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  • hierarchical clustering on correlations in Python scipy/numpy?

    - by user248237
    How can I run hierarchical clustering on a correlation matrix in scipy/numpy? I have a matrix of 100 rows by 9 columns, and I'd like to hierarchically clustering by correlations of each entry across the 9 conditions. I'd like to use 1-pearson correlation as the distances for clustering. Assuming I have a numpy array "X" that contains the 100 x 9 matrix, how can I do this? I tried using hcluster, based on this example: Y=pdist(X, 'seuclidean') Z=linkage(Y, 'single') dendrogram(Z, color_threshold=0) however, pdist is not what I want since that's euclidean distance. Any ideas? thanks.

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  • Semantic Diff Utilities

    - by rubancache
    I'm trying to find some good examples of semantic diff/merge utilities. The traditional paradigm of comparing source code files works by comparing lines and characters.. but are there any utilities out there (for any language) that actually consider the structure of code when comparing files? For example, existing diff programs will report "difference found at character 2 of line 125. File x contains v-o-i-d, where file y contains b-o-o-l". A specialized tool should be able to report "Return type of method doSomething() changed from void to bool". I would argue that this type of semantic information is actually what the user is looking for when comparing code, and should be the goal of next-generation progamming tools. Are there any examples of this in available tools?

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  • How to get a good price on dev books

    - by mgroves
    Does anyone have any tips for getting a good price on new/used programming-related books? I've looked at some of the more popular books (like DDD and GoF), and even used they can be pretty pricey. I'm not saying they aren't worth it, but I feel like there might be a more focused book store or exchange or something just for devs and/or IT professionals that I just don't know about. Any tips at all would be appreciated.

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  • How to figure out optimal C / Gamma parameters in libsvm?

    - by Cuga
    I'm using libsvm for multi-class classification of datasets with a large number of features/attributes (around 5,800 per each item). I'd like to choose better parameters for C and Gamma than the defaults I am currently using. I've already tried running easy.py, but for the datasets I'm using, the estimated time is near forever (ran easy.py at 20, 50, 100, and 200 data samples and got a super-linear regression which projected my necessary runtime to take years). Is there a way to more quickly arrive at better C and Gamma values than the defaults? I'm using the Java libraries, if that makes any difference.

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  • Blackberry - application settings save/load

    - by Max Gontar
    Hi! I know two ways to save/load application settings: use PersistentStore use filesystem (store, since SDCard is optional) I'd like to know what are you're practicies of working with application settings? Using PersistentStore to save/load application settings The persistent store provides a means for objects to persist across device resets. A persistent object consists of a key-value pair. When a persistent object is committed to the persistent store, that object's value is stored in flash memory via a deep copy. The value can then be retrieved at a later point in time via the key. Example of helper class for storing and retrieving settings: class PSOptions { private PersistentObject mStore; private LongHashtableCollection mSettings; private long KEY_URL = 0; private long KEY_ENCRYPT = 1; private long KEY_REFRESH_PERIOD = 2; public PSOptions() { // "AppSettings" = 0x71f1f00b95850cfeL mStore = PersistentStore.getPersistentObject(0x71f1f00b95850cfeL); } public String getUrl() { Object result = get(KEY_URL); return (null != result) ? (String) result : null; } public void setUrl(String url) { set(KEY_URL, url); } public boolean getEncrypt() { Object result = get(KEY_ENCRYPT); return (null != result) ? ((Boolean) result).booleanValue() : false; } public void setEncrypt(boolean encrypt) { set(KEY_ENCRYPT, new Boolean(encrypt)); } public int getRefreshPeriod() { Object result = get(KEY_REFRESH_PERIOD); return (null != result) ? ((Integer) result).intValue() : -1; } public void setRefreshRate(int refreshRate) { set(KEY_REFRESH_PERIOD, new Integer(refreshRate)); } private void set(long key, Object value) { synchronized (mStore) { mSettings = (LongHashtableCollection) mStore.getContents(); if (null == mSettings) { mSettings = new LongHashtableCollection(); } mSettings.put(key, value); mStore.setContents(mSettings); mStore.commit(); } } private Object get(long key) { synchronized (mStore) { mSettings = (LongHashtableCollection) mStore.getContents(); if (null != mSettings && mSettings.size() != 0) { return mSettings.get(key); } else { return null; } } } } Example of use: class Scr extends MainScreen implements FieldChangeListener { PSOptions mOptions = new PSOptions(); BasicEditField mUrl = new BasicEditField("Url:", "http://stackoverflow.com/"); CheckboxField mEncrypt = new CheckboxField("Enable encrypt", false); GaugeField mRefresh = new GaugeField("Refresh period", 1, 60 * 10, 10, GaugeField.EDITABLE|FOCUSABLE); ButtonField mLoad = new ButtonField("Load settings", ButtonField.CONSUME_CLICK); ButtonField mSave = new ButtonField("Save settings", ButtonField.CONSUME_CLICK); public Scr() { add(mUrl); mUrl.setChangeListener(this); add(mEncrypt); mEncrypt.setChangeListener(this); add(mRefresh); mRefresh.setChangeListener(this); HorizontalFieldManager hfm = new HorizontalFieldManager(USE_ALL_WIDTH); add(hfm); hfm.add(mLoad); mLoad.setChangeListener(this); hfm.add(mSave); mSave.setChangeListener(this); loadSettings(); } public void fieldChanged(Field field, int context) { if (field == mLoad) { loadSettings(); } else if (field == mSave) { saveSettings(); } } private void saveSettings() { mOptions.setUrl(mUrl.getText()); mOptions.setEncrypt(mEncrypt.getChecked()); mOptions.setRefreshRate(mRefresh.getValue()); } private void loadSettings() { mUrl.setText(mOptions.getUrl()); mEncrypt.setChecked(mOptions.getEncrypt()); mRefresh.setValue(mOptions.getRefreshPeriod()); } }

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  • Proper way to assert type of variable in Python

    - by Morlock
    In using a function, I wish to ensure that the type of the variables are as expected. How to do it right? Here is an example fake function trying to do just this before going on with its role: def my_print(text, begin, end): """Print text in UPPER between 'begin' and 'end' in lower """ for i in (text, begin, end): assert type(i) == type("") out = begin.lower() + text.upper() + end.lower() print out Is this approach valid? Should I use something else than type(i) == type("") ? Should I use try/except instead? Thanks pythoneers

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  • What languages have a while-else type control structure, and how does it work?

    - by Dan
    A long time ago, I thought I saw a proposal to add an else clause to for or while loops in C or C++... or something like that. I don't remember how it was supposed to work -- did the else clause run if the loop exited normally but not via a break statement? Anyway, this is tough to search for, so I thought maybe I could get some CW answers here for various languages. What languages support adding an else clause to something other than an if statement? What is the meaning of that clause? One language per answer please.

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  • java web development, what skills do I need?

    - by mrblah
    I want to learn, at least at a basic level, how to build java web applications (coming from a .net background). Meaning, I would like to be able to build, deploy a simple cms type application from the ground up. What exactly do I need to learn? Tomcat seems to be a good web server for Java. What options are there for the web? I know there is hibernate for an ORM. Does java have MVC? what about JSP? can MVC and JSP be together? beans? Maybe a book that covers all of these?

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  • How about the "Certified Secure Software Lifecycle Professional"?

    - by Ekkapop
    I have invited to join Certified Secure Software Lifecycle Professional training course, however I have no idea about this course. Course's details give me only an overview of information, for example, this course is about how to gathering requirement about security, how to doing something in more secure ways etc. Did anyone have experience about Certified Secure Software Lifecycle Professional? Is it worth to attend this course?

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  • how much time does grid.py take to run ?

    - by trinity
    Hello all , I am using libsvm for binary classification.. I wanted to try grid.py , as it is said to improve results.. I ran this script for five files in separate terminals , and the script has been running for more than 12 hours.. this is the state of my 5 terminals now : [root@localhost tools]# python grid.py sarts_nonarts_feat.txt>grid_arts.txt Warning: empty z range [61.3997:61.3997], adjusting to [60.7857:62.0137] line 2: warning: Cannot contour non grid data. Please use "set dgrid3d". Warning: empty z range [61.3997:61.3997], adjusting to [60.7857:62.0137] line 4: warning: Cannot contour non grid data. Please use "set dgrid3d". [root@localhost tools]# python grid.py sgames_nongames_feat.txt>grid_games.txt Warning: empty z range [64.5867:64.5867], adjusting to [63.9408:65.2326] line 2: warning: Cannot contour non grid data. Please use "set dgrid3d". Warning: empty z range [64.5867:64.5867], adjusting to [63.9408:65.2326] line 4: warning: Cannot contour non grid data. Please use "set dgrid3d". [root@localhost tools]# python grid.py sref_nonref_feat.txt>grid_ref.txt Warning: empty z range [62.4602:62.4602], adjusting to [61.8356:63.0848] line 2: warning: Cannot contour non grid data. Please use "set dgrid3d". Warning: empty z range [62.4602:62.4602], adjusting to [61.8356:63.0848] line 4: warning: Cannot contour non grid data. Please use "set dgrid3d". [root@localhost tools]# python grid.py sbiz_nonbiz_feat.txt>grid_biz.txt Warning: empty z range [67.9762:67.9762], adjusting to [67.2964:68.656] line 2: warning: Cannot contour non grid data. Please use "set dgrid3d". Warning: empty z range [67.9762:67.9762], adjusting to [67.2964:68.656] line 4: warning: Cannot contour non grid data. Please use "set dgrid3d". [root@localhost tools]# python grid.py snews_nonnews_feat.txt>grid_news.txt Wrong input format at line 494 Traceback (most recent call last): File "grid.py", line 223, in run if rate is None: raise "get no rate" TypeError: exceptions must be classes or instances, not str I had redirected the outputs to files , but those files for now contain nothing.. And , the following files were created : sbiz_nonbiz_feat.txt.out sbiz_nonbiz_feat.txt.png sarts_nonarts_feat.txt.out sarts_nonarts_feat.txt.png sgames_nongames_feat.txt.out sgames_nongames_feat.txt.png sref_nonref_feat.txt.out sref_nonref_feat.txt.png snews_nonnews_feat.txt.out (-- is empty ) There's just one line of information in .out files.. the ".png" files are some GNU PLOTS . But i dont understand what the above GNUplots / warnings convey .. Should i re-run them ? Can anyone please tell me on how much time this script might take if each input file contains about 144000 lines.. Thanks and regards

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  • Neural Network: Handling unavailable inputs (missing or incomplete data)

    - by Mike
    Hopefully the last NN question you'll get from me this weekend, but here goes :) Is there a way to handle an input that you "don't always know"... so it doesn't affect the weightings somehow? Soo... if I ask someone if they are male or female and they would not like to answer, is there a way to disregard this input? Perhaps by placing it squarely in the centre? (assuming 1,0 inputs at 0.5?) Thanks

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  • Multiple levels of 'collection.defaultdict' in Python

    - by Morlock
    Thanks to some great folks on SO, I discovered the possibilities offered by collections.defaultdict, notably in readability and speed. I have put them to use with success. Now I would like to implement three levels of dictionaries, the two top ones being defaultdict and the lowest one being int. I don't find the appropriate way to do this. Here is my attempt: from collections import defaultdict d = defaultdict(defaultdict) a = [("key1", {"a1":22, "a2":33}), ("key2", {"a1":32, "a2":55}), ("key3", {"a1":43, "a2":44})] for i in a: d[i[0]] = i[1] Now this works, but the following, which is the desired behavior, doesn't: d["key4"]["a1"] + 1 I suspect that I should have declared somewhere that the second level defaultdict is of type int, but I didn't find where or how to do so. The reason I am using defaultdict in the first place is to avoid having to initialize the dictionary for each new key. Any more elegant suggestion? Thanks pythoneers!

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  • how to read an address in multiple formats like google maps

    - by ratan
    notice that on google maps you can input the address any way you like. as long as it is a valid address...google maps will read it. In some ruby book I had seen code snippet for something like this, but with phone numbers. Any ideas how this could be done for addresses? in language of your choice. EDIT: i dont care about a "valid" address. I just want to parse an address. so that 123 fake street, WA, 34223 would be an address and so will 123 fake street WA 34223

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  • Why do C compilers prepend underscores to external names?

    - by Michael Burr
    I've been working in C for so long that the fact that compilers typically add an underscore to the start of an extern is just understood... However, another SO question today got me wondering about the real reason why the underscore is added. A wikipedia article claims that a reason is: It was common practice for C compilers to prepend a leading underscore to all external scope program identifiers to avert clashes with contributions from runtime language support I think there's at least a kernel of truth to this, but also it seems to no really answer the question, since if the underscore is added to all externs it won't help much with preventing clashes. Does anyone have good information on the rationale for the leading underscore? Is the added underscore part of the reason that the Unix creat() system call doesn't end with an 'e'? I've heard that early linkers on some platforms had a limit of 6 characters for names. If that's the case, then prepending an underscore to external names would seem to be a downright crazy idea (now I only have 5 characters to play with...).

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  • How Can I up my Street Cred in the coding world

    - by RedEye
    I know this isn't directly related to a specific coding problem. It's a more general programming question. I'm a n00b... Been coding for 1 year, and it's where I belong. I want to get hardcore and put everything I have into it. I started with C++ and now I'm into C#. I love it all. What can I do to up my game and up my respect in the programming world?

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  • Beginner question: What is binding?

    - by JDelage
    Hi, I was trying to understand the difference between early and late binding, and in the process realized that the concept of binding is nebulous to me. I think I understand that it relates to the way data-as-a-word-of-memory is linked to type-as-a-set-of-language-features but I am not sure those are the right concepts. Also, how does understanding this deeply help people become better programmers? Please note: This question is not "what is late v. early binding" or "what are the trade-offs between the 2". Those already exist here. Thanks, JDelage

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  • How to learn flex?

    - by Zenzen
    So I'm starting an internship as a Flex developer in ~2weeks thanks to a friend of mine. The thing is I know squat about Flex - it is an internship after all so I'm supposed to learn there, but nonetheless I want to have some basic understanding of Flex before I start (eventually I want to become a JEE/Flex dev). So my question is simple, which book(s) would you recommend me to start with? Are there any "must have" books, like let's say "Thinking in C++" for C++ etc.? I already heard about a few video tutorials and I will surely check them out but I'd also want to get some decent books.

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  • How do I create a good evaluation function for a new board game?

    - by A. Rex
    I write programs to play board game variants sometimes. The basic strategy is standard alpha-beta pruning or similar searches, sometimes augmented by the usual approaches to endgames or openings. I've mostly played around with chess variants, so when it comes time to pick my evaluation function, I use a basic chess evaluation function. However, now I am writing a program to play a completely new board game. How do I choose a good or even decent evaluation function? The main challenges are that the same pieces are always on the board, so a usual material function won't change based on position, and the game has been played less than a thousand times or so, so humans don't necessarily play it enough well yet to give insight. (PS. I considered a MoGo approach, but random games aren't likely to terminate.) Any ideas? Game details: The game is played on a 10-by-10 board with a fixed six pieces per side. The pieces have certain movement rules, and interact in certain ways, but no piece is ever captured. The goal of the game is to have enough of your pieces in certain special squares on the board. The goal of the computer program is to provide a player which is competitive with or better than current human players.

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  • Core principles, rules, and habits for CS students

    - by Asad Butt
    No doubt there is a lot to read on blogs, in books, and on Stack Overflow, but can we identify some guidelines for CS students to use while studying? For me these are: Finish your course books early and read 4-5 times more material relative to your course work. Programming is the one of the fastest evolving professions. Follow the blogs on a daily basis for the latest updates, news, and technologies. Instead of relying on assignments and exams, do at least one extra, non-graded, small to medium-sized project for every programming course. Fight hard for internships or work placements even if they are unpaid, since 3 months of work 1 year at college. Practice everything, every possible and impossible way. Try doing every bit of your assignments project yourself; i.e. fight for every inch. Rely on documentation as the first source for help and samples, Google, and online forums as the last source. Participate often in online communities and forums to learn the best possible approach for every solution to your problem. (After doing your bit.) Make testing one of your habits as it is getting more important everyday in programming. Make writing one of your habits. Write something productive once or twice a week and publish it.

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  • Understanding Smarty and MVC Frameworks

    - by Korrupzion
    Hello there, I just created this thread to discuss with people who have adopted the smarty system, and how many time it took to you to understand it, because i just can't get the idea, instead of making every easier as everybody says i think it just make more complex to code. More than a problem with only smarty is with the whole MVC model, with CakePHP or KohanaPHP i experience the same problems, u need to do 3x lines of code and files for something that u can do with a few lines of simple php. Maybe u can tell how did u learned to code using MVC model :)

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  • Voice Communication over TCP/IP

    - by Micha
    Hello, I'm currently developing application using DirectSound for communication on an intranet. I've had working solution using UDP but then my boss told me he wants to use TCP/IP for some reason. I've tried to implement it in pretty much the same way as UDP, but with very little success. What I get is basically just noise. 20% of it is the recorded sound and the rest is just weird noise. My guess for the reason is that TCP needs to read all the accepted data several times until it gets the final sound I can play. Now two questions: Am I on the right tracks? Is it even good idea to use TCP/IP for this kind of application (voice conferencing of sorts)? I'm doing it in C# but I don't think this is language specific.

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