From fbc4eaca4cfa537994303a754d42011ec446b809 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Franck=20P=C3=A9rignon?= <franck.perignon@imag.fr>
Date: Mon, 24 Mar 2014 14:14:52 +0000
Subject: [PATCH] Update hdf reader
---
HySoP/hysop/operator/monitors/reader.py | 77 ++++++++++++++++---------
1 file changed, 51 insertions(+), 26 deletions(-)
diff --git a/HySoP/hysop/operator/monitors/reader.py b/HySoP/hysop/operator/monitors/reader.py
index 67ce51eb7..4847fea28 100644
--- a/HySoP/hysop/operator/monitors/reader.py
+++ b/HySoP/hysop/operator/monitors/reader.py
@@ -21,7 +21,7 @@ class Reader(Monitoring):
"""
def __init__(self, variables, topo, prefix,
formattype=None, task_id=None,
- subset=None):
+ subset=None, names=None):
"""
@param variables : list of variables to read.
@param prefix input file name (without ext)
@@ -65,39 +65,62 @@ class Reader(Monitoring):
self._slices = self.topo.mesh.iCompute
self.globalResolution.reverse()
self.step = self.readHDF5
-
- @debug
- @timed_function
- def apply(self, simulation=None):
- self.step()
-
- def finalize(self):
- Monitoring.finalize(self)
-
- def readHDF5(self):
filename = self.prefix + '.h5'
assert os.path.isfile(filename), 'error, file does not exists'
if self.topo.size == 1:
- f = h5py.File(filename, "r")
+ self._file = h5py.File(filename, "r")
else:
- f = h5py.File(filename, 'r', driver='mpio', comm=self.topo.comm)
- # It's necessary to compute the set of indices of the current subset
- # in global notation
+ self._file = h5py.File(filename, 'r', driver='mpio',
+ comm=self.topo.comm)
+ self._globalSlice = []
if self.subset is None:
# Note : g_start and g_end do not include ghost points.
g_start = self.topo.mesh.global_start
g_end = self.topo.mesh.global_end + 1
- sl = [slice(g_start[i], g_end[i])
- for i in xrange(self.domain.dimension)]
+ self._globalSlice = [slice(g_start[i], g_end[i])
+ for i in xrange(self.domain.dimension)]
else:
g_start = self.subset.gstart
# convert self._slices to global position in topo
- sl = self.topo.toIndexGlobal(self._slices)
+ self._globalSlice = self.topo.toIndexGlobal(self._slices)
# And shift using global position of the surface
- sl = [slice(sl[i].start - g_start[i], sl[i].stop - g_start[i])
- for i in xrange(self.domain.dimension)]
- sl.reverse()
- sl = tuple(sl)
+ self._globalSlice = [slice(self._globalSlice[i].start - g_start[i],
+ self._globalSlice[i].stop - g_start[i])
+ for i in xrange(self.domain.dimension)]
+ self._globalSlice.reverse()
+ self._globalSlice = tuple(self._globalSlice)
+ if names is None:
+ self.names = {}
+ names = self.dataset_names()
+ i = 0
+ for field in self.variables:
+ self.names[field] = []
+ for d in xrange(field.nbComponents):
+ self.names[field].append(names[i])
+ i += 1
+ else:
+ self.names = names
+ for field in self.variables:
+ fname = self.names[field]
+ self.names[field] = [v for v in self.dataset_names()
+ if fname in v]
+ assert len(self.names[field]) == field.nbComponents
+
+ @debug
+ @timed_function
+ def apply(self, simulation=None):
+ self.step()
+
+ def dataset_names(self):
+ """
+ Return the list of available names for datasets in
+ the required file.
+ """
+ return self._file.keys()
+
+ def readHDF5(self):
+ # It's necessary to compute the set of indices of the current subset
+ # in global notation
for field in self.variables:
df = field.discreteFields[self.topo]
for d in xrange(df.nbComponents):
@@ -109,10 +132,12 @@ class Reader(Monitoring):
#Note FP : temp method --> use the first name is dataset
# as data for field. Todo : set a list of names
# to be downloaded.
- currentName = f.keys()[0]
- ds = f[currentName]
+ currentName = self.names[field][d]
+ ds = self._file[currentName]
# In parallel, each proc must write in the proper part
# Of the dataset (of site global resolution)
- df.data[d][self._slices] = ds[sl].T
- f.close()
+ df.data[d][self._slices] = ds[self._globalSlice].T
+ def finalize(self):
+ Monitoring.finalize(self)
+ self._file.close()
--
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