gianthk / ciclope Goto Github PK

add material mapping to example 01

WARNING: Discarding https://files.pythonhosted.org/packages/93/4b/979db9e44be09f71e85c9c8cfc42f258adfb7d93ce01deed2788b2948919/logging-0.4.9.6.tar.gz#sha256=26f6b50773f085042d301085bd1bf5d9f3735704db9f37c1ce6d8b85c38f2417 (from https://pypi.org/simple/logging/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
ERROR: Could not find a version that satisfies the requirement logging (from ciclope) (from versions: 0.4.9.6)
ERROR: No maching distribution found for logging

Hello @gianthk
I have a few comments/suggestions about the current version of the paper:

• Line 20: is the package limited to isotropic linear elasticity? If not, please describe what other material models are available.

indeed, 'Linear elastic' in this sentence is ambiguous since it refers only to the first cited study. We have removed 'Linear elastic' leaving the introduction sentence more general. In the examples section (line XX) we have mentioned that the package can be also used for non-linear plastic simulations.

• Lines 32-54 describing the pipeline elements: the first two (image preprocessing and meshing) is in the same paragraph and the third is in a new paragraph. Please make it consistent. Also, please add a description for FE model solution and results postprocessing as well.
• Line 35: what is Otsu's method? I don't see it mentioned in the reference (Walt 2014).

ref to the method for automatic image thresholding (Otsu 1979) added. Walt 2014 is the ref to scikit-image where an algorithm for Otsu's thresholding method is contained.

• Line 36: should be "clusters of voxels"
• Please add the references related to the LHDL project as regular references in the list, and not only as links.
• Line 71: The word "Project" after (LHDL) can be deleted.
• Kine 73: should be "a partner of this project".
• Line 74: the hyphen in linear-elastic can be removed.
• Line 75: what about the Poisson ratio? can it also be calculated?
• What other examples are included besides the described main application?

we have modified the last sentence of the examples section: "Ciclope can be applied to microCT scans other than trabecular bone and in fields other than biomechanics. A simulation of a mechanical test of a whole human teeth, and a non-linear analysis of metal foam plasticity are illustrated in the software examples."

• Please check all the cited software, packages, and repositories if they have citable publications other than the web address.

In ciclope_ex05.1_beamFE-skel.ipynb

When running the ciclope_ex02_tetrauFE_CalculiX example, the error message "TypeError: 'CellBlock' object is not subscriptable" appears. The error message occurs when trying to create the CalculiX FE input file.

Many of the examples reference tiff image stacks that are not available in the test_data folder.

move append call: sys.path.append('~/Applications/ParaView-5.9.0-RC1-MPI-Linux-Python3.8-64bit/lib/python3.8/site-packages') away from ciclope.utils.postprocessing

• rerun all using ciclope==1.3.0
• title all NBs
• correct NB example links to readme file

ciclope.tetraFE.cgal_mesh stuck when running through jupyter

Please add guidelines for external contributors.

• upload small dataset for unit tests
• verify on new installation
• describe test procedure in readme
• describe test procedure in readthedocs
• preprocess.remove_unconnected
• voxelFE.vol2ugrid
• voxelFE.mesh2voxelfe
• tetraFE.shell_mesh
• tetraFE.cgal_mesh
• tetraFE.mesh2tetrafe

CO-AUTHORS reviews:

• enrico
• fulvia
• martino
• new release (pypi an github)

As per JOSS requirements, please add the statement of need to your documentation webpage.

I'm working on the joss review and I'm having some installation difficulties with pip and "optional" dependencies.

1. using pip install ciclope[all] gives me the error no matches found: ciclope[all]. I haven't used options on a pip install before, so I'm not sure what this should look like.
2. There are a bunch of dependencies that are needed beyond what's installed by default. However, ciclope -h can't run without them, so I presume they are not optional. They are dxchange, scipy, scikit-image, pypng
3. pycgal required lots of manual intervention to get things linking and building. Nothing you can do about this, but it certainly makes the installation harder.

As I mentioned in the JOSS review thread, you need to add statements about using data from animals/humans:
https://joss.readthedocs.io/en/latest/policies.html?highlight=animal#joss-policies