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alishakodibagkar edited this page Nov 30, 2020 · 13 revisions

Week of 10/12/20

Meeting Notes - Troubleshoot C++ Plugin

  • Cmake - make output
  • Normal make - type on
  • Issue - diff version of Qt
  • You need to use version of Qt - whatever compiler ur using needs to be version ur compiling of Qt
    • VScode 2015 \
    • VS2008
    • Mingw
      • Suite of compilers u can download
      • Gcc can compile c++
      • Contains C compilers, fortran compilers etc
      • Trying to use an old version
    • Qt - gui handles
      • It wants old version of Qt
      • Im looking at source of old versions
      • Build it into binary (executable) - it needs
    • Change version number???
    • Build from scratch
    • Gcc 4.4

Notes on Plugin Process - Windows Version

  1. Download Vaa3D for windows
  2. Create a windows virtual environment and
    • python -m venv env
    • source env/bin/active
    • .\env\Scripts\activate
  3. Download Qt 4.7.1
  4. Put file in C:\Users\chsha\OneDrive\Documents\Alisha\Vaa3D\pnr-master\pnr-master\pnr-vaa3d>
  5. Process to Make:
    • C:\Qt\4.7.1\bin\qmake Advantra.pro
    • C:\MinGW\msys\1.0\bin\make
  6. Error
    • Error: WARNING: Failure to find: ........\v3d_external\v3d_main\basic_c_fun\v3d_message.cpp
    • Change: move v3d_external file to right spot
  7. Download make for mingw
  8. Add g++ file path into environment path (C:\MinGW\bin)
  9. Download boost and put it in with the app
    • Download from here https://www.boost.org/users/download/
    • Unzip and keep items in pnr-vaa3d folder
    • ........\v3d_external\v3d_main\basic_c_fun/INeuronAssembler.h:
      • Error: #include <boost/container/flat_map.hpp>
      • Change: #include <../../../Vaa3D/pnr-master/pnr-master/pnr-vaa3d/boost/container/flat_map.hpp>
  10. Error
    • Error: ........\v3d_external\v3d_main\basic_c_fun/IPMain4NeuronAssembler.h
    • Change: #include "v3d_core.h" to #include "../../../../v3d_external/v3d_main/v3d/v3d_core.h"
  11. Error
    • Error: ../../../../v3d_external/v3d_main/basic_c_fun/../v3d/../basic_c_fun/stackutil.h:64:10: fatal error: 'tiffio.h' file not found
    • Change: #include "tiffio.h" becomes #include "../../../../v3d_external/matlab_io_basicdatatype/tiffio.h"
  12. Error
    • Error: ../../../../v3d_external/v3d_main/basic_c_fun/../v3d/../cellseg/../v3d/template_matching_cellseg_dialog.h:49:10: fatal error: 'ui_template_matching_cellseg.h' file not found
    • Current change:
      • Remove these from v3d_main/basic_c_fun/v3d_interface.h
      • ///#include "INeuronAssembler.h"
      • //#include "IPMain4NeuronAssembler.h"
      • Might backfire we shall see
  13. Error
    • g++.exe: error: ........v3d_externalv3d_mainbasic_c_funv3d_message.cpp: No such file or directory, g++.exe: fatal error: no input files
    • Change
      • Tried: In toolbox.cpp, Advantra_plugin.cpp I made #include “v3d_message.h” to #include "../../../../v3d_external/v3d_main/basic_c_fun/v3d_message.h"
      • Error is still occurring
      • Add -IC:---> up to basic c_fun into makefile - still figuring this out

Notes on Jovo's Paper

https://docs.google.com/document/d/1AUItU_9Jz7hPW7nAraoDzFMputQDdXSnx9vnfS5nnFw/edit?usp=sharing

Week of 10/19/20

Notes on 2 Papers

https://docs.google.com/document/d/1zeC4O17UBtYuPDIB4qAXq-xqwEiyc20dzeUC2Qzr3Cc/edit?usp=sharing

Week of 10/26/20

Progress & main challenges with implementing the C++ Vaa3D Plugin from Issue #119: Sequential Monte Carlo Paper

Troubleshooting Progress:

  • Cmake - make output
  • Normal make - type on
  • Issue - diff version of Qt
  • You need to use version of Qt - whatever compiler ur using needs to be version ur compiling of Qt
    • VScode 2015 \
    • VS2008
    • Mingw
      • Suite of compilers u can download
      • Gcc can compile c++
      • Contains C compilers, fortran compilers etc
      • Trying to use an old version
    • Qt - gui handles
      • It wants old version of Qt
      • Im looking at source of old versions
      • Build it into binary (executable) - it needs
    • Change version number???
    • Build from scratch
    • Gcc 4.4

Notes on Plugin Process - Windows Version:

  1. Download Vaa3D for windows
  2. Create a windows virtual environment and
    • python -m venv env
    • source env/bin/active
    • .\env\Scripts\activate
  3. Download Qt 4.7.1
  4. Put file in C:\Users\chsha\OneDrive\Documents\Alisha\Vaa3D\pnr-master\pnr-master\pnr-vaa3d>
  5. Process to Make:
    • C:\Qt\4.7.1\bin\qmake Advantra.pro
    • C:\MinGW\msys\1.0\bin\make
  6. Error
    • Error: WARNING: Failure to find: ........\v3d_external\v3d_main\basic_c_fun\v3d_message.cpp
    • Change: move v3d_external file to right spot
  7. Download make for mingw
  8. Add g++ file path into environment path (C:\MinGW\bin)
  9. Download boost and put it in with the app
    • Download from here https://www.boost.org/users/download/
    • Unzip and keep items in pnr-vaa3d folder
    • ........\v3d_external\v3d_main\basic_c_fun/INeuronAssembler.h:
      • Error: #include <boost/container/flat_map.hpp>
      • Change: #include <../../../Vaa3D/pnr-master/pnr-master/pnr-vaa3d/boost/container/flat_map.hpp>
  10. Error
    • Error: ........\v3d_external\v3d_main\basic_c_fun/IPMain4NeuronAssembler.h
    • Change: #include "v3d_core.h" to #include "../../../../v3d_external/v3d_main/v3d/v3d_core.h"
  11. Error
    • Error: ../../../../v3d_external/v3d_main/basic_c_fun/../v3d/../basic_c_fun/stackutil.h:64:10: fatal error: 'tiffio.h' file not found
    • Change: #include "tiffio.h" becomes #include "../../../../v3d_external/matlab_io_basicdatatype/tiffio.h"
  12. Error
    • Error: ../../../../v3d_external/v3d_main/basic_c_fun/../v3d/../cellseg/../v3d/template_matching_cellseg_dialog.h:49:10: fatal error: 'ui_template_matching_cellseg.h' file not found
    • Current change:
      • Remove these from v3d_main/basic_c_fun/v3d_interface.h
      • ///#include "INeuronAssembler.h"
      • //#include "IPMain4NeuronAssembler.h"
      • Might backfire we shall see
  13. Error
    • g++.exe: error: ........v3d_externalv3d_mainbasic_c_funv3d_message.cpp: No such file or directory, g++.exe: fatal error: no input files
    • Unable to solve this error

Main Challenges + Recommendations:

  • Old version of Qt used - incompatible with mac and may be incompatible with windows
  • Unable to understand and debug errors - unsure where to pinpoint errors in code provided/on Windows system (Note: someone with C++/C++ plugin experience may be able to solve these issues)
  • Providing documentation on build, including versions and common errors, would be helpful when this project is picked up in the future

**Microsoft InnerEye - Setup and Basic HelloWorld segmentation model **

Setup and running HelloWorld: Followed instructions on Microsoft InnerEye README.md and was able to do so without errors/no need for extra documentation

HelloWorld segmentation model: https://docs.google.com/document/d/1BujuQrtGIxCz05jIofPw_jmeiL4jQsGeTjCgiAflFSQ/edit?usp=sharing

AzureML documentation exploration

Microsoft Inner Eye Notes

Important Categories:

  • Setting up your environment - done
  • Training a Hello World segmentation model - done
  • Setting up Azure Machine Learning - work through next week
  • Creating a dataset - work through next week
  • Building models in Azure ML - work through next week
  • Sample Segmentation and Classification tasks - work through next week
  • Debugging and monitoring models - read
  • Model diagnostics - read

Week of 11/02/20

https://docs.google.com/document/d/1tidxbeBUsHunTU2fb_YvUmpchPZr18TX4K23Xecct14/edit?usp=sharing

Week of 11/09/20

Meetings to set up AzureML:

InnerEye Setup process doc:

Lesson 1.1 from Andrew Ng's ML course:

Week of 11/16/20

  1. Azure account screenshot
  2. Notes on online InnerEye event
  3. Notes on meeting with Jacopo
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