vais-ral / ccpi-quantification Goto Github PK

Rewrite the python interface currently written in SWIG with boost python.

Create a docker testing container.

Accessible Volume code doesn't deal with exceptions raised by ITK. This should be properly handled inside the code.

• directory structure
• core / wrappers

Each CIL repository (public or private) is organized in subdirectories as follows:

project_name/ 
            CMake/ 
            CMakeLists.txt 
            License.txt 
            Core/ 
            recipes/ 
            Wrappers/ 
                     Python/ 
                     Avizo/  
                     Paraview/  
                     Tomviz/

Disable the nexus reader hdf5 logs.

modify cmake code to build with 7

Replace innosetup with nsis as nsis is better supported with cmake

Documentation

1. Add a section on how to add a new algorithm to the core CCPi toolbox – developer guide
   a. Development environment
   b. Library dependency
   c. Compilation environment
   d. Integration guide
   i. How to integrate the new code with Avizo
   ii. How to integrate the new code with Paraview
   iii. How to integrate the new code with ImageJ
2. Add a section on architecture of CCPi toolbox
3. How to compile CCPi Toolbox into a standalone library
4. Add a main program to the core toolbox to give a command line option
5. Add description of algorithms for
   a. 3D quantification
   b. Particle tracking
   c. Accessible volume
   d. Simple threshold

Building cil_quantification fails on missing tbb/atomic.h
Can be reproduced by conda build recipes/library -c conda-forge
The following is output:

from /home/jenkins/conda-bld/cil_quantification_1548851566206/work/build/Core/QuanWorker.cpp:27:
/home/jenkins/conda-bld/cil_quantification_1548851566206
/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl
acehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/
include/vtk-8.1/vtkAtomic.h:28:24: 
fatal error: tbb/atomic.h: No such file or directory  #include <tbb/atomic.h>

Full failed build at https://anvil.softeng-support.ac.uk/jenkins/job/CILsingle/job/CCPi-Quantification/3/console

Create a conda recipe

Nexus reader for paraview

When Label Quantification module is selected on a label volume it comes up with a VTK exception of no input and crashes avizo

Nexus reader crashes with the axis index type is other than int.

Attempting to load the entry1/tomo_entry/data/rotation_angle variable from this file (https://github.com/DiamondLightSource/Savu/blob/master/test_data/data/24737_fd.nxs) either causes Paraview to crash with a memory allocation error:

ERROR: In /var/pvw/pv/ParaView-SC17-5.5-EGL/src/VTK/Common/Core/vtkGenericDataArray.txx, line 394
vtkDoubleArray (0x6b7d5b0): Unable to allocate 816489068736 elements of size 8 bytes.

or reports that it can't read the data:

HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:
#000: /var/pvw/pv/ParaView-SC17-5.5-EGL/src/VTK/ThirdParty/hdf5/vtkhdf5/src/H5Dio.c line 173 in vtk__H5Dread(): can't read data
major: Dataset
minor: Read failed
#1: /var/pvw/pv/ParaView-SC17-5.5-EGL/src/VTK/ThirdParty/hdf5/vtkhdf5/src/H5Dio.c line 437 in vtk__H5D__read(): no output buffer
major: Invalid arguments to routine
minor: Bad value

This file is being used as a test file for the CCPiReconstruction Paraview plugin and it needs to read in the variable in question.

Get sample data and create test cases for algorithms

Nexus reader for imagej with option to select subset of the data.

CMake for Avizo.
Add ImageJ to the root build.

Avizo plugin windows installer shows up a wrong message.

Change the python wrappers to cython