ImageJ: Help Creating a LOOP that looks through folders and subfolders - loops

I am new to using imageJ and creating my own codes, anyways, I am trying to create a loop that runs all the roi's at once, but I am having trouble doing that. So far this is the code I have:
input = "S:\\Research Projects\\BAC\\machine training set\\Results_1stRound\\2016Data_1stRound\\epoch_based_training_0.7_TPF=0.615_FP=2.110\\SID130871_9999.330357336093230241152104825447607218951\\";
output = input;
function action(input, output, filename) {
open(input + filename);
setThreshold(112, 255);
run("Create Selection");
roiManager("Add");
roiManager("Select", 0);
saveAs("selection", output + filename);
close();
roiManager("Deselect");
roiManager("Delete");
}
list = getFileList(input);
for (i = 0; i < list.length; i++)
action(input, output, list[i]);
What I want the loop to do is to look through all the different SID files that I have so I wouldn't need the specific SID part in the input but I have no idea how to create a loop so that it looks through folders (SID files) and subfolders to create the rois. As of right now, I have to put the specific SID file in the input, so any help on how I can create a loop that looks through the different SID files at once and then create the rois would be great.

You can find some macro examples and examples on the ImageJ mailing list archive how to iterate over nested folders:
https://imagej.nih.gov/ij/macros/BatchProcessFolders.txt
http://imagej.1557.x6.nabble.com/batch-process-macro-td4469342.html

Related

Create text file to write/add of a couple of images name

I tried to get a script to create a text file that could write/add the images name, but the function
FileID = CreateFileForWriting(filename) does not work, it shows that was used by other process
I did not get this, is this function not right format or something is wrong, thx
Number Totaln
totaln=countdocumentwindowsoftype(5)
String filename, text
Number fileID
if (!SaveasDialog( "save text file as",getapplicationdirectory(2,0) + "Imagename.txt", filename))exit(0)
fileID = CreateFileForWriting(filename)
number i
for(i = 0; i <totaln; i++)
{
image imgSRC
imgSRC := GetFrontImage()
string imgname=getname(imgSRC)
WriteFile(fileID,"imgname")
Result("imgname")
}
Your code is nearly fine, but if you use the low-level API for file I/O you need to ensure that you close files you've opened or created.
Your script doesn't. Therefore, it runs fine exactly 1 time but will fail on re-run (when the file is still considered open.)
To fix it, you need to have closefile(fileID) at the end.
( BTW, if you script exits or throws after opening a file but before closing it, you have the same problem. )
However, I would strongly recommend not using the low-level API but the file streaming object instead. It also provides an automated file-closing mechanism so that you don't run into this issue.
Doing what you do in your script would be written as:
void writeCurrentImageNamesToText()
{
number nDoc = CountImageDocuments()
string filename
if (!SaveasDialog( "save text file as",getapplicationdirectory(2,0) + "Imagename.txt", filename)) return
number fileID = CreateFileForWriting(filename)
object fStream = NewStreamFromFileReference(fileID,1) // 1 for auto-close file when out of scope
for( number i = 0; i <nDoc; i++ ){
string name = GetImageDocument(i).ImageDocumentGetName()
fStream.StreamWriteAsText( 0, name + "\n" ) // 0 = use system encoding for text
}
}
writeCurrentImageNamesToText()

Find specific number of a word from the beginning in string

I've been gathering information using api calls from my jira. Information gathered is saved in a body file and it has the following content:
No tickets:
{"startAt":0,"maxResults":50,"total":0,"issues":[]}{"startAt":0,"maxResults":50,"total":0,"issues":[]}
One Ticket:
{"expand":"names,schema","startAt":0,"maxResults":50,"total":1,"issues":[{"expand":"operations,versionedRepresentations,editmeta,changelog,renderedFields","id":"456881","self":"https://myjira...com","key":"TICKET-1111","fields":{"summary":"[TICKET] New Test jira","created":"2018-12-17T01:47:09.000-0800"}}]}{"expand":"names,schema","startAt":0,"maxResults":50,"total":1,"issues":[{"expand":"operations,versionedRepresentations,editmeta,changelog,renderedFields","id":"456881","self":"https://myjira...com","key":"TICKET-1111","fields":{"summary":"[TICKET] New Test jira","created":"2018-12-17T01:47:09.000-0800"}}]}
Two Tickets:
{expand:schema,names,startAt:0,maxResults:50,total:2,issues:[{expand:operations,versionedRepresentations,editmeta,changelog,renderedFields,id:456881,self:https://myjira...com,key:TICKET-1111,fields:{summary:[TICKET] New Test jira,created:2018-12-17T01:47:09.000-0800}},{expand:operations,versionedRepresentations,editmeta,changelog,renderedFields,id:320281,self:https://myjira...com,key:TICKET-2222,fields:{summary:[TICKET] Test jira,created:2016-03-18T07:58:52.000-0700}}]}{expand:schema,names,startAt:0,maxResults:50,total:2,issues:[{expand:operations,versionedRepresentations,editmeta,changelog,renderedFields,id:456881,self:https://myjira...com,key:TICKET-1111,fields:{summary:[TICKET] New Test jira,created:2018-12-17T01:47:09.000-0800}},{expand:operations,versionedRepresentations,editmeta,changelog,renderedFields,id:320281,self:https://myjira...com,key:TICKET-2222,fields:{summary:[TICKET] Test jira,created:2016-03-18T07:58:52.000-0700}}]}
etc..
Using this code I've been able to gather total open tickets:
std::ifstream t("BodyOpenIssues.out");
std::string BodyString((std::istreambuf_iterator<char>(t)),
std::istreambuf_iterator<char>());
// Removing Quotes
BodyString.erase(std::remove(BodyString.begin(), BodyString.end(), '"'), BodyString.end());
int Result = 0;
unsigned first = BodyString.find("total:");
unsigned last = BodyString.find(",issues");
std::string TotalOpenIssues = BodyString.substr(first + 6, last - (first + 6));
Result = std::stoi(TotalOpenIssues);
return Result;
Using a second function I'm trying to get the keys based on total open tickets.
if (GetOpenIssuesNumber() > 0)
{
std::ifstream t("BodyOpenIssues.out");
std::string BodyString((std::istreambuf_iterator<char>(t)),
std::istreambuf_iterator<char>());
// Removing Quotes
BodyString.erase(std::remove(BodyString.begin(), BodyString.end(), '"'), BodyString.end());
unsigned first = BodyString.find("key:TICKET-");
unsigned last = BodyString.find(",fields");
std::string TotalOpenIssues = BodyString.substr(first + 11, last - (first + 11));
String^ Result = gcnew String(TotalOpenIssues.c_str());
return "TICKET-" + Result;
}
else
{
return "No open issues found";
}
What I mean is:
If Total is 1 to search from the beginning and find the first key TICKET-1111.
If Total is 2 to search from the beginning and get the first key TICKET-1111 then to continue from there and to find the next key TICKET-2222.
And based on that total to find that many keys in that string.
I got lost from all the casting between the types as ifstream reads the file and I save the result in std::string. After the find I save the result in System::String to use it in my Label.. I've been researching and found out that I can use char array but I can't make it dynamic based on BodyString.length().
If more information is required please let me know.
Any suggestions are really appreciated! Thank you in advance!
I went for nlohmann json library. It has everything I need. Thank you Walnut!
These are formatted as JSON. You should use a JSON library for C++ and parse the files with that. Using search/replace is unnecessary complicated and you will likely run into corner cases you haven't considered sooner or later (do you really want the code to randomly miss tickets, etc.?). Also String^ is not C++. Are you writing C++/CLI instead of C++? If so, please tag c++-cli instead of c++. – walnut

Create new line in text file X times

I want to write a string to file, n number of times (n being the length of the string). With each insertion being on a new line.
For example, the string "antallabel" (with a length of 10), should be inserted into a file 10 times, with each insertion on its own line. Should I use an array, list or something else?
I'm really new to programming, so I hope this question makes sense.
Check if file exists, then generate 2 files:
if (File.Exists(fullPath)) {
File.Delete(fullPath);
File.WriteAllText(fullPath, totalv + ";" + laste + ";" + antallabels);
File.Create(filePath + #"\" + controlFile).Close();
}
else
{
File.WriteAllText(fullPath, totalv + ";" + laste);
File.Create(filePath + #"\" + controlFile).Close();
I do not think you need this code at all. The WriteAllText(...) function is explained here.
Creates a new file, write the contents to the file, and then closes the file. If the target file already exists, it is overwritten.
So if it not exist it will be created and if it exists it will be deleted and recreated with your content. Please consider also adding the programming language as tag.
for(int i = 0; i < inputVar.length; i++) {
//do sth. as many times as the string is long
File.AppendAllText(path, inputVar + System.Environment.NewLine);
}

How can I password protect a file regardless of its extension in Java 8 ro Java 10

I have tried doing this by encrypting individual files but I have a lot of data (~20GB) and hence it would take a lot of time. In my test it took 2.28 minutes to encrypt a single file of size 80MB.
Is there a quicker way to be able to password protect that would apply to any any file (text/binary/multimedia)?
If you are just trying to hide the file from others, you can try to encrypt the file path instead of encrypting the whole huge file.
For the path you mentioned: text/binary/multimedia, you can try to encrypt it by a method as:
private static String getEncryptedPath(String filePath) {
String[] tokens = filePath.split("/");
List<String> tList = new ArrayList<>();
for (int i = 0; i < tokens.length; i++) {
tList.add(Hashing.md5().newHasher() // com.google.common.hash.Hashing;
.putString(tokens[i] + filePath, StandardCharsets.UTF_8).hash().toString()
.substring(2 * i, 2 * i + 5)); // to make it impossible to encrypt, add your custom secret here;
}
return String.join("/", tList);
}
and then it becomes an encrypted path as:
72b12/9cbb3/4a5f3
Once you know the real path text/binary/multimedia, any time you want to access the file, you can just use this method to get the real file path 72b12/9cbb3/4a5f3.

Is there a way to make the output file of a stream:file?fileName= dynamic?

Given a simple route like this
route.from("direct:foo")
.split()
.tokenize("\n")
.streaming()
.to("stream:file?fileName=target/streaming${header.count}.txt&closeOnDone=true");
which I then trigger with this
#Test
public void splitAndStreamToFile() {
StringBuilder builder = new StringBuilder();
for(int i = 0; i < 500; i++) {
builder.append(i);
builder.append("\n");
}
for(int i = 0; i < 10; i++) {
template.sendBodyAndHeader(builder.toString(), "count", i);
}
}
I get one big file that contains 10 times 500 lines, where I would have hoped to have 10 files that contain 500 lines each.
In other words, it seems that the fileName in the stream:file endpoint is not dynamic. I am wondering if this is at all possible? My google-fu turned up nothing so far.
EDIT:
With Claus' answer, I got it to work like this:
route.from("direct:foo")
.split()
.tokenize("\n")
.streaming()
.recipientList(route.simple("stream:file?fileName=target/streaming${header.count}.txt&closeOnDone=true"));
Its a dynamic to which there is an EIP pattern for:
http://camel.apache.org/how-to-use-a-dynamic-uri-in-to.html
But it could be a good idea to support the file/simple language on the fileName option as the regular file component does. Fell free to log a JIRA ticket about this improvement.
Sourcecode of the StreamProducer looks like it does not support any of the expression languages of Camel yet:
private OutputStream resolveStreamFromFile() throws IOException {
String fileName = endpoint.getFileName();
ObjectHelper.notEmpty(fileName, "fileName");
LOG.debug("About to write to file: {}", fileName);
File f = new File(fileName);
// will create a new file if missing or append to existing
f.getParentFile().mkdirs();
f.createNewFile();
return new FileOutputStream(f, true);
}
See sourecode.
If you need dynamic filenames, you should take a look at the file component, which supports the file language and the CamelFileName header.
In short,
toD uri=stream:file...
will do it.
The "toD" basically translates the "simple" or "file language" before it hits the stream component code...so that works for "fileName=..."

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