Pivot calibration is now implemented in scikit-surgerycalibration

In GitLab by @mianahmad on Mar 27, 2019, 18:37

Merges 1-command-line-app-to-do-callibration -> master

I am requesting for merge in case you want to play with it while I am away.

In GitLab by @mianahmad on Jul 4, 2019, 11:43

Merges 27-documentation-update -> master

Closes #27

I have tested the commands in Mac and Windows. I believe it should work always if the tox complete successfully on the machine. Please merge the changes.

In GitLab by @StephenThompson on Jun 26, 2019, 15:55

3 mm grid is too small for webcams. Better yet include some code for chessboard generation

In GitLab by @StephenThompson on Jun 19, 2019, 16:26

Essential: return -s command line option. It looks to me like the object points have a 1 mm spacing. Which is going to give us bad calibration in most cases.

Nice: It would be nice to have some verbose out put, and some writing out out of annotated images, so we can have a discussion of what's going on.

In GitLab by @StephenThompson on Jul 4, 2019, 15:30

Mac Mojave 10.14.5 macbook pro.
One of our students had one of these. The tracked pointer markers (spheres) do not overlay with the visible image. I do not understand how this could be.

In GitLab by @StephenThompson on Jun 19, 2019, 13:23

In GitLab by @mianahmad on Jul 9, 2019, 11:39

Merges PySide2-version-update -> master

PySide version details changed. Both VTK and Bard has the same versions now.
--Close issue

In GitLab by @MattClarkson on Mar 21, 2019, 14:05

Using opencv-python, this should be a case of implementing a fairly standard grabber.

• See basic functionality in the main BARD user instructions.
• Example python functionality is here. The original C++ code is split over more files, and relies on OpenCV and key bindings. Its probably easier to write a pure python grabber, like I linked to.

Less than 1 days work (hopefully).

In GitLab by @mianahmad on Jul 3, 2019, 10:45

Considering the variable familiarity of students with virtualenv, I think it may be simpler to activate the virtual environment created by tox instead of creating a virtual environment before hand.

This page is in referenced.

In GitLab by @StephenThompson on Jun 25, 2019, 16:31

In GitLab by @StephenThompson on Jul 2, 2019, 15:13

In GitLab by @StephenThompson on Jun 19, 2019, 17:09

i.e. replicate
bard -w ~/build/BARD/Data/ref.txt -i ~/build/BARD/Data/intrinsics.txt -x 1280 -y 720 -p ~/build/BARD/Data/pointer.txt -r -d ~/BARD

In GitLab by @StephenThompson on Jun 27, 2019, 15:14

In GitLab by @StephenThompson on Jul 2, 2019, 12:46

In GitLab by @MattClarkson on Mar 21, 2019, 14:14

In line with current standards... probably best to update the Word doc instructions to Sphinx docs.

• Original BARD instructions are here
• Re-write the manual, testing each bit of code as you go.

In GitLab by @StephenThompson on Mar 11, 2020, 15:49

These could be set in configuration. Buttons, foot pedal, speech?

In GitLab by @MattClarkson on Mar 21, 2019, 14:12

This will require a bit of coordination amoungst all SNAPPY libraries

• Load config from .json file using scikit-surgerycore ConfigurationManager, like SmartLiver does.
• Load VTK models using scikit-surgeryvtk SurfaceModel, like SmartLiver
• Load camera calibration data using standard numpy functions, (use command line parameter, load text file).
• Read Video from webcam using standard opencv-python (from Tom's base class)
• Use overlay widget from scikit-surgeryvtk (from Tom's base class)
• You'll need a GUI program. Look at scikit-surgeryutils for examples.

Then ASK about:

• Save standard models of Aruco tags, and just pre-load them at startup
• Update transformations using scikit-surgerycore TransformationManager
• Load any necessary fiducial points, using standard numpy functions, at startup
• In the main program loop: extract aruco points, compute registrations, update position of tools, compute position of overlay, render.

About 3 to 4 days work I guess, if all the other bits are done in other libraries.

In GitLab by @StephenThompson on Jul 3, 2019, 15:13

In GitLab by @mianahmad on May 1, 2019, 15:11

Merges 6-tidy-ups-with-Matt -> master

@MattClarkson
It would be convenient for me if you merge this branch and then I write the preliminary documentation for usage. During this update entry points are changed and default values are provided.

In GitLab by @StephenThompson on Jul 2, 2019, 15:35

In GitLab by @mianahmad on May 7, 2019, 14:39

Merges 7-make-pivot-calib-unit-test-actually-test-the-result -> master

Closes #7

In GitLab by @StephenThompson on Mar 18, 2020, 11:53

In GitLab by @MattClarkson on Mar 21, 2019, 13:48

Write simple demo app to do video camera calibration

• See this example in C++, here
• Create command line app bard_camera_calibration.py in top level folder
• Create sksurgerybard/ui/bard_camera_calibration_command_line.py
• Create sksurgerybard/ui/bard_camera_calibration_command_app.py
• Use existing app as examples on how to run a command line app, i.e. see code in sksurgerybard commmand line app.
• Add correct line to setup.py
• Convert above mentioned C++ to Python, putting most code in bard_camera_calibration_command_app.py

Hopefully, now you are up to speed, about 1 or 2 days work.

@StephenThompson is familiar with all this, so can provide guidance.

In GitLab by @mianahmad on Jun 11, 2019, 14:23

Merges 7-make-pivot-calib-unit-test-actually-test-the-result-2 -> master

Closes #7

In GitLab by @StephenThompson on Jun 27, 2019, 15:13

setting -o seemed to have no effect

In GitLab by @StephenThompson on Jun 19, 2019, 17:18

At the moment it outputs 7 number without explanation of what they are. It would be more friendly to say what they are and to output a point_tip.txt which can then be put straight into bard.
Could we bring in in matplotlib to visualise point spread?

In GitLab by @mianahmad on Jul 3, 2019, 09:59

I found a bug in the package which is noticed on some computers. When we run

python sksurgerybard.py --config config/reference_only.json

We get the following error.

import cv2.aruco as aruco ModuleNotFoundError: No module named 'cv2.aruco'

This doesn't work properly when we have many targets

In GitLab by @StephenThompson on Jul 2, 2019, 15:12

In GitLab by @StephenThompson on Jun 19, 2019, 17:07

How are we going to support things like this ?
bard -w ~/build/BARD/Data/ref.txt -i ~/build/BARD/Data/intrinsics.txt -x 1280 -y 720
I'm inclined to just use config files?
Also need to update the app so that the above will run OK.

In GitLab by @StephenThompson on Jun 19, 2019, 13:23

Currently this is a bit of a hack that relies on the order in which actors are added

In GitLab by @MattClarkson on Apr 30, 2019, 16:11

• Fix output directory name to be not hard coded
• run_demo should return pivot point
• unit test should assert the right value
• add scikit-surgerycore as dependency in requirements.txt and rebuild .tox folder.
• remove pivot calibration code duplication

In GitLab by @StephenThompson on Jun 19, 2019, 17:19

bard -w ~/build/BARD/Data/ref.txt -i ~/build/BARD/Data/intrinsics.txt -x 1280 -y 720 -p ~/build/BARD/Data/pointer.txt -t -d ~/BARD

should output tip positions so we can do proscrustes. It would be nice if we had some user interface to make grabbing the points easier.

In GitLab by @mianahmad on Jul 3, 2019, 10:26

Merges 25-modulenotfound-cv2_aruco -> master

Closes #25

I think its better to merge the branch because I believe long time ago you mentioned that opencv-python and opencv-contrib-python have overlapping packages.

I noticed that modulenotfound cv2.aruco goes away if we get rid of opencv-python and keep opencv-contrib-python

In GitLab by @mianahmad on Jul 3, 2019, 10:29

I noticed in the class that it was easy to modify input e.g. camera source from 0 to 1 via json file. It will also keep the symmetry of BARD app to get input --config flag and specifying a json file.

In GitLab by @StephenThompson on Mar 18, 2020, 11:54

In GitLab by @StephenThompson on Mar 18, 2020, 11:53

In GitLab by @StephenThompson on Jun 19, 2019, 09:27

When I start the main overlay app, the overlay is wrong until I manually resize the window. Once I've done that everything lines up nicely.

In GitLab by @StephenThompson on Jun 19, 2019, 17:21

We need this.

In GitLab by @MattClarkson on Mar 21, 2019, 13:54

Most pivot calibration code (maths etc) is in scikit-surgerycore. This task is to create a command line app, so we can run it from this project.

Write simple command line app to do pivot calibration.

• See this file for the entry point
• See this file for the maths in C++, which you are now familiar with.
• Create command line app bard_pivot_calibration.py in top level folder
• Create sksurgerybard/ui/bard_pivot_calibration_command_line.py
• Create sksurgerybard/ui/bard_pivot_calibration_command_app.py
• Use existing app as examples on how to run a command line app, i.e. see code in sksurgerybard commmand line app.
• Add correct line to setup.py
• Convert above mentioned C++ to Python, putting most code in bard_pivot_calibration_command_app.py

Hopefully, now you are up to speed, less than 1 days work.

@StephenThompson is familiar with all this, so can provide guidance.

In GitLab by @MattClarkson on Apr 30, 2019, 16:06

• Rename top level python scripts, shorter names.
• Rename name in setup.py
• Update setup.py - "scikit-surgerybard is a Basic Augmented Reality Demo (BARD) based on scikit-surgery (SNAPPY).
• Update setup.py URL to BARD URL
• Update setup.py install_requires should match requirements.txt
• Update README.rst
• Go through all command line apps. Check for description strings, and default values.
• Swap all print statements for six.print_
• In camera calib - decide if you want windows, and make code consistent.

In GitLab by @StephenThompson on Jul 3, 2019, 22:41

There's some sort of mirroring going on. To get the fiducial registration working I had to flip the CT model and fiducuals around the xy plane.

In GitLab by @mianahmad on Jul 8, 2019, 14:23

Merges 26-bardCameraCalibration-input-via-json -> master

Closes #26

This branch modifies calibration process so that it takes input via a configuration file.
The following command (1) will be replaced by command (2) to do the calibration.

(1)
python bardCameraCalibration.py  --xcorners 14 --ycorners 10 --size 24 -i <output_dir> --verbose

(2)
python3 bardCameraCalibration.py --config config/calibration_input.json

I also updated the respective test cases and documentation related to the above change.