fixed errors detected by pylint

src/catalog.py

@@ -3,7 +3,8 @@ import json
 
 
 class DacMetadata(object):
-    """Represents a display_and_comments.txt metadata file"""
+    """Represents a display_and_comments.txt metadata file."""
+    
     def __init__(self, dac_id, dac_file_path):
         """Contructor.
 

src/ijopencv-tester.py

@@ -94,7 +94,6 @@ def print_ijopencvmat(src_mat):
     print("pixel type : %d" % src_mat.type())
 
 
-
 def test_opencv_calc_hist1():
     src_image = opencv_core.Mat([128, 128])
     histogram = opencv_imgproc.cvCalcHist(src_image)  # pylint: disable=unused-variable
@@ -215,6 +214,7 @@ def test_ijopencv_converter():
     # white_mat = imread(white_image_file_path)
     print('mat', mat)
 
+
 def test_ijopencv_morphology_ex():
     print(opencv_core.CV_VERSION())
     # src_image = opencv_core.Mat(128, 128)
@@ -237,7 +237,6 @@ def test_ijopencv_morphology_ex():
     print_ijopencvmat(dst_image)
 
 
-
 def test_opencv():
 
     test_ijopencv_converter()
@@ -247,7 +246,6 @@ def test_opencv():
     test_ijopencv_morphology_ex()
 
 
-
 # If a Jython script is run, the variable __name__ contains the string '__main__'.
 # If a script is loaded as module, __name__ has a different value.
 if __name__ in ['__builtin__', '__main__']:

src/imageengine.py

@@ -78,7 +78,6 @@ class IImageEngine(ABC):
         :param int structuring_element_radius:
         """
 
-
     @abc.abstractmethod
     def replace_border(self, image, band_width):
         """Overwrites the outer band of the image by duplicating the value of the pixels that touch this outer band

src/imagej/ijimageengine.py

@@ -2,8 +2,8 @@
 """
 
 from imageengine import IImage, IImageEngine
-from ij import IJ
-from ij.plugin import ImageCalculator
+from ij import IJ  # pylint: disable=import-error
+from ij.plugin import ImageCalculator  # pylint: disable=import-error
 from ijopencv.ij import ImagePlusMatConverter  # pylint: disable=import-error
 from ijopencv.opencv import MatImagePlusConverter  # pylint: disable=import-error
 import org.bytedeco.javacpp.opencv_core as opencv_core  # pylint: disable=import-error

src/lipase.py

@@ -6,11 +6,11 @@
 # the 'greeting' output parameter, based on its type.
 from ij import IJ  # pylint: disable=import-error
 from ij import ImagePlus  # pylint: disable=import-error
-from ij.process import ByteProcessor  # pylint: disable=import-error
-from ij.process import ImageStatistics
-from ij.plugin import ImageCalculator
-from ij.plugin import ZProjector
-from ij import WindowManager
+# from ij.process import ByteProcessor  # pylint: disable=import-error
+from ij.process import ImageStatistics  # pylint: disable=import-error
+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
 # greeting = "Hello, " + name + "!"
@@ -179,7 +179,9 @@ class Lipase(object):
         return background_image
 
     def estimate_white(self, sequence, channel_id):
-        return preprocessing.estimate_white([sequence], [channel_id], dark=None)
+        white_estimator = preprocessing.WhiteEstimator(open_size=75, close_size=75, average_size=75)
+        white_estimate = white_estimator.estimate_white([sequence], [channel_id], dark=None)
+        return white_estimate
 
     def process_sequence(self, sequence_id):
         '''
@@ -208,7 +210,6 @@ def test_find_white():
     depth_index = lipase.find_depth_index(src_image, white_seq)
 
 
-
 def run_script():
     test_find_white()
 

src/preprocessing.py

@@ -22,7 +22,6 @@ class WhiteEstimator(object):
 
         IImageEngine.get_instance().mean_filter(white_estimate, radius=(self.average_size + 1) / 2)
 
-
     def estimate_white(self, sequences, channel_ids, dark=None):
         """Estimation of the white fluorescence image shape of synchrotron light from experimental images of Telemos microscope.
 
@@ -271,8 +270,8 @@ def test_preprocessing(raw_images_root_path):
     white_estimate = white_estimator.estimate_white([sequence], ['DM300_327-353_fluo'])
     # find_white_reference_image(white_estimate, sequence.get_white())
     print(white_estimate)
-    IImageEngine.get_instance().save_as_tiff( white_estimate, './white_estimate.tiff' )
+    IImageEngine.get_instance().save_as_tiff(white_estimate, './white_estimate.tiff')
     print('end')
 
 if __name__ == '__main__':
-    test_preprocessing()
+    test_preprocessing(raw_images_root_path='/Users/graffy/ownCloud/ipr/lipase/raw-images')

tests/test0001.py

@@ -2,25 +2,24 @@
 """
 # # note: fiji's jython doesn't support encoding keyword
 
-#https://imagej.net/Scripting_Headless
-#@String lipase_src_root_path
-#@String raw_images_root_path
+# https://imagej.net/Scripting_Headless
+# @String lipase_src_root_path
+# @String raw_images_root_path
 
 # String(label="Please enter your name",description="Name field") name
 # OUTPUT String greeting
 import sys
 print('python version %s' % sys.version)  # prints python version
 
-sys.path.append(lipase_src_root_path)  # necessary if run from fiji as script otherwise jython fails to find lipase's modules such as catalog
+# it is necassary to add lipase's root path to the path if run from fiji as script otherwise jython fails to find lipase's modules such as catalog
+sys.path.append(lipase_src_root_path)  # pylint: disable=undefined-variable
 
-from ij import IJ
 # from lipase import Lipase, ImageLogger
-from catalog import ImageCatalog
-from preprocessing import WhiteEstimator
-from preprocessing import test_preprocessing
+from preprocessing import test_preprocessing  # noqa: E402 pylint: disable=import-error,wrong-import-position
+
 
 def run_script():
-    test_preprocessing(raw_images_root_path) # eg '/Users/graffy/ownCloud/ipr/lipase/raw-images'
+    test_preprocessing(raw_images_root_path)  # eg '/Users/graffy/ownCloud/ipr/lipase/raw-images' pylint: disable=undefined-variable
 
 # note : when launched from fiji, __name__ doesn't have the value "__main__", as when launched from python
 run_script()