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Bone app #269

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shekhardw
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[FEA] Bone Segmentation App #198

First version of CT bone segmentation algorithm.

@shekhardw shekhardw added the enhancement New feature or request label Feb 23, 2022
Signed-off-by: Shekhar Dwivedi <shekhard@nvidia.com>
Signed-off-by: Shekhar Dwivedi <shekhard@nvidia.com>
Signed-off-by: Shekhar Dwivedi <shekhard@nvidia.com>
Signed-off-by: Shekhar Dwivedi <shekhard@nvidia.com>
Signed-off-by: Shekhar Dwivedi <shekhard@nvidia.com>
@MMelQin MMelQin linked an issue Feb 23, 2022 that may be closed by this pull request
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MMelQin commented Feb 23, 2022

Please run auto style fixes: ./run check --autofix

BTW, expanding the details of the build/test to see the failures, and also check the version of the checkers (a few) are the same in dev env; it happened to me that the out of sync versions caused me to do quite a number of commits to correct the styling complaints.

@MMelQin MMelQin requested a review from vikashg February 23, 2022 08:52
Signed-off-by: Shekhar Dwivedi <shekhard@nvidia.com>
Signed-off-by: Shekhar Dwivedi <shekhard@nvidia.com>
Signed-off-by: Shekhar Dwivedi <shekhard@nvidia.com>
Signed-off-by: Shekhar Dwivedi <shekhard@nvidia.com>
Signed-off-by: Shekhar Dwivedi <shekhard@nvidia.com>
@vikashg
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vikashg commented Feb 28, 2022

Hi @shekhardw. So, I see that you are using [clcat] (https://pypi.org/project/clcat/). Initially I had no idea about clcat so good to see that there is a clara toolkit. So, I tried installing once

gupta@DIGI1036734:/data/Vikash/Tools/monai_deploy_new/monai-deploy-app-sdk/examples/apps/ct_bone_seg_app$ pip install clcat
Collecting clcat
  Downloading clcat-0.0.3-cp38-cp38-manylinux1_x86_64.whl (196 kB)
     |████████████████████████████████| 196 kB 88 kB/s 
Collecting patchelf
  Downloading patchelf-0.14.5.0-py2.py3-none-manylinux_2_5_x86_64.manylinux1_x86_64.musllinux_1_1_x86_64.whl (326 kB)
     |████████████████████████████████| 326 kB 102 kB/s 
Installing collected packages: patchelf, clcat
Successfully installed clcat-0.0.3 patchelf-0.14.5.0
gupta@DIGI1036734:/data/Vikash/Tools/monai_deploy_new/monai-deploy-app-sdk/examples/apps/ct_bone_seg_app$ ls

However, when I tried to install the same inside a conda environment, I cannot install it

ERROR: Could not find a version that satisfies the requirement clcat (from versions: none)
ERROR: No matching distribution found for clcat
(base) gupta@DIGI1036734:/data/Vikash/Tools/monai_deploy_new/monai-deploy-app-sdk/examples/apps/ct_bone_seg_app$ 

Can you please look into this.
In addition, I was wondering if the bone segmentation app should also be something like the spleen segmentation app.
Another question are the bone segmentation model embeded in clcat ?

@shekhardw
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Hi @vikashg,

Bone segmentation is based on classic computer vision techniques. So the app will be different. I will be preparing some additional documentation and sample datasets to test.
I will look into conda environment install failure.
"clcat" may see a name change and more details are coming around the toolkit in next few days.

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vikashg commented Mar 2, 2022

@shekhardw Sounds good. If the clcat can be installed I can proceed with further testing. Let me know if you need more information to track down that error.

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Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 1 Code Smell

No Coverage information No Coverage information
0.0% 0.0% Duplication

@vikashg
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vikashg commented Oct 4, 2022

@shekhardw Do we have any updates on this? Specifically clcat ?

@shekhardw
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@vikashg This work is on hold due to other high priority items. @rahul-imaging can share his thoughts.

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MMelQin commented Apr 6, 2023

With all indications this PR would not be finalized. Closing it now.

@MMelQin MMelQin closed this Apr 6, 2023
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[FEA] Bone Segmentation App
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