From 3095f783f8b23bf6d39e6038dbaceb53e9725d00 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                                 |  5 +++++
 labs/pyradiomics-dcm/pyradiomics-dcm.py | 19 ++++++-------------
 2 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/.flake8 b/.flake8
index 7916a372..61a545ee 100644
--- a/.flake8
+++ b/.flake8
@@ -33,6 +33,11 @@ ignore:
     E701,
     # .has_key() is deprecated, use 'in'
     W601,
+    # line break after binary operator
+    W504,
+    # invalid escape sequence
+    W605,
+
 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!")