Zach Mor Journal

Activity: learn about relevant CV processes that ParaView operates (slicing, threshold, tinting, cropping, higher level methods), discuss what you cant do in ParaView

Deliverable: Guide about importing, transforming, processing, exporting VTK files, for example, I will attempt to blur the rat heart vessel.

[editted and fleshed out here]

2/6: hours: 2

- read about ultrasound imaging: 2d, 3d reconstruction from sound
- read about nrrd, .stl, .dcm, .sx file format: to do, add description to wiki contrasting experiences

2/9: hours: 1

- explored researchers at that may have sound data to be visualized
- ultrasound and fast particle movement were some research interests I discovered

2/13: hours: 3

- Research into 3d computer vision
- drafted project plan

2/19: hours: 5

- Browsed a bunch of different 3d scene datasets
- researched RGB d file type, along with polygonal meshes
- researching python packages to interface with VTK files

2/21: hours: 4

- met with Chris about his research
- researched xray imaging, reconstruction
- imported the Rat Heart Vessel into Python

2/23: hours: 3

- finished processing
  - segmented into four parallel slices
  - added space between them
  - concatenated to an inverted copy

2/25: hours: 1.5

- exported file as a vtu... thought it would be .vtk
- failed to visualize on my laptop
- trouble shooting different ways around the problem
- added information on wiki about rgbd data

3/3: hours: 1.5

- learned more about vtu file
- still unsure about increase in size
- scaled down to 30% and actually rendered!

3/4: hours: 2

- reading more about vtk low level and high level libraries
  - the vtk documentation is AWFUL
- read a paper related to my project
  - https://conference.scipy.org/proceedings/scipy2015/pdfs/cory_quammen.pdf
- done with the vtu for now
- started new process file (material for another guide)
  - goal: normalize and add normalized array to file

3/11: hours: 8

- began publishing guides in collaboratory

3/28: hours: 6

- worked on geometry guide
  - explored visualization libraries mat plot lib and plotly
  - explored the creation of volumes like trivariate normal distributions

3/29: hours: 5

- finished geometry guide
  - settled on data example
  - redrafted instructions

3/30: hours: 4

- finished geometry guide
- began intravalue guide
  - examples and operations

3/31: hours: 2

- finished intravalue guide
  - intro, conclusion
  - descriptions
  - redrafted to passive voice

PROJECT 2 PLAN

JOURNAL EVALUATION

relevance - 4, beginning was for a a project I'm no longer doing
documented - 2, been keeping personal messy records, though I ought to edit them and publish on wiki
noted time - 5
pacing - 4, missing a week; caught up with plan/use of python to implement range of densities

4/1: hours: 1000000000

- finished project 2
- April fools

4/2: hours: 7

- Got familiar with Cristoph's dataset (add link here)
- read about different similar data formats
  - 360º scans vs Tilt series
- read about how tilt series are collected
- penetrating waves

4/3: hours: 3

- learn about computed tomography
  - sinograms
  - inverse radon transform

4/4: hours: 4

- researched techniques for accomplishing computed tomography (CT)
  - fourier transforms
  - back projection
  - algebraic reconstruction technique
  - had missing pieces to aid accuracy: flat and dark field images, used to reduce sensor noise

4/7: hours: 7

- tried making my own reconstruction algo
  - this was a waste of time. there are labs dedicated to researching how to do this effectively. I should have known to use a module from the beginning

4/10: hours: 2

- researched different libraries
  - decided on TomoPy

4/12: hours: 4

- had to install with conda
  - researched what conda is/ what its for
- downloaded
- had lots of problems getting it set up
- wouldnt find the packages which were reportedly dowloaded
- messed up path variable most probably

4/13 hours: 5

- kept finicking with system settings, researching problems
- somehow got it to run but i guess without fixing the problem
  - it worked once then i had the same problem not being able to import packages

4/14 hours: 5

- succesfully imported data into python
- full res
- discovered ffmpeg
  - command line tool used to convert video to frames

4/16 hours: 3

- preprocessing
  - why -log(data)
  - how does finding the rotation center work
    - minimize entropy between frames
  - segfault error when algorithmically finding the center so i had to estimate

4/20: hours: 8

- reconstruction attempts
- troubleshooting to increase accuracy (reconstructions were 100% noise)
  - different preprocessing schemes
  - looked into source code for tomopy methods
  - other ways to find the center????

4/25: hours: 8

- stuck :(
- decided it wont work with tomopy
- tried doing their tomopy tutorial but it wouldnt work either
  - dxchange, tooth data set
- perhaps my computer is not set up properly

5/1: hours: 7

- tomopy guide
  - ported to colab notebooks but realized its incompatible as far as Conda environments

5/3: hours: 2

- write-ups for all the libraries I used and how they can help a python dev trying to work with visualizing data

5/5: hours: 2

- redrafted most of my documentation

5/10: hours: 10

- played with tomviz
  - lots of crashing, weird bugs, such as reportedly using 125GB of my RAM (i have 16)
  - misaligned axis meant having to recompute the pipeline multiple times
  - it worked in the end!!!!!

5/11: hours: 2

- tomviz activity guide

5/14: hours: 6

- tomviz software page
- python page
- tomopy tutorial
- tomopy software page

Zach Project Evaluation by David 02/07/20

:-( no project plan

Giuse Project Evaluation 2/8/20

None