From 494d2e61f89d63e393741677b8ad79a6d979984a Mon Sep 17 00:00:00 2001
From: Cristian C Lalescu <Cristian.Lalescu@ds.mpg.de>
Date: Mon, 9 May 2016 16:27:51 +0200
Subject: [PATCH] add io of vector<int> and vector<double>
---
bfps/_base.py | 35 ++++++++++++++++++++++--
bfps/cpp/base.hpp | 1 +
bfps/cpp/io_tools.cpp | 62 +++++++++++++++++++++++++++++++++++++++++++
bfps/cpp/io_tools.hpp | 41 ++++++++++++++++++++++++++++
setup.py | 1 +
tests/test_io.py | 2 ++
6 files changed, 140 insertions(+), 2 deletions(-)
create mode 100644 bfps/cpp/io_tools.cpp
create mode 100644 bfps/cpp/io_tools.hpp
diff --git a/bfps/_base.py b/bfps/_base.py
index 395c423e..e0c686f0 100644
--- a/bfps/_base.py
+++ b/bfps/_base.py
@@ -60,6 +60,13 @@ class _base(object):
src_txt += 'int ' + key[i] + ';\n'
elif type(parameters[key[i]]) == str:
src_txt += 'char ' + key[i] + '[{0}];\n'.format(self.string_length)
+ elif type(parameters[key[i]]) == np.ndarray:
+ src_txt += 'std::vector<'
+ if parameters[key[i]].dtype == np.float64:
+ src_txt += 'double'
+ elif parameters[key[i]].dtype == np.int:
+ src_txt += 'int'
+ src_txt += '> ' + key[i] + ';\n'
else:
src_txt += 'double ' + key[i] + ';\n'
return src_txt
@@ -80,7 +87,8 @@ class _base(object):
'sprintf(fname, "%s.h5", simname);\n' +
'parameter_file = H5Fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT);\n')
for i in range(len(key)):
- src_txt += 'dset = H5Dopen(parameter_file, "/{0}/{1}", H5P_DEFAULT);\n'.format(file_group, key[i])
+ src_txt += 'dset = H5Dopen(parameter_file, "/{0}/{1}", H5P_DEFAULT);\n'.format(
+ file_group, key[i])
if type(parameters[key[i]]) == int:
src_txt += 'H5Dread(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &{0});\n'.format(key[i])
elif type(parameters[key[i]]) == str:
@@ -93,6 +101,13 @@ class _base(object):
'free(string_data);\n' +
'H5Sclose(space);\n' +
'H5Tclose(memtype);\n')
+ elif type(parameters[key[i]]) == np.ndarray:
+ if parameters[key[i]].dtype in [np.int, np.int64, np.int32]:
+ template_par = 'int'
+ elif parameters[key[i]].dtype == np.float64:
+ template_par = 'double'
+ src_txt += '{0} = read_vector<{1}>(parameter_file, "/{2}/{0}");\n'.format(
+ key[i], template_par, file_group)
else:
src_txt += 'H5Dread(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &{0});\n'.format(key[i])
src_txt += 'H5Dclose(dset);\n'
@@ -107,6 +122,19 @@ class _base(object):
src_txt += 'DEBUG_MSG("'+ key[i] + ' = %d\\n", ' + key[i] + ');\n'
elif type(self.parameters[key[i]]) == str:
src_txt += 'DEBUG_MSG("'+ key[i] + ' = %s\\n", ' + key[i] + ');\n'
+ elif type(self.parameters[key[i]]) == np.ndarray:
+ src_txt += ('for (int array_counter=0; array_counter<' +
+ key[i] +
+ '.size(); array_counter++)\n' +
+ '{\n' +
+ 'DEBUG_MSG("' + key[i] + '[%d] = %')
+ if self.parameters[key[i]].dtype == np.int:
+ src_txt += 'd'
+ elif self.parameters[key[i]].dtype == np.float64:
+ src_txt += 'g'
+ src_txt += ('\\n", array_counter, ' +
+ key[i] +
+ '[array_counter]);\n}\n')
else:
src_txt += 'DEBUG_MSG("'+ key[i] + ' = %g\\n", ' + key[i] + ');\n'
return src_txt
@@ -152,7 +180,10 @@ class _base(object):
with h5py.File(os.path.join(self.work_dir, self.simname + '.h5'), 'r') as data_file:
for k in data_file['parameters'].keys():
if k in self.parameters.keys():
- self.parameters[k] = type(self.parameters[k])(data_file['parameters/' + k].value)
+ if type(self.parameters[k]) in [int, str, float]:
+ self.parameters[k] = type(self.parameters[k])(data_file['parameters/' + k].value)
+ else:
+ self.parameters[k] = data_file['parameters/' + k].value
return None
def pars_from_namespace(
self,
diff --git a/bfps/cpp/base.hpp b/bfps/cpp/base.hpp
index f3df9c71..ee2d74d5 100644
--- a/bfps/cpp/base.hpp
+++ b/bfps/cpp/base.hpp
@@ -28,6 +28,7 @@
#include <stdarg.h>
#include <iostream>
#include <typeinfo>
+#include "io_tools.hpp"
#ifndef BASE
diff --git a/bfps/cpp/io_tools.cpp b/bfps/cpp/io_tools.cpp
new file mode 100644
index 00000000..224803dc
--- /dev/null
+++ b/bfps/cpp/io_tools.cpp
@@ -0,0 +1,62 @@
+/**********************************************************************
+* *
+* Copyright 2015 Max Planck Institute *
+* for Dynamics and Self-Organization *
+* *
+* This file is part of bfps. *
+* *
+* bfps is free software: you can redistribute it and/or modify *
+* it under the terms of the GNU General Public License as published *
+* by the Free Software Foundation, either version 3 of the License, *
+* or (at your option) any later version. *
+* *
+* bfps is distributed in the hope that it will be useful, *
+* but WITHOUT ANY WARRANTY; without even the implied warranty of *
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
+* GNU General Public License for more details. *
+* *
+* You should have received a copy of the GNU General Public License *
+* along with bfps. If not, see <http://www.gnu.org/licenses/> *
+* *
+* Contact: Cristian.Lalescu@ds.mpg.de *
+* *
+**********************************************************************/
+
+
+
+#include <typeinfo>
+#include <cassert>
+#include "io_tools.hpp"
+
+
+template <typename number>
+std::vector<number> read_vector(
+ hid_t group,
+ std::string dset_name)
+{
+ std::vector<number> result;
+ hsize_t vector_length;
+ // first, read size of array
+ hid_t dset, dspace;
+ hid_t mem_dtype;
+ if (typeid(number) == typeid(int))
+ mem_dtype = H5Tcopy(H5T_NATIVE_INT);
+ else if (typeid(number) == typeid(double))
+ mem_dtype = H5Tcopy(H5T_NATIVE_DOUBLE);
+ dset = H5Dopen(group, dset_name.c_str(), H5P_DEFAULT);
+ dspace = H5Dget_space(dset);
+ assert(H5Sget_simple_extent_ndims(dspace) == 1);
+ H5Sget_simple_extent_dims(dspace, &vector_length, NULL);
+ result.resize(vector_length);
+ H5Dread(dset, mem_dtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, &result.front());
+ H5Sclose(dspace);
+ H5Dclose(dset);
+ H5Tclose(mem_dtype);
+ return result;
+}
+
+template std::vector<int> read_vector(
+ hid_t, std::string);
+template std::vector<double> read_vector(
+ hid_t, std::string);
+
diff --git a/bfps/cpp/io_tools.hpp b/bfps/cpp/io_tools.hpp
new file mode 100644
index 00000000..69c0e8bb
--- /dev/null
+++ b/bfps/cpp/io_tools.hpp
@@ -0,0 +1,41 @@
+/**********************************************************************
+* *
+* Copyright 2015 Max Planck Institute *
+* for Dynamics and Self-Organization *
+* *
+* This file is part of bfps. *
+* *
+* bfps is free software: you can redistribute it and/or modify *
+* it under the terms of the GNU General Public License as published *
+* by the Free Software Foundation, either version 3 of the License, *
+* or (at your option) any later version. *
+* *
+* bfps is distributed in the hope that it will be useful, *
+* but WITHOUT ANY WARRANTY; without even the implied warranty of *
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
+* GNU General Public License for more details. *
+* *
+* You should have received a copy of the GNU General Public License *
+* along with bfps. If not, see <http://www.gnu.org/licenses/> *
+* *
+* Contact: Cristian.Lalescu@ds.mpg.de *
+* *
+**********************************************************************/
+
+
+
+#include <hdf5.h>
+#include <vector>
+#include <string>
+
+#ifndef IO_TOOLS
+
+#define IO_TOOLS
+
+template <typename number>
+std::vector<number> read_vector(
+ hid_t group,
+ std::string dset_name);
+
+#endif//IO_TOOLS
+
diff --git a/setup.py b/setup.py
index b3245758..6c4c277e 100644
--- a/setup.py
+++ b/setup.py
@@ -99,6 +99,7 @@ src_file_list = ['field',
'interpolator_base',
'fluid_solver',
'fluid_solver_base',
+ 'io_tools',
'fftw_tools',
'spline_n1',
'spline_n2',
diff --git a/tests/test_io.py b/tests/test_io.py
index 327889ec..ce825c80 100644
--- a/tests/test_io.py
+++ b/tests/test_io.py
@@ -41,6 +41,8 @@ class test_io(_code):
self.parameters['other_string_parameter'] = 'another test string'
self.parameters['niter_todo'] = 0
self.parameters['real_number'] = 1.21
+ self.parameters['real_array'] = np.array([1.3, 1.5, 0.4])
+ self.parameters['int_array'] = np.array([1, 3, 5, 4])
self.main_start += self.cprint_pars()
return None
--
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