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Home Page: https://afm-spm.github.io/topostats-training
License: Other
TopoStats Training Material
Home Page: https://afm-spm.github.io/topostats-training
License: Other
Process images, gather dataset, get commands, make a few slides, and test myself.
We require a sample dataset for this tutorial so that there is a standard set of images for users to process as they work through the different stages.
I realised whilst working on #11 that we probably don't want to copy over the files and directory structure used in the Unix Shell Software Carpentry and would be better served to have a set of AFM images in a hierarchical structure which we can use to demonstrate directory structure and navigation in the Command Line sections and how TopoStats scans for images across the base_dir
and how that in turn influences the structure of output.
For this I feel we need more than just minicircles.spm
that is used in the TopoStats test suite.
It would also be worthwhile including an image that doesn't process so that we can demonstrate what happens when this arises and how to handle such cases.
If anyone has images that are not under Non-Disclosure Agreements and is able to share them please provide links in reply to this issue (or email me the Google Drive link, no need to send the image).
Assumed knowledge of Atomic Force Microscopy and the steps involved in processing images such as...
Basic familiarity with computers is required but no familiarity with the Command Line Interface, or Conda environments is required, this is the content covered by the course. Python programming is not required as we are teaching users how to use TopoStats. Learning how to use the individual stages (as in existing notebooks) actually requires some Python basics and will, hopefully, be covered in future material that is developed.
After undertaking the course attendees should have an understanding of and be able to perform the following.
pwd
/ cd
)ls
)cp
/ mv
).We would like to use some of the Software Carpentries | UNIX Shell material as a basis for teaching the basics of the command line.
Sections we want to have covered, not necessarily in as much detail...
Need to make sure attribution is clearly given to comply with Creative Commons License under which the material is licensed.
Develop an explanation of the configuration file and what the options are, what they could be and how to edit them.
We would like to use some of the Conda environments for effective and reproducible research material as a basis for teaching the basics of the command line.
Sections we want to have covered, not necessarily in as much detail...
pip
and Conda
--from-history
to limit what is captured.environment.yaml
Need to make sure attribution is clearly given to comply with Creative Commons License under which the material is licensed.
In addition to the documentation @SylviaWhittle has been developing a TopoStats User Guide which will need further bulking out with examples and explanations showing the impact of settings much in the vein already being used which shows the effects of...
Much of this material can then be incorporated into this website for teaching and the TopoStats Documentation so we have examples available on a public facing website.
Further to #9, both Linux and OSX are bundled with terminals/shells (Bash) that will work with the training material. It is better to try and preempt the problems that may arise from variation, to which end the Setup instructions need augmenting.
M$-Win however has a crude command-prompt with its own language.
In order to make life simpler and have one set of instructions that work across all operating systems we will have to include instructions for Windows users to install Git for Windows which includes a Bash shell. We can use the section described in the Software Carpentry : Unix Shell - Summary & Setup for Windows which links to Windows instructions.
We may wish to also link to instructions for Bash under OSX (see the OSX tab) as the default is ZSH (which will likely work, I use ZSH all the time under GNU/Linux and the instructions work).
Bash is the default on Linux, but users may use something else (personally I use ZSH, there is KSH, FISH and more). We should to link to instructions for Bash under Linux (see the Linux tab).
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