:23Z

ok got it! how about adding 5,6 on the right, to give the user the possibility to correct for them? what are the cons?

Do you mean 2? ( I assumed FILE_WITH_LABELS_2-3-4 contained only label 2, 3 and 4 ).
The user can already add 5,6 on the image (they are not defined yet).

yes i meant 2, sorry

lrouhier · 2019-11-21T00:26:00Z

I don't see any cons to it right now. I'll implement it and report if I find any problem with it.

… label. refactoring to use sct function.

jcohenadad

before starting my review, i would like to clarify the following points that are listed under TODO in the body text of this PR:

Decide what to do when the user fail to enter enough label. example : sct_label_utils -i t2.nii.gz -ilabel labels.nii.gz -create-viewer 1,2 will give an error if labels.nii.gz contains already more than two points. Should we raise an error before or increase the value argument to cover at least the number of existing point ?

I would suggest to increase the value argument to cover at least the number of existing point.

Modify the code to project the existing point onto the mid_saggital plane.

wasn't it implemented in commit efb4b71?

lrouhier · 2019-11-27T19:56:30Z

I will modify the TO DO right now. Both of these are now implemented.

jcohenadad · 2019-11-27T20:50:20Z

scripts/sct_label_utils.py

@@ -725,6 +762,11 @@ def get_parser():
 mandatory=False,
 example="t2_labels_cross.nii.gz",
 default_value="labels.nii.gz")
+ parser.add_option(name="-ilabel",


move this option right below -create-viewer. It will be more intuitive

jcohenadad

looks good!
there is just one thing to change, as it is not intuitive: if the user inputs a file with, let,s say, labels 2,3, and he is asking to label 4,5,6, once the window pops up, if the user clicks on the window, the label 2 will be changed (whereas it is already present). I would indicate in a text, that the user has to manually click on the check box on the left the label he would like to create (in that case, the user would click on 4). The text could be placed right above the labels on the left column.

…only when using the -ilabel option as requested

…b.com/neuropoly/spinalcordtoolbox into lrouhier/sct_utils_guiwexisting_point

jcohenadad

👍

…e-viewer option (#2520) * first commit : Pints are added but are weirdly modified by 90 degree at each opening.WIP * Fixed orientation Issue. Will open PR to discuss option about possible value or error. * correction after first review. All previous point are now saved in the mid_slice (if not modified) * First version to remove the existing but not asked label. Trying to improve on the version. * more elegant solution * Added projection of existing point onto mid sagittal plane. Remove debugging ellemnt previously created * typo and PEP8 * remove empty lines * remove extra lines. * Code modified to show every previous label found as well as asked for label. refactoring to use sct function. * PEP-8 modification * PEP-8 formatting * removing extra line. Modifying help description * formatting * moved the option following review. Added a warning message displayed only when using the -ilabel option as requested Former-commit-id: 646f83f

lurou_admin added 2 commits November 7, 2019 17:08

first commit : Pints are added but are weirdly modified by 90 degree …

26da423

…at each opening.WIP

Fixed orientation Issue. Will open PR to discuss option about possibl…

f149e6a

…e value or error.

lrouhier changed the title ~~(WIP) sct_label_utils : add existing albel in the create-viewer option~~ (WIP) sct_label_utils : add existing label in the create-viewer option Nov 11, 2019

jcohenadad reviewed Nov 11, 2019

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lurou_admin added 6 commits November 11, 2019 13:16

correction after first review. All previous point are now saved in t…

3ee95b7

…he mid_slice (if not modified)

First version to remove the existing but not asked label. Trying to i…

2a9a44b

…mprove on the version.

more elegant solution

80c7024

Added projection of existing point onto mid sagittal plane. Remove de…

efb4b71

…bugging ellemnt previously created

typo and PEP8

0b06d4e

remove empty lines

138f608

jcohenadad reviewed Nov 12, 2019

View reviewed changes

remove extra lines.

8ba2e3c

lrouhier changed the title ~~(WIP) sct_label_utils : add existing label in the create-viewer option~~ sct_label_utils : add existing label in the create-viewer option Nov 20, 2019

lrouhier added 5 commits November 21, 2019 15:22

Code modified to show every previous label found as well as asked for…

77831b7

… label. refactoring to use sct function.

PEP-8 modification

2413344

PEP-8 formatting

ebbbf5a

removing extra line. Modifying help description

c1c71b0

Merge branch 'master' into lrouhier/sct_utils_guiwexisting_point

9d442c8

jcohenadad changed the title ~~sct_label_utils : add existing label in the create-viewer option~~ Now possible to add existing label from an external file in the create-viewer option Nov 26, 2019

jcohenadad added this to the 4.1.1 milestone Nov 26, 2019

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

jcohenadad added 2 commits November 26, 2019 12:59

Merge branch 'master' into lrouhier/sct_utils_guiwexisting_point

f3f2ac5

Merge branch 'master' into lrouhier/sct_utils_guiwexisting_point

957fc2a

lrouhier requested a review from jcohenadad November 27, 2019 14:28

formatting

8e55f7d

jcohenadad reviewed Nov 27, 2019

View reviewed changes

jcohenadad requested changes Nov 27, 2019

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lrouhier added 3 commits November 28, 2019 11:50

moved the option following review. Added a warning message displayed …

73b4414

…only when using the -ilabel option as requested

Merge branch 'lrouhier/sct_utils_guiwexisting_point' of https://githu…

91ca091

…b.com/neuropoly/spinalcordtoolbox into lrouhier/sct_utils_guiwexisting_point

Merge branch 'master' into lrouhier/sct_utils_guiwexisting_point

ed77585

jcohenadad approved these changes Nov 28, 2019

View reviewed changes

jcohenadad merged commit 646f83f into master Nov 28, 2019

jcohenadad deleted the lrouhier/sct_utils_guiwexisting_point branch November 28, 2019 19:47

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Now possible to add existing label from an external file in the create-viewer option #2520

Now possible to add existing label from an external file in the create-viewer option #2520

lrouhier commented Nov 11, 2019 •

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Now possible to add existing label from an external file in the create-viewer option #2520

Now possible to add existing label from an external file in the create-viewer option #2520

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