Package omero :: Package plugins :: Module cecog :: Class CecogControl
[hide private]
[frames] | no frames]

Class CecogControl

source code


CeCog integration plugin.

Provides actions for prepairing data and otherwise integrating with Cecog. See the Run_Cecog_4.1.py script.

Instance Methods [hide private]
 
_configure(self, parser) source code
 
merge(self, args)
Uses PIL to read multiple planes from a local folder.
source code
 
rois(self, args)
Parses an object_details text file, as generated by CeCog Analyzer and saves the data as ROIs on an Image in OMERO.
source code

Inherited from cli.BaseControl: __init__

Class Variables [hide private]
  regex_token = re.compile(r'(?P<Token>.+)\.')
  regex_time = re.compile(r'T(?P<T>\d+)')
  regex_channel = re.compile(r'_C(?P<C>.+?)(_|$)')
  regex_zslice = re.compile(r'_Z(?P<Z>\d+)')
Method Details [hide private]

merge(self, args)

source code 

Uses PIL to read multiple planes from a local folder.

Planes are combined and uploaded to OMERO as new images with additional T, C, Z dimensions.

It should be run as a local script (not via scripting service) in order that it has access to the local users file system. Therefore need EMAN2 or PIL installed locally.

Example usage: will$ bin/omero cecog merge /Applications/CecogPackage/Data/Demo_data/0037/

Since this dir does not contain folders, this will upload images in '0037' into a Dataset called Demo_data in a Project called 'Data'.

will$ bin/omero cecog merge /Applications/CecogPackage/Data/Demo_data/

Since this dir does contain folders, this will look for images in all subdirectories of 'Demo_data' and upload images into a Dataset called Demo_data in a Project called 'Data'.

Images will be combined in Z, C and T according to the MetaMorph_PlateScanPackage naming convention. E.g. tubulin_P0037_T00005_Cgfp_Z1_S1.tiff is Point 37, Timepoint 5, Channel gfp, Z 1. S? see /Applications/CecogPackage/CecogAnalyzer.app/Contents/Resources/resources/naming_schemes.conf

rois(self, args)

source code 

Parses an object_details text file, as generated by CeCog Analyzer and saves the data as ROIs on an Image in OMERO.

Text file is of the form:

frame objID classLabel className centerX centerY mean sd 1 10 6 lateana 1119 41 76.8253796095 54.9305640673

Example usage: bin/omero cecog rois -f Data/Demo_output/analyzed/0037/statistics/P0037__object_details.txt -i 502