migrating shell scripts to library
This commit is contained in:
Martin Diehl
parent
5fcff876f9
commit
a0e0f28e51
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@ -5,7 +5,6 @@ import sys
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from io import StringIO
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from optparse import OptionParser
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from scipy import ndimage
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import numpy as np
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import damask
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@ -15,18 +14,6 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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def taintedNeighborhood(stencil,trigger=[],size=1):
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me = stencil[stencil.shape[0]//2]
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if len(trigger) == 0:
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return np.any(stencil != me)
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if me in trigger:
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trigger = set(trigger)
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trigger.remove(me)
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trigger = list(trigger)
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return np.any(np.in1d(stencil,np.array(trigger)))
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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@ -67,19 +54,12 @@ options.trigger = np.array(options.trigger, dtype=int)
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if filenames == []: filenames = [None]
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for name in filenames:
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damask.util.report(scriptName,name)
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damask.util.report(scriptName,name)
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geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
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geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
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offset = np.nanmax(geom.microstructure) if options.offset is None else options.offset
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damask.util.croak(geom.vicinity_offset(options.vicinity,options.offset,options.trigger,
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True if options.mode is 'wrap' else False))
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geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
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damask.util.croak(geom.update(np.where(ndimage.filters.generic_filter(
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geom.microstructure,
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taintedNeighborhood,
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size=1+2*options.vicinity,mode=options.mode,
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extra_arguments=(),
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extra_keywords={"trigger":options.trigger,"size":1+2*options.vicinity}),
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geom.microstructure + offset,geom.microstructure)))
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geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
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geom.to_file(sys.stdout if name is None else name,pack=False)
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geom.to_file(sys.stdout if name is None else name,pack=False)
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@ -278,7 +278,7 @@ class Geom:
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Parameters
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----------
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fname : str or file handle
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geometry file to read.
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Geometry file to read.
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"""
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try:
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@ -345,15 +345,15 @@ class Geom:
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Parameters
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----------
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grid : numpy.ndarray of shape (3)
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number of grid points in x,y,z direction.
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Number of grid points in x,y,z direction.
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size : list or numpy.ndarray of shape (3)
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physical size of the microstructure in meter.
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Physical size of the microstructure in meter.
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seeds : numpy.ndarray of shape (:,3)
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position of the seed points in meter. All points need to lay within the box.
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Position of the seed points in meter. All points need to lay within the box.
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weights : numpy.ndarray of shape (seeds.shape[0])
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weights of the seeds. Setting all weights to 1.0 gives a standard Voronoi tessellation.
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Weights of the seeds. Setting all weights to 1.0 gives a standard Voronoi tessellation.
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periodic : Boolean, optional
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perform a periodic tessellation. Defaults to True.
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Perform a periodic tessellation. Defaults to True.
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"""
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if periodic:
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@ -391,13 +391,13 @@ class Geom:
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Parameters
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----------
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grid : numpy.ndarray of shape (3)
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number of grid points in x,y,z direction.
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Number of grid points in x,y,z direction.
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size : list or numpy.ndarray of shape (3)
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physical size of the microstructure in meter.
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Physical size of the microstructure in meter.
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seeds : numpy.ndarray of shape (:,3)
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position of the seed points in meter. All points need to lay within the box.
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Position of the seed points in meter. All points need to lay within the box.
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periodic : Boolean, optional
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perform a periodic tessellation. Defaults to True.
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Perform a periodic tessellation. Defaults to True.
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"""
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coords = grid_filters.cell_coord0(grid,size).reshape(-1,3)
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@ -415,9 +415,9 @@ class Geom:
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Parameters
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----------
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fname : str or file handle
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geometry file to write.
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Geometry file to write.
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pack : bool, optional
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compress geometry with 'x of y' and 'a to b'.
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Compress geometry with 'x of y' and 'a to b'.
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"""
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header = self.get_header()
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@ -481,7 +481,7 @@ class Geom:
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Parameters
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----------
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fname : str, optional
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vtk file to write. If no file is given, a string is returned.
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Vtk file to write. If no file is given, a string is returned.
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"""
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v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
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@ -508,9 +508,9 @@ class Geom:
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Parameters
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----------
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directions : iterable containing str
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direction(s) along which the microstructure is mirrored. Valid entries are 'x', 'y', 'z'.
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Direction(s) along which the microstructure is mirrored. Valid entries are 'x', 'y', 'z'.
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reflect : bool, optional
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reflect (include) outermost layers.
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Reflect (include) outermost layers.
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"""
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valid = {'x','y','z'}
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@ -540,7 +540,7 @@ class Geom:
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Parameters
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----------
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grid : numpy.ndarray of shape (3)
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number of grid points in x,y,z direction.
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Number of grid points in x,y,z direction.
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"""
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#ToDo: self.add_comments('geom.py:scale v{}'.format(version)
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@ -563,7 +563,7 @@ class Geom:
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Parameters
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----------
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stencil : int, optional
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size of smoothing stencil.
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Size of smoothing stencil.
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"""
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def mostFrequent(arr):
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@ -596,9 +596,9 @@ class Geom:
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Parameters
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----------
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R : damask.Rotation
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rotation to apply to the microstructure.
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Rotation to apply to the microstructure.
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fill : int or float, optional
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microstructure index to fill the corners. Defaults to microstructure.max() + 1.
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Microstructure index to fill the corners. Defaults to microstructure.max() + 1.
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"""
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if fill is None: fill = np.nanmax(self.microstructure) + 1
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@ -631,11 +631,11 @@ class Geom:
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Parameters
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----------
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grid : numpy.ndarray of shape (3)
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number of grid points in x,y,z direction.
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Number of grid points in x,y,z direction.
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offset : numpy.ndarray of shape (3)
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offset (measured in grid points) from old to new microstructue[0,0,0].
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Offset (measured in grid points) from old to new microstructure[0,0,0].
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fill : int or float, optional
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microstructure index to fill the corners. Defaults to microstructure.max() + 1.
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Microstructure index to fill the corners. Defaults to microstructure.max() + 1.
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"""
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if fill is None: fill = np.nanmax(self.microstructure) + 1
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@ -658,14 +658,14 @@ class Geom:
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def substitute(self,from_microstructure,to_microstructure):
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"""
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Substitude microstructure indices.
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Substitute microstructure indices.
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Parameters
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----------
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from_microstructure : iterable of ints
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microstructure indices to be substituted.
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Microstructure indices to be substituted.
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to_microstructure : iterable of ints
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new microstructure indices.
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New microstructure indices.
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"""
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substituted = self.get_microstructure()
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@ -674,3 +674,50 @@ class Geom:
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#ToDo: self.add_comments('geom.py:substitute v{}'.format(version)
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return self.update(substituted)
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def vicinity_offset(self,vicinity=1,offset=None,trigger=[],periodic=True):
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"""
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Offset microstructure index of points in the vicinity of xxx.
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Different from themselves (or listed as triggers) within a given (cubic) vicinity,
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i.e. within the region close to a grain/phase boundary.
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ToDo: use include/exclude as in seeds.from_geom
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Parameters
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----------
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vicinity : int, optional
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Voxel distance checked for presence of other microstructure.
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Defaults to 1.
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offset : int, optional
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Offset (positive or negative) to tag microstructure indices,
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defaults to microstructure.max() + 1.
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trigger : list of ints, optional
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List of microstructure indices triggering a change.
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Defaults to [], meaning that different neigboors trigger a change.
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periodic : Boolean, optional
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Assume geometry to be periodic. Defaults to True.
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"""
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def tainted_neighborhood(stencil,trigger):
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me = stencil[stencil.shape[0]//2]
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if len(trigger) == 0:
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return np.any(stencil != me)
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if me in trigger:
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trigger = set(trigger)
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trigger.remove(me)
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trigger = list(trigger)
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return np.any(np.in1d(stencil,np.array(trigger)))
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offset_ = np.nanmax(self.microstructure) if offset is None else offset
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mask = ndimage.filters.generic_filter(self.microstructure,
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tainted_neighborhood,
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size=1+2*vicinity,
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mode=('wrap' if periodic else 'nearest'),
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extra_keywords={'trigger':trigger})
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microstructure = np.ma.MaskedArray(self.microstructure + offset_, np.logical_not(mask))
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#ToDo: self.add_comments('geom.py:vicinity_offset v{}'.format(version)
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return self.update(microstructure)
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@ -77,9 +77,19 @@ class TestGeom:
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with pytest.raises(ValueError):
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default.update(default.microstructure[1:,1:,1:],size=np.ones(2))
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def test_invalid_microstructure(self,default):
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def test_invalid_origin(self,default):
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with pytest.raises(ValueError):
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default.update(default.microstructure[1])
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default.update(default.microstructure[1:,1:,1:],origin=np.ones(4))
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def test_invalid_microstructure_size(self,default):
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microstructure=np.ones((3,3))
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with pytest.raises(ValueError):
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default.update(microstructure)
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def test_invalid_microstructure_type(self,default):
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microstructure=np.random.randint(1,300,(3,4,5))==1
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with pytest.raises(TypeError):
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default.update(microstructure)
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def test_invalid_homogenization(self,default):
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with pytest.raises(TypeError):
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@ -172,6 +182,33 @@ class TestGeom:
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e = default.grid
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assert np.all(modified.microstructure[:e[0],:e[1],:e[2]] == default.microstructure)
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@pytest.mark.parametrize('trigger',[[1],[]])
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def test_vicinity_offset(self,trigger):
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offset = np.random.randint(2,4)
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vicinity = np.random.randint(2,4)
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g=np.random.randint(28,40,(3))
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m=np.ones(g,'i')
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x=(g*np.random.permutation(np.array([.5,1,1]))).astype('i')
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m[slice(0,x[0]),slice(0,x[1]),slice(0,x[2])]=2
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m2=copy.deepcopy(m)
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for i in [0,1,2]:
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m2[(np.roll(m,+vicinity,i)-m)!=0] +=offset
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m2[(np.roll(m,-vicinity,i)-m)!=0] +=offset
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if len(trigger) > 0:
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m2[m==1]=1
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geom = Geom(m,np.random.rand(3))
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geom.vicinity_offset(vicinity,offset,trigger=trigger)
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assert np.all(m2==geom.microstructure)
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@pytest.mark.parametrize('periodic',[True,False])
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def test_vicinity_offset_invariant(self,default,periodic):
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old = default.get_microstructure()
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default.vicinity_offset(trigger=[old.max()+1,old.min()-1])
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assert np.all(old==default.microstructure)
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@pytest.mark.parametrize('periodic',[True,False])
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def test_tessellation_approaches(self,periodic):
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grid = np.random.randint(10,20,3)
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