|
From: Lauren Fisher <lfisher@scripps.edu>
|
|
Date: February 24, 2011 10:59:48 AM PST
|
|
To: Jeffrey Speir <speir@scripps.edu>
|
|
Subject: Re: Any way to make new stack from selected particle images?
|
|
|
|
I did submit an issue in redmine for the include selected particles feature and I have already written the code to add the feature in. It is in code review right now and hopefully will be functional soon. If you want I can add you as a watcher on the issue so you will be cc'ed on all updates.
|
|
|
|
As for the center particles issue, the error check for the outer mask prevents you from selecting a mask that is more than 1/2 the boxsize. On your dataset (11jan12a, stack6-sub6) I only got this error message: ERROR: Mask radius too large, must be smaller than 240 pixels when I set the boxsize above 240. When set to 240 or less it was fine. The same thing goes for maximum shift; it prevents you from selecting a shift larger than 1/2 your boxsize and I got this message: ERROR: Shift too large, must be smaller than 240 pixels when setting the shift to anything above 240. On stack5-sub8 it looks like the database lost the boxsize of the stack and therefore thinks everything above 0 is too large. I just did a little digging and it looks like this is a bug within sortjunk. I actually found another bug as well...the side menu does not tell you when a sort junk stack is running/queued/complete. So you can go ahead and submit a bug in redmine for this and assign it to me if you want. For now, if you want to do use a mask/shift during centering, center the stack before you sort the junk.
|
|
|
|
The second issue you ran into sounds like a minor bug with the default naming. It sets the stack runname based on the stack id of the stack you are centering....for example, stack5-sub8 is ID: 9 so it wanted to name the centered stack stack5-centered9. I am not sure why this would give you problems with not committing and then committing unless there is an error check to see if that directory and stack already exist. I can look into this a little more, but it's always a good idea to double check that the default runname that appion provides for you does not already exist because on occasion I have noticed it does get confused for reasons unknown to me.
|
|
|
|
Hope this all helps,
|
|
Lauren
|
|
|
|
On Feb 23, 2011, at 7:38 PM, Jeff Speir wrote:
|
|
Thanks for the workaround Lauren. I don't mind being the guinea pig when you and Christopher are so quick to help. I'm keeping notes and putting in feature requests as I run into things. I'll put this one in as a feature request as well if you haven't already.
|
|
|
|
Speaking of - ran into two more issues. I made a sub-stack using the exclude method and then went to Center Particles. If I put anything in the outer mask radius or maximum shift boxes, an error message would come up saying it was out of range, must be less than 0 (!?). The job ran if I left them blank.
|
|
|
|
The second issue was with the same centering job. I first ran it as a test, so did not commit to database. Then ran it again using the same job name, but now selected commit to database. It didn't go into the database the second time. I had to change the job name to something else to get it to show up in the database. It looked like the second job overwrote the older files, but the database import was not executed.
|
|
|
|
If you can confirm those two issues, I'll submit them as bugs. Otherwise, please tell me where I went wrong.
|
|
|
|
Cheers,
|
|
|
|
Jeff
|
|
|
|
|
|
On Feb 23, 2011, at 3:08 PM, Lauren Fisher wrote:
|
|
Sorry for all of the confusion, Jeff. Unfortunately, you are kind of a guinea pig for getting collaborators within Scripps running on appion. Obviously we are still working out the kinks in the process, so I apologize.
|
|
|
|
If I understand your last email correctly, you want to create a new template for template picking using a subset of an existing stack. One way to do this is to go to your completed stacks, click on "[Show original stack summary page]", find the stack you want and select "[Create Substack]". This allows you to choose a range of particles or a certain number of randomly selected particles. However, this does not allow you to choose specific particles that are not in sequential order. The stack viewer only allows you to exclude particles right now, not include selected particles. There is a workaround though, if you want to attempt it here are the steps:
|
|
|
|
-Select all of the particles you want with selection mode set to "exclude"
|
|
-Click "remove particles" which will direct you to a new webform
|
|
-Enter a description
|
|
-Click "Just Show Command" (Make sure you do not click "create substack" because this will remove all of your desired particles)
|
|
-Copy and paste the command into a terminal, but before you submit change the "--exclude" parameter to "--include" (Below is an example of a full command)
|
|
|
|
EX: subStack.py --old-stack-id=6 --description="testing particle inclusion command line" --include=0,1,2,3,4,5,6,7,8,9,11,17,18,37,19,20,23,24,25,27,26,30,10,40,72,152,153,154,155,161,144,145,146,147,148,149,150,151,169 --commit --rundir=/ami/data00/appion/11jan12a/stacks/sub6 --runname=sub6 --projectid=292 --expId=8404 --jobtype=makestack
|
|
|
|
I ran the above command on amibox03 which created stack6-sub6, so it should work for you as well, but let me know if it doesn't.
|
|
|
|
Best,
|
|
Lauren
|
|
On Feb 23, 2011, at 2:09 PM, Jeff Speir wrote:
|
|
Hi Lauren,
|
|
|
|
Everything is working now, thanks for the help. My goal was to select 100-200 particles from one stack to make a new smaller stack and then new template for further particle picking. I can select the particles now, but I don't see an option to just make a new stack or sub-stack from the selected particles. Only option given is to make templates.
|
|
|
|
There is an option to remove excluded particles to make a new stack, but I can't find the equivalent for selected particles. Is there a way to do this?
|
|
|
|
Cheers,
|
|
|
|
Jeff
|
|
|
|
|
|
|
|
Lauren Fisher
|
|
Automated Molecular Imaging Group
|
|
Department of Cell Biology
|
|
The Scripps Research Institute
|
|
10550 North Torrey Pines Road, CB 129
|
|
La Jolla, CA 92037
|
|
(858)784-9208
|
|
lfisher@scripps.edu
|
|
|
|
|
|
|
|
Lauren Fisher
|
|
Automated Molecular Imaging Group
|
|
Department of Cell Biology
|
|
The Scripps Research Institute
|
|
10550 North Torrey Pines Road, CB 129
|
|
La Jolla, CA 92037
|
|
(858)784-9208
|
|
lfisher@scripps.edu
|
|
|