[PRE REVIEW]: Dark-field X-ray microscopy visualization

[editorialbot]

Submitting author: !--author-handle-->@trygvrad<!--end-author-handle-- (Trygve Magnus Ræder) Repository: https://github.com/trygvrad/DF-XRM_viz Branch with paper.md (empty if default branch): Version: 2.0.0 Editor: !--editor-->@jgostick<!--end-editor-- Reviewers: @taw10, @marcocamma Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/efcbe012af763b5599dbd68b0913a7a0"><img src="https://joss.theoj.org/papers/efcbe012af763b5599dbd68b0913a7a0/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/efcbe012af763b5599dbd68b0913a7a0/status.svg)](https://joss.theoj.org/papers/efcbe012af763b5599dbd68b0913a7a0)

Author instructions

Thanks for submitting your paper to JOSS @trygvrad. Currently, there isn't a JOSS editor assigned to your paper.

@trygvrad if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

[editorialbot]

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

Checking the BibTeX entries failed with the following error:

Lexical or syntactical errors: 

@online{plotly 

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.90 s (15.6 files/s, 425306.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           7            256            783           1859
SVG                              1              0              0            551
Jupyter Notebook                 1              0         378105            174
Markdown                         2             53              0            117
TeX                              1             14              0             98
YAML                             1              1              4             18
Bourne Shell                     1              1              0             11
-------------------------------------------------------------------------------
SUM:                            14            325         378892           2828
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1319

[editorialbot]

:warning: An error happened when generating the pdf.

[Kevin-Mattheus-Moerman]

@openjournals/dev can you see what is wrong here? :point_up: is it due to the æ symbol in the authors last name Ræder?

[danielskatz]

@Kevin-Mattheus-Moerman - clicking on the error, I see "Problem with affiliations for Trygve Ræder, perhaps the affiliations index need quoting? (Theoj::Error)"

[danielskatz]

looking at the raw file, I think the problem is the second line here

- name: Department of Physics, Technical University of Denmark, Denmark
index: 1

needs to be indented

[Kevin-Mattheus-Moerman]

Thanks @danielskatz !!

[Kevin-Mattheus-Moerman]

@trygvrad can you work on fixing this issue :point_up:

[trygvrad]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[trygvrad]

@Kevin-Mattheus-Moerman , Thanks for the quick turnaround on this. Following the comment from @danielskatz the issue seems to be resolved now.

[trygvrad]

A number of people in the list of potential reviewers have experience with X-ray diffraction/scattering. Based on their previous work, I believe marcocamma and taw10 are particularly well suited to reviewing this submission

[Kevin-Mattheus-Moerman]

@trygvrad thanks for fixing that. I am trying to see if this work is in scope for JOSS. It is on the small side and the main function appears to be web app based visualisation. Although visualisation code can be in scope for JOSS, usually it also features analysis, or at least it is clear that the visualisation clearly impacts the science (or its communication) at hand. A good test is the "Would I cite this?" test. Essentially if your work is important for scientific research (a requirement for JOSS) then researchers would feel the need to cite it in their publications. This would be because the software is more than a simple utility tool (not in scope for JOSS) and directly influences the scientific outcomes. I can see that this work is relevant for "online communication", but does it go beyond that such that one would directly use this for research? If you feel this work is more than a utility tool, can you help sketch a clearer picture here (in a comment, and perhaps also in the paper) as to how this work is relevant/useful (directly) to scientific research. If it has used in studies (and perhaps cited) you can refer to such works too. Thanks.

[trygvrad]

Hi @Kevin-Mattheus-Moerman,

Thank you for the quick response. I see your concern, that supporting tools are less commonly published and cited than tools directly involved in data manipulation and analysis, and visualization appears to be a simple operation. In our field there has been a great need for supporting tools, due to the difficulty of relating the directions in real and reciprocal space involved in Bragg diffraction. However, there is, as you say, little tradition for attribution in this kind of work, and therefore less incentive to create, share, or publish.

The precise alignment of the instrument for any given sample is a complicated calculation where the scattering vector (calculated from the X-ray energy, Bragg reflection, and lattice vectors in reciprocal space) determines a fixed axis around which the sample may rotate freely to describe a family of possible alignments with different imaging planes. The mathematical complexity forms the backbone of this application, so that the correct geometrical alignment can be presented in terms of angles of the goniometer. The parameter space of possible alignments is vast, given different possibilities of sample orientation, X-ray energy, Bragg reflection, and imaging plane. This tool allows for the simulation and exploration of this parameter space.

The need to access and visualize the sample-instrument alignment exists both during planning, execution and during analysis. I highlighted the need during planning in the manuscript, because that is where I have seen the greatest gains after the creation of this tool. When collecting data for the experiments in arXiv:2210.08366, one of seven days of experimental time at the X-ray free electron laser was lost due to a miscommunication of the angle of the sample mount. The angle was correct, but attributed to the wrong reference. This type of error has been a recurring theme in our field. The associated loss of scientific output is difficult to quantify, but it appears to be significant, and is addressed with the introduction of this tool.

For ongoing experiments, I have been informed that this tool typically occupies at least one monitor at the ESRF at all times (while DF-XRM experiments are being performed). I believe this results in significantly increased scientific output, although, again, this is difficult to quantify. This use touches a number of publications each year (See https://www.esrf.fr/home/UsersAndScience/Experiments/StructMaterials/id06---hard-x-ray-microscope/publications.html for previous publications from the DF-XRM microscope at ESRF. The microscope is currently being moved to a dedicated, and should operate at double throughput once it re-opens)

In our group we use this tool also to support analysis and teaching. However, I am not privy to how other groups operate, or other educators teach, so I cannot tell if others operate in the same way.

I hope you will find this within your scope, as a tool that "supports the functioning of research instruments or the execution of research experiments". I am confident that this tool has had, and continues to have significant scientific impact. However, as you no doubt are well aware, scientific impact does not always correlate with citations.

[Kevin-Mattheus-Moerman]

@trygvrad thanks for the detailed response. I (we) fully agree scientific impact does not correlate with citations (and some scientists are a bit obsessed with citation metrics). I suppose what I was getting at is that something is clearly research software if it needed to reproduce the results (and if that is the case one would need to mention and cite it). Perhaps "planning tools" should be mentioned/cited more often like you hint at, and they do have scientific impact. I think you've given me enough detail in your comment to sketch the importance to research. The handling editor may still have concerns on scope but I'll now proceed to find a handling editor.

[Kevin-Mattheus-Moerman]

@editorialbot invite @jgostick as editor

[editorialbot]

Invitation to edit this submission sent!

[jgostick]

@editorialbot assign @jgostick as editor

[editorialbot]

Assigned! @jgostick is now the editor

[trygvrad]

@Kevin-Mattheus-Moerman Thank you for passing this on!

[jgostick]

@editorialbot add @taw10 as reviewer

[editorialbot]

@taw10 added to the reviewers list!

[jgostick]

@editorialbot add @marcocamma as reviewer

[editorialbot]

@marcocamma added to the reviewers list!

[jgostick]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5177.