Close #152 Represent Bools as Enums

.travis.yml

@@ -42,6 +42,7 @@ before_script:
   - lsb_release -a
   - echo "$SRC"
   - ls -hal $SRC
+  - ls -hal /usr/include
 # PPA providing hdf5 >= 1.8.6 and OpenMPI >= 1.5.1
 # -> remove legacy hdf5 and mpi packages/deps from travis
   - sudo apt-get remove -qq libhdf5* libopenmpi* openmpi-bin
@@ -58,4 +59,10 @@ before_script:
   - sudo apt-get install -qq -f libboost-program-options-dev
   - sudo apt-get -t o=LP-PPA-james-page-openmpi install -q -f $APTMPI
   - sudo apt-get -t o=LP-PPA-axel-huebl-libsplash install -q -f $APTHDF5
+  - sudo apt-get install python-numpy cython
+  - sudo -H pip install --upgrade pip
+#   numpy and cython should be already satisfied
+  - export HDF5_DIR=/usr
+  - export C_INCLUDE_PATH=/usr/lib/openmpi/include
+  - pip install --user h5py
   - mkdir -p $BUILD ~/lib

doc/INSTALL.md

@@ -17,7 +17,8 @@ To use the CMakeLists.txt file which comes with the source code, you must have
 The splashtools and some tests also require an **MPI 2.2** compatible MPI library,
 e.g. **OpenMPI 1.5.1** or higher.
 
-Tests require the development version of the **CppUnit** library.
+Our *tests* require the development version of the **CppUnit** library and
+python support for `h5py` & `numpy`.
 
 
 Compiling

src/include/splash/basetypes/ColTypeBool.hpp

@@ -1,5 +1,5 @@
 /**
- * Copyright 2013 Felix Schmitt, René Widera
+ * Copyright 2013, 2015 Felix Schmitt, René Widera, Axel Huebl
  *
  * This file is part of libSplash. 
  * 
@@ -8,6 +8,7 @@
  * the GNU Lesser General Public License as published by 
  * the Free Software Foundation, either version 3 of the License, or 
  * (at your option) any later version. 
+ *
  * libSplash 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 
@@ -18,7 +19,6 @@
  * and the GNU Lesser General Public License along with libSplash. 
  * If not, see <http://www.gnu.org/licenses/>. 
  */ 
-
 
 
 #ifndef COLTYPEBOOL_H
@@ -35,8 +35,15 @@ class ColTypeBool : public CollectionType
 
     ColTypeBool()
     {
-        const hsize_t dim[] = {sizeof (bool)};
-        this->type = H5Tarray_create(H5T_NATIVE_B8, 1, dim);
+        // 8 bit (very) short int, see
+        //   http://www.hdfgroup.org/HDF5/doc/RM/PredefDTypes.html
+        // this is a h5py compatible implementation for bool, see:
+        //   http://docs.h5py.org/en/latest/faq.html
+        this->type = H5Tenum_create(H5T_NATIVE_INT8);
+        const char *names[2] = {"true", "false"};
+        const int64_t val[2] = {1, 0};
+        H5Tenum_insert(this->type, names[0], &val[0]);
+        H5Tenum_insert(this->type, names[1], &val[1]);
     }
 
     ~ColTypeBool()

src/include/splash/version.hpp

@@ -31,7 +31,7 @@
 /** we can always handle files from the same major release
  *  changes in the minor number have to be backwards compatible
  */
-#define SPLASH_FILE_FORMAT_MAJOR 2
-#define SPLASH_FILE_FORMAT_MINOR 1
+#define SPLASH_FILE_FORMAT_MAJOR 3
+#define SPLASH_FILE_FORMAT_MINOR 0
 
 #endif	/* VERSION_HPP */

tests/CMakeLists.txt

@@ -108,3 +108,8 @@ FOREACH(TEST_FILE ${TEST_FILES})
 
     TARGET_LINK_LIBRARIES(${FILE}.out ${LIBS})
 ENDFOREACH()
+
+# copy scripts to "build" dir for easy testing
+FILE(COPY readBool.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+FILE(COPY run_tests DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+FILE(COPY run_parallel_tests DESTINATION ${CMAKE_CURRENT_BINARY_DIR})

tests/SimpleDataTest.cpp

@@ -40,7 +40,8 @@ using namespace splash;
 
 SimpleDataTest::SimpleDataTest() :
 ctUInt32(),
-ctUInt64()
+ctUInt64(),
+ctBool()
 {
     dataCollector = new SerialDataCollector(10);
     srand(time(NULL));
@@ -74,9 +75,13 @@ bool SimpleDataTest::subtestWriteRead(Dimensions gridSize, Dimensions borderSize
     // initial part of the test: data is written to the file, once with and once
     // without borders
     uint64_t *dataWrite = new uint64_t[bufferSize];
+    bool     *boolWrite = new bool[bufferSize];
 
     for (uint64_t i = 0; i < bufferSize; i++)
+    {
         dataWrite[i] = i;
+        boolWrite[i] = ( i%2 == 0 );
+    }
 
     dataCollector->write(10, ctUInt64, dimensions, Selection(gridSize), "deep/folders/data", dataWrite);
     datasetNames.insert("deep/folders/data");
@@ -85,6 +90,13 @@ bool SimpleDataTest::subtestWriteRead(Dimensions gridSize, Dimensions borderSize
             borderSize), "deep/folders/data_without_borders", dataWrite);
     datasetNames.insert("deep/folders/data_without_borders");
 
+    dataCollector->write(10, ctBool, dimensions, Selection(gridSize), "deep/folders/data_bool", boolWrite);
+    datasetNames.insert("deep/folders/data_bool");
+
+    dataCollector->write(20, ctBool, dimensions, Selection(gridSize, smallGridSize,
+            borderSize), "deep/folders/data_bool_without_borders", boolWrite);
+    datasetNames.insert("deep/folders/data_bool_without_borders");
+
     dataCollector->close();
 
     // first part of the test: read data with borders to a cleared
@@ -103,14 +115,17 @@ bool SimpleDataTest::subtestWriteRead(Dimensions gridSize, Dimensions borderSize
     int32_t *ids = NULL;
     size_t numIDs = 0;
     dataCollector->getEntryIDs(NULL, &numIDs);
+#if defined TESTS_DEBUG
+    printf("number of entry IDs=%d\n", numIDs);
+#endif
     CPPUNIT_ASSERT(numIDs == 2);
     ids = new int32_t[numIDs];
     dataCollector->getEntryIDs(ids, NULL);
 
     for (uint32_t j = 0; j < numIDs; ++j)
     {
         dataCollector->getEntriesForID(ids[j], NULL, &numEntries);
-        CPPUNIT_ASSERT(numEntries == 1);
+        CPPUNIT_ASSERT(numEntries == 2);
         entries = new DataCollector::DCEntry[numEntries];
         dataCollector->getEntriesForID(ids[j], entries, NULL);
 
@@ -129,26 +144,44 @@ bool SimpleDataTest::subtestWriteRead(Dimensions gridSize, Dimensions borderSize
     delete[] ids;
 
     uint64_t *dataRead = new uint64_t[bufferSize];
+    bool *boolRead = new bool[bufferSize];
     for (uint64_t i = 0; i < bufferSize; i++)
+    {
         dataRead[i] = UINT64_MAX;
+        boolRead[i] = false;
+    }
 
     Dimensions resultSize;
     dataCollector->read(10, "deep/folders/data", resultSize, dataRead);
 
     for (uint32_t i = 0; i < 3; i++)
         CPPUNIT_ASSERT(resultSize[i] == gridSize[i]);
 
+    dataCollector->read(10, "deep/folders/data_bool", resultSize, boolRead);
+
     for (uint64_t i = 0; i < bufferSize; i++)
+    {
         if (dataRead[i] != dataWrite[i])
         {
 #if defined TESTS_DEBUG
-            std::cout << i << ": " << dataRead[i] << " != exptected " << dataWrite[i] << std::endl;
+            std::cout << i << ": " << dataRead[i] << " != expected " << dataWrite[i] << std::endl;
+#endif
+            resultsCorrect = false;
+            break;
+        }
+        if (boolRead[i] != boolWrite[i])
+        {
+#if defined TESTS_DEBUG
+            std::cout << i << ": " << boolRead[i] << " != expected " << boolWrite[i] << std::endl;
 #endif
             resultsCorrect = false;
             break;
         }
+    }
 
     delete[] dataRead;
+    delete[] boolRead;
+    delete[] boolWrite;
 
     CPPUNIT_ASSERT_MESSAGE("simple write/read failed", resultsCorrect);
 

tests/include/SimpleDataTest.h

@@ -34,8 +34,8 @@ class SimpleDataTest : public CPPUNIT_NS::TestFixture
 {
     CPPUNIT_TEST_SUITE(SimpleDataTest);
 
-    CPPUNIT_TEST(testWriteRead);
     CPPUNIT_TEST(testNullWrite);
+    CPPUNIT_TEST(testWriteRead);
 
     CPPUNIT_TEST_SUITE_END();
 
@@ -63,6 +63,7 @@ class SimpleDataTest : public CPPUNIT_NS::TestFixture
 
     ColTypeUInt32 ctUInt32;
     ColTypeUInt64 ctUInt64;
+    ColTypeBool   ctBool;
     DataCollector *dataCollector;
 };
 

tests/readBool.py

@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+#
+# Copyright 2015 Axel Huebl
+#
+# This file is part of libSplash.
+#
+# libSplash is free software: you can redistribute it and/or modify
+# it under the terms of of either the GNU General Public License or
+# the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# libSplash 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 and the GNU Lesser General Public License
+# for more details.
+#
+# You should have received a copy of the GNU General Public License
+# and the GNU Lesser General Public License along with libSplash.
+# If not, see <http://www.gnu.org/licenses/>.
+#
+
+import h5py
+import numpy as np
+
+f = h5py.File("h5/testWriteRead_0_0_0.h5", "r")
+data = f["data/10/deep/folders/data_bool"]
+
+len = data.size
+data1d = data[:,:,:].reshape(len)
+
+for i in np.arange(len):
+    val = ( i%2 == 0 );
+    if data1d[i] != val:
+        exit(1)
+
+exit(0)

tests/run_tests

@@ -26,6 +26,7 @@ function testMPI()
 }
 
 testSerial ./SimpleDataTest.cpp.out "Testing simple data read/write..."
+testSerial ./readBool.py "Testing h5py compatible read..."
 
 testSerial ./AttributesTest.cpp.out "Testing reading/writing attributes..."