no image showing in viewers

This is a question from mbycliaw:

....when I used manual application to collect an uncorrected image. I can not see its image on web browser (dbem_1_4_1) either By image viewer or 3 way viewer.

I also try the test data come with dbem_1_4_1 package and still no image shown. Only an image file name display at the window which Supposed to show image.

I click on different image file name on list and same result. Is it because I have not finished calbration and preset? Because when I use IE on XP to browse it and I see the program seems to get some information from preset.

Anchi

Replies (8)

no image showing in viewers - Added by Anchi Cheng over 17 years ago

I don't know all the details about the viewer installation but what you describe seems to be more an installation problem that lacks the component that reads mrc files properly.

I can answer the last part, though. You should be able to view images collected from Manual application without reference images or preset. Images from Manual application have a fake preset called manual for the viewer. The pixel size might be a problem. However, since you don't even see the test image, I doubt that is the cause.

Anchi

- Added by Jim Pulokas over 17 years ago

To get a status report of your PHP web server installation, create a file in your top level web server directory (htdocs, or whatever it is called on your system) called "info.php" with the following contents:

<html>

<head>

<title><? echo $SERVER_NAME ?></title>

</head>

<body  bgproperties="fixed" leftmargin="10" topmargin="5" marginwidth="0" marginheight="5" alink="#00CCCC" vlink="#006699" link="#006699"> 

<?
phpinfo();
?>
</body>
</html>

Then go to that page with your web browser. It should print out a lot of information about the php modules you have installed. Make sure you have the following listed in the output of info.php:

- mrc

- gd

- mysql

Also tell us what version of php is reported by info.php, and also what version of each of those modules.

- Added by Yen-Chywan Liaw over 17 years ago

My php version is 5.1.2

my mysql version is 5.0.18

I can not find gd and mrc.

I install php gd extension

then I find gd version is 2.1.10

But I still can not find mrc.

I did follow the instruction to copy

cp ext/php_mrc_1_2-apache2_0-i586-suse-linux.so /usr/lib/php5/extensions

I also try php5 -re mrc.so

and program fail to find mrc.so. But it is in /usr/lib/php5/extensions/mrc.so

????

- Added by Anonymous over 17 years ago

It looks like php shared library mrc.so is not loaded.

create a file called: info.php

add:

<?php
phpinfo();
?>

in a web browser, got to: http://[your host]/info.php

you'll find a list of loaded module.

Note: to be able to view mrc files you'll need the default php image library "gd" installed as well.

here is a How to with some example:

http://emg.nysbc.org/software/mrctools/mrc_so.php

- Added by Yen-Chywan Liaw over 17 years ago

Yes,

Now I can see image for test data come with dbem_1_4_1.

Also info.php shows mrc with version 1.3 and fft enable.

But for those images collected previously, I can either see white image or black image. Even more is when I click the "i" bottom. instead of showing image information, I see a empty page. ????

- Added by Yen-Chywan Liaw over 17 years ago

In addition, I did the ex1.php and ex2.php to test display the test data mymrc.mrc and both ok! which means the new compiled mrc.so should be OK!

then I ln -s those images I collected previously to mymrc.mrc and

php5 -c /etc/php5/apache2 -q ex1.php | display

They work ok!

So the problem is from viewimage.php or others, not mrc.so.

I forgot to mentioned when I view the images I collected previosly

In http://localhost/dbem_1_4_1/viewimage.php

the bottom show a line say "transfering data from localhost...."

and on the right top corner the circle is running, which means the

php page is doing something.

- Added by Anchi Cheng over 17 years ago

The message "Transfering data from xxx" is normal. So does the "running" indicator.

Am I correct that you see an image, not a broken link, in the display? The image is either white or black?

If it is the case, the image is loaded but not displayed right. The image viewer shows the mean as gray and some (5, I think) set standard deviation above and below as max and min, respectively. If there are large spike, it won't display right. If you click on the settings icon (a hand pointing to a list of menu), you will open a window in which you can change the color table. Uncheck AutoScale, and move the max/min tab on the scale, then click on Update. If you saw white image originally, you mayl need to move both max/min very close to the left for it to show gray.

We just ran into similar problem with an old camera installed on a new microscope. We might find out how to get it to go away soon.

Anchi

pixel size and imgreport - Added by Anchi Cheng over 17 years ago

I just confirmed that pixel size calibration PRIOR To image acquisition is indeed needed for displaying the image report page. Displaying the image itself should not be affected. Once you do calibrate the pixel size for the magnification, you can cheat the query by changing the date in the database but you do have to have one to start with. Inserting a new entry can go very wrong if you don't know every required field.

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