Fix roi_info saving in project and save #241

Czaki · 2021-04-14T14:23:17Z

This PR adds saving whole ROInfo in history, removes duplicated roi information from ProjectInfo (it is stored inside roi_info parameter.

…nfo_save

codecov · 2021-04-14T14:32:23Z

Codecov Report

Merging #241 (bcc9998) into develop (8200e6e) will increase coverage by 0.24%.
The diff coverage is 88.16%.

@@             Coverage Diff             @@
##           develop     #241      +/-   ##
===========================================
+ Coverage    67.69%   67.94%   +0.24%     
===========================================
  Files          139      139              
  Lines        16739    16750      +11     
===========================================
+ Hits         11332    11380      +48     
+ Misses        5407     5370      -37

Impacted Files	Coverage Δ
package/PartSeg/_roi_mask/batch_proceed.py	`45.45% <0.00%> (ø)`
package/PartSeg/plugins/itk_snap_save/__init__.py	`0.00% <0.00%> (ø)`
...artSeg/plugins/modeling_save/save_modeling_data.py	`0.00% <0.00%> (ø)`
package/PartSeg/plugins/old_partseg/old_partseg.py	`0.00% <0.00%> (ø)`
package/PartSeg/_roi_analysis/main_window.py	`55.51% <40.00%> (+0.41%)`	⬆️
...ackage/PartSegCore/napari_plugins/save_mask_roi.py	`56.25% <50.00%> (+2.91%)`	⬆️
package/PartSegCore/mask_create.py	`95.45% <80.00%> (+0.49%)`	⬆️
package/PartSeg/_roi_mask/stack_settings.py	`81.41% <82.92%> (-3.85%)`	⬇️
package/PartSeg/_roi_analysis/partseg_settings.py	`92.04% <88.00%> (-0.82%)`	⬇️
package/PartSegCore/mask/io_functions.py	`84.98% <91.30%> (-0.58%)`	⬇️
... and 22 more

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lgtm-com · 2021-04-14T14:52:32Z

This pull request fixes 1 alert when merging 153cdf3 into 8200e6e - view on LGTM.com

fixed alerts:

1 for Unused local variable

lgtm-com · 2021-04-14T18:36:54Z

This pull request fixes 1 alert when merging 54f0f4a into 8200e6e - view on LGTM.com

fixed alerts:

1 for Unused local variable

lgtm-com · 2021-04-14T18:47:41Z

This pull request fixes 1 alert when merging a3c0f7b into 8200e6e - view on LGTM.com

fixed alerts:

1 for Unused local variable

lgtm-com · 2021-04-15T01:12:13Z

This pull request fixes 1 alert when merging 9c7ee45 into 8200e6e - view on LGTM.com

fixed alerts:

1 for Unused local variable

lgtm-com · 2021-04-15T10:22:06Z

This pull request fixes 1 alert when merging ba6c67d into 8200e6e - view on LGTM.com

fixed alerts:

1 for Unused local variable

lgtm-com · 2021-04-15T22:09:21Z

This pull request introduces 1 alert and fixes 1 when merging 993dcc9 into 8200e6e - view on LGTM.com

new alerts:

1 for Module is imported with 'import' and 'import from'

fixed alerts:

1 for Unused local variable

lgtm-com · 2021-04-15T22:22:32Z

This pull request introduces 1 alert and fixes 1 when merging a2e53c8 into 8200e6e - view on LGTM.com

new alerts:

1 for Module is imported with 'import' and 'import from'

fixed alerts:

1 for Unused local variable

sourcery-ai · 2021-04-15T22:49:44Z

Sourcery Code Quality Report

❌ Merging this PR will decrease code quality in the affected files by 0.07%.

Quality metrics	Before	After	Change
Complexity	4.26 ⭐	4.11 ⭐	-0.15 👍
Method Length	53.32 ⭐	54.23 ⭐	0.91 👎
Working memory	10.23 😞	10.31 😞	0.08 👎
Quality	65.64% 🙂	65.57% 🙂	-0.07% 👎

Other metrics	Before	After	Change
Lines	8960	9222	262

Changed files	Quality Before	Quality After	Quality Change
package/PartSeg/_roi_analysis/main_window.py	57.49% 🙂	57.45% 🙂	-0.04% 👎
package/PartSeg/_roi_analysis/partseg_settings.py	72.24% 🙂	72.46% 🙂	0.22% 👍
package/PartSeg/_roi_mask/batch_proceed.py	47.40% 😞	47.40% 😞	0.00%
package/PartSeg/_roi_mask/main_window.py	60.49% 🙂	60.49% 🙂	0.00%
package/PartSeg/_roi_mask/stack_settings.py	53.72% 🙂	58.43% 🙂	4.71% 👍
package/PartSeg/common_backend/base_settings.py	85.10% ⭐	85.10% ⭐	0.00%
package/PartSeg/plugins/itk_snap_save/init.py	95.25% ⭐	95.25% ⭐	0.00%
package/PartSeg/plugins/modeling_save/save_modeling_data.py	55.67% 🙂	55.50% 🙂	-0.17% 👎
package/PartSeg/plugins/old_partseg/old_partseg.py	42.31% 😞	42.23% 😞	-0.08% 👎
package/PartSegCore/io_utils.py	81.72% ⭐	82.28% ⭐	0.56% 👍
package/PartSegCore/json_hooks.py	62.56% 🙂	61.96% 🙂	-0.60% 👎
package/PartSegCore/mask_create.py	54.68% 🙂	54.10% 🙂	-0.58% 👎
package/PartSegCore/project_info.py	98.95% ⭐	82.53% ⭐	-16.42% 👎
package/PartSegCore/roi_info.py	76.73% ⭐	74.89% 🙂	-1.84% 👎
package/PartSegCore/analysis/calculate_pipeline.py	74.23% 🙂	74.18% 🙂	-0.05% 👎
package/PartSegCore/analysis/io_utils.py	91.55% ⭐	92.72% ⭐	1.17% 👍
package/PartSegCore/analysis/load_functions.py	66.59% 🙂	64.54% 🙂	-2.05% 👎
package/PartSegCore/analysis/save_functions.py	51.85% 🙂	50.65% 🙂	-1.20% 👎
package/PartSegCore/analysis/batch_processing/batch_backend.py	62.29% 🙂	62.30% 🙂	0.01% 👍
package/PartSegCore/mask/history_utils.py	80.57% ⭐	80.57% ⭐	0.00%
package/PartSegCore/mask/io_functions.py	51.85% 🙂	50.36% 🙂	-1.49% 👎
package/PartSegCore/napari_plugins/load_mask_project.py	84.69% ⭐	84.69% ⭐	0.00%
package/PartSegCore/napari_plugins/loader.py	57.58% 🙂	57.31% 🙂	-0.27% 👎
package/PartSegCore/napari_plugins/save_mask_roi.py	67.08% 🙂	66.77% 🙂	-0.31% 👎
package/PartSegCore/segmentation/algorithm_base.py	85.84% ⭐	86.02% ⭐	0.18% 👍
package/PartSegCore/segmentation/restartable_segmentation_algorithms.py	65.33% 🙂	65.33% 🙂	0.00%
package/PartSegCore/segmentation/segmentation_algorithm.py	75.41% ⭐	75.41% ⭐	0.00%
package/tests/conftest.py	71.63% 🙂	71.52% 🙂	-0.11% 👎
package/tests/test_PartSeg/test_settings.py	75.80% ⭐	74.59% 🙂	-1.21% 👎
package/tests/test_PartSeg/test_viewer.py	65.37% 🙂	65.35% 🙂	-0.02% 👎
package/tests/test_PartSegCore/test_io.py	65.19% 🙂	64.47% 🙂	-0.72% 👎
package/tests/test_PartSegCore/test_json_hooks.py	70.52% 🙂	72.09% 🙂	1.57% 👍
package/tests/test_PartSegCore/test_pipeline.py	64.95% 🙂	64.83% 🙂	-0.12% 👎
package/tests/test_PartSegCore/test_segmentation.py	68.43% 🙂	68.43% 🙂	0.00%
package/tests/test_PartSegCore/segmentation/test_algorithm_base.py	66.44% 🙂	66.44% 🙂	0.00%

Here are some functions in these files that still need a tune-up:

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
package/PartSeg/_roi_mask/batch_proceed.py	BatchProceed.run_calculation	25 😞	311 ⛔	19 ⛔	20.08% ⛔	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions
package/PartSegCore/analysis/batch_processing/batch_backend.py	CalculationProcess.do_calculation.FileData.add_data_part	26 😞	248 ⛔	22 ⛔	20.27% ⛔	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions
package/PartSegCore/mask/io_functions.py	save_stack_segmentation	20 😞	437 ⛔	19 ⛔	21.13% ⛔	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions
pack AE91 age/PartSegCore/segmentation/restartable_segmentation_algorithms.py	ThresholdBaseAlgorithm.calculation_run	22 😞	402 ⛔	16 ⛔	22.76% ⛔	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions
package/PartSegCore/analysis/load_functions.py	load_project	18 🙂	368 ⛔	19 ⛔	23.49% ⛔	Try splitting into smaller methods. Extract out complex expressions

Legend and Explanation

The emojis denote the absolute quality of the code:

⭐ excellent
🙂 good
😞 poor
⛔ very poor

The 👍 and 👎 indicate whether the quality has improved or gotten worse with this pull request.

Please see our documentation here for details on how these metrics are calculated.

We are actively working on this report - lots more documentation and extra metrics to come!

Let us know what you think of it by mentioning @sourcery-ai in a comment.

lgtm-com · 2021-04-15T22:55:43Z

This pull request fixes 1 alert when merging bcc9998 into 8200e6e - view on LGTM.com

fixed alerts:

1 for Unused local variable

Czaki added 4 commits April 12, 2021 23:41

fix roi_info setting when use set_project_info in analysis

5b2e1f7

Merge remote-tracking branch 'origin/develop' into bugix/additional_i…

79880be

…nfo_save

fix names

5cea4bc

make roi deprecated in ProjectInfo classes

05af28b

fix notebook, ad changelog

153cdf3

Czaki added 3 commits April 14, 2021 17:01

fix deepsource warnings

d9f8b3a

save annotations and alternatives in project. part 1

54f0f4a

fix deepsource

a3c0f7b

add test for roi set

9c7ee45

Czaki added 3 commits April 15, 2021 12:01

add few base settings tests

42731de

add test for dump numpy 8000 types

ba6c67d

json hooks tests

506513f

Czaki added 3 commits April 15, 2021 14:29

add HistoryElement tests

1f4c73c

add test for saving and load history

2bf4d18

fix deepsource warnings

993dcc9

fix lgtm warning

a2e53c8

fix lgtm warning 2

bcc9998

Czaki changed the title ~~Fix roi_info setting when use set_project_info in analysis~~ Fix roi_info saving in project and save Apr 16, 2021

Czaki merged commit 96c3b66 into develop Apr 16, 2021

Czaki deleted the bugix/additional_info_save branch April 16, 2021 07:15

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Fix roi_info saving in project and save #241

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