From bf60cffab5510fda2598c6d20308b30f3514ddb2 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Thu, 30 May 2019 14:07:49 +0200 Subject: [PATCH] cleaning --- processing/pre/geom_addPrimitive.py | 14 ++++---- processing/pre/geom_canvas.py | 8 ++--- processing/pre/geom_check.sh | 2 +- processing/pre/geom_clean.py | 2 +- processing/pre/geom_fromDREAM3D.py | 22 ++++++------ processing/pre/geom_fromMinimalSurface.py | 2 +- processing/pre/geom_fromOsteonGeometry.py | 8 ++--- processing/pre/geom_fromScratch.py | 2 +- processing/pre/geom_fromTable.py | 20 +++++------ .../pre/geom_fromVoronoiTessellation.py | 34 +++++++++---------- processing/pre/geom_grainGrowth.py | 12 +++---- processing/pre/geom_mirror.py | 10 +++--- processing/pre/geom_pack.py | 4 +-- processing/pre/geom_renumber.py | 6 ++-- processing/pre/geom_rescale.py | 4 +-- processing/pre/geom_rotate.py | 6 ++-- processing/pre/geom_toTable.py | 8 ++--- processing/pre/geom_translate.py | 6 ++-- processing/pre/geom_unpack.py | 4 +-- processing/pre/geom_vicinityOffset.py | 4 +-- 20 files changed, 89 insertions(+), 89 deletions(-) diff --git a/processing/pre/geom_addPrimitive.py b/processing/pre/geom_addPrimitive.py index b8b1ddf6e..99035c8fe 100755 --- a/processing/pre/geom_addPrimitive.py +++ b/processing/pre/geom_addPrimitive.py @@ -24,7 +24,7 @@ These objects can be boxes, cylinders, or ellipsoids. """, version = scriptID) parser.add_option('-c', '--center', - dest='center', + dest='center', type='float', nargs = 3, metavar=' '.join(['float']*3), help='a,b,c origin of primitive %default') parser.add_option('-d', '--dimension', @@ -78,7 +78,7 @@ parser.set_defaults(center = (.0,.0,.0), (options, filenames) = parser.parse_args() if options.dimension is None: - parser.error('no dimension specified.') + parser.error('no dimension specified.') if [options.angleaxis,options.quaternion].count(None) == 0: parser.error('more than one rotation specified.') @@ -94,7 +94,7 @@ if filenames == []: filenames = [None] 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) grid = geom.get_grid() size = geom.get_size() @@ -106,7 +106,7 @@ for name in filenames: else: center = (np.array(options.center) + 0.5)/grid r = np.array(options.dimension)/grid/2.0 - + if np.any(center<0.0) or np.any(center>=1.0): print('error') offset = np.ones(3)*0.5 if options.periodic else center @@ -120,17 +120,17 @@ for name in filenames: for z in range(grid[2]): coords = np.array([x+0.5,y+0.5,z+0.5])/grid mask[x,y,z] = np.sum(np.abs((rotation*(coords-offset))/r)**e) < 1 - + if options.periodic: shift = ((offset-center)*grid).astype(int) mask = np.roll(mask,shift,(0,1,2)) - + if options.inside: mask = np.logical_not(mask) fill = np.nanmax(geom.microstructure)+1 if options.fill is None else options.fill damask.util.croak(geom.update(np.where(mask,geom.microstructure,fill))) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) - + if name is None: sys.stdout.write(str(geom.show())) else: diff --git a/processing/pre/geom_canvas.py b/processing/pre/geom_canvas.py index fe8e69981..b0748dcf3 100755 --- a/processing/pre/geom_canvas.py +++ b/processing/pre/geom_canvas.py @@ -45,7 +45,7 @@ if filenames == []: filenames = [None] 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) grid = geom.get_grid() @@ -56,13 +56,13 @@ for name in filenames: new = np.full(grid,options.fill if options.fill is not None else np.nanmax(geom.microstructure)+1,geom.microstructure.dtype) - + for x in range(geom.microstructure.shape[0]): X = x + options.offset[0] - if not 0 <= X < new.shape[0]: continue + if not 0 <= X < new.shape[0]: continue for y in range(geom.microstructure.shape[1]): Y = y + options.offset[1] - if not 0 <= Y < new.shape[1]: continue + if not 0 <= Y < new.shape[1]: continue for z in range(geom.microstructure.shape[2]): Z = z + options.offset[2] if not 0 <= Z < new.shape[2]: continue diff --git a/processing/pre/geom_check.sh b/processing/pre/geom_check.sh index 2a690918e..fbae91043 100755 --- a/processing/pre/geom_check.sh +++ b/processing/pre/geom_check.sh @@ -5,7 +5,7 @@ if [[ "$1" == "-f" || "$1" == "--float" ]]; then arg='--float' else arg='' -fi +fi for geom in "$@" do diff --git a/processing/pre/geom_clean.py b/processing/pre/geom_clean.py index 8e477c1c1..aeafe4f09 100755 --- a/processing/pre/geom_clean.py +++ b/processing/pre/geom_clean.py @@ -43,7 +43,7 @@ if filenames == []: filenames = [None] 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(geom.update(ndimage.filters.generic_filter( diff --git a/processing/pre/geom_fromDREAM3D.py b/processing/pre/geom_fromDREAM3D.py index 02a2fe0da..5d41e05b9 100755 --- a/processing/pre/geom_fromDREAM3D.py +++ b/processing/pre/geom_fromDREAM3D.py @@ -78,7 +78,7 @@ for name in filenames: damask.util.report(scriptName,name) errors = [] - + inFile = h5py.File(name, 'r') group_geom = os.path.join(rootDir,options.basegroup,'_SIMPL_GEOMETRY') try: @@ -88,8 +88,8 @@ for name in filenames: origin = inFile[os.path.join(group_geom,'ORIGIN')][...] except: errors.append('Geometry data ({}) not found'.format(group_geom)) - - + + group_pointwise = os.path.join(rootDir,options.basegroup,options.pointwise) if options.average is None: label = 'Point' @@ -100,33 +100,33 @@ for name in filenames: rot = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in quats] except: 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: errors.append('Pointwise phase data ({}) not readable'.format(dataset)) - + microstructure = np.arange(1,np.product(grid)+1,dtype=int).reshape(grid,order='F') - + else: label = 'Grain' - + 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: errors.append('Link between pointwise and grain average data ({}) not readable'.format(dataset)) - + group_average = os.path.join(rootDir,options.basegroup,options.average) - + 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: 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) @@ -148,7 +148,7 @@ for name in filenames: 'crystallite 1', '(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(phase[i],i+1), ] - + header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\ + config_header geom = damask.Geom(microstructure,size,origin, diff --git a/processing/pre/geom_fromMinimalSurface.py b/processing/pre/geom_fromMinimalSurface.py index 2b2887ada..19686f763 100755 --- a/processing/pre/geom_fromMinimalSurface.py +++ b/processing/pre/geom_fromMinimalSurface.py @@ -85,7 +85,7 @@ for x in range(options.grid[0]): for y in range(options.grid[1]): for z in range(options.grid[2]): microstructure[x,y,z]=options.microstructure[int(options.threshold < surface[options.type](X[x],Y[y],Z[z]))] - + geom=damask.Geom(microstructure,options.size, homogenization=options.homogenization, comments=[scriptID + ' ' + ' '.join(sys.argv[1:])]) diff --git a/processing/pre/geom_fromOsteonGeometry.py b/processing/pre/geom_fromOsteonGeometry.py index d312220a7..98d2cf9ea 100755 --- a/processing/pre/geom_fromOsteonGeometry.py +++ b/processing/pre/geom_fromOsteonGeometry.py @@ -52,7 +52,7 @@ parser.add_option( '--aspect', dest='aspect', type='float', metavar = 'float', help='vertical/horizontal osteon aspect ratio [%default]') -parser.add_option('-w', '--omega', +parser.add_option('-w', '--omega', dest='omega', type='float', metavar = 'float', help='rotation angle around normal of osteon [%default]') @@ -112,7 +112,7 @@ for y in range(grid[1]): microstructure[x,y] = i Alpha[i] = alpha[x,y] Beta [i] = beta [x,y] - i+=1 + i+=1 config_header = ['', '[canal]', @@ -122,7 +122,7 @@ for i in range(3,np.max(microstructure)): config_header += ['[Point{}]'.format(i-2), '(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 0'.format(Alpha[i],Beta[i]) ] - + config_header = ['', '[canal]', 'crystallite 1', @@ -143,7 +143,7 @@ geom = damask.Geom(microstructure.reshape(grid), size,-size/2, homogenization=options.homogenization,comments=header) damask.util.croak(geom) - + if name is None: sys.stdout.write(str(geom.show())) else: diff --git a/processing/pre/geom_fromScratch.py b/processing/pre/geom_fromScratch.py index b76e0012a..e943f7e3e 100755 --- a/processing/pre/geom_fromScratch.py +++ b/processing/pre/geom_fromScratch.py @@ -63,7 +63,7 @@ geom = damask.Geom(microstructure=np.full(options.grid,options.fill,dtype=dtype) homogenization=options.homogenization, comments=scriptID + ' ' + ' '.join(sys.argv[1:])) damask.util.croak(geom) - + if name is None: sys.stdout.write(str(geom.show())) else: diff --git a/processing/pre/geom_fromTable.py b/processing/pre/geom_fromTable.py index 1ef9822a4..c0b327d7d 100755 --- a/processing/pre/geom_fromTable.py +++ b/processing/pre/geom_fromTable.py @@ -18,7 +18,7 @@ scriptID = ' '.join([scriptName,damask.version]) # -------------------------------------------------------------------- parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """ -Converts ASCII table. Input can be microstructure or orientation (as quaternion). For the latter, +Converts ASCII table. Input can be microstructure or orientation (as quaternion). For the latter, phase information can be given additionally. """, version = scriptID) @@ -78,7 +78,7 @@ for name in filenames: table = damask.ASCIItable(name = name,readonly=True) table.head_read() # read ASCII header info -# ------------------------------------------ sanity checks --------------------------------------- +# ------------------------------------------ sanity checks --------------------------------------- coordDim = table.label_dimension(options.pos) @@ -89,7 +89,7 @@ for name in filenames: errors.append('input "{}" needs to have dimension {}.'.format(label,dim)) if options.phase and table.label_dimension(options.phase) != 1: errors.append('phase column "{}" is not scalar.'.format(options.phase)) - + if errors != []: damask.util.croak(errors) continue @@ -97,7 +97,7 @@ for name in filenames: table.data_readArray([options.pos] \ + (label if isinstance(label, list) else [label]) \ + ([options.phase] if options.phase else [])) - + if coordDim == 2: table.data = np.insert(table.data,2,np.zeros(len(table.data)),axis=1) # add zero z coordinate for two-dimensional input if options.phase is None: @@ -112,7 +112,7 @@ for name in filenames: indices = np.lexsort((table.data[:,0],table.data[:,1],table.data[:,2])) # indices of position when sorting x fast, z slow microstructure = np.empty(grid,dtype = int) # initialize empty microstructure i = 0 - + if inputtype == 'microstructure': for z in range(grid[2]): for y in range(grid[1]): @@ -124,21 +124,21 @@ for name in filenames: elif inputtype == 'quaternion': unique,unique_inverse = np.unique(table.data[:,3:8],return_inverse=True,axis=0) - + for z in range(grid[2]): for y in range(grid[1]): for x in range(grid[0]): microstructure[x,y,z] = unique_inverse[indices[i]]+1 i+=1 - + config_header = [''] for i,data in enumerate(unique): ori = damask.Rotation(data[0:4]) config_header += ['[Grain{}]'.format(i+1), '(gauss)\tphi1 {:g}\tPhi {:g}\tphi2 {:g}'.format(*ori.asEulers(degrees = True)), ] - if options.axes is not None: config_header += ['axes\t{} {} {}'.format(*options.axes)] - + if options.axes is not None: config_header += ['axes\t{} {} {}'.format(*options.axes)] + config_header += [''] for i,data in enumerate(unique): config_header += ['[Grain{}]'.format(i+1), @@ -151,7 +151,7 @@ for name in filenames: geom = damask.Geom(microstructure,size,origin, homogenization=options.homogenization,comments=header) damask.util.croak(geom) - + if name is None: sys.stdout.write(str(geom.show())) else: diff --git a/processing/pre/geom_fromVoronoiTessellation.py b/processing/pre/geom_fromVoronoiTessellation.py index 08b069410..dd2e5e8ea 100755 --- a/processing/pre/geom_fromVoronoiTessellation.py +++ b/processing/pre/geom_fromVoronoiTessellation.py @@ -1,7 +1,7 @@ #!/usr/bin/env python3 import os -import sys +import sys import multiprocessing from optparse import OptionParser,OptionGroup @@ -22,7 +22,7 @@ def laguerreTessellation(undeformed, coords, weights, grains, periodic = True, c tmp = np.repeat(point.reshape(3,1), len(seeds), axis=1).T dist = np.sum((tmp - seeds)**2,axis=1) -myWeights return np.argmin(dist) # seed point closest to point - + copies = \ np.array([ [ -1,-1,-1 ], @@ -60,7 +60,7 @@ def laguerreTessellation(undeformed, coords, weights, grains, periodic = True, c repeatweights = np.tile(weights,len(copies)).flatten(order='F') # Laguerre weights (1,2,3,1,2,3,...,1,2,3) for i,vec in enumerate(copies): # periodic copies of seed points ... try: seeds = np.append(seeds, coords+vec, axis=0) # ... (1+a,2+a,3+a,...,1+z,2+z,3+z) - except NameError: seeds = coords+vec + except NameError: seeds = coords+vec if (repeatweights == 0.0).all(): # standard Voronoi (no weights, KD tree) myKDTree = spatial.cKDTree(seeds) @@ -81,7 +81,7 @@ def laguerreTessellation(undeformed, coords, weights, grains, periodic = True, c closestSeeds[i] = findClosestSeed(arg) # closestSeed is modulo number of original seed points (i.e. excluding periodic copies) - return grains[closestSeeds%coords.shape[0]] + return grains[closestSeeds%coords.shape[0]] # -------------------------------------------------------------------- @@ -202,7 +202,7 @@ if filenames == []: filenames = [None] for name in filenames: damask.util.report(scriptName,name) - + table = damask.ASCIItable(name = name, readonly = True) @@ -210,17 +210,17 @@ for name in filenames: table.head_read() info,extra_header = table.head_getGeom() - + if options.grid is not None: info['grid'] = options.grid if options.size is not None: info['size'] = options.size if options.origin is not None: info['origin'] = options.origin - -# ------------------------------------------ sanity checks --------------------------------------- + +# ------------------------------------------ sanity checks --------------------------------------- remarks = [] errors = [] labels = [] - + hasGrains = table.label_dimension(options.microstructure) == 1 hasEulers = table.label_dimension(options.eulers) == 3 hasWeights = table.label_dimension(options.weight) == 1 and options.laguerre @@ -250,8 +250,8 @@ for name in filenames: table.close(dismiss=True) continue -# ------------------------------------------ read seeds --------------------------------------- - +# ------------------------------------------ read seeds --------------------------------------- + table.data_readArray(labels) coords = table.data[:,table.label_indexrange(options.pos)] * info['size'] if options.normalized \ else table.data[:,table.label_indexrange(options.pos)] - info['origin'] @@ -271,13 +271,13 @@ for name in filenames: z = (np.arange(info['grid'][2])+0.5)*info['size'][2]/info['grid'][2] X,Y,Z = np.meshgrid(x, y, z,indexing='ij') grid = np.stack((X,Y,Z),axis=-1).reshape((info['grid'].prod(),3),order='F') - + damask.util.croak('tessellating...') indices = laguerreTessellation(grid, coords, weights, grains, options.periodic, options.cpus) - + config_header = [] if options.config: - + if hasEulers: config_header += [''] for ID in grainIDs: @@ -286,7 +286,7 @@ for name in filenames: '(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*eulers[eulerID]) ] if options.axes is not None: config_header += ['axes\t{} {} {}'.format(*options.axes)] - + config_header += [''] for ID in grainIDs: config_header += ['[Grain{}]'.format(ID), @@ -295,13 +295,13 @@ for name in filenames: ] config_header += [''] - + header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\ + config_header geom = damask.Geom(indices.reshape(info['grid'],order='F'),info['size'],info['origin'], homogenization=options.homogenization,comments=header) damask.util.croak(geom) - + if name is None: sys.stdout.write(str(geom.show())) else: diff --git a/processing/pre/geom_grainGrowth.py b/processing/pre/geom_grainGrowth.py index 479f6f6fc..93f43d3b3 100755 --- a/processing/pre/geom_grainGrowth.py +++ b/processing/pre/geom_grainGrowth.py @@ -60,9 +60,9 @@ if filenames == []: filenames = [None] 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) - + grid_original = geom.get_grid() damask.util.croak(geom) microstructure = np.tile(geom.microstructure,np.where(grid_original == 1, 2,1)) # make one copy along dimensions with grid == 1 @@ -71,15 +71,15 @@ for name in filenames: # --- initialize support data --------------------------------------------------------------------- # store a copy the initial microstructure to find locations of immutable indices - microstructure_original = np.copy(microstructure) + microstructure_original = np.copy(microstructure) if not options.ndimage: X,Y,Z = np.mgrid[0:grid[0],0:grid[1],0:grid[2]] - + # Calculates gaussian weights for simulating 3d diffusion gauss = np.exp(-(X*X + Y*Y + Z*Z)/(2.0*options.d*options.d),dtype=np.float32) \ /np.power(2.0*np.pi*options.d*options.d,(3.0 - np.count_nonzero(grid_original == 1))/2.,dtype=np.float32) - + gauss[:,:,:grid[2]//2:-1] = gauss[:,:,1:(grid[2]+1)//2] # trying to cope with uneven (odd) grid size gauss[:,:grid[1]//2:-1,:] = gauss[:,1:(grid[1]+1)//2,:] gauss[:grid[0]//2:-1,:,:] = gauss[1:(grid[0]+1)//2,:,:] @@ -102,7 +102,7 @@ for name in filenames: grid[2]//2:-grid[2]//2] # transform bulk volume (i.e. where interfacial energy remained zero), store index of closest boundary voxel - index = ndimage.morphology.distance_transform_edt(periodic_interfaceEnergy == 0., + index = ndimage.morphology.distance_transform_edt(periodic_interfaceEnergy == 0., return_distances = False, return_indices = True) diff --git a/processing/pre/geom_mirror.py b/processing/pre/geom_mirror.py index 408eb15a8..8d3f3d798 100755 --- a/processing/pre/geom_mirror.py +++ b/processing/pre/geom_mirror.py @@ -32,7 +32,7 @@ parser.add_option('-d','--direction', parser.add_option( '--periodic', dest = 'periodic', action = 'store_true', - help = 'omit periodic copies of outermost layers in mirror direction') + help = 'omit periodic copies of outermost layers in mirror direction') parser.set_defaults(periodic = False) @@ -52,9 +52,9 @@ if filenames == []: filenames = [None] 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) - + microstructure = geom.get_microstructure() if 'z' in options.directions: microstructure = np.concatenate([microstructure,microstructure[:,:,limits[0]:limits[1]:-1]],2) @@ -62,10 +62,10 @@ for name in filenames: microstructure = np.concatenate([microstructure,microstructure[:,limits[0]:limits[1]:-1,:]],1) if 'x' in options.directions: microstructure = np.concatenate([microstructure,microstructure[limits[0]:limits[1]:-1,:,:]],0) - + damask.util.croak(geom.update(microstructure,rescale=True)) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) - + if name is None: sys.stdout.write(str(geom.show())) else: diff --git a/processing/pre/geom_pack.py b/processing/pre/geom_pack.py index 2bd993770..786a40b95 100755 --- a/processing/pre/geom_pack.py +++ b/processing/pre/geom_pack.py @@ -33,7 +33,7 @@ for name in filenames: damask.util.croak(geom) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) - + compressType = None former = start = -1 reps = 0 @@ -65,7 +65,7 @@ for name in filenames: reps = 1 former = current - + if compressType == '.': f.write('{}\n'.format(former)) elif compressType == 'to': diff --git a/processing/pre/geom_renumber.py b/processing/pre/geom_renumber.py index 403aeaf5b..2eee189e1 100755 --- a/processing/pre/geom_renumber.py +++ b/processing/pre/geom_renumber.py @@ -30,16 +30,16 @@ if filenames == []: filenames = [None] 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) - + renumbered = np.empty(geom.get_grid(),dtype=geom.microstructure.dtype) for i, oldID in enumerate(np.unique(geom.microstructure)): renumbered = np.where(geom.microstructure == oldID, i+1, renumbered) damask.util.croak(geom.update(renumbered)) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) - + if name is None: sys.stdout.write(str(geom.show())) else: diff --git a/processing/pre/geom_rescale.py b/processing/pre/geom_rescale.py index 57b43c165..5acdf87d6 100755 --- a/processing/pre/geom_rescale.py +++ b/processing/pre/geom_rescale.py @@ -41,7 +41,7 @@ if filenames == []: filenames = [None] 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) grid = geom.get_grid() @@ -55,7 +55,7 @@ for name in filenames: np.array([o*float(n.lower().replace('x','')) if n.lower().endswith('x') \ else float(n) for o,n in zip(size,options.size)],dtype=float) - damask.util.croak(geom.update(microstructure = + damask.util.croak(geom.update(microstructure = ndimage.interpolation.zoom( geom.microstructure, new_grid/grid,output=geom.microstructure.dtype, diff --git a/processing/pre/geom_rotate.py b/processing/pre/geom_rotate.py index 852693304..09da7b044 100755 --- a/processing/pre/geom_rotate.py +++ b/processing/pre/geom_rotate.py @@ -76,7 +76,7 @@ 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) - + microstructure = geom.get_microstructure() fill = np.nanmax(microstructure)+1 if options.fill is None else options.fill dtype = float if np.isnan(fill) or int(fill) != fill or microstructure.dtype==np.float else int @@ -89,10 +89,10 @@ for name in filenames: prefilter=False,output=dtype,cval=fill) # rotation around x microstructure = ndimage.rotate(microstructure,eulers[0],(0,1),order=0, prefilter=False,output=dtype,cval=fill) # rotation around z - + damask.util.croak(geom.update(microstructure,rescale=True)) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) - + if name is None: sys.stdout.write(str(geom.show())) else: diff --git a/processing/pre/geom_toTable.py b/processing/pre/geom_toTable.py index 2b8257cfa..ed33d9c85 100755 --- a/processing/pre/geom_toTable.py +++ b/processing/pre/geom_toTable.py @@ -30,17 +30,17 @@ if filenames == []: filenames = [None] 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(geom) - + # --- generate grid -------------------------------------------------------------------------------- grid = geom.get_grid() size = geom.get_size() origin = geom.get_origin() - + x = (0.5 + np.arange(grid[0],dtype=float))/grid[0]*size[0]+origin[0] y = (0.5 + np.arange(grid[1],dtype=float))/grid[1]*size[1]+origin[1] z = (0.5 + np.arange(grid[2],dtype=float))/grid[2]*size[2]+origin[2] diff --git a/processing/pre/geom_translate.py b/processing/pre/geom_translate.py index 127c63bc6..4b91920ae 100755 --- a/processing/pre/geom_translate.py +++ b/processing/pre/geom_translate.py @@ -48,13 +48,13 @@ if filenames == []: filenames = [None] 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) - + substituted = geom.get_microstructure() for old,new in zip(sub[0::2],sub[1::2]): substituted[substituted==old] = new # substitute microstructure indices substituted += options.microstructure # constant shift - + damask.util.croak(geom.update(substituted,origin=geom.get_origin()+options.origin)) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) diff --git a/processing/pre/geom_unpack.py b/processing/pre/geom_unpack.py index b1b12d2cc..2a2d54130 100755 --- a/processing/pre/geom_unpack.py +++ b/processing/pre/geom_unpack.py @@ -30,10 +30,10 @@ 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(geom) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) - + if name is None: sys.stdout.write(str(geom.show())) else: diff --git a/processing/pre/geom_vicinityOffset.py b/processing/pre/geom_vicinityOffset.py index bda6b6c5f..3a4853121 100755 --- a/processing/pre/geom_vicinityOffset.py +++ b/processing/pre/geom_vicinityOffset.py @@ -68,7 +68,7 @@ if filenames == []: filenames = [None] 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) offset = np.nanmax(geom.microstructure) if options.offset is None else options.offset @@ -81,7 +81,7 @@ for name in filenames: extra_keywords={"trigger":options.trigger,"size":1+2*options.vicinity}), geom.microstructure + offset,geom.microstructure))) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) - + if name is None: sys.stdout.write(str(geom.show())) else: