From c45a0ce55e59e94ad36af4d5bdd834a23d048b38 Mon Sep 17 00:00:00 2001 From: Yannick Naunheim Date: Thu, 11 Jun 2015 10:06:53 +0000 Subject: [PATCH] improved stability for geom_fromAng. no longer depends on correct header information. geom_fromVPSC with correct size determination now --- processing/pre/geom_fromAng.py | 67 ++++++++++++++++++--------------- processing/pre/geom_fromTIFF.py | 3 +- processing/pre/geom_fromVPSC.py | 30 ++++++++++----- 3 files changed, 59 insertions(+), 41 deletions(-) diff --git a/processing/pre/geom_fromAng.py b/processing/pre/geom_fromAng.py index 40783a50d..f27027c5a 100755 --- a/processing/pre/geom_fromAng.py +++ b/processing/pre/geom_fromAng.py @@ -70,47 +70,53 @@ else: 'output':open(name+'_tmp','w'), 'croak':sys.stdout, }) - #--- loop over input files ------------------------------------------------------------------------ for file in files: file['croak'].write('\033[1m' + scriptName + '\033[0m: ' + (file['name'] if file['name'] != 'STDIN' else '') + '\n') info = { - 'grid': np.ones (3,'i'), + 'grid': np.zones(3,'i'), 'size': np.zeros(3,'d'), 'origin': np.zeros(3,'d'), 'microstructures': 0, - 'homogenization': options.homogenization, + 'homogenization': options.homogenization } + + coords = [{},{},{1:True}] + pos = {'min':[ float("inf"), float("inf")], + 'max':[-float("inf"),-float("inf")]} - step = [0,0] - point = 0 + phase = [] + eulerangles = [] +# --------------- read data ----------------------------------------------------------------------- for line in file['input']: - words = line.split() - if len(words) == 0: continue # ignore empty lines - if words[0] == '#': # process initial comments/header block - if len(words) > 2: - if words[2].lower() == 'hexgrid': - file['croak'].write('The file has HexGrid format. Please first convert to SquareGrid...\n') - break - if words[1] == 'XSTEP:': step[0] = float(words[2]) - if words[1] == 'YSTEP:': step[1] = float(words[2]) - if words[1] == 'NCOLS_ODD:': # ignore order of NROWS/NCOLS - info['grid'][0] = int(words[2]) - eulerangles = np.empty((info['grid'].prod(),3),dtype='f') - phase = np.empty(info['grid'].prod(),dtype='i') - if words[1] == 'NROWS:': # ignore order of NROWS/NCOLS - info['grid'][1] = int(words[2]) - eulerangles = np.empty((info['grid'].prod(),3),dtype='f') - phase = np.empty(info['grid'].prod(),dtype='i') - else: # finished with comments block - phase[point] = options.phase[int(float(words[options.column-1]) > options.threshold)] - eulerangles[point,...] = map(lambda x: math.degrees(float(x)), words[:3]) - point += 1 + if line.strip(): + words = line.split() + if words[0] == '#': # process initial comments/header block + if len(words) > 2: + if words[2].lower() == 'hexgrid': + file['croak'].write('The file has HexGrid format. Please first convert to SquareGrid...\n') + break + else: + currPos = words[3:5] + for i in xrange(2): + coords[i][currPos[i]] = True + currPos = map(float,currPos) + for i in xrange(2): + pos['min'][i] = min(pos['min'][i],currPos[i]) + pos['max'][i] = max(pos['max'][i],currPos[i]) + eulerangles.append(map(math.degrees,map(float,words[:3]))) + phase.append(options.phase[int(float(words[options.column-1]) > options.threshold)]) + +# --------------- determine size and grid --------------------------------------------------------- + info['grid'] = np.array(map(len,coords),'i') + info['size'][0:2] = info['grid'][0:2]/(info['grid'][0:2]-1.0)* \ + np.array([pos['max'][0]-pos['min'][0], + pos['max'][1]-pos['min'][1]],'d') + info['size'][2]=info['size'][0]/info['grid'][0] + eulerangles = np.array(eulerangles,dtype='f').reshape(info['grid'].prod(),3) + phase = np.array(phase,dtype='i').reshape(info['grid'].prod()) - if info['grid'].prod() != point: - file['croak'].write('Error: found %s microstructures. Header info in ang file might be wrong.\n'%point) - continue limits = [360,180,360] if any([np.any(eulerangles[:,i]>=limits[i]) for i in [0,1,2]]): file['croak'].write('Error: euler angles out of bound. Ang file might contain unidexed poins.\n') @@ -128,7 +134,7 @@ for file in files: euleranglesRadInt = (eulerangles*10**int(options.precision)).astype('int') # scale by desired precision and convert to int eulerKeys = np.array([int(''.join(map(formatString.format,euleranglesRadInt[i,:]))) \ for i in xrange(info['grid'].prod())]) # create unique integer key from three euler angles by concatenating the string representation with leading zeros and store as integer - devNull, texture, eulerKeys_idx = np.unique(eulerKeys, return_index = True, return_inverse=True)# search unique euler angle keys. Texture IDs are the indices of the first occurence, the inverse is used to construct the microstructure + devNull, texture, eulerKeys_idx = np.unique(eulerKeys, return_index = True, return_inverse=True)# search unique euler angle keys. Texture IDs are the indices of the first occurrence, the inverse is used to construct the microstructure msFull = np.array([[eulerKeys_idx[i],phase[i]] for i in xrange(info['grid'].prod())],'i8') # create a microstructure (texture/phase pair) for each point using unique texture IDs. Use longInt (64bit, i8) because the keys might be long devNull,msUnique,matPoints = np.unique(msFull.view('c16'),True,True) matPoints+=1 @@ -155,7 +161,6 @@ for file in files: ] info['microstructures'] = len(microstructure) - info['size'] = step[0]*info['grid'][0],step[1]*info['grid'][1],min(step) #--- report --------------------------------------------------------------------------------------- file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + diff --git a/processing/pre/geom_fromTIFF.py b/processing/pre/geom_fromTIFF.py index 08fefb49a..7925dbf86 100755 --- a/processing/pre/geom_fromTIFF.py +++ b/processing/pre/geom_fromTIFF.py @@ -90,7 +90,8 @@ for file in files: "homogenization\t%i"%info['homogenization'], ] file['output'].write('\n'.join(['%i\theader'%(len(header))] + header) + '\n') - np.savetxt(file['output'],imarray.reshape([info['grid'][1]*info['grid'][2],info['grid'][0]]),fmt='%03d') + np.savetxt(file['output'],imarray.reshape([info['grid'][1]*info['grid'][2],info['grid'][0]]), + fmt='%0'+str(1+int(math.log10(np.amax(imarray))))+'d' #--- output finalization -------------------------------------------------------------------------- if file['name'] != 'STDIN': diff --git a/processing/pre/geom_fromVPSC.py b/processing/pre/geom_fromVPSC.py index b58caf442..930cd265b 100755 --- a/processing/pre/geom_fromVPSC.py +++ b/processing/pre/geom_fromVPSC.py @@ -74,24 +74,36 @@ for file in files: 'microstructures': 0, 'homogenization': options.homogenization } + + coords = [{},{},{}] + pos = {'min':[ float("inf"), float("inf"), float("inf")], + 'max':[-float("inf"),-float("inf"),-float("inf")]} phase = [] eulerangles = [] - point = 0 +# --------------- read data ----------------------------------------------------------------------- for line in file['input']: if line.strip(): words = line.split() - currPos = map(float,words[3:6]) + currPos = words[3:6] for i in xrange(3): - if currPos[i] > info['grid'][i]: - info['size'][i] = currPos[i] - info['grid'][i]+=1 - eulerangles.append(map(float,words[:3])) + coords[i][currPos[i]] = True + currPos = map(float,currPos) + for i in xrange(3): + pos['min'][i] = min(pos['min'][i],currPos[i]) + pos['max'][i] = max(pos['max'][i],currPos[i]) + eulerangles.append(map(math.degrees,map(float,words[:3]))) phase.append(options.phase[int(float(words[options.column-1]) > options.threshold)]) - + +# --------------- determine size and grid --------------------------------------------------------- + info['grid'] = np.array(map(len,coords),'i') + info['size'] = info['grid']/np.maximum(np.ones(3,'d'),info['grid']-1.0)* \ + np.array([pos['max'][0]-pos['min'][0], + pos['max'][1]-pos['min'][1], + pos['max'][2]-pos['min'][2]],'d') eulerangles = np.array(eulerangles,dtype='f').reshape(info['grid'].prod(),3) phase = np.array(phase,dtype='i').reshape(info['grid'].prod()) - + limits = [360,180,360] if any([np.any(eulerangles[:,i]>=limits[i]) for i in [0,1,2]]): file['croak'].write('Error: euler angles out of bound. Ang file might contain unidexed poins.\n') @@ -164,7 +176,7 @@ for file in files: ] file['output'].write('\n'.join(['%i\theader'%(len(header))] + header) + '\n') if options.compress: - matPoints = matPoints.reshape((info['grid'][1],info['grid'][0])) + matPoints = matPoints.reshape([info['grid'][1]*info['grid'][2],info['grid'][0]]) np.savetxt(file['output'],matPoints,fmt='%0'+str(1+int(math.log10(np.amax(matPoints))))+'d') else: file['output'].write("1 to %i\n"%(info['microstructures']))