Appion

I think the only problem is there is a flag in the php code that disables the input box, which prevents user input. For example in uploadstack.php the code for the Output directory box is:

echo docpop('outdir','<b>Output directory:</b>');
echo "<br/>\n";
echo "<input type='text' name='disoutdir' value='$outdir' size='40' disabled/>\n";
echo "<input type='hidden' name='outdir' value='$outdir'/>\n";

When I remove the "disabled" flag in the code output directory box becomes active. Is there any reason why the programmer initially wanted this feature disabled? What are the problems if the user cannot control the output directory? I think I can handle this bug if you want to reassign it to me, Eric.

Make sure output directories are all active and able to be edited by user. PHP code review on:
uploadTemplateStack.php - r15097, r15110
jumpSubStack.php - r15098, r15104
uploadstack.php - r15099, r15105
uploadtemplate.php - r15100, r15107
uploadimage.php - r15101, r15109
alignSubStack.php - r15111
applyJunkCutoff.php - r15147
coranSubStack.php - r15148
postproc.php - r15149
sortJunk.php - r15150
runClusterCoran.php - r15151, r15200
uploadrecon.php, uploadXmippRecon.php - r15183
uploadFrealign.php =- r15185

r15184 reset uploadimage.php to the original layout which has no output directory input. Anchi pointed out that if you are uploading images to a new session there will be no default output directory and the user would have to input one from scratch. This is dangerous. In addition, if you are uploading more images to a session they must all go to the same location. Giving the user the ability to input the directory opens up a lot of room for error and will most certainly cause problems down the road if they are uploading images in the same session to different directories. If there are any other tools that have been changed that will present problems such as this one, let me know and I will change them back. Also, I am refraining from editing the tomography tools at this point because I have never used them and do not know how they work. If someone else wants to take these on, please do so.

runClusterCoran.php and other clustering routines may not be a good candidate for editable outdir because it uses the feature analysis runname and does not record its own path in the database. However, I see that apClusterStackData does have path taken from rundir

Neil, would there be a problem if the feature analysis and clustering use different rundir?

Clustering needs to be run in the same directory as feature analysis, they are linked together.

r15200 disabled the output directory in runClusterCoran.php and added a note explaining to the user why it can't be edited. This is linked to bug #1097 as well.