I have a need to go through a set of DICOM files and modify certain tags to be current with the data maintained in the database of an external system. I am looking to use GDCM. I am new to GDCM. A search through stack overflow posts demonstrates that the anonymizer class can be used to change tag values.
Generating a simple CT DICOM image using GDCM
My question is if this is the best use of the GDCM API or if there is a better approach for changing the values of individual tags such as patient name or accession number. I am unfamiliar with all of the API options but have a link to the API documentation. It looks like the DataElement SetValue member could be used, but it doesn't appear that there is a valid constructor for doing this in the Value class. Any assistance would appreciated. This is my current approach:
Anonymizer anon = new Anonymizer();
anon.SetFile(myFile);
anon.Replace(new Tag(0x0010, 0x0010), "BUGS^BUNNY");
Quite late, but maybe it would be still useful. You have not mention if you write in C++ or C#, but I assume the latter, as you do not use pointers. Generally, your approach is correct (unless you use System.IO.File instead of gdcm.File). The value (second parameter of Replace function) has to be a plain string so no special constructor is needed. You should probably start with doxygen documentation of gdcm, and there is especially one complete example. It is in C++, but there should be no problems with translation.
There are two different ways to pad dicom tags:
Anonymizer
gdcm::Anonymizer anon;
anon.SetFile(file);
anon.Replace(gdcm::Tag(0x0002, 0x0013), "Implementation Version Name");
//Implementation Version Name
DatsElement
gdcm::Attribute<0x0018, 0x0088> ss;
ss.SetValue(10.0);
ds.Insert(ss.GetAsDataElement());
I'm doing some competitions on a website called topcoder.com where the objective is to solve algorithmic problems. I'm using Eclipse for this purpose, and I code in Java, it would be help me to have some predefined templates or macros that I can use for common coding tasks. For example I would like to write methods to be able to find the max value in and int[] array, or the longest sequence in an int[] array, and so on (there should be quite many of these). Note I can't write these methods as libraries because as part of the competition I need to submit everything in one file.
Therefore ideally, I would like to have some shortcut available to generate code both as a method and as a calling statement at once. Any ideas if this is possible?
Sure you can - I think that's a nifty way to auto-insert boilerplate or helper code. To the point of commenters, you probably want to group the code as a helper class, but the general idea sounds good to me:
You can see it listed in your available templates:
Then as you code your solution, you can Control+Space, type the first few characters of the name you gave your template, and you can preview it:
And then you can insert it. Be sure if you use a class structure to position it as an inner class:
Lastly - if you want to have a template inserts a call to method from a template, I think you would just use two templates. One like shown above (to print the helper code) and another that might look like this, which calls a util method and drops the cursor after it (or between the parentheses if you'd like, etc):
MyUtils.myUtilMethod1();${cursor}
EDIT: I completely re-wrote the question since it seems like I was not clear enough in my first two versions. Thanks for the suggestions so far.
I would like to internationalize the source code for a tutorial project (please notice, not the runtime application). Here is an example (in Java):
/** A comment */
public String doSomething() {
System.out.println("Something was done successfully");
}
in English , and then have the French version be something like:
/** Un commentaire */
public String faitQuelqueChose() {
System.out.println("Quelque chose a été fait avec succès.");
}
and so on. And then have something like a properties file somewhere to edit these translations with usual tools, such as:
com.foo.class.comment1=A comment
com.foo.class.method1=doSomething
com.foo.class.string1=Something was done successfully
and for other languages:
com.foo.class.comment1=Un commentaire
com.foo.class.method1=faitQuelqueChose
com.foo.class.string1=Quelque chose a été fait avec succès.
I am trying to find the easiest, most efficient and unobtrusive way to do this with the least amount of manual grunt work (other than obviously translating the actual text). Preferably working under Eclipse. For example, the original code would be written in English, then externalized (to properties, preferably leaving the original source untouched), translated (humanly) and then re-generated (as a separate source file / project).
Some trails I have found (other than what AlexS suggested):
AntLR, a language parser / generator. There seems to be a supporting Eclipse plugin
Using Eclipse's AST (Abstract Syntax Tree) and I guess building some kind of plugin.
I am just surprised there isn't a tool out there that does this already.
I'd use unique strings as methodnames (or anything you want to be replaced by localized versions.
public String m37hod_1() {
System.out.println(m355a6e_1);
}
then I'd define a propertyfile for each language like this:
m37hod_1=doSomething
m355a6e_1="Something was done successfully"
And then I'd write a small program parsing the sourcefiles and replacing the strings. So everything just outside eclipse.
Or I'd use the ant task Replace and propertyfiles as well, instead of a standalone translation program.
Something like that:
<replace
file="${src}/*.*"
value="defaultvalue"
propertyFile="${language}.properties">
<replacefilter
token="m37hod_1"
property="m37hod_1"/>
<replacefilter
token="m355a6e_1"
property="m355a6e_1"/>
</replace>
Using one of these methods you won't have to explain anything about localization in your tutorials (except you want to), but can concentrate on your real topic.
What you want is a massive code change engine.
ANTLR won't do the trick; ASTs are necessary but not sufficient. See my essay on Life After Parsing. Eclipse's "AST" may be better, if the Eclipse package provides some support for name and type resolution; otherwise you'll never be able to figure out how to replace each "doSomething" (might be overloaded or local), unless you are willing to replace them all identically (and you likely can't do that, because some symbols refer to Java library elements).
Our DMS Software Reengineering Toolkit could be used to accomplish your task. DMS can parse Java to ASTs (including comment capture), traverse the ASTs in arbitrary ways, analyze/change ASTs, and the export modified ASTs as valid source code (including the comments).
Basically you want to enumerate all comments, strings, and declarations of identifiers, export them to an external "database" to be mapped (manually? by Google Translate?) to an equivalent. In each case you want to note not only the item of interest, but its precise location (source file, line, even column) because items that are spelled identically in the original text may need different spellings in the modified text.
Enumeration of strings is pretty easy if you have the AST; simply crawl the tree and look for tree nodes containing string literals. (ANTLR and Eclipse can surely do this, too).
Enumeration of comments is also straightforward if the parser you have captures comments. DMS does. I'm not quite sure if ANTLR's Java grammar does, or the Eclipse AST engine; I suspect they are both capable.
Enumeration of declarations (classes, methods, fields, locals) is relatively straightforward; there's rather more cases to worry about (e.g., anonymous classes containing extensions to base classes). You can code a procedure to walk the AST and match the tree structures, but here's the place that DMS starts to make a difference: you can write surface-syntax patterns that look like the source code you want to match. For instance:
pattern local_for_loop_index(i: IDENTIFIER, t: type, e: expression, e2: expression, e3:expression): for_loop_header
= "for (\t \i = \e,\e2,\e3)"
will match declarations of local for loop variables, and return subtrees for the IDENTIFIER, the type, and the various expressions; you'd want to capture just the identifier (and its location, easily done by taking if from the source position information that DMS stamps on every tree node). You'd probably need 10-20 such patterns to cover the cases of all the different kinds of identifiers.
Capture step completed, something needs to translate all the captured entities to your target language. I'll leave that to you; what's left is to put the translated entities back.
The key to this is the precise source location. A line number isn't good enough in practice; you may have several translated entities in the same line, in the worst case, some with different scopes (imagine nested for loops for example). The replacement process for comments, strings and the declarations are straightforward; rescan the tree for nodes that match any of the identified locations, and replace the entity found there with its translation. (You can do this with DMS and ANTLR. I think Eclipse ADT requires you generate a "patch" but I guess that would work.).
The fun part comes in replacing the identifier uses. For this, you need to know two things:
for any use of an identifier, what is the declaration is uses; if you know this, you can replace it with the new name for the declaration; DMS provides full name and type resolution as well as a usage list, making this pretty easy, and
Do renamed identifiers shadow one another in scopes differently than the originals? This is harder to do in general. However, for the Java language, we have a "shadowing" check, so you can at least decide after renaming that you have an issues. (There's even a renaming procedure that can be used to resolve such shadowing conflicts
After patching the trees, you simply rewrite the patched tree back out as a source file using DMS's built-in prettyprinter. I think Eclipse AST can write out its tree plus patches. I'm not sure ANTLR provides any facilities for regenerating source code from ASTs, although somebody may have coded one for the Java grammar. This is harder to do than it sounds, because of all the picky detail. YMMV.
Given your goal, I'm a little surprised that you don't want a sourcefile "foo.java" containing "class foo { ... }" to get renamed to .java. This would require not only writing the transformed tree to the translated file name (pretty easy) but perhaps even reconstructing the directory tree (DMS provides facilities for doing directory construction and file copies, too).
If you want to do this for many languages, you'd need to run the process once per language. If you wanted to do this just for strings (the classic internationalization case), you'd replace each string (that needs changing, not all of them do) by a call on a resource access with a unique resource id; a runtime table would hold the various strings.
One approach would be to finish the code in one language, then translate to others.
You could use Eclipse to help you.
Copy the finished code to language-specific projects.
Then:
Identifiers: In the Outline view (Window>Show View>Outline), select each item and Refactor>Rename (Alt+Shift+R). This takes care of renaming the identifier wherever it's used.
Comments: Use Search>File to find all instances of "/*" or "//". Click on each and modify.
Strings:
Use Source>Externalize strings to find all of the literal strings.
Search>File for "Messages.getString()".
Click on each result and modify.
On each file, ''Edit>Find/Replace'', replacing "//\$NON-NLS-.*\$" with empty string.
for the printed/logged string, java possess some internatization functionnalities, aka ResourceBundle. There is a tutorial about this on oracle site
Eclipse also possess a funtionnality for this ("Externalize String", as i recall).
for the function name, i don't think there anything out, since this will require you to maintain the code source on many version...
regards
Use .properties file, like:
Locale locale = new Locale(language, country);
ResourceBundle captions= ResourceBundle.getBundle("Messages",locale);
This way, Java picks the Messages.properties file according to the current local (which is acquired from the operating system or Java locale settings)
The file should be on the classpath, called Messages.properties (the default one), or Messages_de.properties for German, etc.
See this for a complete tutorial:
http://docs.oracle.com/javase/tutorial/i18n/intro/steps.html
As far as the source code goes, I'd strongly recommend staying with English. Method names like getUnternehmen() are worse to the average developer then plain English ones.
If you need to familiarize foreign developers to your code, write a proper developer documentation in their language.
If you'd like to have Javadoc in both English and other languages, see this SO thread.
You could write your code using freemarker templates (or another templating language such as velocity).
doSomething.tml
/** ${lang['doSomething.comment']} */
public String ${lang['doSomething.methodName']}() {
System.out.println("${lang['doSomething.message']}");
}
lang_en.prop
doSomething.comment=A comment
doSomething.methodName=doSomething
doSomething.message=Something was done successfully
And then merge the template with each language prop file during your build (using Ant / Gradle / Maven etc.)
I posted a question on the DOxygen forums and also am posting it here for a better response.
I have a moderately sized C project of about 2,900 functions. I am using DOxygen 1.5.9 and it is successfully generating a call graph for the functions. Is there a way to extract this out for further analysis? A simple paired list would be sufficient, e.g.
Caller,Callee
FunctionX, FunctionY
...
I am comfortable with XSLT but I must say that the DOxygen XML output is complex. Has anyone done this before and can provide some guidance on how to parse the XML files?
Thanks in advance!
Based on what I see in the contrived example that I created,
Parse files with a name similar to ^_(.+)\d+(c|cpp|h|hpp)\.xml$, if my regex-foo is right.
Find all <memberdef kind="function">. It has a unique id attribute. I believe the XPath for this is //memberdef[#kind='function'].
Within that element, find all <references>.
For each of those tags, the refid attribute uniquely refers to the id attribute of the corresponding <memberdef> that is being called.
The text node within each <references> corresponds to the <name> of the corresponding <memberdef> that is being called.
This seems like a nice, straightforward way to express call graphs. You should have no trouble using XSLT or any other sane XML-parsing suite to get the desired results.
I don't quite understand how to use application specific YAML tags, and maybe its because my desired use of them is purely wrong. I am using YAML for a configuration file and was hoping to use tags to provide my configuration loader with a hint as to what datatype it should parse the data into - application specific datatypes.
I'm also using libyaml with C.
So I'm trying to do something like...
shapes:
square: "0,4,8,16"
circle: "5,10"
In my app I'd like to use tags as hints so I can load the values of square into my square data structure, and the values of circle into my circle data structure (these values mean nothing in this example).
So I'm currently doing:
shapes:
square: !square "0,4,8,16"
circle: !circle "5,10"
Libyaml will provide a tag of "!square" when I'm passed the scalar "0,4,8,16". Is it valid to use this tag to provide my loader with a hint of how to process the scalar?
Since it does work for me, I'm more curious to know if its proper. And if not, how would I go about making this more proper.
Thanks.
I know that this is an ancient question, but anyway I've seen !int, etc being used in yaml files before so I went to look up the specs at Yaml 1.2 Spec # Tags
application specific tag: !something |
The semantics of the tag
above may be different for
different documents.
As per the document, it does look like your intended usage of tags is correct for application specific tag.