From 931fa9d36a855149daef6e0e3507f9b73e1cecdd Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 30 May 2019 10:20:07 +0200
Subject: [PATCH] standardized and cleaned

-write to file if given
-type casting is done in the geom class
---
 processing/pre/geom_fromScratch.py | 58 ++++++++++++++----------------
 python/damask/geom.py              |  2 +-
 2 files changed, 28 insertions(+), 32 deletions(-)

diff --git a/processing/pre/geom_fromScratch.py b/processing/pre/geom_fromScratch.py
index 822a7f5f2..b76e0012a 100755
--- a/processing/pre/geom_fromScratch.py
+++ b/processing/pre/geom_fromScratch.py
@@ -1,37 +1,36 @@
 #!/usr/bin/env python3
-# -*- coding: UTF-8 no BOM -*-
 
 import os
 import sys
+from optparse import OptionParser
+
 import numpy as np
+
 import damask
 
-from optparse import OptionParser
 
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
+
 # --------------------------------------------------------------------
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [geomfile(s)]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
 Generate homogeneous geometry.
 
 """, version = scriptID)
 
-parser.add_option('-g',
-                  '--grid',
+parser.add_option('-g','--grid',
                   dest = 'grid',
-                  type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
+                  type = 'int', nargs = 3, metavar = ' '.join(['int']*3),
                   help = 'a,b,c grid of hexahedral box %default')
-parser.add_option('-s',
-                  '--size',
+parser.add_option('-s', '--size',
                   dest = 'size',
                   type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
                   help = 'x,y,z of geometry size %default')
-parser.add_option('-o',
-                  '--origin',
+parser.add_option('-o','--origin',
                   dest = 'origin',
                   type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
                   help = 'x,y,z of geometry origin %default')
@@ -39,36 +38,33 @@ parser.add_option('--homogenization',
                   dest = 'homogenization',
                   type = 'int', metavar = 'int',
                   help = 'homogenization index [%default]')
-parser.add_option('-f',
-                  '--fill',
+parser.add_option('-f','--fill',
                   dest = 'fill',
-                  type = 'float', metavar = 'float',
+                  type = 'float', metavar = 'int',
                   help = 'microstructure index [%default]')
 
-parser.set_defaults(grid = [16,16,16],
-                    size = [1.,1.,1.],
-                    origin = [0.,0.,0.],
+parser.set_defaults(grid = (16,16,16),
+                    size = (1.,1.,1.),
+                    origin = (0.,0.,0.),
                     homogenization = 1,
                     fill = 1,
                    )
 
-(options, filenames) = parser.parse_args()
+(options, filename) = parser.parse_args()
+
+
+name = None if filename == [] else filename[0]
+damask.util.report(scriptName,name)
 
 dtype = float if np.isnan(options.fill) or int(options.fill) != options.fill else int
-grid   = list(map(  int,options.grid))
-size   = list(map(float,options.size))
-origin = list(map(float,options.origin))
-homogenization = int(options.homogenization)
-fill = float(options.fill)
-
-damask.util.report(scriptName,'')
-
-geom = damask.Geom(microstructure=(fill * np.ones(grid)).astype(dtype),
-                   size=size,
-                   origin=origin,
-                   homogenization=homogenization,
+geom = damask.Geom(microstructure=np.full(options.grid,options.fill,dtype=dtype),
+                   size=options.size,
+                   origin=options.origin,
+                   homogenization=options.homogenization,
                    comments=scriptID + ' ' + ' '.join(sys.argv[1:]))
-
 damask.util.croak(geom)
   
-sys.stdout.write(str(geom.show()))
+if name is None:
+  sys.stdout.write(str(geom.show()))
+else:
+  geom.to_file(name)
diff --git a/python/damask/geom.py b/python/damask/geom.py
index 1d0161ebb..397684fe1 100644
--- a/python/damask/geom.py
+++ b/python/damask/geom.py
@@ -192,7 +192,7 @@ class Geom():
     """Writes to file"""
     header = self.get_header()
     grid   = self.get_grid()
-    format_string = '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure)-1)))) if self.microstructure.dtype == int \
+    format_string = '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure))))) if self.microstructure.dtype == int \
                else '%g'
     np.savetxt(fname,
                self.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T,