new implementation

[michal367]

New implementation of gamma index including:

• DataReader for reading DICOM RT Dose
• structures for storing and managing 1D, 2D and 3D images
• functions calculating 2D, 2.5D and 3D gamma index
• linear, bilinear and trilinear interpolation
• examples of usage and code documentation

[reviewpad[bot]]

AI-Generated Summary: This pull request introduces a variety of new files and updates for the 'yet Another Gamma Index Tool' project. It includes new source, header, and test files, as well as build and dependency management files. The key additions are the core library files for gamma index calculation (Gamma.cpp, Gamma.hpp, GammaParameters.hpp, and GammaResult.hpp) and associated data structures and utility classes (DoseData.hpp, DoseData.cpp, DataStructs.hpp, ImageData.hpp, ImageData.tpp, Image.hpp, and DataReader.hpp). Test files (test.cpp, test2.cpp, and test3.cpp) are also included for testing purposes. Furthermore, the pull request provides build instructions in the README.md file and related build scripts (bar.bat and CMakeLists.txt), a Conan package manager configuration file (conanfile.txt), and the addition of the GDCM dependency. Note that some files are marked as temporary and that there are recommendations to add newlines at the end of certain files to avoid potential issues.

[reviewpad[bot]]

Thank you @michal367 for this first contribution!

[reviewpad[bot]]

Reviewpad Report

:warning: Warnings

• Please link an issue to the pull request

:bangbang: Errors

• Unconventional commit detected: 'new data reader, data class and classic gamma implementation' (b7cb0404cb2924ba0ee73d6423bdece5fdfb2ea0)
• Unconventional commit detected: 'clean up, add getImageData3D and stats functions in ImageData' (f53f949dccdfc211e2f3c72316629d2bb1934654)
• Unconventional commit detected: 'add linear interpolations' (f87f7531df49206db79f48a28bd3c28e82848e4a)
• Unconventional commit detected: 'add examples and start code documentation' (69573ed09b999b975859a6974c04456e3d34e2ac)
• Unconventional commit detected: 'code documentation' (b27a11e10fadff0883701daaa738d8acf014f916)
• Unconventional commit detected: 'change templated ImageData to float ImageData' (d4025a054bbfde3213ec7a94d4154ed2e5be3d6c)
• Unconventional commit detected: 'remove manual tests' (7bbdb038f923e30685ff62d82b16c5efcf9b43b7)
• Unconventional commit detected: 'review fixes and clean up' (a79721a942404c11a32c8aeb2939b3b9abd2bc5e)
• Unconventional commit detected: 'change license message in source files' (4990609853be4e24e377b0a892ec541c9e2ebff3)
• Unconventional commit detected: 'update test.yml' (e87778972e89ddffe606e8094fc650065cd16125)
• Unconventional commit detected: 'update test.yml 2' (3643a58fa6ad441de75ab1af41093c167a5f3f26)
• Unconventional commit detected: 'change letter case' (3b674097500555215951ad90a4b0c35a952fc41e)
• Unconventional commit detected: 'update test.yml' (74b3b7b182645d0de1d67552d0c9e6b392808c87)
• Unconventional commit detected: 'Merge branch 'master' of https://github.com/DataMedSci/gi-yagit into new-implementation' (cd3f65dd7e6e26194fa0d038db0cc9ad092196e9)
• Unconventional commit detected: 'shorten structs member names' (1f2b33f442c0811a424b3ea023038fa7559ccd65)
• Unconventional commit detected: 'adapt code to c++17 standard' (46642676e1bec7aca5d3df18b657503146c8a38c)
• Unconventional commit detected: 'review fixes' (3a76212c3edd09c746265bf8a1df9ec0c871e3e2)
• Unconventional title detected: 'new implementation' illegal 'n' character in commit message type: col=00

[grzanka]

On clean Linux installation fails:

grzanka@workspace:~/workspace/gi-yagit/build$ cmake ..
CMake Error at /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:146 (message):
  Could NOT find Boost (missing: Boost_INCLUDE_DIR system filesystem
  unit_test_framework)
Call Stack (most recent call first):
  /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:393 (_FPHSA_FAILURE_MESSAGE)
  /usr/share/cmake-3.16/Modules/FindBoost.cmake:2179 (find_package_handle_standard_args)
  gi_core/CMakeLists.txt:26 (find_package)

-- Configuring incomplete, errors occurred!
See also "/data/grzanka/workspace/gi-yagit/build/CMakeFiles/CMakeOutput.log".

[grzanka]

OK, previous comment not valid, I was in a wrong directory. Now trying again:

grzanka@workspace:~/workspace/gi-yagit/new$ mkdir build && cd build
grzanka@workspace:~/workspace/gi-yagit/new/build$ cmake ..
CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
  CMake 3.23.0 or higher is required.  You are running version 3.16.3

-- Configuring incomplete, errors occurred!
grzanka@workspace:~/workspace/gi-yagit/new/build$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 20.04.6 LTS
Release:        20.04
Codename:       focal

[grzanka]

OK, works on newest Ubuntu:

grzanka@grzankax1:~/workspace/gi-yagit/new/build$ ./examples/gammaImage 
Reference image:
[[0.93, 0.95],
 [0.97, 1]]
size: (1, 2, 2)
offset: (0, 0, -1)
spacing: (0, 1, 1)
------------------------------
Evaluated image:
[[0.95, 0.97],
 [1, 1.03]]
size: (1, 2, 2)
offset: (0, -1, 0)
spacing: (0, 1, 1)
------------------------------
Gamma index image:
[[0.816496, 0.333333],
 [0.942809, 0.333333]]
GIPR: 100%
Gamma mean: 0.606493
Gamma min: 0.333333
Gamma max: 0.942809
grzanka@grzankax1:~/workspace/gi-yagit/new/build$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 23.04
Release:        23.04
Codename:       lunar

[reviewpad[bot]]

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