From 8eb1a35dfb649aef6590b03cc04b672cda93ed89 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 13 Apr 2019 11:11:32 +0200
Subject: [PATCH] first version of a library to parse HDF5

- preliminarly called DADF5 (DAMASK HDF5)
- script to write (empty undeformed) geometries is also added
---
 processing/post/DADF5_vtk_cells.py | 64 ++++++++++++++++++++++++++++++
 python/damask/__init__.py          |  1 +
 python/damask/dadf5.py             | 38 ++++++++++++++++++
 3 files changed, 103 insertions(+)
 create mode 100755 processing/post/DADF5_vtk_cells.py
 create mode 100644 python/damask/dadf5.py

diff --git a/processing/post/DADF5_vtk_cells.py b/processing/post/DADF5_vtk_cells.py
new file mode 100755
index 000000000..008ac5f66
--- /dev/null
+++ b/processing/post/DADF5_vtk_cells.py
@@ -0,0 +1,64 @@
+#!/usr/bin/env python3
+# -*- coding: UTF-8 no BOM -*-
+
+import os,vtk
+import numpy as np
+import argparse
+import damask
+
+scriptName = os.path.splitext(os.path.basename(__file__))[0]
+scriptID   = ' '.join([scriptName,damask.version])
+
+# --------------------------------------------------------------------
+#                                MAIN
+# --------------------------------------------------------------------
+parser = argparse.ArgumentParser()
+
+#ToDo:  We need to decide on a way of handling arguments of variable lentght
+#https://stackoverflow.com/questions/15459997/passing-integer-lists-to-python
+
+#parser.add_argument('--version', action='version', version='%(prog)s {}'.format(scriptID))
+parser.add_argument('filenames', nargs='+',
+                    help='DADF5 files')
+
+options = parser.parse_args()
+
+
+# --- loop over input files ------------------------------------------------------------------------
+
+for filename in options.filenames:
+  data = damask.DADF5(filename)
+  
+  if data.structured:                                                                               # for grid solvers use rectilinear grid
+    rGrid = vtk.vtkRectilinearGrid()
+    coordArray = [vtk.vtkDoubleArray(),
+                  vtk.vtkDoubleArray(),
+                  vtk.vtkDoubleArray(),
+                 ]
+
+    rGrid.SetDimensions(*data.grid)
+    for dim in [0,1,2]:
+      for c in np.linspace(0,data.size[dim],1+data.grid[dim]):
+        coordArray[dim].InsertNextValue(c)
+
+    rGrid.SetXCoordinates(coordArray[0])
+    rGrid.SetYCoordinates(coordArray[1])
+    rGrid.SetZCoordinates(coordArray[2])
+
+
+  for i,inc in enumerate(data.increments):
+    if not inc['active']: pass
+    
+    if data.structured:
+      writer = vtk.vtkXMLRectilinearGridWriter()
+
+    writer.SetCompressorTypeToZLib()
+    writer.SetDataModeToBinary()
+    writer.SetFileName(os.path.join(os.path.split(filename)[0],
+                                    os.path.splitext(os.path.split(filename)[1])[0] +
+                                    '_inc{:04d}'.format(i) +                                        # ToDo: adjust to lenght of increments
+                                    '.' + writer.GetDefaultFileExtension()))
+    if data.structured:
+      writer.SetInputData(rGrid)
+    
+    writer.Write()
diff --git a/python/damask/__init__.py b/python/damask/__init__.py
index d7ed4a9f9..2dfdac567 100644
--- a/python/damask/__init__.py
+++ b/python/damask/__init__.py
@@ -14,6 +14,7 @@ from .asciitable  import ASCIItable       # noqa
 from .config      import Material         # noqa
 from .colormaps   import Colormap, Color  # noqa
 from .orientation import Symmetry, Lattice, Rotation, Orientation # noqa
+from .dadf5       import DADF5 # noqa
 
 #from .block       import Block           # only one class
 from .result      import Result           # noqa
diff --git a/python/damask/dadf5.py b/python/damask/dadf5.py
new file mode 100644
index 000000000..6342b18e7
--- /dev/null
+++ b/python/damask/dadf5.py
@@ -0,0 +1,38 @@
+# -*- coding: UTF-8 no BOM -*-
+import h5py
+import re
+
+# ------------------------------------------------------------------
+class DADF5():
+  """Read and write to DADF5 files"""
+  
+# ------------------------------------------------------------------
+  def __init__(self,
+               filename,
+               mode     = 'r',
+              ):
+    
+    if mode not in ['a','r']:
+      print('Invalid file access mode')
+      with h5py.File(filename,mode):
+        pass
+      
+    with h5py.File(filename,'r') as f:
+      
+      if f.attrs['DADF5-major'] != 0 or f.attrs['DADF5-minor'] != 1:
+        print('Unsupported DADF5 version {} '.format(f.attrs['DADF5-version']))
+    
+      self.structured = 'grid' in f['mapping'].attrs.keys()
+    
+      if self.structured:
+        self.grid = f['mapping'].attrs['grid']
+        self.size = f['mapping'].attrs['size']
+        
+      r=re.compile('inc[0-9]+')
+      self.increments = [{'group':  u,
+                          'time':   f[u].attrs['time/s'],
+                          'active': True
+                          }   for u in f.keys() if r.match(u)]
+
+    self.filename   = filename
+    self.mode       = mode