TWO .stl file alignment and measurement

muratmaga · April 21, 2021, 3:37pm

There is the screen capture of the resultant alignment run through Model to Model distance:

There is no tutorial, since there is not much to the module. You specify the reference model from which the distances will be calculated (fixed in this case) and then the target and choose to create a new model file as output. I slightly modified the visualization so anything within -1 to 1mm range is rendered green.

muratmaga · April 21, 2021, 3:39pm

Depending on the question, you may skip the deformable registration. Rigid will only rotate and translate the mesh. Whereas deformable will non-linearly deform the mesh to match the others. Whether you need deformable or not depends on what you want to measure.

manjula · April 21, 2021, 3:44pm

I learned via this tutorial,

manjula · April 21, 2021, 3:46pm

thank you for testing. Yes i managed to get the same with your settings. i was not using the settings properly as I was confused with the tooltips. Many thanks for the help.

seanchoi0519 · April 21, 2021, 4:31pm

Thank you. Some great points here.
If you wouldn’t mind, I had a couple follow-up questions.

Is it possible for me to modify the -1 to 1mm threshold? For example I would like to be a little more precise, down to maybe within -0.3 to 0.3mm range.
Is it possible for me to see the difference of the “inside” of the model? I’ve tried reducing the opacity however it doesn’t seem to do much. For example, I have 2 tooth models - one of them has a hollow cavity preparation (it has been drilled), while the other has not. The model to model distance allows me to see the outside surface, however, I would like to see the distance INSIDE of the tooth as well if possible. Please see attached for reference.
Screen Shot 2021-04-22 at 2.25.57 AM1426×1686 365 KB

Screen Shot 2021-04-22 at 2.26.14 AM1192×1428 276 KB

seanchoi0519 · April 21, 2021, 4:33pm

Thanks manjula. Everything is fine with model-to-model distance, but somehow when I load the vtk file for shape population viewer, I get a weird result and am thinking I must be doing something wrong. Would you be able to have a look

seanchoi0519 · April 21, 2021, 4:37pm

Ok I see. Thank you. I should be able to get away with just the rigid function!

muratmaga · April 21, 2021, 4:47pm

I am not familiar with population shape viewer module. Instead I used the Models module’s Scalar Tab, after running the Model to Model Distance. There you can modify what values to be displayed by playing around with the Scalar Range Mode, and the Displayed Range settings.

manjula · April 22, 2021, 10:01am

@seanchoi0519

@muratmaga Thank you for the help with ALPACA and as you can see I am now able to get good results.

seanchoi0519 · April 23, 2021, 2:38pm

Thanks a lot for all your help

seanchoi0519 · April 23, 2021, 2:41pm

Hello Arthur. This would be a great change as it would simplify the alignment process drastically.
Would you guys have any plans to work on this?

I am trying to see if I can create a UI where I can simply drag and drop two .ply models (without the need for landmark transfer) and get the alignment done in a single step.

Any input would be appreciated.

muratmaga · April 23, 2021, 3:05pm

Because ALPACA as a module is currently being reviewed in a paper, we are unlikely to make a change like that interim. Most likely that interactive alignment of meshes would be a separate module.

seanchoi0519 · April 23, 2021, 3:12pm

I see thank you. I’m so glad I ran into ALPACA, it really works like magic.
In the meanwhile, as my research project is due this coming July, would you guys mind if I attempt to make progress myself?

Any direction & pointers as to how I can achieve it would be appreciated. I’m looking to

Replace the file selectors by node selectors (ex. drag & drop 3D models)
Remove the need for .fcsv file

I have some basic programming knowledge so I am not sure if I can achieve it, but as Andras has mentioned, it is likely a trivial change so I hope I will be able to make some progress.

Thank you in advance

muratmaga · April 23, 2021, 3:13pm

Source code of alpaca is here: SlicerMorph/ALPACA.py at master · SlicerMorph/SlicerMorph · GitHub

@smrolfe and @agporto can help with your questions.

seanchoi0519 · April 23, 2021, 3:30pm

Thank you. I had a read through the code and it seems like I may have to modify

io.read_point_cloud function to another function that will take the node as the input instead of file path. Please correct me if I’m wrong.

Would also love to implement a drag & drop function somehow!

@smrolfe @agporto can’t thank you enough - any advice would be appreciated

pieper · April 23, 2021, 4:22pm

This is great @seanchoi0519, thanks for jumping in

Here’s an example of how the drag-and-drop works in python. If you search through the code for the qt methods it uses you’ll see how this integrates with other ways drops are handled.

github.com

Slicer/Slicer/blob/0094e9a35bd266cc8b0e677858dabce797c9928f/Modules/Scripted/DICOM/DICOM.py#L504


      if not slicer.util.confirmYesNoDisplay("Import of files that have special (non-ASCII) characters in their names is not supported."
          " It is recommended to move files into a different folder and retry. Try to import from current location anyway?"):
        self.directoriesToAdd = []
        return


    slicer.util.selectModule('DICOM')
    slicer.modules.DICOMInstance.browserWidget.dicomBrowser.importDirectories(self.directoriesToAdd)
    self.directoriesToAdd = []




class DICOMLoadingByDragAndDropEventFilter(qt.QWidget):
  """This event filter is used for overriding drag-and-drop behavior while
  the DICOM module is active. To simplify DICOM import, while DICOM module is active
  then files or folders that are drag-and-dropped to the application window
  are always interpreted as DICOM data.
  """


  def eventFilter(self, object, event):
    """
    Custom event filter for Slicer Main Window.

agporto · April 23, 2021, 6:12pm

Hi Sean,
A while ago, I started working on a module for pointcloud registration that I didn’t have time to finish. Perhaps that would be a good starting point (and I can help you a bit in updating it).
It can be found at :

github.com

agporto/PointCloud-Registration/blob/main/PointCloudRegistration.py

##BASE PYTHON
import os
import unittest
import logging
import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
from slicer.util import VTKObservationMixin
import glob
import copy
import multiprocessing
import vtk.util.numpy_support as vtk_np
import numpy as np

#
# PointCloudRegistration
#

class PointCloudRegistration(ScriptedLoadableModule):
  """Uses ScriptedLoadableModule base class, available at:
    https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py

This file has been truncated. show original

With regard to the io.read_point_cloud function, you can load a model from the scene with something like this:
m = getNode(“Segment_1”)
p = arrayFromModelPoints(m)
cloud = o3d.geometry.PointCloud()
cloud.points = o3d.utility.Vector3dVector(p)
Anyway, if you want to start working on this, I can either give you access to the repo or you can create a branch and I can make some commits to it.

seanchoi0519 · April 29, 2021, 3:26pm

Hello,

Thank you all for the feedbacks. I’ve spent some time to digest the code from the scripts this past week - however, I will admit that as a dental student with only basic coding background, it has not been easy creating modifications.

By any chance, would any of you be interested in developing & creating extensions to the ALPACA with some funding? I do have some grants available that I can apply for from my university - and if it means accelerating the timeline of this project & improving the quality of the final product, I am happy to look into this. The funding amount varies from $500-$1000 USD.

Here are some of the functionalities that I’m looking for:

Enable drag-and-drop feature (something similar to attached pic)
Upon drag-and-drop and alignment, highlight areas for correction - (for ex. red = needs to be trimmed down, blue = must be added). I think this is possible via shape population viewer already - would be nice to integrate this with ALPACA.
General UI simplification (ex. remove unnecessary toolbar items). I was thinking slicelet could be appropriate for this?
Bonus: provide a score (%) based on total difference. The less, the better.

Any feedbacks & interest would be appreciated.
If this project is successful, it is sure to make a difference in the dental field.

Sean

@smrolfe @agporto @muratmaga @pieper

lassoan · April 30, 2021, 3:53am

Can you tell a bit more about this application? How the colored overlay display helps the dentist?
Do you see potential further improvements, additional features that could be useful?

The amount of funding that you mentioned to develop this might be sufficient for a software developer/engineering student looking for a summer project. If you cannot find a suitable student then you could contact one of the Slicer commercial partners but probably they would ask for about one magnitude more funding to get started on a new project. There seem to be many dental applications of Slicer, so it could also make sense to coordinate with others in the community who are in this field and see if you can find some good common topics to work on and join forces to find funding and developers together.

seanchoi0519 · June 20, 2021, 1:45pm

Upon research it looks like it may be beneficial to create a custom slicelet with the drag-and-drop function + ALPACA function. Could someone please confirm?

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TWO .stl file alignment and measurement

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