From 68784b0e23125cc3cfe32557a0b4c7ac69c6bddd Mon Sep 17 00:00:00 2001 From: Jan Benda Date: Sun, 13 Dec 2020 09:43:44 +0100 Subject: [PATCH] random fixes and notes --- Makefile | 2 +- chapter.mk | 2 ++ codestyle/lecture/codestyle.tex | 1 + header.tex | 2 +- plotting/lecture/plotting.tex | 28 +++++++++--------- .../lecture/pointprocessscetchA.eps | 4 +-- .../lecture/pointprocessscetchA.pdf | Bin 2786 -> 2786 bytes .../lecture/pointprocessscetchB.eps | 4 +-- .../lecture/pointprocessscetchB.pdf | Bin 4694 -> 4694 bytes scientificcomputing-script.tex | 15 +++++----- 10 files changed, 30 insertions(+), 28 deletions(-) diff --git a/Makefile b/Makefile index a743d0a..b59d881 100644 --- a/Makefile +++ b/Makefile @@ -3,7 +3,7 @@ BASENAME=scientificcomputing-script SUBDIRS=programming debugging plotting codestyle statistics bootstrap regression likelihood pointprocesses designpattern SUBTEXS=$(foreach subd, $(SUBDIRS), $(subd)/lecture/$(subd).tex) -all : script chapters +all : plots chapters index script chapters : for sd in $(SUBDIRS); do $(MAKE) -C $$sd/lecture chapter; done diff --git a/chapter.mk b/chapter.mk index 3afd160..0482aed 100644 --- a/chapter.mk +++ b/chapter.mk @@ -10,6 +10,8 @@ pythonplots : $(PYPDFFILES) $(PYPDFFILES) : %.pdf: %.py ../../plotstyle.py PYTHONPATH="../../" python3 $< + #ps2pdf $@ $(@:.pdf=-temp.pdf) # strip fonts, saves only about 1.5MB + #mv $(@:.pdf=-temp.pdf) $@ cleanpythonplots : rm -f $(PYPDFFILES) diff --git a/codestyle/lecture/codestyle.tex b/codestyle/lecture/codestyle.tex index 01d1d12..8e2ee7e 100644 --- a/codestyle/lecture/codestyle.tex +++ b/codestyle/lecture/codestyle.tex @@ -4,6 +4,7 @@ more months might as well have been written by someone else.}{Eagleson's law} +\noindent Cultivating a good code style is not just a matter of good taste but rather is a key ingredient for readability and maintainability of code and, in the end, facilitates reproducibility of scientific diff --git a/header.tex b/header.tex index fcaaa87..ab412ef 100644 --- a/header.tex +++ b/header.tex @@ -319,7 +319,7 @@ % \newboolean{showexercisesolutions} \setboolean{showexercisesolutions}{true} -\newcommand{\exercisesolutions}{chapter} % 0: here, 1: chapter, 2: end +\newcommand{\exercisesolutions}{end} % 0: here, 1: chapter, 2: end % we need this also as numbers: \ifthenelse{\equal{\exercisesolutions}{end}}{\newcommand{\exercisesolutionsnum}{2}}{% \ifthenelse{\equal{\exercisesolutions}{chapter}}{\newcommand{\exercisesolutionsnum}{1}}{% diff --git a/plotting/lecture/plotting.tex b/plotting/lecture/plotting.tex index b27b919..1d30084 100644 --- a/plotting/lecture/plotting.tex +++ b/plotting/lecture/plotting.tex @@ -74,20 +74,20 @@ the data was changed or the same kind of plot has to be created for a number of datasets. \begin{important}[Why manual editing should be avoided.] - On first glance the manual editing of a figure using tools such as - Corel draw, Illustrator, etc.\,appears much more convenient and less - complex than coding everything into the analysis scripts. This, - however, is not entirely true. What if the figure has to be re-drawn - or updated? Then the editing work starts all over again. Rather, - there is a great risk associated with the manual editing - approach. Axes may be shifted, fonts have not been embedded into the - final document, annotations have been copy pasted between figures - and are not valid. All of these mistakes can be found in - publications and then require an erratum, which is not - desirable. Even if it appears more cumbersome in the beginning one - should always try to create publication-ready figures directly from - the data analysis tool using scripts or functions to properly layout - the plot. + On first glance manual editing of a figure using tools such as + inkscape, Corel draw, Illustrator, etc.\,appears much more + convenient and less complex than coding everything into the analysis + scripts. This, however, is not entirely true. What if the figure has + to be re-drawn or updated, because, for example, you got more data? + Then the editing work starts all over again. In addition, there is a + great risk associated with the manual editing approach. Axes may be + shifted, fonts have not been embedded into the final document, + annotations have been copy-pasted between figures and are not + valid. All of these mistakes can be found in publications and then + require an erratum, which is not desirable. Even if it appears more + cumbersome in the beginning, one should always try to generate + publication-ready figures directly from the data analysis tool using + scripts or functions to properly layout and annotate the plot. \end{important} \subsection{Simple plotting} diff --git a/pointprocesses/lecture/pointprocessscetchA.eps b/pointprocesses/lecture/pointprocessscetchA.eps index 441b034..5a4bb00 100644 --- a/pointprocesses/lecture/pointprocessscetchA.eps +++ b/pointprocesses/lecture/pointprocessscetchA.eps @@ -1,7 +1,7 @@ %!PS-Adobe-2.0 EPSF-2.0 %%Title: pointprocessscetchA.tex %%Creator: gnuplot 4.6 patchlevel 4 -%%CreationDate: Fri Dec 11 21:08:22 2020 +%%CreationDate: Sun Dec 13 09:18:35 2020 %%DocumentFonts: %%BoundingBox: 50 50 373 135 %%EndComments @@ -433,7 +433,7 @@ SDict begin [ /Author (jan) % /Producer (gnuplot) % /Keywords () - /CreationDate (Fri Dec 11 21:08:22 2020) + /CreationDate (Sun Dec 13 09:18:35 2020) /DOCINFO pdfmark end } ifelse diff --git a/pointprocesses/lecture/pointprocessscetchA.pdf b/pointprocesses/lecture/pointprocessscetchA.pdf index 3d417334e8f4f0885323a9268c63697c84990acd..b06226f27816fe77a57084746e940457f8cc9dc1 100644 GIT binary patch delta 309 zcmaDP`bc!cQD$CK3nODwGlL{ub5moB$pLKglRq+NVG(U-vEecfF|f2Uw6HQZoqU!> zLn62|PeIouRX157#L(DE!N3YEX=OT@m$eCt3AKgA`nBvr%33M61?WN2()X=q_=x|x%+hB4O3)Y8<{)YZbo z+|bR^#n{Ed(8ATy&C%S^#nIBx$kffwhMRntYZ; zL&B{nQ$g1yRX157#L&=6!N>|MX=OB-m$eCt3AKgA`nBvr%33M61?WC%nC7Dh&!IXP<>W6jOXj4TbEja|&l zEDemEoehnQEM1)~fTGT(&TdXlb~Xf6#B$l$aTS*&7L`;KrKWKinHU>$sj9mAyKw;k D@|;U- diff --git a/pointprocesses/lecture/pointprocessscetchB.eps b/pointprocesses/lecture/pointprocessscetchB.eps index b9863a7..a0b1ee2 100644 --- a/pointprocesses/lecture/pointprocessscetchB.eps +++ b/pointprocesses/lecture/pointprocessscetchB.eps @@ -1,7 +1,7 @@ %!PS-Adobe-2.0 EPSF-2.0 %%Title: pointprocessscetchB.tex %%Creator: gnuplot 4.6 patchlevel 4 -%%CreationDate: Fri Dec 11 21:08:22 2020 +%%CreationDate: Sun Dec 13 09:18:35 2020 %%DocumentFonts: %%BoundingBox: 50 50 373 237 %%EndComments @@ -433,7 +433,7 @@ SDict begin [ /Author (jan) % /Producer (gnuplot) % /Keywords () - /CreationDate (Fri Dec 11 21:08:22 2020) + /CreationDate (Sun Dec 13 09:18:35 2020) /DOCINFO pdfmark end } ifelse diff --git a/pointprocesses/lecture/pointprocessscetchB.pdf b/pointprocesses/lecture/pointprocessscetchB.pdf index d172e5c62c65027bc4b578fa5f6b7634f9b9e8ef..6d49213180fa4a5b33b784fef75bb8f5208c60a8 100644 GIT binary patch delta 266 zcmcbna!qA}B{#3Bg^{tTnL(1Sxv8D^SDeWM<;zY~pHUVrXJyVQFS*>}+XbX5{Q@Wa?yQ R;p}4MY-dAA#bj$CX#h%9KrR3P delta 266 zcmcbna!qA}B{#28l97q2fw`%!xru@0WC33J$*J5~7@`W3|8QG#8HN}cS{Yba85vD> zX3A!Z0BYLquZoWL^~vQTfe}dDEGML1w$8 zCMy^kD!}cG6_8{%G%_@>Ff!U)D^SDeWN7YW;b>@JY-VN*q+CqR9Zg-Foy`rMUCqoK Qoh*#)YzV2CY%L@W00J>TyZ`_I diff --git a/scientificcomputing-script.tex b/scientificcomputing-script.tex index 4847455..21daaba 100644 --- a/scientificcomputing-script.tex +++ b/scientificcomputing-script.tex @@ -71,19 +71,18 @@ \includechapter{regression} +\includechapter{likelihood} + % add chapter on generalized linear models (versus ANOVA) -% add chapter on nonlinear fitting (methods, initial values, local minima) - -\includechapter{likelihood} +% add chapter on nonlinear fitting (methods, initial values, local minima, power law fits on log-log data) \includechapter{pointprocesses} % add chapter on time series (amplitude distribution, autocorrelation, crosscorrelation) - %\includechapter{spectral} -% add chapter on digital filtering +% add chapter on filtering and envelopes % add chapter on event detection, signal detection, ROC @@ -97,11 +96,11 @@ %\part{Tools} % Latex -% markdown +% markdown, html % Makefile % version control (git and github) only put source files into repository! % distributed computing (ssh and grid engines) -% data handling (structure, data bases, storage (rsync), backup) +% data handling (structure, storage (rsync), backup, data bases) % data annotation, meta data %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% @@ -111,7 +110,7 @@ %\chapter{Cheat-Sheet} %%%% solutions: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% \printallsolutions +\printallsolutions %%%% indices: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%