def writeFields_(graph, options):
fn = str(graph.from_fn)
f = h5py.File(fn, 'r')
fn, _ = myutils.splitH5PathsFromFilename(fn)
#search_groups.append('po2/adaption/vessels_after_adaption')
#search_groups = ['po2/adaption/vessels_after_adaption/po2field']
search_groups = []
search_groups.append(str(options.writeFields))
e = extractVtkFields.Extractor(f, search_groups, recursive=True)
print 'found field datasets:'
pprint.pprint(e.getDatasetPaths())
e.write(options.outfn % 'fields')
del e
dirs = set()
for fn in goodArguments.vesselFileNames:
if not os.path.isfile(fn.name):
raise AssertionError('The file %s is not present!'%fn)
with h5py.File(fn.name, 'r') as f:
d = myutils.walkh5(f, goodArguments.grp_pattern)
if not len(d)>0:
raise AssertionError('pattern "%s" not found in "%s"!' % (grp_pattern, fn))
else:
dirs = set.union(dirs,d)
except Exception, e:
print e.message
sys.exit(-1)
for fn in filenames:
fn, _ = myutils.splitH5PathsFromFilename(fn)
f = h5py.File(fn, 'r')
dirs = myutils.walkh5(f['/'], pattern)
if goodArguments.outfn:
print("you chose: %s as outfilename" % goodArguments.outfn)
goodArguments.outfn = goodArguments.outfn + '_%s.vtk'
else:
goodArguments.outfn = outfn = "%s-%%s.vtk" % (os.path.splitext(os.path.basename(fn))[0])
for d in dirs:
if 'vessels' in d and 'po2' not in d:
vesselgroup = f[join('/',d)]['.']
new = False
if new:
graph = krebsutils.read_vessels_from_hdf(vesselgroup, ['position', 'radius', 'hematocrit', 'pressure', 'flow', 'flags','shearforce','nodeflags','edge_boundary'] + datalist, return_graph=True)
else:
graph = krebsutils.read_vessels_from_hdf(vesselgroup, ['position', 'radius', 'hematocrit', 'pressure', 'flow', 'flags','shearforce'] + datalist, return_graph=True)
def getDatasetPaths(self):
def it(x0):
for x1 in x0:
for x2 in x1:
yield x2.name
return list(it(self.data.itervalues()))
if __name__ == "__main__":
from os.path import basename, dirname, join, splitext
import pprint
args = sys.argv[1:]
# process
fn, (grpname, ) = myutils.splitH5PathsFromFilename(args[0])
f = h5py.File(fn, 'r')
e = Extractor(f, [grpname], recursive=True)
print 'found datasets:'
pprint.pprint(e.getDatasetPaths())
out = basename(fn)
if out.endswith('.h5'):
out = splitext(out)[0]
if grpname and grpname <> '.':
tmp = grpname.replace('/', '-')
if not tmp.startswith('-'):
tmp = '-' + tmp
out += tmp