Monitoring the Buffer cycle

[leginonbot]

---

Author Name: Anonymous (Anonymous) Original Redmine Issue: 2019, https://emg.nysbc.org/redmine/issues/2019 Original Date: 2012-08-27

---

Hi,

We have a problem in our T12 microscope system to empty buffer or to do buffer cycle during the continuous exposures with valves open and screen lift. The result of this is the microscope IGP is going beyond 30 and creating problem.

It is not the problem of Leginon, but our system which is prototype. We monitored the values like P3 and came to conclusion that closing the column valves every 2.30 hrs is good.

We are trying to solve this issue from FEI and may be it takes a longer time or also NO from FEI.

The idea is, use the same feature like queue timeout activated, where Leginon closes the column valves. But here instead of that we also need a feature to close the column valves every three hours.

If it is possible, it would be of great help for the system.

regards, venkata

[leginonbot]

---

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2012-10-13T00:19:44Z

---

Venkata,

I am going to work on this in the next few days. I think what you need here is not to close the column valve but just a trigger to run buffer cycle, at a set interval, right?

[leginonbot]

---

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2012-10-15T22:25:01Z

---

r17181 is the first iteration of this feature. Need testing on a real scope. This will be used to expand to other target-less condition fixing such as autofiller triggering.

[leginonbot]

---

Original Redmine Comment Author Name: Anonymous (Anonymous) Original Date: 2012-10-16T06:22:27Z

---

Hi Anchi,

Yes, that would be perfect. I was just mentioning that since Leginon has this feature already, may be it easy to deal with. As you said, the perfect solution will be to trigger the buffer cycle. But the Image acquisition should stop or the images taken during the buffer cycle need to be discarded manually after the session.

sorry for late reply, I was away from work due to ill health past few days.

regards, venkata

Anchi Cheng wrote:

Venkata,

I am going to work on this in the next few days. I think what you need here is not to close the column valve but just a trigger to run buffer cycle, at a set interval, right?

[leginonbot]

---

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2012-10-16T14:02:12Z

---

Hi, Venkata,

I just need final testing on a scope before sending you the files. Which version do you have currently. I do not plan to commit this to the official releases until next cycle, which will be months since we just got 2.2 out and there are users using that already. Let me know what version you plan to use this and I will give you the appropriate files (8 of them) for you to replace.

Yes, Leginon will pause when this happens, no worry.

[leginonbot]

---

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2012-10-17T20:00:46Z

---

r17193 fix confirmEvent after testing on the scope. r17194 commit all changes for this issue to 2.2 branch r17195 commit all changes for this issue to 2.2-redux

[leginonbot]

---

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2012-10-17T21:14:45Z

---

Venkata,

I've committed the changes to 2.2 and 2.2-redux (the CentOS6 and php 5.3 compatible version) branches. I am also attaching the replacement files you could use if you decide to stay at 2.1 for a while.

Once you have updated your installation with these, you can modify the application you use to add the conditioner which currently only does buffer cycling.

Follow the instruction in [[Use the Application Editor to create Leginon applications|Use the Application Editor to create or edit Leginon applications]] to add a node from Conditioner class to the application you currently use. Create a FixConditionEvent binding from the acquisition node where you want Leginon to run buffer cycle before processing a target list (targets from the same parent image). I recommend that you do this from "Exposure" node (i.e., the last of the MSI sequence) if this is MSI-T application.

When you run the new application, you should see your new node. The settings should be easy to understand. The default is Bypass, so you must deactive the bypass to use it.

Let me know if you have problem.

Again, the files attached are for 2.1 version only.

[leginonbot]

---

Original Redmine Comment Author Name: Anonymous (Anonymous) Original Date: 2012-10-18T05:28:35Z

---

Hi Anchi,

Thanks for the changes. Yesterday, I was checking and confused about whether should I use it directly in 2.2 or 2.1. Now you made me clear with making it compatible in both versions. Because I have both versions installed in parallel with two computers. The installation of 2.2 in RHEL6 machine was kept aside, since as you said to wait untill begining of this month.

Now as per your information, I feel 2.2-redux version is compatible to RHEL6 and hope it works smoothly. So, then I will try in 2.1 as per your instructions and try 2.2-redux later when I finish installation in the new RHEL6 machine. Also, give me your final opinion about 2.2-redux.

regards, venkata Anchi Cheng wrote:

Venkata,

I've committed the changes to 2.2 and 2.2-redux (the CentOS6 and php 5.3 compatible version) branches. I am also attaching the replacement files you could use if you decide to stay at 2.1 for a while.

Once you have updated your installation with these, you can modify the application you use to add the conditioner which currently only does buffer cycling.

Follow the instruction in [[Use the Application Editor to create Leginon applications|Use the Application Editor to create or edit Leginon applications]] to add a node from Conditioner class to the application you currently use. Create a FixConditionEvent binding from the acquisition node where you want Leginon to run buffer cycle before processing a target list (targets from the same parent image). I recommend that you do this from "Exposure" node (i.e., the last of the MSI sequence) if this is MSI-T application.

When you run the new application, you should see your new node. The settings should be easy to understand. The default is Bypass, so you must deactive the bypass to use it.

Let me know if you have problem.

Again, the files attached are for 2.1 version only.

[leginonbot]

---

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2013-12-16T20:10:48Z

---

no news for a year, consider done.