From 3e8518d861e68146f31fecc9c13c90634125858d Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sun, 24 Nov 2019 19:25:01 +0100
Subject: [PATCH] following prospector guidelines

---
 processing/pre/geom_fromDREAM3D.py | 12 ++++++------
 processing/pre/geom_renumber.py    |  4 +---
 processing/pre/geom_rescale.py     |  5 ++---
 python/damask/geom.py              |  2 +-
 4 files changed, 10 insertions(+), 13 deletions(-)

diff --git a/processing/pre/geom_fromDREAM3D.py b/processing/pre/geom_fromDREAM3D.py
index b20749b45..159793cd8 100755
--- a/processing/pre/geom_fromDREAM3D.py
+++ b/processing/pre/geom_fromDREAM3D.py
@@ -86,7 +86,7 @@ for name in filenames:
            * inFile[os.path.join(group_geom,'SPACING')][...]
     grid   = inFile[os.path.join(group_geom,'DIMENSIONS')][...]
     origin = inFile[os.path.join(group_geom,'ORIGIN')][...]
-  except:
+  except KeyError:
     errors.append('Geometry data ({}) not found'.format(group_geom))
 
 
@@ -98,13 +98,13 @@ for name in filenames:
     try:
       quats = np.reshape(inFile[dataset][...],(np.product(grid),4))
       rot   = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in quats]
-    except:
+    except KeyError:
       errors.append('Pointwise orientation (quaternion) data ({}) not readable'.format(dataset))
 
     dataset = os.path.join(group_pointwise,options.phase)
     try:
       phase = np.reshape(inFile[dataset][...],(np.product(grid)))
-    except:
+    except KeyError:
       errors.append('Pointwise phase data ({}) not readable'.format(dataset))
 
     microstructure = np.arange(1,np.product(grid)+1,dtype=int).reshape(grid,order='F')
@@ -116,7 +116,7 @@ for name in filenames:
     dataset = os.path.join(group_pointwise,options.microstructure)
     try:
       microstructure = np.transpose(inFile[dataset][...].reshape(grid[::-1]),(2,1,0))               # convert from C ordering
-    except:
+    except KeyError:
       errors.append('Link between pointwise and grain average data ({}) not readable'.format(dataset))
 
     group_average = os.path.join(rootDir,options.basegroup,options.average)
@@ -124,13 +124,13 @@ for name in filenames:
     dataset = os.path.join(group_average,options.quaternion)
     try:
       rot = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in inFile[dataset][...][1:]]         # skip first entry (unindexed)
-    except:
+    except KeyError:
       errors.append('Average orientation data ({}) not readable'.format(dataset))
 
     dataset = os.path.join(group_average,options.phase)
     try:
       phase = [i[0] for i in inFile[dataset][...]][1:]                                              # skip first entry (unindexed)
-    except:
+    except KeyError:
       errors.append('Average phase data ({}) not readable'.format(dataset))
 
   if errors != []:
diff --git a/processing/pre/geom_renumber.py b/processing/pre/geom_renumber.py
index 1e28ca921..b1db6ed13 100755
--- a/processing/pre/geom_renumber.py
+++ b/processing/pre/geom_renumber.py
@@ -5,8 +5,6 @@ import sys
 from io import StringIO
 from optparse import OptionParser
 
-import numpy as np
-
 import damask
 
 
@@ -32,6 +30,6 @@ for name in filenames:
   damask.util.report(scriptName,name)
 
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-  damask.util.croak(self.renumber)
+  damask.util.croak(geom.renumber)
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
   geom.to_file(sys.stdout if name is None else name,pack=False)
diff --git a/processing/pre/geom_rescale.py b/processing/pre/geom_rescale.py
index 55c2e57a2..b1a15593c 100755
--- a/processing/pre/geom_rescale.py
+++ b/processing/pre/geom_rescale.py
@@ -2,11 +2,10 @@
 
 import os
 import sys
-import numpy as np
-
 from io import StringIO
 from optparse import OptionParser
-from scipy import ndimage
+
+import numpy as np
 
 import damask
 
diff --git a/python/damask/geom.py b/python/damask/geom.py
index e2dcd9bcb..69dfa9ec3 100644
--- a/python/damask/geom.py
+++ b/python/damask/geom.py
@@ -469,7 +469,7 @@ class Geom():
 
     def scale(self,grid):
         """
-        Scale microstructure to new grid 
+        Scale microstructure to new grid.
 
         Parameters
         ----------