From 9cdb0e76571ae8827f20bbf618fd5dd5a1a16866 Mon Sep 17 00:00:00 2001
From: Manuel Guenther <manuel.guenther@idiap.ch>
Date: Wed, 13 Aug 2014 17:13:50 +0200
Subject: [PATCH] Reverted some modifications for which we now found a better
solution.
---
bob/io/base/bobskin.cpp | 121 +++++--
bob/io/base/bobskin.h | 17 +-
bob/io/base/codec.cpp | 3 +-
bob/io/base/{csv.cpp => cpp/CSVFile.cpp} | 90 +++--
bob/io/base/cpp/CodecRegistry.cpp | 22 +-
bob/io/base/cpp/File.cpp | 10 +
.../{hdf5plugin.cpp => cpp/HDF5ArrayFile.cpp} | 68 +++-
bob/io/base/cpp/HDF5Attribute.cpp | 22 +-
bob/io/base/cpp/HDF5Dataset.cpp | 25 +-
bob/io/base/cpp/HDF5File.cpp | 4 +-
bob/io/base/cpp/HDF5Group.cpp | 15 +-
bob/io/base/cpp/HDF5Types.cpp | 114 +++----
bob/io/base/cpp/HDF5Utils.cpp | 15 +-
bob/io/base/{torch3.cpp => cpp/T3File.cpp} | 113 ++++---
.../{tensor.cpp => cpp/TensorArrayFile.cpp} | 58 +++-
bob/io/base/cpp/TensorFile.cpp | 31 +-
bob/io/base/cpp/TensorFile.h | 19 +-
bob/io/base/cpp/TensorFileHeader.cpp | 67 ++--
bob/io/base/cpp/TensorFileHeader.h | 11 +-
bob/io/base/cpp/array.cpp | 134 ++++++++
bob/io/base/cpp/array_type.cpp | 126 +++++++
bob/io/base/cpp/blitz_array.cpp | 69 ++--
bob/io/base/cpp/reorder.cpp | 288 ++++++++++++++++
bob/io/base/{ => cpp}/utils.cpp | 29 +-
bob/io/base/file.cpp | 87 ++++-
bob/io/base/hdf5.cpp | 1 -
.../bob.io.base}/CodecRegistry.h | 12 +-
bob/io/base/include/bob.io.base/File.h | 39 ++-
bob/io/base/include/bob.io.base/HDF5Dataset.h | 1 -
bob/io/base/include/bob.io.base/HDF5File.h | 3 +-
bob/io/base/include/bob.io.base/HDF5Group.h | 8 +-
bob/io/base/include/bob.io.base/HDF5Types.h | 26 +-
bob/io/base/include/bob.io.base/HDF5Utils.h | 4 +-
bob/io/base/include/bob.io.base/api.h | 306 ++---------------
bob/io/base/include/bob.io.base/array.h | 173 +++++++++-
bob/io/base/include/bob.io.base/array_type.h | 162 +++++++++
bob/io/base/include/bob.io.base/array_utils.h | 50 ++-
bob/io/base/include/bob.io.base/blitz_array.h | 43 ++-
bob/io/base/include/bob.io.base/reorder.h | 94 ++++++
bob/io/base/include/bob.io.base/utils.h | 105 ++++++
bob/io/base/main.cpp | 114 +------
bob/io/base/plugin.h | 39 ---
bob/io/base/reorder.cpp | 317 ------------------
bob/io/base/typeinfo.cpp | 251 --------------
setup.py | 31 +-
45 files changed, 1855 insertions(+), 1482 deletions(-)
rename bob/io/base/{csv.cpp => cpp/CSVFile.cpp} (73%)
create mode 100644 bob/io/base/cpp/File.cpp
rename bob/io/base/{hdf5plugin.cpp => cpp/HDF5ArrayFile.cpp} (70%)
rename bob/io/base/{torch3.cpp => cpp/T3File.cpp} (68%)
rename bob/io/base/{tensor.cpp => cpp/TensorArrayFile.cpp} (56%)
create mode 100644 bob/io/base/cpp/array.cpp
create mode 100644 bob/io/base/cpp/array_type.cpp
create mode 100644 bob/io/base/cpp/reorder.cpp
rename bob/io/base/{ => cpp}/utils.cpp (52%)
rename bob/io/base/{cpp => include/bob.io.base}/CodecRegistry.h (86%)
create mode 100644 bob/io/base/include/bob.io.base/array_type.h
create mode 100644 bob/io/base/include/bob.io.base/reorder.h
create mode 100644 bob/io/base/include/bob.io.base/utils.h
delete mode 100644 bob/io/base/plugin.h
delete mode 100644 bob/io/base/reorder.cpp
delete mode 100644 bob/io/base/typeinfo.cpp
diff --git a/bob/io/base/bobskin.cpp b/bob/io/base/bobskin.cpp
index 8a23c66..494bdaf 100644
--- a/bob/io/base/bobskin.cpp
+++ b/bob/io/base/bobskin.cpp
@@ -5,46 +5,129 @@
* @brief Implementation of our bobskin class
*/
-#define BOB_IO_BASE_MODULE
#include "bobskin.h"
#include <stdexcept>
-bobskin::bobskin(PyObject* array, int dtype) {
+bobskin::bobskin(PyObject* array, bob::io::base::array::ElementType eltype) {
if (!PyArray_CheckExact(array)) {
PyErr_SetString(PyExc_TypeError, "input object to bobskin constructor is not (exactly) a numpy.ndarray");
throw std::runtime_error("error is already set");
}
- if (!BobIoTypeinfo_SignedSetWithStrides(&m_type, dtype,
- PyArray_NDIM((PyArrayObject*)array),
- PyArray_DIMS((PyArrayObject*)array),
- PyArray_STRIDES((PyArrayObject*)array))) {
- throw std::runtime_error("error is already set");
- }
+ m_type.set<npy_intp>(eltype, PyArray_NDIM((PyArrayObject*)array),
+ PyArray_DIMS((PyArrayObject*)array),
+ PyArray_STRIDES((PyArrayObject*)array));
m_ptr = PyArray_DATA((PyArrayObject*)array);
}
-bobskin::bobskin(PyArrayObject* array, int dtype) {
+bobskin::bobskin(PyArrayObject* array, bob::io::base::array::ElementType eltype) {
- if (!BobIoTypeinfo_SignedSetWithStrides(&m_type, dtype,
- PyArray_NDIM((PyArrayObject*)array),
- PyArray_DIMS((PyArrayObject*)array),
- PyArray_STRIDES((PyArrayObject*)array))) {
- throw std::runtime_error("error is already set");
- }
+ m_type.set<npy_intp>(eltype, PyArray_NDIM((PyArrayObject*)array),
+ PyArray_DIMS((PyArrayObject*)array),
+ PyArray_STRIDES((PyArrayObject*)array));
m_ptr = PyArray_DATA((PyArrayObject*)array);
}
+static bob::io::base::array::ElementType signed_integer_type(int bits) {
+ switch(bits) {
+ case 8:
+ return bob::io::base::array::t_int8;
+ case 16:
+ return bob::io::base::array::t_int16;
+ case 32:
+ return bob::io::base::array::t_int32;
+ case 64:
+ return bob::io::base::array::t_int64;
+ default:
+ PyErr_Format(PyExc_TypeError, "unsupported signed integer element type with %d bits", bits);
+ }
+ return bob::io::base::array::t_unknown;
+}
+
+static bob::io::base::array::ElementType unsigned_integer_type(int bits) {
+ switch(bits) {
+ case 8:
+ return bob::io::base::array::t_uint8;
+ case 16:
+ return bob::io::base::array::t_uint16;
+ case 32:
+ return bob::io::base::array::t_uint32;
+ case 64:
+ return bob::io::base::array::t_uint64;
+ default:
+ PyErr_Format(PyExc_TypeError, "unsupported unsigned signed integer element type with %d bits", bits);
+ }
+ return bob::io::base::array::t_unknown;
+}
+
+static bob::io::base::array::ElementType num_to_type (int num) {
+ switch(num) {
+ case NPY_BOOL:
+ return bob::io::base::array::t_bool;
+
+ //signed integers
+ case NPY_BYTE:
+ return signed_integer_type(NPY_BITSOF_CHAR);
+ case NPY_SHORT:
+ return signed_integer_type(NPY_BITSOF_SHORT);
+ case NPY_INT:
+ return signed_integer_type(NPY_BITSOF_INT);
+ case NPY_LONG:
+ return signed_integer_type(NPY_BITSOF_LONG);
+ case NPY_LONGLONG:
+ return signed_integer_type(NPY_BITSOF_LONGLONG);
+
+ //unsigned integers
+ case NPY_UBYTE:
+ return unsigned_integer_type(NPY_BITSOF_CHAR);
+ case NPY_USHORT:
+ return unsigned_integer_type(NPY_BITSOF_SHORT);
+ case NPY_UINT:
+ return unsigned_integer_type(NPY_BITSOF_INT);
+ case NPY_ULONG:
+ return unsigned_integer_type(NPY_BITSOF_LONG);
+ case NPY_ULONGLONG:
+ return unsigned_integer_type(NPY_BITSOF_LONGLONG);
+
+ //floats
+ case NPY_FLOAT32:
+ return bob::io::base::array::t_float32;
+ case NPY_FLOAT64:
+ return bob::io::base::array::t_float64;
+#ifdef NPY_FLOAT128
+ case NPY_FLOAT128:
+ return bob::io::base::array::t_float128;
+#endif
+
+ //complex
+ case NPY_COMPLEX64:
+ return bob::io::base::array::t_complex64;
+ case NPY_COMPLEX128:
+ return bob::io::base::array::t_complex128;
+#ifdef NPY_COMPLEX256
+ case NPY_COMPLEX256:
+ return bob::io::base::array::t_complex256;
+#endif
+
+ default:
+ PyErr_Format(PyExc_TypeError, "unsupported NumPy element type (%d)", num);
+ }
+
+ return bob::io::base::array::t_unknown;
+}
+
bobskin::bobskin(PyBlitzArrayObject* array) {
- if (!BobIoTypeinfo_SignedSetWithStrides(&m_type, array->type_num,
- array->ndim, array->shape, array->stride)) {
+ bob::io::base::array::ElementType eltype = num_to_type(array->type_num);
+ if (eltype == bob::io::base::array::t_unknown) {
throw std::runtime_error("error is already set");
}
+ m_type.set<Py_ssize_t>(num_to_type(array->type_num), array->ndim,
+ array->shape, array->stride);
m_ptr = array->data;
}
@@ -60,8 +143,8 @@ void bobskin::set(boost::shared_ptr<interface>) {
throw std::runtime_error("error is already set");
}
-void bobskin::set (const BobIoTypeinfo&) {
- PyErr_SetString(PyExc_NotImplementedError, "setting C++ bobskin with (const type-information&) implemented - DEBUG ME!");
+void bobskin::set (const bob::io::base::array::typeinfo&) {
+ PyErr_SetString(PyExc_NotImplementedError, "setting C++ bobskin with (const typeinfo&) implemented - DEBUG ME!");
throw std::runtime_error("error is already set");
}
diff --git a/bob/io/base/bobskin.h b/bob/io/base/bobskin.h
index a503562..7e69132 100644
--- a/bob/io/base/bobskin.h
+++ b/bob/io/base/bobskin.h
@@ -10,8 +10,13 @@
#define PYTHON_BOB_IO_BOBSKIN_H
#include <Python.h>
+
#include <bob.io.base/array.h>
-#include <bob.blitz/cppapi.h>
+
+extern "C" {
+#include <bob.blitz/capi.h>
+}
+
/**
* Wraps a PyArrayObject such that we can access it from bob::io
@@ -23,12 +28,12 @@ class bobskin: public bob::io::base::array::interface {
/**
* @brief Builds a new skin from an array like object
*/
- bobskin(PyObject* array, int dtype);
+ bobskin(PyObject* array, bob::io::base::array::ElementType eltype);
/**
* @brief Builds a new skin from a numpy array object
*/
- bobskin(PyArrayObject* array, int dtype);
+ bobskin(PyArrayObject* array, bob::io::base::array::ElementType eltype);
/**
* @brief Builds a new skin around a blitz array object
@@ -55,12 +60,12 @@ class bobskin: public bob::io::base::array::interface {
* @brief Re-allocates this interface taking into consideration new
* requirements. The internal memory should be considered uninitialized.
*/
- virtual void set (const BobIoTypeinfo& req);
+ virtual void set (const bob::io::base::array::typeinfo& req);
/**
* @brief Type information for this interface.
*/
- virtual const BobIoTypeinfo& type() const { return m_type; }
+ virtual const bob::io::base::array::typeinfo& type() const { return m_type; }
/**
* @brief Borrows a reference from the underlying memory. This means
@@ -80,7 +85,7 @@ class bobskin: public bob::io::base::array::interface {
private: //representation
- BobIoTypeinfo m_type; ///< type information
+ bob::io::base::array::typeinfo m_type; ///< type information
void* m_ptr; ///< pointer to the data
};
diff --git a/bob/io/base/codec.cpp b/bob/io/base/codec.cpp
index 767fd20..bfc3eb9 100644
--- a/bob/io/base/codec.cpp
+++ b/bob/io/base/codec.cpp
@@ -7,9 +7,8 @@
#define BOB_IO_BASE_MODULE
#include <bob.io.base/api.h>
-#include "cpp/CodecRegistry.h"
-int PyBobIoCodec_Register (const char* extension, const char* description, BobIoFileFactory factory) {
+int PyBobIoCodec_Register (const char* extension, const char* description, bob::io::base::file_factory_t factory) {
boost::shared_ptr<bob::io::base::CodecRegistry> instance =
bob::io::base::CodecRegistry::instance();
diff --git a/bob/io/base/csv.cpp b/bob/io/base/cpp/CSVFile.cpp
similarity index 73%
rename from bob/io/base/csv.cpp
rename to bob/io/base/cpp/CSVFile.cpp
index 7932ad8..1200523 100644
--- a/bob/io/base/csv.cpp
+++ b/bob/io/base/cpp/CSVFile.cpp
@@ -8,10 +8,6 @@
* Copyright (C) Idiap Research Institute, Martigny, Switzerland
*/
-#define BOB_IO_BASE_MODULE
-#include <bob.io.base/api.h>
-#include <bob.io.base/File.h>
-
#include <sstream>
#include <fstream>
#include <string>
@@ -24,6 +20,8 @@
#include <boost/shared_array.hpp>
#include <boost/algorithm/string.hpp>
+#include <bob.io.base/CodecRegistry.h>
+
typedef boost::tokenizer<boost::escaped_list_separator<char> > Tokenizer;
class CSVFile: public bob::io::base::File {
@@ -64,16 +62,16 @@ class CSVFile: public bob::io::base::File {
return;
}
- m_arrayset_type.dtype = NPY_FLOAT64;
+ m_arrayset_type.dtype = bob::io::base::array::t_float64;
m_arrayset_type.nd = 1;
m_arrayset_type.shape[0] = entries;
- BobIoTypeinfo_UpdateStrides(&m_arrayset_type);
+ m_arrayset_type.update_strides();
m_array_type = m_arrayset_type;
m_array_type.nd = 2;
m_array_type.shape[0] = m_pos.size();
m_array_type.shape[1] = entries;
- BobIoTypeinfo_UpdateStrides(&m_array_type);
+ m_array_type.update_strides();
}
CSVFile(const char* path, char mode):
@@ -118,11 +116,11 @@ class CSVFile: public bob::io::base::File {
return m_filename.c_str();
}
- virtual const BobIoTypeinfo& type() const {
+ virtual const bob::io::base::array::typeinfo& type() const {
return m_arrayset_type;
}
- virtual const BobIoTypeinfo& type_all() const {
+ virtual const bob::io::base::array::typeinfo& type_all() const {
return m_array_type;
}
@@ -138,7 +136,7 @@ class CSVFile: public bob::io::base::File {
if (m_newfile)
throw std::runtime_error("uninitialized CSV file cannot be read");
- if (!BobIoTypeinfo_IsCompatible(&buffer.type(), &m_array_type)) buffer.set(m_array_type);
+ if (!buffer.type().is_compatible(m_array_type)) buffer.set(m_array_type);
//read contents
std::string line;
@@ -158,7 +156,7 @@ class CSVFile: public bob::io::base::File {
if (m_newfile)
throw std::runtime_error("uninitialized CSV file cannot be read");
- if (!BobIoTypeinfo_IsCompatible(&buffer.type(), &m_arrayset_type))
+ if (!buffer.type().is_compatible(m_arrayset_type))
buffer.set(m_arrayset_type);
if (index >= m_pos.size()) {
@@ -186,12 +184,12 @@ class CSVFile: public bob::io::base::File {
virtual size_t append (const bob::io::base::array::interface& buffer) {
- const BobIoTypeinfo& type = buffer.type();
+ const bob::io::base::array::typeinfo& type = buffer.type();
if (m_newfile) {
- if (type.nd != 1 || type.dtype != NPY_FLOAT64) {
+ if (type.nd != 1 || type.dtype != bob::io::base::array::t_float64) {
boost::format m("cannot append %s to file '%s' - CSV files only accept 1D double precision float arrays");
- m % BobIoTypeinfo_Str(&type) % m_filename;
+ m % type.str() % m_filename;
throw std::runtime_error(m.str());
}
m_pos.clear();
@@ -203,9 +201,9 @@ class CSVFile: public bob::io::base::File {
else {
//check compatibility
- if (!BobIoTypeinfo_IsCompatible(&m_arrayset_type, &buffer.type())) {
+ if (!m_arrayset_type.is_compatible(buffer.type())) {
boost::format m("CSV file '%s' only accepts arrays of type %s");
- m % m_filename % BobIoTypeinfo_Str(&m_arrayset_type);
+ m % m_filename % m_arrayset_type.str();
throw std::runtime_error(m.str());
}
@@ -217,19 +215,19 @@ class CSVFile: public bob::io::base::File {
for (size_t k=1; k<type.shape[0]; ++k) m_file << *(p++) << ",";
m_file << *(p++);
m_array_type.shape[0] = m_pos.size();
- BobIoTypeinfo_UpdateStrides(&m_array_type);
+ m_array_type.update_strides();
return (m_pos.size()-1);
}
virtual void write (const bob::io::base::array::interface& buffer) {
- const BobIoTypeinfo& type = buffer.type();
+ const bob::io::base::array::typeinfo& type = buffer.type();
if (m_newfile) {
- if (type.nd != 2 || type.dtype != NPY_FLOAT64) {
+ if (type.nd != 2 || type.dtype != bob::io::base::array::t_float64) {
boost::format m("cannot write %s to file '%s' - CSV files only accept a single 2D double precision float array as input");
- m % BobIoTypeinfo_Str(&type) % m_filename;
+ m % type.str() % m_filename;
throw std::runtime_error(m.str());
}
const double* p = static_cast<const double*>(buffer.ptr());
@@ -243,7 +241,7 @@ class CSVFile: public bob::io::base::File {
m_arrayset_type = type;
m_arrayset_type.nd = 1;
m_arrayset_type.shape[0] = type.shape[1];
- BobIoTypeinfo_UpdateStrides(&m_arrayset_type);
+ m_arrayset_type.update_strides();
m_array_type = type;
m_newfile = false;
return;
@@ -258,8 +256,8 @@ class CSVFile: public bob::io::base::File {
std::fstream m_file;
std::string m_filename;
bool m_newfile;
- BobIoTypeinfo m_array_type;
- BobIoTypeinfo m_arrayset_type;
+ bob::io::base::array::typeinfo m_array_type;
+ bob::io::base::array::typeinfo m_arrayset_type;
std::vector<std::streampos> m_pos; ///< dictionary of line starts
static std::string s_codecname;
@@ -269,10 +267,48 @@ class CSVFile: public bob::io::base::File {
std::string CSVFile::s_codecname = "bob.csv";
/**
- * Registration method: use an unique name. Copy the definition to "plugin.h"
- * and then call it on "main.cpp" to register the codec.
+ * From this point onwards we have the registration procedure. If you are
+ * looking at this file for a coding example, just follow the procedure bellow,
+ * minus local modifications you may need to apply.
+ */
+
+/**
+ * This defines the factory method F that can create codecs of this type.
+ *
+ * Here are the meanings of the mode flag that should be respected by your
+ * factory implementation:
+ *
+ * 'r': opens for reading only - no modifications can occur; it is an
+ * error to open a file that does not exist for read-only operations.
+ * 'w': opens for reading and writing, but truncates the file if it
+ * exists; it is not an error to open files that do not exist with
+ * this flag.
+ * 'a': opens for reading and writing - any type of modification can
+ * occur. If the file does not exist, this flag is effectively like
+ * 'w'.
+ *
+ * Returns a newly allocated File object that can read and write data to the
+ * file using a specific backend.
+ *
+ * @note: This method can be static.
*/
-boost::shared_ptr<bob::io::base::File>
- make_csv_file (const char* path, char mode) {
+static boost::shared_ptr<bob::io::base::File> make_file (const char* path, char mode) {
return boost::make_shared<CSVFile>(path, mode);
}
+
+/**
+ * Takes care of codec registration per se.
+ */
+static bool register_codec() {
+
+ boost::shared_ptr<bob::io::base::CodecRegistry> instance =
+ bob::io::base::CodecRegistry::instance();
+
+ instance->registerExtension(".csv", "Comma-Separated Values", &make_file);
+ instance->registerExtension(".txt", "Comma-Separated Values", &make_file);
+
+ return true;
+
+}
+
+static bool codec_registered = register_codec();
diff --git a/bob/io/base/cpp/CodecRegistry.cpp b/bob/io/base/cpp/CodecRegistry.cpp
index 483215e..229d580 100644
--- a/bob/io/base/cpp/CodecRegistry.cpp
+++ b/bob/io/base/cpp/CodecRegistry.cpp
@@ -7,16 +7,15 @@
* Copyright (C) Idiap Research Institute, Martigny, Switzerland
*/
-#define BOB_IO_BASE_MODULE
-#include <bob.core/logging.h>
-
-#include "CodecRegistry.h"
-
#include <vector>
#include <boost/filesystem.hpp>
#include <boost/format.hpp>
+#include <bob.io.base/CodecRegistry.h>
+
+#include <bob/core/logging.h>
+
boost::shared_ptr<bob::io::base::CodecRegistry> bob::io::base::CodecRegistry::instance() {
static boost::shared_ptr<bob::io::base::CodecRegistry> s_instance(new CodecRegistry());
return s_instance;
@@ -33,7 +32,7 @@ const char* bob::io::base::CodecRegistry::getDescription(const char* ext) {
return it->second.c_str();
}
-void bob::io::base::CodecRegistry::deregisterFactory(BobIoFileFactory factory) {
+void bob::io::base::CodecRegistry::deregisterFactory(bob::io::base::file_factory_t factory) {
std::vector<std::string> to_remove;
for (auto it = s_extension2codec.begin(); it != s_extension2codec.end(); ++it) {
@@ -48,7 +47,7 @@ void bob::io::base::CodecRegistry::deregisterFactory(BobIoFileFactory factory) {
}
void bob::io::base::CodecRegistry::registerExtension(const char* extension,
- const char* description, BobIoFileFactory codec) {
+ const char* description, bob::io::base::file_factory_t codec) {
auto it = s_extension2codec.find(extension);
@@ -59,8 +58,7 @@ void bob::io::base::CodecRegistry::registerExtension(const char* extension,
else if (!s_ignore) {
boost::format m("extension already registered: %s - ignoring second registration with description `%s'");
m % extension % description;
- auto& error_stream = PyBobCoreLogging_Error();
- error_stream << m.str() << std::endl;
+ bob::core::error << m.str() << std::endl;
throw std::runtime_error(m.str());
}
@@ -73,13 +71,13 @@ bool bob::io::base::CodecRegistry::isRegistered(const char* ext) {
return (s_extension2codec.find(lower_extension) != s_extension2codec.end());
}
-BobIoFileFactory bob::io::base::CodecRegistry::findByExtension (const char* ext) {
+bob::io::base::file_factory_t bob::io::base::CodecRegistry::findByExtension (const char* ext) {
std::string extension(ext);
std::string lower_extension = extension;
std::transform(extension.begin(), extension.end(), lower_extension.begin(), ::tolower);
- std::map<std::string, BobIoFileFactory>::iterator it =
+ std::map<std::string, bob::io::base::file_factory_t >::iterator it =
s_extension2codec.find(lower_extension);
if (it == s_extension2codec.end()) {
@@ -92,7 +90,7 @@ BobIoFileFactory bob::io::base::CodecRegistry::findByExtension (const char* ext)
}
-BobIoFileFactory bob::io::base::CodecRegistry::findByFilenameExtension
+bob::io::base::file_factory_t bob::io::base::CodecRegistry::findByFilenameExtension
(const char* filename) {
return findByExtension(boost::filesystem::path(filename).extension().c_str());
diff --git a/bob/io/base/cpp/File.cpp b/bob/io/base/cpp/File.cpp
new file mode 100644
index 0000000..bbdfedf
--- /dev/null
+++ b/bob/io/base/cpp/File.cpp
@@ -0,0 +1,10 @@
+/**
+ * @date Tue Oct 25 23:25:46 2011 +0200
+ * @author Andre Anjos <andre.anjos@idiap.ch>
+ *
+ * Copyright (C) Idiap Research Institute, Martigny, Switzerland
+ */
+
+#include <bob.io.base/File.h>
+
+bob::io::base::File::~File() { }
diff --git a/bob/io/base/hdf5plugin.cpp b/bob/io/base/cpp/HDF5ArrayFile.cpp
similarity index 70%
rename from bob/io/base/hdf5plugin.cpp
rename to bob/io/base/cpp/HDF5ArrayFile.cpp
index 5982adf..8a9aa97 100644
--- a/bob/io/base/hdf5plugin.cpp
+++ b/bob/io/base/cpp/HDF5ArrayFile.cpp
@@ -7,15 +7,13 @@
* Copyright (C) Idiap Research Institute, Martigny, Switzerland
*/
-#define BOB_IO_BASE_MODULE
-#include <bob.io.base/api.h>
-#include <bob.io.base/File.h>
-#include <bob.io.base/HDF5File.h>
-
#include <boost/make_shared.hpp>
#include <boost/filesystem.hpp>
#include <boost/format.hpp>
+#include <bob.io.base/CodecRegistry.h>
+#include <bob.io.base/HDF5File.h>
+
/**
* Read and write arrays in HDF5 format
*/
@@ -67,11 +65,11 @@ class HDF5ArrayFile: public bob::io::base::File {
return m_filename.c_str();
}
- virtual const BobIoTypeinfo& type_all () const {
+ virtual const bob::io::base::array::typeinfo& type_all () const {
return m_type_array;
}
- virtual const BobIoTypeinfo& type () const {
+ virtual const bob::io::base::array::typeinfo& type () const {
return m_type_arrayset;
}
@@ -91,7 +89,7 @@ class HDF5ArrayFile: public bob::io::base::File {
throw std::runtime_error(f.str());
}
- if(!BobIoTypeinfo_IsCompatible(&buffer.type(), &m_type_array)) buffer.set(m_type_array);
+ if(!buffer.type().is_compatible(m_type_array)) buffer.set(m_type_array);
m_file.read_buffer(m_path, 0, buffer.type(), buffer.ptr());
}
@@ -104,7 +102,7 @@ class HDF5ArrayFile: public bob::io::base::File {
throw std::runtime_error(f.str());
}
- if(!BobIoTypeinfo_IsCompatible(&buffer.type(), &m_type_arrayset)) buffer.set(m_type_arrayset);
+ if(!buffer.type().is_compatible(m_type_arrayset)) buffer.set(m_type_arrayset);
m_file.read_buffer(m_path, index, buffer.type(), buffer.ptr());
}
@@ -154,8 +152,8 @@ class HDF5ArrayFile: public bob::io::base::File {
bob::io::base::HDF5File m_file;
std::string m_filename;
- BobIoTypeinfo m_type_array; ///< type for reading all data at once
- BobIoTypeinfo m_type_arrayset; ///< type for reading data by sub-arrays
+ bob::io::base::array::typeinfo m_type_array; ///< type for reading all data at once
+ bob::io::base::array::typeinfo m_type_arrayset; ///< type for reading data by sub-arrays
size_t m_size_arrayset; ///< number of arrays in arrayset mode
std::string m_path; ///< default path to use
bool m_newfile; ///< path check optimization
@@ -167,11 +165,32 @@ class HDF5ArrayFile: public bob::io::base::File {
std::string HDF5ArrayFile::s_codecname = "bob.hdf5";
/**
- * Registration method: use an unique name. Copy the definition to "plugin.h"
- * and then call it on "main.cpp" to register the codec.
+ * From this point onwards we have the registration procedure. If you are
+ * looking at this file for a coding example, just follow the procedure bellow,
+ * minus local modifications you may need to apply.
+ */
+
+/**
+ * This defines the factory method F that can create codecs of this type.
+ *
+ * Here are the meanings of the mode flag that should be respected by your
+ * factory implementation:
+ *
+ * 'r': opens for reading only - no modifications can occur; it is an
+ * error to open a file that does not exist for read-only operations.
+ * 'w': opens for reading and writing, but truncates the file if it
+ * exists; it is not an error to open files that do not exist with
+ * this flag.
+ * 'a': opens for reading and writing - any type of modification can
+ * occur. If the file does not exist, this flag is effectively like
+ * 'w'.
+ *
+ * Returns a newly allocated File object that can read and write data to the
+ * file using a specific backend.
+ *
+ * @note: This method can be static.
*/
-boost::shared_ptr<bob::io::base::File>
- make_hdf5_file (const char* path, char mode) {
+static boost::shared_ptr<bob::io::base::File> make_file (const char* path, char mode) {
bob::io::base::HDF5File::mode_t h5mode;
if (mode == 'r') h5mode = bob::io::base::HDF5File::in;
@@ -182,3 +201,22 @@ boost::shared_ptr<bob::io::base::File>
return boost::make_shared<HDF5ArrayFile>(path, h5mode);
}
+
+/**
+ * Takes care of codec registration per se.
+ */
+static bool register_codec() {
+ static const char* description = "Hierarchical Data Format v5 (default)";
+
+ boost::shared_ptr<bob::io::base::CodecRegistry> instance =
+ bob::io::base::CodecRegistry::instance();
+
+ instance->registerExtension(".h5", description, &make_file);
+ instance->registerExtension(".hdf5", description, &make_file);
+ instance->registerExtension(".hdf", description, &make_file);
+
+ return true;
+
+}
+
+static bool codec_registered = register_codec();
diff --git a/bob/io/base/cpp/HDF5Attribute.cpp b/bob/io/base/cpp/HDF5Attribute.cpp
index 2d42802..e701ace 100644
--- a/bob/io/base/cpp/HDF5Attribute.cpp
+++ b/bob/io/base/cpp/HDF5Attribute.cpp
@@ -7,12 +7,11 @@
* Copyright (C) Idiap Research Institute, Martigny, Switzerland
*/
-#define BOB_IO_BASE_MODULE
-#include <bob.core/logging.h>
+#include <boost/format.hpp>
-#include <bob.io.base/HDF5Attribute.h>
+#include <bob/core/logging.h>
-#include <boost/format.hpp>
+#include <bob.io.base/HDF5Attribute.h>
static std::runtime_error status_error(const char* f, herr_t s) {
boost::format m("call to HDF5 C-function %s() returned error %d. HDF5 error statck follows:\n%s");
@@ -32,9 +31,8 @@ static void delete_h5dataspace (hid_t* p) {
if (*p >= 0) {
herr_t err = H5Sclose(*p);
if (err < 0) {
- auto& error_stream = PyBobCoreLogging_Error();
- error_stream << "H5Sclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
- error_stream << bob::io::base::format_hdf5_error() << std::endl;
+ bob::core::error << "H5Sclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
+ bob::core::error << bob::io::base::format_hdf5_error() << std::endl;
}
}
delete p;
@@ -64,9 +62,8 @@ static void delete_h5type (hid_t* p) {
if (*p >= 0) {
herr_t err = H5Tclose(*p);
if (err < 0) {
- auto& error_stream = PyBobCoreLogging_Error();
- error_stream << "H5Tclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
- error_stream << bob::io::base::format_hdf5_error() << std::endl;
+ bob::core::error << "H5Tclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
+ bob::core::error << bob::io::base::format_hdf5_error() << std::endl;
}
}
delete p;
@@ -102,9 +99,8 @@ static void delete_h5attribute (hid_t* p) {
if (*p >= 0) {
herr_t err = H5Aclose(*p);
if (err < 0) {
- auto& error_stream = PyBobCoreLogging_Error();
- error_stream << "H5Aclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
- error_stream << bob::io::base::format_hdf5_error() << std::endl;
+ bob::core::error << "H5Aclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
+ bob::core::error << bob::io::base::format_hdf5_error() << std::endl;
}
}
delete p;
diff --git a/bob/io/base/cpp/HDF5Dataset.cpp b/bob/io/base/cpp/HDF5Dataset.cpp
index 3e4b93d..59b2093 100644
--- a/bob/io/base/cpp/HDF5Dataset.cpp
+++ b/bob/io/base/cpp/HDF5Dataset.cpp
@@ -7,13 +7,12 @@
* Copyright (C) Idiap Research Institute, Martigny, Switzerland
*/
-#define BOB_IO_BASE_MODULE
-#include <bob.core/logging.h>
-
#include <boost/format.hpp>
#include <boost/make_shared.hpp>
#include <boost/shared_array.hpp>
+#include <bob/core/logging.h>
+
#include <bob.io.base/HDF5Utils.h>
#include <bob.io.base/HDF5Group.h>
#include <bob.io.base/HDF5Dataset.h>
@@ -31,9 +30,8 @@ static void delete_h5dataset (hid_t* p) {
if (*p >= 0) {
herr_t err = H5Dclose(*p);
if (err < 0) {
- auto& error_stream = PyBobCoreLogging_Error();
- error_stream << "H5Dclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
- error_stream << bob::io::base::format_hdf5_error() << std::endl;
+ bob::core::error << "H5Dclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
+ bob::core::error << bob::io::base::format_hdf5_error() << std::endl;
}
}
delete p;
@@ -63,9 +61,8 @@ static void delete_h5datatype (hid_t* p) {
if (*p >= 0) {
herr_t err = H5Tclose(*p);
if (err < 0) {
- auto& error_stream = PyBobCoreLogging_Error();
- error_stream << "H5Tclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
- error_stream << bob::io::base::format_hdf5_error() << std::endl;
+ bob::core::error << "H5Tclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
+ bob::core::error << bob::io::base::format_hdf5_error() << std::endl;
}
}
delete p;
@@ -89,9 +86,8 @@ static void delete_h5plist (hid_t* p) {
if (*p >= 0) {
herr_t err = H5Pclose(*p);
if (err < 0) {
- auto& error_stream = PyBobCoreLogging_Error();
- error_stream << "H5Pclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
- error_stream << bob::io::base::format_hdf5_error() << std::endl;
+ bob::core::error << "H5Pclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
+ bob::core::error << bob::io::base::format_hdf5_error() << std::endl;
}
}
delete p;
@@ -113,9 +109,8 @@ static void delete_h5dataspace (hid_t* p) {
if (*p >= 0) {
herr_t err = H5Sclose(*p);
if (err < 0) {
- auto& error_stream = PyBobCoreLogging_Error();
- error_stream << "H5Sclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
- error_stream << bob::io::base::format_hdf5_error() << std::endl;
+ bob::core::error << "H5Sclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
+ bob::core::error << bob::io::base::format_hdf5_error() << std::endl;
}
}
delete p;
diff --git a/bob/io/base/cpp/HDF5File.cpp b/bob/io/base/cpp/HDF5File.cpp
index 3f838b4..549069f 100644
--- a/bob/io/base/cpp/HDF5File.cpp
+++ b/bob/io/base/cpp/HDF5File.cpp
@@ -7,10 +7,10 @@
* Copyright (C) Idiap Research Institute, Martigny, Switzerland
*/
-#define BOB_IO_BASE_MODULE
-#include <bob.io.base/HDF5File.h>
#include <boost/format.hpp>
+#include <bob.io.base/HDF5File.h>
+
static unsigned int getH5Access (bob::io::base::HDF5File::mode_t v) {
switch(v) {
case 0: return H5F_ACC_RDONLY;
diff --git a/bob/io/base/cpp/HDF5Group.cpp b/bob/io/base/cpp/HDF5Group.cpp
index 486b7ea..aab9166 100644
--- a/bob/io/base/cpp/HDF5Group.cpp
+++ b/bob/io/base/cpp/HDF5Group.cpp
@@ -7,15 +7,14 @@
* Copyright (C) Idiap Research Institute, Martigny, Switzerland
*/
-#define BOB_IO_BASE_MODULE
-#include <bob.core/logging.h>
-
#include <boost/make_shared.hpp>
#include <boost/shared_array.hpp>
#include <boost/filesystem.hpp>
#include <boost/format.hpp>
#include <boost/algorithm/string.hpp>
+#include <bob/core/logging.h>
+
#include <bob.io.base/HDF5Group.h>
#include <bob.io.base/HDF5Utils.h>
@@ -26,9 +25,8 @@ static void delete_h5g (hid_t* p) {
if (*p >= 0) {
herr_t err = H5Gclose(*p);
if (err < 0) {
- auto& error_stream = PyBobCoreLogging_Error();
- error_stream << "H5Gclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
- error_stream << bob::io::base::format_hdf5_error() << std::endl;
+ bob::core::error << "H5Gclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
+ bob::core::error << bob::io::base::format_hdf5_error() << std::endl;
}
}
delete p;
@@ -313,9 +311,8 @@ static void delete_h5plist (hid_t* p) {
if (*p >= 0) {
herr_t err = H5Pclose(*p);
if (err < 0) {
- auto& error_stream = PyBobCoreLogging_Error();
- error_stream << "H5Pclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
- error_stream << bob::io::base::format_hdf5_error() << std::endl;
+ bob::core::error << "H5Pclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
+ bob::core::error << bob::io::base::format_hdf5_error() << std::endl;
}
}
delete p;
diff --git a/bob/io/base/cpp/HDF5Types.cpp b/bob/io/base/cpp/HDF5Types.cpp
index e628d52..16795bf 100644
--- a/bob/io/base/cpp/HDF5Types.cpp
+++ b/bob/io/base/cpp/HDF5Types.cpp
@@ -7,11 +7,8 @@
* Copyright (C) Idiap Research Institute, Martigny, Switzerland
*/
-#define BOB_IO_BASE_MODULE
-#include <bob.core/logging.h>
-
-#include <sstream>
#include <boost/format.hpp>
+#include <sstream>
#include <boost/make_shared.hpp>
/**
@@ -27,6 +24,8 @@
#warning Disabling MT locks because Boost < 1.35!
#endif
+#include <bob/core/logging.h>
+
#include <bob.io.base/HDF5Types.h>
const char* bob::io::base::stringize (hdf5type t) {
@@ -214,9 +213,8 @@ static void delete_h5datatype (hid_t* p) {
if (*p >= 0) {
herr_t err = H5Tclose(*p);
if (err < 0) {
- auto& error_stream = PyBobCoreLogging_Error();
- error_stream << "H5Tclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
- error_stream << bob::io::base::format_hdf5_error() << std::endl;
+ bob::core::error << "H5Tclose() exited with an error (" << err << "). The stack trace follows:" << std::endl;
+ bob::core::error << bob::io::base::format_hdf5_error() << std::endl;
}
}
delete p;
@@ -416,7 +414,7 @@ static bob::io::base::hdf5type get_datatype
throw std::runtime_error("cannot handle HDF5 datatype on file using one of the native types supported by this API");
}
-bool bob::io::base::HDF5Type::compatible (const BobIoTypeinfo& value) const
+bool bob::io::base::HDF5Type::compatible (const bob::io::base::array::typeinfo& value) const
{
return *this == HDF5Type(value);
}
@@ -620,9 +618,9 @@ bob::io::base::HDF5Type::HDF5Type(const std::string& value):
(const blitz::Array<T,N>& value): \
m_type(E), \
m_shape(value.shape()) { \
- if (N > BOB_BLITZ_MAXDIMS) {\
+ if (N > bob::io::base::array::N_MAX_DIMENSIONS_ARRAY) {\
boost::format m("you passed an array with %d dimensions, but this HDF5 API only supports arrays with up to %d dimensions"); \
- m % N % BOB_BLITZ_MAXDIMS; \
+ m % N % bob::io::base::array::N_MAX_DIMENSIONS_ARRAY; \
throw std::runtime_error(m.str()); \
} \
}
@@ -670,56 +668,53 @@ bob::io::base::HDF5Type::HDF5Type(bob::io::base::hdf5type type, const bob::io::b
{
}
-static bob::io::base::hdf5type array_to_hdf5 (int dtype) {
- switch(dtype) {
- case NPY_NOTYPE:
+static bob::io::base::hdf5type array_to_hdf5 (bob::io::base::array::ElementType eltype) {
+ switch(eltype) {
+ case bob::io::base::array::t_unknown:
return bob::io::base::unsupported;
- case NPY_BOOL:
+ case bob::io::base::array::t_bool:
return bob::io::base::b;
- case NPY_INT8:
+ case bob::io::base::array::t_int8:
return bob::io::base::i8;
- case NPY_INT16:
+ case bob::io::base::array::t_int16:
return bob::io::base::i16;
- case NPY_INT32:
+ case bob::io::base::array::t_int32:
return bob::io::base::i32;
- case NPY_INT64:
+ case bob::io::base::array::t_int64:
return bob::io::base::i64;
- case NPY_UINT8:
+ case bob::io::base::array::t_uint8:
return bob::io::base::u8;
- case NPY_UINT16:
+ case bob::io::base::array::t_uint16:
return bob::io::base::u16;
- case NPY_UINT32:
+ case bob::io::base::array::t_uint32:
return bob::io::base::u32;
- case NPY_UINT64:
+ case bob::io::base::array::t_uint64:
return bob::io::base::u64;
- case NPY_FLOAT32:
+ case bob::io::base::array::t_float32:
return bob::io::base::f32;
- case NPY_FLOAT64:
+ case bob::io::base::array::t_float64:
return bob::io::base::f64;
-# ifdef NPY_FLOAT128
- case NPY_FLOAT128:
+ case bob::io::base::array::t_float128:
return bob::io::base::f128;
-# endif
- case NPY_COMPLEX64:
+ case bob::io::base::array::t_complex64:
return bob::io::base::c64;
- case NPY_COMPLEX128:
+ case bob::io::base::array::t_complex128:
return bob::io::base::c128;
-# ifdef NPY_COMPLEX256
- case NPY_COMPLEX256:
+ case bob::io::base::array::t_complex256:
return bob::io::base::c256;
-# endif
}
throw std::runtime_error("unsupported dtype <=> hdf5 type conversion -- FIXME");
}
-bob::io::base::HDF5Type::HDF5Type(const BobIoTypeinfo& ti):
+bob::io::base::HDF5Type::HDF5Type(const bob::io::base::array::typeinfo& ti):
m_type(array_to_hdf5(ti.dtype)),
m_shape(ti.nd, ti.shape)
{
}
-bob::io::base::HDF5Type::HDF5Type(int dtype, const HDF5Shape& extents):
- m_type(array_to_hdf5(dtype)),
+bob::io::base::HDF5Type::HDF5Type(bob::io::base::array::ElementType eltype,
+ const HDF5Shape& extents):
+ m_type(array_to_hdf5(eltype)),
m_shape(extents)
{
}
@@ -769,63 +764,56 @@ std::string bob::io::base::HDF5Type::str() const {
return retval.str();
}
-int bob::io::base::HDF5Type::element_type() const {
-
+bob::io::base::array::ElementType bob::io::base::HDF5Type::element_type() const {
switch (m_type) {
case b:
- return NPY_BOOL;
+ return bob::io::base::array::t_bool;
case i8:
- return NPY_INT8;
+ return bob::io::base::array::t_int8;
case i16:
- return NPY_INT16;
+ return bob::io::base::array::t_int16;
case i32:
- return NPY_INT32;
+ return bob::io::base::array::t_int32;
case i64:
- return NPY_INT64;
+ return bob::io::base::array::t_int64;
case u8:
- return NPY_UINT8;
+ return bob::io::base::array::t_uint8;
case u16:
- return NPY_UINT16;
+ return bob::io::base::array::t_uint16;
case u32:
- return NPY_UINT32;
+ return bob::io::base::array::t_uint32;
case u64:
- return NPY_UINT64;
+ return bob::io::base::array::t_uint64;
case f32:
- return NPY_FLOAT32;
+ return bob::io::base::array::t_float32;
case f64:
- return NPY_FLOAT64;
-# ifdef NPY_FLOAT128
+ return bob::io::base::array::t_float64;
case f128:
- return NPY_FLOAT128;
-# endif
+ return bob::io::base::array::t_float128;
case c64:
- return NPY_COMPLEX64;
+ return bob::io::base::array::t_complex64;
case c128:
- return NPY_COMPLEX128;
-# ifdef NPY_COMPLEX256
+ return bob::io::base::array::t_complex128;
case c256:
- return NPY_COMPLEX256;
-# endif
+ return bob::io::base::array::t_complex256;
case s:
throw std::runtime_error("Cannot convert HDF5 string type to an element type to be used in blitz::Array's - FIXME: something is wrong in the logic");
default:
break;
}
-
- return NPY_NOTYPE;
-
+ return bob::io::base::array::t_unknown;
}
-void bob::io::base::HDF5Type::copy_to (BobIoTypeinfo& ti) const {
+void bob::io::base::HDF5Type::copy_to (bob::io::base::array::typeinfo& ti) const {
ti.dtype = element_type();
ti.nd = shape().n();
- if (ti.nd > (BOB_BLITZ_MAXDIMS+1)) {
+ if (ti.nd > (BOB_MAX_DIM+1)) {
boost::format f("HDF5 type has more (%d) than the allowed maximum number of dimensions (%d)");
- f % ti.nd % (BOB_BLITZ_MAXDIMS+1);
+ f % ti.nd % (BOB_MAX_DIM+1);
throw std::runtime_error(f.str());
}
for (size_t i=0; i<ti.nd; ++i) ti.shape[i] = shape()[i];
- BobIoTypeinfo_UpdateStrides(&ti);
+ ti.update_strides();
}
bob::io::base::HDF5Descriptor::HDF5Descriptor(const HDF5Type& type, size_t size,
diff --git a/bob/io/base/cpp/HDF5Utils.cpp b/bob/io/base/cpp/HDF5Utils.cpp
index f06bd11..b735be4 100644
--- a/bob/io/base/cpp/HDF5Utils.cpp
+++ b/bob/io/base/cpp/HDF5Utils.cpp
@@ -7,12 +7,11 @@
* Copyright (C) Idiap Research Institute, Martigny, Switzerland
*/
-#define BOB_IO_BASE_MODULE
-#include <bob.core/logging.h>
-
#include <boost/format.hpp>
#include <boost/make_shared.hpp>
+#include <bob/core/logging.h>
+
#include <bob.io.base/HDF5Utils.h>
/**
@@ -22,9 +21,8 @@ static void delete_h5file (hid_t* p) {
if (*p >= 0) {
herr_t err = H5Fclose(*p);
if (err < 0) {
- auto& error_stream = PyBobCoreLogging_Error();
- error_stream << "H5Fclose(hid=" << *p << ") exited with an error (" << err << "). The stack trace follows:" << std::endl;
- error_stream << bob::io::base::format_hdf5_error() << std::endl;
+ bob::core::error << "H5Fclose(hid=" << *p << ") exited with an error (" << err << "). The stack trace follows:" << std::endl;
+ bob::core::error << bob::io::base::format_hdf5_error() << std::endl;
}
}
delete p;
@@ -37,9 +35,8 @@ static void delete_h5p (hid_t* p) {
if (*p >= 0) {
herr_t err = H5Pclose(*p);
if (err < 0) {
- auto& error_stream = PyBobCoreLogging_Error();
- error_stream << "H5Pclose(hid=" << *p << ") exited with an error (" << err << "). The stack trace follows:" << std::endl;
- error_stream << bob::io::base::format_hdf5_error() << std::endl;
+ bob::core::error << "H5Pclose(hid=" << *p << ") exited with an error (" << err << "). The stack trace follows:" << std::endl;
+ bob::core::error << bob::io::base::format_hdf5_error() << std::endl;
return;
}
}
diff --git a/bob/io/base/torch3.cpp b/bob/io/base/cpp/T3File.cpp
similarity index 68%
rename from bob/io/base/torch3.cpp
rename to bob/io/base/cpp/T3File.cpp
index 5910da8..8380a62 100644
--- a/bob/io/base/torch3.cpp
+++ b/bob/io/base/cpp/T3File.cpp
@@ -18,11 +18,6 @@
* Copyright (C) Idiap Research Institute, Martigny, Switzerland
*/
-#define BOB_IO_BASE_MODULE
-#include <bob.io.base/api.h>
-#include <bob.io.base/File.h>
-#include <bob.io.base/blitz_array.h>
-
#include <fstream>
#include <boost/filesystem.hpp>
#include <boost/make_shared.hpp>
@@ -35,6 +30,9 @@
#include <bob.core/check.h>
+#include <bob.io.base/CodecRegistry.h>
+#include <bob.io.base/blitz_array.h>
+
static inline size_t get_filesize(const char* filename) {
struct stat filestatus;
stat(filename, &filestatus);
@@ -71,12 +69,12 @@ class T3File: public bob::io::base::File {
// are those floats or doubles?
if (fsize == (nsamples*framesize*sizeof(float))) {
- m_type_array.dtype = NPY_FLOAT32;
- m_type_arrayset.dtype = NPY_FLOAT32;
+ m_type_array.dtype = bob::io::base::array::t_float32;
+ m_type_arrayset.dtype = bob::io::base::array::t_float32;
}
else if (fsize == (nsamples*framesize*sizeof(double))) {
- m_type_array.dtype = NPY_FLOAT64;
- m_type_arrayset.dtype = NPY_FLOAT64;
+ m_type_array.dtype = bob::io::base::array::t_float64;
+ m_type_arrayset.dtype = bob::io::base::array::t_float64;
}
else {
boost::format s("Cannot read file '%s', mode = '%c': fsize (%d) != %d*%d*sizeof(float32) nor *sizeof(float64)");
@@ -85,8 +83,8 @@ class T3File: public bob::io::base::File {
}
size_t shape[2] = {nsamples, framesize};
- BobIoTypeinfo_Set(&m_type_array, m_type_array.dtype, 2, &shape[0]);
- BobIoTypeinfo_Set(&m_type_arrayset, m_type_arrayset.dtype, 1, &shape[1]);
+ m_type_array.set_shape<size_t>(2, &shape[0]);
+ m_type_arrayset.set_shape<size_t>(1, &shape[1]);
m_newfile = false;
}
@@ -98,11 +96,11 @@ class T3File: public bob::io::base::File {
return m_filename.c_str();
}
- virtual const BobIoTypeinfo& type_all () const {
+ virtual const bob::io::base::array::typeinfo& type_all () const {
return m_type_array;
}
- virtual const BobIoTypeinfo& type () const {
+ virtual const bob::io::base::array::typeinfo& type () const {
return m_type_arrayset;
}
@@ -122,14 +120,14 @@ class T3File: public bob::io::base::File {
throw std::runtime_error(f.str());
}
- if (!BobIoTypeinfo_IsCompatible(&buffer.type(), &m_type_array)) buffer.set(m_type_array);
+ if (!buffer.type().is_compatible(m_type_array)) buffer.set(m_type_array);
//open the file, now for reading the contents...
std::ifstream ifile(m_filename.c_str(), std::ios::binary|std::ios::in);
//skip the first 8 bytes, that contain the header that we already read
ifile.seekg(8, std::ios::beg);
- ifile.read(static_cast<char*>(buffer.ptr()), BobIoTypeinfo_BufferSize(&buffer.type()));
+ ifile.read(static_cast<char*>(buffer.ptr()), buffer.type().buffer_size());
}
@@ -141,26 +139,26 @@ class T3File: public bob::io::base::File {
throw std::runtime_error(f.str());
}
- const BobIoTypeinfo& type = buffer.type();
+ const bob::io::base::array::typeinfo& type = buffer.type();
- if (!BobIoTypeinfo_IsCompatible(&buffer.type(), &m_type_arrayset)) buffer.set(m_type_arrayset);
+ if (!buffer.type().is_compatible(m_type_arrayset)) buffer.set(m_type_arrayset);
//open the file, now for reading the contents...
std::ifstream ifile(m_filename.c_str(), std::ios::binary|std::ios::in);
//skip the first 8 bytes, that contain the header that we already read
- ifile.seekg(8 + (index*BobIoTypeinfo_BufferSize(&type)), std::ios::beg);
- ifile.read(static_cast<char*>(buffer.ptr()), BobIoTypeinfo_BufferSize(&type));
+ ifile.seekg(8 + (index*type.buffer_size()), std::ios::beg);
+ ifile.read(static_cast<char*>(buffer.ptr()), type.buffer_size());
}
virtual size_t append (const bob::io::base::array::interface& buffer) {
- const BobIoTypeinfo& info = buffer.type();
+ const bob::io::base::array::typeinfo& info = buffer.type();
- if (!m_newfile && !BobIoTypeinfo_IsCompatible(&info, &m_type_arrayset)) {
+ if (!m_newfile && !info.is_compatible(m_type_arrayset)) {
boost::format f("input buffer of type %s cannot be appended to already initialized torch3vision binary file of type %s");
- f % BobIoTypeinfo_Str(&info) % BobIoTypeinfo_Str(&m_type_arrayset);
+ f % info.str() % m_type_arrayset.str();
throw std::runtime_error(f.str());
}
@@ -170,15 +168,15 @@ class T3File: public bob::io::base::File {
//can only save uni-dimensional data, so throw if that is not the case
if (info.nd != 1) {
boost::format m("codec for torch3vision binary files can only save uni-dimensional data, but you passed: %s");
- m % BobIoTypeinfo_Str(&info);
+ m % info.str();
throw std::runtime_error(m.str());
}
//can only save float32 or float64, otherwise, throw.
- if ((info.dtype != NPY_FLOAT32) &&
- (info.dtype != NPY_FLOAT64)) {
+ if ((info.dtype != bob::io::base::array::t_float32) &&
+ (info.dtype != bob::io::base::array::t_float64)) {
boost::format f("cannot have T3 bindata files with type %s - only float32 or float64");
- f % PyBlitzArray_TypenumAsString(info.dtype);
+ f % bob::io::base::array::stringize(info.dtype);
throw std::runtime_error(f.str());
}
@@ -207,13 +205,13 @@ class T3File: public bob::io::base::File {
throw std::runtime_error(f.str());
}
- ofile.write(static_cast<const char*>(buffer.ptr()), BobIoTypeinfo_BufferSize(&info));
+ ofile.write(static_cast<const char*>(buffer.ptr()), info.buffer_size());
ofile.close();
//setup new type information
++m_length;
size_t shape[2] = {m_length, info.shape[0]};
- BobIoTypeinfo_Set(&m_type_array, m_type_array.dtype, 2, &shape[0]);
+ m_type_array.set_shape<size_t>(2, &shape[0]);
//update the header information on the file
ofile.open(m_filename.c_str(), std::ios::binary|std::ios::in|std::ios::out);
@@ -232,7 +230,7 @@ class T3File: public bob::io::base::File {
virtual void write (const bob::io::base::array::interface& buffer) {
m_newfile = true; //force file re-setting
- const BobIoTypeinfo& info = buffer.type();
+ const bob::io::base::array::typeinfo& info = buffer.type();
if (info.nd == 1) {//just do a normal append
append(buffer);
@@ -241,10 +239,10 @@ class T3File: public bob::io::base::File {
else if (info.nd == 2) { //append every array individually
const uint8_t* ptr = static_cast<const uint8_t*>(buffer.ptr());
- BobIoTypeinfo slice_info;
- BobIoTypeinfo_Set(&slice_info, info.dtype, 1, &info.shape[1]);
+ bob::io::base::array::typeinfo slice_info(info.dtype, static_cast<size_t>(1),
+ &info.shape[1]);
for (size_t k=0; k<info.shape[0]; ++k) {
- const void* slice_ptr=static_cast<const void*>(ptr+k*BobIoTypeinfo_BufferSize(&slice_info));
+ const void* slice_ptr=static_cast<const void*>(ptr+k*slice_info.buffer_size());
bob::io::base::array::blitz_array slice(const_cast<void*>(slice_ptr), slice_info);
append(slice);
}
@@ -253,7 +251,7 @@ class T3File: public bob::io::base::File {
else {
boost::format f("cannot do single write of torch3vision .bindata file with array with type '%s' - only supports 1D or 2D arrays of types float32 or float64");
- f % BobIoTypeinfo_Str(&info);
+ f % info.str();
throw std::runtime_error(f.str());
}
@@ -263,8 +261,8 @@ class T3File: public bob::io::base::File {
std::string m_filename;
bool m_newfile;
- BobIoTypeinfo m_type_array;
- BobIoTypeinfo m_type_arrayset;
+ bob::io::base::array::typeinfo m_type_array;
+ bob::io::base::array::typeinfo m_type_arrayset;
size_t m_length;
static std::string s_codecname;
@@ -274,10 +272,47 @@ class T3File: public bob::io::base::File {
std::string T3File::s_codecname = "torch3.binary";
/**
- * Registration method: use an unique name. Copy the definition to "plugin.h"
- * and then call it on "main.cpp" to register the codec.
+ * From this point onwards we have the registration procedure. If you are
+ * looking at this file for a coding example, just follow the procedure bellow,
+ * minus local modifications you may need to apply.
+ */
+
+/**
+ * This defines the factory method F that can create codecs of this type.
+ *
+ * Here are the meanings of the mode flag that should be respected by your
+ * factory implementation:
+ *
+ * 'r': opens for reading only - no modifications can occur; it is an
+ * error to open a file that does not exist for read-only operations.
+ * 'w': opens for reading and writing, but truncates the file if it
+ * exists; it is not an error to open files that do not exist with
+ * this flag.
+ * 'a': opens for reading and writing - any type of modification can
+ * occur. If the file does not exist, this flag is effectively like
+ * 'w'.
+ *
+ * Returns a newly allocated File object that can read and write data to the
+ * file using a specific backend.
+ *
+ * @note: This method can be static.
*/
-boost::shared_ptr<bob::io::base::File>
- make_torch3_file (const char* path, char mode) {
+static boost::shared_ptr<bob::io::base::File> make_file (const char* path, char mode) {
return boost::make_shared<T3File>(path, mode);
}
+
+/**
+ * Takes care of codec registration per se.
+ */
+static bool register_codec() {
+
+ boost::shared_ptr<bob::io::base::CodecRegistry> instance =
+ bob::io::base::CodecRegistry::instance();
+
+ instance->registerExtension(".bindata", "torch3 binary data format", &make_file);
+
+ return true;
+
+}
+
+static bool codec_registered = register_codec();
diff --git a/bob/io/base/tensor.cpp b/bob/io/base/cpp/TensorArrayFile.cpp
similarity index 56%
rename from bob/io/base/tensor.cpp
rename to bob/io/base/cpp/TensorArrayFile.cpp
index 8d51dbc..d0cb72d 100644
--- a/bob/io/base/tensor.cpp
+++ b/bob/io/base/cpp/TensorArrayFile.cpp
@@ -7,11 +7,8 @@
* Copyright (C) Idiap Research Institute, Martigny, Switzerland
*/
-#define BOB_IO_BASE_MODULE
-#include <bob.io.base/api.h>
-#include <bob.io.base/File.h>
-
-#include "cpp/TensorFile.h"
+#include "TensorFile.h"
+#include <bob.io.base/CodecRegistry.h>
class TensorArrayFile: public bob::io::base::File {
@@ -29,11 +26,11 @@ class TensorArrayFile: public bob::io::base::File {
return m_filename.c_str();
}
- virtual const BobIoTypeinfo& type_all () const {
+ virtual const bob::io::base::array::typeinfo& type_all () const {
return m_type;
}
- virtual const BobIoTypeinfo& type () const {
+ virtual const bob::io::base::array::typeinfo& type () const {
return m_type;
}
@@ -83,7 +80,7 @@ class TensorArrayFile: public bob::io::base::File {
private: //representation
bob::io::base::TensorFile m_file;
- BobIoTypeinfo m_type;
+ bob::io::base::array::typeinfo m_type;
std::string m_filename;
static std::string s_codecname;
@@ -93,11 +90,32 @@ class TensorArrayFile: public bob::io::base::File {
std::string TensorArrayFile::s_codecname = "bob.tensor";
/**
- * Registration method: use an unique name. Copy the definition to "plugin.h"
- * and then call it on "main.cpp" to register the codec.
+ * From this point onwards we have the registration procedure. If you are
+ * looking at this file for a coding example, just follow the procedure bellow,
+ * minus local modifications you may need to apply.
*/
-boost::shared_ptr<bob::io::base::File>
- make_tensor_file (const char* path, char mode) {
+
+/**
+ * This defines the factory method F that can create codecs of this type.
+ *
+ * Here are the meanings of the mode flag that should be respected by your
+ * factory implementation:
+ *
+ * 'r': opens for reading only - no modifications can occur; it is an
+ * error to open a file that does not exist for read-only operations.
+ * 'w': opens for reading and writing, but truncates the file if it
+ * exists; it is not an error to open files that do not exist with
+ * this flag.
+ * 'a': opens for reading and writing - any type of modification can
+ * occur. If the file does not exist, this flag is effectively like
+ * 'w'.
+ *
+ * Returns a newly allocated File object that can read and write data to the
+ * file using a specific backend.
+ *
+ * @note: This method can be static.
+ */
+static boost::shared_ptr<bob::io::base::File> make_file (const char* path, char mode) {
bob::io::base::TensorFile::openmode _mode;
if (mode == 'r') _mode = bob::io::base::TensorFile::in;
@@ -108,3 +126,19 @@ boost::shared_ptr<bob::io::base::File>
return boost::make_shared<TensorArrayFile>(path, _mode);
}
+
+/**
+ * Takes care of codec registration per se.
+ */
+static bool register_codec() {
+
+ boost::shared_ptr<bob::io::base::CodecRegistry> instance =
+ bob::io::base::CodecRegistry::instance();
+
+ instance->registerExtension(".tensor", "torch3vision v2.1 tensor files", &make_file);
+
+ return true;
+
+}
+
+static bool codec_registered = register_codec();
diff --git a/bob/io/base/cpp/TensorFile.cpp b/bob/io/base/cpp/TensorFile.cpp
index d559ba6..66b7216 100644
--- a/bob/io/base/cpp/TensorFile.cpp
+++ b/bob/io/base/cpp/TensorFile.cpp
@@ -7,10 +7,11 @@
* Copyright (C) Idiap Research Institute, Martigny, Switzerland
*/
-#define BOB_IO_BASE_MODULE
-#include <bob.io.base/api.h>
#include "TensorFile.h"
+#include <bob.io.base/reorder.h>
+#include <bob.io.base/array_type.h>
+
bob::io::base::TensorFile::TensorFile(const std::string& filename,
bob::io::base::TensorFile::openmode flag):
m_header_init(false),
@@ -24,7 +25,7 @@ bob::io::base::TensorFile::TensorFile(const std::string& filename,
if(m_stream)
{
m_header.read(m_stream);
- m_buffer.reset(new char[BobIoTypeinfo_BufferSize(&m_header.m_type)]);
+ m_buffer.reset(new char[m_header.m_type.buffer_size()]);
m_header_init = true;
m_n_arrays_written = m_header.m_n_samples;
@@ -39,7 +40,7 @@ bob::io::base::TensorFile::TensorFile(const std::string& filename,
m_stream.open(filename.c_str(), std::ios::out | std::ios::in |
std::ios::binary);
m_header.read(m_stream);
- m_buffer.reset(new char[BobIoTypeinfo_BufferSize(&m_header.m_type)]);
+ m_buffer.reset(new char[m_header.m_type.buffer_size()]);
m_header_init = true;
m_n_arrays_written = m_header.m_n_samples;
m_stream.seekp(0, std::ios::end);
@@ -52,7 +53,7 @@ bob::io::base::TensorFile::TensorFile(const std::string& filename,
m_stream.open(filename.c_str(), std::ios::in | std::ios::binary);
if(m_stream) {
m_header.read(m_stream);
- m_buffer.reset(new char[BobIoTypeinfo_BufferSize(&m_header.m_type)]);
+ m_buffer.reset(new char[m_header.m_type.buffer_size()]);
m_header_init = true;
m_n_arrays_written = m_header.m_n_samples;
@@ -70,7 +71,7 @@ bob::io::base::TensorFile::~TensorFile() {
close();
}
-void bob::io::base::TensorFile::peek(BobIoTypeinfo& info) const {
+void bob::io::base::TensorFile::peek(bob::io::base::array::typeinfo& info) const {
info = m_header.m_type;
}
@@ -82,7 +83,7 @@ void bob::io::base::TensorFile::close() {
m_stream.close();
}
-void bob::io::base::TensorFile::initHeader(const BobIoTypeinfo& info) {
+void bob::io::base::TensorFile::initHeader(const bob::io::base::array::typeinfo& info) {
// Check that data have not already been written
if (m_n_arrays_written > 0 ) {
throw std::runtime_error("cannot init the header of an output stream in which data have already been written");
@@ -94,25 +95,25 @@ void bob::io::base::TensorFile::initHeader(const BobIoTypeinfo& info) {
m_header.write(m_stream);
// Temporary buffer to help with data transposition...
- m_buffer.reset(new char[BobIoTypeinfo_BufferSize(&m_header.m_type)]);
+ m_buffer.reset(new char[m_header.m_type.buffer_size()]);
m_header_init = true;
}
void bob::io::base::TensorFile::write(const bob::io::base::array::interface& data) {
- const BobIoTypeinfo& info = data.type();
+ const bob::io::base::array::typeinfo& info = data.type();
if (!m_header_init) initHeader(info);
else {
//checks compatibility with previously written stuff
- if (!BobIoTypeinfo_IsCompatible(&m_header.m_type, &info))
+ if (!m_header.m_type.is_compatible(info))
throw std::runtime_error("buffer does not conform to expected type");
}
- BobIoReorder_RowToCol(data.ptr(), m_buffer.get(), &info);
+ bob::io::base::row_to_col_order(data.ptr(), m_buffer.get(), info);
- m_stream.write(static_cast<const char*>(m_buffer.get()), BobIoTypeinfo_BufferSize(&info));
+ m_stream.write(static_cast<const char*>(m_buffer.get()), info.buffer_size());
// increment m_n_arrays_written and m_current_array
++m_current_array;
@@ -124,12 +125,12 @@ void bob::io::base::TensorFile::read (bob::io::base::array::interface& buf) {
if(!m_header_init) {
throw std::runtime_error("TensorFile: header is not initialized");
}
- if(!BobIoTypeinfo_IsCompatible(&buf.type(), &m_header.m_type)) buf.set(m_header.m_type);
+ if(!buf.type().is_compatible(m_header.m_type)) buf.set(m_header.m_type);
m_stream.read(reinterpret_cast<char*>(m_buffer.get()),
- BobIoTypeinfo_BufferSize(&m_header.m_type));
+ m_header.m_type.buffer_size());
- BobIoReorder_ColToRow(m_buffer.get(), buf.ptr(), &m_header.m_type);
+ bob::io::base::col_to_row_order(m_buffer.get(), buf.ptr(), m_header.m_type);
++m_current_array;
}
diff --git a/bob/io/base/cpp/TensorFile.h b/bob/io/base/cpp/TensorFile.h
index 2c342a4..35d42bf 100644
--- a/bob/io/base/cpp/TensorFile.h
+++ b/bob/io/base/cpp/TensorFile.h
@@ -10,12 +10,13 @@
#ifndef BOB_IO_TENSORFILE_H
#define BOB_IO_TENSORFILE_H
-#include "TensorFileHeader.h"
-
-#include <bob.io.base/blitz_array.h>
#include <boost/format.hpp>
#include <stdexcept>
+#include <bob.io.base/blitz_array.h>
+
+#include "TensorFileHeader.h"
+
namespace bob { namespace io { namespace base {
/**
@@ -93,9 +94,9 @@ namespace bob { namespace io { namespace base {
void read (size_t index, bob::io::base::array::interface& data);
/**
- * Peeks the file and returns the currently set type information
+ * Peeks the file and returns the currently set typeinfo
*/
- void peek(BobIoTypeinfo& info) const;
+ void peek(bob::io::base::array::typeinfo& info) const;
/**
* Gets the number of samples/arrays written so far
@@ -129,7 +130,7 @@ namespace bob { namespace io { namespace base {
/**
* Initializes the tensor file with the given type and shape.
*/
- inline void initTensorFile(const BobIoTypeinfo& info) {
+ inline void initTensorFile(const bob::io::base::array::typeinfo& info) {
initHeader(info);
}
@@ -160,7 +161,7 @@ namespace bob { namespace io { namespace base {
* Initializes the header of the (output) stream with the given type
* and shape
*/
- void initHeader(const BobIoTypeinfo& info);
+ void initHeader(const bob::io::base::array::typeinfo& info);
public:
@@ -185,7 +186,7 @@ namespace bob { namespace io { namespace base {
* multiarrays saved have the same dimensions.
*/
template <typename T, int D> inline blitz::Array<T,D> read() {
- BobIoTypeinfo info;
+ bob::io::base::array::typeinfo info;
peek(info);
bob::io::base::array::blitz_array buf(info);
read(buf);
@@ -194,7 +195,7 @@ namespace bob { namespace io { namespace base {
template <typename T, int D> inline blitz::Array<T,D> read(size_t
index) {
- BobIoTypeinfo info;
+ bob::io::base::array::typeinfo info;
peek(info);
bob::io::base::array::blitz_array buf(info);
read(index, buf);
diff --git a/bob/io/base/cpp/TensorFileHeader.cpp b/bob/io/base/cpp/TensorFileHeader.cpp
index 8d8dfee..fb96a13 100644
--- a/bob/io/base/cpp/TensorFileHeader.cpp
+++ b/bob/io/base/cpp/TensorFileHeader.cpp
@@ -7,11 +7,10 @@
* Copyright (C) Idiap Research Institute, Martigny, Switzerland
*/
-#define BOB_IO_BASE_MODULE
-#include "TensorFileHeader.h"
-#include <bob.blitz/capi.h>
#include <boost/format.hpp>
+#include "TensorFileHeader.h"
+
bob::io::base::detail::TensorFileHeader::TensorFileHeader()
: m_tensor_type(bob::io::base::Char),
m_type(),
@@ -32,28 +31,28 @@ void bob::io::base::detail::TensorFileHeader::read(std::istream& str) {
str.seekg(std::ios_base::beg);
int val;
- str.read(reinterpret_cast<char*>(&val), sizeof(int));
+ str.read( reinterpret_cast<char*>(&val), sizeof(int));
m_tensor_type = (bob::io::base::TensorType)val;
m_type.dtype = bob::io::base::tensorTypeToArrayType(m_tensor_type);
- str.read(reinterpret_cast<char*>(&val), sizeof(int));
+ str.read( reinterpret_cast<char*>(&val), sizeof(int));
m_n_samples = (size_t)val;
- str.read(reinterpret_cast<char*>(&val), sizeof(int));
- size_t nd = (size_t)val;
+ int nd;
+ str.read(reinterpret_cast<char*>(&nd), sizeof(int));
- size_t shape[BOB_BLITZ_MAXDIMS];
+ int shape[BOB_MAX_DIM];
- str.read(reinterpret_cast<char*>(&val), sizeof(int));
+ str.read( reinterpret_cast<char*>(&val), sizeof(int));
shape[0] = (size_t)val;
- str.read(reinterpret_cast<char*>(&val), sizeof(int));
+ str.read( reinterpret_cast<char*>(&val), sizeof(int));
shape[1] = (size_t)val;
str.read( reinterpret_cast<char*>(&val), sizeof(int));
shape[2] = (size_t)val;
str.read( reinterpret_cast<char*>(&val), sizeof(int));
shape[3] = (size_t)val;
- BobIoTypeinfo_Set(&m_type, m_type.dtype, nd, shape);
+ m_type.set_shape(nd, shape);
header_ok();
}
@@ -65,19 +64,19 @@ void bob::io::base::detail::TensorFileHeader::write(std::ostream& str) const
int val;
val = (int)m_tensor_type;
- str.write(reinterpret_cast<char*>(&val), sizeof(int));
+ str.write( reinterpret_cast<char*>(&val), sizeof(int));
val = (int)m_n_samples;
- str.write(reinterpret_cast<char*>(&val), sizeof(int));
+ str.write( reinterpret_cast<char*>(&val), sizeof(int));
val = (int)m_type.nd;
- str.write(reinterpret_cast<char*>(&val), sizeof(int));
+ str.write( reinterpret_cast<char*>(&val), sizeof(int));
val = (int)m_type.shape[0];
- str.write(reinterpret_cast<char*>(&val), sizeof(int));
+ str.write( reinterpret_cast<char*>(&val), sizeof(int));
val = (int)m_type.shape[1];
- str.write(reinterpret_cast<char*>(&val), sizeof(int));
+ str.write( reinterpret_cast<char*>(&val), sizeof(int));
val = (int)m_type.shape[2];
- str.write(reinterpret_cast<char*>(&val), sizeof(int));
+ str.write( reinterpret_cast<char*>(&val), sizeof(int));
val = (int)m_type.shape[3];
- str.write(reinterpret_cast<char*>(&val), sizeof(int));
+ str.write( reinterpret_cast<char*>(&val), sizeof(int));
}
void bob::io::base::detail::TensorFileHeader::header_ok()
@@ -101,7 +100,7 @@ void bob::io::base::detail::TensorFileHeader::header_ok()
// Check the number of samples and dimensions
if( m_type.nd < 1 || m_type.nd > 4) {
boost::format m("header for tensor file indicates an unsupported type: %s");
- m % BobIoTypeinfo_Str(&m_type);
+ m % m_type.str();
throw std::runtime_error(m.str());
}
@@ -131,43 +130,43 @@ void bob::io::base::detail::TensorFileHeader::update()
}
-bob::io::base::TensorType bob::io::base::arrayTypeToTensorType(int dtype)
+bob::io::base::TensorType bob::io::base::arrayTypeToTensorType(bob::io::base::array::ElementType eltype)
{
- switch(dtype)
+ switch(eltype)
{
- case NPY_INT8:
+ case bob::io::base::array::t_int8:
return bob::io::base::Char;
- case NPY_INT16:
+ case bob::io::base::array::t_int16:
return bob::io::base::Short;
- case NPY_INT32:
+ case bob::io::base::array::t_int32:
return bob::io::base::Int;
- case NPY_INT64:
+ case bob::io::base::array::t_int64:
return bob::io::base::Long;
- case NPY_FLOAT32:
+ case bob::io::base::array::t_float32:
return bob::io::base::Float;
- case NPY_FLOAT64:
+ case bob::io::base::array::t_float64:
return bob::io::base::Double;
default:
throw std::runtime_error("unsupported data type found while converting array type to tensor type");
}
}
-int bob::io::base::tensorTypeToArrayType(bob::io::base::TensorType tensortype)
+bob::io::base::array::ElementType bob::io::base::tensorTypeToArrayType(bob::io::base::TensorType tensortype)
{
switch(tensortype)
{
case bob::io::base::Char:
- return NPY_INT8;
+ return bob::io::base::array::t_int8;
case bob::io::base::Short:
- return NPY_INT16;
+ return bob::io::base::array::t_int16;
case bob::io::base::Int:
- return NPY_INT32;
+ return bob::io::base::array::t_int32;
case bob::io::base::Long:
- return NPY_INT64;
+ return bob::io::base::array::t_int64;
case bob::io::base::Float:
- return NPY_FLOAT32;
+ return bob::io::base::array::t_float32;
case bob::io::base::Double:
- return NPY_FLOAT64;
+ return bob::io::base::array::t_float64;
default:
throw std::runtime_error("unsupported data type found while converting tensor type to array type");
}
diff --git a/bob/io/base/cpp/TensorFileHeader.h b/bob/io/base/cpp/TensorFileHeader.h
index 7f3275d..7e852b8 100644
--- a/bob/io/base/cpp/TensorFileHeader.h
+++ b/bob/io/base/cpp/TensorFileHeader.h
@@ -11,9 +11,10 @@
#ifndef BOB_IO_BASE_TENSORFILEHEADER_H
#define BOB_IO_BASE_TENSORFILEHEADER_H
-#include <bob.io.base/api.h>
-#include <blitz/array.h>
#include <fstream>
+#include <blitz/array.h>
+
+#include <bob.io.base/array.h>
namespace bob { namespace io { namespace base {
@@ -28,8 +29,8 @@ namespace bob { namespace io { namespace base {
Double
};
- TensorType arrayTypeToTensorType(int dtype);
- int tensorTypeToArrayType(bob::io::base::TensorType tensortype);
+ TensorType arrayTypeToTensorType(bob::io::base::array::ElementType eltype);
+ bob::io::base::array::ElementType tensorTypeToArrayType(bob::io::base::TensorType tensortype);
namespace detail {
/**
@@ -84,7 +85,7 @@ namespace bob { namespace io { namespace base {
//representation
TensorType m_tensor_type; ///< array element type
- BobIoTypeinfo m_type; ///< the type information
+ bob::io::base::array::typeinfo m_type; ///< the type information
size_t m_n_samples; ///< total number of arrays in the file
size_t m_tensor_size; ///< the number of dimensions in each array
};
diff --git a/bob/io/base/cpp/array.cpp b/bob/io/base/cpp/array.cpp
new file mode 100644
index 0000000..2ffc94d
--- /dev/null
+++ b/bob/io/base/cpp/array.cpp
@@ -0,0 +1,134 @@
+/**
+ * @date Tue Nov 8 15:34:31 2011 +0100
+ * @author Andre Anjos <andre.anjos@idiap.ch>
+ *
+ * @brief Some buffer stuff
+ *
+ * Copyright (C) Idiap Research Institute, Martigny, Switzerland
+ */
+
+#include <boost/format.hpp>
+#include <bob.io.base/array.h>
+
+bob::io::base::array::typeinfo::typeinfo():
+ dtype(bob::io::base::array::t_unknown),
+ nd(0)
+{
+}
+
+bob::io::base::array::typeinfo::typeinfo(const bob::io::base::array::typeinfo& other):
+ dtype(other.dtype)
+{
+ set_shape(other.nd, other.shape);
+}
+
+bob::io::base::array::typeinfo& bob::io::base::array::typeinfo::operator= (const bob::io::base::array::typeinfo& other) {
+ dtype = other.dtype;
+ set_shape(other.nd, other.shape);
+ return *this;
+}
+
+void bob::io::base::array::typeinfo::reset() {
+ dtype = bob::io::base::array::t_unknown;
+ nd = 0;
+}
+
+bool bob::io::base::array::typeinfo::is_valid() const {
+ return (dtype != bob::io::base::array::t_unknown) && (nd > 0) && (nd <= (BOB_MAX_DIM+1)) && has_valid_shape();
+}
+
+void bob::io::base::array::typeinfo::update_strides() {
+ switch (nd) {
+ case 0:
+ return;
+ case 1:
+ stride[0] = 1;
+ return;
+ case 2:
+ stride[1] = 1;
+ stride[0] = shape[1];
+ return;
+ case 3:
+ stride[2] = 1;
+ stride[1] = shape[2];
+ stride[0] = shape[1]*shape[2];
+ return;
+ case 4:
+ stride[3] = 1;
+ stride[2] = shape[3];
+ stride[1] = shape[2]*shape[3];
+ stride[0] = shape[1]*shape[2]*shape[3];
+ return;
+ case 5:
+ stride[4] = 1;
+ stride[3] = shape[4];
+ stride[2] = shape[3]*shape[4];
+ stride[1] = shape[2]*shape[3]*shape[4];
+ stride[0] = shape[1]*shape[2]*shape[3]*shape[4];
+ return;
+ default:
+ break;
+ }
+ throw std::runtime_error("unsupported number of dimensions");
+}
+
+size_t bob::io::base::array::typeinfo::size() const {
+ size_t retval = 1;
+ for (size_t k=0; k<nd; ++k) retval *= shape[k];
+ return retval;
+}
+
+size_t bob::io::base::array::typeinfo::buffer_size() const {
+ return size()*bob::io::base::array::getElementSize(dtype);
+}
+
+static bool same_shape(size_t nd, const size_t* s1, const size_t* s2) {
+ for (size_t k=0; k<nd; ++k) if (s1[k] != s2[k]) return false;
+ return true;
+}
+
+bool bob::io::base::array::typeinfo::is_compatible(const bob::io::base::array::typeinfo& other) const {
+ return (dtype == other.dtype) && (nd == other.nd) && same_shape(nd, shape, other.shape);
+}
+
+std::string bob::io::base::array::typeinfo::str() const {
+ boost::format s("dtype: %s (%d); shape: [%s]; size: %d bytes");
+ size_t sz = 0;
+ size_t buf_sz = 0;
+ if (dtype != bob::io::base::array::t_unknown) {
+ //otherwise it throws
+ sz = item_size();
+ buf_sz = buffer_size();
+ }
+ s % item_str() % sz;
+ switch (nd) {
+ case 0:
+ s % "";
+ break;
+ case 1:
+ s % (boost::format("%d") % shape[0]).str();
+ break;
+ case 2:
+ s % (boost::format("%d,%d") % shape[0] % shape[1]).str();
+ break;
+ case 3:
+ s % (boost::format("%d,%d,%d") % shape[0] % shape[1] % shape[2]).str();
+ break;
+ case 4:
+ s % (boost::format("%d,%d,%d,%d") % shape[0] % shape[1] % shape[2] % shape[3]).str();
+ break;
+ default:
+ s % ">4 dimensions?";
+ break;
+ }
+ s % buf_sz;
+ return s.str();
+}
+
+void bob::io::base::array::typeinfo::reset_shape() {
+ shape[0] = 0;
+}
+
+bool bob::io::base::array::typeinfo::has_valid_shape() const {
+ return shape[0] != 0;
+}
diff --git a/bob/io/base/cpp/array_type.cpp b/bob/io/base/cpp/array_type.cpp
new file mode 100644
index 0000000..d42368e
--- /dev/null
+++ b/bob/io/base/cpp/array_type.cpp
@@ -0,0 +1,126 @@
+/**
+ * @date Sat Apr 9 18:10:10 2011 +0200
+ * @author Laurent El Shafey <Laurent.El-Shafey@idiap.ch>
+ *
+ * @brief Some type-related array utilities
+ *
+ * Copyright (C) Idiap Research Institute, Martigny, Switzerland
+ */
+
+#include <bob.io.base/array_type.h>
+#include <boost/format.hpp>
+
+static const char* t_bool_string = "bool";
+static const char* t_int8_string = "int8";
+static const char* t_int16_string = "int16";
+static const char* t_int32_string = "int32";
+static const char* t_int64_string = "int64";
+static const char* t_uint8_string = "uint8";
+static const char* t_uint16_string = "uint16";
+static const char* t_uint32_string = "uint32";
+static const char* t_uint64_string = "uint64";
+static const char* t_float32_string = "float32";
+static const char* t_float64_string = "float64";
+static const char* t_float128_string = "float128";
+static const char* t_complex64_string = "complex64";
+static const char* t_complex128_string = "complex128";
+static const char* t_complex256_string = "complex256";
+static const char* t_unknown_string = "unknown";
+
+size_t bob::io::base::array::getElementSize(ElementType t) {
+ switch(t) {
+ case bob::io::base::array::t_bool:
+ return sizeof(bool);
+ case bob::io::base::array::t_int8:
+ return sizeof(int8_t);
+ case bob::io::base::array::t_int16:
+ return sizeof(int16_t);
+ case bob::io::base::array::t_int32:
+ return sizeof(int32_t);
+ case bob::io::base::array::t_int64:
+ return sizeof(int64_t);
+ case bob::io::base::array::t_uint8:
+ return sizeof(uint8_t);
+ case bob::io::base::array::t_uint16:
+ return sizeof(uint16_t);
+ case bob::io::base::array::t_uint32:
+ return sizeof(uint32_t);
+ case bob::io::base::array::t_uint64:
+ return sizeof(uint64_t);
+ case bob::io::base::array::t_float32:
+ return sizeof(float);
+ case bob::io::base::array::t_float64:
+ return sizeof(double);
+ case bob::io::base::array::t_float128:
+ return sizeof(long double);
+ case bob::io::base::array::t_complex64:
+ return sizeof(std::complex<float>);
+ case bob::io::base::array::t_complex128:
+ return sizeof(std::complex<double>);
+ case bob::io::base::array::t_complex256:
+ return sizeof(std::complex<long double>);
+ default:
+ {
+ boost::format m("unsupported element type (%d)");
+ m % (int)t;
+ throw std::runtime_error(m.str());
+ }
+ }
+}
+
+const char* bob::io::base::array::stringize(ElementType t) {
+ switch(t) {
+ case bob::io::base::array::t_bool:
+ return t_bool_string;
+ case bob::io::base::array::t_int8:
+ return t_int8_string;
+ case bob::io::base::array::t_int16:
+ return t_int16_string;
+ case bob::io::base::array::t_int32:
+ return t_int32_string;
+ case bob::io::base::array::t_int64:
+ return t_int64_string;
+ case bob::io::base::array::t_uint8:
+ return t_uint8_string;
+ case bob::io::base::array::t_uint16:
+ return t_uint16_string;
+ case bob::io::base::array::t_uint32:
+ return t_uint32_string;
+ case bob::io::base::array::t_uint64:
+ return t_uint64_string;
+ case bob::io::base::array::t_float32:
+ return t_float32_string;
+ case bob::io::base::array::t_float64:
+ return t_float64_string;
+ case bob::io::base::array::t_float128:
+ return t_float128_string;
+ case bob::io::base::array::t_complex64:
+ return t_complex64_string;
+ case bob::io::base::array::t_complex128:
+ return t_complex128_string;
+ case bob::io::base::array::t_complex256:
+ return t_complex256_string;
+ default:
+ return t_unknown_string;
+ }
+}
+
+bob::io::base::array::ElementType bob::io::base::array::unstringize(const char* s) {
+ std::string sc(s);
+ if (sc == t_bool_string) return bob::io::base::array::t_bool;
+ if (sc == t_int8_string) return bob::io::base::array::t_int8;
+ if (sc == t_int16_string) return bob::io::base::array::t_int16;
+ if (sc == t_int32_string) return bob::io::base::array::t_int32;
+ if (sc == t_int64_string) return bob::io::base::array::t_int64;
+ if (sc == t_uint8_string) return bob::io::base::array::t_uint8;
+ if (sc == t_uint16_string) return bob::io::base::array::t_uint16;
+ if (sc == t_uint32_string) return bob::io::base::array::t_uint32;
+ if (sc == t_uint64_string) return bob::io::base::array::t_uint64;
+ if (sc == t_float32_string) return bob::io::base::array::t_float32;
+ if (sc == t_float64_string) return bob::io::base::array::t_float64;
+ if (sc == t_float128_string) return bob::io::base::array::t_float128;
+ if (sc == t_complex64_string) return bob::io::base::array::t_complex64;
+ if (sc == t_complex128_string) return bob::io::base::array::t_complex128;
+ if (sc == t_complex256_string) return bob::io::base::array::t_complex256;
+ return bob::io::base::array::t_unknown;
+}
diff --git a/bob/io/base/cpp/blitz_array.cpp b/bob/io/base/cpp/blitz_array.cpp
index 9439a4c..2bc723a 100644
--- a/bob/io/base/cpp/blitz_array.cpp
+++ b/bob/io/base/cpp/blitz_array.cpp
@@ -7,10 +7,10 @@
* Copyright (C) Idiap Research Institute, Martigny, Switzerland
*/
-#define BOB_IO_BASE_MODULE
-#include <bob.io.base/blitz_array.h>
#include <stdexcept>
+#include <bob.io.base/blitz_array.h>
+
bob::io::base::array::blitz_array::blitz_array(boost::shared_ptr<blitz_array> other) {
set(other);
}
@@ -27,26 +27,21 @@ bob::io::base::array::blitz_array::blitz_array(const interface& other) {
set(other);
}
-bob::io::base::array::blitz_array::blitz_array(const BobIoTypeinfo& info) {
+bob::io::base::array::blitz_array::blitz_array(const typeinfo& info) {
set(info);
}
-bob::io::base::array::blitz_array::blitz_array(void* data, const BobIoTypeinfo& info):
- m_type(),
+bob::io::base::array::blitz_array::blitz_array(void* data, const typeinfo& info):
+ m_type(info),
m_ptr(data),
m_is_blitz(false) {
- if (!BobIoTypeinfo_Copy(&m_type, &info)) {
- throw std::runtime_error("error already set");
- }
}
bob::io::base::array::blitz_array::~blitz_array() {
}
void bob::io::base::array::blitz_array::set(boost::shared_ptr<blitz_array> other) {
- if (!BobIoTypeinfo_Copy(&m_type, &other->m_type)) {
- throw std::runtime_error("error already set");
- }
+ m_type = other->m_type;
m_ptr = other->m_ptr;
m_is_blitz = other->m_is_blitz;
m_data = other->m_data;
@@ -54,13 +49,11 @@ void bob::io::base::array::blitz_array::set(boost::shared_ptr<blitz_array> other
void bob::io::base::array::blitz_array::set(const interface& other) {
set(other.type());
- memcpy(m_ptr, other.ptr(), BobIoTypeinfo_BufferSize(&m_type));
+ memcpy(m_ptr, other.ptr(), m_type.buffer_size());
}
void bob::io::base::array::blitz_array::set(boost::shared_ptr<interface> other) {
- if (!BobIoTypeinfo_Copy(&m_type, &other->type())) {
- throw std::runtime_error("error already set");
- }
+ m_type = other->type();
m_ptr = other->ptr();
m_is_blitz = false;
m_data = other;
@@ -112,66 +105,58 @@ static boost::shared_ptr<void> make_array(size_t nd, const size_t* shape,
throw std::runtime_error("unsupported number of dimensions -- debug me");
}
-void bob::io::base::array::blitz_array::set (const BobIoTypeinfo& req) {
- if (BobIoTypeinfo_IsCompatible(&m_type, &req)) return; ///< double-check requirement first!
-
- //have to go through reallocation
- if (!BobIoTypeinfo_Copy(&m_type, &req)) {
- throw std::runtime_error("error already set");
- }
+void bob::io::base::array::blitz_array::set (const bob::io::base::array::typeinfo& req) {
+ if (m_type.is_compatible(req)) return; ///< double-check requirement first!
+ //ok, have to go through reallocation
+ m_type = req;
m_is_blitz = true;
-
switch (m_type.dtype) {
- case NPY_BOOL:
+ case bob::io::base::array::t_bool:
m_data = make_array<bool>(req.nd, req.shape, m_ptr);
return;
- case NPY_INT8:
+ case bob::io::base::array::t_int8:
m_data = make_array<int8_t>(req.nd, req.shape, m_ptr);
return;
- case NPY_INT16:
+ case bob::io::base::array::t_int16:
m_data = make_array<int16_t>(req.nd, req.shape, m_ptr);
return;
- case NPY_INT32:
+ case bob::io::base::array::t_int32:
m_data = make_array<int32_t>(req.nd, req.shape, m_ptr);
return;
- case NPY_INT64:
+ case bob::io::base::array::t_int64:
m_data = make_array<int64_t>(req.nd, req.shape, m_ptr);
return;
- case NPY_UINT8:
+ case bob::io::base::array::t_uint8:
m_data = make_array<uint8_t>(req.nd, req.shape, m_ptr);
return;
- case NPY_UINT16:
+ case bob::io::base::array::t_uint16:
m_data = make_array<uint16_t>(req.nd, req.shape, m_ptr);
return;
- case NPY_UINT32:
+ case bob::io::base::array::t_uint32:
m_data = make_array<uint32_t>(req.nd, req.shape, m_ptr);
return;
- case NPY_UINT64:
+ case bob::io::base::array::t_uint64:
m_data = make_array<uint64_t>(req.nd, req.shape, m_ptr);
return;
- case NPY_FLOAT32:
+ case bob::io::base::array::t_float32:
m_data = make_array<float>(req.nd, req.shape, m_ptr);
return;
- case NPY_FLOAT64:
+ case bob::io::base::array::t_float64:
m_data = make_array<double>(req.nd, req.shape, m_ptr);
return;
-# ifdef NPY_FLOAT128
- case NPY_FLOAT128:
+ case bob::io::base::array::t_float128:
m_data = make_array<long double>(req.nd, req.shape, m_ptr);
return;
-# endif
- case NPY_COMPLEX64:
+ case bob::io::base::array::t_complex64:
m_data = make_array<std::complex<float> >(req.nd, req.shape, m_ptr);
return;
- case NPY_COMPLEX128:
+ case bob::io::base::array::t_complex128:
m_data = make_array<std::complex<double> >(req.nd, req.shape, m_ptr);
return;
-# ifdef NPY_COMPLEX256
- case NPY_COMPLEX256:
+ case bob::io::base::array::t_complex256:
m_data = make_array<std::complex<long double> >(req.nd, req.shape, m_ptr);
return;
-# endif
default:
break;
}
diff --git a/bob/io/base/cpp/reorder.cpp b/bob/io/base/cpp/reorder.cpp
new file mode 100644
index 0000000..cda5ab3
--- /dev/null
+++ b/bob/io/base/cpp/reorder.cpp
@@ -0,0 +1,288 @@
+/**
+ * @date Tue Nov 22 11:24:44 2011 +0100
+ * @author Andre Anjos <andre.anjos@idiap.ch>
+ *
+ * @brief Implementation of row-major/column-major reordering
+ *
+ * Copyright (C) Idiap Research Institute, Martigny, Switzerland
+ */
+
+#include <boost/format.hpp>
+#include <cstring> //for memcpy
+
+#include <bob.io.base/reorder.h>
+
+void bob::io::base::rc2d(size_t& row, size_t& col, const size_t i, const size_t j,
+ const size_t* shape) {
+ row = (i * shape[1]) + j;
+ col = (j * shape[0]) + i;
+}
+
+void bob::io::base::rc3d(size_t& row, size_t& col, const size_t i, const size_t j,
+ const size_t k, const size_t* shape) {
+ row = ( (i * shape[1]) + j ) * shape[2] + k;
+ col = ( (k * shape[1]) + j ) * shape[0] + i;
+}
+
+void bob::io::base::rc4d(size_t& row, size_t& col, const size_t i, const size_t j,
+ const size_t k, const size_t l, const size_t* shape) {
+ row = ( ( i * shape[1] + j ) * shape[2] + k ) * shape[3] + l;
+ col = ( ( l * shape[2] + k ) * shape[1] + j ) * shape[0] + i;
+}
+
+void bob::io::base::row_to_col_order(const void* src_, void* dst_,
+ const bob::io::base::array::typeinfo& info) {
+
+ size_t dsize = info.item_size();
+
+ //cast to byte type so we can manipulate the pointers...
+ const uint8_t* src = static_cast<const uint8_t*>(src_);
+ uint8_t* dst = static_cast<uint8_t*>(dst_);
+
+ switch(info.nd) {
+
+ case 1:
+ std::memcpy(dst, src, info.buffer_size());
+ break;
+
+ case 2:
+ for (size_t i=0; i<info.shape[0]; ++i)
+ for (size_t j=0; j<info.shape[1]; ++j) {
+ size_t row_major, col_major;
+ bob::io::base::rc2d(row_major, col_major, i, j, info.shape);
+ row_major *= dsize;
+ col_major *= dsize;
+ std::memcpy(&dst[col_major], &src[row_major], dsize);
+ }
+ break;
+
+ case 3:
+ for (size_t i=0; i<info.shape[0]; ++i)
+ for (size_t j=0; j<info.shape[1]; ++j)
+ for (size_t k=0; k<info.shape[2]; ++k) {
+ size_t row_major, col_major;
+ bob::io::base::rc3d(row_major, col_major, i, j, k, info.shape);
+ row_major *= dsize;
+ col_major *= dsize;
+ std::memcpy(&dst[col_major], &src[row_major], dsize);
+ }
+ break;
+
+ case 4:
+ for (size_t i=0; i<info.shape[0]; ++i)
+ for (size_t j=0; j<info.shape[1]; ++j)
+ for (size_t k=0; k<info.shape[2]; ++k)
+ for (size_t l=0; l<info.shape[3]; ++l) {
+ size_t row_major, col_major;
+ bob::io::base::rc4d(row_major, col_major, i, j, k, l, info.shape);
+ row_major *= dsize;
+ col_major *= dsize;
+ std::memcpy(&dst[col_major], &src[row_major], dsize);
+ }
+ break;
+
+ default:
+ {
+ boost::format m("row_to_col_order() can only flip arrays with up to %u dimensions - you passed one with %u dimensions");
+ m % BOB_MAX_DIM % info.nd;
+ throw std::runtime_error(m.str());
+ }
+ }
+}
+
+void bob::io::base::col_to_row_order(const void* src_, void* dst_,
+ const bob::io::base::array::typeinfo& info) {
+
+ size_t dsize = info.item_size();
+
+ //cast to byte type so we can manipulate the pointers...
+ const uint8_t* src = static_cast<const uint8_t*>(src_);
+ uint8_t* dst = static_cast<uint8_t*>(dst_);
+
+ switch(info.nd) {
+
+ case 1:
+ std::memcpy(dst, src, info.buffer_size());
+ break;
+
+ case 2:
+ for (size_t i=0; i<info.shape[0]; ++i)
+ for (size_t j=0; j<info.shape[1]; ++j) {
+ size_t row_major, col_major;
+ bob::io::base::rc2d(row_major, col_major, i, j, info.shape);
+ row_major *= dsize;
+ col_major *= dsize;
+ std::memcpy(&dst[row_major], &src[col_major], dsize);
+ }
+ break;
+
+ case 3:
+ for (size_t i=0; i<info.shape[0]; ++i)
+ for (size_t j=0; j<info.shape[1]; ++j)
+ for (size_t k=0; k<info.shape[2]; ++k) {
+ size_t row_major, col_major;
+ bob::io::base::rc3d(row_major, col_major, i, j, k, info.shape);
+ row_major *= dsize;
+ col_major *= dsize;
+ std::memcpy(&dst[row_major], &src[col_major], dsize);
+ }
+ break;
+
+ case 4:
+ for (size_t i=0; i<info.shape[0]; ++i)
+ for (size_t j=0; j<info.shape[1]; ++j)
+ for (size_t k=0; k<info.shape[2]; ++k)
+ for (size_t l=0; l<info.shape[3]; ++l) {
+ size_t row_major, col_major;
+ bob::io::base::rc4d(row_major, col_major, i, j, k, l, info.shape);
+ row_major *= dsize;
+ col_major *= dsize;
+ std::memcpy(&dst[row_major], &src[col_major], dsize);
+ }
+ break;
+
+ default:
+ {
+ boost::format m("col_to_row_order() can only flip arrays with up to %u dimensions - you passed one with %u dimensions");
+ m % BOB_MAX_DIM % info.nd;
+ throw std::runtime_error(m.str());
+ }
+ }
+}
+
+void bob::io::base::row_to_col_order_complex(const void* src_, void* dst_re_,
+ void* dst_im_, const bob::io::base::array::typeinfo& info) {
+
+ size_t dsize = info.item_size();
+ size_t dsize2 = dsize/2; ///< size of each complex component (real, imaginary)
+
+ //cast to byte type so we can manipulate the pointers...
+ const uint8_t* src = static_cast<const uint8_t*>(src_);
+ uint8_t* dst_re = static_cast<uint8_t*>(dst_re_);
+ uint8_t* dst_im = static_cast<uint8_t*>(dst_im_);
+
+ switch(info.nd) {
+
+ case 1:
+ for (size_t i=0; i<info.shape[0]; ++i) {
+ std::memcpy(&dst_re[dsize2*i], &src[dsize*i] , dsize2);
+ std::memcpy(&dst_im[dsize2*i], &src[dsize*i]+dsize2, dsize2);
+ }
+ break;
+
+ case 2:
+ for (size_t i=0; i<info.shape[0]; ++i)
+ for (size_t j=0; j<info.shape[1]; ++j) {
+ size_t row_major, col_major;
+ bob::io::base::rc2d(row_major, col_major, i, j, info.shape);
+ row_major *= dsize;
+ col_major *= dsize2;
+ std::memcpy(&dst_re[col_major], &src[row_major] , dsize2);
+ std::memcpy(&dst_im[col_major], &src[row_major]+dsize2, dsize2);
+ }
+ break;
+
+ case 3:
+ for (size_t i=0; i<info.shape[0]; ++i)
+ for (size_t j=0; j<info.shape[1]; ++j)
+ for (size_t k=0; k<info.shape[2]; ++k) {
+ size_t row_major, col_major;
+ bob::io::base::rc3d(row_major, col_major, i, j, k, info.shape);
+ row_major *= dsize;
+ col_major *= dsize2;
+ std::memcpy(&dst_re[col_major], &src[row_major] , dsize2);
+ std::memcpy(&dst_im[col_major], &src[row_major]+dsize2, dsize2);
+ }
+ break;
+
+ case 4:
+ for (size_t i=0; i<info.shape[0]; ++i)
+ for (size_t j=0; j<info.shape[1]; ++j)
+ for (size_t k=0; k<info.shape[2]; ++k)
+ for (size_t l=0; l<info.shape[3]; ++l) {
+ size_t row_major, col_major;
+ bob::io::base::rc4d(row_major, col_major, i, j, k, l, info.shape);
+ row_major *= dsize;
+ col_major *= dsize2;
+ std::memcpy(&dst_re[col_major], &src[row_major] , dsize2);
+ std::memcpy(&dst_im[col_major], &src[row_major]+dsize2, dsize2);
+ }
+ break;
+
+ default:
+ {
+ boost::format m("row_to_col_order_complex() can only flip arrays with up to %u dimensions - you passed one with %u dimensions");
+ m % BOB_MAX_DIM % info.nd;
+ throw std::runtime_error(m.str());
+ }
+ }
+}
+
+void bob::io::base::col_to_row_order_complex(const void* src_re_, const void* src_im_,
+ void* dst_, const bob::io::base::array::typeinfo& info) {
+
+ size_t dsize = info.item_size();
+ size_t dsize2 = dsize/2; ///< size of each complex component (real, imaginary)
+
+ //cast to byte type so we can manipulate the pointers...
+ const uint8_t* src_re = static_cast<const uint8_t*>(src_re_);
+ const uint8_t* src_im = static_cast<const uint8_t*>(src_im_);
+ uint8_t* dst = static_cast<uint8_t*>(dst_);
+
+ switch(info.nd) {
+
+ case 1:
+ for (size_t i=0; i<info.shape[0]; ++i) {
+ std::memcpy(&dst[dsize*i] , &src_re[dsize2*i], dsize2);
+ std::memcpy(&dst[dsize*i]+dsize2, &src_im[dsize2*i], dsize2);
+ }
+ break;
+
+ case 2:
+ for (size_t i=0; i<info.shape[0]; ++i)
+ for (size_t j=0; j<info.shape[1]; ++j) {
+ size_t row_major, col_major;
+ bob::io::base::rc2d(row_major, col_major, i, j, info.shape);
+ row_major *= dsize;
+ col_major *= dsize2;
+ std::memcpy(&dst[row_major], &src_re[col_major], dsize2);
+ std::memcpy(&dst[row_major]+dsize2, &src_im[col_major], dsize2);
+ }
+ break;
+
+ case 3:
+ for (size_t i=0; i<info.shape[0]; ++i)
+ for (size_t j=0; j<info.shape[1]; ++j)
+ for (size_t k=0; k<info.shape[2]; ++k) {
+ size_t row_major, col_major;
+ bob::io::base::rc3d(row_major, col_major, i, j, k, info.shape);
+ row_major *= dsize;
+ col_major *= dsize2;
+ std::memcpy(&dst[row_major] , &src_re[col_major], dsize2);
+ std::memcpy(&dst[row_major]+dsize2, &src_im[col_major], dsize2);
+ }
+ break;
+
+ case 4:
+ for (size_t i=0; i<info.shape[0]; ++i)
+ for (size_t j=0; j<info.shape[1]; ++j)
+ for (size_t k=0; k<info.shape[2]; ++k)
+ for (size_t l=0; l<info.shape[3]; ++l) {
+ size_t row_major, col_major;
+ bob::io::base::rc4d(row_major, col_major, i, j, k, l, info.shape);
+ row_major *= dsize;
+ col_major *= dsize2;
+ std::memcpy(&dst[row_major] , &src_re[col_major], dsize2);
+ std::memcpy(&dst[row_major]+dsize2, &src_im[col_major], dsize2);
+ }
+ break;
+
+ default:
+ {
+ boost::format m("col_to_row_order_complex() can only flip arrays with up to %u dimensions - you passed one with %u dimensions");
+ m % BOB_MAX_DIM % info.nd;
+ throw std::runtime_error(m.str());
+ }
+ }
+}
+
diff --git a/bob/io/base/utils.cpp b/bob/io/base/cpp/utils.cpp
similarity index 52%
rename from bob/io/base/utils.cpp
rename to bob/io/base/cpp/utils.cpp
index 53ebd5f..3467b99 100644
--- a/bob/io/base/utils.cpp
+++ b/bob/io/base/cpp/utils.cpp
@@ -7,31 +7,24 @@
* Copyright (C) Idiap Research Institute, Martigny, Switzerland
*/
-#define BOB_IO_BASE_MODULE
-#include <bob.io.base/api.h>
-#include <bob.io.base/File.h>
-#include "cpp/CodecRegistry.h"
+#include <bob.io.base/CodecRegistry.h>
+#include <bob.io.base/utils.h>
-boost::shared_ptr<bob::io::base::File> BobIoFile_Open
- (const char* filename, char mode) {
-
- boost::shared_ptr<bob::io::base::CodecRegistry> instance = bob::io::base::CodecRegistry::instance();
- return instance->findByFilenameExtension(filename)(filename, mode);
-
-}
-
-boost::shared_ptr<bob::io::base::File> BobIoFile_OpenWithExtension (const char* filename,
+boost::shared_ptr<bob::io::base::File> bob::io::base::open (const char* filename,
char mode, const char* pretend_extension) {
-
boost::shared_ptr<bob::io::base::CodecRegistry> instance = bob::io::base::CodecRegistry::instance();
return instance->findByExtension(pretend_extension)(filename, mode);
+}
+boost::shared_ptr<bob::io::base::File> bob::io::base::open (const char* filename, char mode) {
+ boost::shared_ptr<bob::io::base::CodecRegistry> instance = bob::io::base::CodecRegistry::instance();
+ return instance->findByFilenameExtension(filename)(filename, mode);
}
-void BobIoFile_Peek (const char* filename, BobIoTypeinfo* info) {
- BobIoTypeinfo_Copy(info, &BobIoFile_Open(filename, 'r')->type());
+bob::io::base::array::typeinfo bob::io::base::peek (const char* filename) {
+ return open(filename, 'r')->type();
}
-void BobIoFile_PeekAll (const char* filename, BobIoTypeinfo* info) {
- BobIoTypeinfo_Copy(info, &BobIoFile_Open(filename, 'r')->type_all());
+bob::io::base::array::typeinfo bob::io::base::peek_all (const char* filename) {
+ return open(filename, 'r')->type_all();
}
diff --git a/bob/io/base/file.cpp b/bob/io/base/file.cpp
index 3f36c38..58d760c 100644
--- a/bob/io/base/file.cpp
+++ b/bob/io/base/file.cpp
@@ -8,12 +8,14 @@
#define BOB_IO_BASE_MODULE
#include "bobskin.h"
#include <bob.io.base/api.h>
-#include <bob.io.base/File.h>
#include <numpy/arrayobject.h>
#include <bob.blitz/capi.h>
#include <bob.blitz/cleanup.h>
#include <stdexcept>
+#include <bob.io.base/CodecRegistry.h>
+#include <bob.io.base/utils.h>
+
#define FILETYPE_NAME "File"
PyDoc_STRVAR(s_file_str, BOB_EXT_MODULE_PREFIX "." FILETYPE_NAME);
@@ -119,10 +121,10 @@ static int PyBobIoFile_Init(PyBobIoFileObject* self, PyObject *args, PyObject* k
try {
if (pretend_extension) {
- self->f = BobIoFile_OpenWithExtension(c_filename, mode, pretend_extension);
+ self->f = bob::io::base::open(c_filename, mode, pretend_extension);
}
else {
- self->f = BobIoFile_Open(c_filename, mode);
+ self->f = bob::io::base::open(c_filename, mode);
}
}
catch (std::exception& e) {
@@ -191,6 +193,51 @@ static Py_ssize_t PyBobIoFile_Len (PyBobIoFileObject* self) {
return retval;
}
+int PyBobIo_AsTypenum (bob::io::base::array::ElementType type) {
+
+ switch(type) {
+ case bob::io::base::array::t_bool:
+ return NPY_BOOL;
+ case bob::io::base::array::t_int8:
+ return NPY_INT8;
+ case bob::io::base::array::t_int16:
+ return NPY_INT16;
+ case bob::io::base::array::t_int32:
+ return NPY_INT32;
+ case bob::io::base::array::t_int64:
+ return NPY_INT64;
+ case bob::io::base::array::t_uint8:
+ return NPY_UINT8;
+ case bob::io::base::array::t_uint16:
+ return NPY_UINT16;
+ case bob::io::base::array::t_uint32:
+ return NPY_UINT32;
+ case bob::io::base::array::t_uint64:
+ return NPY_UINT64;
+ case bob::io::base::array::t_float32:
+ return NPY_FLOAT32;
+ case bob::io::base::array::t_float64:
+ return NPY_FLOAT64;
+#ifdef NPY_FLOAT128
+ case bob::io::base::array::t_float128:
+ return NPY_FLOAT128;
+#endif
+ case bob::io::base::array::t_complex64:
+ return NPY_COMPLEX64;
+ case bob::io::base::array::t_complex128:
+ return NPY_COMPLEX128;
+#ifdef NPY_COMPLEX256
+ case bob::io::base::array::t_complex256:
+ return NPY_COMPLEX256;
+#endif
+ default:
+ PyErr_Format(PyExc_TypeError, "unsupported Bob/C++ element type (%s)", bob::io::base::array::stringize(type));
+ }
+
+ return NPY_NOTYPE;
+
+}
+
static PyObject* PyBobIoFile_GetIndex (PyBobIoFileObject* self, Py_ssize_t i) {
if (i < 0) i += self->f->size(); ///< adjust for negative indexing
@@ -200,14 +247,15 @@ static PyObject* PyBobIoFile_GetIndex (PyBobIoFileObject* self, Py_ssize_t i) {
return 0;
}
- const BobIoTypeinfo& info = self->f->type();
+ const bob::io::base::array::typeinfo& info = self->f->type();
npy_intp shape[NPY_MAXDIMS];
for (size_t k=0; k<info.nd; ++k) shape[k] = info.shape[k];
- if (info.dtype == NPY_NOTYPE) return 0; ///< failure
+ int type_num = PyBobIo_AsTypenum(info.dtype);
+ if (type_num == NPY_NOTYPE) return 0; ///< failure
- PyObject* retval = PyArray_SimpleNew(info.nd, shape, info.dtype);
+ PyObject* retval = PyArray_SimpleNew(info.nd, shape, type_num);
if (!retval) return 0;
auto retval_ = make_safe(retval);
@@ -240,17 +288,18 @@ static PyObject* PyBobIoFile_GetSlice (PyBobIoFileObject* self, PySliceObject* s
self->f->size(), &start, &stop, &step, &slicelength) < 0) return 0;
//creates the return array
- const BobIoTypeinfo& info = self->f->type();
+ const bob::io::base::array::typeinfo& info = self->f->type();
- if (info.dtype == NPY_NOTYPE) return 0; ///< failure
+ int type_num = PyBobIo_AsTypenum(info.dtype);
+ if (type_num == NPY_NOTYPE) return 0; ///< failure
- if (slicelength <= 0) return PyArray_SimpleNew(0, 0, info.dtype);
+ if (slicelength <= 0) return PyArray_SimpleNew(0, 0, type_num);
npy_intp shape[NPY_MAXDIMS];
shape[0] = slicelength;
for (size_t k=0; k<info.nd; ++k) shape[k+1] = info.shape[k];
- PyObject* retval = PyArray_SimpleNew(info.nd+1, shape, info.dtype);
+ PyObject* retval = PyArray_SimpleNew(info.nd+1, shape, type_num);
if (!retval) return 0;
auto retval_ = make_safe(retval);
@@ -334,14 +383,15 @@ static PyObject* PyBobIoFile_Read(PyBobIoFileObject* self, PyObject *args, PyObj
// reads the whole file in a single shot
- const BobIoTypeinfo& info = self->f->type_all();
+ const bob::io::base::array::typeinfo& info = self->f->type_all();
npy_intp shape[NPY_MAXDIMS];
for (size_t k=0; k<info.nd; ++k) shape[k] = info.shape[k];
- if (info.dtype == NPY_NOTYPE) return 0; ///< failure
+ int type_num = PyBobIo_AsTypenum(info.dtype);
+ if (type_num == NPY_NOTYPE) return 0; ///< failure
- PyObject* retval = PyArray_SimpleNew(info.nd, shape, info.dtype);
+ PyObject* retval = PyArray_SimpleNew(info.nd, shape, type_num);
if (!retval) return 0;
auto retval_ = make_safe(retval);
@@ -494,12 +544,13 @@ Returns the current position of the newly written array.\n\
"
);
-PyObject* PyBobIo_TypeinfoAsTuple (const BobIoTypeinfo& ti) {
+PyObject* PyBobIo_TypeInfoAsTuple (const bob::io::base::array::typeinfo& ti) {
- if (ti.dtype == NPY_NOTYPE) return 0;
+ int type_num = PyBobIo_AsTypenum(ti.dtype);
+ if (type_num == NPY_NOTYPE) return 0;
PyObject* retval = Py_BuildValue("NNN",
- reinterpret_cast<PyObject*>(PyArray_DescrFromType(ti.dtype)),
+ reinterpret_cast<PyObject*>(PyArray_DescrFromType(type_num)),
PyTuple_New(ti.nd), //shape
PyTuple_New(ti.nd) //strides
);
@@ -525,12 +576,12 @@ static PyObject* PyBobIoFile_Describe(PyBobIoFileObject* self, PyObject *args, P
PyObject* all = 0;
if (!PyArg_ParseTupleAndKeywords(args, kwds, "|O", kwlist, &all)) return 0;
- const BobIoTypeinfo* info = 0;
+ const bob::io::base::array::typeinfo* info = 0;
if (all && PyObject_IsTrue(all)) info = &self->f->type_all();
else info = &self->f->type();
/* Now return type description and tuples with shape and strides */
- return PyBobIo_TypeinfoAsTuple(*info);
+ return PyBobIo_TypeInfoAsTuple(*info);
}
PyDoc_STRVAR(s_describe_str, "describe");
diff --git a/bob/io/base/hdf5.cpp b/bob/io/base/hdf5.cpp
index 1b56fa6..dcb4249 100644
--- a/bob/io/base/hdf5.cpp
+++ b/bob/io/base/hdf5.cpp
@@ -7,7 +7,6 @@
#define BOB_IO_BASE_MODULE
#include <bob.io.base/api.h>
-#include <bob.io.base/HDF5File.h>
#include <boost/make_shared.hpp>
#include <numpy/arrayobject.h>
diff --git a/bob/io/base/cpp/CodecRegistry.h b/bob/io/base/include/bob.io.base/CodecRegistry.h
similarity index 86%
rename from bob/io/base/cpp/CodecRegistry.h
rename to bob/io/base/include/bob.io.base/CodecRegistry.h
index aa9501e..019bb57 100644
--- a/bob/io/base/cpp/CodecRegistry.h
+++ b/bob/io/base/include/bob.io.base/CodecRegistry.h
@@ -14,7 +14,7 @@
#include <string>
#include <boost/shared_ptr.hpp>
-#include <bob.io.base/api.h>
+#include <bob.io.base/File.h>
namespace bob { namespace io { namespace base {
@@ -47,9 +47,9 @@ namespace bob { namespace io { namespace base {
public: //object access
void registerExtension(const char* extension, const char* description,
- BobIoFileFactory factory);
+ file_factory_t factory);
- void deregisterFactory(BobIoFileFactory factory);
+ void deregisterFactory(file_factory_t factory);
void deregisterExtension(const char* ext);
/**
@@ -58,8 +58,8 @@ namespace bob { namespace io { namespace base {
*/
const char* getDescription(const char* ext);
- BobIoFileFactory findByExtension(const char* ext);
- BobIoFileFactory findByFilenameExtension(const char* fn);
+ file_factory_t findByExtension(const char* ext);
+ file_factory_t findByFilenameExtension(const char* fn);
bool isRegistered(const char* ext);
@@ -70,7 +70,7 @@ namespace bob { namespace io { namespace base {
// Not implemented
CodecRegistry( const CodecRegistry&);
- std::map<std::string, BobIoFileFactory> s_extension2codec;
+ std::map<std::string, file_factory_t> s_extension2codec;
std::map<std::string, std::string> s_extension2description;
bool s_ignore; ///< shall I ignore double-registrations?
diff --git a/bob/io/base/include/bob.io.base/File.h b/bob/io/base/include/bob.io.base/File.h
index 1b71c93..e41bccd 100644
--- a/bob/io/base/include/bob.io.base/File.h
+++ b/bob/io/base/include/bob.io.base/File.h
@@ -11,8 +11,9 @@
#ifndef BOB_IO_BASE_FILE_H
#define BOB_IO_BASE_FILE_H
-#include <bob.io.base/blitz_array.h>
#include <boost/shared_ptr.hpp>
+#include <bob.io.base/array.h>
+#include <bob.io.base/blitz_array.h>
namespace bob { namespace io { namespace base {
@@ -24,7 +25,7 @@ namespace bob { namespace io { namespace base {
public: //abstract API
- virtual ~File() {};
+ virtual ~File();
/**
* The filename this array codec current points to
@@ -32,16 +33,16 @@ namespace bob { namespace io { namespace base {
virtual const char* filename() const =0;
/**
- * The type information of data within this file, if it is supposed to be
- * read as as a sequence of arrays
+ * The typeinfo of data within this file, if it is supposed to be read as
+ * as a sequence of arrays
*/
- virtual const BobIoTypeinfo& type() const =0;
+ virtual const bob::io::base::array::typeinfo& type() const =0;
/**
- * The type information of data within this file, if it is supposed to be
- * read as a single array.
+ * The typeinfo of data within this file, if it is supposed to be read as
+ * a single array.
*/
- virtual const BobIoTypeinfo& type_all() const =0;
+ virtual const bob::io::base::array::typeinfo& type_all() const =0;
/**
* The number of arrays available in this file, if it is supposed to be
@@ -156,6 +157,28 @@ namespace bob { namespace io { namespace base {
};
+ /**
+ * @brief This defines the factory method F that can create codecs. Your
+ * task, as a codec developer is to create one of such methods for each of
+ * your codecs and statically register them to the codec registry.
+ *
+ * Here are the meanings of the mode flag that should be respected by your
+ * factory implementation:
+ *
+ * 'r': opens for reading only - no modifications can occur; it is an
+ * error to open a file that does not exist for read-only operations.
+ * 'w': opens for reading and writing, but truncates the file if it
+ * exists; it is not an error to open files that do not exist with
+ * this flag.
+ * 'a': opens for reading and writing - any type of modification can
+ * occur. If the file does not exist, this flag is effectively like
+ * 'w'.
+ *
+ * Returns a newly allocated File object that can read and write data to the
+ * file using a specific backend.
+ */
+ typedef boost::shared_ptr<File> (*file_factory_t) (const char* filename, char mode);
+
}}}
#endif /* BOB_IO_BASE_FILE_H */
diff --git a/bob/io/base/include/bob.io.base/HDF5Dataset.h b/bob/io/base/include/bob.io.base/HDF5Dataset.h
index 9059bab..5572410 100644
--- a/bob/io/base/include/bob.io.base/HDF5Dataset.h
+++ b/bob/io/base/include/bob.io.base/HDF5Dataset.h
@@ -13,7 +13,6 @@
#include <vector>
#include <boost/shared_ptr.hpp>
-#include <boost/weak_ptr.hpp>
#include <blitz/array.h>
#include <hdf5.h>
diff --git a/bob/io/base/include/bob.io.base/HDF5File.h b/bob/io/base/include/bob.io.base/HDF5File.h
index 4c80604..31c6594 100644
--- a/bob/io/base/include/bob.io.base/HDF5File.h
+++ b/bob/io/base/include/bob.io.base/HDF5File.h
@@ -12,9 +12,10 @@
#ifndef BOB_IO_BASE_HDF5FILE_H
#define BOB_IO_BASE_HDF5FILE_H
-#include <bob.io.base/HDF5Utils.h>
#include <boost/format.hpp>
+#include <bob.io.base/HDF5Utils.h>
+
namespace bob { namespace io { namespace base {
/**
diff --git a/bob/io/base/include/bob.io.base/HDF5Group.h b/bob/io/base/include/bob.io.base/HDF5Group.h
index 9071403..9dcd7a6 100644
--- a/bob/io/base/include/bob.io.base/HDF5Group.h
+++ b/bob/io/base/include/bob.io.base/HDF5Group.h
@@ -10,14 +10,14 @@
#ifndef BOB_IO_BASE_HDF5GROUP_H
#define BOB_IO_BASE_HDF5GROUP_H
-#include <bob.io.base/HDF5Types.h>
-#include <bob.io.base/HDF5Dataset.h>
-#include <bob.io.base/HDF5Attribute.h>
-
#include <boost/shared_ptr.hpp>
#include <boost/enable_shared_from_this.hpp>
#include <hdf5.h>
+#include <bob.io.base/HDF5Types.h>
+#include <bob.io.base/HDF5Dataset.h>
+#include <bob.io.base/HDF5Attribute.h>
+
namespace bob { namespace io { namespace base { namespace detail { namespace hdf5 {
class File;
diff --git a/bob/io/base/include/bob.io.base/HDF5Types.h b/bob/io/base/include/bob.io.base/HDF5Types.h
index 01c5cc5..d19eab3 100644
--- a/bob/io/base/include/bob.io.base/HDF5Types.h
+++ b/bob/io/base/include/bob.io.base/HDF5Types.h
@@ -10,6 +10,12 @@
#ifndef BOB_IO_BASE_HDF5TYPES_H
#define BOB_IO_BASE_HDF5TYPES_H
+#include <vector>
+#include <string>
+#include <boost/shared_ptr.hpp>
+#include <blitz/array.h>
+#include <hdf5.h>
+
/**
* Checks if the version of HDF5 installed is greater or equal to some set of
* values. (extracted from hdf5-1.8.7)
@@ -23,12 +29,6 @@
#include <bob.io.base/array.h>
-#include <vector>
-#include <string>
-#include <boost/shared_ptr.hpp>
-#include <blitz/array.h>
-#include <hdf5.h>
-
namespace bob { namespace io { namespace base {
/**
@@ -340,14 +340,14 @@ namespace bob { namespace io { namespace base {
HDF5Type(hdf5type type);
/**
- * Creates a HDF5Type from an BobIoTypeinfo
+ * Creates a HDF5Type from an bob::io::base::array::typeinfo
*/
- HDF5Type(const BobIoTypeinfo& ti);
+ HDF5Type(const bob::io::base::array::typeinfo& ti);
/**
* Creates a HDF5Type from a type enumeration and an explicit shape
*/
- HDF5Type(int dtype, const HDF5Shape& extents);
+ HDF5Type(bob::io::base::array::ElementType eltype, const HDF5Shape& extents);
/**
* Creates a HDF5Type from a type enumeration and an explicit shape
@@ -400,7 +400,7 @@ namespace bob { namespace io { namespace base {
/**
* Checks if an existing object is compatible with my type
*/
- bool compatible (const BobIoTypeinfo& value) const;
+ bool compatible (const bob::io::base::array::typeinfo& value) const;
/**
* Returns the HDF5Shape of this type
@@ -436,12 +436,12 @@ namespace bob { namespace io { namespace base {
* Returns a mapping between the current type and the supported element
* types in bob::io::base::array
*/
- int element_type() const;
+ bob::io::base::array::ElementType element_type() const;
/**
- * Copies this type information to a stock BobIoTypeinfo
+ * Copies this type information to a stock bob::io::base::array::typeinfo
*/
- void copy_to (BobIoTypeinfo& ti) const;
+ void copy_to (bob::io::base::array::typeinfo& ti) const;
private: //representation
diff --git a/bob/io/base/include/bob.io.base/HDF5Utils.h b/bob/io/base/include/bob.io.base/HDF5Utils.h
index d380dfd..670430e 100644
--- a/bob/io/base/include/bob.io.base/HDF5Utils.h
+++ b/bob/io/base/include/bob.io.base/HDF5Utils.h
@@ -27,13 +27,13 @@
#ifndef BOB_IO_BASE_HDF5UTILS_H
#define BOB_IO_BASE_HDF5UTILS_H
-#include <bob.io.base/HDF5Group.h>
-
#include <boost/filesystem.hpp>
#include <boost/shared_ptr.hpp>
#include <boost/enable_shared_from_this.hpp>
#include <hdf5.h>
+#include <bob.io.base/HDF5Group.h>
+
namespace bob { namespace io { namespace base { namespace detail { namespace hdf5 {
/**
diff --git a/bob/io/base/include/bob.io.base/api.h b/bob/io/base/include/bob.io.base/api.h
index 59b1dbb..001e8d4 100644
--- a/bob/io/base/include/bob.io.base/api.h
+++ b/bob/io/base/include/bob.io.base/api.h
@@ -13,11 +13,13 @@
#define BOB_IO_BASE_PREFIX "bob.io.base"
#define BOB_IO_BASE_FULL_NAME "bob.io.base._library"
-/* Maximum number of dimensions supported at this library */
-#define BOB_BLITZ_MAXDIMS 4
-
#include <Python.h>
+
#include <bob.io.base/config.h>
+#include <bob.io.base/File.h>
+#include <bob.io.base/CodecRegistry.h>
+#include <bob.io.base/HDF5File.h>
+
#include <boost/shared_ptr.hpp>
/*******************
@@ -27,37 +29,12 @@
/* Enum defining entries in the function table */
enum _PyBobIo_ENUM{
PyBobIo_APIVersion_NUM = 0,
- // C/C++ Type Information
- BobIoTypeinfo_Init_NUM,
- BobIoTypeinfo_Copy_NUM,
- BobIoTypeinfo_Set_NUM,
- BobIoTypeinfo_SetWithStrides_NUM,
- BobIoTypeinfo_SignedSet_NUM,
- BobIoTypeinfo_SignedSetWithStrides_NUM,
- BobIoTypeinfo_Reset_NUM,
- BobIoTypeinfo_IsValid_NUM,
- BobIoTypeinfo_HasValidShape_NUM,
- BobIoTypeinfo_ResetShape_NUM,
- BobIoTypeinfo_UpdateStrides_NUM,
- BobIoTypeinfo_Size_NUM,
- BobIoTypeinfo_BufferSize_NUM,
- BobIoTypeinfo_IsCompatible_NUM,
- BobIoTypeinfo_Str_NUM,
- // Data reordering
- BobIoReorder_RowToCol_NUM,
- BobIoReorder_ColToRow_NUM,
- BobIoReorder_RowToColComplex_NUM,
- BobIoReorder_ColToRowComplex_NUM,
// Bindings for bob.io.base.File
PyBobIoFile_Type_NUM,
PyBobIoFileIterator_Type_NUM,
- // File loading and data type peeking
- BobIoFile_Open_NUM,
- BobIoFile_OpenWithExtension_NUM,
- BobIoFile_Peek_NUM,
- BobIoFile_PeekAll_NUM,
// I/O generic bindings
- PyBobIo_TypeinfoAsTuple_NUM,
+ PyBobIo_AsTypenum_NUM,
+ PyBobIo_TypeInfoAsTuple_NUM,
PyBobIo_FilenameConverter_NUM,
// HDF5 bindings
PyBobIoHDF5File_Type_NUM,
@@ -78,88 +55,11 @@ enum _PyBobIo_ENUM{
#define PyBobIo_APIVersion_TYPE int
-/********************
- * Type Information *
- ********************/
-
-typedef struct {
-
- int dtype; ///< data type
- size_t nd; ///< number of dimensions
- size_t shape[BOB_BLITZ_MAXDIMS+1]; ///< length along each dimension
- size_t stride[BOB_BLITZ_MAXDIMS+1]; ///< strides along each dimension
-
-} BobIoTypeinfo;
-
-
-#define BobIoTypeinfo_Init_RET void
-#define BobIoTypeinfo_Init_PROTO (BobIoTypeinfo*)
-
-#define BobIoTypeinfo_Copy_RET int
-#define BobIoTypeinfo_Copy_PROTO (BobIoTypeinfo*, const BobIoTypeinfo*)
-
-#define BobIoTypeinfo_Set_RET int
-#define BobIoTypeinfo_Set_PROTO (BobIoTypeinfo*, int, size_t, const size_t*)
-
-#define BobIoTypeinfo_SetWithStrides_RET int
-#define BobIoTypeinfo_SetWithStrides_PROTO (BobIoTypeinfo*, int, size_t, const size_t*, const size_t*)
-
-#define BobIoTypeinfo_SignedSet_RET int
-#define BobIoTypeinfo_SignedSet_PROTO (BobIoTypeinfo*, int, Py_ssize_t, const Py_ssize_t*)
-
-#define BobIoTypeinfo_SignedSetWithStrides_RET int
-#define BobIoTypeinfo_SignedSetWithStrides_PROTO (BobIoTypeinfo*, int, Py_ssize_t, const Py_ssize_t*, const Py_ssize_t*)
-
-#define BobIoTypeinfo_Reset_RET void
-#define BobIoTypeinfo_Reset_PROTO (BobIoTypeinfo*)
-
-#define BobIoTypeinfo_IsValid_RET bool
-#define BobIoTypeinfo_IsValid_PROTO (const BobIoTypeinfo*)
-
-#define BobIoTypeinfo_HasValidShape_RET bool
-#define BobIoTypeinfo_HasValidShape_PROTO (const BobIoTypeinfo*)
-
-#define BobIoTypeinfo_ResetShape_RET void
-#define BobIoTypeinfo_ResetShape_PROTO (BobIoTypeinfo*)
-
-#define BobIoTypeinfo_UpdateStrides_RET int
-#define BobIoTypeinfo_UpdateStrides_PROTO (BobIoTypeinfo*)
-
-#define BobIoTypeinfo_Size_RET size_t
-#define BobIoTypeinfo_Size_PROTO (const BobIoTypeinfo*)
-
-#define BobIoTypeinfo_BufferSize_RET size_t
-#define BobIoTypeinfo_BufferSize_PROTO (const BobIoTypeinfo*)
-
-#define BobIoTypeinfo_IsCompatible_RET bool
-#define BobIoTypeinfo_IsCompatible_PROTO (const BobIoTypeinfo*, const BobIoTypeinfo*)
-
-#define BobIoTypeinfo_Str_RET std::string
-#define BobIoTypeinfo_Str_PROTO (const BobIoTypeinfo*)
-
-/********************
- * Array reordering *
- ********************/
-
-#define BobIoReorder_RowToCol_RET int
-#define BobIoReorder_RowToCol_PROTO (const void*, void*, const BobIoTypeinfo*)
-
-#define BobIoReorder_ColToRow_RET int
-#define BobIoReorder_ColToRow_PROTO (const void*, void*, const BobIoTypeinfo*)
-
-#define BobIoReorder_RowToColComplex_RET int
-#define BobIoReorder_RowToColComplex_PROTO (const void*, void*, void*, const BobIoTypeinfo*)
-
-#define BobIoReorder_ColToRowComplex_RET int
-#define BobIoReorder_ColToRowComplex_PROTO (const void*, const void*, void*, const BobIoTypeinfo*)
-
/**********************************
* Bindings for bob.io.base.File *
**********************************/
/* Type definition for PyBobIoFileObject */
-
-namespace bob { namespace io { namespace base { class File; }}}
typedef struct {
PyObject_HEAD
@@ -181,28 +81,15 @@ typedef struct {
#define PyBobIoFileIterator_Type_TYPE PyTypeObject
-/**************************************
- * File loading and data type peeking *
- **************************************/
-
-#define BobIoFile_Open_RET boost::shared_ptr<bob::io::base::File>
-#define BobIoFile_Open_PROTO (const char*, char)
-
-#define BobIoFile_OpenWithExtension_RET boost::shared_ptr<bob::io::base::File>
-#define BobIoFile_OpenWithExtension_PROTO (const char*, char, const char*)
-
-#define BobIoFile_Peek_RET void
-#define BobIoFile_Peek_PROTO (const char*, BobIoTypeinfo*)
-
-#define BobIoFile_PeekAll_RET void
-#define BobIoFile_PeekAll_PROTO (const char*, BobIoTypeinfo*)
-
/************************
* I/O generic bindings *
************************/
-#define PyBobIo_TypeinfoAsTuple_RET PyObject*
-#define PyBobIo_TypeinfoAsTuple_PROTO (const BobIoTypeinfo& ti)
+#define PyBobIo_AsTypenum_RET int
+#define PyBobIo_AsTypenum_PROTO (bob::io::base::array::ElementType et)
+
+#define PyBobIo_TypeInfoAsTuple_RET PyObject*
+#define PyBobIo_TypeInfoAsTuple_PROTO (const bob::io::base::array::typeinfo& ti)
#define PyBobIo_FilenameConverter_RET int
#define PyBobIo_FilenameConverter_PROTO (PyObject* o, PyObject** b)
@@ -211,7 +98,6 @@ typedef struct {
* HDF5 bindings *
*****************/
-namespace bob { namespace io { namespace base { class HDF5File; }}}
typedef struct {
PyObject_HEAD
@@ -232,30 +118,8 @@ typedef struct {
* Code Registration and De-registration *
*****************************************/
-/**
- * @brief This defines the factory method F that can create codecs. Your
- * task, as a codec developer is to create one of such methods for each of
- * your codecs and statically register them to the codec registry.
- *
- * Here are the meanings of the mode flag that should be respected by your
- * factory implementation:
- *
- * 'r': opens for reading only - no modifications can occur; it is an
- * error to open a file that does not exist for read-only operations.
- * 'w': opens for reading and writing, but truncates the file if it
- * exists; it is not an error to open files that do not exist with
- * this flag.
- * 'a': opens for reading and writing - any type of modification can
- * occur. If the file does not exist, this flag is effectively like
- * 'w'.
- *
- * Returns a newly allocated File object that can read and write data to the
- * file using a specific backend.
- */
-typedef boost::shared_ptr<bob::io::base::File> (*BobIoFileFactory) (const char* filename, char mode);
-
#define PyBobIoCodec_Register_RET int
-#define PyBobIoCodec_Register_PROTO (const char* extension, const char* description, BobIoFileFactory factory)
+#define PyBobIoCodec_Register_PROTO (const char* extension, const char* description, bob::io::base::file_factory_t factory)
#define PyBobIoCodec_Deregister_RET int
#define PyBobIoCodec_Deregister_PROTO (const char* extension)
@@ -276,52 +140,6 @@ typedef boost::shared_ptr<bob::io::base::File> (*BobIoFileFactory) (const char*
extern int PyBobIo_APIVersion;
- /********************
- * Type Information *
- ********************/
-
- BobIoTypeinfo_Init_RET BobIoTypeinfo_Init BobIoTypeinfo_Init_PROTO;
-
- BobIoTypeinfo_Copy_RET BobIoTypeinfo_Copy BobIoTypeinfo_Copy_PROTO;
-
- BobIoTypeinfo_Set_RET BobIoTypeinfo_Set BobIoTypeinfo_Set_PROTO;
-
- BobIoTypeinfo_SetWithStrides_RET BobIoTypeinfo_SetWithStrides BobIoTypeinfo_SetWithStrides_PROTO;
-
- BobIoTypeinfo_SignedSet_RET BobIoTypeinfo_SignedSet BobIoTypeinfo_SignedSet_PROTO;
-
- BobIoTypeinfo_SignedSetWithStrides_RET BobIoTypeinfo_SignedSetWithStrides BobIoTypeinfo_SignedSetWithStrides_PROTO;
-
- BobIoTypeinfo_Reset_RET BobIoTypeinfo_Reset BobIoTypeinfo_Reset_PROTO;
-
- BobIoTypeinfo_IsValid_RET BobIoTypeinfo_IsValid BobIoTypeinfo_IsValid_PROTO;
-
- BobIoTypeinfo_HasValidShape_RET BobIoTypeinfo_HasValidShape BobIoTypeinfo_HasValidShape_PROTO;
-
- BobIoTypeinfo_ResetShape_RET BobIoTypeinfo_ResetShape BobIoTypeinfo_ResetShape_PROTO;
-
- BobIoTypeinfo_UpdateStrides_RET BobIoTypeinfo_UpdateStrides BobIoTypeinfo_UpdateStrides_PROTO;
-
- BobIoTypeinfo_Size_RET BobIoTypeinfo_Size BobIoTypeinfo_Size_PROTO;
-
- BobIoTypeinfo_BufferSize_RET BobIoTypeinfo_BufferSize BobIoTypeinfo_BufferSize_PROTO;
-
- BobIoTypeinfo_IsCompatible_RET BobIoTypeinfo_IsCompatible BobIoTypeinfo_IsCompatible_PROTO;
-
- BobIoTypeinfo_Str_RET BobIoTypeinfo_Str BobIoTypeinfo_Str_PROTO;
-
- /********************
- * Array reordering *
- ********************/
-
- BobIoReorder_RowToCol_RET BobIoReorder_RowToCol BobIoReorder_RowToCol_PROTO;
-
- BobIoReorder_ColToRow_RET BobIoReorder_ColToRow BobIoReorder_ColToRow_PROTO;
-
- BobIoReorder_RowToColComplex_RET BobIoReorder_RowToColComplex BobIoReorder_RowToColComplex_PROTO;
-
- BobIoReorder_ColToRowComplex_RET BobIoReorder_ColToRowComplex BobIoReorder_ColToRowComplex_PROTO;
-
/**********************************
* Bindings for bob.io.base.File *
**********************************/
@@ -329,29 +147,19 @@ typedef boost::shared_ptr<bob::io::base::File> (*BobIoFileFactory) (const char*
extern PyBobIoFile_Type_TYPE PyBobIoFile_Type;
extern PyBobIoFileIterator_Type_TYPE PyBobIoFileIterator_Type;
- /**************************************
- * File loading and data type peeking *
- **************************************/
-
- BobIoFile_Open_RET BobIoFile_Open BobIoFile_Open_PROTO;
-
- BobIoFile_OpenWithExtension_RET BobIoFile_OpenWithExtension BobIoFile_OpenWithExtension_PROTO;
-
- BobIoFile_Peek_RET BobIoFile_Peek BobIoFile_Peek_PROTO;
-
- BobIoFile_PeekAll_RET BobIoFile_PeekAll BobIoFile_PeekAll_PROTO;
-
/************************
* I/O generic bindings *
************************/
- PyBobIo_TypeinfoAsTuple_RET PyBobIo_TypeinfoAsTuple PyBobIo_TypeinfoAsTuple_PROTO;
+ PyBobIo_AsTypenum_RET PyBobIo_AsTypenum PyBobIo_AsTypenum_PROTO;
+
+ PyBobIo_TypeInfoAsTuple_RET PyBobIo_TypeInfoAsTuple PyBobIo_TypeInfoAsTuple_PROTO;
PyBobIo_FilenameConverter_RET PyBobIo_FilenameConverter PyBobIo_FilenameConverter_PROTO;
- /*****************
- * HDF5 bindings *
- *****************/
+/*****************
+ * HDF5 bindings *
+ *****************/
extern PyBobIoHDF5File_Type_TYPE PyBobIoHDF5File_Type;
@@ -359,17 +167,17 @@ typedef boost::shared_ptr<bob::io::base::File> (*BobIoFileFactory) (const char*
PyBobIoHDF5File_Converter_RET PyBobIoHDF5File_Converter PyBobIoHDF5File_Converter_PROTO;
- /*****************************************
- * Code Registration and De-registration *
- *****************************************/
+/*****************************************
+ * Code Registration and De-registration *
+ *****************************************/
- PyBobIoCodec_Register_RET PyBobIoCodec_Register PyBobIoCodec_Register_PROTO;
+ PyBobIoCodec_Register_RET PyBobIoCodec_Register PyBobIoCodec_Register_PROTO;
- PyBobIoCodec_Deregister_RET PyBobIoCodec_Deregister PyBobIoCodec_Deregister_PROTO;
+ PyBobIoCodec_Deregister_RET PyBobIoCodec_Deregister PyBobIoCodec_Deregister_PROTO;
- PyBobIoCodec_IsRegistered_RET PyBobIoCodec_IsRegistered PyBobIoCodec_IsRegistered_PROTO;
+ PyBobIoCodec_IsRegistered_RET PyBobIoCodec_IsRegistered PyBobIoCodec_IsRegistered_PROTO;
- PyBobIoCodec_GetDescription_RET PyBobIoCodec_GetDescription PyBobIoCodec_GetDescription_PROTO;
+ PyBobIoCodec_GetDescription_RET PyBobIoCodec_GetDescription PyBobIoCodec_GetDescription_PROTO;
#else
@@ -391,52 +199,6 @@ typedef boost::shared_ptr<bob::io::base::File> (*BobIoFileFactory) (const char*
# define PyBobIo_APIVersion (*(PyBobIo_APIVersion_TYPE *)PyBobIo_API[PyBobIo_APIVersion_NUM])
- /********************
- * Type Information *
- ********************/
-
-# define BobIoTypeinfo_Init (*(BobIoTypeinfo_Init_RET (*)BobIoTypeinfo_Init_PROTO) PyBobIo_API[BobIoTypeinfo_Init_NUM])
-
-# define BobIoTypeinfo_Copy (*(BobIoTypeinfo_Copy_RET (*)BobIoTypeinfo_Copy_PROTO) PyBobIo_API[BobIoTypeinfo_Copy_NUM])
-
-# define BobIoTypeinfo_Set (*(BobIoTypeinfo_Set_RET (*)BobIoTypeinfo_Set_PROTO) PyBobIo_API[BobIoTypeinfo_Set_NUM])
-
-# define BobIoTypeinfo_SetWithStrides (*(BobIoTypeinfo_SetWithStrides_RET (*)BobIoTypeinfo_SetWithStrides_PROTO) PyBobIo_API[BobIoTypeinfo_SetWithStrides_NUM])
-
-# define BobIoTypeinfo_SignedSet (*(BobIoTypeinfo_SignedSet_RET (*)BobIoTypeinfo_SignedSet_PROTO) PyBobIo_API[BobIoTypeinfo_SignedSet_NUM])
-
-# define BobIoTypeinfo_SignedSetWithStrides (*(BobIoTypeinfo_SignedSetWithStrides_RET (*)BobIoTypeinfo_SignedSetWithStrides_PROTO) PyBobIo_API[BobIoTypeinfo_SignedSetWithStrides_NUM])
-
-# define BobIoTypeinfo_Reset (*(BobIoTypeinfo_Reset_RET (*)BobIoTypeinfo_Reset_PROTO) PyBobIo_API[BobIoTypeinfo_Reset_NUM])
-
-# define BobIoTypeinfo_IsValid (*(BobIoTypeinfo_IsValid_RET (*)BobIoTypeinfo_IsValid_PROTO) PyBobIo_API[BobIoTypeinfo_IsValid_NUM])
-
-# define BobIoTypeinfo_HasValidShape (*(BobIoTypeinfo_HasValidShape_RET (*)BobIoTypeinfo_HasValidShape_PROTO) PyBobIo_API[BobIoTypeinfo_HasValidShape_NUM])
-
-# define BobIoTypeinfo_ResetShape (*(BobIoTypeinfo_ResetShape_RET (*)BobIoTypeinfo_ResetShape_PROTO) PyBobIo_API[BobIoTypeinfo_ResetShape_NUM])
-
-# define BobIoTypeinfo_UpdateStrides (*(BobIoTypeinfo_UpdateStrides_RET (*)BobIoTypeinfo_UpdateStrides_PROTO) PyBobIo_API[BobIoTypeinfo_UpdateStrides_NUM])
-
-# define BobIoTypeinfo_Size (*(BobIoTypeinfo_Size_RET (*)BobIoTypeinfo_Size_PROTO) PyBobIo_API[BobIoTypeinfo_Size_NUM])
-
-# define BobIoTypeinfo_BufferSize (*(BobIoTypeinfo_BufferSize_RET (*)BobIoTypeinfo_BufferSize_PROTO) PyBobIo_API[BobIoTypeinfo_BufferSize_NUM])
-
-# define BobIoTypeinfo_IsCompatible (*(BobIoTypeinfo_IsCompatible_RET (*)BobIoTypeinfo_IsCompatible_PROTO) PyBobIo_API[BobIoTypeinfo_IsCompatible_NUM])
-
-# define BobIoTypeinfo_Str (*(BobIoTypeinfo_Str_RET (*)BobIoTypeinfo_Str_PROTO) PyBobIo_API[BobIoTypeinfo_Str_NUM])
-
- /********************
- * Array reordering *
- ********************/
-
-# define BobIoReorder_RowToCol (*(BobIoReorder_RowToCol_RET (*)BobIoReorder_RowToCol_PROTO) PyBobIo_API[BobIoReorder_RowToCol_NUM])
-
-# define BobIoReorder_ColToRow (*(BobIoReorder_ColToRow_RET (*)BobIoReorder_ColToRow_PROTO) PyBobIo_API[BobIoReorder_ColToRow_NUM])
-
-# define BobIoReorder_RowToColComplex (*(BobIoReorder_RowToColComplex_RET (*)BobIoReorder_RowToColComplex_PROTO) PyBobIo_API[BobIoReorder_RowToColComplex_NUM])
-
-# define BobIoReorder_ColToRowComplex (*(BobIoReorder_ColToRowComplex_RET (*)BobIoReorder_ColToRowComplex_PROTO) PyBobIo_API[BobIoReorder_ColToRowComplex_NUM])
-
/*****************************
* Bindings for bob.io.File *
*****************************/
@@ -444,23 +206,13 @@ typedef boost::shared_ptr<bob::io::base::File> (*BobIoFileFactory) (const char*
# define PyBobIoFile_Type (*(PyBobIoFile_Type_TYPE *)PyBobIo_API[PyBobIoFile_Type_NUM])
# define PyBobIoFileIterator_Type (*(PyBobIoFileIterator_Type_TYPE *)PyBobIo_API[PyBobIoFileIterator_Type_NUM])
- /**************************************
- * File loading and data type peeking *
- **************************************/
-
-# define BobIoFile_Open (*(BobIoFile_Open_RET (*)BobIoFile_Open_PROTO) PyBobIo_API[BobIoFile_Open_NUM])
-
-# define BobIoFile_OpenWithExtension (*(BobIoFile_OpenWithExtension_RET (*)BobIoFile_OpenWithExtension_PROTO) PyBobIo_API[BobIoFile_OpenWithExtension_NUM])
-
-# define BobIoFile_Peek (*(BobIoFile_Peek_RET (*)BobIoFile_Peek_PROTO) PyBobIo_API[BobIoFile_Peek_NUM])
-
-# define BobIoFile_PeekAll (*(BobIoFile_PeekAll_RET (*)BobIoFile_PeekAll_PROTO) PyBobIo_API[BobIoFile_PeekAll_NUM])
-
/************************
* I/O generic bindings *
************************/
-# define PyBobIo_TypeinfoAsTuple (*(PyBobIo_TypeinfoAsTuple_RET (*)PyBobIo_TypeinfoAsTuple_PROTO) PyBobIo_API[PyBobIo_TypeinfoAsTuple_NUM])
+# define PyBobIo_AsTypenum (*(PyBobIo_AsTypenum_RET (*)PyBobIo_AsTypenum_PROTO) PyBobIo_API[PyBobIo_AsTypenum_NUM])
+
+# define PyBobIo_TypeInfoAsTuple (*(PyBobIo_TypeInfoAsTuple_RET (*)PyBobIo_TypeInfoAsTuple_PROTO) PyBobIo_API[PyBobIo_TypeInfoAsTuple_NUM])
# define PyBobIo_FilenameConverter (*(PyBobIo_FilenameConverter_RET (*)PyBobIo_FilenameConverter_PROTO) PyBobIo_API[PyBobIo_FilenameConverter_NUM])
diff --git a/bob/io/base/include/bob.io.base/array.h b/bob/io/base/include/bob.io.base/array.h
index 5bbe268..570c09f 100644
--- a/bob/io/base/include/bob.io.base/array.h
+++ b/bob/io/base/include/bob.io.base/array.h
@@ -11,15 +11,14 @@
#ifndef BOB_IO_BASE_ARRAY_INTERFACE_H
#define BOB_IO_BASE_ARRAY_INTERFACE_H
-#include <bob.blitz/cppapi.h>
-#include <bob.io.base/api.h>
-
#include <stdexcept>
#include <string>
#include <boost/shared_ptr.hpp>
#include <blitz/array.h>
+#include <bob.io.base/array_type.h>
+
/* MinGW flags */
#ifdef _WIN32
#undef interface
@@ -30,6 +29,170 @@
*/
namespace bob { namespace io { namespace base { namespace array {
+ /**
+ * @brief Encapsulation of special type information of interfaces.
+ */
+ struct typeinfo {
+
+ ElementType dtype; ///< data type
+ size_t nd; ///< number of dimensions
+ size_t shape[BOB_MAX_DIM+1]; ///< length along each dimension
+ size_t stride[BOB_MAX_DIM+1]; ///< strides along each dimension
+
+ /**
+ * @brief Default constructor
+ */
+ typeinfo();
+
+ /**
+ * @brief Simplification to build a typeinfo from a size
+ */
+ template <typename T> typeinfo(ElementType dtype_, T nd_) {
+ set(dtype_, nd_);
+ }
+
+ /**
+ * @brief Simplification to build a typeinfo from a shape pointer.
+ */
+ template <typename T> typeinfo(ElementType dtype_, T nd_, const T* shape_) {
+ set(dtype_, nd_, shape_);
+ }
+
+ /**
+ * @brief Copies information from another typeinfo
+ */
+ typeinfo(const typeinfo& other);
+
+ /**
+ * @brief Assignment
+ */
+ typeinfo& operator= (const typeinfo& other);
+
+ /**
+ * @brief Builds with type and number of dimensions, but set the shape and
+ * strides to all zeros.
+ */
+ template <typename T>
+ void set(ElementType dtype_, T nd_) {
+ dtype = dtype_;
+ nd = nd_;
+ reset_shape();
+ }
+
+ /**
+ * @brief Set to specific values
+ */
+ template <typename T>
+ void set(ElementType dtype_, T nd_, const T* shape_) {
+ dtype = dtype_;
+ set_shape(nd_, shape_);
+ }
+
+ /**
+ * @brief Set to specific values, including strides
+ */
+ template <typename T>
+ void set(ElementType dtype_, T nd_, const T* shape_,
+ const T* stride_) {
+ dtype = dtype_;
+ nd = nd_;
+ for (size_t k=0; k<nd; ++k) {
+ shape[k] = shape_[k];
+ stride[k] = stride_[k];
+ }
+ }
+
+ /**
+ * @brief Reset to defaults -- as if uninitialized.
+ */
+ void reset();
+
+ /**
+ * @brief Is this a valid type information?
+ */
+ bool is_valid() const;
+
+ /**
+ * @brief Does this has a valid shape information?
+ */
+ bool has_valid_shape() const;
+
+ /**
+ * @brief sets the shape
+ */
+ template <typename T> void set_shape(T nd_, const T* shape_) {
+ if (nd_ > (BOB_MAX_DIM+1))
+ throw std::runtime_error("unsupported number of dimensions");
+ nd = nd_;
+ for (size_t k=0; k<nd; ++k) shape[k] = shape_[k];
+ update_strides();
+ }
+
+ /**
+ * @brief resets the shape to all zeros
+ */
+ void reset_shape();
+
+ /**
+ * @brief Update my own stride vector. Called automatically after any use
+ * of set_shape().
+ */
+ void update_strides();
+
+ /**
+ * @brief Returns the total number of elements available
+ */
+ size_t size() const;
+
+ /**
+ * @brief Returns the size of each element
+ */
+ inline size_t item_size() const { return getElementSize(dtype); }
+
+ /**
+ * @brief Returns the total size (in bytes) of the buffer that I'm
+ * associated with.
+ */
+ size_t buffer_size() const;
+
+ /**
+ * @brief Returns the item type description
+ */
+ const char* item_str() const { return stringize(dtype); }
+
+ /**
+ * @brief Checks compatibility with other typeinfo
+ */
+ bool is_compatible(const typeinfo& other) const;
+
+ /**
+ * @brief Formats and returns a string containing the full typeinfo
+ * description.
+ */
+ std::string str() const;
+
+ /**
+ * @brief Make it easy to set for blitz::Array<T,N>
+ */
+ template <typename T, int N> void set(const blitz::Array<T,N>& array) {
+ dtype = getElementType<T>();
+ set_shape(array.shape());
+ }
+
+ template <typename T, int N>
+ void set(boost::shared_ptr<blitz::Array<T,N> >& array) {
+ dtype = getElementType<T>();
+ set_shape(array->shape());
+ }
+
+ template <int N> void set_shape(const blitz::TinyVector<int,N>& tv_shape) {
+ nd = N;
+ for (size_t k=0; k<nd; ++k) shape[k] = tv_shape(k);
+ update_strides();
+ }
+
+ };
+
/**
* @brief The interface manager introduces a concept for managing the
* interfaces that can be handled as C-style arrays. It encapsulates methods
@@ -62,12 +225,12 @@ namespace bob { namespace io { namespace base { namespace array {
* @brief Re-allocates this interface taking into consideration new
* requirements. The internal memory should be considered uninitialized.
*/
- virtual void set (const BobIoTypeinfo& req) =0;
+ virtual void set (const typeinfo& req) =0;
/**
* @brief Type information for this interface.
*/
- virtual const BobIoTypeinfo& type() const =0;
+ virtual const typeinfo& type() const =0;
/**
* @brief Borrows a reference from the underlying memory. This means
diff --git a/bob/io/base/include/bob.io.base/array_type.h b/bob/io/base/include/bob.io.base/array_type.h
new file mode 100644
index 0000000..89eb1e2
--- /dev/null
+++ b/bob/io/base/include/bob.io.base/array_type.h
@@ -0,0 +1,162 @@
+/**
+ * @date Sat Apr 9 18:10:10 2011 +0200
+ * @author Laurent El Shafey <Laurent.El-Shafey@idiap.ch>
+ *
+ * @brief This file contains information about the supported arrays
+ *
+ * Copyright (C) Idiap Research Institute, Martigny, Switzerland
+ */
+
+#ifndef BOB_IO_BASE_ARRAY_TYPE_H
+#define BOB_IO_BASE_ARRAY_TYPE_H
+
+#include <stdint.h>
+#include <cstdlib>
+#include <complex>
+
+/**
+ * @ingroup IO_ARRAY
+ * @brief This macro defines the maximum number of dimensions supported by bob.
+ * A variable in the bob.io.array namespace is created from this macro
+ * receiving the same value. Use that variable on your programs, or this macro
+ * on your preprocessor code.
+ */
+#define BOB_MAX_DIM 4
+
+namespace bob { namespace io { namespace base { namespace array {
+
+ /**
+ * @brief Enumeration of the supported type for multidimensional arrays
+ * @warning float128 and complex256 are defined but currently not
+ * supported
+ */
+ typedef enum ElementType {
+ t_unknown=0,
+ t_bool=1,
+ t_int8=2,
+ t_int16=3,
+ t_int32=4,
+ t_int64=5,
+ t_uint8=6,
+ t_uint16=7,
+ t_uint32=8,
+ t_uint64=9,
+ t_float32=10,
+ t_float64=11,
+ t_float128=12,
+ t_complex64=13,
+ t_complex128=14,
+ t_complex256=15
+ } ElementType;
+
+ /**
+ * @brief Maximum number of supported dimensions for multidimensional
+ * arrays.
+ */
+ const size_t N_MAX_DIMENSIONS_ARRAY = BOB_MAX_DIM;
+
+ /**
+ * @brief These are some type to element type conversions
+ */
+ template<typename T> ElementType getElementType() {
+ return t_unknown;
+ }
+
+ /**
+ * @brief Some specializations that convert type to element type.
+ */
+ template<> inline ElementType getElementType<bool>() { return t_bool; }
+ template<> inline ElementType getElementType<int8_t>() { return t_int8; }
+ template<> inline ElementType getElementType<int16_t>()
+ { return t_int16; }
+ template<> inline ElementType getElementType<int32_t>()
+ { return t_int32; }
+ template<> inline ElementType getElementType<int64_t>()
+ { return t_int64; }
+ template<> inline ElementType getElementType<uint8_t>()
+ { return t_uint8; }
+ template<> inline ElementType getElementType<uint16_t>()
+ { return t_uint16; }
+ template<> inline ElementType getElementType<uint32_t>()
+ { return t_uint32; }
+ template<> inline ElementType getElementType<uint64_t>()
+ { return t_uint64; }
+ template<> inline ElementType getElementType<float>()
+ { return t_float32; }
+ template<> inline ElementType getElementType<double>()
+ { return t_float64; }
+ template<> inline ElementType getElementType<long double>()
+ { return t_float128; }
+ template<> inline ElementType getElementType<std::complex<float> >()
+ { return t_complex64; }
+ template<> inline ElementType getElementType<std::complex<double> >()
+ { return t_complex128; }
+ template<> inline ElementType getElementType<std::complex<long double> >()
+ { return t_complex256; }
+
+ /**
+ * @brief These are some type to element size conversions
+ */
+ template<typename T> size_t getElementSize() {
+ return 0;
+ }
+
+ /**
+ * @brief Some specializations that convert the types we handle properly
+ */
+ template<> inline size_t getElementSize<bool>() { return sizeof(bool); }
+ template<> inline size_t getElementSize<int8_t>()
+ { return sizeof(int8_t); }
+ template<> inline size_t getElementSize<int16_t>()
+ { return sizeof(int16_t); }
+ template<> inline size_t getElementSize<int32_t>()
+ { return sizeof(int32_t); }
+ template<> inline size_t getElementSize<int64_t>()
+ { return sizeof(int64_t); }
+ template<> inline size_t getElementSize<uint8_t>()
+ { return sizeof(uint8_t); }
+ template<> inline size_t getElementSize<uint16_t>()
+ { return sizeof(uint16_t); }
+ template<> inline size_t getElementSize<uint32_t>()
+ { return sizeof(uint32_t); }
+ template<> inline size_t getElementSize<uint64_t>()
+ { return sizeof(uint64_t); }
+ template<> inline size_t getElementSize<float>()
+ { return sizeof(float); }
+ template<> inline size_t getElementSize<double>()
+ { return sizeof(double); }
+ template<> inline size_t getElementSize<long double>()
+ { return sizeof(long double); }
+ template<> inline size_t getElementSize<std::complex<float> >()
+ { return sizeof(std::complex<float>); }
+ template<> inline size_t getElementSize<std::complex<double> >()
+ { return sizeof(std::complex<double>); }
+ template<> inline size_t getElementSize<std::complex<long double> >()
+ { return sizeof(std::complex<long double>); }
+
+ /**
+ * @brief Returns the type size given the enumeration
+ */
+ size_t getElementSize(ElementType t);
+
+ /**
+ * @brief Gets a string representation of an element type value
+ */
+ const char* stringize(ElementType t);
+
+ /**
+ * @brief Equivalent to call stringize() on the result of
+ * getElementType<T>().
+ */
+ template<typename T> const char* stringize() {
+ return stringize(getElementType<T>());
+ }
+
+ /**
+ * @brief Returns the ElementType given the string representation
+ */
+ ElementType unstringize(const char* name);
+
+}}}}
+
+#endif /* BOB_IO_BASE_ARRAY_TYPE_H */
diff --git a/bob/io/base/include/bob.io.base/array_utils.h b/bob/io/base/include/bob.io.base/array_utils.h
index 2ccf320..8fdfa77 100644
--- a/bob/io/base/include/bob.io.base/array_utils.h
+++ b/bob/io/base/include/bob.io.base/array_utils.h
@@ -22,9 +22,9 @@
namespace bob { namespace io { namespace base { namespace array {
/**
- * @brief Fills in shape and stride starting from a type information object
+ * @brief Fills in shape and stride starting from a typeinfo object
*/
- template <int N> void set_shape_and_stride(const BobIoTypeinfo& info,
+ template <int N> void set_shape_and_stride(const typeinfo& info,
blitz::TinyVector<int,N>& shape, blitz::TinyVector<int,N>& stride) {
for (int k=0; k<N; ++k) {
shape[k] = info.shape[k];
@@ -43,19 +43,19 @@ namespace bob { namespace io { namespace base { namespace array {
template <typename T, int N>
blitz::Array<T,N> wrap(const interface& buf) {
- const BobIoTypeinfo& type = buf.type();
+ const typeinfo& type = buf.type();
if (!buf.ptr()) throw std::runtime_error("empty buffer");
- if (type.dtype != PyBlitzArrayCxx_CToTypenum<T>()) {
+ if (type.dtype != bob::io::base::array::getElementType<T>()) {
boost::format m("cannot efficiently retrieve blitz::Array<%s,%d> from buffer of type '%s'");
- m % PyBlitzArray_TypenumAsString(PyBlitzArrayCxx_CToTypenum<T>()) % N % BobIoTypeinfo_Str(&type);
+ m % stringize<T>() % N % type.str();
throw std::runtime_error(m.str());
}
if (type.nd != N) {
boost::format m("cannot retrieve blitz::Array<%s,%d> from buffer of type '%s'");
- m % PyBlitzArray_TypenumAsString(PyBlitzArrayCxx_CToTypenum<T>()) % N % BobIoTypeinfo_Str(&type);
+ m % stringize<T>() % N % type.str();
throw std::runtime_error(m.str());
}
@@ -80,49 +80,45 @@ namespace bob { namespace io { namespace base { namespace array {
template <typename T, int N>
blitz::Array<T,N> cast(const interface& buf) {
- const BobIoTypeinfo& type = buf.type();
+ const typeinfo& type = buf.type();
if (type.nd != N) {
boost::format m("cannot cast blitz::Array<%s,%d> from buffer of type '%s'");
- m % PyBlitzArray_TypenumAsString(PyBlitzArrayCxx_CToTypenum<T>()) % N % BobIoTypeinfo_Str(&type);
+ m % stringize<T>() % N % type.str();
throw std::runtime_error(m.str());
}
switch (type.dtype) {
- case NPY_BOOL:
+ case bob::io::base::array::t_bool:
return bob::core::array::cast<T>(wrap<bool,N>(buf));
- case NPY_INT8:
+ case bob::io::base::array::t_int8:
return bob::core::array::cast<T>(wrap<int8_t,N>(buf));
- case NPY_INT16:
+ case bob::io::base::array::t_int16:
return bob::core::array::cast<T>(wrap<int16_t,N>(buf));
- case NPY_INT32:
+ case bob::io::base::array::t_int32:
return bob::core::array::cast<T>(wrap<int32_t,N>(buf));
- case NPY_INT64:
+ case bob::io::base::array::t_int64:
return bob::core::array::cast<T>(wrap<int64_t,N>(buf));
- case NPY_UINT8:
+ case bob::io::base::array::t_uint8:
return bob::core::array::cast<T>(wrap<uint8_t,N>(buf));
- case NPY_UINT16:
+ case bob::io::base::array::t_uint16:
return bob::core::array::cast<T>(wrap<uint16_t,N>(buf));
- case NPY_UINT32:
+ case bob::io::base::array::t_uint32:
return bob::core::array::cast<T>(wrap<uint32_t,N>(buf));
- case NPY_UINT64:
+ case bob::io::base::array::t_uint64:
return bob::core::array::cast<T>(wrap<uint64_t,N>(buf));
- case NPY_FLOAT32:
+ case bob::io::base::array::t_float32:
return bob::core::array::cast<T>(wrap<float,N>(buf));
- case NPY_FLOAT64:
+ case bob::io::base::array::t_float64:
return bob::core::array::cast<T>(wrap<double,N>(buf));
-# ifdef NPY_FLOAT128
- case NPY_FLOAT128:
+ case bob::io::base::array::t_float128:
return bob::core::array::cast<T>(wrap<long double,N>(buf));
-# endif
- case NPY_COMPLEX64:
+ case bob::io::base::array::t_complex64:
return bob::core::array::cast<T>(wrap<std::complex<float>,N>(buf));
- case NPY_COMPLEX128:
+ case bob::io::base::array::t_complex128:
return bob::core::array::cast<T>(wrap<std::complex<double>,N>(buf));
-# ifdef NPY_COMPLEX256
- case NPY_COMPLEX256:
+ case bob::io::base::array::t_complex256:
return bob::core::array::cast<T>(wrap<std::complex<long double>,N>(buf));
-# endif
default:
break;
}
diff --git a/bob/io/base/include/bob.io.base/blitz_array.h b/bob/io/base/include/bob.io.base/blitz_array.h
index f784156..9927e00 100644
--- a/bob/io/base/include/bob.io.base/blitz_array.h
+++ b/bob/io/base/include/bob.io.base/blitz_array.h
@@ -11,17 +11,18 @@
#ifndef BOB_IO_BASE_BLITZ_ARRAY_H
#define BOB_IO_BASE_BLITZ_ARRAY_H
-#include <bob.io.base/array.h>
-#include <bob.io.base/array_utils.h>
+#include <stdexcept>
+#include <boost/make_shared.hpp>
+#include <boost/format.hpp>
+#include <blitz/array.h>
#include <bob.core/check.h>
#include <bob.core/cast.h>
#include <bob.core/array_copy.h>
-#include <stdexcept>
-#include <boost/make_shared.hpp>
-#include <boost/format.hpp>
-#include <blitz/array.h>
+#include <bob.io.base/array.h>
+#include <bob.io.base/array_utils.h>
+#include <bob.io.base/array_type.h>
namespace bob { namespace io { namespace base { namespace array {
@@ -55,13 +56,13 @@ namespace bob { namespace io { namespace base { namespace array {
/**
* @brief Starts with an uninitialized, pre-allocated array.
*/
- blitz_array(const BobIoTypeinfo& info);
+ blitz_array(const typeinfo& info);
/**
* @brief Borrows the given pointer - if you use this constructor, you
* must make sure the pointed data outlives this object.
*/
- blitz_array(void* data, const BobIoTypeinfo& info);
+ blitz_array(void* data, const typeinfo& info);
/**
* @brief Destroyes me
@@ -82,7 +83,7 @@ namespace bob { namespace io { namespace base { namespace array {
* @brief Re-allocates this buffer taking into consideration new
* requirements. The internal memory should be considered uninitialized.
*/
- virtual void set (const BobIoTypeinfo& req);
+ virtual void set (const typeinfo& req);
/**
* @brief Refers to the data of another blitz array.
@@ -90,9 +91,9 @@ namespace bob { namespace io { namespace base { namespace array {
void set(boost::shared_ptr<blitz_array> other);
/**
- * @brief type information
+ * @brief Element type
*/
- virtual const BobIoTypeinfo& type() const { return m_type; }
+ virtual const typeinfo& type() const { return m_type; }
/**
* @brief Borrows a reference from the underlying memory. This means
@@ -151,20 +152,16 @@ namespace bob { namespace io { namespace base { namespace array {
template <typename T, int N>
void set(boost::shared_ptr<blitz::Array<T,N> > data) {
- if (PyBlitzArrayCxx_CToTypenum<T>() == NPY_NOTYPE)
+ if (getElementType<T>() == t_unknown)
throw std::runtime_error("unsupported element type on blitz::Array<>");
- if (N > BOB_BLITZ_MAXDIMS)
+ if (N > BOB_MAX_DIM)
throw std::runtime_error("unsupported number of dimensions on blitz::Array<>");
if (!isCContiguous(*data.get()))
throw std::runtime_error("cannot buffer'ize non-c contiguous array");
- m_type.dtype = PyBlitzArrayCxx_CToTypenum<T>();
- m_type.nd = data->ndim();
- for (size_t k=0; k<m_type.nd; ++k) {
- m_type.shape[k] = data->shape(k);
- m_type.stride[k] = data->stride(k);
- }
+ m_type.set(data);
+
m_data = data;
m_ptr = reinterpret_cast<void*>(data->data());
m_is_blitz = true;
@@ -212,15 +209,15 @@ namespace bob { namespace io { namespace base { namespace array {
if (!m_data) throw std::runtime_error("empty blitz array");
- if (m_type.dtype != PyBlitzArrayCxx_CToTypenum<T>()) {
+ if (m_type.dtype != getElementType<T>()) {
boost::format m("cannot efficiently retrieve blitz::Array<%s,%d> from buffer of type '%s'");
- m % PyBlitzArray_TypenumAsString(PyBlitzArrayCxx_CToTypenum<T>()) % N % BobIoTypeinfo_Str(&m_type);
+ m % stringize<T>() % N % m_type.str();
throw std::runtime_error(m.str());
}
if (m_type.nd != N) {
boost::format m("cannot retrieve blitz::Array<%s,%d> from buffer of type '%s'");
- m % PyBlitzArray_TypenumAsString(PyBlitzArrayCxx_CToTypenum<T>()) % N % BobIoTypeinfo_Str(&m_type);
+ m % stringize<T>() % N % m_type.str();
throw std::runtime_error(m.str());
}
@@ -252,7 +249,7 @@ namespace bob { namespace io { namespace base { namespace array {
private: //representation
- BobIoTypeinfo m_type; ///< type information
+ typeinfo m_type; ///< type information
void* m_ptr; ///< pointer to the data
bool m_is_blitz; ///< true if initiated with a blitz::Array<>
boost::shared_ptr<void> m_data; ///< Pointer to the data owner
diff --git a/bob/io/base/include/bob.io.base/reorder.h b/bob/io/base/include/bob.io.base/reorder.h
new file mode 100644
index 0000000..09ebf50
--- /dev/null
+++ b/bob/io/base/include/bob.io.base/reorder.h
@@ -0,0 +1,94 @@
+/**
+ * @date Tue Nov 22 11:24:44 2011 +0100
+ * @author Andre Anjos <andre.anjos@idiap.ch>
+ *
+ * @brief Row-major to column-major reordering and vice-versa
+ *
+ * Copyright (C) Idiap Research Institute, Martigny, Switzerland
+ */
+
+#ifndef BOB_IO_BASE_REORDER_H
+#define BOB_IO_BASE_REORDER_H
+
+#include <stdint.h>
+
+#include <bob.io.base/array.h>
+
+namespace bob { namespace io { namespace base {
+
+ /**
+ * Returns, on the first argument, the linear indexes by calculating the
+ * linear positions relative to both row-major and column-major order
+ * matrixes given a certain index accessing a position in the matrix and the
+ * matrix shape
+ *
+ * @param row The resulting row-major linear index.
+ * (row,col) is a 2-tuple with the results: row-major and
+ * column-major linear indexes
+ * @param col The resulting column-major linear index. (see above)
+ * @param i Index of the column.
+ * (i,j) a 2-tuple with the indexes as would be accessed
+ * [col][row]; this is the same as accessing the matrix like
+ * on directions [y][x]
+ * @param j Index of the row. (see above)
+ * @param shape a 2-tuple with the matrix shape like [col][row]; this is the
+ * same as thinking about the extends of the matrix like on directions
+ * [y][x]
+ *
+ * Detailed arithmetics with graphics and explanations can be found here:
+ * http://webster.cs.ucr.edu/AoA/Windows/HTML/Arraysa2.html
+ */
+ void rc2d(size_t& row, size_t& col, const size_t i, const size_t j,
+ const size_t* shape);
+
+ /**
+ * Same as above, but for a 3D array organized as [depth][column][row]
+ */
+ void rc3d(size_t& row, size_t& col, const size_t i, const size_t j,
+ const size_t k, const size_t* shape);
+
+ /**
+ * Same as above, but for a 4D array organized as [time][depth][column][row]
+ */
+ void rc4d(size_t& row, size_t& col, const size_t i, const size_t j,
+ const size_t k, const size_t l, const size_t* shape);
+
+ /**
+ * Converts the data from row-major order (C-Style) to column major order
+ * (Fortran style). Input parameters are the src data in row-major order, the
+ * destination (pre-allocated) array of the same size and the type
+ * information.
+ */
+ void row_to_col_order(const void* src_, void* dst_, const
+ bob::io::base::array::typeinfo& info);
+
+ /**
+ * Converts the data from column-major order (Fortran-Style) to row major
+ * order (C style), which is required by bob. Input parameters are the src
+ * data in column-major order, the destination (pre-allocated) array of the
+ * same size and the type information.
+ */
+ void col_to_row_order(const void* src_, void* dst_,
+ const bob::io::base::array::typeinfo& info);
+
+ /**
+ * Converts the data from row-major order (C-Style) to column major order
+ * (Fortran style). Input parameters are the src data in row-major order, the
+ * destination (pre-allocated) array of the same size and the type
+ * information.
+ */
+ void row_to_col_order_complex(const void* src_, void* dst_re_,
+ void* dst_im_, const bob::io::base::array::typeinfo& info);
+
+ /**
+ * Converts the data from column-major order (Fortran-Style) to row major
+ * order (C style), which is required by bob. Input parameters are the src
+ * data in column-major order, the destination (pre-allocated) array of the
+ * same size and the type information.
+ */
+ void col_to_row_order_complex(const void* src_re_, const void* src_im_,
+ void* dst_, const bob::io::base::array::typeinfo& info);
+
+}}}
+
+#endif /* BOB_IO_BASE_REORDER_H */
diff --git a/bob/io/base/include/bob.io.base/utils.h b/bob/io/base/include/bob.io.base/utils.h
new file mode 100644
index 0000000..c42b1fa
--- /dev/null
+++ b/bob/io/base/include/bob.io.base/utils.h
@@ -0,0 +1,105 @@
+/**
+ * @author Andre Anjos <andre.anjos@idiap.ch>
+ * @date Wed 3 Oct 07:46:49 2012
+ *
+ * @brief Utilities for easy manipulation of filed data.
+ */
+
+#ifndef BOB_IO_BASE_BASE_UTILS_H
+#define BOB_IO_BASE_BASE_UTILS_H
+
+#include <boost/shared_ptr.hpp>
+
+#include <bob.io.base/File.h>
+
+namespace bob { namespace io { namespace base {
+
+ /**
+ * Creates a new array codec using the filename extension to determine which
+ * codec to use. The opening mode is passed to the underlying registered File
+ * implementation.
+ *
+ * Here are the meanings of the mode flag:
+ *
+ * 'r': opens for reading only - no modifications can occur; it is an
+ * error to open a file that does not exist for read-only operations.
+ * 'w': opens for reading and writing, but truncates the file if it
+ * exists; it is not an error to open files that do not exist with
+ * this flag.
+ * 'a': opens for reading and writing - any type of modification can
+ * occur. If the file does not exist, this flag is effectively like
+ * 'w'.
+ */
+ boost::shared_ptr<File> open (const char* filename, char mode);
+
+ /**
+ * Opens the file pretending it has a different extension (that is, using a
+ * different codec) then the one expected (if any). This allows you to write
+ * a file with the extension you want, but still using one of the available
+ * codecs.
+ */
+ boost::shared_ptr<File> open (const char* filename, char mode,
+ const char* pretend_extension);
+
+ /**
+ * Peeks the file and returns the typeinfo for reading individual frames (or
+ * samples) from the file.
+ *
+ * This method is equivalent to calling open() with 'r' as mode flag and then
+ * calling type() on the returned bob::io::base::File object.
+ */
+ bob::io::base::array::typeinfo peek (const char* filename);
+
+ /**
+ * Peeks the file and returns the typeinfo for reading the whole contents in
+ * a single shot.
+ *
+ * This method is equivalent to calling open() with 'r' as mode flag and then
+ * calling type_all() on the returned bob::io::base::File object.
+ */
+ bob::io::base::array::typeinfo peek_all (const char* filename);
+
+ /**
+ * Opens for reading and load all contents
+ *
+ * This method is equivalent to calling open() with 'r' as mode flag and then
+ * calling read_all() on the returned bob::io::base::File object.
+ */
+ template <typename T, int N> blitz::Array<T,N> load (const char* filename) {
+ return open(filename, 'r')->read_all<T,N>();
+ }
+
+ /**
+ * Opens for reading and load a particular frame (or sample)
+ *
+ * This method is equivalent to calling open() with 'r' as mode flag and then
+ * calling read(index) on the returned bob::io::base::File object.
+ */
+ template <typename T, int N> blitz::Array<T,N> load (const char* filename, size_t index) {
+ return open(filename, 'r')->read<T,N>(index);
+ }
+
+ /**
+ * Opens for appending and add an array to it
+ *
+ * This method is equivalent to calling open() with 'a' as mode flag and then
+ * calling append(data) on the returned bob::io::base::File object.
+ */
+ template <typename T, int N> void append (const char* filename, const blitz::Array<T,N>& data) {
+ open(filename, 'a')->append(data);
+ }
+
+ /**
+ * Opens for writing and write an array to it. If the file exists before the
+ * call to this method, it is truncated.
+ *
+ * This method is equivalent to calling open() with 'w' as mode flag and then
+ * calling write(data) on the returned bob::io::base::File object.
+ */
+ template <typename T, int N> void save (const char* filename, const blitz::Array<T,N>& data) {
+ open(filename, 'w')->write(data);
+ }
+
+}}}
+
+#endif /* BOB_IO_BASE_BASE_UTILS_H */
diff --git a/bob/io/base/main.cpp b/bob/io/base/main.cpp
index 50eaabd..f7dfb87 100644
--- a/bob/io/base/main.cpp
+++ b/bob/io/base/main.cpp
@@ -13,10 +13,6 @@
#endif
#include <bob.blitz/capi.h>
#include <bob.blitz/cleanup.h>
-#include <bob.core/logging.h>
-
-#include "cpp/CodecRegistry.h"
-#include "plugin.h"
/**
* Creates an str object, from a C or C++ string. Returns a **new
@@ -124,52 +120,6 @@ static PyObject* create_module (void) {
PyBobIo_API[PyBobIo_APIVersion_NUM] = (void *)&PyBobIo_APIVersion;
- /********************
- * Type Information *
- ********************/
-
- PyBobIo_API[BobIoTypeinfo_Init_NUM] = (void *)&BobIoTypeinfo_Init;
-
- PyBobIo_API[BobIoTypeinfo_Copy_NUM] = (void *)&BobIoTypeinfo_Copy;
-
- PyBobIo_API[BobIoTypeinfo_Set_NUM] = (void *)&BobIoTypeinfo_Set;
-
- PyBobIo_API[BobIoTypeinfo_SetWithStrides_NUM] = (void *)&BobIoTypeinfo_SetWithStrides;
-
- PyBobIo_API[BobIoTypeinfo_SignedSet_NUM] = (void *)&BobIoTypeinfo_SignedSet;
-
- PyBobIo_API[BobIoTypeinfo_SignedSetWithStrides_NUM] = (void *)&BobIoTypeinfo_SignedSetWithStrides;
-
- PyBobIo_API[BobIoTypeinfo_Reset_NUM] = (void *)&BobIoTypeinfo_Reset;
-
- PyBobIo_API[BobIoTypeinfo_IsValid_NUM] = (void *)&BobIoTypeinfo_IsValid;
-
- PyBobIo_API[BobIoTypeinfo_HasValidShape_NUM] = (void *)&BobIoTypeinfo_HasValidShape;
-
- PyBobIo_API[BobIoTypeinfo_ResetShape_NUM] = (void *)&BobIoTypeinfo_ResetShape;
-
- PyBobIo_API[BobIoTypeinfo_UpdateStrides_NUM] = (void *)&BobIoTypeinfo_UpdateStrides;
-
- PyBobIo_API[BobIoTypeinfo_Size_NUM] = (void *)&BobIoTypeinfo_Size;
-
- PyBobIo_API[BobIoTypeinfo_BufferSize_NUM] = (void *)&BobIoTypeinfo_BufferSize;
-
- PyBobIo_API[BobIoTypeinfo_IsCompatible_NUM] = (void *)&BobIoTypeinfo_IsCompatible;
-
- PyBobIo_API[BobIoTypeinfo_Str_NUM] = (void *)&BobIoTypeinfo_Str;
-
- /********************
- * Array reordering *
- ********************/
-
- PyBobIo_API[BobIoReorder_RowToCol_NUM] = (void *)&BobIoReorder_RowToCol;
-
- PyBobIo_API[BobIoReorder_ColToRow_NUM] = (void *)&BobIoReorder_ColToRow;
-
- PyBobIo_API[BobIoReorder_RowToColComplex_NUM] = (void *)&BobIoReorder_RowToColComplex;
-
- PyBobIo_API[BobIoReorder_ColToRowComplex_NUM] = (void *)&BobIoReorder_ColToRowComplex;
-
/**********************************
* Bindings for bob.io.base.File *
**********************************/
@@ -178,23 +128,13 @@ static PyObject* create_module (void) {
PyBobIo_API[PyBobIoFileIterator_Type_NUM] = (void *)&PyBobIoFileIterator_Type;
- /**************************************
- * File loading and data type peeking *
- **************************************/
-
- PyBobIo_API[BobIoFile_Open_NUM] = (void *)&BobIoFile_Open;
-
- PyBobIo_API[BobIoFile_OpenWithExtension_NUM] = (void *)&BobIoFile_OpenWithExtension;
-
- PyBobIo_API[BobIoFile_Peek_NUM] = (void *)&BobIoFile_Peek;
-
- PyBobIo_API[BobIoFile_PeekAll_NUM] = (void *)&BobIoFile_PeekAll;
-
/************************
* I/O generic bindings *
************************/
- PyBobIo_API[PyBobIo_TypeinfoAsTuple_NUM] = (void *)PyBobIo_TypeinfoAsTuple;
+ PyBobIo_API[PyBobIo_AsTypenum_NUM] = (void *)PyBobIo_AsTypenum;
+
+ PyBobIo_API[PyBobIo_TypeInfoAsTuple_NUM] = (void *)PyBobIo_TypeInfoAsTuple;
PyBobIo_API[PyBobIo_FilenameConverter_NUM] = (void *)PyBobIo_FilenameConverter;
@@ -208,9 +148,9 @@ static PyObject* create_module (void) {
PyBobIo_API[PyBobIoHDF5File_Converter_NUM] = (void *)&PyBobIoHDF5File_Converter;
- /*****************************************
- * Code Registration and De-registration *
- *****************************************/
+/*****************************************
+ * Code Registration and De-registration *
+ *****************************************/
PyBobIo_API[PyBobIoCodec_Register_NUM] = (void *)&PyBobIoCodec_Register;
@@ -237,13 +177,6 @@ static PyObject* create_module (void) {
if (PyModule_AddObject(m, "_C_API", c_api_object) < 0) return 0;
- /* imports dependencies */
- if (import_bob_core_logging() < 0) {
- PyErr_Print();
- PyErr_Format(PyExc_ImportError, "cannot import `%s'", BOB_EXT_MODULE_NAME);
- return 0;
- }
-
/* imports dependencies */
if (import_bob_blitz() < 0) {
PyErr_Print();
@@ -251,41 +184,6 @@ static PyObject* create_module (void) {
return 0;
}
- /* activates built-in plugins */
- if (!PyBobIoCodec_Register(".csv", "Comma-Separated Values (built-in)",
- &make_csv_file)) {
- PyErr_Print();
- }
-
- if (!PyBobIoCodec_Register(".txt", "Comma-Separated Values (built-in)",
- &make_csv_file)) {
- PyErr_Print();
- }
-
- if (!PyBobIoCodec_Register(".h5", "Hierarchical Data Format v5 (libhdf5)",
- &make_hdf5_file)) {
- PyErr_Print();
- }
-
- if (!PyBobIoCodec_Register(".hdf5", "Hierarchical Data Format v5 (libhdf5)",
- &make_hdf5_file)) {
- PyErr_Print();
- }
-
- if (!PyBobIoCodec_Register(".hdf", "Hierarchical Data Format v5 (libhdf5)",
- &make_hdf5_file)) {
- PyErr_Print();
- }
-
- if (!PyBobIoCodec_Register(".bindata", "Torch3 binary data format (built-in)",
- &make_torch3_file)) {
- PyErr_Print();
- }
-
- if (!PyBobIoCodec_Register(".tensor", "Torch3vision v2.1 tensor format (built-in)", &make_tensor_file)) {
- PyErr_Print();
- }
-
Py_INCREF(m);
return m;
diff --git a/bob/io/base/plugin.h b/bob/io/base/plugin.h
deleted file mode 100644
index 735ff37..0000000
--- a/bob/io/base/plugin.h
+++ /dev/null
@@ -1,39 +0,0 @@
-/**
- * @author Andre Anjos <andre.anjos@idiap.ch>
- * @date Wed 14 May 14:42:34 2014 CEST
- *
- * @brief Implements the matlab (.mat) array codec using matio
- *
- * Copyright (C) 2011-2014 Idiap Research Institute, Martigny, Switzerland
- */
-
-#ifndef BOB_IO_BASE_PLUGIN_H
-#define BOB_IO_BASE_PLUGIN_H
-
-#include <boost/shared_ptr.hpp>
-#include <bob.io.base/File.h>
-
-/**
- * This defines the factory method F that can create codecs of this type.
- *
- * Here are the meanings of the mode flag that should be respected by your
- * factory implementation:
- *
- * 'r': opens for reading only - no modifications can occur; it is an
- * error to open a file that does not exist for read-only operations.
- * 'w': opens for reading and writing, but truncates the file if it
- * exists; it is not an error to open files that do not exist with
- * this flag.
- * 'a': opens for reading and writing - any type of modification can
- * occur. If the file does not exist, this flag is effectively like
- * 'w'.
- *
- * Returns a newly allocated File object that can read and write data to the
- * file using a specific backend.
- */
-boost::shared_ptr<bob::io::base::File> make_csv_file (const char* path, char mode);
-boost::shared_ptr<bob::io::base::File> make_hdf5_file (const char* path, char mode);
-boost::shared_ptr<bob::io::base::File> make_torch3_file (const char* path, char mode);
-boost::shared_ptr<bob::io::base::File> make_tensor_file (const char* path, char mode);
-
-#endif /* BOB_IO_BASE_PLUGIN_H */
diff --git a/bob/io/base/reorder.cpp b/bob/io/base/reorder.cpp
deleted file mode 100644
index b07ac50..0000000
--- a/bob/io/base/reorder.cpp
+++ /dev/null
@@ -1,317 +0,0 @@
-/**
- * @date Tue Nov 22 11:24:44 2011 +0100
- * @author Andre Anjos <andre.anjos@idiap.ch>
- *
- * @brief Implementation of row-major/column-major reordering
- *
- * Copyright (C) Idiap Research Institute, Martigny, Switzerland
- */
-
-#define BOB_IO_BASE_MODULE
-#include <bob.io.base/api.h>
-#include <bob.blitz/capi.h>
-#include <cstring> //for memcpy
-
-/**
- * Returns, on the first argument, the linear indexes by calculating the
- * linear positions relative to both row-major and column-major order
- * matrixes given a certain index accessing a position in the matrix and the
- * matrix shape
- *
- * @param row The resulting row-major linear index.
- * (row,col) is a 2-tuple with the results: row-major and
- * column-major linear indexes
- * @param col The resulting column-major linear index. (see above)
- * @param i Index of the column.
- * (i,j) a 2-tuple with the indexes as would be accessed
- * [col][row]; this is the same as accessing the matrix like
- * on directions [y][x]
- * @param j Index of the row. (see above)
- * @param shape a 2-tuple with the matrix shape like [col][row]; this is the
- * same as thinking about the extends of the matrix like on directions
- * [y][x]
- *
- * Detailed arithmetics with graphics and explanations can be found here:
- * http://webster.cs.ucr.edu/AoA/Windows/HTML/Arraysa2.html
- */
-static void rc2d(size_t& row, size_t& col, const size_t i, const size_t j,
- const size_t* shape) {
-
- row = (i * shape[1]) + j;
- col = (j * shape[0]) + i;
-
-}
-
-/**
- * Same as above, but for a 3D array organized as [depth][column][row]
- */
-static void rc3d(size_t& row, size_t& col, const size_t i, const size_t j,
- const size_t k, const size_t* shape) {
-
- row = ( (i * shape[1]) + j ) * shape[2] + k;
- col = ( (k * shape[1]) + j ) * shape[0] + i;
-
-}
-
-/**
- * Same as above, but for a 4D array organized as [time][depth][column][row]
- */
-static void rc4d(size_t& row, size_t& col, const size_t i, const size_t j,
- const size_t k, const size_t l, const size_t* shape) {
-
- row = ( ( i * shape[1] + j ) * shape[2] + k ) * shape[3] + l;
- col = ( ( l * shape[2] + k ) * shape[1] + j ) * shape[0] + i;
-
-}
-
-int BobIoReorder_RowToCol(const void* src_, void* dst_,
- const BobIoTypeinfo* info) {
-
- size_t dsize = PyBlitzArray_TypenumSize(info->dtype);
-
- //cast to byte type so we can manipulate the pointers...
- const uint8_t* src = static_cast<const uint8_t*>(src_);
- uint8_t* dst = static_cast<uint8_t*>(dst_);
-
- switch(info->nd) {
-
- case 1:
- std::memcpy(dst, src, BobIoTypeinfo_BufferSize(info));
- break;
-
- case 2:
- for (size_t i=0; i<info->shape[0]; ++i)
- for (size_t j=0; j<info->shape[1]; ++j) {
- size_t row_major, col_major;
- rc2d(row_major, col_major, i, j, info->shape);
- row_major *= dsize;
- col_major *= dsize;
- std::memcpy(&dst[col_major], &src[row_major], dsize);
- }
- break;
-
- case 3:
- for (size_t i=0; i<info->shape[0]; ++i)
- for (size_t j=0; j<info->shape[1]; ++j)
- for (size_t k=0; k<info->shape[2]; ++k) {
- size_t row_major, col_major;
- rc3d(row_major, col_major, i, j, k, info->shape);
- row_major *= dsize;
- col_major *= dsize;
- std::memcpy(&dst[col_major], &src[row_major], dsize);
- }
- break;
-
- case 4:
- for (size_t i=0; i<info->shape[0]; ++i)
- for (size_t j=0; j<info->shape[1]; ++j)
- for (size_t k=0; k<info->shape[2]; ++k)
- for (size_t l=0; l<info->shape[3]; ++l) {
- size_t row_major, col_major;
- rc4d(row_major, col_major, i, j, k, l, info->shape);
- row_major *= dsize;
- col_major *= dsize;
- std::memcpy(&dst[col_major], &src[row_major], dsize);
- }
- break;
-
- default:
- PyErr_Format(PyExc_RuntimeError, "can only flip arrays with up to %u dimensions - you passed one with %zu dimensions", BOB_BLITZ_MAXDIMS, info->nd);
- return 0;
- }
-
- return 1;
-}
-
-int BobIoReorder_ColToRow(const void* src_, void* dst_,
- const BobIoTypeinfo* info) {
-
- size_t dsize = PyBlitzArray_TypenumSize(info->dtype);
-
- //cast to byte type so we can manipulate the pointers...
- const uint8_t* src = static_cast<const uint8_t*>(src_);
- uint8_t* dst = static_cast<uint8_t*>(dst_);
-
- switch(info->nd) {
-
- case 1:
- std::memcpy(dst, src, BobIoTypeinfo_BufferSize(info));
- break;
-
- case 2:
- for (size_t i=0; i<info->shape[0]; ++i)
- for (size_t j=0; j<info->shape[1]; ++j) {
- size_t row_major, col_major;
- rc2d(row_major, col_major, i, j, info->shape);
- row_major *= dsize;
- col_major *= dsize;
- std::memcpy(&dst[row_major], &src[col_major], dsize);
- }
- break;
-
- case 3:
- for (size_t i=0; i<info->shape[0]; ++i)
- for (size_t j=0; j<info->shape[1]; ++j)
- for (size_t k=0; k<info->shape[2]; ++k) {
- size_t row_major, col_major;
- rc3d(row_major, col_major, i, j, k, info->shape);
- row_major *= dsize;
- col_major *= dsize;
- std::memcpy(&dst[row_major], &src[col_major], dsize);
- }
- break;
-
- case 4:
- for (size_t i=0; i<info->shape[0]; ++i)
- for (size_t j=0; j<info->shape[1]; ++j)
- for (size_t k=0; k<info->shape[2]; ++k)
- for (size_t l=0; l<info->shape[3]; ++l) {
- size_t row_major, col_major;
- rc4d(row_major, col_major, i, j, k, l, info->shape);
- row_major *= dsize;
- col_major *= dsize;
- std::memcpy(&dst[row_major], &src[col_major], dsize);
- }
- break;
-
- default:
- PyErr_Format(PyExc_RuntimeError, "can only flip arrays with up to %u dimensions - you passed one with %zu dimensions", BOB_BLITZ_MAXDIMS, info->nd);
- return 0;
- }
-
- return 1;
-}
-
-int BobIoReorder_RowToColComplex(const void* src_, void* dst_re_,
- void* dst_im_, const BobIoTypeinfo* info) {
-
- size_t dsize = PyBlitzArray_TypenumSize(info->dtype);
- size_t dsize2 = dsize/2; ///< size of each complex component (real, imaginary)
-
- //cast to byte type so we can manipulate the pointers...
- const uint8_t* src = static_cast<const uint8_t*>(src_);
- uint8_t* dst_re = static_cast<uint8_t*>(dst_re_);
- uint8_t* dst_im = static_cast<uint8_t*>(dst_im_);
-
- switch(info->nd) {
-
- case 1:
- for (size_t i=0; i<info->shape[0]; ++i) {
- std::memcpy(&dst_re[dsize2*i], &src[dsize*i] , dsize2);
- std::memcpy(&dst_im[dsize2*i], &src[dsize*i]+dsize2, dsize2);
- }
- break;
-
- case 2:
- for (size_t i=0; i<info->shape[0]; ++i)
- for (size_t j=0; j<info->shape[1]; ++j) {
- size_t row_major, col_major;
- rc2d(row_major, col_major, i, j, info->shape);
- row_major *= dsize;
- col_major *= dsize2;
- std::memcpy(&dst_re[col_major], &src[row_major] , dsize2);
- std::memcpy(&dst_im[col_major], &src[row_major]+dsize2, dsize2);
- }
- break;
-
- case 3:
- for (size_t i=0; i<info->shape[0]; ++i)
- for (size_t j=0; j<info->shape[1]; ++j)
- for (size_t k=0; k<info->shape[2]; ++k) {
- size_t row_major, col_major;
- rc3d(row_major, col_major, i, j, k, info->shape);
- row_major *= dsize;
- col_major *= dsize2;
- std::memcpy(&dst_re[col_major], &src[row_major] , dsize2);
- std::memcpy(&dst_im[col_major], &src[row_major]+dsize2, dsize2);
- }
- break;
-
- case 4:
- for (size_t i=0; i<info->shape[0]; ++i)
- for (size_t j=0; j<info->shape[1]; ++j)
- for (size_t k=0; k<info->shape[2]; ++k)
- for (size_t l=0; l<info->shape[3]; ++l) {
- size_t row_major, col_major;
- rc4d(row_major, col_major, i, j, k, l, info->shape);
- row_major *= dsize;
- col_major *= dsize2;
- std::memcpy(&dst_re[col_major], &src[row_major] , dsize2);
- std::memcpy(&dst_im[col_major], &src[row_major]+dsize2, dsize2);
- }
- break;
-
- default:
- PyErr_Format(PyExc_RuntimeError, "can only flip arrays with up to %u dimensions - you passed one with %zu dimensions", BOB_BLITZ_MAXDIMS, info->nd);
- return 0;
- }
-
- return 1;
-}
-
-int BobIoReorder_ColToRowComplex(const void* src_re_,
- const void* src_im_, void* dst_, const BobIoTypeinfo* info) {
-
- size_t dsize = PyBlitzArray_TypenumSize(info->dtype);
- size_t dsize2 = dsize/2; ///< size of each complex component (real, imaginary)
-
- //cast to byte type so we can manipulate the pointers...
- const uint8_t* src_re = static_cast<const uint8_t*>(src_re_);
- const uint8_t* src_im = static_cast<const uint8_t*>(src_im_);
- uint8_t* dst = static_cast<uint8_t*>(dst_);
-
- switch(info->nd) {
-
- case 1:
- for (size_t i=0; i<info->shape[0]; ++i) {
- std::memcpy(&dst[dsize*i] , &src_re[dsize2*i], dsize2);
- std::memcpy(&dst[dsize*i]+dsize2, &src_im[dsize2*i], dsize2);
- }
- break;
-
- case 2:
- for (size_t i=0; i<info->shape[0]; ++i)
- for (size_t j=0; j<info->shape[1]; ++j) {
- size_t row_major, col_major;
- rc2d(row_major, col_major, i, j, info->shape);
- row_major *= dsize;
- col_major *= dsize2;
- std::memcpy(&dst[row_major], &src_re[col_major], dsize2);
- std::memcpy(&dst[row_major]+dsize2, &src_im[col_major], dsize2);
- }
- break;
-
- case 3:
- for (size_t i=0; i<info->shape[0]; ++i)
- for (size_t j=0; j<info->shape[1]; ++j)
- for (size_t k=0; k<info->shape[2]; ++k) {
- size_t row_major, col_major;
- rc3d(row_major, col_major, i, j, k, info->shape);
- row_major *= dsize;
- col_major *= dsize2;
- std::memcpy(&dst[row_major] , &src_re[col_major], dsize2);
- std::memcpy(&dst[row_major]+dsize2, &src_im[col_major], dsize2);
- }
- break;
-
- case 4:
- for (size_t i=0; i<info->shape[0]; ++i)
- for (size_t j=0; j<info->shape[1]; ++j)
- for (size_t k=0; k<info->shape[2]; ++k)
- for (size_t l=0; l<info->shape[3]; ++l) {
- size_t row_major, col_major;
- rc4d(row_major, col_major, i, j, k, l, info->shape);
- row_major *= dsize;
- col_major *= dsize2;
- std::memcpy(&dst[row_major] , &src_re[col_major], dsize2);
- std::memcpy(&dst[row_major]+dsize2, &src_im[col_major], dsize2);
- }
- break;
-
- default:
- PyErr_Format(PyExc_RuntimeError, "can only flip arrays with up to %u dimensions - you passed one with %zu dimensions", BOB_BLITZ_MAXDIMS, info->nd);
- return 0;
- }
-
- return 1;
-}
diff --git a/bob/io/base/typeinfo.cpp b/bob/io/base/typeinfo.cpp
deleted file mode 100644
index 386843f..0000000
--- a/bob/io/base/typeinfo.cpp
+++ /dev/null
@@ -1,251 +0,0 @@
-/**
- * @date Tue Nov 8 15:34:31 2011 +0100
- * @author Andre Anjos <andre.anjos@idiap.ch>
- *
- * @brief Some buffer stuff
- *
- * Copyright (C) Idiap Research Institute, Martigny, Switzerland
- */
-
-#define BOB_IO_BASE_MODULE
-#include <bob.blitz/capi.h>
-#include <bob.io.base/api.h>
-#include <boost/format.hpp>
-
-void BobIoTypeinfo_Init(BobIoTypeinfo* self) {
- BobIoTypeinfo_Reset(self);
-}
-
-int BobIoTypeinfo_Copy (BobIoTypeinfo* self, const BobIoTypeinfo* other) {
-
- self->dtype = other->dtype;
-
- if (other->nd > (BOB_BLITZ_MAXDIMS+1)) {
- PyErr_Format(PyExc_RuntimeError, "unsupported number of dimensions (%" PY_FORMAT_SIZE_T "d) while the maximum is %d", other->nd, BOB_BLITZ_MAXDIMS);
- return 0;
- }
-
- self->nd = other->nd;
- for (size_t k=0; k<self->nd; ++k) self->shape[k] = other->shape[k];
-
- return BobIoTypeinfo_UpdateStrides(self);
-
-}
-
-int BobIoTypeinfo_Set (BobIoTypeinfo* self, int dtype, size_t nd,
- const size_t* shape) {
-
- self->dtype = dtype;
-
- if (nd > (BOB_BLITZ_MAXDIMS+1)) {
- PyErr_Format(PyExc_RuntimeError, "unsupported number of dimensions (%" PY_FORMAT_SIZE_T "d) while the maximum is %d", nd, BOB_BLITZ_MAXDIMS);
- return 0;
- }
-
- self->nd = nd;
- for (size_t k=0; k<nd; ++k) self->shape[k] = shape[k];
-
- return BobIoTypeinfo_UpdateStrides(self);
-
-}
-
-int BobIoTypeinfo_SignedSet (BobIoTypeinfo* self, int dtype, Py_ssize_t nd,
- const Py_ssize_t* shape) {
-
- self->dtype = dtype;
-
- if (nd > (BOB_BLITZ_MAXDIMS+1)) {
- PyErr_Format(PyExc_RuntimeError, "unsupported number of dimensions (%" PY_FORMAT_SIZE_T "d) while the maximum is %d", nd, BOB_BLITZ_MAXDIMS);
- return 0;
- }
-
- self->nd = nd;
- for (Py_ssize_t k=0; k<nd; ++k) self->shape[k] = shape[k];
-
- return BobIoTypeinfo_UpdateStrides(self);
-
-}
-
-int BobIoTypeinfo_SetWithStrides (BobIoTypeinfo* self, int dtype,
- size_t nd, const size_t* shape, const size_t* stride) {
- self->dtype = dtype;
-
- if (nd > (BOB_BLITZ_MAXDIMS+1)) {
- PyErr_Format(PyExc_RuntimeError, "unsupported number of dimensions (%" PY_FORMAT_SIZE_T "d) while the maximum is %d", nd, BOB_BLITZ_MAXDIMS);
- return 0;
- }
-
- self->nd = nd;
- for (Py_ssize_t k=0; k<nd; ++k) {
- self->shape[k] = shape[k];
- self->stride[k] = stride[k];
- }
-
- return 1;
-
-}
-
-int BobIoTypeinfo_SignedSetWithStrides (BobIoTypeinfo* self, int dtype,
- Py_ssize_t nd, const Py_ssize_t* shape, const Py_ssize_t* stride) {
- self->dtype = dtype;
-
- if (nd > (BOB_BLITZ_MAXDIMS+1)) {
- PyErr_Format(PyExc_RuntimeError, "unsupported number of dimensions (%" PY_FORMAT_SIZE_T "d) while the maximum is %d", nd, BOB_BLITZ_MAXDIMS);
- return 0;
- }
-
- self->nd = nd;
- for (Py_ssize_t k=0; k<nd; ++k) {
- self->shape[k] = shape[k];
- self->stride[k] = stride[k];
- }
-
- return 1;
-
-}
-
-void BobIoTypeinfo_Reset(BobIoTypeinfo* self) {
-
- self->dtype = NPY_NOTYPE;
- self->nd = 0;
-
-}
-
-bool BobIoTypeinfo_IsValid(const BobIoTypeinfo* self) {
-
- return (self->dtype != NPY_NOTYPE) && (self->nd > 0) && (self->nd <= (BOB_BLITZ_MAXDIMS+1)) && BobIoTypeinfo_HasValidShape(self);
-
-}
-
-int BobIoTypeinfo_UpdateStrides(BobIoTypeinfo* self) {
-
- auto* stride = self->stride;
- auto* shape = self->shape;
-
- switch (self->nd) {
-
- case 0:
- return 1;
-
- case 1:
- stride[0] = 1;
- return 1;
-
- case 2:
- stride[1] = 1;
- stride[0] = shape[1];
- return 1;
-
- case 3:
- stride[2] = 1;
- stride[1] = shape[2];
- stride[0] = shape[1]*shape[2];
- return 1;
-
- case 4:
- stride[3] = 1;
- stride[2] = shape[3];
- stride[1] = shape[2]*shape[3];
- stride[0] = shape[1]*shape[2]*shape[3];
- return 1;
-
- case 5:
- stride[4] = 1;
- stride[3] = shape[4];
- stride[2] = shape[3]*shape[4];
- stride[1] = shape[2]*shape[3]*shape[4];
- stride[0] = shape[1]*shape[2]*shape[3]*shape[4];
- return 1;
-
- default:
- break;
-
- }
-
- PyErr_Format(PyExc_RuntimeError, "unsupported number of dimensions (%" PY_FORMAT_SIZE_T "d) while the maximum is %d", self->nd, BOB_BLITZ_MAXDIMS);
- return 0;
-
-}
-
-size_t BobIoTypeinfo_Size(const BobIoTypeinfo* self) {
-
- size_t retval = 1;
- for (size_t k=0; k<self->nd; ++k) retval *= self->shape[k];
- return retval;
-
-}
-
-size_t BobIoTypeinfo_BufferSize(const BobIoTypeinfo* self) {
-
- return BobIoTypeinfo_Size(self) * PyBlitzArray_TypenumSize(self->dtype);
-
-}
-
-static bool same_shape(size_t nd, const size_t* s1, const size_t* s2) {
-
- for (size_t k=0; k<nd; ++k) if (s1[k] != s2[k]) return false;
- return true;
-
-}
-
-bool BobIoTypeinfo_IsCompatible(const BobIoTypeinfo* self,
- const BobIoTypeinfo* other) {
-
- return (self->dtype == other->dtype) && (self->nd == other->nd) && same_shape(self->nd, self->shape, other->shape);
-
-}
-
-std::string BobIoTypeinfo_Str(const BobIoTypeinfo* self) {
-
- boost::format s("dtype: %s (%d); shape: [%s]; size: %d bytes");
- size_t sz = 0;
- size_t buf_sz = 0;
- if (self->dtype != NPY_NOTYPE) {
- //otherwise it throws
- sz = PyBlitzArray_TypenumSize(self->dtype);
- buf_sz = BobIoTypeinfo_BufferSize(self);
- }
- s % PyBlitzArray_TypenumAsString(self->dtype) % sz;
-
- auto* shape = self->shape;
-
- switch (self->nd) {
-
- case 0:
- s % "";
- break;
-
- case 1:
- s % (boost::format("%d") % shape[0]).str();
- break;
-
- case 2:
- s % (boost::format("%d,%d") % shape[0] % shape[1]).str();
- break;
-
- case 3:
- s % (boost::format("%d,%d,%d") % shape[0] % shape[1] % shape[2]).str();
- break;
-
- case 4:
- s % (boost::format("%d,%d,%d,%d") % shape[0] % shape[1] % shape[2] % shape[3]).str();
- break;
-
- default:
- s % ">4 dimensions?";
- break;
-
- }
-
- s % buf_sz;
- return s.str();
-
-}
-
-void BobIoTypeinfo_ResetShape (BobIoTypeinfo* self) {
- self->shape[0] = 0;
-}
-
-bool BobIoTypeinfo_HasValidShape(const BobIoTypeinfo* self) {
- return self->shape[0] != 0;
-}
diff --git a/setup.py b/setup.py
index 967e9b5..d3eac6e 100644
--- a/setup.py
+++ b/setup.py
@@ -14,6 +14,7 @@ package_dir = os.path.dirname(os.path.realpath(__file__))
package_dir = os.path.join(package_dir, 'bob', 'io', 'base', 'include')
include_dirs = [package_dir, bob.core.get_include()]
+packages = ['bob-core >= 1.2.2']
version = '2.0.0a0'
def libhdf5_version(header):
@@ -147,7 +148,6 @@ setup(
install_requires=[
'setuptools',
'bob.blitz',
- 'bob.core',
],
namespace_packages=[
@@ -160,46 +160,47 @@ setup(
[
"bob/io/base/version.cpp",
],
+ packages = packages,
include_dirs = include_dirs,
define_macros = define_macros,
extra_compile_args = extra_compile_args,
version = version,
- packages = ['boost'],
),
Extension("bob.io.base._library",
[
- "bob/io/base/cpp/blitz_array.cpp",
- "bob/io/base/cpp/TensorFileHeader.cpp",
- "bob/io/base/cpp/TensorFile.cpp",
"bob/io/base/cpp/CodecRegistry.cpp",
+ "bob/io/base/cpp/CSVFile.cpp",
+ "bob/io/base/cpp/File.cpp",
+ "bob/io/base/cpp/HDF5ArrayFile.cpp",
"bob/io/base/cpp/HDF5Attribute.cpp",
"bob/io/base/cpp/HDF5Dataset.cpp",
"bob/io/base/cpp/HDF5File.cpp",
"bob/io/base/cpp/HDF5Group.cpp",
"bob/io/base/cpp/HDF5Types.cpp",
"bob/io/base/cpp/HDF5Utils.cpp",
+ "bob/io/base/cpp/reorder.cpp",
+ "bob/io/base/cpp/T3File.cpp",
+ "bob/io/base/cpp/TensorArrayFile.cpp",
+ "bob/io/base/cpp/TensorFileHeader.cpp",
+ "bob/io/base/cpp/utils.cpp",
+ "bob/io/base/cpp/TensorFile.cpp",
+ "bob/io/base/cpp/array.cpp",
+ "bob/io/base/cpp/array_type.cpp",
+ "bob/io/base/cpp/blitz_array.cpp",
- "bob/io/base/file.cpp",
- "bob/io/base/utils.cpp",
- "bob/io/base/csv.cpp",
- "bob/io/base/hdf5plugin.cpp",
- "bob/io/base/torch3.cpp",
- "bob/io/base/tensor.cpp",
- "bob/io/base/reorder.cpp",
- "bob/io/base/typeinfo.cpp",
"bob/io/base/bobskin.cpp",
"bob/io/base/codec.cpp",
+ "bob/io/base/file.cpp",
"bob/io/base/hdf5.cpp",
"bob/io/base/main.cpp",
],
+ packages = packages,
include_dirs = include_dirs,
library_dirs = library_dirs,
libraries = libraries,
define_macros = define_macros,
extra_compile_args = extra_compile_args,
version = version,
- packages = ['boost'],
- boost_modules = ['iostreams', 'filesystem'],
),
],
--
GitLab