renamed preprocessing.py as telemos.py because it contains functions that have been translated from matlab telemos toolbox

src/ij-plugins/Ipr/Lipase/Display_Sequence.py

@@ -25,7 +25,7 @@ from lipase.settings import UserSettings
 # from lipase import Lipase, ImageLogger
 from lipase.imageengine import IImageEngine
 from lipase.imagej.ijimageengine import IJImageEngine
-from lipase.preprocessing import WhiteEstimator
+from lipase.telemos import WhiteEstimator
 from lipase.catalog import ImageCatalog
 from lipase.imagej import open_sequence_in_imagej
 

src/lipase/lipase.py

@@ -12,7 +12,7 @@ from ij.plugin import ImageCalculator  # pylint: disable=import-error
 from ij.plugin import ZProjector  # pylint: disable=import-error
 from ij import WindowManager  # pylint: disable=import-error
 from catalog import Sequence, ImageCatalog
-import preprocessing
+import telemos
 # greeting = "Hello, " + name + "!"
 
 # image prefix :
@@ -180,7 +180,7 @@ class Lipase(object):
         return background_image
 
     def estimate_white(self, sequence, channel_id):
-        white_estimator = preprocessing.WhiteEstimator(open_size=75, close_size=75, average_size=75)
+        white_estimator = telemos.WhiteEstimator(open_size=75, close_size=75, average_size=75)
         white_estimate = white_estimator.estimate_white([sequence], [channel_id], dark=None)
         return white_estimate
 

src/lipase/telemos.py

@@ -27,7 +27,7 @@ class WhiteEstimator(object):
         :param list(str) channel_ids: the channels to consider, eg ['DM300_327-353_fluo']
         :param ImagePlus or None dark:
         :rtype ImagePlus:
-        Code adapted from matlab telemosToolbx's estimatedwhiteFluoImageTelemos function
+        Code adapted from matlab telemosToolbx's estimatewhiteFluoImageTelemos function
 
         % this function is specific of Telemos images (DISCO line SOLEIL)
             % acquired using micromanager software linked to imageJ

src/lipase/traps_detector.py

@@ -3,7 +3,7 @@ from catalog import ImageCatalog, Sequence
 # from imageengine import Toto
 from imageengine import IImageEngine, Aabb, StackImageFeeder
 from imageengine import PixelType
-from preprocessing import WhiteEstimator, correct_non_uniform_lighting
+from telemos import WhiteEstimator, correct_non_uniform_lighting
 from maxima_finder import Match
 from template_matcher import TemplateMatcher
 

tests/test0001.py

@@ -9,7 +9,7 @@ import unittest  # unittest2 doesn't exist in fiji
 import sys
 from lipase.imageengine import IImageEngine, PixelType, Aabb  # pylint: disable=import-error
 from lipase.imagej.ijimageengine import IJImageEngine, IJImage  # pylint: disable=import-error
-from lipase.preprocessing import WhiteEstimator, correct_non_uniform_lighting  # pylint: disable=import-error
+from lipase.telemos import WhiteEstimator, correct_non_uniform_lighting  # pylint: disable=import-error
 from lipase.maxima_finder import MaximaFinder  # pylint: disable=import-error
 from lipase.template_matcher import TemplateMatcher  # pylint: disable=import-error
 from lipase.traps_detector import TrapsDetector  # pylint: disable=import-error