dcbia-ortholab / shapevariationanalyzer Goto Github PK

Dear SVA Team,

My name is Shoaib Attar and I am a new user of the software SlicerSALT (4.0.1). I have been trying to input a set of groomed femurs (n=4) to create a PCA chart. But I keep getting an error. I am attaching a screenshot of the error. I am confused about what could be the mistake in this case. Can you please help me solve this problem?

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Please do let me know if I should send you the vtk files of the groomed femurs. I am trying to make a comparison between the PCA results of SlicerSALT and Shapeworks software. This particular dataset did work with shapeworks software but it keeps giving me an error in slicerSALT.

I am looking forward to hearing back from you soon.

with regards,
Shoaib Attar

When the button "process and export csv" is pressed in the PCA tab, the layout of slicer automatically changes to "four-up quantitative" and it should be "standard quantitative" so the 3D view can be seen.

Hello.
The module ShapeVariationAnalyzer is not working/being launched in the Slicer 4.11.0-2020-07-18! (Windows 10)
Maybe the figure bellow can help to solve this.
*Ps: I remember that I could use this module for the last time before the slicer change from python 2 to python3.

@jcfr @bpaniagua @luciacev

https://www.slicer.org/wiki/Documentation/4.10/Modules/ShapeVariationAnalyzer

Also, please add SALT grant number and update github repo.

ShapeVariationAnalyzer does not work under Slicer 5.2.1

[Qt] Switch to module:  "shapepcalib"
[Qt] Warning, there is no UI for the module "shapepcalib"

Currently points to https://github.com/pdedumast/ShapeVariationAnalyzer.

@jcfr @allemangD @bpaniagua

Hi

ShapeVariationAnalyzer is not working/cannot find module after installing SlicerCMF. Thanks!

Could you associate the 3d-slicer-extension GitHub topic so that it is listed here: https://github.com/topics/3d-slicer-extension

To learn more about topic, read https://help.github.com/en/articles/about-topics

@pdedumast To avoid confusion, could you delete your project pdedumast/ShapeVariationAnalyzer and re-fork the one hosted in the DCBIA-OrthoLab organization. See https://github.com/DCBIA-OrthoLab/ShapeVariationAnalyzer

The fork graph currently shows this:

@ClementMirabel, @ninatubau, @juanprietob (for NIRALUser) : After @pdedumast is done, you may have to do the same.

Thanks 🙏

The reading logic should be improved so that successful loading of a csv file does not depend on the current working directory.

Instead the function pcaExplorer.readCSVFile( should be updated to resolve relative path based on the location of the csv file.

Once this is implement, use of the following context manager should not be needed:

Similar to what is needed at DCBIA-OrthoLab/MFSDA_Python#26

Slicer recently upgraded from Python 3.6.7 to Python 3.9.10 in Slicer/Slicer@34e48e8. There are now observed build errors of the ShapeVariationAnalyzer Slicer extension as seen at https://slicer.cdash.org/viewBuildError.php?buildid=2618477. This is because the python requirements file in the repo is including hashes that are only for Python 3.6 wheels. These need to be updated for Python 3.9 wheels which also means the actual version of packages here will need to be updated as some older versions simply don't have Python 3.9 wheels because that version was released before Python 3.9 was even released. For example scikit-learn==0.23.1 does not have Python 3.9 wheels available from PyPI (see here).

Hello, I have added ShapeVariationAnalyzer as an extension but I cannot see it as a module. I have downloaded Slicer 5.2.2.. Please help.

We are getting ready to integrate this module in SlicerSALT,
Please Integrate changes ref: #31 #30 in @lopezmt repository (https://github.com/lopezmt/ShapeVariationAnalyzer) into this repo.

@juanprietob

Hi @lopezmt @juanprietob

I installed manually sklearn and scipy for the SVA extension downloaded from the extension manager in Ubuntu 16.04. The extension fails to install some python libraries.

Here is the message:
Traceback (most recent call last):
File "", line 1, in
File "/home/bpaniagua/.config/NA-MIC/Extensions-27534/ShapeVariationAnalyzer/lib/Slicer-4.11/qt-scripted-modules/ShapeVariationAnalyzer.py", line 24, in
import shapepcalib as shapca

Could you please look into that?
Thanks,
Bea

sklearn is not packaged with Slicer. This causes ShapeVariationAnalyzer to fail to load.

We should separate the PCA calculation / mean calculation etc and shape learning/classification into two different modules / CLIs

@vicory @juanprietob Mateo Lopez

The PCA sliders seem to be doing something weird with an example dataset. I am using intercranial shapes from the CONTE dataset for which I have already QC'ed for a different experiment (regression).
PC1 correctly captures the size change in the dataset, but when exploring that principal direction, the shape deforms in an impossible way.

See animation below.

Following the integration of commit 976e22c (ENH: Add Export tab) adding test_ShapeVariationAnalyzer, the file hippo.csv. is referenced as input but missing.

@juanprietob Do you happen to know how to generate or look up that specific file ? Or hints on how to update the test using a different input. 🙏

cc: @jamesfishbaugh