fixed wrong variable name when using pre-existing microstructures from table.
added switch to skip effort for tolerance == 0.
This commit is contained in:
Philip Eisenlohr
parent
87daed84e6
commit
6de6b8b87f
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@ -191,15 +191,13 @@ for name in filenames:
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colOri = table.label_index(label)+(3-coordDim) # column(s) of orientation data (following 3 or 2 coordinates that were expanded to 3!)
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if inputtype == 'microstructure':
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microstructure = table.data[:,colOri]
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nGrains = len(np.unique(microstructure))
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grain = table.data[:,colOri]
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nGrains = len(np.unique(grain))
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else:
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# --- start background messaging
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if options.verbose:
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bg = damask.util.backgroundMessage()
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bg.start()
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if options.verbose: bg = damask.util.backgroundMessage(); bg.start() # start background messaging
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colPhase = -1 # column of phase data comes last
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if options.verbose: bg.set_message('sorting positions...')
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@ -250,28 +248,29 @@ for name in filenames:
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cos_disorientations = -np.ones(1,dtype='f') # largest possible disorientation
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closest_grain = -1 # invalid neighbor
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neighbors = np.array(KDTree.query_ball_point([x,y,z], 3)) # point indices within radius
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neighbors = neighbors[(neighbors < myPos) & \
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(table.data[index[neighbors],colPhase] == myPhase)] # filter neighbors: skip myself, anyone further ahead (cannot yet have a grain ID), and other phases
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grains = np.unique(grain[neighbors]) # unique grain IDs among valid neighbors
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if options.tolerance > 0.0: # only try to compress orientations if asked to
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neighbors = np.array(KDTree.query_ball_point([x,y,z], 3)) # point indices within radius
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neighbors = neighbors[(neighbors < myPos) & \
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(table.data[index[neighbors],colPhase] == myPhase)] # filter neighbors: skip myself, anyone further ahead (cannot yet have a grain ID), and other phases
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grains = np.unique(grain[neighbors]) # unique grain IDs among valid neighbors
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if len(grains) > 0: # check immediate neighborhood first
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cos_disorientations = np.array([o.disorientation(orientations[grainID],
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SST = False)[0].quaternion.w \
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for grainID in grains]) # store disorientation per grainID
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closest_grain = np.argmax(cos_disorientations) # find grain among grains that has closest orientation to myself
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match = 'local'
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if cos_disorientations[closest_grain] < threshold: # orientation not close enough?
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grains = existingGrains[np.atleast_1d( ( np.array(phases) == myPhase ) & \
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( np.in1d(existingGrains,grains,invert=True) ) )] # check every other already identified grain (of my phase)
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if len(grains) > 0:
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if len(grains) > 0: # check immediate neighborhood first
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cos_disorientations = np.array([o.disorientation(orientations[grainID],
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SST = False)[0].quaternion.w \
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for grainID in grains]) # store disorientation per grainID
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closest_grain = np.argmax(cos_disorientations) # find grain among grains that has closest orientation to myself
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match = 'global'
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match = 'local'
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if cos_disorientations[closest_grain] < threshold: # orientation not close enough?
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grains = existingGrains[np.atleast_1d( ( np.array(phases) == myPhase ) & \
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( np.in1d(existingGrains,grains,invert=True) ) )] # check every other already identified grain (of my phase)
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if len(grains) > 0:
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cos_disorientations = np.array([o.disorientation(orientations[grainID],
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SST = False)[0].quaternion.w \
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for grainID in grains]) # store disorientation per grainID
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closest_grain = np.argmax(cos_disorientations) # find grain among grains that has closest orientation to myself
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match = 'global'
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if cos_disorientations[closest_grain] >= threshold: # orientation now close enough?
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grainID = grains[closest_grain]
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@ -281,12 +280,12 @@ for name in filenames:
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multiplicity[grainID] += 1
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statistics[match] += 1
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else:
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grain[myPos] = nGrains # ... and assign to me
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grain[myPos] = nGrains # assign new grain to me ...
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nGrains += 1 # ... and update counter
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orientations.append(o) # store new orientation for future comparison
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multiplicity.append(1) # having single occurrence so far
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phases.append(myPhase) # store phase info for future reporting
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nGrains += 1 # update counter ...
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existingGrains = np.arange(nGrains)
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existingGrains = np.arange(nGrains) # update list of existing grains
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myPos += 1
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@ -296,6 +295,8 @@ for name in filenames:
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damask.util.croak("{} seconds total.\n{} local and {} global matches.".\
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format(time.clock()-tick,statistics['local'],statistics['global']))
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grain += 1 # offset from starting index 0 to 1
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# --- generate header ----------------------------------------------------------------------------
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info = {
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@ -343,7 +344,7 @@ for name in filenames:
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# --- write microstructure information ------------------------------------------------------------
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table.data = grain.reshape(info['grid'][1]*info['grid'][2],info['grid'][0]) + 1 # offset from starting index 0 to 1
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table.data = grain.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
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table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
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#--- output finalization --------------------------------------------------------------------------
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