From 3b322fb7a312677fb10f6d957a6b1d24ccfb2dc6 Mon Sep 17 00:00:00 2001
From: Gennady Pospelov <g.pospelov@fz-juelich.de>
Date: Wed, 28 Oct 2015 14:50:18 +0100
Subject: [PATCH] New doxygen group for input/output classes.
---
Core/InputOutput/IntensityDataIOFactory.cpp | 21 +----------
Core/InputOutput/IntensityDataIOFactory.h | 29 +++++++++++----
Core/InputOutput/OutputDataReadFactory.h | 2 +-
Core/InputOutput/OutputDataReadStrategy.h | 8 ++--
Core/InputOutput/OutputDataReader.h | 2 +-
Core/InputOutput/OutputDataWriteFactory.h | 2 +-
Core/InputOutput/OutputDataWriteStrategy.h | 8 ++--
Core/InputOutput/OutputDataWriter.h | 2 +-
Core/InputOutput/TiffHandler.h | 2 +-
.../src/IntensityDataIOFactory.pypp.cpp | 37 +++++--------------
Doc/Doxygen/defgroups.doc | 8 +++-
Doc/Doxygen/userapi.doc | 3 ++
.../python/utils/plot_intensity_data_diff.py | 22 +++++------
dev-tools/python-bindings/settings_core.py | 2 +-
14 files changed, 68 insertions(+), 80 deletions(-)
diff --git a/Core/InputOutput/IntensityDataIOFactory.cpp b/Core/InputOutput/IntensityDataIOFactory.cpp
index e91a16a4e7d..381598e97da 100644
--- a/Core/InputOutput/IntensityDataIOFactory.cpp
+++ b/Core/InputOutput/IntensityDataIOFactory.cpp
@@ -31,17 +31,12 @@ OutputData<double > *IntensityDataIOFactory::readOutputData(
return P_reader->getOutputData();
}
-IHistogram *IntensityDataIOFactory::readHistogram(const std::string &file_name)
+IHistogram *IntensityDataIOFactory::readIntensityData(const std::string &file_name)
{
boost::scoped_ptr<OutputData<double> > data(readOutputData(file_name));
return IHistogram::createHistogram(*data);
}
-IHistogram *IntensityDataIOFactory::readIntensityData(const std::string &file_name)
-{
- return readHistogram(file_name);
-}
-
/* ************************************************************************* */
@@ -54,21 +49,9 @@ void IntensityDataIOFactory::writeOutputData(const OutputData<double>& data,
return P_writer->writeOutputData(data);
}
-//void IntensityDataIOFactory::writeOutputData(const IHistogram &histogram,
-// const std::string &file_name)
-//{
-// writeHistogram(histogram, file_name);
-//}
-
-void IntensityDataIOFactory::writeHistogram(const IHistogram &histogram,
- const std::string &file_name)
+void IntensityDataIOFactory::writeIntensityData(const IHistogram &histogram, const std::string &file_name)
{
boost::scoped_ptr<OutputData<double> > data(histogram.createOutputData());
writeOutputData(*data, file_name);
}
-void IntensityDataIOFactory::writeIntensityData(const IHistogram &histogram, const std::string &file_name)
-{
- writeHistogram(histogram, file_name);
-}
-
diff --git a/Core/InputOutput/IntensityDataIOFactory.h b/Core/InputOutput/IntensityDataIOFactory.h
index 114a4b17e7e..5bd191e2ff5 100644
--- a/Core/InputOutput/IntensityDataIOFactory.h
+++ b/Core/InputOutput/IntensityDataIOFactory.h
@@ -28,24 +28,39 @@ class IHistogram;
//! @class IntensityDataIOFactory
//! @ingroup input_output
//! @brief Provides users with possibility to read and write IntensityData from/to files
-//! in different format.
+//! in different format. Type of the file will be deduced from file name.
+//! *.txt - ASCII file with 2D array [nrow][ncol], layout as in numpy.
+//! *.int - BornAgain internal ASCII format.
+//! *.tif - 32-bits tiff file.
+//! If file name ends woth "*.gz" or "*.bz2" the file will be zipped on the fly using
+//! appropriate algorithm.
+
+/*! Usage:
+\code{.py}
+# reading from ASCII file or g-zipped ASCII file
+histogram = IntensityDataIOFactory.readIntensityData("filename.txt")
+histogram = IntensityDataIOFactory.readIntensityData("filename.txt.gz")
+
+# writing to 32-bits tiff file or b-zipped tiff file
+IntensityDataIOFactory.writeIntensityData(histogram, "filename.tif")
+IntensityDataIOFactory.writeIntensityData(histogram, "filename.tif.bz2")
+\endcode
+*/
class BA_CORE_API_ IntensityDataIOFactory
{
public:
+ //! Reads file and returns newly created OutputData object
static OutputData<double > *readOutputData(const std::string& file_name);
- static IHistogram *readHistogram(const std::string& file_name);
-
+ //! Reads file and returns newly created Histogram object
static IHistogram *readIntensityData(const std::string& file_name);
-
+ //! Writes OutputData in file
static void writeOutputData(const OutputData<double>& data,
const std::string& file_name);
- static void writeHistogram(const IHistogram &histogram,
- const std::string& file_name);
-
+ //! Writes histogram in file
static void writeIntensityData(const IHistogram &histogram,
const std::string& file_name);
diff --git a/Core/InputOutput/OutputDataReadFactory.h b/Core/InputOutput/OutputDataReadFactory.h
index c27f1a9f588..cd62f83ef45 100644
--- a/Core/InputOutput/OutputDataReadFactory.h
+++ b/Core/InputOutput/OutputDataReadFactory.h
@@ -23,7 +23,7 @@
class IOutputDataReadStrategy;
//! @class OutputDataReadFactory
-//! @ingroup input_output
+//! @ingroup input_output_internal
//! @brief Creates reader appropariate for given type of files
class BA_CORE_API_ OutputDataReadFactory
diff --git a/Core/InputOutput/OutputDataReadStrategy.h b/Core/InputOutput/OutputDataReadStrategy.h
index ca05637ad68..b18368b9ca0 100644
--- a/Core/InputOutput/OutputDataReadStrategy.h
+++ b/Core/InputOutput/OutputDataReadStrategy.h
@@ -22,7 +22,7 @@ template <class T> class OutputData;
//! @class IOutputDataReadStrategy
-//! @ingroup input_output
+//! @ingroup input_output_internal
//! @brief Interface for reading strategy of OutputData from file
class BA_CORE_API_ IOutputDataReadStrategy
{
@@ -34,7 +34,7 @@ private:
//! @class OutputDataReadINTStrategy
-//! @ingroup input_output
+//! @ingroup input_output_internal
//! @brief Strategy to read BornAgain native IntensityData from ASCII file
class OutputDataReadINTStrategy : public IOutputDataReadStrategy
{
@@ -43,7 +43,7 @@ public:
};
//! @class OutputDataReadNumpyTXTStrategy
-//! @ingroup input_output
+//! @ingroup input_output_internal
//! @brief Strategy to read OutputData from simple ASCII file with the layout as in numpy.savetxt
class OutputDataReadNumpyTXTStrategy : public IOutputDataReadStrategy
{
@@ -57,7 +57,7 @@ public:
class TiffHandler;
//! @class OutputDataReadTiffStrategy
-//! @ingroup input_output
+//! @ingroup input_output_internal
//! @brief Reads tiff files
class BA_CORE_API_ OutputDataReadTiffStrategy : public IOutputDataReadStrategy
diff --git a/Core/InputOutput/OutputDataReader.h b/Core/InputOutput/OutputDataReader.h
index e07a409e68b..e8260dcebbc 100644
--- a/Core/InputOutput/OutputDataReader.h
+++ b/Core/InputOutput/OutputDataReader.h
@@ -25,7 +25,7 @@
template <class T> class OutputData;
//! @class OutputDataReader
-//! @ingroup input_output
+//! @ingroup input_output_internal
//! @brief Reads OutputData from file using different reading strategies.
class BA_CORE_API_ OutputDataReader
diff --git a/Core/InputOutput/OutputDataWriteFactory.h b/Core/InputOutput/OutputDataWriteFactory.h
index 1143d95e605..161497fe1f3 100644
--- a/Core/InputOutput/OutputDataWriteFactory.h
+++ b/Core/InputOutput/OutputDataWriteFactory.h
@@ -23,7 +23,7 @@
class IOutputDataWriteStrategy;
//! @class OutputDataWriteFactory
-//! @ingroup input_output
+//! @ingroup input_output_internal
//! @brief Creates writer appropariate for given type of files
class BA_CORE_API_ OutputDataWriteFactory
diff --git a/Core/InputOutput/OutputDataWriteStrategy.h b/Core/InputOutput/OutputDataWriteStrategy.h
index d91eead9d0c..18fc4774b30 100644
--- a/Core/InputOutput/OutputDataWriteStrategy.h
+++ b/Core/InputOutput/OutputDataWriteStrategy.h
@@ -23,7 +23,7 @@ template <class T> class OutputData;
//! @class IOutputDataWriteStrategy
-//! @ingroup input_output
+//! @ingroup input_output_internal
//! @brief Strategy interface to write OututData in file
class BA_CORE_API_ IOutputDataWriteStrategy
@@ -38,7 +38,7 @@ protected:
};
//! @class OutputDataWriteINTStrategy
-//! @ingroup input_output
+//! @ingroup input_output_internal
//! @brief Strategy to write OutputData to special BornAgain ASCII format
class OutputDataWriteINTStrategy : public IOutputDataWriteStrategy
{
@@ -47,7 +47,7 @@ public:
};
//! @class OutputDataWriteNumpyTXTStrategy
-//! @ingroup input_output
+//! @ingroup input_output_internal
//! @brief Strategy to write OutputData to simple ASCII file with the layout as in numpy.savetxt
class OutputDataWriteNumpyTXTStrategy : public IOutputDataWriteStrategy
{
@@ -61,7 +61,7 @@ public:
class TiffHandler;
//! @class OutputDataWriteTiffStrategy
-//! @ingroup input_output
+//! @ingroup input_output_internal
//! @brief Strategy to write OutputData to tiff files
class OutputDataWriteTiffStrategy : public IOutputDataWriteStrategy
{
diff --git a/Core/InputOutput/OutputDataWriter.h b/Core/InputOutput/OutputDataWriter.h
index 04f4a631d2c..ad5e180a933 100644
--- a/Core/InputOutput/OutputDataWriter.h
+++ b/Core/InputOutput/OutputDataWriter.h
@@ -24,7 +24,7 @@
template <class T> class OutputData;
//! @class OutputDataWriter
-//! @ingroup input_output
+//! @ingroup input_output_internal
//! @brief Write OutputData to file using different witing strategies
class BA_CORE_API_ OutputDataWriter
{
diff --git a/Core/InputOutput/TiffHandler.h b/Core/InputOutput/TiffHandler.h
index 8b1b37bc7c1..d0333dab505 100644
--- a/Core/InputOutput/TiffHandler.h
+++ b/Core/InputOutput/TiffHandler.h
@@ -26,7 +26,7 @@
#include <boost/scoped_ptr.hpp>
//! @class TiffHandler
-//! @ingroup input_output
+//! @ingroup input_output_internal
//! @brief Reads/write tiff files, should be used through TiffReadStrategy
class BA_CORE_API_ TiffHandler
diff --git a/Core/PythonAPI/src/IntensityDataIOFactory.pypp.cpp b/Core/PythonAPI/src/IntensityDataIOFactory.pypp.cpp
index db22ab74cfd..68198a45f64 100644
--- a/Core/PythonAPI/src/IntensityDataIOFactory.pypp.cpp
+++ b/Core/PythonAPI/src/IntensityDataIOFactory.pypp.cpp
@@ -30,19 +30,8 @@ void register_IntensityDataIOFactory_class(){
{ //::IntensityDataIOFactory
typedef bp::class_< IntensityDataIOFactory > IntensityDataIOFactory_exposer_t;
- IntensityDataIOFactory_exposer_t IntensityDataIOFactory_exposer = IntensityDataIOFactory_exposer_t( "IntensityDataIOFactory", "Provides users with possibility to read and write IntensityData from/to files in different format." );
+ IntensityDataIOFactory_exposer_t IntensityDataIOFactory_exposer = IntensityDataIOFactory_exposer_t( "IntensityDataIOFactory" );
bp::scope IntensityDataIOFactory_scope( IntensityDataIOFactory_exposer );
- { //::IntensityDataIOFactory::readHistogram
-
- typedef ::IHistogram * ( *readHistogram_function_type )( ::std::string const & );
-
- IntensityDataIOFactory_exposer.def(
- "readHistogram"
- , readHistogram_function_type( &::IntensityDataIOFactory::readHistogram )
- , ( bp::arg("file_name") )
- , bp::return_value_policy< bp::manage_new_object >() );
-
- }
{ //::IntensityDataIOFactory::readIntensityData
typedef ::IHistogram * ( *readIntensityData_function_type )( ::std::string const & );
@@ -51,7 +40,8 @@ void register_IntensityDataIOFactory_class(){
"readIntensityData"
, readIntensityData_function_type( &::IntensityDataIOFactory::readIntensityData )
, ( bp::arg("file_name") )
- , bp::return_value_policy< bp::manage_new_object >() );
+ , bp::return_value_policy< bp::manage_new_object >()
+ , "Reads file and returns newly created Histogram object." );
}
{ //::IntensityDataIOFactory::readOutputData
@@ -62,17 +52,8 @@ void register_IntensityDataIOFactory_class(){
"readOutputData"
, readOutputData_function_type( &::IntensityDataIOFactory::readOutputData )
, ( bp::arg("file_name") )
- , bp::return_value_policy< bp::manage_new_object >() );
-
- }
- { //::IntensityDataIOFactory::writeHistogram
-
- typedef void ( *writeHistogram_function_type )( ::IHistogram const &,::std::string const & );
-
- IntensityDataIOFactory_exposer.def(
- "writeHistogram"
- , writeHistogram_function_type( &::IntensityDataIOFactory::writeHistogram )
- , ( bp::arg("histogram"), bp::arg("file_name") ) );
+ , bp::return_value_policy< bp::manage_new_object >()
+ , "Reads file and returns newly created OutputData object." );
}
{ //::IntensityDataIOFactory::writeIntensityData
@@ -82,7 +63,8 @@ void register_IntensityDataIOFactory_class(){
IntensityDataIOFactory_exposer.def(
"writeIntensityData"
, writeIntensityData_function_type( &::IntensityDataIOFactory::writeIntensityData )
- , ( bp::arg("histogram"), bp::arg("file_name") ) );
+ , ( bp::arg("histogram"), bp::arg("file_name") )
+ , "Writes histogram in file." );
}
{ //::IntensityDataIOFactory::writeOutputData
@@ -92,13 +74,12 @@ void register_IntensityDataIOFactory_class(){
IntensityDataIOFactory_exposer.def(
"writeOutputData"
, writeOutputData_function_type( &::IntensityDataIOFactory::writeOutputData )
- , ( bp::arg("data"), bp::arg("file_name") ) );
+ , ( bp::arg("data"), bp::arg("file_name") )
+ , "Writes OutputData in file." );
}
- IntensityDataIOFactory_exposer.staticmethod( "readHistogram" );
IntensityDataIOFactory_exposer.staticmethod( "readIntensityData" );
IntensityDataIOFactory_exposer.staticmethod( "readOutputData" );
- IntensityDataIOFactory_exposer.staticmethod( "writeHistogram" );
IntensityDataIOFactory_exposer.staticmethod( "writeIntensityData" );
IntensityDataIOFactory_exposer.staticmethod( "writeOutputData" );
}
diff --git a/Doc/Doxygen/defgroups.doc b/Doc/Doxygen/defgroups.doc
index 134973e722b..7afb0a16c54 100644
--- a/Doc/Doxygen/defgroups.doc
+++ b/Doc/Doxygen/defgroups.doc
@@ -51,7 +51,13 @@
@brief Different tools.
\defgroup tools_internal
-@brief More different tools.
+@brief Tools internal classes.
+
+\defgroup input_output Input and output
+@brief Various routines for input/output.
+
+\defgroup input_output_internal
+@brief Input/output internal classes.
*/
diff --git a/Doc/Doxygen/userapi.doc b/Doc/Doxygen/userapi.doc
index daf004d227d..7ccd006fe41 100644
--- a/Doc/Doxygen/userapi.doc
+++ b/Doc/Doxygen/userapi.doc
@@ -18,6 +18,8 @@ List of implemented interference functions
Additional routines
<li> \ref tools "Tools" <BR>
Different tools mainly to deal with intensity data
+<li> \ref input_output "Input and output" <BR>
+Various routines to write intensity data on disk and to import user data.
<li> \ref fitting "Fitting" <BR>
Fitting routines
</ul>
@@ -32,6 +34,7 @@ Here is a list of additional classes from internal API.
<li> \ref interference_internal "Interference functions (internal)"
<li> \ref algorithms_internal "Algorithms (internal)" <BR>
<li> \ref tools_internal "Tools (internal)" <BR>
+<li> \ref input_output_internal "Input/output (internal)" <BR>
<li> \ref fitting_internal "Fitting (internal)" <BR>
</ul>
diff --git a/Examples/python/utils/plot_intensity_data_diff.py b/Examples/python/utils/plot_intensity_data_diff.py
index 871c9daf2e4..9cdb91b59fa 100644
--- a/Examples/python/utils/plot_intensity_data_diff.py
+++ b/Examples/python/utils/plot_intensity_data_diff.py
@@ -4,27 +4,27 @@
import numpy
import matplotlib
-import pylab
+from matplotlib import pyplot as plt
from bornagain import *
def plot_intensity_data(ref, data):
- phi_min = rad2deg(ref.getAxis(0).getMin())
- phi_max = rad2deg(ref.getAxis(0).getMax())
- alpha_min = rad2deg(ref.getAxis(1).getMin())
- alpha_max = rad2deg(ref.getAxis(1).getMax())
- im = pylab.imshow(numpy.rot90(data, 1), norm=matplotlib.colors.LogNorm(),
- extent=[phi_min, phi_max, alpha_min, alpha_max])
- cb = pylab.colorbar(im)
+ im = plt.imshow(data,
+ norm=matplotlib.colors.LogNorm(),
+ extent=[ref.getXmin()/deg, ref.getXmax()/deg, ref.getYmin()/deg, ref.getYmax()/deg],
+ aspect='auto')
+
+ cb = plt.colorbar(im)
cb.set_label(r'Intensity (arb. u.)', size=16)
- pylab.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- pylab.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- pylab.show()
+ plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
+ plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
+ plt.show()
if __name__ == '__main__':
if len(sys.argv)!=3:
exit("Usage: python plot_intensity_data_diff.py intensity_reference.int.gz intensity_other.int.gz")
+ print "xxx"
intensity_ref = IntensityDataIOFactory.readIntensityData(sys.argv[1])
intensity_other = IntensityDataIOFactory.readIntensityData(sys.argv[2])
data = numpy.abs((intensity_ref.getArray() - intensity_other.getArray())/intensity_ref.getArray())
diff --git a/dev-tools/python-bindings/settings_core.py b/dev-tools/python-bindings/settings_core.py
index 1e4ea74184d..319a0650af2 100644
--- a/dev-tools/python-bindings/settings_core.py
+++ b/dev-tools/python-bindings/settings_core.py
@@ -410,7 +410,7 @@ def ManualClassTunings(mb):
cl = mb.class_("IntensityDataIOFactory")
cl.member_function("readOutputData").call_policies = call_policies.return_value_policy(call_policies.manage_new_object)
- cl.member_function("readHistogram").call_policies = call_policies.return_value_policy(call_policies.manage_new_object)
+ # cl.member_function("readHistogram").call_policies = call_policies.return_value_policy(call_policies.manage_new_object)
cl.member_function("readIntensityData").call_policies = call_policies.return_value_policy(call_policies.manage_new_object)
--
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