Merge branch 'with-to-file-methods' into 'development'

modified file writing of geom and table to a general to_file() that takes a "format=" argument

See merge request damask/DAMASK!213

PRIVATE

@@ -1 +1 @@
-Subproject commit 1ca2223c68475bbcb9da633353dbe4a98c18db0d
+Subproject commit c6dc3f116fc6007caf076772d5c29f0a0523544d

processing/legacy/addAPS34IDEstrainCoords.py

@@ -49,4 +49,4 @@ for name in filenames:
 
     table.add('coord',rot_to_TSL.broadcast_to(coord.shape[0]) @ coord,scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_ASCII(sys.stdout if name is None else name)
+    table.to_file(sys.stdout if name is None else name)

processing/legacy/addCumulative.py

@@ -45,4 +45,4 @@ for name in filenames:
                   np.cumprod(table.get(label),0) if options.product else np.cumsum(table.get(label),0),
                   scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_ASCII(sys.stdout if name is None else name)
+    table.to_file(sys.stdout if name is None else name)

processing/post/DADF5_postResults.py

@@ -60,4 +60,4 @@ for filename in options.filenames:
             os.mkdir(dirname,0o755)
         file_out = '{}_inc{}.txt'.format(os.path.splitext(os.path.split(filename)[-1])[0],
                                          inc[3:].zfill(N_digits))
-        table.to_ASCII(os.path.join(dirname,file_out))
+        table.to_file(os.path.join(dirname,file_out))

processing/post/addCompatibilityMismatch.py

@@ -191,4 +191,4 @@ for name in filenames:
               volumeMismatch.reshape(-1,1,order='F'),
               scriptID+' '+' '.join(sys.argv[1:]))
 
-  table.to_ASCII(sys.stdout if name is None else name)
+  table.to_file(sys.stdout if name is None else name)

processing/post/addCurl.py

@@ -55,4 +55,4 @@ for name in filenames:
                   curl.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape),order='F'),
                   scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_ASCII(sys.stdout if name is None else name)
+    table.to_file(sys.stdout if name is None else name)

processing/post/addDerivative.py

@@ -71,4 +71,4 @@ for name in filenames:
                   derivative(table.get(options.coordinates),table.get(label)),
                   scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_ASCII(sys.stdout if name is None else name)
+    table.to_file(sys.stdout if name is None else name)

processing/post/addDisplacement.py

@@ -60,7 +60,7 @@ for name in filenames:
         table.add('fluct({}).{}'.format(options.f,options.pos),
                   damask.grid_filters.node_displacement_fluct(size,F).reshape(-1,3,order='F'),
                   scriptID+' '+' '.join(sys.argv[1:]))
-        table.to_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'_nodal.txt')
+        table.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'_nodal.txt')
     else:
         table.add('avg({}).{}'.format(options.f,options.pos),
                   damask.grid_filters.cell_displacement_avg(size,F).reshape(-1,3,order='F'),
@@ -68,4 +68,4 @@ for name in filenames:
         table.add('fluct({}).{}'.format(options.f,options.pos),
                   damask.grid_filters.cell_displacement_fluct(size,F).reshape(-1,3,order='F'),
                   scriptID+' '+' '.join(sys.argv[1:]))
-        table.to_ASCII(sys.stdout if name is None else name)
+        table.to_file(sys.stdout if name is None else name)

processing/post/addDivergence.py

@@ -55,4 +55,4 @@ for name in filenames:
                   div.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)//3,order='F'),
                   scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_ASCII(sys.stdout if name is None else name)
+    table.to_file(sys.stdout if name is None else name)

processing/post/addEuclideanDistance.py

@@ -184,4 +184,4 @@ for name in filenames:
                   distance[i,:],
                   scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_ASCII(sys.stdout if name is None else name)
+    table.to_file(sys.stdout if name is None else name)

processing/post/addGaussian.py

@@ -73,4 +73,4 @@ for name in filenames:
                                                   mode = 'wrap' if options.periodic else 'nearest'),
                   scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_ASCII(sys.stdout if name is None else name)
+    table.to_file(sys.stdout if name is None else name)

processing/post/addGradient.py

@@ -55,4 +55,4 @@ for name in filenames:
                   grad.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)*3,order='F'),
                   scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_ASCII(sys.stdout if name is None else name)
+    table.to_file(sys.stdout if name is None else name)

processing/post/addIndexed.py

@@ -61,4 +61,4 @@ for name in filenames:
     for data in options.label:
         table.add(data+'_addIndexed',indexedTable.get(data)[idx],scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_ASCII(sys.stdout if name is None else name)
+    table.to_file(sys.stdout if name is None else name)

processing/post/addOrientations.py

@@ -147,4 +147,4 @@ for name in filenames:
     if 'axisangle' in options.output:
         table.add('om({})'.format(label),o.as_axisangle(options.degrees), scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_ASCII(sys.stdout if name is None else name)
+    table.to_file(sys.stdout if name is None else name)

processing/post/addSchmidfactors.py

@@ -189,4 +189,4 @@ for name in filenames:
     for i,label in enumerate(labels):
         table.add(label,S[:,i],scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_ASCII(sys.stdout if name is None else name)
+    table.to_file(sys.stdout if name is None else name)

processing/post/permuteData.py

@@ -58,4 +58,4 @@ for name in filenames:
         rng.shuffle(uniques)
         table.set(label,uniques[inverse], scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_ASCII(sys.stdout if name is None else name)
+    table.to_file(sys.stdout if name is None else name)

processing/pre/geom_fromDREAM3D.py

@@ -154,4 +154,4 @@ for name in filenames:
                      homogenization=options.homogenization,comments=header)
   damask.util.croak(geom)
 
-  geom.to_file(os.path.splitext(name)[0]+'.geom',pack=False)
+  geom.to_file(os.path.splitext(name)[0]+'.geom',format='ASCII',pack=False)

processing/pre/geom_fromMinimalSurface.py

@@ -89,4 +89,4 @@ geom=damask.Geom(microstructure,options.size,
                  comments=[scriptID + ' ' + ' '.join(sys.argv[1:])])
 damask.util.croak(geom)
 
-geom.to_file(sys.stdout if name is None else name,pack=False)
+geom.to_file(sys.stdout if name is None else name,format='ASCII',pack=False)

processing/pre/geom_fromOsteonGeometry.py

@@ -142,4 +142,4 @@ geom = damask.Geom(microstructure.reshape(grid),
                    homogenization=options.homogenization,comments=header)
 damask.util.croak(geom)
 
-geom.to_file(sys.stdout if name is None else name,pack=False)
+geom.to_file(sys.stdout if name is None else name,format='ASCII',pack=False)

processing/pre/geom_fromTable.py

@@ -105,4 +105,5 @@ for name in filenames:
                        homogenization=options.homogenization,comments=header)
     damask.util.croak(geom)
 
-    geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',pack=False)
+    geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',
+                 format='ASCII',pack=False)

processing/pre/geom_fromVoronoiTessellation.py

@@ -228,4 +228,5 @@ for name in filenames:
                        homogenization=options.homogenization,comments=header)
     damask.util.croak(geom)
 
-    geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',pack=False)
+    geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',
+                 format='ASCII',pack=False)

processing/pre/geom_grainGrowth.py

@@ -172,4 +172,4 @@ for name in filenames:
   geom=geom.duplicate(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]])
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  geom.to_file(sys.stdout if name is None else name,pack=False)
+  geom.to_file(sys.stdout if name is None else name,format='ASCII',pack=False)

processing/pre/seeds_fromDistribution.py

@@ -90,7 +90,7 @@ class myThread (threading.Thread):
           direction[i]*=2.
           i+= 1
       perturbedSeedsTable.set('pos',coords)
-      perturbedSeedsTable.to_ASCII(perturbedSeedsVFile)
+      perturbedSeedsTable.to_file(perturbedSeedsVFile)
 
 #--- do tesselation with perturbed seed file ------------------------------------------------------
       perturbedGeomVFile.close()

processing/pre/seeds_fromGeom.py

@@ -65,5 +65,5 @@ for name in filenames:
 
     table = damask.Table(seeds[mask],{'pos':(3,)},comments)
     table.add('microstructure',microstructure[mask])
-    table.to_ASCII(sys.stdout if name is None else \
+    table.to_file(sys.stdout if name is None else \
                   os.path.splitext(name)[0]+'.seeds')

processing/pre/seeds_fromPokes.py

@@ -92,5 +92,5 @@ for name in filenames:
 
     table = damask.Table(seeds,{'pos':(3,),'microstructure':(1,)},comments)
     table.set('microstructure',table.get('microstructure').astype(np.int))
-    table.to_ASCII(sys.stdout if name is None else \
+    table.to_file(sys.stdout if name is None else \
-                   os.path.splitext(name)[0]+'_poked_{}.seeds'.format(options.N))
+                  os.path.splitext(name)[0]+f'_poked_{options.N}.seeds')

processing/pre/seeds_fromRandom.py

@@ -162,4 +162,4 @@ for name in filenames:
              else np.random.normal(loc = options.mean, scale = options.sigma, size = options.N)
         table.add('weight',weights)
 
-    table.to_ASCII(sys.stdout if name is None else name)
+    table.to_file(sys.stdout if name is None else name)

python/damask/_colormap.py

@@ -300,9 +300,9 @@ class Colormap(mpl.colors.ListedColormap):
 
         if fhandle is None:
             with open(colormap.name.replace(' ','_')+'.txt', 'w') as f:
-                t.to_ASCII(f,True)
+                t.to_file(f,new_style=True)
         else:
-            t.to_ASCII(fhandle,True)
+            t.to_file(fhandle,new_style=True)
 
     @staticmethod
     def _export_GOM(colormap,fhandle=None):

python/damask/_geom.py

@@ -447,36 +447,54 @@ class Geom:
                    )
 
 
-    def to_file(self,fname,pack=None):
+    def to_file(self,fname,format='vtr',pack=None):
         """
         Writes a geom file.
 
         Parameters
         ----------
+        fname : str or file handle
+            Geometry file to write.
+        format : {'vtr', 'ASCII'}, optional
+            File format, defaults to 'vtr'. Available formats are:
+            - vtr: VTK rectilinear grid file, extension '.vtr'.
+            - ASCII: Plain text file, extension '.geom'.
+        pack : bool, optional
+            Compress ASCII geometry with 'x of y' and 'a to b'.
+
+        """
+        def _to_ASCII(geom,fname,pack=None):
+            """
+            Writes a geom file.
+
+            Parameters
+            ----------
+            geom : Geom object
+                Geometry to write.
             fname : str or file handle
                 Geometry file to write.
             pack : bool, optional
                 Compress geometry with 'x of y' and 'a to b'.
 
             """
-        header =  [f'{len(self.comments)+4} header'] + self.comments
+            header =  [f'{len(geom.comments)+4} header'] + geom.comments
-        header.append('grid   a {} b {} c {}'.format(*self.get_grid()))
+            header.append('grid   a {} b {} c {}'.format(*geom.get_grid()))
-        header.append('size   x {} y {} z {}'.format(*self.get_size()))
+            header.append('size   x {} y {} z {}'.format(*geom.get_size()))
-        header.append('origin x {} y {} z {}'.format(*self.get_origin()))
+            header.append('origin x {} y {} z {}'.format(*geom.get_origin()))
-        header.append(f'homogenization {self.get_homogenization()}')
+            header.append(f'homogenization {geom.get_homogenization()}')
 
-        grid = self.get_grid()
+            grid = geom.get_grid()
 
             if pack is None:
-            plain = grid.prod()/self.N_microstructure < 250
+                plain = grid.prod()/geom.N_microstructure < 250
             else:
                 plain = not pack
 
             if plain:
-            format_string = '%g' if self.microstructure.dtype in np.sctypes['float'] else \
+                format_string = '%g' if geom.microstructure.dtype in np.sctypes['float'] else \
-                            '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure)))))
+                                '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(geom.microstructure)))))
                 np.savetxt(fname,
-                       self.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T,
+                           geom.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T,
                            header='\n'.join(header), fmt=format_string, comments='')
             else:
                 try:
@@ -487,7 +505,7 @@ class Geom:
                 compressType = None
                 former = start = -1
                 reps = 0
-            for current in self.microstructure.flatten('F'):
+                for current in geom.microstructure.flatten('F'):
                     if abs(current - former) == 1 and (start - current) == reps*(former - current):
                         compressType = 'to'
                         reps += 1
@@ -518,31 +536,39 @@ class Geom:
                     f.write(f'{reps} of {former}\n')
 
 
-    def to_vtr(self,fname=None):
+        def _to_vtr(geom,fname=None):
             """
             Generates vtk rectilinear grid.
 
             Parameters
             ----------
+            geom : Geom object
+                Geometry to write.
             fname : str, optional
                 Filename to write. If no file is given, a string is returned.
                 Valid extension is .vtr, it will be appended if not given.
 
             """
-        v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
+            v = VTK.from_rectilinearGrid(geom.grid,geom.size,geom.origin)
-        v.add(self.microstructure.flatten(order='F'),'materialpoint')
+            v.add(geom.microstructure.flatten(order='F'),'materialpoint')
-        v.add_comments(self.comments)
+            v.add_comments(geom.comments)
 
             if fname:
                 v.to_file(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
             else:
                 sys.stdout.write(v.__repr__())
 
+        if format.lower() == 'ascii':
+            return _to_ASCII(self,fname,pack)
+        elif format.lower() == 'vtr':
+            return _to_vtr(self,fname)
+        else:
+            raise TypeError(f'Unknown format {format}.')
 
-    def as_ASCII(self):
+    def as_ASCII(self,pack=False):
         """Format geometry as human-readable ASCII."""
         f = StringIO()
-        self.to_file(f)
+        self.to_file(f,'ASCII',pack)
         f.seek(0)
         return ''.join(f.readlines())
 

python/damask/_table.py

@@ -313,12 +313,29 @@ class Table:
                 self.shapes[key] = other.shapes[key]
 
 
-    def to_ASCII(self,fname,new_style=False):
+    def to_file(self,fname,format='ASCII',new_style=False):
         """
         Store as plain text file.
 
         Parameters
         ----------
+        fname : file, str, or pathlib.Path
+            Filename or file for writing.
+        format : {ASCII'}, optional
+            File format, defaults to 'ASCII'. Available formats are:
+            - ASCII: Plain text file, extension '.txt'.
+        new_style : Boolean, optional
+            Write table in new style, indicating header lines by comment sign ('#') only.
+
+        """
+        def _to_ASCII(table,fname,new_style=False):
+            """
+            Store as plain text file.
+
+            Parameters
+            ----------
+            table : Table object
+                Table to write.
             fname : file, str, or pathlib.Path
                 Filename or file for writing.
             new_style : Boolean, optional
@@ -327,21 +344,18 @@ class Table:
             """
             seen = set()
             labels = []
-        for l in [x for x in self.data.columns if not (x in seen or seen.add(x))]:
+            for l in [x for x in table.data.columns if not (x in seen or seen.add(x))]:
-            if self.shapes[l] == (1,):
+                if table.shapes[l] == (1,):
                     labels.append(f'{l}')
-            elif len(self.shapes[l]) == 1:
+                elif len(table.shapes[l]) == 1:
                     labels += [f'{i+1}_{l}' \
-                          for i in range(self.shapes[l][0])]
+                              for i in range(table.shapes[l][0])]
                 else:
-                labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
+                    labels += [f'{util.srepr(table.shapes[l],"x")}:{i+1}_{l}' \
-                          for i in range(np.prod(self.shapes[l]))]
+                              for i in range(np.prod(table.shapes[l]))]
 
-        if new_style:
+            header = [f'# {comment}' for comment in table.comments] if new_style else \
-            header = [f'# {comment}' for comment in self.comments]
+                     [f'{len(table.comments)+1} header'] + table.comments
-        else:
-            header = [f'{len(self.comments)+1} header'] \
-                   + self.comments \
 
             try:
                 f = open(fname,'w')
@@ -349,4 +363,9 @@ class Table:
                 f = fname
 
             for line in header + [' '.join(labels)]: f.write(line+'\n')
-        self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False)
+            table.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False)
+
+        if format.lower() == 'ascii':
+            return _to_ASCII(self,fname,new_style)
+        else:
+            raise TypeError(f'Unknown format {format}.')

python/tests/test_Geom.py

@@ -63,13 +63,13 @@ class TestGeom:
 
 
     def test_write_read_str(self,default,tmpdir):
-        default.to_file(str(tmpdir/'default.geom'))
+        default.to_file(str(tmpdir/'default.geom'),format='ASCII')
         new = Geom.from_file(str(tmpdir/'default.geom'))
         assert geom_equal(default,new)
 
     def test_write_read_file(self,default,tmpdir):
         with open(tmpdir/'default.geom','w') as f:
-            default.to_file(f,pack=True)
+            default.to_file(f,format='ASCII',pack=True)
         with open(tmpdir/'default.geom') as f:
             new = Geom.from_file(f)
         assert geom_equal(default,new)
@@ -82,8 +82,7 @@ class TestGeom:
         assert geom_equal(default,new)
 
     def test_read_write_vtr(self,default,tmpdir):
-        default.to_vtr(tmpdir/'default')
+        default.to_file(tmpdir/'default',format='vtr')
-        print(default.to_vtr())
         for _ in range(10):
             time.sleep(.2)
             if os.path.exists(tmpdir/'default.vtr'): break
@@ -110,7 +109,7 @@ class TestGeom:
 
     @pytest.mark.parametrize('pack',[True,False])
     def test_pack(self,default,tmpdir,pack):
-        default.to_file(tmpdir/'default.geom',pack=pack)
+        default.to_file(tmpdir/'default.geom',format='ASCII',pack=pack)
         new = Geom.from_file(tmpdir/'default.geom')
         assert geom_equal(new,default)
 
@@ -140,6 +139,10 @@ class TestGeom:
         with pytest.raises(TypeError):
             default.set_homogenization(homogenization=0)
 
+    def test_invalid_write_format(self,default):
+        with pytest.raises(TypeError):
+            default.to_file(format='invalid')
+
     @pytest.mark.parametrize('directions,reflect',[
                                                    (['x'],        False),
                                                    (['x','y','z'],True),
@@ -196,7 +199,7 @@ class TestGeom:
         current = default.clean(stencil,selection,periodic)
         reference = reference_dir/f'clean_{stencil}_{"+".join(map(str,[None] if selection is None else selection))}_{periodic}'
         if update and stencil > 1:
-            current.to_vtr(reference)
+            current.to_file(reference,format='vtr')
             for _ in range(10):
                 time.sleep(.2)
                 if os.path.exists(reference.with_suffix('.vtr')): break

python/tests/test_Table.py

@@ -35,7 +35,7 @@ class TestTable:
 
     @pytest.mark.parametrize('mode',['str','path'])
     def test_write_read(self,default,tmpdir,mode):
-        default.to_ASCII(tmpdir/'default.txt')
+        default.to_file(tmpdir/'default.txt')
         if   mode == 'path':
             new = Table.from_ASCII(tmpdir/'default.txt')
         elif mode == 'str':
@@ -43,19 +43,22 @@ class TestTable:
         assert all(default.data==new.data) and default.shapes == new.shapes
 
     def test_write_read_file(self,default,tmpdir):
-        with open(tmpdir.join('default.txt'),'w') as f:
+        with open(tmpdir/'default.txt','w') as f:
-            default.to_ASCII(f)
+            default.to_file(f)
-        with open(tmpdir.join('default.txt')) as f:
+        with open(tmpdir/'default.txt') as f:
             new = Table.from_ASCII(f)
         assert all(default.data==new.data) and default.shapes == new.shapes
 
     def test_write_read_new_style(self,default,tmpdir):
-        with open(tmpdir.join('new_style.txt'),'w') as f:
+        with open(tmpdir/'new_style.txt','w') as f:
-            default.to_ASCII(f,new_style=True)
+            default.to_file(f,new_style=True)
-        with open(tmpdir.join('new_style.txt')) as f:
+        with open(tmpdir/'new_style.txt') as f:
             new = Table.from_ASCII(f)
         assert all(default.data==new.data) and default.shapes == new.shapes
 
+    def test_write_invalid_format(self,default,tmpdir):
+        with pytest.raises(TypeError):
+            default.to_file(tmpdir/'shouldnotbethere.txt',format='invalid')
 
     @pytest.mark.parametrize('mode',['str','path'])
     def test_read_ang(self,reference_dir,mode):