diff --git a/processing/pre/geom_grainGrowth.py b/processing/pre/geom_grainGrowth.py index bdf8d8efe..6d1985ee3 100755 --- a/processing/pre/geom_grainGrowth.py +++ b/processing/pre/geom_grainGrowth.py @@ -169,7 +169,7 @@ for name in filenames: # undo any changes involving immutable microstructures microstructure = np.where(immutable, microstructure_original,microstructure) - damask.util.croak(geom.update(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]])) + 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) diff --git a/python/damask/_colormap.py b/python/damask/_colormap.py index e2b317d63..59f3b749d 100644 --- a/python/damask/_colormap.py +++ b/python/damask/_colormap.py @@ -280,7 +280,7 @@ class Colormap(mpl.colors.ListedColormap): colors+=[i]+c out = [{ - 'Creator':util.version_date('Colormap'), + 'Creator':util.execution_stamp('Colormap'), 'ColorSpace':'RGB', 'Name':colormap.name, 'DefaultMap':True, @@ -296,7 +296,7 @@ class Colormap(mpl.colors.ListedColormap): def _export_ASCII(colormap,fhandle=None): """Write colormap to ASCII table.""" labels = {'RGBA':4} if colormap.colors.shape[1] == 4 else {'RGB': 3} - t = Table(colormap.colors,labels,f'Creator: {util.version_date("Colormap")}') + t = Table(colormap.colors,labels,f'Creator: {util.execution_stamp("Colormap")}') if fhandle is None: with open(colormap.name.replace(' ','_')+'.txt', 'w') as f: diff --git a/python/damask/_geom.py b/python/damask/_geom.py index 6632eb5ed..8a5dfcdc9 100644 --- a/python/damask/_geom.py +++ b/python/damask/_geom.py @@ -24,15 +24,15 @@ class Geom: Parameters ---------- microstructure : numpy.ndarray - microstructure array (3D) + Microstructure array (3D) size : list or numpy.ndarray - physical size of the microstructure in meter. + Physical size of the microstructure in meter. origin : list or numpy.ndarray, optional - physical origin of the microstructure in meter. + Physical origin of the microstructure in meter. homogenization : int, optional - homogenization index. + Homogenization index. comments : list of str, optional - comments lines. + Comment lines. """ self.set_microstructure(microstructure) @@ -63,63 +63,73 @@ class Geom: return self.__copy__() - def update(self,microstructure=None,size=None,origin=None,rescale=False): + def duplicate(self,microstructure=None,size=None,origin=None,comments=None,autosize=False): """ - Update microstructure and size. + Create a duplicate having updated microstructure, size, and origin. Parameters ---------- microstructure : numpy.ndarray, optional - microstructure array (3D). + Microstructure array (3D). size : list or numpy.ndarray, optional - physical size of the microstructure in meter. + Physical size of the microstructure in meter. origin : list or numpy.ndarray, optional - physical origin of the microstructure in meter. - rescale : bool, optional - ignore size parameter and rescale according to change of grid points. + Physical origin of the microstructure in meter. + comments : list of str, optional + Comment lines. + autosize : bool, optional + Ignore size parameter and rescale according to change of grid points. """ - grid_old = self.get_grid() - size_old = self.get_size() - origin_old = self.get_origin() - unique_old = self.N_microstructure - max_old = np.nanmax(self.microstructure) + if size is not None and autosize: + raise ValueError('Auto-sizing conflicts with explicit size parameter.') - if size is not None and rescale: - raise ValueError('Either set size explicitly or rescale automatically') + grid_old = self.get_grid() + dup = self.copy() + dup.set_microstructure(microstructure) + dup.set_origin(origin) - self.set_microstructure(microstructure) - self.set_origin(origin) + if comments is not None: + dup.set_comments(comments) if size is not None: - self.set_size(size) - elif rescale: - self.set_size(self.get_grid()/grid_old*self.size) + dup.set_size(size) + elif autosize: + dup.set_size(dup.get_grid()/grid_old*self.get_size()) - message = [f'grid a b c: {util.srepr(grid_old," x ")}'] - if np.any(grid_old != self.get_grid()): - message[-1] = util.delete(message[-1]) - message.append(util.emph(f'grid a b c: {util.srepr(self.get_grid()," x ")}')) + return dup - message.append(f'size x y z: {util.srepr(size_old," x ")}') - if np.any(size_old != self.get_size()): - message[-1] = util.delete(message[-1]) - message.append(util.emph(f'size x y z: {util.srepr(self.get_size()," x ")}')) - message.append(f'origin x y z: {util.srepr(origin_old," ")}') - if np.any(origin_old != self.get_origin()): - message[-1] = util.delete(message[-1]) - message.append(util.emph(f'origin x y z: {util.srepr(self.get_origin()," ")}')) + def diff(self,other): + """ + Report property differences of self relative to other. - message.append(f'# microstructures: {unique_old}') - if unique_old != self.N_microstructure: - message[-1] = util.delete(message[-1]) - message.append(util.emph(f'# microstructures: {self.N_microstructure}')) + Parameters + ---------- + other : Geom + Geometry to compare self against. - message.append(f'max microstructure: {max_old}') - if max_old != np.nanmax(self.microstructure): - message[-1] = util.delete(message[-1]) - message.append(util.emph(f'max microstructure: {np.nanmax(self.microstructure)}')) + """ + message = [] + if np.any(other.get_grid() != self.get_grid()): + message.append(util.delete(f'grid a b c: {util.srepr(other.get_grid()," x ")}')) + message.append(util.emph( f'grid a b c: {util.srepr( self.get_grid()," x ")}')) + + if np.any(other.get_size() != self.get_size()): + message.append(util.delete(f'size x y z: {util.srepr(other.get_size()," x ")}')) + message.append(util.emph( f'size x y z: {util.srepr( self.get_size()," x ")}')) + + if np.any(other.get_origin() != self.get_origin()): + message.append(util.delete(f'origin x y z: {util.srepr(other.get_origin()," ")}')) + message.append(util.emph( f'origin x y z: {util.srepr( self.get_origin()," ")}')) + + if other.N_microstructure != self.N_microstructure: + message.append(util.delete(f'# materialpoints: {other.N_microstructure}')) + message.append(util.emph( f'# materialpoints: { self.N_microstructure}')) + + if np.nanmax(other.microstructure) != np.nanmax(self.microstructure): + message.append(util.delete(f'max materialpoint: {np.nanmax(other.microstructure)}')) + message.append(util.emph( f'max materialpoint: {np.nanmax( self.microstructure)}')) return util.return_message(message) @@ -131,7 +141,7 @@ class Geom: Parameters ---------- comments : list of str - new comments. + All comments. """ self.comments = [] @@ -145,7 +155,7 @@ class Geom: Parameters ---------- comments : list of str - new comments. + New comments. """ self.comments += [str(c) for c in comments] if isinstance(comments,list) else [str(comments)] @@ -172,6 +182,10 @@ class Geom: else: self.microstructure = np.copy(microstructure) + if self.microstructure.dtype in np.sctypes['float'] and \ + np.all(self.microstructure == self.microstructure.astype(int).astype(float)): + self.microstructure = self.microstructure.astype(int) + if len(self.microstructure.shape) != 3: raise ValueError(f'Invalid microstructure shape {microstructure.shape}') elif self.microstructure.dtype not in np.sctypes['float'] + np.sctypes['int']: @@ -185,7 +199,7 @@ class Geom: Parameters ---------- size : list or numpy.ndarray - physical size of the microstructure in meter. + Physical size of the microstructure in meter. """ if size is not None: @@ -202,7 +216,7 @@ class Geom: Parameters ---------- origin : list or numpy.ndarray - physical origin of the microstructure in meter + Physical origin of the microstructure in meter. """ if origin is not None: @@ -219,12 +233,12 @@ class Geom: Parameters ---------- homogenization : int - homogenization index + Homogenization index. """ if homogenization is not None: if not isinstance(homogenization,int) or homogenization < 1: - raise TypeError(f'Invalid homogenization {homogenization}') + raise TypeError(f'Invalid homogenization {homogenization}.') else: self.homogenization = homogenization @@ -286,13 +300,16 @@ class Geom: f = fname f.seek(0) - header_length,keyword = f.readline().split()[:2] - header_length = int(header_length) - content = f.readlines() - + try: + header_length,keyword = f.readline().split()[:2] + header_length = int(header_length) + except ValueError: + header_length,keyword = (-1, 'invalid') if not keyword.startswith('head') or header_length < 3: raise TypeError('Header length information missing or invalid') + content = f.readlines() + comments = [] for i,line in enumerate(content[:header_length]): items = line.split('#')[0].lower().strip().split() @@ -345,11 +362,12 @@ class Geom: """ v = VTK.from_file(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr') - grid = np.array(v.geom.GetDimensions())-1 - bbox = np.array(v.geom.GetBounds()).reshape(3,2).T + comments = v.get_comments() + grid = np.array(v.vtk_data.GetDimensions())-1 + bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T size = bbox[1] - bbox[0] - return Geom(v.get('materialpoint').reshape(grid,order='F'),size,bbox[0]) + return Geom(v.get('materialpoint').reshape(grid,order='F'),size,bbox[0],comments=comments) @staticmethod @@ -398,8 +416,9 @@ class Geom: else: microstructure = microstructure.reshape(grid) - creator = util.version_date('Geom','from_Laguerre_tessellation') - return Geom(microstructure+1,size,homogenization=1,comments=creator) + return Geom(microstructure+1,size,homogenization=1, + comments=util.execution_stamp('Geom','from_Laguerre_tessellation'), + ) @staticmethod @@ -423,8 +442,9 @@ class Geom: KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds) devNull,microstructure = KDTree.query(coords) - creator = util.version_date('Geom','from_Voronoi_tessellation') - return Geom(microstructure.reshape(grid)+1,size,homogenization=1,comments=creator) + return Geom(microstructure.reshape(grid)+1,size,homogenization=1, + comments=util.execution_stamp('Geom','from_Voronoi_tessellation'), + ) def to_file(self,fname,pack=None): @@ -511,6 +531,7 @@ class Geom: """ v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin) v.add(self.microstructure.flatten(order='F'),'materialpoint') + v.add_comments(self.comments) if fname: v.write(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr') @@ -518,9 +539,9 @@ class Geom: sys.stdout.write(v.__repr__()) - def show(self): - """Show raw content (as in file).""" - f=StringIO() + def as_ASCII(self): + """Format geometry as human-readable ASCII.""" + f = StringIO() self.to_file(f) f.seek(0) return ''.join(f.readlines()) @@ -550,10 +571,10 @@ class Geom: R : damask.Rotation, optional Rotation of primitive. Defaults to no rotation. inverse : Boolean, optional - Retain original microstructure within primitive and fill - outside. Defaults to False. + Retain original microstructure within primitive and fill outside. + Defaults to False. periodic : Boolean, optional - Repeat primitive over boundaries. Defaults to False. + Repeat primitive over boundaries. Defaults to True. """ # normalized 'radius' and center @@ -563,11 +584,11 @@ class Geom: (np.array(center) - self.origin)/self.size coords = grid_filters.cell_coord0(self.grid,np.ones(3)) \ - - (np.ones(3)*0.5 if periodic else c) # center if periodic + - ((np.ones(3)-(1./self.grid if np.array(center).dtype in np.sctypes['int'] else 0))*0.5 if periodic else c) # periodic center is always at CoG coords_rot = R.broadcast_to(tuple(self.grid))@coords - with np.errstate(over='ignore',under='ignore'): - mask = np.where(np.sum(np.abs(coords_rot/r)**(2.0**exponent),axis=-1) < 1,True,False) + with np.errstate(all='ignore'): + mask = np.where(np.sum(np.power(coords_rot/r,2.0**exponent),axis=-1) > 1.0,True,False) if periodic: # translate back to center mask = np.roll(mask,((c-np.ones(3)*.5)*self.grid).astype(int),(0,1,2)) @@ -575,8 +596,9 @@ class Geom: fill_ = np.full_like(self.microstructure,np.nanmax(self.microstructure)+1 if fill is None else fill) ms = np.ma.MaskedArray(fill_,np.logical_not(mask) if inverse else mask) - self.add_comments(util.version_date('Geom','add_primitive')) - return self.update(ms) + return self.duplicate(ms, + comments=self.get_comments()+[util.execution_stamp('Geom','add_primitive')], + ) def mirror(self,directions,reflect=False): @@ -589,10 +611,10 @@ class Geom: Direction(s) along which the microstructure is mirrored. Valid entries are 'x', 'y', 'z'. reflect : bool, optional - Reflect (include) outermost layers. + Reflect (include) outermost layers. Defaults to False. """ - valid = {'x','y','z'} + valid = ['x','y','z'] if not set(directions).issubset(valid): raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.') @@ -606,8 +628,31 @@ class Geom: if 'x' in directions: ms = np.concatenate([ms,ms[limits[0]:limits[1]:-1,:,:]],0) - self.add_comments(util.version_date('Geom','mirror')) - return self.update(ms,rescale=True) + return self.duplicate(ms, + comments=self.get_comments()+[util.execution_stamp('Geom','mirror')], + autosize=True) + + + def flip(self,directions): + """ + Flip microstructure along given directions. + + Parameters + ---------- + directions : iterable containing str + Direction(s) along which the microstructure is flipped. + Valid entries are 'x', 'y', 'z'. + + """ + valid = ['x','y','z'] + if not set(directions).issubset(valid): + raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.') + + ms = np.flip(self.microstructure, (valid.index(d) for d in directions if d in valid)) + + return self.duplicate(ms, + comments=self.get_comments()+[util.execution_stamp('Geom','flip')], + ) def scale(self,grid,periodic=True): @@ -622,17 +667,16 @@ class Geom: Assume geometry to be periodic. Defaults to True. """ - self.add_comments(util.version_date('Geom','scale')) - return self.update( - ndimage.interpolation.zoom( - self.microstructure, - grid/self.get_grid(), - output=self.microstructure.dtype, - order=0, - mode=('wrap' if periodic else 'nearest'), - prefilter=False - ) - ) + return self.duplicate(ndimage.interpolation.zoom( + self.microstructure, + grid/self.get_grid(), + output=self.microstructure.dtype, + order=0, + mode=('wrap' if periodic else 'nearest'), + prefilter=False + ), + comments=self.get_comments()+[util.execution_stamp('Geom','scale')], + ) def clean(self,stencil=3,selection=None,periodic=True): @@ -657,15 +701,15 @@ class Geom: else: return me - self.add_comments(util.version_date('Geom','clean')) - return self.update(ndimage.filters.generic_filter( - self.microstructure, - mostFrequent, - size=(stencil if selection is None else stencil//2*2+1,)*3, - mode=('wrap' if periodic else 'nearest'), - extra_keywords=dict(selection=selection), - ).astype(self.microstructure.dtype) - ) + return self.duplicate(ndimage.filters.generic_filter( + self.microstructure, + mostFrequent, + size=(stencil if selection is None else stencil//2*2+1,)*3, + mode=('wrap' if periodic else 'nearest'), + extra_keywords=dict(selection=selection), + ).astype(self.microstructure.dtype), + comments=self.get_comments()+[util.execution_stamp('Geom','clean')], + ) def renumber(self): @@ -674,8 +718,9 @@ class Geom: for i, oldID in enumerate(np.unique(self.microstructure)): renumbered = np.where(self.microstructure == oldID, i+1, renumbered) - self.add_comments(util.version_date('Geom','renumber')) - return self.update(renumbered) + return self.duplicate(renumbered, + comments=self.get_comments()+[util.execution_stamp('Geom','renumber')], + ) def rotate(self,R,fill=None): @@ -709,8 +754,11 @@ class Geom: origin = self.origin-(np.asarray(microstructure_in.shape)-self.grid)*.5 * self.size/self.grid - self.add_comments(util.version_date('Geom','rotate')) - return self.update(microstructure_in,origin=origin,rescale=True) + return self.duplicate(microstructure_in, + origin=origin, + comments=self.get_comments()+[util.execution_stamp('Geom','rotate')], + autosize=True, + ) def canvas(self,grid=None,offset=None,fill=None): @@ -724,16 +772,14 @@ class Geom: offset : numpy.ndarray of shape (3) Offset (measured in grid points) from old to new microstructure[0,0,0]. fill : int or float, optional - Microstructure index to fill the corners. Defaults to microstructure.max() + 1. + Microstructure index to fill the background. Defaults to microstructure.max() + 1. """ - if fill is None: fill = np.nanmax(self.microstructure) + 1 if offset is None: offset = 0 - dtype = float if int(fill) != fill or self.microstructure.dtype==np.float else int + if fill is None: fill = np.nanmax(self.microstructure) + 1 + dtype = float if int(fill) != fill or self.microstructure.dtype in np.sctypes['float'] else int - canvas = np.full(self.grid if grid is None else grid, - np.nanmax(self.microstructure)+1 if fill is None else fill, - dtype) + canvas = np.full(self.grid if grid is None else grid,fill,dtype) LL = np.clip( offset, 0,np.minimum(self.grid, grid+offset)) UR = np.clip( offset+grid, 0,np.minimum(self.grid, grid+offset)) @@ -742,8 +788,11 @@ class Geom: canvas[ll[0]:ur[0],ll[1]:ur[1],ll[2]:ur[2]] = self.microstructure[LL[0]:UR[0],LL[1]:UR[1],LL[2]:UR[2]] - self.add_comments(util.version_date('Geom','canvas')) - return self.update(canvas,origin=self.origin+offset*self.size/self.grid,rescale=True) + return self.duplicate(canvas, + origin=self.origin+offset*self.size/self.grid, + comments=self.get_comments()+[util.execution_stamp('Geom','canvas')], + autosize=True, + ) def substitute(self,from_microstructure,to_microstructure): @@ -762,8 +811,9 @@ class Geom: for from_ms,to_ms in zip(from_microstructure,to_microstructure): substituted[self.microstructure==from_ms] = to_ms - self.add_comments(util.version_date('Geom','substitute')) - return self.update(substituted) + return self.duplicate(substituted, + comments=self.get_comments()+[util.execution_stamp('Geom','substitute')], + ) def vicinity_offset(self,vicinity=1,offset=None,trigger=[],periodic=True): @@ -804,9 +854,10 @@ class Geom: mask = ndimage.filters.generic_filter(self.microstructure, tainted_neighborhood, size=1+2*vicinity, - mode=('wrap' if periodic else 'nearest'), + mode='wrap' if periodic else 'nearest', extra_keywords={'trigger':trigger}) microstructure = np.ma.MaskedArray(self.microstructure + offset_, np.logical_not(mask)) - self.add_comments(util.version_date('Geom','vicinity_offset')) - return self.update(microstructure) + return self.duplicate(microstructure, + comments=self.get_comments()+[util.execution_stamp('Geom','vicinity_offset')], + ) diff --git a/python/damask/_result.py b/python/damask/_result.py index d739db8f5..1af403ab1 100644 --- a/python/damask/_result.py +++ b/python/damask/_result.py @@ -1,6 +1,5 @@ import multiprocessing as mp import re -import inspect import glob import os import datetime @@ -537,7 +536,7 @@ class Result: 'meta': { 'Unit': x['meta']['Unit'], 'Description': f"Absolute value of {x['label']} ({x['meta']['Description']})", - 'Creator': inspect.stack()[0][3][1:] + 'Creator': 'add_absolute' } } def add_absolute(self,x): @@ -565,7 +564,7 @@ class Result: 'meta': { 'Unit': kwargs['unit'], 'Description': f"{kwargs['description']} (formula: {kwargs['formula']})", - 'Creator': inspect.stack()[0][3][1:] + 'Creator': 'add_calculation' } } def add_calculation(self,label,formula,unit='n/a',description=None): @@ -599,7 +598,7 @@ class Result: 'Description': "Cauchy stress calculated " f"from {P['label']} ({P['meta']['Description']})" f" and {F['label']} ({F['meta']['Description']})", - 'Creator': inspect.stack()[0][3][1:] + 'Creator': 'add_Cauchy' } } def add_Cauchy(self,P='P',F='F'): @@ -625,7 +624,7 @@ class Result: 'meta': { 'Unit': T['meta']['Unit'], 'Description': f"Determinant of tensor {T['label']} ({T['meta']['Description']})", - 'Creator': inspect.stack()[0][3][1:] + 'Creator': 'add_determinant' } } def add_determinant(self,T): @@ -649,7 +648,7 @@ class Result: 'meta': { 'Unit': T['meta']['Unit'], 'Description': f"Deviator of tensor {T['label']} ({T['meta']['Description']})", - 'Creator': inspect.stack()[0][3][1:] + 'Creator': 'add_deviator' } } def add_deviator(self,T): @@ -680,7 +679,7 @@ class Result: 'meta' : { 'Unit': T_sym['meta']['Unit'], 'Description': f"{label} eigenvalue of {T_sym['label']} ({T_sym['meta']['Description']})", - 'Creator': inspect.stack()[0][3][1:] + 'Creator': 'add_eigenvalue' } } def add_eigenvalue(self,T_sym,eigenvalue='max'): @@ -713,7 +712,7 @@ class Result: 'Unit': '1', 'Description': f"Eigenvector corresponding to {label} eigenvalue" f" of {T_sym['label']} ({T_sym['meta']['Description']})", - 'Creator': inspect.stack()[0][3][1:] + 'Creator': 'add_eigenvector' } } def add_eigenvector(self,T_sym,eigenvalue='max'): @@ -746,7 +745,7 @@ class Result: 'Unit': '8-bit RGB', 'Lattice': q['meta']['Lattice'], 'Description': 'Inverse Pole Figure (IPF) colors along sample direction [{} {} {}]'.format(*m), - 'Creator': inspect.stack()[0][3][1:] + 'Creator': 'add_IPF_color' } } def add_IPF_color(self,q,l): @@ -772,7 +771,7 @@ class Result: 'meta': { 'Unit': T_sym['meta']['Unit'], 'Description': f"Maximum shear component of {T_sym['label']} ({T_sym['meta']['Description']})", - 'Creator': inspect.stack()[0][3][1:] + 'Creator': 'add_maximum_shear' } } def add_maximum_shear(self,T_sym): @@ -799,7 +798,7 @@ class Result: 'meta': { 'Unit': T_sym['meta']['Unit'], 'Description': f"Mises equivalent {t} of {T_sym['label']} ({T_sym['meta']['Description']})", - 'Creator': inspect.stack()[0][3][1:] + 'Creator': 'add_Mises' } } def add_Mises(self,T_sym): @@ -835,7 +834,7 @@ class Result: 'meta': { 'Unit': x['meta']['Unit'], 'Description': f"{o}-norm of {t} {x['label']} ({x['meta']['Description']})", - 'Creator': inspect.stack()[0][3][1:] + 'Creator': 'add_norm' } } def add_norm(self,x,ord=None): @@ -863,7 +862,7 @@ class Result: 'Description': "2. Piola-Kirchhoff stress calculated " f"from {P['label']} ({P['meta']['Description']})" f" and {F['label']} ({F['meta']['Description']})", - 'Creator': inspect.stack()[0][3][1:] + 'Creator': 'add_PK2' } } def add_PK2(self,P='P',F='F'): @@ -899,7 +898,7 @@ class Result: 'Unit': '1', 'Description': '{} coordinates of stereographic projection of pole (direction/plane) in crystal frame'\ .format('Polar' if polar else 'Cartesian'), - 'Creator': inspect.stack()[0][3][1:] + 'Creator': 'add_pole' } } def add_pole(self,q,p,polar=False): @@ -927,7 +926,7 @@ class Result: 'meta': { 'Unit': F['meta']['Unit'], 'Description': f"Rotational part of {F['label']} ({F['meta']['Description']})", - 'Creator': inspect.stack()[0][3][1:] + 'Creator': 'add_rotational_part' } } def add_rotational_part(self,F): @@ -951,7 +950,7 @@ class Result: 'meta': { 'Unit': T['meta']['Unit'], 'Description': f"Spherical component of tensor {T['label']} ({T['meta']['Description']})", - 'Creator': inspect.stack()[0][3][1:] + 'Creator': 'add_spherical' } } def add_spherical(self,T): @@ -975,7 +974,7 @@ class Result: 'meta': { 'Unit': F['meta']['Unit'], 'Description': f"Strain tensor of {F['label']} ({F['meta']['Description']})", - 'Creator': inspect.stack()[0][3][1:] + 'Creator': 'add_strain_tensor' } } def add_strain_tensor(self,F='F',t='V',m=0.0): @@ -1007,7 +1006,7 @@ class Result: 'Unit': F['meta']['Unit'], 'Description': '{} stretch tensor of {} ({})'.format('Left' if t.upper() == 'V' else 'Right', F['label'],F['meta']['Description']), - 'Creator': inspect.stack()[0][3][1:] + 'Creator': 'add_stretch_tensor' } } def add_stretch_tensor(self,F='F',t='V'): diff --git a/python/damask/_table.py b/python/damask/_table.py index b4822bea9..fd8cf0fe3 100644 --- a/python/damask/_table.py +++ b/python/damask/_table.py @@ -49,7 +49,7 @@ class Table: def _add_comment(self,label,shape,info): if info is not None: specific = f'{label}{" "+str(shape) if np.prod(shape,dtype=int) > 1 else ""}: {info}' - general = util.version_date('Table') + general = util.execution_stamp('Table') self.comments.append(f'{specific} / {general}') @@ -136,7 +136,7 @@ class Table: content = f.readlines() - comments = [util.version_date('Table','from_ang')] + comments = [util.execution_stamp('Table','from_ang')] for line in content: if line.startswith('#'): comments.append(line.strip()) diff --git a/python/damask/_vtk.py b/python/damask/_vtk.py index 349e158ca..bbc2d2e69 100644 --- a/python/damask/_vtk.py +++ b/python/damask/_vtk.py @@ -20,18 +20,19 @@ class VTK: High-level interface to VTK. """ - def __init__(self,geom): + def __init__(self,vtk_data): """ - Set geometry and topology. + Initialize from vtk dataset. Parameters ---------- - geom : subclass of vtk.vtkDataSet - Description of geometry and topology. Valid types are vtk.vtkRectilinearGrid, - vtk.vtkUnstructuredGrid, or vtk.vtkPolyData. + vtk_data : subclass of vtk.vtkDataSet + Description of geometry and topology, optionally with attached data. + Valid types are vtk.vtkRectilinearGrid, vtk.vtkUnstructuredGrid, + or vtk.vtkPolyData. """ - self.geom = geom + self.vtk_data = vtk_data @staticmethod @@ -51,15 +52,15 @@ class VTK: Spatial origin. """ - geom = vtk.vtkRectilinearGrid() - geom.SetDimensions(*(grid+1)) + vtk_data = vtk.vtkRectilinearGrid() + vtk_data.SetDimensions(*(grid+1)) coord = [np_to_vtk(np.linspace(origin[i],origin[i]+size[i],grid[i]+1),deep=True) for i in [0,1,2]] [coord[i].SetName(n) for i,n in enumerate(['x','y','z'])] - geom.SetXCoordinates(coord[0]) - geom.SetYCoordinates(coord[1]) - geom.SetZCoordinates(coord[2]) + vtk_data.SetXCoordinates(coord[0]) + vtk_data.SetYCoordinates(coord[1]) + vtk_data.SetZCoordinates(coord[2]) - return VTK(geom) + return VTK(vtk_data) @staticmethod @@ -87,11 +88,11 @@ class VTK: connectivity),axis=1).ravel() cells.SetCells(connectivity.shape[0],np_to_vtkIdTypeArray(T,deep=True)) - geom = vtk.vtkUnstructuredGrid() - geom.SetPoints(vtk_nodes) - geom.SetCells(eval(f'vtk.VTK_{cell_type.split("_",1)[-1].upper()}'),cells) + vtk_data = vtk.vtkUnstructuredGrid() + vtk_data.SetPoints(vtk_nodes) + vtk_data.SetCells(eval(f'vtk.VTK_{cell_type.split("_",1)[-1].upper()}'),cells) - return VTK(geom) + return VTK(vtk_data) @staticmethod @@ -110,10 +111,10 @@ class VTK: vtk_points = vtk.vtkPoints() vtk_points.SetData(np_to_vtk(points)) - geom = vtk.vtkPolyData() - geom.SetPoints(vtk_points) + vtk_data = vtk.vtkPolyData() + vtk_data.SetPoints(vtk_points) - return VTK(geom) + return VTK(vtk_data) @staticmethod @@ -131,18 +132,20 @@ class VTK: """ ext = Path(fname).suffix - if ext == '.vtk' or dataset_type: + if ext == '.vtk' or dataset_type is not None: reader = vtk.vtkGenericDataObjectReader() reader.SetFileName(str(fname)) - reader.Update() if dataset_type is None: raise TypeError('Dataset type for *.vtk file not given.') elif dataset_type.lower().endswith('rectilineargrid'): - geom = reader.GetRectilinearGridOutput() + reader.Update() + vtk_data = reader.GetRectilinearGridOutput() elif dataset_type.lower().endswith('unstructuredgrid'): - geom = reader.GetUnstructuredGridOutput() + reader.Update() + vtk_data = reader.GetUnstructuredGridOutput() elif dataset_type.lower().endswith('polydata'): - geom = reader.GetPolyDataOutput() + reader.Update() + vtk_data = reader.GetPolyDataOutput() else: raise TypeError(f'Unknown dataset type {dataset_type} for vtk file') else: @@ -157,9 +160,9 @@ class VTK: reader.SetFileName(str(fname)) reader.Update() - geom = reader.GetOutput() + vtk_data = reader.GetOutput() - return VTK(geom) + return VTK(vtk_data) @staticmethod def _write(writer): @@ -177,11 +180,11 @@ class VTK: Write data in parallel background process. Defaults to True. """ - if isinstance(self.geom,vtk.vtkRectilinearGrid): + if isinstance(self.vtk_data,vtk.vtkRectilinearGrid): writer = vtk.vtkXMLRectilinearGridWriter() - elif isinstance(self.geom,vtk.vtkUnstructuredGrid): + elif isinstance(self.vtk_data,vtk.vtkUnstructuredGrid): writer = vtk.vtkXMLUnstructuredGridWriter() - elif isinstance(self.geom,vtk.vtkPolyData): + elif isinstance(self.vtk_data,vtk.vtkPolyData): writer = vtk.vtkXMLPolyDataWriter() default_ext = writer.GetDefaultFileExtension() @@ -191,7 +194,7 @@ class VTK: writer.SetFileName(str(Path(fname).with_suffix('.'+default_ext))) writer.SetCompressorTypeToZLib() writer.SetDataModeToBinary() - writer.SetInputData(self.geom) + writer.SetInputData(self.vtk_data) if parallel: try: @@ -218,8 +221,8 @@ class VTK: Data label. """ - N_points = self.geom.GetNumberOfPoints() - N_cells = self.geom.GetNumberOfCells() + N_points = self.vtk_data.GetNumberOfPoints() + N_cells = self.vtk_data.GetNumberOfCells() if isinstance(data,np.ndarray): if label is None: @@ -232,9 +235,9 @@ class VTK: d.SetName(label) if data.shape[0] == N_cells: - self.geom.GetCellData().AddArray(d) + self.vtk_data.GetCellData().AddArray(d) elif data.shape[0] == N_points: - self.geom.GetPointData().AddArray(d) + self.vtk_data.GetPointData().AddArray(d) else: raise ValueError(f'Invalid shape {data.shape[0]}') elif isinstance(data,pd.DataFrame): @@ -259,22 +262,22 @@ class VTK: Data label. """ - celldata = self.geom.GetCellData() - for a in range(celldata.GetNumberOfArrays()): - if celldata.GetArrayName(a) == label: - return vtk_to_np(celldata.GetArray(a)) + cell_data = self.vtk_data.GetCellData() + for a in range(cell_data.GetNumberOfArrays()): + if cell_data.GetArrayName(a) == label: + return vtk_to_np(cell_data.GetArray(a)) - pointdata = self.geom.GetPointData() - for a in range(celldata.GetNumberOfArrays()): - if pointdata.GetArrayName(a) == label: - return vtk_to_np(pointdata.GetArray(a)) + point_data = self.vtk_data.GetPointData() + for a in range(point_data.GetNumberOfArrays()): + if point_data.GetArrayName(a) == label: + return vtk_to_np(point_data.GetArray(a)) raise ValueError(f'array "{label}" not found') def get_comments(self): """Return the comments.""" - fielddata = self.geom.GetFieldData() + fielddata = self.vtk_data.GetFieldData() for a in range(fielddata.GetNumberOfArrays()): if fielddata.GetArrayName(a) == 'comments': comments = fielddata.GetAbstractArray(a) @@ -284,7 +287,7 @@ class VTK: def set_comments(self,comments): """ - Set Comments. + Set comments. Parameters ---------- @@ -296,12 +299,12 @@ class VTK: s.SetName('comments') for c in [comments] if isinstance(comments,str) else comments: s.InsertNextValue(c) - self.geom.GetFieldData().AddArray(s) + self.vtk_data.GetFieldData().AddArray(s) def add_comments(self,comments): """ - Add Comments. + Add comments. Parameters ---------- @@ -309,15 +312,15 @@ class VTK: Comments to add. """ - self.set_comments(self.get_comments + ([comments] if isinstance(comments,str) else comments)) + self.set_comments(self.get_comments() + ([comments] if isinstance(comments,str) else comments)) def __repr__(self): """ASCII representation of the VTK data.""" writer = vtk.vtkDataSetWriter() - writer.SetHeader(f'# {util.version_date("VTK")}') + writer.SetHeader(f'# {util.execution_stamp("VTK")}') writer.WriteToOutputStringOn() - writer.SetInputData(self.geom) + writer.SetInputData(self.vtk_data) writer.Write() return writer.GetOutputString() @@ -329,7 +332,7 @@ class VTK: See http://compilatrix.com/article/vtk-1 for further ideas. """ mapper = vtk.vtkDataSetMapper() - mapper.SetInputData(self.geom) + mapper.SetInputData(self.vtk_data) actor = vtk.vtkActor() actor.SetMapper(mapper) diff --git a/python/damask/util.py b/python/damask/util.py index f7c40416e..a04ee47de 100644 --- a/python/damask/util.py +++ b/python/damask/util.py @@ -22,7 +22,7 @@ __all__=[ 'scale_to_coprime', 'return_message', 'extendableOption', - 'version_date' + 'execution_stamp' ] #################################################################################################### @@ -178,10 +178,10 @@ def scale_to_coprime(v): return m -def version_date(class_name,function_name=None): - """tbd.""" - _function_name = '' if function_name is None else f'.{function_name}' +def execution_stamp(class_name,function_name=None): + """Timestamp the execution of a (function within a) class.""" now = datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z') + _function_name = '' if function_name is None else f'.{function_name}' return f'damask.{class_name}{_function_name} v{version} ({now})' diff --git a/python/tests/conftest.py b/python/tests/conftest.py index 51da90671..9c58eedd9 100644 --- a/python/tests/conftest.py +++ b/python/tests/conftest.py @@ -26,13 +26,13 @@ def patch_datetime_now(monkeypatch): monkeypatch.setattr(datetime, 'datetime', mydatetime) @pytest.fixture -def version_date(monkeypatch): - """Set damask.util.version_date for reproducible tests results.""" - def version_date(class_name,function_name=None): +def execution_stamp(monkeypatch): + """Set damask.util.execution_stamp for reproducible tests results.""" + def execution_stamp(class_name,function_name=None): _function_name = '' if function_name is None else f'.{function_name}' return f'damask.{class_name}{_function_name} v{patched_version} ({patched_date})' - monkeypatch.setattr(damask.util, 'version_date', version_date) + monkeypatch.setattr(damask.util, 'execution_stamp', execution_stamp) def pytest_addoption(parser): diff --git 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+++ b/python/tests/reference/Geom/clean_4_1_True.vtr @@ -1,23 +1,23 @@ - - + + - - AQAAAACAAAAALQAANQAAAA==eF7t1CECACAMxLBj/380fhYwIyK2spWkmnWgt6b3AF65/avfegAAAAAAAAAAAMy0AfYtC2k= + + AQAAAACAAAAABQAAZAAAAA==eF7t0rcSglAARFEHE0bAgBkE8///oAWnF8b2bXP6nRv1mkXBv+xzwCFHHDPmhFPOOOeCSyZMmXHFNTfcMueOex545IlnXliw5JUVa95454NPvvjmh79+DXYzdNisbYdfSqMHMg== - - AQAAAACAAACoAAAAVQAAAA==eF5jYICAWTNBYKU9hN5pb2IMAoeh/JP2EFUXoOKX7dPTQOAaVP6m/dkzIHAHqu4BVPwhVP1jqPwTqL5nUHUvoOpeQtW9hqp7A1X3Dqrugz0ASSZF3Q== + + AQAAAACAAABIAAAAOgAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2D3IeNxx9YfV6DiN+22x9tFGsbchco/sAMA/fQl6g== - - AQAAAACAAACYAAAAVgAAAA==eF5jYIAAmeOFQLTGHkLvsQ8Fg6NQ/hn7IjDjIlT8qr1F32MgugGVv2MPMeUBVN1D+8cQBVD1T+3BymSeQ/W9sF8FBq+g+t/Yg4Ut3kHN+WAPAAVdQE4= + + AQAAAACAAAAwAAAAKwAAAA==eF5jYICAvrdbF3w/tsEOQh+wC30iUFisdRLKv2D3MeNxx9YfV+wAD5wZgw== - - AQAAAACAAABIAAAAIgAAAA==eF5jYEAGB+wh9AUofQNKP4DST6D0Cyj9Bkp/sAcAAU8I6Q== + + AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w= diff --git 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28 27 26 +25 24 23 22 21 20 19 18 +17 16 15 14 13 12 11 10 + 9 8 7 6 5 4 3 2 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 diff --git a/python/tests/reference/Geom/flip_directions=x.geom b/python/tests/reference/Geom/flip_directions=x.geom new file mode 100644 index 000000000..9d4ee74a9 --- /dev/null +++ b/python/tests/reference/Geom/flip_directions=x.geom @@ -0,0 +1,25 @@ +4 header +grid a 8 b 5 c 4 +size x 8e-06 y 5e-06 z 4e-06 +origin x 0.0 y 0.0 z 0.0 +homogenization 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 9 8 7 6 5 4 3 2 +17 16 15 14 13 12 11 10 +25 24 23 22 21 20 19 18 +33 32 31 30 29 28 27 26 +41 40 39 38 37 36 35 34 + 2 2 2 2 2 2 2 2 + 2 2 2 2 2 2 2 2 + 2 2 2 2 2 2 2 2 + 2 2 2 2 2 2 2 2 + 2 2 2 2 2 2 2 2 + 8 7 6 5 4 3 2 1 +16 15 14 13 12 11 10 9 +24 23 22 21 20 19 18 17 +32 31 30 29 28 27 26 25 +40 39 38 37 36 35 34 33 diff --git a/python/tests/reference/Geom/flip_directions=y-z.geom b/python/tests/reference/Geom/flip_directions=y-z.geom new file mode 100644 index 000000000..ecd22f902 --- /dev/null +++ b/python/tests/reference/Geom/flip_directions=y-z.geom @@ -0,0 +1,25 @@ +4 header +grid a 8 b 5 c 4 +size x 8e-06 y 5e-06 z 4e-06 +origin x 0.0 y 0.0 z 0.0 +homogenization 1 +33 34 35 36 37 38 39 40 +25 26 27 28 29 30 31 32 +17 18 19 20 21 22 23 24 + 9 10 11 12 13 14 15 16 + 1 2 3 4 5 6 7 8 + 2 2 2 2 2 2 2 2 + 2 2 2 2 2 2 2 2 + 2 2 2 2 2 2 2 2 + 2 2 2 2 2 2 2 2 + 2 2 2 2 2 2 2 2 +34 35 36 37 38 39 40 41 +26 27 28 29 30 31 32 33 +18 19 20 21 22 23 24 25 +10 11 12 13 14 15 16 17 + 2 3 4 5 6 7 8 9 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 diff --git a/python/tests/reference/Geom/flip_directions=z-x-y.geom b/python/tests/reference/Geom/flip_directions=z-x-y.geom new file mode 100644 index 000000000..99e55ad7f --- /dev/null +++ b/python/tests/reference/Geom/flip_directions=z-x-y.geom @@ -0,0 +1,25 @@ +4 header +grid a 8 b 5 c 4 +size x 8e-06 y 5e-06 z 4e-06 +origin x 0.0 y 0.0 z 0.0 +homogenization 1 +40 39 38 37 36 35 34 33 +32 31 30 29 28 27 26 25 +24 23 22 21 20 19 18 17 +16 15 14 13 12 11 10 9 + 8 7 6 5 4 3 2 1 + 2 2 2 2 2 2 2 2 + 2 2 2 2 2 2 2 2 + 2 2 2 2 2 2 2 2 + 2 2 2 2 2 2 2 2 + 2 2 2 2 2 2 2 2 +41 40 39 38 37 36 35 34 +33 32 31 30 29 28 27 26 +25 24 23 22 21 20 19 18 +17 16 15 14 13 12 11 10 + 9 8 7 6 5 4 3 2 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 + 1 1 1 1 1 1 1 1 diff --git a/python/tests/test_Colormap.py b/python/tests/test_Colormap.py index 870ff9761..22c208551 100644 --- a/python/tests/test_Colormap.py +++ b/python/tests/test_Colormap.py @@ -17,8 +17,8 @@ def reference_dir(reference_dir_base): class TestColormap: @pytest.fixture(autouse=True) - def _version_date(self, version_date): - print('patched damask.util.version_date') + def _execution_stamp(self, execution_stamp): + print('patched damask.util.execution_stamp') def test_conversion(self): specials = np.array([[0.,0.,0.], diff --git a/python/tests/test_Geom.py b/python/tests/test_Geom.py index 479dd43fc..91cb61591 100644 --- a/python/tests/test_Geom.py +++ b/python/tests/test_Geom.py @@ -13,7 +13,8 @@ from damask import util def geom_equal(a,b): return np.all(a.get_microstructure() == b.get_microstructure()) and \ np.all(a.get_grid() == b.get_grid()) and \ - np.allclose(a.get_size(), b.get_size()) + np.allclose(a.get_size(), b.get_size()) and \ + str(a.diff(b)) == str(b.diff(a)) @pytest.fixture def default(): @@ -32,15 +33,26 @@ def reference_dir(reference_dir_base): class TestGeom: - def test_update(self,default): - modified = default.copy() - modified.update( - default.get_microstructure(), - default.get_size(), - default.get_origin() - ) + @pytest.mark.parametrize('flavor',['plain','explicit']) + def test_duplicate(self,default,flavor): + if flavor == 'plain': + modified = default.duplicate() + elif flavor == 'explicit': + modified = default.duplicate( + default.get_microstructure(), + default.get_size(), + default.get_origin() + ) print(modified) - assert geom_equal(modified,default) + assert geom_equal(default,modified) + + def test_diff_equal(self,default): + assert str(default.diff(default)) == '' + + def test_diff_not_equal(self,default): + new = Geom(default.microstructure[1:,1:,1:]+1,default.size*.9,np.ones(3)-default.origin,comments=['modified']) + assert str(default.diff(new)) != '' + @pytest.mark.parametrize('masked',[True,False]) def test_set_microstructure(self,default,masked): @@ -53,24 +65,25 @@ class TestGeom: def test_write_read_str(self,default,tmpdir): default.to_file(str(tmpdir/'default.geom')) new = Geom.from_file(str(tmpdir/'default.geom')) - assert geom_equal(new,default) + 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) + default.to_file(f,pack=True) with open(tmpdir/'default.geom') as f: new = Geom.from_file(f) - assert geom_equal(new,default) + assert geom_equal(default,new) - def test_write_show(self,default,tmpdir): + def test_write_as_ASCII(self,default,tmpdir): with open(tmpdir/'str.geom','w') as f: - f.write(default.show()) + f.write(default.as_ASCII()) with open(tmpdir/'str.geom') as f: new = Geom.from_file(f) - assert geom_equal(new,default) + assert geom_equal(default,new) def test_read_write_vtr(self,default,tmpdir): default.to_vtr(tmpdir/'default') + print(default.to_vtr()) for _ in range(10): time.sleep(.2) if os.path.exists(tmpdir/'default.vtr'): break @@ -78,6 +91,13 @@ class TestGeom: new = Geom.from_vtr(tmpdir/'default.vtr') assert geom_equal(new,default) + def test_invalid_geom(self,tmpdir): + with open('invalid_file','w') as f: + f.write('this is not a valid header') + with open('invalid_file','r') as f: + with pytest.raises(TypeError): + Geom.from_file(f) + def test_invalid_vtr(self,tmpdir): v = VTK.from_rectilinearGrid(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0) v.write(tmpdir/'no_materialpoint.vtr') @@ -96,25 +116,25 @@ class TestGeom: def test_invalid_combination(self,default): with pytest.raises(ValueError): - default.update(default.microstructure[1:,1:,1:],size=np.ones(3), rescale=True) + default.duplicate(default.microstructure[1:,1:,1:],size=np.ones(3), autosize=True) def test_invalid_size(self,default): with pytest.raises(ValueError): - default.update(default.microstructure[1:,1:,1:],size=np.ones(2)) + default.duplicate(default.microstructure[1:,1:,1:],size=np.ones(2)) def test_invalid_origin(self,default): with pytest.raises(ValueError): - default.update(default.microstructure[1:,1:,1:],origin=np.ones(4)) + default.duplicate(default.microstructure[1:,1:,1:],origin=np.ones(4)) def test_invalid_microstructure_size(self,default): microstructure = np.ones((3,3)) with pytest.raises(ValueError): - default.update(microstructure) + default.duplicate(microstructure) def test_invalid_microstructure_type(self,default): microstructure = np.random.randint(1,300,(3,4,5))==1 with pytest.raises(TypeError): - default.update(microstructure) + default.duplicate(microstructure) def test_invalid_homogenization(self,default): with pytest.raises(TypeError): @@ -128,31 +148,61 @@ class TestGeom: ] ) def test_mirror(self,default,update,reference_dir,directions,reflect): - modified = default.copy() - modified.mirror(directions,reflect) + modified = default.mirror(directions,reflect) tag = f'directions={"-".join(directions)}_reflect={reflect}' reference = reference_dir/f'mirror_{tag}.geom' if update: modified.to_file(reference) - assert geom_equal(modified,Geom.from_file(reference)) + assert geom_equal(Geom.from_file(reference), + modified) @pytest.mark.parametrize('directions',[(1,2,'y'),('a','b','x'),[1]]) def test_mirror_invalid(self,default,directions): with pytest.raises(ValueError): default.mirror(directions) + + @pytest.mark.parametrize('directions',[ + ['x'], + ['x','y','z'], + ['z','x','y'], + ['y','z'], + ] + ) + def test_flip(self,default,update,reference_dir,directions): + modified = default.flip(directions) + tag = f'directions={"-".join(directions)}' + reference = reference_dir/f'flip_{tag}.geom' + if update: modified.to_file(reference) + assert geom_equal(Geom.from_file(reference), + modified) + + def test_flip_invariant(self,default): + assert geom_equal(default,default.flip([])) + + @pytest.mark.parametrize('direction',[['x'],['x','y']]) + def test_flip_double(self,default,direction): + assert geom_equal(default,default.flip(direction).flip(direction)) + + @pytest.mark.parametrize('directions',[(1,2,'y'),('a','b','x'),[1]]) + def test_flip_invalid(self,default,directions): + with pytest.raises(ValueError): + default.flip(directions) + + @pytest.mark.parametrize('stencil',[1,2,3,4]) - @pytest.mark.parametrize('selection',[None,1,2]) + @pytest.mark.parametrize('selection',[None,[1],[1,2,3]]) @pytest.mark.parametrize('periodic',[True,False]) - def test_clean(self,update,reference_dir,stencil,selection,periodic): - current = Geom.from_vtr((reference_dir/'clean').with_suffix('.vtr')) - current.clean(stencil,None if selection is None else [selection],periodic) - reference = reference_dir/f'clean_{stencil}_{selection}_{periodic}' - if update and stencil !=1: + def test_clean(self,default,update,reference_dir,stencil,selection,periodic): + 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) for _ in range(10): time.sleep(.2) if os.path.exists(reference.with_suffix('.vtr')): break - assert geom_equal(current,Geom.from_vtr(reference if stencil !=1 else reference_dir/'clean')) + assert geom_equal(Geom.from_vtr(reference) if stencil > 1 else default, + current + ) @pytest.mark.parametrize('grid',[ (10,11,10), @@ -164,33 +214,29 @@ class TestGeom: ] ) def test_scale(self,default,update,reference_dir,grid): - modified = default.copy() - modified.scale(grid) + modified = default.scale(grid) tag = f'grid={util.srepr(grid,"-")}' reference = reference_dir/f'scale_{tag}.geom' if update: modified.to_file(reference) - assert geom_equal(modified,Geom.from_file(reference)) + assert geom_equal(Geom.from_file(reference), + modified) def test_renumber(self,default): - modified = default.copy() - microstructure = modified.get_microstructure() + microstructure = default.get_microstructure() for m in np.unique(microstructure): microstructure[microstructure==m] = microstructure.max() + np.random.randint(1,30) - modified.update(microstructure) + modified = default.duplicate(microstructure) assert not geom_equal(modified,default) - modified.renumber() - assert geom_equal(modified,default) + assert geom_equal(default, + modified.renumber()) def test_substitute(self,default): - modified = default.copy() - microstructure = modified.get_microstructure() offset = np.random.randint(1,500) - microstructure += offset - modified.update(microstructure) + modified = default.duplicate(default.get_microstructure() + offset) assert not geom_equal(modified,default) - modified.substitute(np.arange(default.microstructure.max())+1+offset, - np.arange(default.microstructure.max())+1) - assert geom_equal(modified,default) + assert geom_equal(default, + modified.substitute(np.arange(default.microstructure.max())+1+offset, + np.arange(default.microstructure.max())+1)) @pytest.mark.parametrize('axis_angle',[np.array([1,0,0,86.7]), np.array([0,1,0,90.4]), np.array([0,0,1,90]), np.array([1,0,0,175]),np.array([0,-1,0,178]),np.array([0,0,1,180])]) @@ -198,40 +244,58 @@ class TestGeom: modified = default.copy() for i in range(np.rint(360/axis_angle[3]).astype(int)): modified.rotate(Rotation.from_axis_angle(axis_angle,degrees=True)) - assert geom_equal(modified,default) + assert geom_equal(default,modified) @pytest.mark.parametrize('Eulers',[[32.0,68.0,21.0], [0.0,32.0,240.0]]) def test_rotate(self,default,update,reference_dir,Eulers): - modified = default.copy() - modified.rotate(Rotation.from_Eulers(Eulers,degrees=True)) + modified = default.rotate(Rotation.from_Eulers(Eulers,degrees=True)) tag = f'Eulers={util.srepr(Eulers,"-")}' reference = reference_dir/f'rotate_{tag}.geom' if update: modified.to_file(reference) - assert geom_equal(modified,Geom.from_file(reference)) + assert geom_equal(Geom.from_file(reference), + modified) def test_canvas(self,default): + grid = default.grid grid_add = np.random.randint(0,30,(3)) - modified = default.copy() - modified.canvas(modified.grid + grid_add) - e = default.grid - assert np.all(modified.microstructure[:e[0],:e[1],:e[2]] == default.microstructure) + modified = default.canvas(grid + grid_add) + assert np.all(modified.microstructure[:grid[0],:grid[1],:grid[2]] == default.microstructure) - @pytest.mark.parametrize('center1,center2',[(np.random.random(3)*.5,np.random.random(3)), + @pytest.mark.parametrize('center1,center2',[(np.random.random(3)*.5,np.random.random()*8), (np.random.randint(4,8,(3)),np.random.randint(9,12,(3)))]) @pytest.mark.parametrize('diameter',[np.random.random(3)*.5, - np.random.randint(4,10,(3))]) - def test_add_primitive(self,diameter,center1,center2): + np.random.randint(4,10,(3)), + np.random.rand(), + np.random.randint(30)]) + @pytest.mark.parametrize('exponent',[np.random.random(3)*.5, + np.random.randint(4,10,(3)), + np.random.rand()*4, + np.random.randint(20)]) + def test_add_primitive_shift(self,center1,center2,diameter,exponent): """Same volume fraction for periodic microstructures and different center.""" o = np.random.random(3)-.5 g = np.random.randint(8,32,(3)) s = np.random.random(3)+.5 - G_1 = Geom(np.ones(g,'i'),s,o) - G_2 = Geom(np.ones(g,'i'),s,o) - G_1.add_primitive(diameter,center1,1) - G_2.add_primitive(diameter,center2,1) + G_1 = Geom(np.ones(g,'i'),s,o).add_primitive(diameter,center1,exponent) + G_2 = Geom(np.ones(g,'i'),s,o).add_primitive(diameter,center2,exponent) assert np.count_nonzero(G_1.microstructure!=2) == np.count_nonzero(G_2.microstructure!=2) + @pytest.mark.parametrize('center',[np.random.randint(4,10,(3)), + np.random.randint(2,10), + np.random.rand()*4, + np.random.rand(3)*10]) + @pytest.mark.parametrize('inverse',[True,False]) + @pytest.mark.parametrize('periodic',[True,False]) + def test_add_primitive_rotation(self,center,inverse,periodic): + """Rotation should not change result for sphere (except for discretization errors).""" + g = np.array([32,32,32]) + fill = np.random.randint(10)+2 + eu=np.array([np.random.randint(4),np.random.randint(2),np.random.randint(4)])*.5*np.pi + G_1 = Geom(np.ones(g,'i'),[1.,1.,1.]).add_primitive(.3,center,1,fill,inverse=inverse,periodic=periodic) + G_2 = Geom(np.ones(g,'i'),[1.,1.,1.]).add_primitive(.3,center,1,fill,Rotation.from_Eulers(eu),inverse,periodic=periodic) + assert geom_equal(G_1,G_2) + @pytest.mark.parametrize('trigger',[[1],[]]) def test_vicinity_offset(self,trigger): offset = np.random.randint(2,4) @@ -248,8 +312,7 @@ class TestGeom: if len(trigger) > 0: m2[m==1] = 1 - geom = Geom(m,np.random.rand(3)) - geom.vicinity_offset(vicinity,offset,trigger=trigger) + geom = Geom(m,np.random.rand(3)).vicinity_offset(vicinity,offset,trigger=trigger) assert np.all(m2==geom.microstructure) diff --git a/python/tests/test_VTK.py b/python/tests/test_VTK.py index 91ff4033c..ab9c4fa8b 100644 --- a/python/tests/test_VTK.py +++ b/python/tests/test_VTK.py @@ -13,8 +13,19 @@ def reference_dir(reference_dir_base): """Directory containing reference results.""" return reference_dir_base/'VTK' +@pytest.fixture +def default(): + """Simple VTK.""" + grid = np.array([5,6,7],int) + size = np.array([.6,1.,.5]) + return VTK.from_rectilinearGrid(grid,size) + class TestVTK: + @pytest.fixture(autouse=True) + def _execution_stamp(self, execution_stamp): + print('patched damask.util.execution_stamp') + def test_rectilinearGrid(self,tmp_path): grid = np.random.randint(5,10,3)*2 size = np.random.random(3) + 1.0 @@ -77,10 +88,36 @@ class TestVTK: @pytest.mark.parametrize('name,dataset_type',[('this_file_does_not_exist.vtk', None), ('this_file_does_not_exist.vtk','vtk'), ('this_file_does_not_exist.vtx', None)]) - def test_invalid_dataset_type(self,dataset_type,name): + def test_invalid_dataset_type(self,name,dataset_type): with pytest.raises(TypeError): - VTK.from_file('this_file_does_not_exist.vtk',dataset_type) + VTK.from_file(name,dataset_type) + def test_invalid_extension_write(self,default): + with pytest.raises(ValueError): + default.write('default.txt') + + def test_invalid_get(self,default): + with pytest.raises(ValueError): + default.get('does_not_exist') + + def test_invalid_add_shape(self,default): + with pytest.raises(ValueError): + default.add(np.ones(3),'valid') + + def test_invalid_add_missing_label(self,default): + data = np.random.randint(9,size=np.prod(np.array(default.vtk_data.GetDimensions())-1)) + with pytest.raises(ValueError): + default.add(data) + + def test_invalid_add_type(self,default): + with pytest.raises(TypeError): + default.add('invalid_type','valid') + + def test_comments(self,tmp_path,default): + default.add_comments(['this is a comment']) + default.write(tmp_path/'with_comments',parallel=False) + new = VTK.from_file(tmp_path/'with_comments.vtr') + assert new.get_comments() == ['this is a comment'] def test_compare_reference_polyData(self,update,reference_dir,tmp_path): points=np.dstack((np.linspace(0.,1.,10),np.linspace(0.,2.,10),np.linspace(-1.,1.,10))).squeeze() @@ -90,7 +127,8 @@ class TestVTK: polyData.write(reference_dir/'polyData') else: reference = VTK.from_file(reference_dir/'polyData.vtp') - assert polyData.__repr__() == reference.__repr__() + assert polyData.__repr__() == reference.__repr__() and \ + np.allclose(polyData.get('coordinates'),points) def test_compare_reference_rectilinearGrid(self,update,reference_dir,tmp_path): grid = np.array([5,6,7],int) @@ -104,5 +142,5 @@ class TestVTK: rectilinearGrid.write(reference_dir/'rectilinearGrid') else: reference = VTK.from_file(reference_dir/'rectilinearGrid.vtr') - assert rectilinearGrid.__repr__() == reference.__repr__() - + assert rectilinearGrid.__repr__() == reference.__repr__() and \ + np.allclose(rectilinearGrid.get('cell'),c)