Leginon

Hi, Quentin,

I do not know for sure, but your problem might be that the path leginon saves its images is not accessable by the dbemtool you use.

The reason I suspect this is that your image path is called simply

/leginon/08mar25a/rawdata/08mar25a_00001ma_0.mrc

It is hard to imagine that you have created a directory from the top level that is accessable from other computers.

I've tried this on my computer saving the image in /tmp/leginon/....

Since our web server is not on this same computer, I have the exact problem as you did.

What you should try is to make sure the image path that Leginon generates is

the full linux path. Specify this in leginon.cfg under

[Images]

path: /nramm/data00/leginon

,for example.

If you are running Leginon on Windows, the combination of your drive mapping and the image path (written in Windows format) should be the full linux path.

With the above example, let's say that /nramm/data00 is mapped on Windows as Z drive. You should put the following in your leginon.cfg on the PC as

[Images]

path: Z:\leginon

[Drive Mapping]

Z: /nramm/data00

Another thing you should check is where the file is actually saved. Make sure the image file does end up where you told it to. I've notice this on Windows that when it had trouble accessing the disk it needs to get to, instead of an error message, it simply create a folder of the same name under its C drive. This path is of course not recognized from outside because the leginon database assumes that the file is saved at where it says at the global level.

I will update the documentation to make this more clear under Windows installation.

Seeing test image in the viewer only tells you that the components for dbemtools are working so that you can read an mrc image locally. It does not tell you whether it can access a file in other file path.

Anchi

Just moving the previous thread (viewtopic.php?f=2&t=287 ) here since it is more related to this topic.

I am going to be obtaining most of my data through the Linux machine, so mapping my drives is not actually necessary. However, is there any (hopefully simple) way that I can have the choice of obtaining my data either from the Linux machine or from the microscope (Windows) computer? I was thinking that if I made a "dummy" user profile (by copying the leginon.cfg file to its user folder) that I might be able to get away with this. That is, it would allow the windows machine to send images to the Linux /data/leginon folder by mapping the drive, but leave still give me the choice of doing so from the Linux machine.

We're probably going to go with the Linux machine most of the time, but I was just wondering if this was possible. I did some digging in the WIndows hard drive and I found the .mrc files we were taking on the microscope manually; they seem to be saving on the folder C:\data\leginon and not in the Linux machine folder /data/leginon, but the webviewer is still updating project data to show that they exist (it just can't see it).

Thanks again for aid up to this point! Now we just need to do the calibrations...that and updatecom.py is still not working properly. (viewtopic.php?f=8&t=286 )

Hi, Carlos,

The drive mapping as described by Jim in viewtopic.php?f=2&t=285 is supposed to allow the Windows machine to save the images on the data disk on Samba server. Since you found your files on the Windows machine instead, it was not done right. Read that carefully. You can check if Windows has access to the network drive you mapped (Let's say it is Z:) by navigate to that drive similar to you would to do to go to C: drive. Windows will attempt to connect to the network drive and show you the content of the share point. If that works and you still find images saved to the wrong place, you might want to show us your leginon.cfg and what you typed exactly when you mapped the drive in Windows Menu.

Anchi