[ome-users] Running Bio-Formats from a plugin

[Ved P. Sharma]

Thanks for your answer Jmarie! Running BF Importer in a new thread did
improve its performance. Now, I have a new problem and wondering if you can
help me.

After opening files using BF Importer (in a new thread) I am performing
some operations on the images. It seems to me that Event Dispatch Thread
(EDT) starts running "some operations" before images are even open. How do
I stop EDT until new thread is finished opening the files? For example, the
following code logs "Number of open images= 0" and then opens the images.
Any ideas on how to fix this?

public void actionPerformed(ActionEvent e) {
        Thread queryThread = new Thread() {
            public void run() {
                IJ.run("Bio-Formats Importer",
"open=[d:\\Users\\ved\\Test\\image.dv] autoscale color_mode=Default
split_channels view=[Standard ImageJ] stack_order=Default");
            }
          };
queryThread.start();

int n = WindowManager.getImageCount();
IJ.log("Number of open images= "+n);
// perform some operations




On Tue, Jun 30, 2015 at 11:05 AM, Jean-Marie Burel (Staff) <
j.burel at dundee.ac.uk> wrote:

>  Dear Ved
>
>  This is due to a threading issue
> When your frame is displayed and you click on the button,
>  you are “blocking”  the UI when Bio-Formats is reading the file.
>
>  If you do not invoke Bio-Formats in the UI thread, you should see the
> same performance
> For demo
>
>  public void actionPerformed(ActionEvent e) {
>
>         Thread queryThread = new Thread() {
>
>             public void run() {
>
>                 IJ.run("Bio-Formats Importer",
> "open=[d:\\Users\\ved\\Test\\image.dv] autoscale color_mode=Default
> split_channels view=[Standard ImageJ] stack_order=Default");
>
>             }
>
>           };
>
>           queryThread.start();
>
>
>
>     }
>
>
>
>  Cheers
>
>  Jmarie
>
>   From: "Ved P. Sharma" <vedsharma at gmail.com>
> Reply-To: "ved.sharma at gmail.com" <ved.sharma at gmail.com>, OME User Support
> List <ome-users at lists.openmicroscopy.org.uk>
> Date: Friday, 26 June 2015 18:51
> To: "Balaji Ramalingam (Staff)" <b.ramalingam at dundee.ac.uk>
> Cc: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] Running Bio-Formats from a plugin
>
>    Dear Balaji,
>
>  I think the ActionListener in my plugin is slowing the BF Importer. Take
> a look at a sample code below. The first call to BF importer from inside
> BF_plugin() opens image quickly but when I press the "open image" button,
> it takes 5-10 sec to open the same image. Any thoughts on why
> ActionListener is slowing things down and how to remedy this?
>
>  Thanks,
>
>  Ved
>
>
>  // ******************* plugin starts here ****************************
> import ij.plugin.frame.*;
> import java.awt.event.*;
> import ij.*;
> import ij.gui.*;
> import javax.swing.*;
>
> public class BF_plugin extends PlugInFrame implements ActionListener {
>     private JPanel panel;
>     public BF_plugin() {
>         super("BF_plugin");
>         panel = new JPanel();
>         JButton b = new JButton("open image");
>         b.addActionListener(this);
>         panel.add(b);
>         add(panel);
>         pack();
>         GUI.center(this);
>         setVisible(true);
>         IJ.run("Bio-Formats Importer",
> "open=[d:\\Users\\ved\\Test\\image.dv] autoscale color_mode=Default
> split_channels view=[Standard ImageJ] stack_order=Default");
>     }
>     public void actionPerformed(ActionEvent e) {
>         IJ.run("Bio-Formats Importer",
> "open=[d:\\Users\\ved\\Test\\image.dv] autoscale color_mode=Default
> split_channels view=[Standard ImageJ] stack_order=Default");
>     }
> }
> // ******************* plugin ends here ****************************
>
>
> On Fri, Jun 26, 2015 at 10:33 AM, Balaji Ramalingam (Staff) <
> b.ramalingam at dundee.ac.uk> wrote:
>
>>  Hi,
>>
>>  Thank you for reporting your issue.
>> It would be great if you could expand the “options” that were used to
>> open the image within the plugin.
>>
>>  Could you please check the following,
>>
>>    1. open ImageJ. Go to Plugins—>Macro—> Record
>>    2. In the Macro Recorder window , please use the drop down menu for
>>    “Record” and select “Java” as the option.
>>    3. Repeat the Manual workflow described in your post (which opens the
>>    file within a fraction of a second).This will record the api method call ,
>>    in the Recorder window.
>>    4. And check if the “options” in your plugin, matches the “options”
>>    in the Macro Recorder, for the IJ.Run method.
>>
>> If they match, there should be no difference in terms of performance in
>> the import call.
>> Please let us know, if you find otherwise.
>>
>>  Best,
>> Balaji
>>
>>  __________________
>>
>> Mr Balaji Ramalingam
>>
>> Software Developer
>>
>> OME Team
>>
>> College of Life Sciences
>>
>> University of Dundee
>>
>>   From: "Ved P. Sharma" <vedsharma at gmail.com>
>> Reply-To: "ved.sharma at gmail.com" <ved.sharma at gmail.com>, OME User
>> Support List <ome-users at lists.openmicroscopy.org.uk>
>> Date: Thursday, 25 June 2015 20:11
>> To: "ome-users at lists.openmicroscopy.org.uk" <
>> ome-users at lists.openmicroscopy.org.uk>
>> Subject: [ome-users] Running Bio-Formats from a plugin
>>
>>    Hi,
>>
>>  When I run *Bio-Formats Importer* from ImageJ, it opens an image file
>> of size ~ 20MB within a fraction of a second. When I open the same image
>> file by calling *Bio-Formats Importer* from inside a plugin using
>> IJ.run("Bio-Formats Importer", "options"), it takes a long time to open the
>> file (~ 10 sec). It starts with a white background and then after about
>> ~5-10 seconds, the image is displayed. Can anybody tell me what am I doing
>> wrong when calling BF Importer from inside a plugin?
>>
>> *System info:* I have ImageJ 1.49v running on WIndows 7, 64-bit computer
>> and I have installed bioformats_package.jar (ver 5.1.2) in the plugins
>> folder of ImageJ.
>>
>>  Thanks,
>>
>>  Ved
>>
>> _________________________________
>> Ved P. Sharma, PhD
>> Dept. of Anatomy and Structural Biology
>> Albert Einstein College of Medicine
>> Bronx, NY 10461
>>
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
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