From 0314208124043f1bec2bc66cf8d25f46d8091b8a Mon Sep 17 00:00:00 2001 From: Fabian Sinz Date: Thu, 30 Oct 2014 14:04:55 +0100 Subject: [PATCH] project template added --- projects/Makefile | 4 +- projects/disclaimer.tex | 50 ++-- .../pca_natural_images.tex | 217 ------------------ .../Makefile | 6 +- projects/project_template/template.tex | 42 ++++ 5 files changed, 83 insertions(+), 236 deletions(-) delete mode 100755 projects/project_PCA_natural_images/pca_natural_images.tex rename projects/{project_PCA_natural_images => project_template}/Makefile (54%) create mode 100755 projects/project_template/template.tex diff --git a/projects/Makefile b/projects/Makefile index 986268d..dbdf636 100644 --- a/projects/Makefile +++ b/projects/Makefile @@ -1,7 +1,7 @@ all: for d in `ls -d project_*/`; do \ echo "Processing $$d" ; \ - cd $$d; $(MAKE) zip ; \ + cd $$d; $(MAKE) zip ; cd .. ; \ done mv project_*/*zip . @@ -9,7 +9,7 @@ all: clean: for d in `ls -d project_*/`; do \ echo "Cleaning up $$d" ; \ - cd $$d; $(MAKE) clean ; \ + cd $$d; $(MAKE) clean ; cd .. ; \ done rm -f *.zip diff --git a/projects/disclaimer.tex b/projects/disclaimer.tex index 11e7bab..261c2a4 100644 --- a/projects/disclaimer.tex +++ b/projects/disclaimer.tex @@ -1,15 +1,37 @@ - \fbox{\parbox{0.985\linewidth}{ \small Please answer all questions - in an electronic file (.txt, .doc are ok, but we prefer .pdf) and - submit in ILIAS. If the assignments include programming - exercises, hand in a pdf for the questions, the .py files for - the programs, and the data in one zip file. - - Use complete and correct sentences unless otherwise - noted. Please be succinct. Use your own words. Write down a - concise reasoning, not just the result. We expect you to do - exercises on your own, but you are encouraged to discuss the - exercises with your fellow students. If you blindly copy your - results from others, you miss out on a chance to learn something - new. Use all resources available to you, but always make sure - that you truly understand why you give the answer you give. + \fbox{\parbox{0.985\linewidth}{ \small + + {\bf Evaluation criteria:} + + Each project has three elements that are graded: (i) the code, + (ii) the slides/figures, and (iii) the presentation. + + \vspace{.5cm} + + The {\bf code} and the {\bf presentation} should be uploaded to + ILIAS before the presentations start on Thursday. Everything + should be bundeled into a {\em single} zip-file. The + presentation should be handed in as pdf. + + \vspace{.5cm} + + The {\bf code} should be exectuable without any further + adjustments from us. This means that you should include all + additional functions you wrote and the data into the + zip-file. The {\em main script} should produce the same {\em + figures} that you use in your slides. The figures should follow + the guidelines for proper plotting as discussed in the first + statistics lecture. The code should be properly commented and + comprehensible by third persons (use proper and consistent + variable names). + + \vspace{.5cm} + + The {\bf slides} should be handed in along with the code and in + pdf format. We will store them all on one computer to allow fast + transitions between talks. The {\bf presentation} itself should + be {\em at most} 10min long and be held in English. In the + presentation you should (i) briefly describe the problem, (ii) + explain how you solved it algorithmically (don't show your + entire code), and (iii) present figures showing your results. + }} \ No newline at end of file diff --git a/projects/project_PCA_natural_images/pca_natural_images.tex b/projects/project_PCA_natural_images/pca_natural_images.tex deleted file mode 100755 index 25f903c..0000000 --- a/projects/project_PCA_natural_images/pca_natural_images.tex +++ /dev/null @@ -1,217 +0,0 @@ -\documentclass[addpoints,10pt]{exam} -\usepackage{url} -\usepackage{color} -\usepackage{hyperref} - -\pagestyle{headandfoot} -\runningheadrule -\firstpageheadrule - -\firstpageheader{Essential Statistics}{Homework 01 due 10/29/2014 23:59 am}{23. October 2014} -\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014} -\firstpagefooter{}{}{} -\runningfooter{}{}{} -\pointsinmargin -\bracketedpoints - -%\printanswers -\shadedsolutions - - -\begin{document} -%%%%%%%%%%%%%%%%%%%%% Submission instructions %%%%%%%%%%%%%%%%%%%%%%%%% -\sffamily -\begin{flushright} -\gradetable[h][questions] -\end{flushright} - -\begin{center} - \fbox{\parbox{0.985\linewidth}{ \small Please answer all questions - in an electronic file (.txt, .doc are ok, but we prefer .pdf) and - submit in ILIAS. - - Use complete and correct sentences unless otherwise - noted. Please be succinct. Use your own words. Write down a - concise reasoning, not just the result. We expect you to do - exercises on your own, but you are encouraged to discuss the - exercises with your fellow students. If you blindly copy your - results from others, you miss out on a chance to learn something - new. Use all resources available to you, but always make sure - that you truly understand why you give the answer you give. - }} -\end{center} - -%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%% - -\begin{questions} - \question {\bf Reading assignment: Do not submit answers to this - question! } - - Read chapter 1. up to 2.4 (including) of Samuels/Wittmer/Schaffner. - - Pay special attention to the following questions. - \begin{enumerate} - \item What types of scientific evidence do the authors list? How - strong are these evidences? - \item What are the different types of data encountered in - statistical analysis? - \item What is a population? What is a random sample? What are - sampling errors? What are nonsampling errors? - \item What is a descriptive statistic? - \item What property do robust statistics have? - \end{enumerate} - - \question Install python and a suitable editor on your computer. - \begin{parts} - \part For installing python, I recommend the anaconda - distribution: \url{http://continuum.io/downloads}. It does not - matter whether you install python 2.7 or 3.4. I will use python - 3.4 syntax. - - \part As editor I recommend either sublime text (for people new to - programming) or pycharm (for people with programming - experience). I do not recommend to use a text editor that comes - with your operating system (like word pad). Text processing - programs like Mircosoft Word or Libre-Office {\bf won't work at - all}. Programming needs a little more than just typing text and - you will make your life unnecessarily hard by using an editor not - suited for it. - \part Find out how to run a python program on your operating - system and how to install new python packages. Install the - packages {\tt pandas} and {\tt seaborn}. - \end{parts} - - \question To publish scientific results, you will usually need - to use statistical methods. Some journals provide you with a brief - description of how they expect you to apply statistical methods. One - example can be found in the author guidelines of the journal - Nature - - \begin{center} - \url{http://www.nature.com/neuro/pdf/sm_checklist.pdf} - \end{center} - - Please read the ‘checklist’ and answer the following questions: - - \begin{parts} - \part[2] Why is it important that statistical methods are applied - correctly? - - \begin{solution} - When not applied correctly, the results of statistical methods - might not support your hypothesis and can lead to false - conclusions. - \end{solution} - - \part[2] Name two common descriptive statistics and what you have - to specify for them in nature. - - \begin{solution} - \begin{itemize} - \item A clearly defined number $n$ of data points should be - specified. If the sample is small, plot points instead of - using descriptive statistics. Errorbars should be clearly - defined. - \item measure of center: mean, median - \item measure of variability: standard deviation, range - \end{itemize} - \end{solution} - - \part[3] Name one statistical test that you have heard of or - used. If you were to apply any of them, what would you have to - specify to follow the Nature guidelines? - - \begin{solution} - {\bf Student's T-Test} for testing whether the mean of two - populations is the same - \begin{itemize} - \item a clearly defined $n$ for the test - \item a justification for the sample size used - \item a clear description of the statistical method: since the - t-test is very common, stating that a two independent sample - t-test was used should be sufficient. - \item Justify that the data meets the definition: the two - populations should be normally distributed with the same - variance; the data was sampled independently from the two - populations being compared. - \item Is the variance in the different groups different. - \item was it one-sided or two-sided - \end{itemize} - \end{solution} - - \part[3] Why are you asked to justify each incidence in which - you exclude some of the data that you collected? What could be a - valid reason to exclude a data point? - - \begin{solution} - Excluded data points might make a sample from a population not - representative anymore, and can therefore alter the outcome and - conclusions of a study. They might be excluded if there is a - good reason to believe that they are not part of the population - under investigation. - \end{solution} - - \end{parts} - - \question {\bf Robust statistics} In 1888, P. Topinard published - data on the brain weights of hundreds of French men and women. Here - are ten brain weights (in Gramm) of female brains from the dataset - \begin{center} [1125, 1027, 1112, 983, 1090, 1247, 1045, 983, 972, 1045] - \end{center} - - Open a new file ``brain\_weight.py'' with you text editor to write - the following python program (please hand in the plots and the program). - \begin{parts} - \part[2] Create a list that contains the above brain weights. - \part[2] Create a new list that contains the following ten means: - Each mean is computed from the original list after removing one - element (hint use slicing and adding lists for that; we did this - in the lecture already). {\bf Warning:} I {\em do not} expect you - to use {\tt for}-loops. Only use them if you know them already. If - you do use them, be prepared to explain your code to me to get - credits for this task. - \part[2] Create yet another list that does the same, only for the - median. - \part[2] Make a boxplot with the different means and medias (like - in the lecture). To show the plot at the end of the program - you need to put a {\tt plt.show()} at the end of the program. If - you want to save the plot, put the command {\tt - plt.gcf().savefig('YOUR\_NAME\_homework01.pdf')} before that. Label - the y-axis by using the function {\tt plt.ylabel('FILL IN YOUR LABEL')} - \part[2] What can you observe and what does that tell you about - the robustness of the statistic? - \end{parts} - \begin{solution} - \begin{verbatim} -import matplotlib.pyplot as plt -import seaborn as sns -import numpy as np - -sns.set_context("paper", font_scale=1.5, rc={"lines.linewidth": 2.5}) - -w = [1125, 1027, 1112, 983, 1090, 1247, 1045, 983, 972, 1045] - -brain_means = [ np.mean(w[1:]), np.mean(w[:1] + w[2:]), np.mean(w[:2] + w[3:]), \ - np.mean(w[:3] + w[4:]), np.mean(w[:4] + w[5:]), np.mean(w[:5] + w[6:]), \ - np.mean(w[:6] + w[7:]), np.mean(w[:7] + w[8:]), np.mean(w[:8] + w[9:]),\ - np.mean(w[:9]) ] -brain_medians = [ np.median(w[1:]), np.median(w[:1] + w[2:]), np.median(w[:2] + w[3:]), \ - np.median(w[:3] + w[4:]), np.median(w[:4] + w[5:]), np.median(w[:5] + w[6:]), \ - np.median(w[:6] + w[7:]), np.median(w[:7] + w[8:]), np.median(w[:8] + w[9:]),\ - np.median(w[:9]) ] - -sns.boxplot([brain_means, brain_medians], names=['means', 'medians']) -plt.ylabel('brain weight [g]') -plt.gcf().savefig('fabian_sinz_homework01.pdf') -plt.show() - \end{verbatim} - \end{solution} - - -\end{questions} - - - - - -\end{document} diff --git a/projects/project_PCA_natural_images/Makefile b/projects/project_template/Makefile similarity index 54% rename from projects/project_PCA_natural_images/Makefile rename to projects/project_template/Makefile index b7abffb..585d602 100644 --- a/projects/project_PCA_natural_images/Makefile +++ b/projects/project_template/Makefile @@ -1,9 +1,9 @@ latex: - pdflatex *.tex - pdflatex *.tex + pdflatex *.tex > /dev/null + pdflatex *.tex > /dev/null clean: - rm -f *.log *.aux *.zip *.out + rm -f *.log *.aux *.zip *.out auto rm -f `basename *.tex .tex`.pdf zip: latex diff --git a/projects/project_template/template.tex b/projects/project_template/template.tex new file mode 100755 index 0000000..61f2e1a --- /dev/null +++ b/projects/project_template/template.tex @@ -0,0 +1,42 @@ +\documentclass[addpoints,10pt]{exam} +\usepackage{url} +\usepackage{color} +\usepackage{hyperref} + +\pagestyle{headandfoot} +\runningheadrule +\firstpageheadrule +\firstpageheader{Scientific Computing}{Project Assignment}{11/05/2014 + -- 11/06/2014} +%\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014} +\firstpagefooter{}{}{} +\runningfooter{}{}{} +\pointsinmargin +\bracketedpoints + +%\printanswers +%\shadedsolutions + + +\begin{document} +%%%%%%%%%%%%%%%%%%%%% Submission instructions %%%%%%%%%%%%%%%%%%%%%%%%% +\sffamily +% \begin{flushright} +% \gradetable[h][questions] +% \end{flushright} + +\begin{center} + \input{../disclaimer.tex} +\end{center} + +%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%% + +\begin{questions} + \question What was the questions for 42? +\end{questions} + + + + + +\end{document}