From c49cd71d6eea5dfb41f8571cea4c23074be24a37 Mon Sep 17 00:00:00 2001
From: Andre Anjos <andre.anjos@idiap.ch>
Date: Mon, 13 Jan 2014 17:07:16 +0100
Subject: [PATCH] Base Activation class fully implemented with all details from
original
---
setup.py | 2 +-
xbob/machine/activation.cpp | 355 +++++++++++++++++++-----
xbob/machine/include/xbob.machine/api.h | 9 +-
3 files changed, 289 insertions(+), 77 deletions(-)
diff --git a/setup.py b/setup.py
index 0f9ce08..ecb1f92 100644
--- a/setup.py
+++ b/setup.py
@@ -52,7 +52,7 @@ setup(
),
Extension("xbob.machine._library",
[
- #"xbob/machine/activation.cpp",
+ "xbob/machine/activation.cpp",
"xbob/machine/main.cpp",
],
packages = packages,
diff --git a/xbob/machine/activation.cpp b/xbob/machine/activation.cpp
index a06e7f1..7acb1fa 100644
--- a/xbob/machine/activation.cpp
+++ b/xbob/machine/activation.cpp
@@ -7,8 +7,13 @@
* Copyright (C) 2011-2014 Idiap Research Institute, Martigny, Switzerland
*/
-#include <cleanup.h>
+#define XBOB_MACHINE_MODULE
+#include "cleanup.h"
+#include <xbob.machine/api.h>
+#include <xbob.io/api.h>
+#include <xbob.blitz/cppapi.h>
#include <bob/machine/Activation.h>
+#include <boost/bind.hpp>
#include <boost/function.hpp>
#include <structmember.h>
@@ -45,56 +50,32 @@ static int PyBobMachineActivation_init(PyBobMachineActivationObject* self, PyObj
}
-PyDoc_STRVAR(s_call_str, "f");
-PyDoc_STRVAR(s_call_doc,
-"o.f(z, [res]) -> array | scalar
-
-Computes the activated value, given an input array or scalar\n\
-``z``, placing results in ``res`` (and returning it).
-
-If ``z`` is an array, then you can pass another array in ``res``\n\
-to store the results and, in this case, we won't allocate a new\n\
-one for that purpose. This can be a speed-up in certain scenarios.\n\
-Note this does not work for scalars as it makes little sense to\n\
-avoid scalar allocation at this level.\n\
-\n\
-If you decide to pass an array in ``res``, note this array should\n\
-have the exact same dimensions as the input array ``z``. It is an
-error otherwise.\n\
-\n\
-.. note::\n\
-\n\
- This method only accepts 64-bit float arrays as input or\n\
- output.\n\
-\n\
-");
-
/**
* Maps all elements of arr through function() into retval
*/
static int apply(boost::function<double (double)> function,
PyBlitzArrayObject* z, PyBlitzArrayObject* res) {
- if (arr->ndim == 1) {
- blitz::Array<double,1>* z_ = PyBlitzArrayCxx_AsBlitz<double,1>(z);
- blitz::Array<double,1>* res_ = PyBlitzArrayCxx_AsBlitz<double,1>(res);
+ if (z->ndim == 1) {
+ auto z_ = PyBlitzArrayCxx_AsBlitz<double,1>(z);
+ auto res_ = PyBlitzArrayCxx_AsBlitz<double,1>(res);
for (int k=0; k<z_->extent(0); ++k)
res_->operator()(k) = function(z_->operator()(k));
return 1;
}
- else if (array->ndim == 2) {
- blitz::Array<double,2>* z_ = PyBlitzArrayCxx_AsBlitz<double,2>(z);
- blitz::Array<double,2>* res_ = PyBlitzArrayCxx_AsBlitz<double,2>(res);
+ else if (z->ndim == 2) {
+ auto z_ = PyBlitzArrayCxx_AsBlitz<double,2>(z);
+ auto res_ = PyBlitzArrayCxx_AsBlitz<double,2>(res);
for (int k=0; k<z_->extent(0); ++k)
for (int l=0; l<z_->extent(1); ++l)
res_->operator()(k,l) = function(z_->operator()(k,l));
return 1;
}
- else if (array->ndim == 3) {
- blitz::Array<double,3>* z_ = PyBlitzArrayCxx_AsBlitz<double,3>(z);
- blitz::Array<double,3>* res_ = PyBlitzArrayCxx_AsBlitz<double,3>(res);
+ else if (z->ndim == 3) {
+ auto z_ = PyBlitzArrayCxx_AsBlitz<double,3>(z);
+ auto res_ = PyBlitzArrayCxx_AsBlitz<double,3>(res);
for (int k=0; k<z_->extent(0); ++k)
for (int l=0; l<z_->extent(1); ++l)
for (int m=0; m<z_->extent(2); ++m)
@@ -102,9 +83,9 @@ static int apply(boost::function<double (double)> function,
return 1;
}
- else if (array->ndim == 4) {
- blitz::Array<double,4>* z_ = PyBlitzArrayCxx_AsBlitz<double,4>(z);
- blitz::Array<double,4>* res_ = PyBlitzArrayCxx_AsBlitz<double,4>(res);
+ else if (z->ndim == 4) {
+ auto z_ = PyBlitzArrayCxx_AsBlitz<double,4>(z);
+ auto res_ = PyBlitzArrayCxx_AsBlitz<double,4>(res);
for (int k=0; k<z_->extent(0); ++k)
for (int l=0; l<z_->extent(1); ++l)
for (int m=0; m<z_->extent(2); ++m)
@@ -118,14 +99,18 @@ static int apply(boost::function<double (double)> function,
}
static PyObject* PyBobMachineActivation_call1(PyBobMachineActivationObject* o,
+ double (bob::machine::Activation::*method) (double) const,
PyObject* args, PyObject* kwds) {
+ /* Parses input arguments in a single shot */
+ static const char* const_kwlist[] = {"z", 0};
+ static char** kwlist = const_cast<char**>(const_kwlist);
+
PyObject* z = 0;
if (!PyArg_ParseTupleAndKeywords(args, kwds, "O", kwlist, &z)) return 0;
- //protects acquired resources through this scope
- auto z_ = make_safe(z);
+ //note: object z is borrowed
if (PyBlitzArray_Check(z) || PyArray_Check(z)) {
@@ -149,7 +134,8 @@ static PyObject* PyBobMachineActivation_call1(PyBobMachineActivationObject* o,
auto res_ = make_safe(res);
// processes the data
- int ok = apply(boost::bind(&bob::machine::Activation::f, *(o->base), _1), z_converted, res);
+ int ok = apply(boost::bind(method, o->base, _1),
+ z_converted, reinterpret_cast<PyBlitzArrayObject*>(res));
if (!ok) {
PyErr_SetString(PyExc_RuntimeError, "unexpected error occurred applying C++ activation function to input array (DEBUG ME)");
@@ -165,7 +151,8 @@ static PyObject* PyBobMachineActivation_call1(PyBobMachineActivationObject* o,
PyObject* z_float = PyNumber_Float(z);
auto z_float_ = make_safe(z_float);
- double res_c = o->base->f(PyFloat_AsDouble(z_float);
+ auto bound_method = boost::bind(method, o->base, _1);
+ double res_c = bound_method(PyFloat_AsDouble(z_float));
return PyFloat_FromDouble(res_c);
}
@@ -176,6 +163,7 @@ static PyObject* PyBobMachineActivation_call1(PyBobMachineActivationObject* o,
}
static PyObject* PyBobMachineActivation_call2(PyBobMachineActivationObject* o,
+ double (bob::machine::Activation::*method) (double) const,
PyObject* args, PyObject* kwds) {
/* Parses input arguments in a single shot */
@@ -217,14 +205,14 @@ static PyObject* PyBobMachineActivation_call2(PyBobMachineActivationObject* o,
for (Py_ssize_t i=0; i<z->ndim; ++i) {
if (z->shape[i] != res->shape[i]) {
- PyErr_Format(PyExc_RuntimeError, "Input and output arrays should have matching sizes, but dimension %" PY_FORMAT_SIZE_T "d of input array `z' has %" PY_FORMAT_SIZE_T "d positions while output array `res' has %" PY_FORMAT_SIZE_T "d positions", z->shape[i], res->shape[i]);
+ PyErr_Format(PyExc_RuntimeError, "Input and output arrays should have matching sizes, but dimension %" PY_FORMAT_SIZE_T "d of input array `z' has %" PY_FORMAT_SIZE_T "d positions while output array `res' has %" PY_FORMAT_SIZE_T "d positions", i, z->shape[i], res->shape[i]);
return 0;
}
}
//at this point all checks are done, we can proceed into calling C++
- int ok = apply(boost::bind(&bob::machine::Activation::f, *(o->base), _1), z, res);
+ int ok = apply(boost::bind(method, o->base, _1), z, res);
if (!ok) {
PyErr_SetString(PyExc_RuntimeError, "unexpected error occurred applying C++ activation function to input array (DEBUG ME)");
@@ -232,10 +220,34 @@ static PyObject* PyBobMachineActivation_call2(PyBobMachineActivationObject* o,
}
Py_INCREF(res);
- return res;
+ return reinterpret_cast<PyObject*>(res);
}
+PyDoc_STRVAR(s_call_str, "f");
+PyDoc_STRVAR(s_call_doc,
+"o.f(z, [res]) -> array | scalar\n\
+\n\
+Computes the activated value, given an input array or scalar\n\
+``z``, placing results in ``res`` (and returning it).\n\
+\n\
+If ``z`` is an array, then you can pass another array in ``res``\n\
+to store the results and, in this case, we won't allocate a new\n\
+one for that purpose. This can be a speed-up in certain scenarios.\n\
+Note this does not work for scalars as it makes little sense to\n\
+avoid scalar allocation at this level.\n\
+\n\
+If you decide to pass an array in ``res``, note this array should\n\
+have the exact same dimensions as the input array ``z``. It is an\n\
+error otherwise.\n\
+\n\
+.. note::\n\
+\n\
+ This method only accepts 64-bit float arrays as input or\n\
+ output.\n\
+\n\
+");
+
static PyObject* PyBobMachineActivation_call(PyBobMachineActivationObject* o,
PyObject* args, PyObject* kwds) {
@@ -244,11 +256,117 @@ static PyObject* PyBobMachineActivation_call(PyBobMachineActivationObject* o,
switch (nargs) {
case 1:
- return PyBobMachineActivation_call1(self, args, kwds);
+ return PyBobMachineActivation_call1
+ (o, &bob::machine::Activation::f, args, kwds);
+ break;
+
+ case 2:
+ return PyBobMachineActivation_call2
+ (o, &bob::machine::Activation::f, args, kwds);
+ break;
+
+ default:
+
+ PyErr_Format(PyExc_RuntimeError, "number of arguments mismatch - %s requires 1 or 2 arguments, but you provided %" PY_FORMAT_SIZE_T "d (see help)", s_call_str, nargs);
+
+ }
+
+ return 0;
+
+}
+
+PyDoc_STRVAR(s_f_prime_str, "f_prime");
+PyDoc_STRVAR(s_f_prime_doc,
+"o.f_prime(z, [res]) -> array | scalar\n\
+\n\
+Computes the derivative of the activated value, given an input\n\
+array or scalar ``z``, placing results in ``res`` (and returning\n\
+it).\n\
+\n\
+If ``z`` is an array, then you can pass another array in ``res``\n\
+to store the results and, in this case, we won't allocate a new\n\
+one for that purpose. This can be a speed-up in certain scenarios.\n\
+Note this does not work for scalars as it makes little sense to\n\
+avoid scalar allocation at this level.\n\
+\n\
+If you decide to pass an array in ``res``, note this array should\n\
+have the exact same dimensions as the input array ``z``. It is an\n\
+error otherwise.\n\
+\n\
+.. note::\n\
+\n\
+ This method only accepts 64-bit float arrays as input or\n\
+ output.\n\
+\n\
+");
+
+static PyObject* PyBobMachineActivation_f_prime(PyBobMachineActivationObject* o,
+ PyObject* args, PyObject* kwds) {
+
+ Py_ssize_t nargs = args?PyTuple_Size(args):0 + kwds?PyDict_Size(kwds):0;
+
+ switch (nargs) {
+
+ case 1:
+ return PyBobMachineActivation_call1
+ (o, &bob::machine::Activation::f_prime, args, kwds);
+ break;
+
+ case 2:
+ return PyBobMachineActivation_call2
+ (o, &bob::machine::Activation::f_prime, args, kwds);
+ break;
+
+ default:
+
+ PyErr_Format(PyExc_RuntimeError, "number of arguments mismatch - %s requires 1 or 2 arguments, but you provided %" PY_FORMAT_SIZE_T "d (see help)", s_call_str, nargs);
+
+ }
+
+ return 0;
+
+}
+
+PyDoc_STRVAR(s_f_prime_from_f_str, "f_prime_from_f");
+PyDoc_STRVAR(s_f_prime_from_f_doc,
+"o.f_prime_from_f(a, [res]) -> array | scalar\n\
+\n\
+Computes the derivative of the activated value, given the\n\
+derivative value ``a``, placing results in ``res`` (and returning\n\
+it).\n\
+\n\
+If ``a`` is an array, then you can pass another array in ``res``\n\
+to store the results and, in this case, we won't allocate a new\n\
+one for that purpose. This can be a speed-up in certain scenarios.\n\
+Note this does not work for scalars as it makes little sense to\n\
+avoid scalar allocation at this level.\n\
+\n\
+If you decide to pass an array in ``res``, note this array should\n\
+have the exact same dimensions as the input array ``a``. It is an\n\
+error otherwise.\n\
+\n\
+.. note::\n\
+\n\
+ This method only accepts 64-bit float arrays as input or\n\
+ output.\n\
+\n\
+");
+
+static PyObject* PyBobMachineActivation_f_prime_from_f(PyBobMachineActivationObject* o,
+ PyObject* args, PyObject* kwds) {
+
+ Py_ssize_t nargs = args?PyTuple_Size(args):0 + kwds?PyDict_Size(kwds):0;
+
+ switch (nargs) {
+
+ case 1:
+ return PyBobMachineActivation_call1
+ (o, &bob::machine::Activation::f_prime_from_f, args, kwds);
break;
case 2:
- return PyBobMachineActivation_call2(self, args, kwds);
+ return PyBobMachineActivation_call2
+ (o, &bob::machine::Activation::f_prime_from_f, args, kwds);
break;
default:
@@ -261,6 +379,87 @@ static PyObject* PyBobMachineActivation_call(PyBobMachineActivationObject* o,
}
+PyDoc_STRVAR(s_unique_id_str, "unique_identifier");
+PyDoc_STRVAR(s_unique_id_doc,
+"o.unique_identifier() -> str\n\
+\n\
+Returns a unique (string) identifier, used by this class\n\
+in connection with the Activation registry.\n\
+\n\
+");
+
+static PyObject* PyBobMachineActivation_UniqueIdentifier (PyBobMachineActivationObject* o) {
+ return Py_BuildValue("s", o->base->unique_identifier().c_str());
+}
+
+PyDoc_STRVAR(s_load_str, "load");
+PyDoc_STRVAR(s_load_doc,
+"o.load(f) -> None\n\
+\n\
+Loads itself from a :py:class:`xbob.io.HDF5File`\n\
+\n\
+");
+
+static PyObject* PyBobMachineActivation_Load(PyBobMachineActivationObject* o,
+ PyObject* f) {
+
+ if (!PyBobIoHDF5File_Check(f)) {
+ PyErr_Format(PyExc_TypeError, "Activation function cannot load itself from `%s', only from an HDF5 file", f->ob_type->tp_name);
+ return 0;
+ }
+
+ auto h5f = reinterpret_cast<PyBobIoHDF5FileObject*>(f);
+
+ try {
+ o->base->load(*h5f->f);
+ }
+ catch (std::exception& e) {
+ PyErr_SetString(PyExc_RuntimeError, e.what());
+ return 0;
+ }
+ catch (...) {
+ PyErr_Format(PyExc_RuntimeError, "cannot read data from file `%s' (at group `%s'): unknown exception caught", h5f->f->filename().c_str(),
+ h5f->f->cwd().c_str());
+ return 0;
+ }
+
+ Py_RETURN_NONE;
+}
+
+PyDoc_STRVAR(s_save_str, "save");
+PyDoc_STRVAR(s_save_doc,
+"o.save(f) -> None\n\
+\n\
+Loads itself from a :py:class:`xbob.io.HDF5File`\n\
+\n\
+");
+
+static PyObject* PyBobMachineActivation_Save(PyBobMachineActivationObject* o,
+ PyObject* f) {
+
+ if (!PyBobIoHDF5File_Check(f)) {
+ PyErr_Format(PyExc_TypeError, "Activation function cannot write itself to `%s', only to an HDF5 file", f->ob_type->tp_name);
+ return 0;
+ }
+
+ auto h5f = reinterpret_cast<PyBobIoHDF5FileObject*>(f);
+
+ try {
+ o->base->save(*h5f->f);
+ }
+ catch (std::exception& e) {
+ PyErr_SetString(PyExc_RuntimeError, e.what());
+ return 0;
+ }
+ catch (...) {
+ PyErr_Format(PyExc_RuntimeError, "cannot write data to file `%s' (at group `%s'): unknown exception caught", h5f->f->filename().c_str(),
+ h5f->f->cwd().c_str());
+ return 0;
+ }
+
+ Py_RETURN_NONE;
+}
+
static PyMethodDef PyBobMachineActivation_methods[] = {
{
s_call_str,
@@ -268,8 +467,38 @@ static PyMethodDef PyBobMachineActivation_methods[] = {
METH_VARARGS|METH_KEYWORDS,
s_call_doc
},
+ {
+ s_f_prime_str,
+ (PyCFunction)PyBobMachineActivation_f_prime,
+ METH_VARARGS|METH_KEYWORDS,
+ s_f_prime_doc
+ },
+ {
+ s_f_prime_from_f_str,
+ (PyCFunction)PyBobMachineActivation_f_prime_from_f,
+ METH_VARARGS|METH_KEYWORDS,
+ s_f_prime_from_f_doc
+ },
+ {
+ s_unique_id_str,
+ (PyCFunction)PyBobMachineActivation_UniqueIdentifier,
+ METH_NOARGS,
+ s_unique_id_doc
+ },
+ {
+ s_load_str,
+ (PyCFunction)PyBobMachineActivation_Load,
+ METH_O,
+ s_load_doc
+ },
+ {
+ s_save_str,
+ (PyCFunction)PyBobMachineActivation_Save,
+ METH_O,
+ s_save_doc
+ },
{0} /* Sentinel */
-}
+};
static int PyBobMachineActivation_Check(PyObject* o) {
return PyObject_IsInstance(o, reinterpret_cast<PyObject*>(&PyBobMachineActivation_Type));
@@ -287,11 +516,11 @@ static PyObject* PyBobMachineActivation_RichCompare (PyBobMachineActivationObjec
switch (op) {
case Py_EQ:
- if (*(self->base) == *(other_->base)) Py_RETURN_TRUE;
+ if (self->base->str() == other_->base->str()) Py_RETURN_TRUE;
Py_RETURN_FALSE;
break;
case Py_NE:
- if (*(self->base) != *(other_->base)) Py_RETURN_TRUE;
+ if (self->base->str() != other_->base->str()) Py_RETURN_TRUE;
Py_RETURN_FALSE;
break;
default:
@@ -301,6 +530,10 @@ static PyObject* PyBobMachineActivation_RichCompare (PyBobMachineActivationObjec
}
+static PyObject* PyBobMachineActivation_Str (PyBobMachineActivationObject* o) {
+ return Py_BuildValue("s", o->base->str().c_str());
+}
+
PyTypeObject PyBobMachineActivation_Type = {
PyObject_HEAD_INIT(0)
0, /* ob_size */
@@ -317,8 +550,8 @@ PyTypeObject PyBobMachineActivation_Type = {
0, /* tp_as_sequence */
0, /* tp_as_mapping */
0, /* tp_hash */
- 0, /* tp_call */
- 0, /* tp_str */
+ (ternaryfunc)PyBobMachineActivation_call, /* tp_call */
+ (reprfunc)PyBobMachineActivation_Str, /* tp_str */
0, /* tp_getattro */
0, /* tp_setattro */
0, /* tp_as_buffer */
@@ -342,23 +575,3 @@ PyTypeObject PyBobMachineActivation_Type = {
0, /* tp_alloc */
0, /* tp_new */
};
-
-/**
- .def("__call__", &activation_f_ndarray_1, (arg("self"), arg("z"), arg("res")), "Computes the activated value, given an input array ``z``, placing results in ``res`` (and returning it)")
- .def("__call__", &activation_f_ndarray_2, (arg("self"), arg("z")), "Computes the activated value, given an input array ``z``. Returns a newly allocated array with the same size as ``z``")
- .def("__call__", &bob::machine::Activation::f, (arg("self"), arg("z")), "Computes the activated value, given an input ``z``")
- .def("f_prime", &activation_f_prime_ndarray_1, (arg("self"), arg("z"), arg("res")), "Computes the derivative of the activated value, placing results in ``res`` (and returning it)")
- .def("f_prime", &activation_f_prime_ndarray_2, (arg("self"), arg("z")), "Computes the derivative of the activated value, given an input array ``z``. Returns a newly allocated array with the same size as ``z``")
- .def("f_prime", &bob::machine::Activation::f_prime, (arg("self"), arg("z")), "Computes the derivative of the activated value.")
- .def("f_prime_from_f", &activation_f_prime_from_f_ndarray_1, (arg("self"), arg("a"), arg("res")), "Computes the derivative of the activated value, given **the activated value** ``a``, placing results in ``res`` (and returning it)")
- .def("f_prime_from_f", &activation_f_prime_from_f_ndarray_2, (arg("self"), arg("z")), "Computes the derivative of the activated value, given **the activated value** ``a``. Returns a newly allocated array with the same size as ``a`` with the answer.")
- .def("f_prime_from_f", &bob::machine::Activation::f_prime_from_f, (arg("self"), arg("a")), "Computes the derivative of the activation value, given **the activated value** ``a``.")
- .def("save", &bob::machine::Activation::save, (arg("self"), arg("h5f")),
- "Saves itself to a :py:class:`bob.io.HDF5File`")
- .def("load", &bob::machine::Activation::load, (arg("self"), arg("h5f")),
- "Loads itself from a :py:class:`bob.io.HDF5File`")
- .def("unique_identifier",
- &bob::machine::Activation::unique_identifier, (arg("self")),
- "Returns a unique identifier, used by this class in connection to the Activation registry.")
- .def("__str__", &bob::machine::Activation::str)
-**/
diff --git a/xbob/machine/include/xbob.machine/api.h b/xbob/machine/include/xbob.machine/api.h
index 26cc62a..4cecbcd 100644
--- a/xbob/machine/include/xbob.machine/api.h
+++ b/xbob/machine/include/xbob.machine/api.h
@@ -10,7 +10,6 @@
#include <Python.h>
#include <xbob.machine/config.h>
-#include <bob/config.h>
#include <bob/machine/Activation.h>
#define XBOB_MACHINE_MODULE_PREFIX xbob.machine
@@ -31,14 +30,14 @@
* Bindings for xbob.io.Activation *
***********************************/
-/* Type definition for PyBobIoFileObject */
+/* Type definition for PyBobMachineActivationObject */
typedef struct {
PyObject_HEAD
/* Type-specific fields go here. */
bob::machine::Activation* base;
-} PyBobMachineActivation;
+} PyBobMachineActivationObject;
#define PyBobMachineActivation_Type_NUM 1
#define PyBobMachineActivation_Type_TYPE PyTypeObject
@@ -48,7 +47,7 @@ typedef struct {
#ifdef XBOB_MACHINE_MODULE
- /* This section is used when compiling `xbob.core.random' itself */
+ /* This section is used when compiling `xbob.machine' itself */
/**************
* Versioning *
@@ -98,7 +97,7 @@ typedef struct {
* Bindings for xbob.machine.Activation *
****************************************/
-# define PyBobMachineActivation_Type (*(PyBobMachineActivation_Type_TYPE *)PyXbobIo_API[PyBobMachineActivation_Type_NUM])
+# define PyBobMachineActivation_Type (*(PyBobMachineActivation_Type_TYPE *)PyXbobMachine_API[PyBobMachineActivation_Type_NUM])
# if !defined(NO_IMPORT_ARRAY)
--
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