From 83b510c33a8a4fbf9e0cd2c534e10b29c070b851 Mon Sep 17 00:00:00 2001
From: Joost van Griethuysen <j.v.griethuysen@nki.nl>
Date: Mon, 12 Nov 2018 11:32:27 +0100
Subject: [PATCH] STYL: Fix flake8 errors

Add ignores for 504 and 605 (new line after binary operator and invalid escape sequence, both were giving false positives)

Fix Regex match pattern errors (missing `r` prefix to the pattern strings).
---
 .flake8                                 |  3 +++
 labs/pyradiomics-dcm/pyradiomics-dcm.py | 19 ++++++-------------
 radiomics/featureextractor.py           |  2 +-
 radiomics/imageoperations.py            |  2 +-
 4 files changed, 11 insertions(+), 15 deletions(-)

diff --git a/.flake8 b/.flake8
index 7916a372..02fe528b 100644
--- a/.flake8
+++ b/.flake8
@@ -33,6 +33,9 @@ ignore:
     E701,
     # .has_key() is deprecated, use 'in'
     W601,
+    # line break after binary operator
+    W504,
+
 select: C,E,W,F,I
 # flake8-import-order
 application-import-names: radiomics,testUtils
diff --git a/labs/pyradiomics-dcm/pyradiomics-dcm.py b/labs/pyradiomics-dcm/pyradiomics-dcm.py
index 9b4f0939..b355852c 100644
--- a/labs/pyradiomics-dcm/pyradiomics-dcm.py
+++ b/labs/pyradiomics-dcm/pyradiomics-dcm.py
@@ -210,15 +210,15 @@ def prefix2codes(self, prefix):
                         "modifierValue": self.makePrivateCode("Exponent transformation")})
 
     # parameterized processing operations
-    elif re.match("wavelet-([HL]{2,3})", prefix):
-      match = re.match("wavelet-([HL]{2,3})", prefix)
+    elif re.match(r"wavelet-([HL]{2,3})", prefix):
+      match = re.match(r"wavelet-([HL]{2,3})", prefix)
       modifiers.append({"modifier": imageTransformationConcept,
                         "modifierValue": self.makePrivateCode("Wavelet transformation")})
       modifiers.append({"modifier": self.makePrivateCode("Wavelet sub-band"),
                         "modifierValue": self.makePrivateCode(match.group(1))})
 
-    elif re.match("log-sigma-([\d]+)-([\d]+)-([a-z]+)", prefix):
-      match = re.match("log-sigma-([\d]+)-([\d]+)-([a-z]+)", prefix)
+    elif re.match(r"log-sigma-([\d]+)-([\d]+)-([a-z]+)", prefix):
+      match = re.match(r"log-sigma-([\d]+)-([\d]+)-([a-z]+)", prefix)
 
       units = match.group(3)
       if units == "mm":
@@ -286,11 +286,7 @@ def addMeasurement(
           quantityCode)
         return
     except Exception as e:
-      scriptlogger.error(
-        "Exception checking for NaN: " +
-        str(e) +
-        " " +
-        value)
+      scriptlogger.error("Exception checking for NaN: %s %s", str(e), value)
       return
 
     measurement["value"] = '%E' % Decimal(value)
@@ -559,10 +555,7 @@ def main():
     dcm = pydicom.read_file(outputSRTempFile)
     shutil.move(
       outputSRTempFile,
-      os.path.join(
-        args.outputDir,
-        dcm.SOPInstanceUID +
-        ".dcm"))
+      os.path.join(args.outputDir, dcm.SOPInstanceUID + ".dcm"))
   except BaseException:
     scriptlogger.error("Failed to move output SR!")
 
diff --git a/radiomics/featureextractor.py b/radiomics/featureextractor.py
index 630b0475..e60bb278 100644
--- a/radiomics/featureextractor.py
+++ b/radiomics/featureextractor.py
@@ -532,7 +532,7 @@ def loadImage(self, ImageFilePath, MaskFilePath):
     return image, mask
 
   def computeFeatures(self, image, mask, imageTypeName, **kwargs):
-    """
+    r"""
     Compute signature using image, mask, \*\*kwargs settings.
 
     This function computes the signature for just the passed image (original or derived), it does not preprocess or
diff --git a/radiomics/imageoperations.py b/radiomics/imageoperations.py
index 2ae3e177..7bf2bcd3 100644
--- a/radiomics/imageoperations.py
+++ b/radiomics/imageoperations.py
@@ -539,7 +539,7 @@ def normalizeImage(image, **kwargs):
 
 
 def resegmentMask(imageNode, maskNode, **kwargs):
-  """
+  r"""
   Resegment the Mask based on the range specified by the threshold(s) in ``resegmentRange``. Either 1 or 2 thresholds
   can be defined. In case of 1 threshold, all values equal to or higher than that threshold are included. If there are
   2 thresholds, all voxels with a value inside the closed-range defined by these thresholds is included