Hey I am new very new to programming in ImageJ macro, I would like to average all images in a folder, save that single average image in a separate folder
Presuming your images are logically ordered (e.g., image001, image002, image003 etc...) - try this:
setBatchMode(true);
//retrieve images from directory
dir = getDirectory("Choose a directory of images...");
list = getFileList(dir);
for (i=0; i <list.length; i++) {
path = dir + list[i];
open(path);
}
run("Images to Stack", "name=Stack title=[] use");
stackImage = getTitle();
//make an average intensity image
run("Z Project...", "projection=[Average Intensity]");
//save out to new folder
outputPath = dir + File.separator + "separateFolder";
if (!File.exists(outputPath)) File.makeDirectory(outputPath);
newPath = outputPath + File.separator + "averagedImage";
run("Save","save=[newPath]");
close(stackImage);
close();
setBatchMode(false);
Related
I am trying to get the folder size for some S3 folders with scala from my command line EMR.
I have JSON data stored as GZ files in S3. I find I can count the number of JSON records within my files:
spark.read.json("s3://mybucket/subfolder/subsubfolder/").count
But now I need to know how much GB that data accounts for.
I am finding options to get the size for distinct files, but not for a whole folder all up.
I am finding options to get the size for distinct files, but not for a
whole folder all up.
Solution :
Option1:
Get the s3 access by FileSystem
val fs = FileSystem.get(new URI(ipPath), spark.sparkContext.hadoopConfiguration)
Note :
1) new URI is important other wise it will connect to
hadoop file system path instread of s3 file system(object store :-)) path . using new URI you are giving scheme s3://
here.
2) org.apache.commons.io.FileUtils.byteCountToDisplaySize will
give display sizes of file system in GB MB etc...
/**
* recursively print file sizes
*
* #param filePath
* #param fs
* #return
*/
#throws[FileNotFoundException]
#throws[IOException]
def getDisplaysizesOfS3Files(filePath: org.apache.hadoop.fs.Path, fs: org.apache.hadoop.fs.FileSystem): scala.collection.mutable.ListBuffer[String] = {
val fileList = new scala.collection.mutable.ListBuffer[String]
val fileStatus = fs.listStatus(filePath)
for (fileStat <- fileStatus) {
println(s"file path Name : ${fileStat.getPath.toString} length is ${fileStat.getLen}")
if (fileStat.isDirectory) fileList ++= (getDisplaysizesOfS3Files(fileStat.getPath, fs))
else if (fileStat.getLen > 0 && !fileStat.getPath.toString.isEmpty) {
println("fileStat.getPath.toString" + fileStat.getPath.toString)
fileList += fileStat.getPath.toString
val size = fileStat.getLen
val display = org.apache.commons.io.FileUtils.byteCountToDisplaySize(size)
println(" length zero files \n " + fileStat)
println("Name = " + fileStat.getPath().getName());
println("Size = " + size);
println("Display = " + display);
} else if (fileStat.getLen == 0) {
println(" length zero files \n " + fileStat)
}
}
fileList
}
based on your requirement, you can modify the code... you can sum up all the distinct files.
Option 2 : Simple and crispy using getContentSummary
implicit val spark = SparkSession.builder().appName("ObjectSummary").getOrCreate()
/**
* getDisplaysizesOfS3Files
* #param path
* #param spark [[org.apache.spark.sql.SparkSession]]
*/
def getDisplaysizesOfS3Files(path: String)( implicit spark: org.apache.spark.sql.SparkSession): Unit = {
val filePath = new org.apache.hadoop.fs.Path(path)
val fileSystem = filePath.getFileSystem(spark.sparkContext.hadoopConfiguration)
val size = fileSystem.getContentSummary(filePath).getLength
val display = org.apache.commons.io.FileUtils.byteCountToDisplaySize(size)
println("path = " + path);
println("Size = " + size);
println("Display = " + display);
}
Note : Any option showed above will work for
local or
hdfs or
s3
as well
I'm trying to merge all my text files into one file.
The problem I am having is that the file names are based on data previously captured in my app. I don't know how to define my path to where the text files are, maybe. I keep getting a error, but the path to the files are correct.
What am I missing?
string filesread = System.AppDomain.CurrentDomain.BaseDirectory + #"\data\Customers\" + CustComboB.SelectedItem + #"\";
Directory.GetFiles(filesread);
using (var output = File.Create("allfiles.txt"))
{
foreach (var file in new[] { filesread })
{
using (var input = File.OpenRead(file))
{
input.CopyTo(output);
}
}
}
System.Diagnostics.Process.Start("allfiles.txt");
my error:
System.IO.DirectoryNotFoundException
HResult=0x80070003
Message=Could not find a part of the path 'C:\Users\simeo\source\repos\UpMarker\UpMarker\bin\Debug\data\Customers\13Dec2018\'.
I cant post a pic, but let me try and give some more details on my form.
I select a combobox item, this item is a directory. then I have a listbox that displays the files in my directory. I then have a button that executes my desires of combining the files. thanks
I finally got it working.
string path = #"data\Customers\" + CustComboB.SelectedItem;
string topath = #"data\Customers\";
string files = "*.txt";
string[] txtFiles;
txtFiles = Directory.GetFiles(path, files);
using (StreamWriter writer = new StreamWriter(topath + #"\allfiles.txt"))
{
for (int i = 0; i < txtFiles.Length; i++)
{
using (StreamReader reader = File.OpenText(txtFiles[i]))
{
writer.Write(reader.ReadToEnd());
}
}
System.Diagnostics.Process.Start(topath + #"\allfiles.txt");
}
I tried to merge the red and the green channel images to generate a composite image. My code reads like :
path = getDirectory("Choose a Directory");
filename = getFileList(path);
newDir = path + "Single_Channel" + File.separator;
File.makeDirectory(newDir);
for (i=0; i<filename.length; i++)
{
if(endsWith(filename[i], ".tif"))
{
open(path+filename[i]);
filenameG = filename[i]+" (green)";
filenameR = filename[i+1]+" (red)";
run("Merge Channels...","c1=[" + filenameR + "] c2=[" + filenameG + "] create");
rename(filename[i]+"_composite");
saveAs("tiff", newDir+getTitle);
close();
}
}
The error am getting is : The file ".........." is not for channel C1 (red).
Because of this am unable to proceed to further processing of my image.
Any feedback is appreciated.
Thank you.
I have list of files saved in a folder and i am putting this logic to get them in a array..still it is showing just the first name can u please help me out..
filePath = Environment.getExternalStorageDirectory() + "/openedpages/";
file = new File(filePath);
if (file.exists()) {
filenew = file.listFiles();
for (int i = 0; i < file.listFiles().length; i++) {
arr = new ArrayList<String>();
arr.add(filenew[i].getName());
}
System.out.println("print arr " + arr);
}
Thanks
please keep arr = new ArrayList(); out of for lop and try.
Is it possible to move files programmatically based on virus scan status?
What I want to do is have a set of folders:
Incoming
Scanned
Scanned/Clean
Scanned/Infected
Not Scanned
Files would be dropped into the Incoming folder. At that point, I would like to kick off the antivirus and scan the files in the Incoming folder. Once complete, the files would then need to be moved to the appropriate folder, either Clean or Infected. If, for whatever reason, the file could not be scanned or had trouble scanning, it would be moved to the Not Scanned folder.
I was hoping there would be a way to script this out. Has anyone ever done anything like this before?
public void Scan()
{
string[] uploadPath = Directory.GetFiles(ConfigurationManager.AppSettings["UploadPath"]);
foreach(string filePath in uploadPath)
{
string fileName = Path.GetFileName(filePath);
string cleanPath = Path.Combine(ConfigurationManager.AppSettings["CleanPath"], fileName);
try
{
Process AV = new Process();
AV.StartInfo.UseShellExecute = false;
AV.StartInfo.RedirectStandardOutput = true;
AV.StartInfo.FileName = ConfigurationManager.AppSettings["VSApp"];
AV.StartInfo.Arguments = " -Scan -ScanType 3 -file " + ConfigurationManager.AppSettings["UploadPath"] + " -DisableRemediation";
AV.Start();
string output = AV.StandardOutput.ReadToEnd();
AV.WaitForExit();
if (AV.ExitCode == 0)
{
File.Move(filePath, cleanPath);
}
else if (AV.ExitCode == 2)
{
using (TextWriter tw = new StreamWriter(ConfigurationManager.AppSettings["FailedPath"] + fileName + ".txt"))
{
tw.WriteLine("2");
tw.Close();
}
using (TextWriter tw1 = new StreamWriter(ConfigurationManager.AppSettings["FailedFiles"] + fileName + ".txt"))
{
tw1.WriteLine(AV.StandardOutput);
tw1.Close();
}
File.Delete(filePath);
}
AV.Close();
}
catch (Exception ex)
{
if (ex.ToString().Contains("Could not find file"))
{
string failedFile = ConfigurationManager.AppSettings["FailedPath"] + fileName + ".txt";
string failedFileDesc = ConfigurationManager.AppSettings["FailedPath"] + fileName + "_ErrorDesc" + ".txt";
using (TextWriter tw = new StreamWriter(failedFile))
{
tw.WriteLine("2");
tw.Close();
}
using (TextWriter tw1 = new StreamWriter(failedFileDesc))
{
tw1.WriteLine(ex.ToString());
tw1.Close();
}
}
else
{
Thread.Sleep(2000);
if (runCounter == 0)
{
Scan();
}
runCounter++;
string errorFile = ConfigurationManager.AppSettings["ProcessErrorPath"] + fileName + ".txt";
using (TextWriter tw = new StreamWriter(errorFile))
{
tw.WriteLine(ex.ToString());
tw.Close();
}
}
}
}
}
I created this as a Windows Service. My OnStart method creates my FileSystemWatcher to watch the Upload Path. For On Created, I have a method that runs my Scan method and creates my counter and sets it to 0. My On Error event just logs. I had an issue where the FileSystemWatcher was trying to open the file before it had been uploaded, hence why I added the sleep.
Finally, I am using Microsoft Forefront's command line scanner. File path: C:\Program Files\Microsoft Security Client\mpcmdrun.exe.
Let me know if any questions.