openeyes/oph-in-visualfields

This package is abandoned and no longer maintained. No replacement package was suggested.

There is no license information available for the latest version (v1.12) of this package.

Module capable of communicating with Visual Fields machine to import images

v1.12 2016-02-11 13:26 UTC

Requires

• openeyes/module-installer: *

Unknown License

README

As of Openeyes release 1.12.1, this module has been merged into the core openeyes repository.

This repository is kept for historic purposes only

OphInVisualfields

This description requires extra information for the Import standard fields section. Using the Openeyes Vagrant vm might help run the legacy import below faster.

Importing Legacy Events: OpenEyes

Requirements:

• Latest version of the OphInVisualfields module and an OpenEyes instance to support it.
• OpenEyes has already been set up, and all necessary modules imported and necessary database migrations ran.

The legacy import script in the OphInVisualfields/commands directory is used to import .fmes files. For help on the command, simply run (from protected/):

./yiic importlegacyvf help

The arguments are very much similar to the import performed on the client, only with differently named options:

--importDir: specifies which directory to import legacy files from;
--archiveDir: move successfully imported measurements to specified directory;
--errorDir: where to move files that were not successfully imported;
--dupDir: where to place files that have already been imported to OpenEyes
--interval: an acceptable time span that exists between tests for a given patient; specified as a PHP time interval (e.g. PT1H30M);

Create folders required by import process

1 - ssh the VM - vagrant ssh
2 - Create directories
	cd /var/www/protected; \
	mkdir runtime/fields;  \
	mkdir runtime/fields/legacy; \
	mkdir runtime/fields/out; \
	mkdir runtime/fields/err; \
	mkdir runtime/fields/dups;
3 - copy test legacy fmes files  - cp  modules/OphInVisualfields/tests/fields/legacy/* runtime/fields/legacy/
4 - These files have sample numbers that might not match your patient ID, change the number part in patient ids in the xml to map a user in your system

Run the command below to import the legacy events:

    ./yiic importlegacyvf import --importDir=runtime/fields/legacy --archiveDir=runtime/fields/out --errorDir=runtime/fields/err --dupDir=runtime/fields/dups

Note that if import is successful a list of legacy events will appear under "Legacy events" on the patien's Episodes and events page. Also the command informs of the result for each attempted import

Importing Standard Fields

(This is not tested and left only for future reference)

Once all legacy field events have been imported, standard (that is, non-legacy) fields can be imported. The import process for standard imports is very different to the legacy import method - standard fields are sent to OpenEyes using HTTP to access the OpenEyes API.

In order to import the fields via the API, a new user must be set up, via the admin (localhost/admin) page. You can use a current user but it's best to set up a fields user specifically for this task. This can be done via the admin interface. The user will need 3 roles when created, API access, Admin and User. "Yes" should be chosen for "doctor". The config/local/common.php needs to be updated, using 'local_users' => array('admin','fields_user').

Again, like the legacy import, there are several folders that are used to marshal files into: -a (archive, where successfully transferred files are moved to), -d (directory to watch for newly arrived files from the fields machine), -e (error directory) and -u (duplicate directory), -t (outgoing - when a file is not sent due to a network error it is moved here to be re-scheduled for sending). There are also some extra arguments to take into account:

-c,--credentials : Supply (necessary) username/password (comma separated); if no password is given after the comma it is prompted for when the process runs; -g,--global-search-path : Specify the location of the imagemagick installation; necessary only on Windows installations. -i,--interval : Time in seconds to sleep between checks for the in-directory. -o,--image-options : Set up by default but can be parameterised. Specify location and segment of humphrey test to extract, along with scaling parameters. Format: x,y,w,h,x1,y1 where x,y is the the location to cut image with wxh size, scaled to x1,y1. Scaling parameters (x1,y1) are optional and can be omitted. -p,--port : Port to connect to on server. Default 80. Local 8888. -r,--regex : Regular expression to determine valid patient identifiers. Defaults to ^([0-9]{1,9})$ -s,--host : Specify server to send messages to. -t,--outgoing : Directory to place measurement files that were not successfully sent. -u,--duplicates : Duplicate files (successfully transferred) are moved to this directory. -x,--xml-source: Include XML source file information with captured data. Default is false.

For example, to send fields to the server 'openeyes' with username fields_user and password admin, with ImageMagick being installed in ImageMagick-6.8.8-Q16, the following would import all file from fields/in and post them to the server:

sh target/appassembler/bin/fields -d fields/in -e fields/err -u fields/dups -a fields/out -t fields/resend -c fields_user,admin -s localhost -p 8888 Note that the credentials could have been specified as -c fields, and the password will be prompted for at the command line.