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Bug 1154 - batch save Java exception: access is denied
batch save Java exception: access is denied
Status: RESOLVED INVALID
Product: Fiji
Classification: Unclassified
Component: Other
unspecified
PC Windows
: P5 blocker
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-09-04 17:04 CDT by Aleksandra Denisin
Modified: 2015-10-13 14:46 CDT
1 user (show)

See Also:
Description Aleksandra Denisin 2015-09-04 17:04:01 CDT 
Hello
I am trying to run a batch process using a macro in ImageJ (using the Fiji version) and I get a Java warning when I try to batch save. The warning is a pop-up box with the following:
java.io.FileNotFoundException: "the path of my file" (Access is denied)
I tried to change the settings on Java by giving the C:Program Files\Java folder full control permissions on my machine and also always run Fiji as administrator. I've poked around online but have not found a solution to this problem. I am including my macro below, which references another plugin. I get the batch saving problem all the time, even when not doing a complex task with the open images.

Thank you so much for your help!
-Sasha

Macro:
  dir = getDirectory("Choose a Directory ");
  count = 1;
  listFiles(dir);
  setBatchMode(true);

  function listFiles(dir) {
  list=getFileList(dir);
  for (i = 300; i < list.length; i++) {
open (list[i]);
run("iterative PIV(Basic)..." , "piv1=64 sw1=128 piv2=32 sw2=96 piv3=0 sw3=0 correlation=0.80 what=[Accept this PIV and output] noise=0.20 threshold=5 c1=3 c2=1 batch path=["+dir+"]"); 
close();
    }
}
setBatchMode(false);


Information about your version of Java - this information is useful for the Fiji developers:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: CHECK_TURNED_OFF

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\PROGRA~1\Fiji.app/java/win64/jdk1.6.0_24/jre/
  ij.dir => C:\PROGRA~1\Fiji.app

Information about the version of each plugin:

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Comment 1 Curtis Rueden 2015-10-13 14:46:04 CDT 
It is not recommended to install Fiji to Program Files.
  http://imagej.net/Downloads#Installation

Instead, unpack the distribution somewhere you control, such as 'My Documents' or 'Desktop' in your home directory.

(As an aside: in the future, we will likely have an installer for ImageJ that installs into 'Program Files' like other software does, and sets the permissions appropriately. See https://github.com/imagej/imagej/issues/72 for details.)

By the way, it looks like you are running a _really_ old version of Fiji! You might want to try updating. But back up your existing installation first -- it will be a big update. ;-)