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Topic Title: How do you set the 'Remote Reference:' in Columbus if it is missing
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Created On: 10/9/2018 1:25 PM
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10/9/2018 1:25 PM
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Jace

Posts: 23
Joined: 5/9/2014

In ColumbusPlus the Remote Reference is a requirement for the Cluster system to access a measurement's corresponding images and perform a batch analysis. You will find Remote Reference under the Measurement Info tab in the Browse view. If the Remote Reference is missing a Cluster analysis will fail. If your system has been in use and data imported prior to being upgraded to ColumbusPlus you will find that any existing measurement data will not have a Remote Reference. To set the Remote Reference manually using measurement data available in Columbus:

Export to the shared file system

- Switch to the Export View

- Select Export Options - Method - Export to Disk (*)

- Export Folder - the path to the shared file system used by the Columbus Cluster

- Image Data - tick checkbox and select SinglePlane TIF

- Start Export

If you are uncertain of the Export Folder path refer to the import_path parameter in the /etc/columbus/*.config file

For purposes of this example the Export Folder is

/columbus_cluster/data/images

To export to this path the acapella user requires write access. This would normally be the case if the shared file system is owned by columbus (acapella user typically being in the same group) but if you see a warning to the effect:

Selected directory /columbus_cluster/data/image1 does not exist.

Check and potentially change the permissions to allow acapella to write, if writable you will see:

Selected directory /columbus_cluster/data/images OK.

Once exported by default the folder created will bear the name of the Screen appended with the Screen ID within []

For purposes of this example Reference Screen is the name of the Screen and the Screen ID in Columbus is [3152]. Therefore the first folder created is Reference Screen[3152] then a plate and finally the measurement folders containing the images. The full path in this example being:

/columbus_cluster/data/images/Reference Screen[3152]/Plate[3202]/2008-06-12T123202+0100[3252]/2008-06-12T123202+0100[3252]

Confirming the above path on the Columbus Server

- Log into the Columbus server using ssh

- Navigate to the top level folder in the Export Folder path i.e the measurement level (keep changing directory until you can list the TIF files)

- Get the path, for instance using a command such as:

$ pwd

- Switch to the Browse view in Columbus interface

- Edit the Remote Reference adding the path such as above but append ‘file://‘ to the beginning.

When adding the remote reference be mindful of any escape characters, for instance spaces in the path. In this example the Screen started with 'Reference Data' in which case \ would need to preceed any spaces i.e ‘Reference\ Data'. If a special character has not been accounted for you will typically see the following error on attempting cluster analysis:
  1. Error Message: tcgetattr: Inappropriate ioctl for device Connection to gcc1 closed.
Ammended path for this example:

file:///columbus_cluster/data/images/Reference\ Screen[3152]/Plate[3202]/2008-06-12T123202+0100[3252]/2008-06-12T123202+0100[3252]
  1. (*) If you are only exporting a single measurement as oppose to a large Screen and do not need to preserve the folder hieracy the exported subfolders can be simplify by choosing: Screen or Screen+Plate or left at default Screen+Plate+Measurement in Generate Subfolders. You will find this under the left drop down arrow at the bottom of the Select Export Options section.



Edited: 10/10/2018 at 6:53 AM by Jace
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