自分の学術雑誌への投稿論文原稿に対して，１名の審査員からは「そのまま出版するので良いと思う」て意見だったのだけれど，おそらく審査員も兼ねている編集者から 18 箇所の修正要求（示唆）があり，10 箇所は受け入れたけれど，8箇所は修正要求を拒絶しました。
自分の論文投稿の経験の中でも総量の多い方で，公開すれば学術雑誌に投稿しようとする人に参考になるかと思うので，公開することにします。クレームが来れば，すぐに削除します。
Nov 29, 2024 Response to the Editor’s comments
Comment #1. I suggest a change in title to read: “Deconvolution treatment about the sample transparency aberration effect on the peak position when interfered by opaque and translucent sample holders in Bragg-Bretano geometry.
Response to comment #1: (0Yes/1No)
Original title is “Deconvolutional treatment about sample transparency aberration interfered by opaque and translucent sample holders in Bragg-Brentano geometry”.
Firstly, the “deconvolutional treatment” defined by the author is definitely different from the deconvolution, in mathematical and computer-technological senses. Secondly, sample transparency aberration does not only affect the peak position, but also affect the peak profile. The author has not changed the title in the revised manuscript.
Comment #2-a. I. Introduction
(very minor). Figure1 on right side the diagram for the strip-type X-ray detector has “grey” lines parallel with the goniometer axis. Do these lines represent the detector decoding the position of an incident photon along the length of the line? To me I would have thought that the lines would be perpendicular to the goniometer axis.
Response to comment #2-a: (0Yes/2No)
The author is sure that each of the “X-ray detector strips” has a shape elongated along the parallel direction and arranged along the perpendicular direction to the goniometer axis.
The reason why the author is sure may be that the author was working on spectroscopy of ultra-visible (UV), visible (VIS), and near infrared (NIR) light, when he was young.
The design commonly used for Bragg-Brentano diffractometers is similar to the design commonly used for Czerny-Turner spectrometers the author was partly working on. The combination of a knife-edge slit and zero-dimensional photosensor used in the Czerny-Turner spectrometers had rapidly been replaced by “PIN photodiode array” in 1990’s, while the similar replacement started in late 2000’s in the field of powder X-ray diffraction.
Some old “X-ray crystallographers” may be confused, because they know there existed “position sensitive detectors”, in the field of X-ray detection technology.
The one-dimensional position-sensitive detectors have a shape elongated perpendicular to the goniometer axis. They have two electrodes to detect the photocurrents at the edges of the rod-shape detector, and the position of the detected X-ray was determined by the difference of the photocurrents detected by the two electrodes.
In contrast, a “semiconductor detector strip” does not have “position sensitivity” at all, in a sense, but it can be used, as if it were a position sensitive detector, because the modern semiconductor technology makes it possible that all the electronic circuits for amplification, filtering, comparation, counting of electric signal pulses, and so on, be settled within the average width of 0.1 mm.
Comment #2-b Line 2 below Figure 1 caption: “X-ray” likely should be plural, i.e. “X-rays”
Response to comment #2-b: (0Yes/3No)
The author could find some “spectroscopic profile of source X-ray” with internet search engines, but no “spectroscopic profile of source X-rays”. The author has not changed “X-ray” to “X-rays” in the revised manuscript.
Comment #2-c Line 4. Suggest to read: “….it is not purely an instrumental ……”
Response to comment #2-c: (1Yes/3No)
The author agrees with the suggestion to change the expression “…it is not purely instrumental ……”. The author has changed to “…it is not a purely instrumental ……” in the revised manuscript.
Comment #2-d Line 9. Suggest it read (changes bold): “important information for phase identification, quantitative analysis…..”
Response to comment #2-d: (1Yes/4No)
Peak locations are important for identification, qualitative analysis, and precise estimation of lattice parameters. Precise lattice parameters may be used for quantitative analysis of solid solutions, based on the Vegard’s law, but the diffraction intensities are rather important for quantitative phase analysis (QPA).
The suggested modification has not been applied in the revised manuscript.
Comment #2-e Line 10. Suggest it read (changes bold): Asymmetric peak profiles lead to challenges in determining peak locations.
Response to comment #2-e: (1Yes/5No)
Asymmetric peak profile leads ambiguity of peak location as written in the original manuscript. Average peak location, peak-top location, and median peak location are different in asymmetric peak profile, while they are coincided in symmetric monomodal peak profile.
The author has not changed the expression suggested in comment #2-e in the revised manuscript.
Comment #2-f Lines 14-16. Suggest this read: “In principle, application of FPA method will automatically correct the peak shift and asymmetric deformation of the peak profile.”
Response to comment #2-f: (2Yes/5No)
The expression has been changed to
“In principle, application of FPA method will automatically correct the peak shift and asymmetric deformation of the peak profile.”
in the revised manuscript.
Comment #3-a. Section II. Theoretical
Paragraph 2. line 1 likely should read: “There are 5 cases (see Figure 2) for the formulation of the sample transparency aberration, …..”
Response to comment #3-a: (3Yes/5No)
The expression has been changed to
“There are 5 cases (a), (b), (c), (c’), and (d) (see Figure 2) for the formulation of the sample transparency aberration, when an opaque sample holder is used.”
in the revised manuscript.
Comment #4-a. caption for Figure 6
I see just 3 vertical lines, not 4 as implied by “cases (a), (b), (c), and (d).
Response to comment #4-a: (3Yes/6No)
It is written in the caption of Figure 6,
“Vertical lines indicate the locations of the boundaries between the cases (a), (b), (c), and (d), for an opaque sample holder.”
There are four cases, and the boundaries are three.
Figure 6 and the caption of Figure 6 have not been changed in the revised manuscript.
The author expects that the most impressive part of this manuscript to the readers (or viewers) would be Figure 2. It includes five illustrations.
Some readers will notice that there should be four cases, when they use a real XRD measurement system.
The caption of Figure 2 has slightly been changed from “… as shown in the illustrations.” to “… as shown in the schematic illustrations.” in the revised manuscript.
Comment #5. Applies to the entire document, but noted particularly where Figure 6 and caption is followed by test (I believe) that reads “Figure 7 shows a magnified plot about ….” The distinction between manuscript text and Figure captions is not clear. Please check the Notes for Authors to see if these should be presented differently.
Response to comment #5: (4Yes/6No)
Certainly, it is written in the Notes for Authors of Powder Diffraction Journal,
“The captions of all figures should be listed together in a separate page after the tables. When submitting your paper, do not embed the figures with the text of the paper inside the word processor file. “
The author has removed embedded tables, figures and captions, and separately attached them after the main text in the revised manuscript.
Comment #6. Figure 6 caption near the end states “….between the cases (a), (b), (c), and (d), for….” I can not see a “vertical line (a) in the Figure. Seems either the Figure caption is incomplete or the Figure 6 is missing a vertical line below the (a).
Response to comment #6: (5Yes/6No)
As written in the response to the comment #4-a, there are four cases and three boundaries. Figure 6 and the caption have not been changed in the revised manuscript.
Comment #7-a. In IV. Analytical, section A. Deconvolutional treatment.
Paragraph 2, line 5 you mention “SciPy library”. Seems to me this should have a reference so reader can be sure of where to “find” this.
Response to comment #7-a: (6Yes/6No)
The following reference and citation about SciPy have been added in the revised manuscript;
“Virtanen, P., Gommers, R., Oliphant, T. E., Haberland, M., Tyler Reddy, T., Cournapeau, D., Burovski, E., Peterson, P., Weckesser, W., Bright, J., van der Walt, S.J., Brett, M., Wilson, J., Millman, K. J., Mayorov, N., Nelson, A.R.J., Jones, E., Kern, R., Larson, E., Carey, CJ., Polat, İ, Feng, Y., Moore, E.W., VanderPlas, J., Laxalde, D., Perktold, J., Cimrman, R., Henriksen, I., Quintero, E.A., Harris, C.R, Archibald, A.M., Ribeiro, A.H., Pedregosa, F., and van Mulbregt, P. (2020) “SciPy 1.0: Fundamental Algorithms for Scientific Computing in Python”, Nature Methods, 17(3), 261-272. DOI: 10.1038/s41592-019-0686-2″
Comment #7-b. Last paragraph of Section IV. A. it seems that “NumPy and SciPy libraries needs a reference.
Response to commennt #7-b: (7Yes/6No)
The following reference about NumPy library has been added, in addition to the reference of SciPy, in the revised manuscript;
“Harris, C.R., Millman, K.J., van der Walt, S.J., Gommers, R., Virtanen, P., Cournapeau, D., Wieser, E., Taylor, J., Berg, S., Smith, N.J., Kern, R., Picus, M., Hoyer, S., van Kerkwijk, M.H., Brett, M., Haldane, A., Fernández del Río, J., Wiebe, M., Peterson, P., Gérard-Marchant, P., Sheppard, K., Reddy, T., Weckesser, W., Abbasi, H., Gohlke, C., and Oliphant, T.E. (2020) “Array programming with NumPy” Nature 585, 357–362 (2020). DOI: 10.1038/s41586-020-2649-2″
Comment #8-a. V. Results
Paragraph 2, beginning with “Figures 9, 10, and 11 ….” uses abbreviation “DCT”. Has “DCT” been defined earlier? If not give the name followed by “, DCT,”.
Response to comment #8-a: (7Yes/7No)
In the section I. Introduction, paragraph 8, it is written
“The author has proposed a deconvolutional treatment (DCT) that introduces multiplication by the complex absolute value of the Fourier transform of the instrumental function, into the pure deconvolution process, which is equivalent to that the symmetrized instrumental function is used as the smoothing function (Ida and Toraya, 2002).”
in the original manuscript.
The author has not added more descriptions about the definition in the revised manuscript.
Comment #8-b. Line 2 should have “profile” plural. That is, “profiles”.
Response to comment #8-b: (8Yes/7No)
V. Results – Line 2 has been changed to
“Figures 9, 10, and 11 show the raw data, DCT data, and results of IPPF analysis for Si 111, 422, and 533-reflections. DCT data certainly show more symmetric peak profiles, as compared with the raw data.”
in the revised manuscript.
Comment #9-a. Figures 9, 10 and 11
Each figure has three different vertical scales. There should be a larger gap (suggest about 1/8 inch or so) between the three different vertical scales. The current vehicle scales in Figure 10 (selecting one of the three) has the zero of the upper scale too close to the 1500 of the lower scale. Suggest you add an additional 1/8 inch or so.
Response to comment #9-a: (9Yes/7No)
Margins between the upper and lower panels in Figures 9, 10 and 11 have been added in the revised manuscript.
Comment #10-a. Caption for Table I.
Line two has “…, and fixed values of the standard……” The word “fixed” is not clear. It wasn’t clear why the sigma and ketosis were “fixed”.
Response to comment #10-a: (9Yes/8No)
How the sigma and kurtosis were fixed is explained in the subsection “IV. B Peak profile fitting analysis”.
The emission area (focal line) on the copper target in the X-ray tube is nominally 1 mm-width by 10 mm-length, and the take-off angle of X-ray is 6 degrees, based on the information given to the author from the manufacturer of the X-ray diffraction instrument (Rigaku). The author has assumed homogeneous intensity distribution in the emitting range, because the manufacturer (assembler?) of the X-ray diffraction instrument (Rigaku) does not know the intensity distribution in the emitting range of the X-ray tube manufacturer (Canon Electron Tubes & Devices) they are applying as OEM (Original Equipment Manufacturing).
It is not likely that the intensity distribution in the nominal X-ray emitting area of the X-ray tube could be homogeneous. Now, the author is trying to construct the methodology to evaluate the intensity distribution emitted from the real X-ray tube, and a practical theoretical model, but the insufficiency and inaccuracy of the information available from the manufacturer (assembler) are the biggest obstacles against the establishment of the methodology.
The author thinks that the only possible way to solve the problem is education.
#11. Just above Figure 12 the value of Delta S in the text and in the figure are slightly different: -0.0863 and -0.0864. Which is the best value?
Res;
pomse to comment #11 (10Yes/8No)
The value of the optimized offset error in the text has been changed to -0.0864(3) in the revised manuscript.
Such a difference of the last significant number often causes in the currently affordable computing system, but some PDJ readers may certainly be confused.
In summary — I look forward to you contribution being published in Powder Diffraction following addressing the minor comments given above.
Response:
The author deeply appreciates the suggestions and comments from the current editor of Powder Diffraction Journal.
The author would like the paper to be published as an open access article.
The author is willing to pay the article processing charge (APC) for open access, from the budget he can settle by himself now, if it is 1000 USD or 2000 USD, for example. But it is difficult for the author to find how the article could be open-accessed on the web pages of ICDD and Cambridge University Press, about Powder Diffraction Journal.
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