Tab names for slice tabs as file names. #2973

maharshi-gor · 2023-11-10T19:43:28Z

Changes

This PR introduces a data field saying file name

The behavior to observe:

On the page a field Filename got added with the file name next to it.

I have updated all the test cases accordingly to take care of file while unpacking the images data.

skoudoro · 2023-11-30T02:34:39Z

What is the status of this PR ? Can you provide a description and some picture (before/after)? I do not understand the title and not sure what this PR is supposed to do/fix.

Thank you in advance for your feedback

maharshi-gor · 2023-11-30T20:50:34Z

Hi @skoudoro ,

I am waiting to test this PR on a Windows machine as the naming strategy relies on splitting the path based on '/'. I do not know how Python is handling the path for Windows. I tested this on a mac and a linux machine works perfectly fine.

I would attach a few screen shots of expectations

maharshi-gor · 2023-12-05T17:42:24Z

dipy/viz/horizon/app.py

@@ -443,7 +442,8 @@ def build_show(self, scene):
            img_count = 0
            synchronize_slices = check_img_shapes(self.images)
            for img in self.images:
-                data, affine = img
+                data, affine, fname = img
+                fname = fname.split("/")[-1]


splitting the file path and extracting the name

Are you sure it works on windows? I will be surprised because they usually use \\. I recommend you to use os.path.basename. You can also look at the Pathlib python module.

maharshi-gor · 2023-12-05T17:43:28Z

dipy/viz/horizon/app.py

@@ -460,19 +460,17 @@ def build_show(self, scene):
                            world_coords=self.world_coords,
                            percentiles=[0, 100])
                        self.__tabs.append(SlicesTab(
-                            slices_viz, slice_id=img_count + 1,
-                            force_render=self._show_force_render))


Removed id parameter which only was providing count to present in the slice tab.

codecov · 2023-12-05T18:53:36Z

Codecov Report

Attention: Patch coverage is 92.18750% with 5 lines in your changes are missing coverage. Please review.

Project coverage is 82.43%. Comparing base (529a3fd) to head (32fe9a1).
Report is 5 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2973      +/-   ##
==========================================
+ Coverage   82.34%   82.43%   +0.08%     
==========================================
  Files         146      146              
  Lines       20664    20707      +43     
  Branches     3328     3334       +6     
==========================================
+ Hits        17015    17069      +54     
+ Misses       2817     2805      -12     
- Partials      832      833       +1

Files	Coverage Δ
dipy/testing/decorators.py	`77.55% <100.00%> (+0.95%)`	⬆️
dipy/viz/horizon/app.py	`47.16% <100.00%> (+1.61%)`	⬆️
dipy/viz/horizon/util.py	`98.18% <100.00%> (+0.50%)`	⬆️
dipy/workflows/viz.py	`85.32% <100.00%> (ø)`
dipy/viz/horizon/tab/base.py	`75.25% <95.23%> (+4.23%)`	⬆️
dipy/viz/horizon/tab/slice.py	`51.42% <77.77%> (+2.18%)`	⬆️

... and 1 file with indirect coverage changes

skoudoro

Thanks @maharshi-gor,

See below some comments to fix before I try on my latptop.

Can you also confirm that this work only at the startup. if we resize the window, it does not refresh the filename, right ?

skoudoro · 2023-12-06T17:19:49Z

dipy/viz/horizon/app.py

@@ -443,7 +442,8 @@ def build_show(self, scene):
            img_count = 0
            synchronize_slices = check_img_shapes(self.images)
            for img in self.images:
-                data, affine = img
+                data, affine, fname = img
+                fname = fname.split("/")[-1]


Are you sure it works on windows? I will be surprised because they usually use \\. I recommend you to use os.path.basename. You can also look at the Pathlib python module.

skoudoro · 2023-12-06T17:25:05Z

dipy/viz/horizon/util.py

+    string
+        File name with the extension in it.
+    """
+    if extension[0] != '.':


if not extension.startswith('.') instead

skoudoro · 2023-12-06T17:42:51Z

dipy/viz/horizon/tab/base.py

+            )
+
+    def _handle_title_overflow(self, title_text, title_block):
+        tab_text = remove_extension(title_text, 'nii')


Not sure you need a function for that....

tab_text = title_text.split('.', 1)[0] should just be enough.....

in pathlib module, you also have suffixes()

dipy/viz/horizon/tab/base.py

skoudoro · 2023-12-06T17:46:45Z

dipy/viz/horizon/app.py

-                for act in actors:
-                    scene.rm(act)
-                    scene.add(act)
+            def get_size(actor):


Why did you add this function? where do you use it ?

maharshi-gor · 2023-12-07T18:20:50Z

Thanks @maharshi-gor,

See below some comments to fix before I try on my latptop.

Can you also confirm that this work only at the startup. if we resize the window, it does not refresh the filename, right ?

The resize window will required more changes. The current PR only targets the startup.

maharshi-gor · 2023-12-07T18:44:08Z

Hello @skoudoro , I have resolved all the mentioned comments and also added a few test cases for the util file.

Thank you, for the thorough review!

commit 2170d22 Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Tue Feb 20 10:40:45 2024 -0500 scene removed from tab manager commit 337bc2f Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Wed Jan 31 10:53:01 2024 -0500 test case fix commit 4ee6416 Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Tue Jan 30 15:39:07 2024 -0500 file name working commit 64aa0c2 Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Tue Jan 30 11:46:02 2024 -0500 ellipsis test added commit 99821ad Merge: 1167146 7e1d10a Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Tue Jan 30 11:40:56 2024 -0500 Merge branch 'master' into feature/tab-names commit 1167146 Merge: eb501db cf636e7 Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Mon Jan 29 14:05:37 2024 -0500 Merge branch 'feature/tab-names' of github.com:maharshi-gor/dipy into feature/tab-names commit cf636e7 Author: maharshigor <gor.maharshi@gmail.com> Date: Tue Dec 12 15:16:29 2023 -0500 changes for horizon code case commit 225a207 Merge: a3b1b42 b825c14 Author: maharshigor <gor.maharshi@gmail.com> Date: Tue Dec 12 14:24:01 2023 -0500 Merge remote-tracking branch 'upstream/master' into feature/tab-names commit a3b1b42 Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Thu Dec 7 13:42:22 2023 -0500 comments fixed and util test cases added commit 063bcb8 Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Tue Dec 5 12:28:56 2023 -0500 Fix all test cases commit 9fe236d Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Thu Nov 30 16:39:53 2023 -0500 test cases fixed commit 68da7d2 Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Thu Nov 16 14:15:38 2023 -0500 windows test left commit fd49628 Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Fri Nov 10 14:20:05 2023 -0500 changes for tab names commit e8ffcbf Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Fri Nov 10 13:02:44 2023 -0500 tab names fixed commit eb501db Merge: 2fca5f0 1419292 Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Fri Dec 8 17:20:49 2023 -0500 Merge branch 'master' into feature/tab-names commit 2fca5f0 Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Thu Dec 7 13:42:22 2023 -0500 comments fixed and util test cases added commit 208d892 Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Tue Dec 5 12:28:56 2023 -0500 Fix all test cases commit 5361104 Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Thu Nov 30 16:39:53 2023 -0500 test cases fixed commit 898c106 Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Thu Nov 16 14:15:38 2023 -0500 windows test left commit 07218a6 Merge: 269a459 f92f595 Author: Maharshi <39947025+maharshi-gor@users.noreply.github.com> Date: Sat Nov 11 10:41:26 2023 -0500 Merge branch 'master' into feature/tab-names commit 269a459 Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Wed Nov 8 14:17:37 2023 -0500 bugfix for --force issue commit c929fac Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Tue Nov 7 16:22:53 2023 -0500 opacity and slider toggle fixed commit 41afb35 Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Fri Nov 10 14:20:05 2023 -0500 changes for tab names commit e831925 Author: Maharshi Gor <gor.maharshi@gmail.com> Date: Fri Nov 10 13:02:44 2023 -0500 tab names fixed

skoudoro

Hi @maharshi-gor,

Can you merge master on this PR or rebase to fix the conflicts.

is it normal to have 3 dots (ellipsis) at the beginning of the filename ? it is weird, see below the weird filename:

EDIT: the name should be mni_icbm152_t1_tal_nlin_asym_09c.nii

skoudoro

ok, all good, thanks @maharshi-gor!

merging

skoudoro added the type:Enhancement label Nov 30, 2023

maharshi-gor changed the title ~~Feature/tab names~~ Tab names for slice tabs as file names. Dec 5, 2023

maharshi-gor requested review from skoudoro and guaje December 5, 2023 17:41

maharshi-gor self-assigned this Dec 5, 2023

maharshi-gor commented Dec 5, 2023

View reviewed changes

skoudoro reviewed Dec 6, 2023

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skoudoro force-pushed the master branch from dc5f269 to c4bbb40 Compare December 7, 2023 16:05

maharshi-gor added the category:visualization everything related to viz label Dec 7, 2023

maharshi-gor requested a review from skoudoro December 7, 2023 18:44

skoudoro force-pushed the master branch 6 times, most recently from 1419292 to ca6268a Compare December 8, 2023 22:25

maharshi-gor force-pushed the feature/tab-names branch from 865646e to a3b1b42 Compare December 12, 2023 18:33

skoudoro force-pushed the master branch 3 times, most recently from 5935e1e to 765963e Compare January 24, 2024 19:24

maharshi-gor force-pushed the feature/tab-names branch from 2170d22 to f03dfd7 Compare March 1, 2024 22:03

skoudoro requested changes Mar 4, 2024

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maharshi-gor added 3 commits March 4, 2024 10:36

Merge branch 'master' into feature/tab-names

526acdc

size increased

6acd47e

ellipse mac issue

32fe9a1

skoudoro mentioned this pull request Mar 4, 2024

[UPCOMING] Release preparation for 1.9.0 #3095

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skoudoro merged commit e0cd7db into dipy:master Mar 5, 2024
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Tab names for slice tabs as file names. #2973

Tab names for slice tabs as file names. #2973

maharshi-gor commented Nov 10, 2023 •

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Tab names for slice tabs as file names. #2973

Tab names for slice tabs as file names. #2973

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maharshi-gor commented Nov 10, 2023 • edited

Changes

The behavior to observe:

skoudoro commented Nov 30, 2023

maharshi-gor commented Nov 30, 2023

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